Purdue University Logo
Department of Horticulture and Landscape Architecture
Horticulture Home Page
Agriculture Home Page
Purdue Home Page
HORT640 Home Page
N Use By Plants
Nitrate Assimilation
Ammonia Assimilation
Glu, Gln, Asn, Gly, Ser
Asp, Ala, GABA
Val, Leu, Ileu, Thr, Lys
Pro, Arg, Orn
Non-protein AAs
Sulfate Assimilation
Cys, Met, AdoMet, ACC
His, Phe, Tyr, Tryp
Secondary Products
Onium Compounds
HORT640 - Metabolic Plant Physiology

References, Escherichia

Abadjieva A, Hilven P, Pauwels K, Crabeel M. The yeast ARG7 gene product is autoproteolyzed to two subunit peptides, yielding active ornithine acetyltransferase. J. Biol. Chem. 275: 11361-11367 (2000).

Abaibou H, Pommier J, Benoit S, Giordano G, Mandrand-Berthelot MA. Expression and characterization of the Escherichia coli fdo locus and a possible physiological role for aerobic formate dehydrogenase. J. Bacteriol. 177: 7141-7149 (1995).

Abd Rahman RN, Fujiwara S, Takagi M, Kanaya S, Imanaka T. Effect of heat treatment on proper oligomeric structure formation of thermostable glutamate dehydrogenase from a hyperthermophilic archaeon. Biochem. Biophys. Res. Commun. 241: 646-652 (1997).

Abdel-Ghany SE, Ye H, Garifullina GF, Zhang L, Pilon-Smits EA, Pilon M. Iron-sulfur cluster biogenesis in chloroplasts. Involvement of the scaffold protein CpIsca. Plant Physiol. 138: 161-172 (2005).

Abdel-Hamid AM, Attwood MM, Guest JR. Pyruvate oxidase contributes to the aerobic growth efficiency of Escherichia coli. Microbiology 147: 1483-1498 (2001).

AbdelRaheim SR, McLennan AG. The Caenorhabditis elegans Y87G2A.14 Nudix hydrolase is a peroxisomal coenzyme A diphosphatase. BMC Biochem. 3: 5 (2002).

Abe I, Utsumi Y, Oguro S, Noguchi H. The first plant type III polyketide synthase that catalyzes formation of aromatic heptaketide. FEBS Lett. 562: 171-176 (2004).

Abebe T, Guenzi AC, Martin B, Cushman JC. Tolerance of mannitol-accumulating transgenic wheat to water stress and salinity. Plant Physiol. 131: 1748-1755 (2003).

Abee T, Wouters JA. Microbial stress response in minimal processing Int. J. Food Microbiol. 50: 65-91 (1999).

Abel S, Nguyen MD, Chow W, Theologis A. ACS4, a primary indoleacetic acid-responsive gene encoding 1-aminocyclopropane-1-carboxylate synthase in Arabidopsis thaliana. Structural characterization, expression in Escherichia coli, and expression characteristics in response to auxin. J. Biol. Chem. 270: 19093-19099 (1995).

Abell LM, Schineller J, Keck PJ, Villafranca JJ. Effect of metal-ligand mutations on phosphoryl transfer reactions catalyzed by Escherichia coli glutamine synthetase. Biochemistry 34: 16695-16702 (1995).

Abell LM, Villafranca JJ. Investigation of the mechanism of phosphinothricin inactivation of Escherichia coli glutamine synthetase using rapid quench kinetic technique. Biochemistry 30: 6135-6141 (1991).

Abell LM, Villafranca JJ. Effect of metal ions and adenylylation state on the internal thermodynamics of phosphoryl transfer in the Escherichia coli glutamine synthetase reaction. Biochemistry 30: 1413-1418 (1991).

Abraham Z, Martinez M, Carbonero P, Diaz I. Structural and functional diversity within the cystatin gene family of Hordeum vulgare. J. Exp. Bot. 57: 4245-4255 (2006).

Abrahams GL, Abratt VR. The NADH-dependent glutamate dehydrogenase enzyme of Bacteroides fragilis Bf1 is induced by peptides in the growth medium. Microbiology 144: 1659-1667 (1998).

Abrahamson JL, Baker LG, Stephenson JT, Wood JM. Proline dehydrogenase from Escherichia coli K12. Properties of the membrane-associated enzyme. Eur. J. Biochem. 134: 77-82 (1983).

Abramson J, Smirnova I, Kasho V, Verner G, Kaback HR, Iwata S. Structure and mechanism of the lactose permease of Escherichia coli. Science 301: 610-615 (2003).

Abratt VR, Mbewe M, Woods DR. Cloning of an EF-P homologue from Bacteroides fragilis that increases B. fragilis glutamine synthetase activity in Escherichia coli. Mol. Gen. Genet. 258: 363-372 (1998).

Abratt VR, Zappe H, Woods DR. A reporter gene vector to investigate the regulation of glutamine synthetase in Bacteroides fragilis Bf1. J. Gen. Microbiol. 139: 59-65 (1993).

Abuoun M, Suthers PF, Jones GI, Carter BR, Saunders MP, Maranas CD, Woodward MJ, Anjun MF. Genome scale reconstruction of a Salmonella metabolic model: comparison of similarity and differences with a commensal Escherichia coli strain. J. Biol. Chem. Aug 18 [Epub ahead of print] (2009).

Acerenza L, Ortega F. Metabolic control analysis for large changes: extension to variable elasticity coefficients. Syst. Biol. (Stevenage) 153: 323-326 (2006).

Achebach S, Tran QH, Vlamis-Gardikas A, Mullner M, Holmgren A, Unden G. Stimulation of Fe-S cluster insertion into apoFNR by Escherichia coli glutaredoxins 1, 2 and 3 in vitro. FEBS Lett. 565: 203-206 (2004).

Adam Z, Zaltsman A, Sinvany-Villalobo G, Sakamoto W. FtsH proteases in chloroplasts and cyanobacteria. Physiol. Plant. 123: 386-390 (2005).

Adams J, Johnson K, Matthews R, Benkovic SJ. Effects of distal point-site mutations on the binding and catalysis of dihydrofolate reductase from Escherichia coli. Biochemistry 28: 6611-6618 (1989).

Adler SP, Purich D, Stadtman ER. Cascade control of Escherichia coli glutamine synthetase. Properties of the PII regulatory protein and the uridylyltransferase-uridylyl-removing enzyme. J. Biol. Chem. 250: 6264-6272 (1975).

Adul Rahman RN, Jongsareejit B, Fujiwara S, Imanaka T. Characterization of recombinant glutamine synthetase from the hyperthermophilic archaeon Pyrococcus sp. strain KOD1. Appl. Environ. Microbiol. 63: 2472-2476 (1997).

Aertsen A, De Spiegeleer P, Vanoirbeek K, Lavilla M, Michiels CW. Induction of oxidative stress by high hydrostatic pressure in Escherichia coli. Appl. Environ. Microbiol. 71: 2226-2231 (2005).

Agarwal AK, Qi Y, Bhat DG, Woerner BM, Brown SM. Gene isolation and characterization of two acyl CoA oxidases from soybean with broad substrate specificities and enhanced expression in the growing seedling axis. Plant Mol. Biol. 47: 519-531 (2001).

Aghajanian S, Worrall DM. Identification and characterization of the gene encoding the human phosphopantetheine adenylyltransferase and dephospho-CoA kinase bifunctional enzyme (CoA synthase). Biochem. J. 365: 13-18 (2002).

Agrawal S, Kumar A, Srivastava V, Mishra BN. Cloning, expression, activity and folding studies of serine hydroxymethyltransferase: a target enzyme for cancer chemotherapy. J. Mol. Microbiol. Biotechnol. 6: 67-75 (2003).

Aguiar JM, Franco OL, Rigden DJ, Bloch C Jr, Monteiro AC, Flores VM, Jacinto T, Xavier-Filho J, Oliveira AE, Grossi-de-Sa MF, Fernandes KV. Molecular modeling and inhibitory activity of cowpea cystatin against bean bruchid pests. Proteins 63: 662-670 (2006).

Aharoni A, Giri AP, Verstappen FW, Bertea CM, Sevenier R, Sun Z, Jongsma MA, Schwab W, Bouwmeester HJ. Gain and loss of fruit flavor compounds produced by wild and cultivated strawberry species. Plant Cell 16: 3110-3131 (2004).

Aharoni A, Keizer LC, Bouwmeester HJ, Sun Z, Alvarez-Huerta M, Verhoeven HA, Blaas J, van Houwelingen AM, De Vos RC, van Der Voet H, Jansen RC, Guis M, Mol J, Davis RW, Schena M, van Tunen AJ, O'Connell AP. Identification of the SAAT gene involved in strawberry flavor biogenesis by use of DNA microarrays. Plant Cell 12: 647-662 (2000).

Ahmad S, Jensen RA. The prephenate dehydrogenase component of the bifunctional T-protein in enteric bacteria can utilize L-arogenate. FEBS Lett. 216: 133-139 (1987).

Ahmad S, Jensen RA. The phylogenetic origin of the bifunctional tyrosine-pathway protein in the enteric lineage of bacteria. Mol. Biol. Evol. 5: 282-297 (1988).

Ahmed SA, Martin B, Miles EW. Beta-elimination of indole from L-tryptophan catalyzed by bacterial tryptophan synthase: a comparison between reactions catalyzed by tryptophanase and tryptophan synthase. Biochemistry 25: 4233-4240 (1986).

Ahn KS, Henney HR Jr. Nucleotide sequence and developmental expression of Acanthamoeba S-adenosylmethionine synthetase gene. Biochim. Biophys. Acta 1351: 223-230 (1997).

Ahn SJ, Shin R, Schachtman DP. Expression of KT/KUP genes in Arabidopsis and the role of root hairs in K+ uptake. Plant Physiol. 134: 1135-1145 (2004).

Akad F, Teverovsky E, David A, Czosnek H, Gidoni D, Gera A, Loebenstein G. A cDNA from tobacco codes for an inhibitor of virus replication (IVR)-like protein. Plant Mol. Biol. 40: 969-976 (1999).

Akama K, Akihiro T, Kitagawa M, Takaiwa F. Rice (Oryza sativa) contains a novel isoform of glutamate decarboxylase that lacks an authentic calmodulin-binding domain at the C-terminus. Biochim. Biophys. Acta 1522: 143-150 (2001).

Akashi T, Aoki T, Ayabe S. Molecular and biochemical characterization of 2-hydroxyisoflavanone dehydratase. Involvement of carboxylesterase-like proteins in leguminous isoflavone biosynthesis. Plant Physiol. 137: 882-891 (2005).

Akashi T, Vanetten HD, Sawada Y, Wasmann CC, Uchiyama H, Ayabe SI. Catalytic specificity of pea O-methyltransferases suggests gene duplication for (+)-pisatin biosynthesis. Phytochemistry 67: 2525-2530 (2006).

Akesson M, Karlsson EN, Hagander P, Axelsson JP, Tocaj A. On-line detection of acetate formation in Escherichia coli cultures using dissolved oxygen responses to feed transients. Biotechnol. Bioeng. 64: 590-598 (1999).

Akhtar TA, McQuinn RP, Naponelli V, Gregory JF 3rd, Giovannoni JJ, Hanson AD. Tomato gamma-glutamylhydrolases: expression, characterization, and evidence for heterodimer formation. Plant Physiol. 148: 775-785 (2008).

Akinterinwa O, Cirino PC. Heterologous expression of d-xylulokinase from Pichia stipitis enables high levels of xylitol production by engineered Escherichia coli growing on xylose. Metab. Eng. 11: 48-55 (2009).

Akinterinwa O, Khankal R, Cirino PC. Metabolic engineering for bioproduction of sugar alcohols. Curr. Opin. Biotechnol. 19: 461-467 (2008).

Akiyama T, Pillai MA, Sentoku N. Cloning, characterization and expression of OsGLN2, a rice endo-1,3-beta-glucanase gene regulated developmentally in flowers and hormonally in germinating seeds. Planta 220: 129-139 (2004).

Akiyama T, Shibuya M, Liu HM, Ebizuka Y. p-Coumaroyltriacetic acid synthase, a new homologue of chalcone synthase, from Hydrangea macrophylla var. thunbergii. Eur. J. Biochem. 263: 834-839 (1999).

Akowski JP, Bauerle R. Steady-state kinetics and inhibitor binding of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (tryptophan sensitive) from Escherichia coli. Biochemistry 36: 15817-15822 (1997).

Al-Taweel K, Iwaki T, Yabuta Y, Shigeoka S, Murata N, Wadano A. A bacterial transgene for catalase protects translation of D1 protein during exposure of salt-stressed tobacco leaves to strong light. Plant Physiol. 145: 258-265 (2007).

Alahari A, Apte SK. A novel potassium deficiency-induced stimulon in Anabaena torulosa. J. Biosci. 29: 153-161 (2004).

Aldridge P, Metzger M, Geider K. Genetics of sorbitol metabolism in Erwinia amylovora and its influence on bacterial virulence. Mol. Gen. Genet. 256: 611-619 (1997).

Alex D, Bach TJ, Chye ML. Expression of Brassica juncea 3-hydroxy-3-methylglutaryl CoA synthase is developmentally regulated and stress-responsive. Plant J. 22: 415-426 (2000).

Alexander LG, Sessions RB, Clarke AR, Tatham AS, Shewry PR, Napier JA. Characterization and modelling of the hydrophobic domain of a sunflower oleosin. Planta 214: 546-551 (2002).

Alexander RW. Teasing apart the Taxol pathway. Trends Biochem. Sci. 26: 152-153 (2001).

Alfadhli S, Rathod PK. Gene organization of a Plasmodium falciparum serine hydroxymethyltransferase and its functional expression in Escherichia coli. Mol. Biochem. Parasitol. 110: 283-291 (2000).

Ali R, Zielinski RE, Berkowitz GA. Expression of plant cyclic nucleotide-gated cation channels in yeast. J. Exp. Bot. 57: 125-138 (2006).

Alibhai M, Villafranca JJ. Kinetic and mutagenic studies of the role of the active site residues Asp-50 and Glu-327 of Escherichia coli glutamine synthetase. Biochemistry 33: 682-686 (1994).

Almaas E, Kovacs B, Vicsek T, Oltvai ZN, Barabasi AL. Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature 427: 839-843 (2004).

Almaas E, Oltvai ZN, Barabasi AL. The activity reaction core and plasticity of metabolic networks. PLoS Comput. Biol. 1: e68 (2005).

Alper H, Jin YS, Moxley JF, Stephanopoulos G. Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli. Metab. Eng. 7: 155-164 (2005).

Alper H, Stephanopoulos G. Uncovering the gene knockout landscape for improved lycopene production in E. coli. Appl. Microbiol. Biotechnol. 78: 801-810 (2008).

Altaras NE, Cameron DC. Metabolic engineering of a 1,2-propanediol pathway in Escherichia coli. Appl. Environ. Microbiol. 65: 1180-1185 (1999).

Alvarez R, Garcia-Maurino S, Feria AB, Vidal J, Echevarria C. A conserved 19-amino acid synthetic peptide from the carboxy terminus of phosphoenolpyruvate carboxylase inhibits the in vitro phosphorylation of the enzyme by the calcium-independent phosphoenolpyruvate carboxylase kinase. Plant Physiol. 132: 1097-1106 (2003).

Amaratunga M, Fluhr K, Jarrett JT, Drennan CL, Ludwig ML, Matthews RG, Scholten JD. A synthetic module for the metH gene permits facile mutagenesis of the cobalamin-binding region of Escherichia coli methionine synthase: initial characterization of seven mutant proteins. Biochemistry 35: 2453-2463 (1996).

Ambikapathy J, Marshall JS, Hocart CH, Hardham AR. The role of proline in osmoregulation in Phytophthora nicotianae. Fungal Genet. Biol. 35: 287-299 (2002).

Ament K, Van Schie CC, Bouwmeester HJ, Haring MA, Schuurink RC. Induction of a leaf specific geranylgeranyl pyrophosphate synthase and emission of (E,E)-4,8,12-trimethyltrideca-1,3,7,11-tetraene in tomato are dependent on both jasmonic acid and salicylic acid signaling pathways. Planta 224: 1197-1208 (2006).

Amezaga MR, Booth IR. Osmoprotection of Escherichia coli by peptone is mediated by the uptake and accumulation of free proline but not of proline-containing peptides. Appl. Environ. Microbiol. 65: 5272-5278 (1999).

Amon J, Brau T, Grimrath A, HanBler E, Hasselt K, Holler M, JeBberger N, Ott L, Szokol J, Titgemeyer F, Burkovski A. Nitrogen control in Mycobacterium smegmatis: nitrogen-dependent expression of ammonium transport and assimilation proteins depends on OmpR-type regulator GlnR. J. Bacteriol. 190: 7108-7116 (2008).

Ananvoranich S, Varin L, Gulick P, Ibrahim R. Cloning and regulation of flavonol 3-sulfotransferase in cell-suspension cultures of Flaveria bidentis. Plant Physiol. 106: 485-491 (1994).

Anderson LA, McNairn E, Leubke T, Pau RN, Boxer DH. ModE-dependent molybdate regulation of the molybdenum cofactor operon moa in Escherichia coli J. Bacteriol. 182: 7035-7043 (2000).

Andersson C, Helmerius J, Hodge D, Berglund KA, Rova U. Inhibition of succinic acid production in metabolically engineered Escherichia coli by neutralizing agent, organic acids, and osmolarity. Biotechnol. Prog. 25: 116-123 (2009).

Andrade SL, Dickmanns A, Ficner R, Einsle O. Crystal structure of the archaeal ammonium transporter Amt-1 from Archaeoglobus fulgidus. Proc. Natl. Acad. Sci. U.S.A. 102: 14994-14999 (2005).

Andreasson E, Taipalensuu J, Rask L, Meijer J. Age-dependent wound induction of a myrosinase-associated protein from oilseed rape (Brassica napus). Plant Mol. Biol. 41: 171-180 (1999).

Andreou AZ, Vanko M, Bezakova L, Feussner I. Properties of a mini 9R-lipoxygenase from Nostoc sp. PCC 7120 and its mutant forms. Phytochemistry 69: 1832-1837 (2008).

Andresen PA, Kaasen I, Styrvold OB, Boulnois G, Strom AR. Molecular cloning, physical mapping and expression of the bet genes governing the osmoregulatory choline-glycine betaine pathway of Escherichia coli. J. Gen. Microbiol. 134: 1737-1746 (1988).

Anesiadis N, Cluett WR, Mahadevan R. Dynamic metabolic engineering for increasing bioprocess productivity. Metab. Eng. 10: 255-266 (2008).

Angel Rubio M, Barrado P, Carlos Espinosa J, Jimenez A, Lobato MF. The pur6 gene of the puromycin biosynthetic gene cluster from Streptomyces alboniger encodes a tyrosinyl-aminonucleoside synthetase. FEBS Lett. 577: 371-375 (2004).

Angeles TS, Hunsley JR, Viola RE. Reversal of enzyme regiospecificity with alternative substrates for aspartokinase I from Escherichia coli. Biochemistry 31: 799-805 (1992).

Angeles TS, Smanik PA, Borders CL Jr, Viola RE. Aspartokinase-homoserine dehydrogenase I from Escherichia coli: pH and chemical modification studies of the kinase activity. Biochemistry 28: 8771-8777 (1989).

Angeles TS, Viola RE. The kinetic mechanisms of the bifunctional enzyme aspartokinase-homoserine dehydrogenase I from Escherichia coli. Arch. Biochem. Biophys. 283: 96-101 (1990).

Angelidis AS, Smith GM. Role of the glycine betaine and carnitine transporters in adaptation of Listeria monocytogenes to chill stress in defined medium. Appl. Environ. Microbiol. 69: 7492-7498 (2003).

Angove HC, Cole JA, Richardson DJ, Butt JN. Protein film voltammetry reveals distinctive fingerprints of nitrite and hydroxylamine reduction by a cytochrome C nitrite reductase. J. Biol. Chem. 277: 23374-23381 (2002).

Anguera MC, Liu X, Stover PJ. Cloning, expression, and purification of 5,10-methenyltetrahydrofolate synthetase from Mus musculus. Protein Expr. Purif. 35: 276-283 (2004).

Ankri S, Serebrijski I, Reyes O, Leblon G. Mutations in the Corynebacterium glutamicum proline biosynthetic pathway: a natural bypass of th proA step. J. Bacteriol. 178: 4412-4419 (1996).

Ansari MI, Lee RH, Chen SCG. A novel senescence-associated gene encoding gamma-aminobutyric acid (GABA): pyruvate transaminase is upregulated during rice leaf senescence. Physiol. Plant. 123: 1-8 (2005).

Anterola A, Gobel C, Hornung E, Sellhorn G, Feussner I, Grimes H. Physcomitrella patens has lipoxygenases for both eicosanoid and octadecanoid pathways. Phytochemistry 70: 40-52 (2009).

Anthoni U, Christophersen C, Hougaard L, Nielsen PH. Quaternay ammonium compounds in the biosphere - an example of a versatile adaptive strategy. Comp. Biochem. Physiol. [B] 99: 1-18 (1991).

Anthony JR, Anthony LC, Nowroozi F, Kwon G, Newman JD, Keasling JD. Optimization of the mevalonate-based isoprenoid biosynthetic pathway in Escherichia coli for production of the anti-malarial drug precursor amorpha-4,11-diene. Metab. Eng. 11: 13-19 (2009).

Antoine W, Stewart JM, de los Reyes BG. The rice homolog of the sodium/lithium tolerance gene functions as molecular chaperon in vitro. Physiol. Plant. 125: 299-310 (2005).

Antoniewicz MR, Kraynie DF, Laffend LA, González-Lergier J, Kelleher JK, Stephanopoulos G. Metabolic flux analysis in a nonstationary system: fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol. Metab. Eng. 9: 277-292 (2007).

Aoki K, Ogata Y, Shibata D. Approaches for extracting practical information from gene co-expression networks in plant biology. Plant Cell Physiol. 48: 381-390 (2007).

Aoshima M, Oshima T. Stabilization of Escherichia coli isopropylmalate dehydrogenase by single amino acid substitution. Protein Eng. 10: 249-254 (1997).

Arai Y, Hayashi M, Nishimura M. Proteomic identification and characterization of a novel peroxisomal adenine nucleotide transporter supplying ATP for fatty acid beta-oxidation in soybean and Arabidopsis. Plant Cell 20: 3227-3240 (2008).

Arakawa K, Yamada Y, Shinoda K, Nakayama Y, Tomita M. GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes. BMC Bioinformatics 7: 168 (2006).

Archer JA, Solow-Cordero DE, Sinskey AJ. A C-terminal deletion in Corynebacterium glutamicum homoserine dehydrogenase abolishes allosteric inhibition by L-threonine. Gene 107: 53-59 (1991).

Arenas-Diaz G, Mercado LA, Marshall SH. Bacterial aspartate kinase-like activity in human platelet. Cell Mol. Biol. Res. 41: 461-465 (1995).

Arend J, Warzecha H, Hefner T, Stockigt J. Utilizing genetically engineered bacteria to produce plant-specific glucosides. Biotechnol. Bioeng. 76: 126-131 (2001).

Argos P, Hanei M, Wilson JM, Kelley WN. A possible nucleotide-binding domain in the tertiary fold of phosphoribosyltransferases. J. Biol. Chem. 258: 6450-6457 (1983).

Arias-Negrete S, Jimenez-Romero LA, Soliis-Martiinez MO, Ramiirez-Emiliano J, Avila EE, Cuellar-Mata P. Indirect determination of nitric oxide production by reduction of nitrate with a freeze-thawing-resistant nitrate reductase from Escherichia coli MC1061. Anal. Biochem. 328: 14-21 (2004).

Arisi AC, Noctor G, Foyer CH, Jouanin L. Modification of thiol contents in poplars (Populus tremula x P. alba) overexpressing enzymes involved in glutathione synthesis. Planta 203: 362-372 (1997).

Aristidou AA, San KY, Bennett GN. Metabolic flux analysis of Escherichia coli expressing the Bacillus subtilis acetolactate synthase in batch and continuous cultures. Biotechnol. Bioeng. 63: 737-749 (1999).

Aristidou AA, San KY, Bennett GN. Metabolic engineering of Escherichia coli to enhance recombinant protein production through acetate reduction. Biotechnol. Prog. 11: 475-478 (1995).

Arita M. In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism. Genome Res. 13: 2455-2466 (2003).

Arkin IT, Xu H, Jensen MO, Arbely E, Bennett ER, Bowers KJ, Chow E, Dror RO, Eastwood MP, Flitman-Tene R, Gregersen BA, Klepeis JL, Kolossváry I, Shan Y, Shaw DE. Mechanism of Na+/H+ antiporting. Science 317: 799-803 (2007).

Armengaud J, Fernandez B, Chaumont V, Rollin-Genetet F, Finet S, Marchetti C, Myllykallio H, Vidaud C, Pellequer JL, Gribaldo S, Forterre P, Gans P. Identification, purification, and characterization of an eukaryotic-like phosphopantetheine adenylyltransferase (coenzyme A biosynthetic pathway) in the hyperthermophilic archaeon Pyrococcus abyssi. J. Biol. Chem. 278: 31078-31087 (2003).

Arnoux P, Sabaty M, Alric J, Frangioni B, Guigliarelli B, Adriano JM, Pignol D. Structural and redox plasticity in the heterodimeric periplasmic nitrate reductase. Nat. Struct. Biol. 10: 928-934 (2003).

Arora A, Sairam RK, Srivastava GC. Oxidative stress and antioxidative system in plants. Curr. Sci. 82: 1227-1238 (2002).

Arrebola E, Cazorla FM, Duran VE, Rivera E, Olea F, Codina JC, Perez-Garcia A, de Vicente A. Mangotoxin: a novel antimetabolite toxin produced by Pseudomonas syringae inhibiting ornithine/arginine biosynthesis. Physiol. Mol. Plant Pathol. 63: 117-127 (2003).

Arredondo-Peter R, Moran JF, Sarath G, Luan P, Klucas RV. Molecular cloning of the cowpea leghemoglobin II gene and expression of its cDNA in Escherichia coli. Purification and characterization of the recombinant protein. Plant Physiol. 114: 493-500 (1997).

Arrendondo-Peter R, Hargrove MS, Sarath G, Moran JF, Lohrman J, Olson JS, Klucas RV. Rice hemoglobins. Gene cloning, analysis, and O2-binding kinetics of a recombinant protein synthesized in Escherichia coli. Plant Physiol. 115: 1259-1266 (1997).

Arsene-Ploetze F, Bringel F. Role of inorganic carbon in lactic acid bacteria metabolism. Lait 84: 49-59 (2004).

Arvizu-Flores AA, Sugich-Miranda R, Arreola R, Garcia-Orozco KD, Velazquez-Contreras EF, Montfort WR, Maley F, Sotelo-Mundo RR. Role of an invariant lysine residue in folate binding on Escherichia coli thymidylate synthase: calorimetric and crystallographic analysis of the K48Q mutant. Int. J. Biochem. Cell Biol. 40: 2206-2217 (2008).

Asanuma N, Iwamoto M, Hino T. Structure and transcriptional regulation of the gene encoding pyruvate formate-lyase of a ruminal bacterium, Streptococcus bovis. Microbiology 145: 151-157 (1999).

Asha H, Gowrishankar J. Regulation of kdp operon expression in Escherichia coli: evidence against turgor as signal for transcriptional control. J. Bacteriol. 175: 4528-4537 (1993).

Ashenafi M, Carrington R, Collins AC, Byrnes WM. The fused TrpEG from Streptomyces venezuelae is an anthranilate synthase, not a 2-amino-4-deoxyisochorismate (ADIC) synthase. Ethn. Dis. 18: S2-S9-S13 (2008).

Atkins WM. Supramolecular self-assembly of Escherichia coli glutamine synthetase: effects of pressure and adenylylation state on dodecamer stacking. Biochemistry 33: 14965-14973 (1994).

Atkins WM, Cader BM, Hemmingsen J, Villafranca JJ. Time-resolved fluorescence and computational studies of adenylylated glutamine synthetase: analysis of intersubunit interactions. Protein Sci. 2: 800-813 (1993).

Atkins WM, Villafranca JJ. Time-resolved fluorescence studies of tryptophan mutants of Escherichia coli glutamine synthetase: conformational analysis of intermediates and transition-state complexes. Protein Sci. 1: 342-355 (1992).

Atkinson MR, Blauwkamp TA, Bondarenko V, Studitsky V, Ninfa AJ. Activation of the glnA, glnK, and nac promoters as Escherichia coli undergoes the transition from nitrogen excess growth to nitrogen starvation. J. Bacteriol. 184: 5358-5363 (2002).

Atkinson MR, Blauwkamp TA, Ninfa AJ. Context-dependent functions of the PII and GlnK signal transduction proteins in Escherichia coli. J. Bacteriol. 184: 5364-5375 (2002).

Atkinson MR, Kamberov ES, Weiss RL, Ninfa AJ. Reversible uridylylation of the Escherichia coli PII signal transduction protein regulates its ability to stimulate the dephosphorylation of the transcription factor nitrogen regulator I (NRI or NtrC). J. Biol. Chem. 269: 28288-28293 (1994).

Atkinson MR, Ninfa AJ. Characterization of the GlnK protein of Escherichia coli. Mol. Microbiol. 32: 301-313 (1999).

Atkinson MR, Ninfa AJ. Characterization of Escherichia coli glnL mutations affecting nitrogen regulation. J. Bacteriol. 174: 4538-4548 (1992).

Atkinson MR, Ninfa AJ. Role of the GlnK signal transduction protein in the regulation of nitrogen assimilation in Escherichia coli. Mol. Microbiol. 29: 431-447 (1998).

Atkinson MR, Pattaramanon N, Ninfa AJ. Governor of the glnAp2 promoter of Escherichia coli. Mol. Microbiol. 46: 1247-1257 (2002).

Atkinson MR, Savageau MA, Myers JT, Ninfa AJ. Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 113: 597-607 (2003).

Atlas JC, Nikolaev EV, Browning ST, Shuler ML. Incorporating genome-wide DNA sequence information into a dynamic whole-cell model of Escherichia coli: application to DNA replication. IET Syst. Biol. 2: 369-382 (2008).

Atsumi S, Liao JC. Metabolic engineering for advanced biofuels production from Escherichia coli. Curr. Opin. Biotechnol. 19: 414-419 (2008).

Attieh J, Djiana R, Koonjul P, Etienne C, Sparace SA, Saini HS. Cloning and functional expression of two plant thiol methyltransferases: a new class of enzymes involved in the biosynthesis of sulfur volatiles. Plant Mol. Biol. 50: 511-521 (2002).

Aubel D, Germond JE, Gilbert C, Atlan D. Isolation of the patC gene encoding the cystathionine beta-lyase of Lactobacillus delbrueckii subsp. bulgaricus and molecular analysis of inter-strain variability in enzyme biosynthesis. Microbiology 148: 2029-2036 (2002).

Auger S, Yuen WH, Danchin A, Martin-Verstraete I. The metIC operon involved in methionine biosynthesis in Bacillus subtilis is controlled by transcription antitermination. Microbiology 148: 507-518 (2002).

Augier V, Asso M, Guigliarelli B, More C, Bertrand P, Santini CL, Blasco F, Chippaux M, Giordano G. Removal of the high-potential [4Fe-4S] center of the beta-subunit from Escherichia coli nitrate reductase. Physiological, biochemical, and EPR characterization of site-directed mutated enzymes. Biochemistry 32: 5099-5108 (1993).

Augier V, Guigliarelli B, Asso M, Bertrand P, Frixon C, Giordano G, Chippaux M, Blasco F. Site-directed mutagenesis of conserved cysteine residues within the beta subunit of Escherichia coli nitrate reductase. Physiological, biochemical, and EPR characterization of the mutated enzymes. Biochemistry 32: 2013-2023 (1993).

Austgen TR, Chen MK, Moore W, Souba WW. Endotoxin and renal glutamine metabolism. Arch. Surg. 126: 23-27 (1991).

Austin-Brown SL, Chapman KD. Inhibition of phospholipase Dalpha by N-acylethanolamines. Plant Physiol. 129: 1892-1898 (2002).

Avila C, Marquez AJ, Pajuelo P, Cannell ME, Wallsgrove RM, Forde BG. Cloning and sequence analysis of a cDNA for barley ferredoxin-dependent glutamate synthase and molecular analysis of photorespiratory mutants deficient in the enzyme. Planta 189: 475-483 (1993).

Awai K, Kakimoto T, Awai C, Kaneko T, Nakamura Y, Takamiya K, Wada H, Ohta H. Comparative genomic analysis revealed a gene for monoglucosyldiacylglycerol synthase, an enzyme for photosynthetic membrane lipid synthesis in cyanobacteria. Plant Physiol. 141: 1120-1127 (2006).

Awai K, Watanabe H, Benning C, Nishida I. Digalactosyldiacylglycerol is required for better photosynthetic growth of Synechocystis sp. PCC6803 under phosphate limitation. Plant Cell Physiol. 48: 1517-1523 (2007).

Azachi M, Sadka A, Fisher M, Goldshlag P, Gokhman I, Zamir A. Salt induction of fatty acid elongase and membrane lipid modifications in the extreme halotolerant alga Dunaliella salina. Plant Physiol. 129: 1320-1329 (2002).

Babajide OJ, Babajide OO, Daramola AO, Mabusela WT. Flavonols and an oxychromonol from Piliostigma reticulatum. Phytochemistry 69: 2245-2250 (2008).

Babu BN, Brown OR. Quantitative effects of redox-cycling chemicals on the oxidant-sensitive enzyme dihydroxy-acid dehydratase. Microbios. 82: 157-170 (1995).

Baedeker M, Schulz GE. Overexpression of a designed 2.2 kb gene of eukaryotic phenylalanine ammonia-lyase in Escherichia coli. FEBS Lett. 457: 57-60 (1999).

Baerson SR, Rodriguez DJ, Tran M, Feng Y, Biest NA, Dill GM. Glyphosate-resistant goosegrass. Identification of a mutation in the target enzyme 5-enolpyruvylshikimate-3-phosphate synthase. Plant Physiol. 129: 1265-1275 (2002).

Baetens M, Legrain C, Boyen A, Glansdorff N. Genes and enzymes of the acetyl cycle of arginine biosynthesis in the extreme thermophilic bacterium Thermus thermophilus HB27. Microbiology 144: 479-492 (1998).

Baga M, Nair RB, Repellin A, Scoles GJ, Chibbar RN. Isolation of a cDNA encoding a granule-bound 152-kilodalton starch-branching enzyme in wheat. Plant Physiol. 124: 253-264 (2000).

Baggio L, Morrison M. The NAD(P)H-utilizing glutamate dehydrogenase of Bacteroides thetaiotaomicron belongs to enzyme family I, and its activity is affected by trans-acting gene(s) positioned downstream of gdhA. J. Bacteriol. 178: 7212-7220 (1996).

Bagni N, Tassoni A. Biosynthesis, oxidation and conjugation of aliphatic polyamines in higher plants. Amino Acids 20: 301-317 (2001).

Bai L, Kim EH, Dellapenna D, Brutnell TP. Novel lycopene epsilon cyclase activities in maize revealed through perturbation of carotenoid biosynthesis. Plant J. 59: 588-599 (2009).

Baich A. The biosynthesis of proline in Escherichia coli. Phosphate-dependent glutamate gamma-semialdehyde dehydrogenase (NADP), the second enzyme in the pathway. Biochim. Biophys. Acta 244: 129-134 (1971).

Baich A. Proline synthesis in Escherichia coli. A proline-inhibitable glutamic acid kinase. Biochim. Biophys. Acta 192: 462-467 (1969).

Bailey-Serres J, Dawe RK. Both 5' and 3' sequences of maize adh1 mRNA are required for enhanced translation under low-oxygen conditions. Plant Physiol. 112: 685-695 (1996).

Bak S, Kahn RA, Nielsen HL, Moller BL, Halkier BA. Cloning of three A-type cytochromes P450, CYP71E1, CYP98, and CYP99 from Sorghum bicolor (L.) Moench by a PCR approach and identification by expression in Escherichia coli of CYP71E1 as a multifunctional cytochrome P450 … Plant Mol. Biol. 36: 393-405 (1998).

Baker KP, Boxer DH. Regulation of the chlA locus of Escherichia coli K12: involvement of molybdenum cofactor. Mol. Microbiol. 5: 901-907 (1991).

Balasundaram D, Tyagi AK. Modulation of arginine decarboxylase activity from Mycobacterium smegmatis. Evidence for pyridoxal-5'-phosphate-mediated conformational changes in the enzyme. Eur. J. Biochem. 183: 339-345 (1989).

Balderas-Hernandez VE, Sabido-Ramos A, Silva P, Cabrera-Valladares N, Hernandez-Chavez G, Baez-Viveros JL, Martinez A, Bolívar F, Gosset G. Metabolic engineering for improving anthranilate synthesis from glucose in Escherichia coli. Microb. Cell Fact. 8: 19 (2009).

Baldwin JC, Karthikeyan AS, Raghothama KG. LEPS2, a phosphorus starvation-induced novel acid phosphatase from tomato. Plant Physiol. 125: 728-737 (2001).

Baliarda A, Robert H, Jebbar M, Blanco C, Le Marrec C. Isolation and characterization of ButA, a secondary glycine betaine transport system operating in Tetragenococcus halophila. Curr. Microbiol. 47: 347-351 (2003).

Ball SG, Morell MK. From bacterial glycogen to starch: understanding the biogenesis of the plant starch granule. Annu. Rev. Plant Biol. 54: 207-233 (2003).

Ballicora MA, Laughlin MJ, Fu Y, Okita TW, Barry GF, Preiss J. Adenosine 5'-diphosphate-glucose pyrophosphorylase from potato tuber. Significance of the N terminus of the small subunit for catalytic properties and heat stability. Plant Physiol. 109: 245-251 (1995).

Baltes N, Hennig-Pauka I, Jacobsen I, Gruber AD, Gerlach GF. Identification of dimethyl sulfoxide reductase in Actinobacillus pleuropneumoniae and its role in infection. Infect. Immun. 71: 6784-6792 (2003).

Baltz RH. Genetic methods and strategies for secondary metabolite yield improvement in actinomycetes. Antonie Van Leewenhoek 79: 251-259 (2001).

Banerjee RV, Frasca V, Ballou DP, Matthews RG. Participation of cob(I) alamin in the reaction catalyzed by methionine synthase from Escherichia coli: a steady-state and rapid reaction kinetic analysis. Biochemistry 29: 11101-11109 (1990).

Bantignies B, Seguin J, Muzac I, Dedaldechamp F, Gulick P, Ibrahim R. Direct evidence for ribonucleolytic activity of a PR-10-like protein from white lupin roots. Plant Mol. Biol. 42: 871-881 (2000).

Bao W, Sheldon PJ, Hutchinson CR. Purification and properties of the Streptomyces peucetius DpsC beta-ketoacyl:acyl carrier protein synthase III that specifies the propionate-starter unit for type II polyketide biosynthesis. Biochemistry 38: 9752-9757 (1999).

Barber MJ, Desai SK, Marohnic CC, Hernandez HH, Pollock VV. Synthesis and bacterial expression of a gene encoding the heme domain of assimilatory nitrate reductase. Arch. Biochem. Biophys. 402: 38-50 (2002).

Barderi P, Campetella O, Frasch AC, Santome JA, Hellman U, Pettersson U, Cazzulo JJ. The NADP+-linked glutamate dehydrogenase from Trypanosoma cruzi: sequence, genomic organization and expression. Biochem. J. 330: 951-958 (1998).

Bardey V, Vallet C, Robas N, Charpentier B, Thouvenot B, Mougin A, Hajnsdorf E, Regnier P, Springer M, Branlant C. Characterization of the molecular mechanisms involved in the differential production of erythrose-4-phosphate dehydrogenase, 3-phosphoglycerate kinase and class II fructose-1,6-bisphosphate aldolase in Escherichia coli. Mol. Microbiol. 57: 1265-1287 (2005).

Baril C, Richaud C, Fournie E, Baranton G, Saint Girons I. Cloning of dapD, aroD and asd of Leptospira interrogans serovar icterohaemorrhagiae, and nucleotide sequence of the asd gene. J. Gen. Microbiol. 138: 47-53 (1992).

Barker JH, Slocombe SP, Ball KL, Hardie DG, Shewry PR, Halford NG. Evidence that barley 3-hydroxy-3-methylglutaryl-coenzyme A reductase kinase is a member of the sucrose nonfermenting-1-related protein kinase family. Plant Physiol. 112: 1141-1149 (1996).

Barkman TJ, Martins TR, Sutton E, Stout JT. Positive selection for single amino acid change promotes substrate discrimination of a plant volatile-producing enzyme. Mol. Biol. Evol. 24: 1320-1329 (2007).

Barra D, Martini F, Angelaccio S, Bossa F, Gavilanes F, Peterson D, Bullis B, Schirch L. Sequence homology between prokaryotic and eukaryotic forms of serine hydroxymethyltransferase. Biochem. Biophys. Res. Commun. 116: 1007-1012 (1983).

Barra L, Pica N, Gouffi K, Walker GC, Blanco C, Trautwetter A. Glucose 6-phosphate dehydrogenase is required for sucrose and trehalose to be efficient osmoprotectants in Sinorhizobium meliloti. FEMS Microbiol. Lett. 229: 183-188 (2003).

Barratt DH, Barber L, Kruger NJ, Smith AM, Wang TL, Martin C. Multiple, distinct isoforms of sucrose synthase in pea. Plant Physiol. 127: 655-664 (2001).

Barrero-Gil J, Rodríguez-Navarro A, Benito B. Cloning of the PpNHAD1 transporter of Physcomitrella patens, a chloroplast transporter highly conserved in photosynthetic eukaryotic organisms. J. Exp. Bot. 58: 2839-2849 (2007).

Barron A, Jung JU, Villarejo M. Purification and characterization of a glycine betaine binding protein from Escherichia coli. J. Biol. Chem. 262: 11841-11846 (1987).

Bartlem D, Lambein I, Okamoto T, Itaya A, Uda Y, Kijima F, Tamaki Y, Nambara E, Naito S. Mutation in the threonine synthase gene results in an over-accumulation of soluble methionine in Arabidopsis. Plant Physiol. 123: 101-110 (2000).

Bartling D, Weiler EW. Leucine aminopeptidase from Arabidopsis thaliana. Molecular evidence for a phylogenetically conserved enzyme of protein turnover in higher plants. Eur. J. Biochem. 205: 425-431 (1992).

Bartsch K, von Johnn-Marteville A, Schulz A. Molecular analysis of two genes of the Escherichia coli gab cluster: nucleotide sequence of the glutamate:succinic semialdehyde transaminase gene (gabT) and characterization of the succinic semialdehyde dehydrogenase gene (gabD). J. Bacteriol. 172: 7035-7042 (1990).

Basset GJ, Quinlivan EP, Ravanel S, Rebeille F, Nichols BP, Shinozaki K, Seki M, Adams-Phillips LC, Giovannoni JJ, Gregory JF 3rd, Hanson AD. Folate synthesis in plants: the p-aminobenzoate branch is initiated by a bifunctional PabA-PabB protein that is targeted to plastids. Proc. Natl. Acad. Sci. U.S.A. 101: 1496-1501 (2004).

Basset GJ, Ravanel S, Quinlivan EP, White R, Giovannoni JJ, Rebeille F, Nichols BP, Shinozaki K, Seki M, Gregory JF 3rd, Hanson AD. Folate synthesis in plants: the last step of the p-aminobenzoate branch is catalyzed by a plastidial aminodeoxychorismate lyase. Plant J. 40: 453-461 (2004).

Bastola DR, Pethe VV, Winicov I. Alfin1, a novel zinc-finger protein in alfalfa roots that binds to promoter elements in the salt-inducible MsPRP2 gene. Plant Mol. Biol. 38: 1123-1135 (1998).

Basurko MJ, Marche M, Darriet M, Cassaigne A. Phosphoserine aminotransferase, the second step-catalyzing enzyme for serine biosynthesis. IUBMB Life 48: 525-529 (1999).

Bate NJ, Sivasankar S, Moxon C, Riley JM, Thompson JE, Rothstein SJ. Molecular characterization of an Arabidopsis gene encoding hydroperoxide lyase, a cytochrome P-450 that is wound inducible. Plant Physiol. 117: 1393-1400 (1998).

Baum G, Chen Y, Arazi T, Takatsuji H, Fromm H. A plant glutamate decarboxylase containing a calmodulin binding domain. Cloning, sequence, and functional analysis. J. Biol. Chem. 268: 19610-19617 (1993).

Beagle JM, Apgar GA, Jones KL, Griswold KE, Radcliffe JS, Qiu X, Lightfoot DA, Iqbal MJ. The digestive fate of Escherichia coli glutamate dehydrogenase deoxyribonucleic acid from transgenic corn in diets fed to weanling pigs. J. Anim. Sci. 84: 597-607 (2006).

Bearne SL, Hekmat O, Macdonnell JE. Inhibition of Escherichia coli CTP synthase by glutamate gamma-semialdehyde and the role of the allosteric effector GTP in glutamine hydrolysis. Biochem. J. 356: 223-232 (2001).

Bearne SL, Wolfenden R. Glutamate gamma-semialdehyde as a natural transition state analogue inhibitor of Escherichia coli glucosamine-6-phosphate synthase. Biochemistry 34: 11515-11520 (1995).

Becker DF, Thomas EA. Redox properties of the PutA protein from Escherichia coli and the influence of the flavin redox state on PutA-DNA interactions. Biochemistry 40: 4714-4721 (2001).

Bedhomme M, Hoffmann M, McCarthy EA, Gambonnet B, Moran RG, Rebeille F, Ravanel S. Folate metabolism in plants: an Arabidopsis homolog of the mammalian mitochondrial folate transporter mediates folate import into chloroplasts. J. Biol. Chem. 280: 34823-34831 (2005).

Bednarek SY, Reynolds TL, Schroeder M, Grabowski R, Hengst L, Gallwitz D, Raikhel NV. A small GTP-binding protein from Arabidopsis thaliana functionally complements the yeast YPT6 null mutant. Plant Physiol. 104: 591-596 (1994).

Beekwilder J, Alvarez-Huerta M, Neef E, Verstappen FW, Bouwmeester HJ, Aharoni A. Functional characterization of enzymes forming volatile esters from strawberry and banana. Plant Physiol. 135: 1865-1878 (2004).

Begam M, Kumar S, Roy S, Campanella JJ, Kapoor HC. Molecular cloning and functional identification of a ribosome inactivating/antiviral protein from leaves of post-flowering stage of Celosia cristata and its expression in E. coli. Phytochemistry 67: 2441-2449 (2006).

Begley TJ, Samson LD. AlkB mystery solved: oxidative demethylation of N1-methyladenine and N3-methylcytosine adducts by a direct reversal mechanism. Trends Biochem. Sci. 28: 2-5 (2003).

Behal RH, Oliver DJ. NAD(+)-dependent isocitrate dehydrogenase from Arabidopsis thaliana. Characterization of two closely related subunits. Plant Mol. Biol. 36: 691-698 (1998).

Behrends V, Ebbels TM, Williams HD, Bundy JG. Time-resolved metabolic footprinting for nonlinear modeling of bacterial substrate utilization. Appl. Environ. Microbiol. 75: 2453-2463 (2009).

Beismann-Driemeyer S, Sterner R. Imidazole glycerol phosphate synthase from Thermotoga maritima - Quaternary structure, steady-state kinetics, and reaction mechanism of the bienzyme complex. J. Biol. Chem. 276: 20387-20396 (2001).

Bejar CM, Ballicora MA, Gomez-Casati DF, Iglesias AA, Preiss J. The ADP-glucose pyrophosphorylase from Escherichia coli comprises two tightly bound distinct domains. FEBS Lett. 573: 99-104 (2004).

Bejar CM, Jin X, Ballicora MA, Preiss J. Molecular architecture of the glucose 1-phosphate site in ADP-glucose pyrophosphorylases. J. Biol. Chem. 281: 40473-40484 (2006).

Belenghi B, Acconcia F, Trovato M, Perazzolli M, Bocedi A, Polticelli F, Ascenzi P, Delledonne M. AtCYS1, a cystatin from Arabidopsis thaliana, suppresses hypersensitive cell death. Eur. J. Biochem. 270: 2593-2604 (2003).

Bell E, Malmberg RL. Analysis of a cDNA encoding arginine decarboxylase from oat reveals similarity to the Escherichia coli arginine decarboxlase and evidence of protein processing. Mol. Gen. Genet. 224: 431-436 (1990).

Bell JK, Pease PJ, Bell JE, Grant GA, Banaszak LJ. De-regulation of D-3-phosphoglycerate dehydrogenase by domain removal. Eur. J. Biochem. 269: 4176-4184 (2002).

Bell KS, Sebaihia M, Pritchard L, Holden MT, Hyman LJ, Holeva MC, Thomson NR, Bentley SD, Churcher LJ, Mungall K, Atkin R, Bason N, Brooks K, Chillingworth T, Clark K, Doggett J, Fraser A, Hance Z, Hauser H, Jagels K, Moule S, Norbertczak H, et al. Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors. Proc. Natl. Acad. Sci. U.S.A. 101: 11105-11110 (2004).

Bell LC, Page MD, Berks BC, Richardson DJ, Ferguson SJ. Insertion of transposon Tn5 into a structural gene of the membrane-bound nitrate reductase of Thiosphaera pantotropha results in anaerobic overexpression of periplasmic nitrate reductase activity. J. Gen. Microbiol. 139: 3205-3214 (1993).

Bellafiore S, Ferris P, Naver H, Gohre V, Rochaix JD. Loss of Albino3 leads to the specific depletion of the light-harvesting system. Plant Cell 14: 2303-2314 (2002).

Bellissimo DB, Privalle LS. Expression of spinach nitrite reductase in Escherichia coli: site-directed mutagenesis of predicted active site amino acids. Arch. Biochem. Biophys. 323: 155-163 (1995).

Bellucci M, Ederli L, De Marchis F, Pasqualini S, Arcioni S. Transformation of Lotus corniculatus plants with Escherichia coli asparagine synthetase A: effect on nitrogen assimilation and plant development. Plant Cell Tissue Organ Cult. 78: 139-150 (2004).

Bender RA, Macaluso A, Magasanik B. Glutamate dehydrogenase: genetic mapping and isolation of regulatory mutants of Klebsiella aerogenes. J. Bacteriol. 127: 141-148 (1976).

Bender RA, Magasanik B. Autogenous regulation of the synthesis of glutamine synthetase in Klebsiella aerogenes. J. Bacteriol. 132: 106-112 (1977).

Benichou M, Li Z, Tournier B, Chaves A, Zegzouti H, Jauneau A, Delalande C, Latche A, Bouzayen M, Spremulli LL, Pech JC. Tomato EF-Ts(mt), a functional mitochondrial translation elongation factor from higher plants. Plant Mol. Biol. 53: 411-422 (2003).

Bennett B, Langan P, Coates L, Mustyakimov M, Schoenborn B, Howell EE, Dealwis C. Neutron diffraction studies of Escherichia coli dihydrofolate reductase complexed with methotrexate. Proc. Natl. Acad. Sci. U.S.A. 103: 18493-18498 (2006).

Bennett GN, San KY. Microbial formation, biotechnological production and applications of 1,2-propanediol. Appl. Microbiol. Biotechnol. 55: 1-9 (2001).

Bennett M, Cullimore J. Expression of three plant glutamine synthetase cDNA in Escherichia coli. Formation of catalytically active isoenzymes, and complementation of a glnA mutant. Eur. J. Biochem. 193: 319-324 (1990).

Berberich MA. Effect of some D-amino acids on the steady-state level of glutamine synthetase in Escherichia coli. J. Bacteriol. 163: 1109-1113 (1985).

Berberich MA. Catabolism and nitrogen control in Escherichia coli. Curr. Top. Cell Regul. 26: 491-502 (1985).

Berducci G, Mazzetti AP, Rotilio G, Battistoni A. Periplasmic competition for zinc uptake between the metallochaperone ZnuA and Cu,Zn superoxide dismutase. FEBS Lett. 569: 289-292 (2004).

Berendt U, Haverkamp T, Prior A, Schwenn JD. Reaction mechanism of thioredoxin: 3'-phospho-adenylylsulfate reductase investigated by site-directed mutagenesis. Eur. J. Biochem. 233: 347-356 (1995).

Bereswill S, Fassbinder F, Volzing C, Haas R, Reuter K, Ficner R, Kist M. Cloning and functional characterization of the genes encoding 3-dehydroquinate synthase (aroB) and tRNA-guanine transglycosylase (tgt) from Helicobacter pylori. Med. Microbiol. Immunol. (Berl.) 186: 125-134 (1997).

Berg BL, Stewart V. Structural genes for nitrate-inducible formate dehydrogenase in Escherichia coli K-12. Genetics 125: 691-702 (1990).

Berg CM, Whalen WA, Archambault LB. Role of alanine-valine transaminase in Salmonella typhimurium and analysis of an avtA::Tn5 mutant. J. Bacteriol. 155: 1009-1014 (1983).

Berg HC. The rotary motor of bacterial flagella. Annu. Rev. Biochem. 72: 19-54 (2003).

Berger A, Meinhard J, Petersen M. Rosmarinic acid synthase is a new member of the superfamily of BAHD acyltransferases. Planta 224: 1503-1510 (2006).

Bergkamp RJ, Geerse RH, Verbakel JM, Musters W, Planta RJ. Cloning and disruption of the LEU2 gene of Kluyveromyces marxianus CBS 6556. Yeast 7: 963-970 (1991).

Berkovitch F, Nicolet Y, Wan JT, Jarrett JT, Drennan CL. Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme. Science 303: 76-79 (2004).

Berlett BS, Friguet B, Yim MB, Chock PB, Stadtman ER. Peroxynitrite-mediated nitration of tyrosine residues in Escherichia coli glutamine synthetase mimics adenylylation: relevance to signal transduction. Proc. Natl. Acad. Sci. U.S.A. 93: 1776-1780 (1996).

Berlett BS, Levine RL, Stadtman ER. Carbon dioxide stimulates peroxynitrite-mediated nitration of tyrosine residues and inhibits oxidation of methionine residues of glutamine synthetase: both modifications mimic effects of adenylylation. Proc. Natl. Acad. Sci. U.S.A. 95: 2784-2789 (1998).

Berlett BS, Levine RL, Stadtman ER. Comparison of the effects of ozone on the modification of amino acid residues in glutamine synthetase and bovine serum albumin. J. Biol. Chem. 271: 4177-4182 (1996).

Berlicki L, Obojska A, Forlani G, Kafarski P. Design, synthesis, and activity of analogues of phosphinothricin as inhibitors of glutamine synthetase. J. Med. Chem. 48: 6340-6449 (2005).

Bernal V, Arense P, Blatz V, Mandrand-Berthelot MA, Cánovas M, Iborra JL. Role of betaine:CoA ligase (CaiC) in the activation of betaines and the transfer of coenzyme A in Escherichia Coli. J. Appl. Microbiol. 105: 42-50 (2008).

Bernard T, Ayache M, Le Rudulier D. Restoration, by glycine betaine, of growth and enzyme activities of Escherichia coli Lac-mutants. C. R. Acad. Sci. III 307: 99-104 (1988).

Bernard T, Jebbar M, Rassouli Y, Himdikabbab S, Hamelin J, Blanco C. Ectoine accumulation and osmotic regulation in Brevibacterium linens. J. Gen. Microbiol. 139: 129-136 (1993).

Bernasconi P, Walters EW, Woodworth AR, Siehl DL, Stone TE, Subramanian MV. Functional expression of Arabidopsis thaliana anthranilate synthase subunit I in Escherichia coli. Plant Physiol. 106: 353-358 (1994).

Bernasconi P, Woodworth AR, Rosen BA, Subramanian MV, Siehl DL. A naturally occurring point mutation confers broad range tolerance to herbicides that target acetolactate synthase. J. Biol. Chem. 270: 17381-17385 (1995).

Bernstein JR, Bulter T, Liao JC. Transfer of the high-GC cyclohexane carboxylate degradation pathway from Rhodopseudomonas palustris to Escherichia coli for production of biotin. Metab. Eng. 10: 131-140 (2008).

Berrios-Rivera SJ, Bennett GN, San KY. The effect of increasing NADH availability on the redistribution of metabolic fluxes in Escherichia coli chemostat cultures. Metab. Eng. 4: 230-237 (2002).

Berrios-Rivera SJ, Bennett GN, San KY. Metabolic engineering of Escherichia coli: increase of NADH availability by overexpressing an NAD(+)-dependent formate dehydrogenase. Metab. Eng. 4: 217-229 (2002).

Berrios-Rivera SJ, San KY, Bennett GN. The effect of NAPRTase overexpression on the total levels of NAD, the NADH/NAD+ ratio, and the distribution of metabolites in Escherichia coli. Metab. Eng. 4: 238-247 (2002).

Berrios-Rivera SJ, Yang YT, Bennett GN, San KY. Effect of glucose analog supplementation on metabolic flux distribution in anaerobic chemostat cultures of Escherichia coli. Metab. Eng. 2: 149-154 (2000).

Berry A. Improving production of aromatic compounds in Escherichia coli by metabolic engineering. Trends Biotechnol. 14: 250-256 (1996).

Bertero MG, Rothery RA, Boroumand N, Palak M, Blasco F, Ginet N, Weiner JH, Strynadka NC. Structural and biochemical characterization of a quinol binding site of Escherichia coli nitrate reductase A. J. Biol. Chem. 280: 14836-14843 (2005).

Bertero MG, Rothery RA, Palak M, Hou C, Lim D, Blasco F, Weiner JH, Strynadka NCJ. Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A. Nat. Struct. Biol. 10: 681-687 (2003).

Bertoldi M, Carbone V, Borri Voltattorni C. Ornithine and glutamate decarboxylases catalyse an oxidative deamination of their alpha-methyl substrates. Biochem. J. 342: 509-512 (1999).

Betti M, Arcondeguy T, Marquez AJ. Molecular analysis of two mutants from Lotus japonicus deficient in plastidic glutamine synthetase: functional properties of purified GLN2 enzymes. Planta 224: 1068-1079 (2006).

Bevers LE, Hagedoorn PL, Krijger GC, Hagen WR. Tungsten transport protein A (WtpA) in Pyrococcus furiosus: the first member of a new class of tungstate and molybdate transporters. J. Bacteriol. 188: 6498-6505 (2006).

Bevers LE, Hagedoorn PL, Santamaria-Araujo JA, Magalon A, Hagen WR, Schwarz G. Function of MoaB proteins in the biosynthesis of the molybdenum and tungsten cofactors. Biochemistry 47: 949-956 (2008).

Bhartiya S, Rawool S, Venkatesh KV. Dynamic model of Escherichia coli tryptophan operon shows an optimal structural design. Eur. J. Biochem. 270: 2644-2651 (2003).

Bhat PJ, Venkatesh KV. Stochastic variation in the concentration of a repressor activates GAL genetic switch: implications in evolution of regulatory network. FEBS Lett. 579: 597-603 (2005).

Bhuiya MW, Sakuraba H, Kujo C, Nunoura-Kominato N, Kawarabayasi Y, Kikuchi H, Ohshima T. Glutamate dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix K1: enzymatic characterization, identification of the encoding gene, and phylogenetic implications. Extremophiles 4: 333-341 (2000).

Biagini A, Puigserver A. Sequence analysis of the aminoacylase-1 family. A new proposed signature for metalloexopeptidases. Comp. Biochem. Physiol. B. Biochem. Mol. Biol. 128: 469-481 (2001).

Biastoff S, Brandt W, Drager B. Putrescine N-methyltransferase - the start for alkaloids. Phytochemistry Aug 1 [Epub ahead of print] (2009).

Bick JA, Aslund F, Chen Y, Leustek T. Glutaredoxin function for the carboxyl-terminal domain of the plant-type 5'-adenylylsulfate reductase. Proc. Natl. Acad. Sci. U.S.A. 95: 8404-8409 (1998).

Bick JA, Dennis JJ, Zylstra GJ, Nowack J, Leustek T. Identification of a new class of 5'-adenylylsulfate (APS) reductases from sulfate-assimilating bacteria. J. Bacteriol. 182: 135-142 (2000).

Bick JA, Setterdahl AT, Knaff DB, Chen Y, Pitcher LH, Zilinskas BA, Leustek T. Regulation of the plant-type 5'-adenylyl sulfate reductase by oxidative stress. Biochemistry 40: 9040-9048 (2001).

Biellmann JF, Eid P, Hirth C. Affinity labeling of the Escherichia coli aspartate-beta-semialdehyde dehydrogenase with an alkylating coenzyme analogue. Half-site reactivity and competition with the substrate alkylating analogue. Eur. J. Biochem. 104: 65-69 (1980).

Biellmann JF, Eid P, Hirth C, Jornvall H. Aspartate-beta-semialdehyde dehydrogenase from Escherichia coli. Affinity labeling with the substrate analogue L-2-amino-4-oxo-5-chloropentanoic acid: an example of half-site reactivity. Eur. J. Biochem. 104: 59-64 (1980).

Biellmann JF, Eid P, Hirth C, Jornvall H. Aspartate-beta-semialdehyde dehydrogenase from Escherichia coli. Purification and general properties. Eur. J. Biochem. 104: 53-58 (1980).

Biemans-Oldehinkel E, Poolman B. On the role of the two extracytoplasmic substrate-binding domains in the ABC transporter OpuA. EMBO J. 22: 5983-5993 (2003).

Bild GS, Boyer PD. Subunit interaction during catalysis: ammonium ion modulation of catalytic steps in the Escherichia coli glutamine synthetase reaction. Biochemistry 19: 5774-5781 (1980).

Bilsel O, Yang L, Zitzewitz JA, Beechem JM, Matthews CR. Time-resolved fluorescence anisotropy study of the refolding reaction of the alpha-subunit of tryptophan synthase reveals nonmonotonic behavior of the rotational correlation time. Biochemistry 38: 4177-4187 (1999).

Bilsel O, Zitzewitz JA, Bowers KE, Matthews CR. Folding mechanism of the alpha-subunit of tryptophan synthase, an alpha/beta barrel protein: global analysis highlights the interconversion of multiple native, intermediate, and unfolded forms through parallel channels. Biochemistry 38: 1018-1029 (1999).

Birolo L, Dal Piaz F, Pucci P, Marino G. Structural characterization of the M* partly folded intermediate of wild type and P138A aspartate aminotransferase from Escherichia coli. J. Biol. Chem. 277: 17428-17437 (2002).

Birolo L, Malashkevich VN, Capitani G, De Luca F, Moretta A, Jansonius JN, Marino G. Functional and structural analysis of cis-proline mutants of Escherichia coli aspartate aminotransferase. Biochemistry 38: 905-913 (1999).

Birolo L, Tutino ML, Fontanella B, Gerday C, Mainolfi K, Pascarella S, Sannia G, Vinci F, Marino G. Aspartate aminotransferase from the Antarctic bacterium Pseudoalteromonas haloplanktis TAC 125. Cloning, expression, properties, and molecular modelling. Eur. J. Biochem. 267: 2790-2802 (2000).

Bischoff M, Rosler J, Raesecke HR, Gorlach J, Amrhein N, Schmid J. Cloning of a cDNA encoding a 3-dehydroquinate synthase from a higher plant, and analysis of the organ-specific and elicitor-induced expression of the corresponding gene. Plant Mol. Biol. 31: 69-76 (1996).

Bischoff M, Schaller A, Bieri F, Kessler F, Amrhein N, Schmid J. Molecular characterization of tomato 3-dehydroquinate dehydratase-shikimate:NADP oxidoreductase. Plant Physiol. 125: 1891-1900 (2001).

Bitonti AJ, McCann PP, Sjoerdsma A. Restriction of bacterial growth by inhibition of polyamine biosynthesis by using monofluoromethylornithine, difluoromethylarginine and dicyclohexylammonium sulphate. Biochem. J. 208: 435-441 (1982).

Blanchard CZ, Lee YM, Frantom PA, Waldrop GL. Mutations at four active site residues of biotin carboxylase abolish substrate-induced synergism by biotin. Biochemistry 38: 3393-3400 (1999).

Blanco-Rivero MC, Takabe T, Viale AM. Functional differences between cyanobacterial DnaK1 chaperones from the halophyte Aphanothece halophytica and the freshwater species Synechococcus elongatus expressed in Escherichia coli. Curr. Microbiol. 51: 164-170 (2005).

Blank LM, Ebert BE, Buhler B, Schmid A. Metabolic capacity estimation of Escherichia coli as a platform for redox biocatalysis: constraint-based modeling and experimental verification. Biotechnol. Bioeng. 100: 1050-1065 (2008).

Blankenhorn D, Phillips J, Slonczewski JL. Acid- and base-induced proteins during aerobic and anaerobic growth of Escherichia coli revealed by two-dimensional gel electrophoresis. J. Bacteriol. 181: 2209-2216 (1999).

Blasco F, Dos Santos JP, Magalon A, Frixon C, Guigliarelli B, Santini CL, Giordano G. NarJ is a specific chaperone required for molybdenum cofactor assembly in nitrate reductase A of Escherichia coli. Mol. Microbiol. 28: 435-447 (1998).

Blasco F, Guigliarelli B, Magalon A, Asso M, Giordano G, Rothery RA. The coordination and function of the redox centres of the membrane-bound nitrate reductases. Cell Mol. Life Sci. 58: 179-193 (2001).

Blasco F, Iobbi C, Giordano G, Chippaux M, Bonnefoy V. Nitrate reductase of Escherichia coli: completion of the nucleotide sequence of the nar operon and reassessment of the role of the alpha and beta subunits in iron binding and electron transfer. Mol. Gen. Genet. 218: 249-256 (1989).

Blasco F, Iobbi C, Ratouchniak J, Bonnefoy V, Chippaux M. Nitrate reductases of Escherichia coli: sequence of the second nitrate reductase and comparison with that encoded by the narGHJI operon. Mol. Gen. Genet. 222: 104-111 (1990).

Blasco F, Pommier J, Augier V, Chippaux M, Giordano G. Involvement of the narJ or narW gene product in the formation of active nitrate reductase in Escherichia coli. Mol. Microbiol. 6: 221-230 (1992).

Blaszczyk A, Sirko L, Hawkesford MJ, Sirko A. Biochemical analysis of transgenic tobacco lines producing bacterial serine acetyltransferase. Plant Sci. 162: 589-597 (2002).

Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y. The complete genome sequence of Escherichia coli K-12. Science 277: 1453-1474 (1997).

Blauwkamp TA, Ninfa AJ. Physiological role of the GlnK signal transduction protein of Escherichia coli: survival of nitrogen starvation. Mol. Microbiol. 46: 203-214 (2002).

Blauwkamp TA, Ninfa AJ. Nac-mediated repression of the serA promoter of Escherichia coli. Mol. Microbiol. 45: 351-363 (2002).

Blickling S, Beisel HG, Bozic D, Knablein J, Laber B, Huber R. Structure of dihydrodipicolinate synthase of Nicotiana sylvestris reveals novel quaternary structure. J. Mol. Biol. 274: 608-621 (1997).

Blickling S, Renner C, Laber B, Pohlenz HD, Holak TA, Huber R. Reaction mechanism of Escherichia coli dihydrodipicolinate synthase investigated by X-ray crystallography and NMR spectroscopy. Biochemistry 36: 24-33 (1997).

Block MA, Tewari AK, Albrieux C, Marechal E, Joyard J. The plant S-adenosyl-L-methionine:Mg-protoporphyrin IX methyltransferase is located in both envelope and thylakoid chloroplast membranes. Eur. J. Biochem. 269: 240-248 (2002).

Blokesch M, Rohrmoser M, Rode S, Bock A. HybF, a zinc-containing protein involved in NiFe. hydrogenase maturation. J. Bacteriol. 186: 2603-2611 (2004).

Bloom F, Smith CJ, Jessee J, Veileux B, Deutch AH. The use of genetically engineered strains of Escherichia coli for the overproduction of free amino acids: proline as a model system. In "Advances in Gene Technology: Molecular Genetics of Plants and Animals", Academic Press, New York, pp. 383-394 (1983).

Bloom FR, Levin MS, Foor F, Tyler B. Regulation of glutamine synthetase formation in Escherichia coli: characterization of mutants lacking the uridylyltransferase. J. Bacteriol. 134: 569-577 (1978).

Bloom FR, Streicher SL, Tyler B. Regulation of enzyme synthesis by the glutamine synthetase of Salmonella typhimurium: a factor in addition to glutamine synthetase is required for activation of enzyme formation. J. Bacteriol. 130: 983-990 (1977).

Bloss T, Clemens S, Nies DH. Characterization of the ZAT1p zinc transporter from Arabidopsis thaliana in microbial model organisms and reconstituted proteoliposomes. Planta 214: 783-791 (2002).

Board PG, Baker RT, Chelvanayagam G, Jermiin LS. Zeta, a novel class of glutathione transferases in a range of species from plants to humans. Biochem. J. 328: 929-935 (1997).

Boch J, Kempf B, Schmid R, Bremer E. Synthesis of the osmoprotectant glycine betaine in Bacillus subtilis: characterization of the gbsAB genes. J. Bacteriol. 178: 5121-5129 (1996).

Boch J, Nau-Wagner G, Kneip S, Bremer E. Glycine betaine aldehyde dehydrogenase from Bacillus subtilis: characterization of an enzyme required for the synthesis of the osmoprotectant glycine betaine. Arch. Microbiol. 168: 282-289 (1997).

Bodei C, Bracciali A, Chiarugi D. On deducing causality in metabolic networks. BMC Bioinformatics 9 Suppl. 4: S8 (2008).

Bodenmiller DM, Spiro S. The yjeB (nsrR) gene of Escherichia coli encodes a nitric oxide-sensitive transcriptional regulator. J. Bacteriol. 188: 874-881 (2006).

Boehlein SK, Richards NG, Walworth ES, Schuster SM. Arginine 30 and asparagine 74 have functional roles in the glutamine dependent activities of Escherichia coli asparagine synthetase B. J. Biol. Chem. 269: 26789-26795 (1994).

Boehlein SK, Schuster SM, Richards NG. Glutamic acid gamma-monohydroxamate and hydroxylamine are alternate substrates for Escherichia coli asparagine synthetase B. Biochemistry 35: 3031-3037 (1996).

Boehlein SK, Stewart JD, Walworth ES, Thirumoorthy R, Richards NG, Schuster SM. Kinetic mechanism of Escherichia coli asparagine synthetase B. Biochemistry 37: 13230-13238 (1998).

Boehlein SK, Walworth ES, Richards NG, Schuster SM. Mutagenesis and chemical rescue indicate residues involved in beta-aspartyl-AMP formation by Escherichia coli asparagine synthetase B. J. Biol. Chem. 272: 12384-12392 (1997).

Boehlein SK, Walworth ES, Schuster SM. Identification of cysteine-523 in the aspartate binding site of Escherichia coli asparagine synthetase B. Biochemistry 36: 10168-10177 (1997).

Bogdanova N, Hell R. Cysteine synthesis in plants: protein-protein interactions of serine acetyltransferase from Arabidopsis thaliana. Plant J. 11: 251-262 (1997).

Boghigian BA, Pfeifer BA. Current status, strategies, and potential for the metabolic engineering of heterologous polyketides in Escherichia coli. Biotechnol. Lett. 30: 1323-1330 (2008).

Bohlmann J, De Luca V, Eilert U, Martin W. Purification and cDNA cloning of anthranilate synthase from Ruta graveolens: modes of expression and properties of native and recombinant enzymes. Plant J. 7: 491-501 (1995).

Bohlmann J, Lins T, Martin W, Eilert U. Anthranilate synthase from Ruta graveolens. Duplicated AS alpha genes encode tryptophan-sensitive and tryptophan-insensitive isoenzymes specific to amino acid and alkaloid biosynthesis. Plant Physiol. 111: 507-514 (1996).

Bohlmann J, Martin D, Oldham NJ, Gershenzon J. Terpenoid secondary metabolism in Arabidopsis thaliana: cDNA cloning, characterization, and functional expression of a myrcene/(E)-beta-ocimene synthase. Arch. Biochem. Biophys. 375: 261-269 (2000).

Bohlmann J, Phillips M, Ramachandiran V, Katoh S, Croteau R. cDNA cloning, characterization, and functional expression of four new monoterpene synthase members of the Tpsd gene family from grand fir (Abies grandis). Arch. Biochem. Biophys. 368: 232-243 (1999).

Boldt R, Edner C, Kolukisaoglu U, Hagemann M, Weckwerth W, Wienkoop S, Morgenthal K, Bauwe H. D-GLYCERATE 3-KINASE, the last unknown enzyme in the photorespiratory cycle in Arabidopsis, belongs to a novel kinase family. Plant Cell 17: 2413-2420 (2005).

Bolognesi A, Polito L, Olivieri F, Valbonesi P, Barbieri L, Battelli MG, Carusi MV, Benvenuto E, Del Vecchio Blanco F, Di Maro A, Parente A, Di Loreto M, Stirpe F. New ribosome-inactivating proteins with polynucleotide:adenosine glycosidase and antiviral activities from Basella rubra L. and bougainvillea spectabilis Willd. Planta 203: 422-429 (1997).

Bolte S, Schiene K, Dietz KJ. Characterization of a small GTP-binding protein of the rab 5 family in Mesembryanthemum crystallinum with increased level of expression during early salt stress. Plant Mol. Biol. 42: 923-936 (2000).

Boncompagni E, Dupont L, Mignot T, Osteras M, Lambert A, Poggi MC, Le Rudulier D. Characterization of a Snorhizobium meliloti ATP-binding cassette histidine transporter also involved in betaine and proline uptake. J. Bacteriol. 182: 3717-3725 (2000).

Bondaryk RP, Paulus H. Cloning and structure of the gene for the subunits of aspartokinase II from Bacillus subtilis. J. Biol. Chem. 260: 585-591 (1985).

Bondaryk RP, Paulus H. Expression of the gene for Bacillus subtilis aspartokinase II in Escherichia coli. J. Biol. Chem. 260: 592-597 (1985).

Bongaerts R, Verpoorte R. HPLC assays for the chorismate utilizing enzymes chorismate pyruvate lyase and para-aminobenzoate synthase. J. Liq. Chromatogr. Relat. Technol. 23: 2703-2713 (2000).

Bonnefoy V, Demoss JA. Nitrate reductases in Escherichia coli. Antonie Van Leeuwenhoek 66: 47-56 (1994).

Bonnefoy V, Ratouchniak J, Blasco F, Chippaux M. Organization of the nar genes at the chlZ locus. FEMS Microbiol. Lett. 147: 147-149 (1997).

Bonner CA, Fischer RS, Ahmad S, Jensen RA. Remnants of an ancient pathway to L-phenylalanine and L-tyrosine in enteric bacteria: evolutionary implications and biotechnological impact. Appl. Environ. Microbiol. 56: 3741-3747 (1990).

Bonner CA, Jensen RA. Cloning of cDNA encoding the bifunctional dehydroquinase.shikimate dehydrogenase of aromatic-amino-acid biosynthesis in Nicotiana tabacum. Biochem. J. 302: 11-14 (1994).

Bono H, Ogata H, Goto S, Kanehisa M. Reconstruction of amino acid biosynthesis pathways from the complete genome sequence. Genome Res. 8: 203-210 (1998).

Bonomo J, Warnecke T, Hume P, Marizcurrena A, Gill RT. A comparative study of metabolic engineering anti-metabolite tolerance in Escherichia coli. Metab. Eng. 8: 227-239 (2006).

Boos W, Ehmann U, Forkl H, Klein W, Rimmele M, Postma P. Trehalose transport and metabolism in Escherichia coli. J. Bacteriol. 172: 3450-3461 (1990).

Bordo D, van Monfort RL, Pijning T, Kalk KH, Reizer J, Saier MH Jr, Dijkstra BW. The three-dimensional structure of the nitrogen regulatory protein IIANtr from Escherichia coli. J. Mol. Biol. 279: 245-255 (1998).

Bork P, Dandekar T, Diaz-Lazcoz Y, Eisenhaber F, Huynen M, Yuan YP. Predicting function: from genes to genomes and back. J. Mol. Biol. 283: 707-725 (1998).

Bormann ER, Eikmanns BJ, Sahm H. Molecular analysis of the Corynebacterium glutamicum gdh gene encoding glutamate dehydrogenase. Mol. Microbiol. 6: 317-326 (1992).

Born TL, Zheng R, Blanchard JS. Hydrolysis of N-succinyl-L,L-diaminopimelic acid by the Haemophilus influenzae dapE-encoded desuccinylase: metal activation, solvent isotope effects, and kinetic mechanism. Biochemistry 37: 10478-10487 (1998).

Bornemann S, Lowe DJ, Thorneley RN. The transient kinetics of Escherichia coli chorismate synthase: substrate consumption, product formation, phosphate dissociation, and characterization of a flavin intermediate. Biochemistry 35: 9907-9916 (1996).

Bornemann S, Ramjee MK, Balasubramanian S, Abell C, Coggins JR, Lowe DJ, Thorneley RN. Escherichia coli chorismate synthase catalyzes the conversion of (6S)-6-fluoro-5-enolpyruvylshikimate-3-phosphate to 6-fluorochorismate. Implications for the enzyme mechanism and the antimicrobial action of (6S)-6-fluoroshikimate. J. Biol. Chem. 270: 22811-22815 (1995).

Borst DW, Blumenthal RM, Matthews RG. Use of an in vivo titration method to study a global regulator: effect of varying Lrp levels on expression of gltBDF in Escherichia coli. J. Bacteriol. 178: 6904-6912 (1996).

Bortolotti C, Cordeiro A, Alcazar R, Borrell A, Culianez-Macia FA, Tiburcio AF, Altabella T. Localization of arginine decarboxylase in tobacco plants. Physiol. Plant. 120: 84-92 (2004).

Boscari A, Mandon K, Dupont L, Poggi MC, Le Rudulier D. BetS is a major glycine betaine/proline betaine transporter required for early osmotic adjustment in Sinorhizobium meliloti. J. Bacteriol. 184: 2654-2663 (2002).

Bose N, Greenspan P, Momany C. Expression of recombinant human betaine: homocysteine S-methyltransferase for X-ray crystallographic studies and further characterization of interaction with S-adenosylmethionine. Protein Expr. Purif. 25: 73-80 (2002).

Bossa F, Maras B, De Biase D, John RA, Barra D. Sequence studies on pyridoxal phosphate-dependent enzymes. Biotechnol. Appl. Biochem. 18: 143-148 (1993).

Bothast RJ, Nichols NN, Dien BS. Fermentations with new recombinant organisms. Biotechnol. Prog. 15: 867-875 (1999).

Bottomley JR, Clayton CL, Chalk PA, Kleanthous C. Cloning, sequencing, expression, purification and preliminary characterization of a type II dehydroquinase from Helicobacter pylori. Biochem. J. 319: 559-565 (1996).

Botzenhardt J, Morbach S, Kramer R. Activity regulation of the betaine transporter BetP of Corynebacterium glutamicum in response to osmotic compensation. Biochim. Biophys. Acta 1667: 229-240 (2004).

Bourgault R, Bewley JD. Variation in its C-terminal amino acids determines whether endo-beta-mannanase is active or inactive in ripening tomato fruits of different cultivars. Plant Physiol. 130: 1254-1262 (2002).

Bourgis F, Kader JC, Barret P, Renard M, Robinson D, Robinson C, Delseny M, Roscoe TJ. A plastidial lysophosphatidic acid acyltransferase from oilseed rape. Plant Physiol. 120: 913-922 (1999).

Bourot S, Sire O, Trautwetter A, Touze T, Wu LF, Blanco C, Bernard T. Glycine betaine-assisted protein folding in a lysA mutant of Escherichia coli. J. Biol. Chem. 275: 1050-1056 (2000).

Bouvier J, Bordes P, Romeo Y, Fourcans A, Bouvier I, Gutierrez C. Characterization of OpuA, a glycine-betaine uptake system of Lactococcus lactis. J. Mol. Microbiol. Biotechnol. 2: 199-205 (2000).

Bouvier J, Richaud C, Higgins W, Bogler O, Stragier P. Cloning, characterization, and expression of the dapE gene of Escherichia coli. J. Bacteriol. 174: 5265-5271 (1992).

Bouwmeester HJ, Kodde J, Verstappen FW, Altug IG, De Kraker JW, Wallaart TE. Isolation and characterization of two germacrene a synthase cDNA clones from chicory. Plant Physiol. 129: 134-144 (2002).

Bowen TL, Union J, Tumbula DL, Whitman WB. Cloning and phylogenetic analysis of the genes encoding acetohydroxyacid synthase from the archaeon Methanococcus aeolicus. Gene 188: 77-84 (1997).

Boxer DH. Involvement of the chlorate resistance loci and the molybdenum cofactor in the biosynthesis of the Escherichia coli nitrate reductase. In "Molecular and Genetic Aspects of Nitrate Assimilation" (JL Wray, JR Kinghorn eds) Oxford Science Publications, Oxford, pp. 27-39 (1989).

Boy E, Borne F, Patte JC. Isolation and identification of mutants constitutive for aspartokinase III synthesis in Escherichia coli K 12. Biochimie 61: 1151-1160 (1979).

Boyaval P, Deborde C, Corre C, Blanco C, Begue E. Stress and osmoprotection in propionibacteria. Lait 79: 59-69 (1999).

Boyd LA, Adam L, Pelcher LE, McHughen A, Hirji R, Selvaraj G. Characterization of an Escherichia coli gene encoding betaine aldehyde dehydrogenase (BADH): structural similarity to mammalian ALDHs and a plant BADH. Gene 103: 45-52 (1991).

Boyen A, Charlier D, Charlier J, Sakanyan V, Mett I, Glansdorff N. Acetylornithine deacetylase, succinyldiaminopimelate desuccinylase and carboxypeptidase G2 are evolutionarily related. Gene 116: 1-6 (1992).

Boyle SM, MacIntyre MF, Sells BH. Polyamine levels in Escherichia coli during nutritional shiftup and exponential growth. Biochim. Biophys. Acta 477: 221-227 (1977).

Brabban AD, Edwards C. The effects of glucosinolates and their hydrolysis products on microbial growth. J. Appl. Bacteriol. 79: 171-177 (1995).

Brandl MT, Lindow SE. Cloning and characterization of a locus encoding an indolepyruvate decarboxylase involved in indole-3-acetic acid synthesis in Erwinia herbicola. Appl. Environ. Microbiol. 62: 4121-4128 (1996).

Braun M, Henstrand JM, Gorlach J, Amrhein N, Schmid J. Enzymatic properties of chorismate synthase isozymes of tomato (Lycopersicon esculentum Mill.). Planta 200: 64-70 (1996).

Braun V, Braun M. Iron transport and signaling in Escherichia coli. FEBS Lett. 529: 78-85 (2002).

Brautaset T, Petersen S, Valla S. An experimental study on carbon flow in Escherichia coli as a function of kinetic properties and expression levels of the enzyme phosphoglucomutase. Biotechnol. Bioeng. 58: 299-302 (1998).

Brautaset T, Petersen SB, Valla S. In vitro determined kinetic properties of mutant phosphoglucomutases and their effects on sugar catabolism in Escherichia coli. Metab. Eng. 2: 104-114 (2000).

Bravo JM, Campo S, Murillo I, Coca M, San Segundo B. Fungus- and wound-induced accumulation of mRNA containing a class II chitinase of the pathogenesis-related protein 4 (PR-4) family of maize. Plant Mol. Biol. 52: 745-759 (2003).

Bray D, Bourret RB, Simon MI. Computer simulation of the phosphorylation cascade controlling bacterial chemotaxis. Mol. Biol. Cell 4: 469-482 (1993).

Brechtel CE, Hu L, King SC. Substrate specificity of the Escherichia coli 4-aminobutyrate carrier encoded by gabP. Uptake and counterflow of structurally diverse molecules. J. Biol. Chem. 271: 783-788 (1996).

Brechtel CE, King SC. 4-Aminobutyrate (GABA) transporters from the amine-polyamine-choline superfamily: substrate specificity and ligand recognition profile of the 4-aminobutyrate permease from Bacillus subtilis. Biochem. J. 333: 565-571 (1998).

Breitenbach J, Fernandez-Gonzalez B, Vioque A, Sandmann G. A higher-plant type zeta-carotene desaturase in the cyanobacterium Synechocystis PCC6803. Plant Mol. Biol. 36: 725-732 (1998).

Breitinger U, Clausen T, Ehlert S, Huber R, Laber B, Schmidt F, Pohl E, Messerschmidt A. The three-dimensional structure of cystathionine beta-lyase from Arabidopsis and its substrate specificity. Plant Physiol. 126: 631-642 (2001).

Breksa AP 3rd, Garrow TA. Random mutagenesis of the zinc-binding motif of betaine-homocysteine methyltransferase reveals that Gly 214 is essential. Arch. Biochem. Biophys. 399: 73-80 (2002).

Brill EM, Abrahams S, Hayes CM, Jenkins CL, Watson JM. Molecular characterisation and expression of a wound-inducible cDNA encoding a novel cinnamyl-alcohol dehydrogenase enzyme in lucerne (Medicago sativa L.) Plant Mol. Biol. 41: 279-291 (1999).

Brinch-Pedersen H, Galili G, Knudsen S, Holm PB. Engineering of the aspartate family biosynthetic pathway in barley (Hordeum vulgare L.) by transformation with heterologous genes encoding feed-back-insensitive aspartate kinase and dihydrodipicolinate synthase. Plant Mol. Biol. 32: 611-620 (1996).

Brinch-Pedersen H, Olsen O, Knudsen S, Holm PB. An evaluation of feed-back insensitive aspartate kinase as a selectable marker for barley (Hordeum vulgare L.) transformation. Hereditas 131: 239-245 (1999).

Brock A, Brandt W, Drager B. The functional divergence of short-chain dehydrogenases involved in tropinone reduction. Plant J. 54: 388-401 (2008).

Brock M, Maerker C, Schutz A, Volker U, Buckel W. Oxidation of propionate to pyruvate in Escherichia coli. Involvement of methylcitrate dehydratase and aconitase. Eur. J. Biochem. 269: 6184-6194 (2002).

Brodelius M, Lundgren A, Mercke P, Brodelius PE. Fusion of farnesyldiphosphate synthase and epi-aristolochene synthase, a sesquiterpene cyclase involved in capsidiol biosynthesis in Nicotiana tabacum. Eur. J. Biochem. 269: 3570-3577 (2002).

Brody SS, Gough SP, Kannangara CG. Predicted structure and fold recognition for the glutamyl tRNA reductase family of proteins. Proteins 37: 485-493 (1999).

Brondijk THC, Fiegen D, Richardson DJ, Cole JA. Roles of NapF, NapG and NapH, subunits of the Escherichia coli periplasmic nitrate reductase, in ubiquinol oxidation. Mol. Microbiol. 44: 245-255 (2002).

Brondijk THC, Nilavongse A, Filenko N, Richardson DJ, Cole JA. NapGH components of the periplasmic nitrate reductase of Escherichia coli K- 12: location, topology and physiological roles in quinol oxidation and redox balancing. Biochem. J. 379: 47-55 (2004).

Bronsoms S, Villanueva J, Canals F, Querol E, Aviles FX. Analysis of the effect of potato carboxypeptidase inhibitor pro-sequence on the folding of the mature protein. Eur. J. Biochem. 270: 3641-3650 (2003).

Brown AP, Affleck V, Fawcett T, Slabas AR. Tandem affinity purification tagging of fatty acid biosynthetic enzymes in Synechocystis sp. PCC6803 and Arabidopsis thaliana. J. Exp. Bot. 57: 1563-1571 (2006).

Brown ED, Wood JM. Redesigned purification yields a fully functional PutA protein dimer from Escherichia coli. J. Biol. Chem. 267: 13086-13092 (1992).

Brown MP, Grillo AO, Boyer M, Royer CA. Probing the role of water in the tryptophan repressor-operator complex. Protein Sci. 8: 1276-1285 (1999).

Brown OR, Smyk-Randall E, Draczynska-Lusiak B, Fee JA. Dihydroxy-acid dehydratase, a [4Fe-4S] cluster-containing enzyme in Escherichia coli: effects of intracellular superoxide dismutase on its inactivation by oxidant stress. Arch. Biochem. Biophys. 319: 10-22 (1995).

Brown TD, Jones-Mortimer MC, Kornberg HL. The enzymic interconversion of acetate and acetyl-coenzyme A in Escherichia coli. J. Gen. Microbiol. 102: 327-336 (1977).

Browning ST, Shuler ML. Towards the development of a minimal cell model by generalization of a model of Escherichia coli: Use of dimensionless rate parameters. Biotechnol. Bioeng. 76: 187-92 (2001).

Bruggeman C, Denger K, Cook AM, Ruff J. Enzymes and genes of taurine and isethionate dissimilation in Paracoccus denitrificans. Microbiology (U.K.) 150: 805-816 (2004).

Bruggeman FJ, Boogerd FC, Westerhoff HV. The multifarious short-term regulation of ammonium assimilation of Escherichia coli: dissection using an in silico replica. FEBS J. 272: 1965-1985 (2005).

Bruggeman FJ, van Heeswijk WC, Boogerd FC, Westerhoff HV. Macromolecular intelligence in microorganisms. Biol. Chem. 381: 965-972 (2000).

Bruggeman FJ, Westerhoff HV, Hoek JB, Kholodenko BN. Modular response analysis of cellular regulatory networks. J. Theor. Biol. 218: 507-520 (2002).

Brugiere N, Jiao S, Hantke S, Zinselmeier C, Roessler JA, Niu X, Jones RJ, Habben JE. Cytokinin oxidase gene expression in maize is localized to the vasculature, and is induced by cytokinins, abscisic acid, and abiotic stress. Plant Physiol. 132: 1228-1240 (2003).

Bruhl A, Haverkamp T, Gisselmann G, Schwenn JD. A cDNA clone from Arabidopsis thaliana encoding plastidic ferredoxin:sulfite reductase. Biochim. Biophys. Acta 1295: 119-124 (1996).

Brunker P, Altenbuchner J, Mattes R. Structure and function of the genes involved in mannitol, arabitol and glucitol utilization from Pseudomonas fluorescens DSM50106. Gene 206: 117-126 (1998).

Brunker P, Hils M, Altenbuchner J, Mattes R. The mannitol utilization genes of Pseudomonas fluorescens are regulated by an activator: cloning, nucleotide sequence and expression of the mtlR gene. Gene 215: 19-27 (1998).

Brzezinski K, Bujacz G, Jaskolski M. Purification, crystallization and preliminary crystallographic studies of plant S-adenosyl-L-homocysteine hydrolase (Lupinus luteus). Acta Crystallogr. Sect. F. Struct. Biol. Cryst. Commun. 64: 671-673 (2008).

Buc J, Santini CL, Blasco F, Giordani R, Cardenas ML, Chippaux M, Cornish-Bowden A, Giordano G. Kinetic studies of a soluble alpha beta complex of nitrate reductase A from Escherichia coli. Use of various alpha beta mutants with altered beta subunits. Eur. J. Biochem. 234: 766-772 (1995).

Buchenau B, Thauer RK. Tetrahydrofolate-specific enzymes in Methanosarcina barkeri and growth dependence of this methanogenic archaeon on folic acid or p-aminobenzoic acid. Arch. Microbiol. 182: 313-325 (2004).

Buckland BC, Drew SW, Connors NC, Chartrain MM, Lee C, Salmon PM, Gbewonyo K, Zhou W, Gailliot P, Singhvi R, Olewinski RC Jr, Sun WJ, Reddy J, Zhang J, Jackey BA, Taylor C, Goklen KE, Junker B, Greasham RL. Microbial conversion of indene to indandiol: a key intermediate in the synthesis of CRIXIVAN. Metab. Eng. 1: 63-74 (1999).

Budhiraja R, Hermkes R, Muller S, Schmidt J, Colby T, Panigrahi K, Coupland G, Bachmair A. Substrates related to chromatin and to RNA-dependent processes are modified by Arabidopsis SUMO isoforms that differ in a conserved residue with influence on desumoylation. Plant Physiol. 149: 1529-1540 (2009).

Bueno R, Pahel G, Magasanik B. Role of glnB and glnD gene products in regulation of the glnALG operon of Escherichia coli. J. Bacteriol. 164: 816-822 (1985).

Bueso J, Cervera J, Fresquet V, Marina A, Lusty CJ, Rubio V. Photoaffinity labeling with the activator IMP and site-directed mutagenesis of histidine 995 of carbamoyl phosphate synthetase from Escherichia coli demonstrate that the binding site for IMP overlaps with that for the inhibitor UMP. Biochemistry 38: 3910-3917 (1999).

Bulow L, Mosbach K. The oligopeptide (Gly-Pro)2-Ala-(Gly-Pro)2 increases the internal proline level and improves NaCl tolerance when produced in Escherichia coli. Gene 109: 125-129 (1991).

Burgard AP, Maranas CD. Optimization-based framework for inferring and testing hypothesized metabolic objective functions. Biotechnol. Bioeng. 82: 670-677 (2003).

Burgard AP, Maranas CD. Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions. Biotechnol. Bioeng. 74: 364-375 (2001).

Burger BT, Cross JM, Shaw JR, Caren JR, Greene TW, Okita TW, Hannah LC. Relative turnover numbers of maize endosperm and potato tuber ADP-glucose pyrophosphorylases in the absence and presence of 3-phosphoglyceric acid. Planta 217: 449-456 (2003).

Burkhead JL, Abdel-Ghany SE, Morrill JM, Pilon-Smits EA, Pilon M. The Arabidopsis thaliana CUTA gene encodes an evolutionarily conserved copper binding chloroplast protein. Plant J. 34: 856-867 (2003).

Burland V, Plunkett G 3rd, Sofia HJ, Daniels DL, Blattner FR. Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes. Nucleic Acids Res. 23: 2105-2119 (1995).

Burlat B, Gwyer JD, Poock S, Clarke T, Cole JA, Hemmings AM, Cheesman MR, Butt JN, Richardson DJ. Cytochrome c nitrite reductase: from structural to physicochemical analysis. Biochem. Soc. Trans. 33: 137-140 (2005).

Burman JD, Harris RL, Hauton KA, Lawson DM, Sawers RG. The iron-sulfur cluster in the L-serine dehydratase TdcG from Escherichia coli is required for enzyme activity. FEBS Lett. 576: 442-444 (2004).

Burnet M, Lafontaine PJ, Hanson AD. Assay, purification, and partial characterization of choline monooxygenase from spinach. Plant Physiol. 108: 581-588 (1995).

Busam G, Junghanns KT, Kneusel RE, Kassemeyer HH, Matern U. Characterization and expression of caffeoyl-coenzyme A 3-O-methyltransferase proposed for the induced resistance response of Vitis vinifera L. Plant Physiol. 115: 1039-1048 (1997).

Busch KB, Fromm H. Plant succinic semialdehyde dehydrogenase. Cloning, purification, localization in mitochondria, and regulation by adenine nucleotides. Plant Physiol. 121: 589-598 (1999).

Busquets A, Keim V, Closa M, Del Arco A, Boronat A, Arro M, Ferrer A. Arabidopsis thaliana contains a single gene encoding squalene synthase. Plant Mol. Biol. 67: 25-36 (2008).

Byng GS, Berry A, Jensen RA. Evolutionary implications of features of aromatic amino acid biosynthesis in the genus Acinetobacter. Arch. Microbiol. 143: 122-129 (1985).

Byrne KM, Smith SK, Ondeyka JG. Biosynthesis of nodulisporic acid A: Precursor studies. J. Am. Chem. Soc. 124: 7055-7060 (2002).

Byrnes WM, Vilker VL. Extrinsic factors potassium chloride and glycerol induce thermostability in recombinant anthranilate synthase from Archaeoglobus fulgidus. Extremophiles 8: 455-462 (2004).

Caban CE, Ginsburg A. Glutamine synthetase adenylyltransferase from Escherichia coli: purification and physical and chemical properties. Biochemistry 15: 1569-1580 (1976).

Cabrera Artiles Y, Martinez Garcia D, Perez Cruz ER, Marquez Perera GJ, Feble ML. Osmoregulated TAQ polymerase gene expression in Escherichia coli. Rev. Latinoam. Microbiol. 44: 14-18 (2002).

Cahoon EB, Shah S, Shanklin J, Browse J. A determinant of substrate specificity predicted from the acyl-acyl carrier protein desaturase of developing cat's claw seed. Plant Physiol. 117: 593-598 (1998).

Cai H, Clarke S. A novel methyltransferase catalyzes the methyl esterification of trans-aconitate in Escherichia coli. J. Biol. Chem. 274: 13470-13479 (1999).

Cai H, Zhou Y, Xiao J, Li X, Zhang Q, Lian X. Overexpressed glutamine synthetase gene modifies nitrogen metabolism and abiotic stress responses in rice. Plant Cell Rep. 28: 527-537 (2009).

Cai XY, Maxon ME, Redfield B, Glass R, Brot N, Weissbach H. Methionine synthesis in Escherichia coli: effect of the MetR protein on metE and metH expression. Proc. Natl. Acad. Sci. U.S.A. 86: 4407-4411 (1989).

Cain CC, Saslowsky DE, Walker RA, Shirley BW. Expression of chalcone synthase and chalcone isomerase proteins in Arabidopsis seedlings. Plant Mol. Biol. 35: 377-381 (1997).

Cakici O, Sikorski M, Stepkowski T, Bujacz G, Jaskolski M. Cloning, expression, purification, crystallization and preliminary X-ray analysis of NodS N-methyltransferase from Bradyrhizobium japonicum WM9. Acta Crystallogr. Sect. F. Struct. Biol. Cryst. Commun. 64: 1149-1152 (2008).

Caldara M, Dupont G, Leroy F, Goldbeter A, De Vuyst L, Cunin R. Arginine biosynthesis in Escherichia coli: experimental perturbation and mathematical modeling. J. Biol. Chem. 283: 6347-6358 (2008).

Caldas T, Demont-Caulet N, Ghazi A, Richarme G. Thermoprotection by glycine betaine and choline. Microbiology 145: 2543-2548 (1999).

Calder RB, Williams RS, Ramaswamy G, Rock CO, Campbell E, Unkles SE, Kinghorn JR, Jackowski S. Cloning and characterization of a eukaryotic pantothenate kinase gene (panK) from Aspergillus nidulans. J. Biol. Chem. 274: 2014-2020 (1999).

Caldwell CR, Turano FJ, McMahon MB. Identification of two cytosolic ascorbate peroxidase cDNAs from soybean leaves and characterization of their products by functional expression in E. coli. Planta 204: 120-126 (1998).

Calvo AP, Nicolas C, Nicolas G, Rodriguez D. Evidence of a cross-talk regulation of a GA 20-oxidase (FsGA20ox1) by gibberellins and ethylene during the breaking of dormancy in Fagus sylvatica seeds. Physiol. Plant. 120: 623-630 (2004).

Camarena L, Poggio S, Campos A, Bastarrachea F, Osorio A. An IS4 insertion at the glnA control region of Escherichia coli creates a new promoter by providing the -35 region of its 3'-end. Plasmid 39: 41-47 (1998).

Camarena L, Poggio S, Garcia N, Osorio A. Transcriptional repression of gdhA in Escherichia coli is mediated by the Nac protein. FEMS Microbiol. Lett. 167: 51-56 (1998).

Camargo A, Llamas A, Schnell RA, Higuera JJ, Gonzalez-Ballester D, Lefebvre PA, Fernandez E, Galvan A. Nitrate signaling by the regulatory gene NIT2 in Chlamydomonas. Plant Cell 19: 3491-3503 (2007).

Cameron DC, Chaplen FW. Developments in metabolic engineering. Curr. Opin. Biotechnol. 8: 175-80 (1997).

Cami B, Clepet C, Patte JC. Evolutionary comparisons of three enzymes of the threonine biosynthetic pathway among several microbial species. Biochimie 75: 487-495 (1993).

Cammack R, Jackson RH, Cornish-Bowden A, Cole JA. Electron-spin-resonance studies of the NADH-dependent nitrite reductase from Escherichia coli K12. Biochem. J. 207: 333-339 (1982).

Campbell EI, Unkles SE, Macro JA, van den Hondel C, Contreras R, Kinghorn JR. Improved transformation efficiency of Aspergillus niger using the homologous niaD gene for nitrate reductase. Curr. Genet. 16: 53-56 (1989).

Campos N, Rodriguez-Concepcion M, Sauret-Gueto S, Gallego F, Lois LM, Boronat A. Escherichia coli engineered to synthesize isopentenyl diphosphate and dimethylallyl diphosphate from mevalonate: a novel system for the genetic analysis of the 2-C-methyl-D-erythritol 4-phosphate pathway for isoprenoid biosynthesis. Biochem. J. 353: 59-67 (2001).

Campos R, Nonogaki H, Suslow T, Saltveit ME. Isolation and characterization of a wound inducible phenylalanine ammonia-lyase gene (LsPAL1) from Romaine lettuce leaves. Physiol. Plant. 121: 429-438 (2004).

Canas RA, Villalobos DP, Diaz-Moreno SM, Canovas FM, Canton FR. Molecular and functional analyses support a role of ornithine-delta-aminotransferase in the provision of glutamate for glutamine biosynthesis during pine germination. Plant Physiol. 148: 77-88 (2008).

Caniuguir A, Cabrera R, Baez M, Vasquez CC, Babul J, Guixe V. Role of Cys-295 on subunit interactions and allosteric regulation of phosphofructokinase-2 from Escherichia coli. FEBS Lett. 579: 2313-2318 (2005).

Cannons AC, Barber MJ, Solomonson LP. Expression and characterization of the heme-binding domain of Chlorella nitrate reductase. J. Biol. Chem. 268: 3268-3271 (1993).

Canonaco F, Hess TA, Heri S, Wang T, Szyperski T, Sauer U. Metabolic flux response to phosphoglucose isomerase knock-out in Escherichia coli and impact of overexpression of the soluble transhydrogenase UdhA. FEMS Microbiol. Lett. 204: 247-252 (2001).

Canovas D, Vargas C, Kneip S, Moron MJ, Ventosa A, Bremer E, Nieto JJ. Genes for the synthesis of the osmoprotectant glycine betaine from choline in the moderately halophilic bacterium Halomonas elongata DSM 3043, USA. Microbiology 146: 455-463 (2000).

Canovas M, Bernal V, Sevilla A, Iborra JL. Salt stress effects on the central and carnitine metabolisms of Escherichia coli. Biotechnol. Bioeng. 96: 722-737 (2007).

Canovas M, Bernal V, Torroglosa T, Ramirez JL, Iborra JL. Link between primary and secondary metabolism in the biotransformation of trimethylammonium compounds by Escherichia coli. Biotechnol. Bioeng. 84: 686-699 (2003).

Canovas M, Maiquez JR, Obon JM, Iborra JL. Modeling of the biotransformation of crotonobetaine into L-(-)-carnitine by Escherichia coli strains. Biotechnol. Bioeng. 77: 764-775 (2002).

Canovas M, Sevilla A, Bernal V, Leal R, Iborra JL. Role of energetic coenzyme pools in the production of L-carnitine by Escherichia coli. Metab. Eng. 8: 603-618 (2006).

Canton FR, Garcia-Gutierrez A, Crespillo R, Canovas FM. High-level expression of Pinus sylvestris glutamine synthetase in Escherichia coli. Production of polyclonal antibodies against the recombinant protein and expression studies in pine seedlings. FEBS Lett. 393: 205-210 (1996).

Cao H, Imparl-Radosevich J, Guan H, Keeling PL, James MG, Myers AM. Identification of the soluble starch synthase activities of maize endosperm. Plant Physiol. 120: 205-216 (1999).

Cardy DL, Murrell JC. Cloning, sequencing and expression of the glutamine synthetase structural gene (glnA) from the obligate methanotroph Methylococcus capsulatus (Bath). J. Gen. Microbiol. 136: 343-352 (1990).

Carlier A, Uroz S, Smadja B, Fray R, Latour X, Dessaux Y, Faure D. The Ti plasmid of Agrobacterium tumefaciens harbors an attM-paralogous gene, aiiB, also encoding N-acyl homoserine lactonase activity. Appl. Environ. Microbiol. 69: 4989-4993 (2003).

Carlson R, Srienc F. Fundamental Escherichia coli biochemical pathways for biomass and energy production: creation of overall flux states. Biotechnol. Bioeng. 86: 149-162 (2004).

Carlson RP. Metabolic systems cost-benefit analysis for interpreting network structure and regulation. Bioinformatics 23: 1258-1264 (2007).

Carlson RP. Decomposition of complex microbial behaviors into resource-based stress responses. Bioinformatics 25: 90-97 (2009).

Carreras CW, Khosla C. Purification and in vitro reconstitution of the essential protein components of an aromatic polyketide synthase. Biochemistry 37: 2084-2088 (1998).

Carretero-Paulet L, Ahumada I, Cunillera N, Rodriguez-Concepcion M, Ferrer A, Boronat A, Campos N. Expression and molecular analysis of the Arabidopsis DXR gene encoding 1-deoxy-D-xylulose 5-phosphate reductoisomerase, the first committed enzyme of the 2-C-methyl-D-erythritol 4-phosphate pathway. Plant Physiol. 129: 1581-1591 (2002).

Carvalho H, Sunkel C, Salema R, Cullimore JV. Heteromeric assembly of the cytosolic glutamine synthetase polypeptides of Medicago truncatula: complementation of a glnA Escherichia coli mutant with a plant domain-swapped enzyme. Plant Mol. Biol. 35: 623-632 (1997).

Casazza AP, Basner A, Hofgen R, Hesse H. Expression of threonine synthase from Solanum tuberosum L. is not metabolically regulated by photosynthesis-related signals or by nitrogenous compounds. Plant Sci. 157: 43-50 (2000).

Cassan M, Boy E, Borne F, Patte JC. Regulation of the lysine biosynthetic pathway in Escherichia coli K-12: isolation of a cis-dominant constitutive mutant for AK III synthesis. J. Bacteriol. 123: 391-399 (1975).

Cassan M, Parsot C, Cohen GN, Patte JC. Nucleotide sequence of lysC gene encoding the lysine-sensitive aspartokinase III of Escherichia coli K12. Evolutionary pathway leading to three isofunctional enzymes. J. Biol. Chem. 261: 1052-1057 (1986).

Cassan M, Ronceray J, Patte JC. Nucleotide sequence of the promoter region of the E. coli lysC gene. Nucleic Acids Res. 11: 6157-6166 (1983).

Castanie-Cornet MP, Penfound TA, Smith D, Elliott JF, Foster JW. Control of acid resistance in Escherichia coli. J. Bacteriol. 181: 3525-3535 (1999).

Castelo R, Roverato A. Reverse engineering molecular regulatory networks from microarray data with qp-graphs. J. Comput. Biol. 16: 213-227 (2009).

Castillo RM, Mizuguchi K, Dhanaraj V, Albert A, Blundell TL, Murzin AG. A six-stranded double-psi beta barrel is shared by several protein superfamilies. Structure Fold. Des. 7: 227-236 (1999).

Castle LA, Siehl DL, Gorton R, Patten PA, Chen YH, Bertain S, Cho HJ, Duck N, Wong J, Liu D, Lassner MW. Discovery and directed evolution of a glyphosate tolerance gene. Science 304: 1151-1154 (2004).

Cataldi AA, Algranati ID. A probable new pathway for the biosynthesis of putrescine in Escherichia coli. Biochem. J. 234: 617-622 (1986).

Cataldi AA, Algranati ID. Polyamines and regulation of ornithine biosynthesis in Escherichia coli. J. Bacteriol. 171: 1998-2002 (1989).

Cavener DR. GMC oxidoreductases. A newly defined family of homologous proteins with diverse catalytic activities. J. Mol. Biol. 223: 811-814 (1992).

Cavicchioli R, Chiang RC, Kalman LV, Gunsalus RP. Role of the periplasmic domain of the Escherichia coli NarX sensor-transmitter protein in nitrate-dependent signal transduction and gene regulation. Mol. Microbiol. 21: 901-911 (1996).

Cavicchioli R, Kolesnikow T, Chiang RC, Gunsalus RP. Characterization of the aegA locus of Escherichia coli: control of gene expression in response to anaerobiosis and nitrate. J. Bacteriol. 178: 6968-6974 (1996).

Cavin JF, Dartois V, Labarre C, Divies C. Cloning of branched chain amino acid biosynthesis genes and assays of alpha-acetolactate synthase activities in Leuconostoc mesenteroides subsp. cremoris. Res. Microbiol. 150: 189-198 (1999).

Cayley S, Lewis BA, Guttman HJ, Record MT Jr. Characterization of the cytoplasm of Escherichia coli K-12 as a function of external osmolarity. Implications for protein-DNA interactions in vivo. J. Mol. Biol. 222: 281-300 (1991).

Cayley S, Lewis BA, Record MT Jr. Origins of the osmoprotective properties of betaine and proline in Escherichia coli K-12. J. Bacteriol. 174: 1586-1595 (1992).

Cayley S, Record MT. Roles of cytoplasmic osmolytes, water, and crowding in the response of Escherichia coli to osmotic stress: biophysical basis of osmoprotection by glycine betaine. Biochemistry 42: 12596-12609 (2003).

Cayley S, Record MT Jr. Large changes in cytoplasmic biopolymer concentration with osmolality indicate that macromolecular crowding may regulate protein-DNA interactions and growth rate in osmotically stressed Escherichia coli K-12. J. Mol. Recognit. 17: 488-496 (2004).

Cayley S, Record MT Jr, Lewis BA. Accumulation of 3-(N-morpholino)propanesulfonate by osmotically stressed Escherichia coli K-12. J. Bacteriol. 171: 3597-3602 (1989).

Cervantes-Cervantes M, Gallagher CE, Zhu C, Wurtzel ET. Maize cDNAs expressed in endosperm encode functional farnesyl diphosphate synthase with geranylgeranyl diphosphate synthase activity. Plant Physiol. 141: 220-231 (2006).

Cha HJ, Wu CF, Valdes JJ, Rao G, Bentley WE. Observations of green fluorescent protein as a fusion partner in genetically engineered Escherichia coli: monitoring protein expression and solubility. Biotechnol. Bioeng. 67: 565-574 (2000).

Cha MK, Kim HK, Kim IH. Thioredoxin-linked "thiol peroxidase" from periplasmic space of Escherichia coli. J. Biol. Chem. 270: 28635-28641 (1995).

Chae MJ, Lee JS, Nam MH, Cho K, Hong JY, Yi SA, Suh SC, Yoon IS. A rice dehydration-inducible SNF1-related protein kinase 2 phosphorylates an abscisic acid responsive element-binding factor and associates with ABA signaling. Plant Mol. Biol. 63: 151-169 (2007).

Chambers S, Kunin CM. The osmoprotective properties of urine for bacteria: the protective effect of betaine and human urine against low pH and high concentrations of electrolytes, sugars, and urea. J. Infect. Dis. 152: 1308-1316 (1985).

Chambers ST, Kunin CM. Osmoprotective activity for Escherichia coli in mammalian renal inner medulla and urine. Correlation of glycine and proline betaines and sorbitol with response to osmotic loads. J. Clin. Invest. 80: 1255-1260 (1987).

Chambers ST, Kunin CM, Miller D, Hamada A. Dimethylthetin can substitute for glycine betaine as an osmoprotectant molecule for Escherichia coli. J. Bacteriol. 169: 4845-4847 (1987).

Chan CS, Howell JM, Workentine ML, Turner RJ. Twin-arginine translocase may have a role in the chaperone function of NarJ from Escherichia coli. Biochem. Biophys. Res. Commun. 343: 244-151 (2006).

Chan MK, Gong W, Rajagopalan PT, Hao B, Tsai CM, Pei D. Crystal structure of the Escherichia coli peptide deformylase. Biochemistry 36: 13904-13909 (1997).

Chan VL, Bingham HL. Complete sequence of the Campylobacter jejuni glyA gene encoding serine hydroxymethyltransferase. Gene 101: 51-58 (1991).

Chandran SS, Yi J, Draths KM, Von Daeniken R, Weber W, Frost JW. Phosphoenolpyruvate availability and the biosynthesis of shikimic acid. Biotechnol. Prog. 19: 808-814 (2003).

Chang AK, Duggleby RG. Expression, purification and characterization of Arabidopsis thaliana acetohydroxyacid synthase. Biochem. J. 327: 161-169 (1997).

Chang AK, Duggleby RG. Herbicide-resistant forms of Arabidopsis thaliana acetohydroxyacid synthase: characterization of the catalytic properties and sensitivity to inhibitors of four defined mutants. Biochem. J. 333: 765-777 (1998).

Chang DE, Jung HC, Rhee JS, Pan JG. Homofermentative production of D- or L-lactate in metabolically engineered Escherichia coli RR1. Appl. Environ. Microbiol. 65: 1384-1389 (1999).

Chang DE, Shin S, Rhee JS, Pan JG. Acetate metabolism in a pta mutant of Escherichia coli W3110: importance of maintaining acetyl coenzyme A flux for growth and survival. J. Bacteriol. 181: 6656-6663 (1999).

Chang HC, Bush DR. Topology of NAT2, a prototypical example of a new family of amino acid transporters. J. Biol. Chem. 272: 30552-30557 28 (1997).

Chang SI, Kang MK, Choi JD, Namgoong SK. Soluble overexpression in Escherichia coli, and purification and characterization of wild-type recombinant tobacco acetolactate synthase. Biochem. Biophys. Res. Commun. 234: 549-553 (1997).

Chang YC, Lee TM. High temperature-induced free proline accumulation in Gracilaria tenuistipitata (Rhodophyta). Bot. Bul. Acad. Sin. 40: 289-294 (1999).

Chang YY, Wang AY, Cronan JE Jr. Molecular cloning, DNA sequencing, and biochemical analyses of Escherichia coli glyoxylate carboligase. An enzyme of the acetohydroxy acid synthase-pyruvate oxidase family. J. Biol. Chem. 268: 3911-3919 (1993).

Chao G, Shen J, Tseng CP, Park SJ, Gunsalus RP. Aerobic regulation of isocitrate dehydrogenase gene (icd) expression in Escherichia coli by the arcA and fnr gene products. J. Bacteriol. 179: 4299-4304 (1997).

Chao KL, Lim K, Lehmann C, Doseeva V, Howard AJ, Schwarz FP, Herzberg O. The Escherichia coli YdcF binds S-adenosyl-L-methionine and adopts an alpha/beta-fold characteristic of nucleotide-utilizing enzymes. Proteins 72: 506-509 (2008).

Charlebois RL, Singh RK, Chan-Weiher CCY, Allard G, Chow C, Confalonieri F, Curtis B, Duguet M, Erauso G, Faguy D, Gaasterland T et al. Gene content and organization of a 281-kbp contig from the genome of the extremely thermophilic archaeon, Sulfolobus solfataricus P2. Genome 43: 116-136 (2000).

Chary P, Dillon D, Schroeder AL, Natvig DO. Superoxide dismutase (sod-1) null mutants of Neurospora crassa: oxidative stress sensitivity, spontaneous mutation rate and response to mutagens. Genetics 137: 723-730 (1994).

Chassagnole C, Fell DA, Rais B, Kudla B, Mazat JP. Control of the threonine-synthesis pathway in Escherichia coli: a theoretical and experimental approach. Biochem. J. 356: 433-444 (2001).

Chassagnole C, Noisommit-Rizzi N, Schmid JW, Mauch K, Reuss M. Dynamic modeling of the central carbon metabolism of Escherichia coli. Biotechnol. Bioeng. 79: 53-73 (2002).

Chassagnole C, Rais B, Quentin E, Fell DA, Mazat JP. An integrated study of threonine-pathway enzyme kinetics in Escherichia coli. Biochem. J. 356: 415-423 (2001).

Chassin Y, Kapri-Pardes E, Sinvany G, Arad T, Adam Z. Expression and characterization of the thylakoid lumen protease DegP1 from Arabidopsis. Plant Physiol. 130: 857-864 (2002).

Chatterjee A, Majee M, Ghosh S, Majumder AL. sll1722, an unassigned open reading frame of Synechocystis PCC 6803, codes for L-myo-inositol 1-phosphate synthase. Planta 218: 989-998 (2004).

Chave KJ, Auger IE, Galivan J, Ryan J. Molecular modeling and site-directed mutagenesis define the catalytic motif in human gamma-glutamyl hydrolase. J. Biol. Chem. 275: 40365-40370 (2000).

Chavez S, Reyes JC, Chauvat F, Florencio FJ, Candau P. The NADP-glutamate dehydrogenase of the cyanobacterium Synechocystis 6803: cloning, transcriptional analysis and disruption of the gdhA gene. Plant Mol. Biol. 28: 173-188 (1995).

Chavez-Bejar MI, Lara AR, Lopez H, Hernandez-Chavez G, Martinez A, Ramirez OT, Bolívar F, Gosset G. Metabolic engineering of Escherichia coli for L-tyrosine production by expression of genes coding for the chorismate mutase domain of the native chorismate mutase-prephenate dehydratase and a cyclohexadienyl dehydrogenase from Zymomonas mobilis. Appl. Environ. Microbiol. 74: 3284-3290 (2008).

Che FS, Watanabe N, Iwano M, Inokuchi H, Takayama S, Yoshida S, Isogai A. Molecular characterization and subcellular localization of protoporphyrinogen oxidase in spinach chloroplasts. Plant Physiol. 124: 59-70 (2000).

Cheah E, Carr PD, Suffolk PM, Vasudevan SG, Dixon NE, Ollis DL. Structure of the Escherichia coli signal transducing protein PII. Structure 2: 981-990 (1994).

Chehab EW, Patharkar OR, Hegeman AD, Taybi T, Cushman JC. Autophosphorylation and subcellular localization dynamics of a salt- and water deficit-induced calcium-dependent protein kinase from ice plant. Plant Physiol. 135: 1430-1446 (2004).

Chen C, Beattie GA. Characterization of the osmoprotectant transporter OpuC from Pseudomonas syringae and demonstration that CBS domains are required for its osmoregulatory function. J. Bacteriol. 189: 6901-6912 (2007).

Chen C, Newman EB. Comparison of the sensitivities of two Escherichia coli genes to in vivo variation of Lrp concentration. J. Bacteriol. 180: 655-659 (1998).

Chen CC, Liao CC, Hsu WH. The cloning and nucleotide sequence of a Corynebacterium glutamicum 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase gene. FEMS Microbiol. Lett. 107: 223-229 (1993).

Chen F, Ro DK, Petri J, Gershenzon J, Bohlmann J, Pichersky E, Tholl D. Characterization of a root-specific Arabidopsis terpene synthase responsible for the formation of the volatile monoterpene 1,8-cineole. Plant Physiol. 135: 1956-1966 (2004).

Chen HM, Ho CW, Liu JW, Lin KY, Wang YT, Lu CH, Liu HL. Production, IMAC purification, and molecular modeling of N-carbamoyl-D-amino acid amidohydrolase C-terminally fused with a six-His peptide. Biotechnol. Prog. 19: 864-873 (2003).

Chen J, Zhang W, Tan L, Wang Y, He G. Optimization of metabolic pathways for bioconversion of lignocellulose to ethanol through genetic engineering. Biotechnol. Adv. 27: 593-598 (2009).

Chen JP, Dabrowski MJ, Atkins WM. Synthesis and characterization of supramolecular protein aggregates: self-assembled, molecularly-ordered, tubes from electrostatic complementation of glutamine synthetase dodecamers. Protein Eng. 10: 1289-1294 (1997).

Chen NY, Hu FM, Paulus H. Nucleotide sequence of the overlapping genes for the subunits of Bacillus subtilis aspartokinase II and their control regions. J. Biol. Chem. 262: 8787-8798 (1987).

Chen NY, Jiang SQ, Klein DA, Paulus H. Organization and nucleotide sequence of the Bacillus subtilis diaminopimelate operon, a cluster of genes encoding the first three enzymes of diaminopimelate synthesis and dipicolinate synthase. J. Biol. Chem. 268: 9448-9465 (1993).

Chen NY, Paulus H. Mechanism of expression of the overlapping genes of Bacillus subtilis aspartokinase II. J. Biol. Chem. 263: 9526-9532 (1988).

Chen R, Hatzimanikatis V, Yap WM, Postma PW, Bailey JE. Metabolic consequences of phosphotransferase (PTS) mutation in a phenylalanine-producing recombinant Escherichia coli. Biotechnol. Prog. 13: 768-775 (1997).

Chen R, Yap WM, Postma PW, Bailey JE. Comparative studies of Escherichia coli strains using different glucose uptake systems: metabolism and energetics. Biotechnol. Bioeng. 56: 583-590 (1997).

Chen S, Glawischnig E, Jorgensen K, Naur P, Jorgensen B, Olsen CE, Hansen CH, Rasmussen H, Pickett JA, Halkier BA. CYP79F1 and CYP79F2 have distinct functions in the biosynthesis of aliphatic glucosinolates in Arabidopsis. Plant J. 33: 923-937 (2003).

Chen S, Vincent S, Wilson DB, Ganem B. Mapping of chorismate mutase and prephenate dehydrogenase domains in the Escherichia coli T-protein. Eur. J. Biochem. 270: 757-763 (2003).

Chen TH, Murata N. Enhancement of tolerance of abiotic stress by metabolic engineering of betaines and other compatible solutes. Curr. Opin. Plant Biol. 5: 250-257 (2002).

Chen W, Wright L, Li S, Cosloy SD, Russell CS. Expression of glutamyl-tRNA reductase in Escherichia coli. Biochim. Biophys. Acta 1309: 109-121 (1996).

Chen YC, Chang HS, Lai HM, Jeng ST. Characterization of the wound-inducible protein ipomoelin from sweet potato. Plant Cell Environ. 28: 251-259 (2005).

Chen YQ, Gulotta M, Cheung HT, Callender R. Light activates reduction of methotrexate by NADPH in the ternary complex with Escherichia coli dihydrofolate reductase. Photochem. Photobiol. 69: 77-85 (1999).

Chen Z, Crippen K, Gulati S, Banerjee R. Purification and kinetic mechanism of a mammalian methionine synthase from pig liver. J. Biol. Chem. 269: 27193-27197 (1994).

Chen ZY, Lavigne LL, Mason CB, Moroney JV. Cloning and overexpression of two cDNAs encoding the low-CO2-inducible chloroplast envelope protein LIP-36 from Chlamydomonas reinhardtii. Plant Physiol. 114: 265-273 (1997).

Cheng Q, Liu HT, Bombelli P, Smith A, Slabas AR. Functional identification of AtFao3, a membrane bound long chain alcohol oxidase in Arabidopsis thaliana. FEBS Lett. 574: 62-68 (2004).

Cherest H, Surdin-Kerjan Y. Genetic analysis of a new mutation conferring cysteine auxotrophy in Saccharomyces cerevisiae: updating of the sulfur metabolism pathway. Genetics 130: 51-58 (1992).

Cherry JL. Genome size and operon content. J. Theor. Biol. 221: 401-410 (2003).

Chiang RC, Cavicchioli R, Gunsalus RP. 'Locked-on' and 'locked-off' signal transduction mutations in the periplasmic domain of the Escherichia coli NarQ and NarX sensors affect nitrate- and nitrite-dependent regulation by NarL and NarP. Mol. Microbiol. 24: 1049-1060 (1997).

Chiang RC, Cavicchioli R, Gunsalus RP. Identification and characterization of narQ, a second nitrate sensor for nitrate-dependent gene regulation in Escherichia coli. Mol. Microbiol. 6: 1913-1923 (1992).

Chilson OP, Kelly-Chilson AE, Siegel NR. Pyrroline-5-carboxylate reductase in soybean nodules: isolation/partial primary structure/evidence for isozymes. Arch. Biochem. Biophys. 288: 350-357 (1991).

Chin JW, Khankal R, Monroe CA, Maranas CD, Cirino PC. Analysis of NADPH supply during xylitol production by engineered Escherichia coli. Biotechnol. Bioeng. 102: 209-220 (2009).

Chinchilla D, Schwarz FP, Eisenstein E. Amino acid substitutions in the C-terminal regulatory domain disrupt allosteric effector binding to biosynthetic threonine deaminase from Escherichia coli. J. Biol. Chem. 273: 23219-23224 (1998).

Chipman D, Barak Z, Schloss JV. Biosynthesis of 2-aceto-2-hydroxy acids: acetolactate synthases and acetohydroxyacid synthases. Biochim. Biophys. Acta 1385: 401-419 (1998).

Chiron H, Drouet A, Claudot AC, Eckerskorn C, Trost M, Heller W, Ernst D, Sandermann H Jr. Molecular cloning and functional expression of a stress-induced multifunctional O-methyltransferase with pinosylvin methyltransferase activity from Scots pine (Pinus sylvestris L.). Plant Mol. Biol. 44: 733-745 (2000).

Chirwa NT, Herrington MB. Role of MetR and PurR in the activation of glyA by CsgD in Escherichia coli K-12. Can. J. Microbiol. 50: 683-690 (2004).

Chittur SV, Chen Y, Davisson VJ. Expression and purification of imidazole glycerol phosphate synthase from Saccharomyces cerevisiae. Protein Expr. Purif. 18: 366-377 (2000).

Cho HS, Lee SS, Kim KD, Hwang I, Lim JS, Park YI, Pai HS. DNA gyrase is involved in chloroplast nucleoid partitioning. Plant Cell 16: 2665-2682 (2004).

Cho JC, Tiedje JM. Quantitative detection of microbial genes by using DNA microarrays. Appl. Environ. Microbiol. 68: 1425-1430 (2002).

Cho SW, Yoon HY, Ahn JY, Lee EY, Lee J. Cassette mutagenesis of lysine 130 of human glutamate dehydrogenase. An essential residue in catalysis. Eur. J. Biochem. 268: 3205-3213 (2001).

Chohnan S, Furukawa H, Fujio T, Nishihara H, Takamura Y. Changes in the size and composition of intracellular pools of nonesterified coenzyme A and coenzyme A thioesters in aerobic and facultatively anaerobic bacteria. Appl. Environ. Microbiol. 63: 553-560 (1997).

Chohnan S, Izawa H, Nishihara H, Takamura Y. Changes in size of intracellular pools of coenzyme A and its thioesters in Escherichia coli K-12 cells to various carbon sources and stresses. Biosci. Biotechnol. Biochem. 62: 1122-1128 (1998).

Choi JK, Yu F, Wurtele ES, Nikolau BJ. Molecular cloning and characterization of the cDNA coding for the biotin-containing subunit of the chloroplastic acetyl-coenzyme A carboxylase. Plant Physiol. 109: 619-625 (1995).

Choi KJ, Noh KM, Kim DE, Ha BH, Kim EE, Yoon MY. Identification of the catalytic subunit of acetohydroxyacid synthase in Haemophilus influenzae and its potent inhibitors. Arch. Biochem. Biophys. 466: 24-30 (2007).

Choi YO, Cheong NE, Lee KO, Jung BG, Hong CH, Jeong JH, Chi YH, Kim K, Cho MJ, Lee SY. Cloning and expression of a new isotype of the peroxiredoxin gene of Chinese cabbage and its comparison to 2Cys-peroxiredoxin isolated from the same plant. Biochem. Biophys. Res. Commun. 258: 768-771 (1999).

Chong CK, Shin HJ, Chang SI, Choi JD. Role of tryptophanyl residues in tobacco acetolactate synthase. Biochem. Biophys. Res. Commun. 259: 136-140 (1999).

Choquet G, Jehan N, Pissavin C, Blanco C, Jebbar M. OusB, a broad-specificity ABC-type transporter from Erwinia chrysanthemi, mediates uptake of glycine betaine and choline with a high affinity. Appl. Environ. Microbiol. 71: 3389-3398 (2005).

Choudhury D, Roy S, Chakrabarti C, Biswas S, Dattagupta JK. Production and recovery of recombinant propapain with high yield. Phytochemistry 70: 465-472 (2009).

Chow IT, Baneyx F. Coordinated synthesis of the two ClpB isoforms improves the ability of Escherichia coli to survive thermal stress. FEBS Lett. 579: 4235-4241 (2005).

Chow IT, Barnett ME, Zolkiewski M, Baneyx F. The N-terminal domain of Escherichia coli ClpB enhances chaperone function. FEBS Lett. 579: 4242-4248 (2005).

Christendat D, Turnbull JL. Identifying groups involved in the binding of prephenate to prephenate dehydrogenase from Escherichia coli. Biochemistry 38: 4782-4793 (1999).

Christensen AB, Gregersen PL, Olsen CE, Collinge DB. A flavonoid 7-O-methyltransferase is expressed in barley leaves in response to pathogen attack. Plant Mol. Biol. 36: 219-227 (1998).

Christensen AB, Gregersen PL, Schroder J, Collinge DB. A chalcone synthase with an unusual substrate preference is expressed in barley leaves in response to UV light and pathogen attack. Plant Mol. Biol. 37: 849-857 (1998).

Christopherson RI. Partial inactivation of chorismate mutase-prephenate dehydrogenase from Escherichia coli in the presence of analogues of chorismate. Int. J. Biochem. Cell Biol. 29: 589-594 (1997).

Christova PK, Christov NK, Imai R. A cold inducible multidomain cystatin from winter wheat inhibits growth of the snow mold fungus, Microdochium nivale. Planta 223: 1207-1218 (2006).

Chronis D, Krishnan HB. Sulfur assimilation in soybean (Glycine max [L.] Merr.): molecular cloning and characterization of a cytosolic isoform of serine acetyltransferase. Planta 218: 417-426 (2004).

Chu J, Shoeman R, Hart J, Coleman T, Mazaitis A, Kelker N, Brot N, Weissbach H. Cloning and expression of the metE gene in Escherichia coli. Arch. Biochem. Biophys. 239: 467-474 (1985).

Chung HK, Rhee SG. Separation of glutamine synthetase species with different states of adenylylation by chromatography on monoclonal anti-AMP antibody affinity columns. Proc. Natl. Acad. Sci. U.S.A. 81: 4677-4681 (1984).

Chung TW, Lee DI, Kim DS, Jin UH, Park C, Kim JG, Kim MG, Ha SD, Kim KS, Lee KH, Kim KY, Chung DH, Kim CH. Molecular cloning and characterization of a large subunit of Salmonella typhimurium glutamate synthase (GOGAT) gene in Escherichia coli. J. Microbiol. 44: 301-310 (2006).

Chye ML. Arabidopsis cDNA encoding a membrane-associated protein with an acyl-CoA binding domain. Plant Mol. Biol. 38: 827-838 (1998).

Chye ML, Li HY, Yung MH. Single amino acid substitutions at the acyl-CoA-binding domain interrupt 14[C]palmitoyl-CoA binding of ACBP2, an Arabidopsis acyl-CoA-binding protein with ankyrin repeats. Plant Mol. Biol. 44: 711-721 (2000).

Cid E, Geremia RA, Guinovart JJ, Ferrer JC. Glycogen synthase: towards a minimum catalytic unit? FEBS Lett. 528: 5-11 (2002).

Cinege G, Kereszt A, Kertesz S, Balogh G, Dusha I. The roles of different regions of the CycH protein in c-type cytochrome biogenesis in Sinorhizobium meliloti. Mol. Genet. Genomics 271: 171-179 (2004).

Cirillo JD, Weisbrod TR, Pascopella L, Bloom BR, Jacobs WR Jr. Isolation and characterization of the aspartokinase and aspartate semialdehyde dehydrogenase operon from mycobacteria. Mol. Microbiol. 11: 629-639 (1994).

Clancy M, Madill KA, Wood JM. Genetic and biochemical requirements for chemotaxis to L-proline in Escherichia coli. J. Bacteriol. 146: 902-906 (1981).

Clark MA, Baumann L, Baumann P. Buchnera aphidicola (Aphid endosymbiont) contains genes encoding enzymes of histidine biosynthesis. Curr. Microbiol. 37: 356-358 (1998).

Clark SM, Di Leo R, Dhanoa PK, Van Cauwenberghe OR, Mullen RT, Shelp BJ. Biochemical characterization, mitochondrial localization, expression, and potential functions for an Arabidopsis gamma-aminobutyrate transaminase that utilizes both pyruvate and glyoxylate. J. Exp. Bot. 60: 1743-1757 (2009).

Clark SM, Di Leo R, Van Cauwenberghe OR, Mullen RT, Shelp BJ. Subcellular localization and expression of multiple tomato gamma-aminobutyrate transaminases that utilize both pyruvate and glyoxylate. J. Exp. Bot. 60: 3255-3267 (2009).

Clarke AK, MacDonald TM, Sjogren LLE. The ATP-dependent Clp protease in chloroplasts of higher plants. Physiol. Plant. 123: 406-412 (2005).

Clarke TA, Hemmings AM, Burlat B, Butt JN, Cole JA, Richardson DJ. Comparison of the structural and kinetic properties of the cytochrome c nitrite reductases from Escherichia coli, Wolinella succinogenes, Sulfurospirillum deleyianum and Desulfovibrio desulfuricans. Biochem. Soc. Trans. 34: 143-145 (2006).

Clarke TA, Holley T, Hartshorne RS, Fredrickson JK, Zachara JM, Shi L, Richardson DJ. The role of multihaem cytochromes in the respiration of nitrite in Escherichia coli and Fe(III) in Shewanella oneidensis. Biochem. Soc. Trans. 36: 1005-1010 (2008).

Clarke TA, Mills PC, Poock SR, Butt JN, Cheesman MR, Cole JA, Hinton JC, Hemmings AM, Kemp G, Söderberg CA, Spiro S, Van Wonderen J, Richardson DJ. Escherichia coli cytochrome c nitrite reductase NrfA. Methods Enzymol. 437: 63-77 (2008).

Clausen T, Wahl MC, Messerschmidt A, Huber R, Fuhrmann JC, Laber B, Streber W, Steegborn C. Cloning, purification and characterisation of cystathionine gamma-synthase from Nicotiana tabacum. Biol. Chem. 380: 1237-1242 (1999).

Clegg S, Yu F, Griffiths L, Cole JA. The roles of the polytopic membrane proteins NarK, NarU and NirC in Escherichia coli K-12: two nitrate and three nitrite transporters. Mol. Microbiol. 44: 143-155 (2002).

Clegg SJ, Jia W, Cole JA. Role of the Escherichia coli nitrate transport protein, NarU, in survival during severe nutrient starvation and slow growth. Microbiology 152: 2091-2100 (2006).

Clemente MT, Marquez AJ. Site-directed mutagenesis of Glu-297 from the alpha-polypeptide of Phaseolus vulgaris glutamine synthetase alters kinetic and structural properties and confers resistance to L-methionine sulfoximine. Plant Mol. Biol. 40: 835-845 (1999).

Clemente MT, Marquez AJ. Functional importance of Asp56 from the alpha-polypeptide of Phaseolus vulgaris glutamine synthetase. An essential residue for transferase but not for biosynthetic enzyme activity. Eur. J. Biochem. 264: 453-460 (1999).

Cock JM, Kim KD, Miller PW, Hutson RG, Schmidt RR. A nuclear gene with many introns encoding ammonium-inducible chloroplastic NADP-specific glutamate dehydrogenase(s) in Chlorella sorokiniana. Plant Mol. Biol. 17: 1023-1044 (1991).

Cody V, Galitsky N, Rak D, Luft JR, Pangborn W, Queener SF. Ligand-induced conformational changes in the crystal structures of Pneumocystis carinii dihydrofolate reductase complexes with folate and NADP+. Biochemistry 38: 4303-4312 (1999).

Colanduoni JA, Villafranca JJ. Labeling of a specific arginine residue at the active site of glutamine synthetase (E.coli). Biochem. Biophys. Res. Commun. 126: 412-418 (1985).

Cole J. Nitrate reduction to ammonia by enteric bacteria: redundancy, or a strategy for survival during oxygen starvation? FEMS Microbiol. Lett. 136: 1-11 (1996).

Cole JA. Physiology, biochemistry, and genetics of nitrite reduction by Escherichia coli. In "Molecular and Genetic Aspects of Nitrate Assimilation" (JL Wray, JR Kinghorn eds) Oxford Science Publications, Oxford, pp. 229-244 (1989).

Collet JF, Gerin I, Rider MH, Veiga-da-Cunha M, Van Schaftingen E. Human L-3-phosphoserine phosphatase: sequence, expression and evidence for a phosphoenzyme intermediate. FEBS Lett. 408: 281-284 (1997).

Collin S, Justin AM, Cantrel C, Arondel V, Kader JC. Identification of AtPIS, a phosphatidylinositol synthase from Arabidopsis. Eur. J. Biochem. 262: 652-658 (1999).

Collins LA, Egan SM, Stewart V. Mutational analysis reveals functional similarity between NARX, a nitrate sensor in Escherichia coli K-12, and the methyl-accepting chemotaxis proteins. J. Bacteriol. 174: 3667-3675 (1992).

Colnaghi R, Rudnick P, He L, Green A, Yan D, Larson E, Kennedy C. Lethality of glnD null mutations in Azotobacter vinelandii is suppressible by prevention of glutamine synthetase adenylylation. Microbiology 147: 1267-1276 (2001).

Colombo G, Villafranca JJ. Amino acid sequence of Escherichia coli glutamine synthetase deduced from the DNA nucleotide sequence. J. Biol. Chem. 261: 10587-10591 (1986).

Comeau DE, Inouye M. A novel method for the cloning of chromosomal mutations in a single step: isolation of two mutant alleles of envZ, an osmoregulatory gene from Escherichia coli. Mol. Gen. Genet. 213: 166-169 (1988).

Commichau FM, Gunka K, Landmann JJ, Stulke J.. Glutamate metabolism in Bacillus subtilis: gene expression and enzyme activities evolved to avoid futile cycles and to allow rapid responses to perturbations of the system J. Bacteriol. 190: 3557-3564 (2008).

Conn S, Curtin C, Bezier A, Franco C, Zhang W. Purification, molecular cloning, and characterization of glutathione S-transferases (GSTs) from pigmented Vitis vinifera L. cell suspension cultures as putative anthocyanin transport proteins. J. Exp. Bot. 59: 3621-3634 (2008).

Conrado RJ, Mansell TJ, Varner JD, Delisa MP. Stochastic reaction-diffusion simulation of enzyme compartmentalization reveals improved catalytic efficiency for a synthetic metabolic pathway. Metab. Eng. 9: 355-363 (2007).

Contador CA, Rizk ML, Asenjo JA, Liao JC. Ensemble modeling for strain development of L-lysine-producing Escherichia coli. Metab. Eng. 11: 221-233 (2009).

Contestabile R, Angelaccio S, Bossa F, Wright HT, Scarsdale N, Kazanina G, Schirch V. Role of tyrosine 65 in the mechanism of serine hydroxymethyltransferase. Biochemistry 39: 7492-7500 (2000).

Contestabile R, Paiardini A, Pascarella S, di Salvo ML, D'Aguanno S, Bossa F. L-Threonine aldolase, serine hydroxymethyltransferase and fungal alanine racemase. A subgroup of strictly related enzymes specialized for different functions. Eur. J. Biochem. 268: 6508-6525 (2001).

Contreras A, Drummond M, Bali A, Blanco G, Garcia E, Bush G, Kennedy C, Merrick M. The product of the nitrogen fixation regulatory gene nfrX of Azotobacter vinelandii is functionally and structurally homologous to the uridylyltransferase encoded by glnD in enteric bacteria. J. Bacteriol. 173: 7741-7749 (1991).

Conzelmann H, Saez-Rodriguez J, Sauter T, Bullinger E, Allgower F, Gilles ED. Reduction of mathematical models of signal transduction networks: simulation-based approach applied to EGF receptor signalling. Syst. Biol. 1: 159-169 (2004).

Cool RH, Veenstra MK, van Klompenburg W, Heyne RI, Muller M, de Vries EG, van Veen HW, Konings WN. S-decyl-glutathione nonspecifically stimulates the ATPase activity of the nucleotide-binding domains of the human multidrug resistance-associated protein, MRP1 (ABCC1). Eur. J. Biochem. 269: 3470-3478 (2002).

Coppee JY, Auger S, Turlin E, Sekowska A, Le Caer JP, Labas V, Vagner V, Danchin A, Martin-Verstraete I. Sulfur-limitation-regulated proteins in Bacillus subtilis: a two-dimensional gel electrophoresis study. Microbiology 147: 1631-1640 (2001).

Corbin RW, Paliy O, Yang F, Shabanowitz J, Platt M, Lyons CE Jr, Root K, McAuliffe J, Jordan MI, Kustu S, Soupene E, Hunt DF. Toward a protein profile of Escherichia coli: comparison to its transcription profile. Proc. Natl. Acad. Sci. U.S.A. 100: 9232-9237 (2003).

Cordes C, Mockel B, Eggeling L, Sahm H. Cloning, organization and functional analysis of ilvA, ilvB and ilvC genes from Corynebacterium glutamicum. Gene 112: 113-116 (1992).

Corigliano EM, Perona JJ. Architectural underpinnings of the genetic code for glutamine. Biochemistry 48: 676-687 (2009).

Cormack BP, Valdivia RH, Falkow S. FACS-optimized mutants of the green fluorescent protein (GFP). Gene 173: 33-38 (1996).

Cornell KA, Riscoe MK. Cloning and expression of Escherichia coli 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase: identification of the pfs gene product. Biochim. Biophys. Acta 1396: 8-14 (1998).

Cornell KA, Winter RW, Tower PA, Riscoe MK. Affinity purification of 5-methylthioribose kinase and 5-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Klebsiella pneumoniae. Biochem. J. 317: 285-290 (1996).

Cosper MM, Jameson GN, Hernandez HL, Krebs C, Huynh BH, Johnson MK. Characterization of the cofactor composition of Escherichia coli biotin synthase. Biochemistry 43: 2007-2021 (2004).

Cosper MM, Jameson GNL, Eidsness MK, Huynh BH, Johnson MK. Recombinant Escherichia coli biotin synthase is a [2Fe-2S](2+) protein in whole cells. FEBS Lett. 529: 332-336 (2002).

Cosquer A, Ficamos M, Jebbar M, Corbel JC, Choquet G, Fontenelle C, Uriac P, Bernard T. Antibacterial activity of glycine of betaine analogues: involvement osmoporters. Bioorg. Med. Chem. Lett. 14: 2061-2065 (2004).

Cosquer A, Pichereau V, Pocard JA, Minet J, Cormier M, Bernard T. Nanomolar levels of dimethylsulfoniopropionate, dimethylsulfonioacetate, and glycine betaine are sufficient to confer osmoprotection to Escherichia coli. Appl. Environ. Microbiol. 65: 3304-3311 (1999).

Cottaz S, Samain E. Genetic engineering of Escherichia coli for the production of NI,NII-diacetylchitobiose (chitinbiose) and its utilization as a primer for the synthesis of complex carbohydrates. Metab. Eng. 7: 311-317 (2005).

Coughlan S, Wang XG, Britton KL, Stillman TJ, Rice DW, Chiaraluce R, Consalvi V, Scandurra R, Engel PC. Contribution of an aspartate residue, D114, in the active site of clostridial glutamate dehydrogenase to the enzyme's unusual pH dependence. Biochim. Biophys. Acta 1544: 10-17 (2001).

Coulter CV, Gerrard JA, Kraunsoe JAE, Pratt AJ. Escherichia coli dihydrodipicolinate synthase and dihydrodipicolinate reductase: kinetic and inhibition studies of two putative herbicide targets. Pestic. Sci. 55: 887-895 (1999).

Coursol S, Pierre JN, Vidal J, Grisvard J. Cloning and characterization of a phospholipase C from the C4 plant Digitaria sanguinalis. J. Exp. Bot. 53: 1521-1524 (2002).

Coutts G, Thomas G, Blakey D, Merrick M. Membrane sequestration of the signal transduction protein GlnK by the ammonium transporter AmtB. EMBO J. 21: 536-545 (2002).

Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. Integrating high-throughput and computational data elucidates bacterial networks. Nature 429: 92-96 (2004).

Covert MW, Palsson BO. Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J. Biol. Chem. 277: 28058-28064 (2002).

Covert MW, Xiao N, Chen TJ, Karr JR. Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. Bioinformatics 24: 2044-2050 (2008).

Covic L, Silva NF, Lew RR. Functional characterization of ARAKIN (ATMEKK1): a possible mediator in an osmotic stress response pathway in higher plants. Biochim. Biophys. Acta 1451: 242-254 (1999).

Cowan JA. Structural and catalytic chemistry of magnesium-dependent enzymes. Biometals 15: 225-235 (2002).

Cox JM, Hawkes TR, Bellini P, Ellis RM, Barrett R, Swanborough JJ, Russell SE, Walker PA, Barnes NJ, Knee AJ, Lewis T, Davies PR. The design and synthesis of inhibitors of imidazoleglycerol phosphate dehydratase as potential herbicides. Pestic. Sci. 50: 297-311 (1997).

Cox SJ, Shalel Levanon S, Bennett GN, San KY. Genetically constrained metabolic flux analysis. Metab. Eng. 7: 445-456 (2005).

Cozzani I, Fazio AM, Felici E, Barletta G. Separation and characterization of NAD- and NADP-specific succinate-semialdehyde dehydrogenase from Escherichia coli K-12 3300. Biochim. Biophys. Acta 613: 309-317 (1980).

Crabeel M, Charlier D, Cunin R, Boyen A, Glansdorff N, Pierard A. Accumulation of arginine precursors in Escherichia coli: effects on growth, enzyme repression, and application to the forward selection of arginine auxotrophs. J. Bacteriol. 123: 898-904 (1975).

Crack JC, Le Brun NE, Thomson AJ, Green J, Jervis AJ. Reactions of nitric oxide and oxygen with the regulator of fumarate and nitrate reduction, a global transcriptional regulator, during anaerobic growth of Escherichia coli. Methods Enzymol. 437: 191-209 (2008).

Cramm R, Strube K. Redox-controlled dinitrosyl formation at the diiron-oxo center of NorA. Methods Enzymol. 437: 103-116 (2008).

Crane BR, Getzoff ED. The relationship between structure and function for the sulfite reductases. Curr. Opin. Struct. Biol. 6: 744-756 (1996).

Crane BR, Siegel LM, Getzoff ED. Sulfite reductase structure at 1.6 A: evolution and catalysis for reduction of inorganic anions. Science 270: 59-67 (1995).

Cremer J, Treptow C, Eggeling L, Sahm H. Regulation of enzymes of lysine biosynthesis in Corynebacterium glutamicum. J. Gen. Microbiol. 134: 3221-3229 (1988).

Crespo JL, Garcia-Dominguez M, Florencio FJ. Nitrogen control of the glnN gene that codes for GS type III, the only glutamine synthetase in the cyanobacterium Pseudanabaena sp. PCC 6903. Mol. Microbiol. 30: 1101-1112 (1998).

Cretin C, Bakrim N, Keryer E, Santi S, Lepiniec L, Vidal J, Gadal P. Production in Escherichia coli of active Sorghum phosphoenolpyruvate carboxylase which can be phosphorylated. Plant Mol. Biol. 17: 83-88 (1991).

Croft JE, Love DR, Bergquist PL. Expression of leucine genes from an extremely thermophilic bacterium in Escherichia coli. Mol. Gen. Genet. 210: 490-497 (1987).

Cronan JE Jr. Beta-alanine synthesis in Escherichia coli. J. Bacteriol. 141: 1291-1297 (1980).

Cronan JE Jr, Littel KJ, Jackowski S. Genetic and biochemical analyses of pantothenate biosynthesis in Escherichia coli and Salmonella typhimurium. J. Bacteriol. 149: 916-922 (1982).

Cross JM, Clancy M, Shaw JR, Boehlein SK, Greene TW, Schmidt RR, Okita TW, Hannah LC. A polymorphic motif in the small subunit of ADP-glucose pyrophosphorylase modulates interactions between the small and large subunits. Plant J. 41: 501-511 (2005).

Cross JM, Clancy M, Shaw JR, Greene TW, Schmidt RR, Okita TW, Hannah LC. Both subunits of ADP-glucose pyrophosphorylase are regulatory. Plant Physiol. 135: 137-144 (2004).

Crossman LC, Moir JW, Enticknap JJ, Richardson DJ, Spiro S. Heterologous expression of heterotrophic nitrification genes. Microbiology 143: 3775-3783 (1997).

Cruz JA, Harfe B, Radkowski CA, Dann MS, McCarty RE. Molecular dissection of the epsilon subunit of the chloroplast ATP synthase of spinach. Plant Physiol. 109: 1379-1388 (1995).

Cruz-Hernandez A, Gomez-Lim MA. Alternative oxidase from mango (Mangifera indica, L.) is differentially regulated during fruit ripening. Planta 197: 569-576 (1995).

Csonka LN. The role of proline in osmoregulation in Salmonella typhimurium and Escherichia coli. Basic Life Sci. 18: 533-542 (1981).

Csonka LN, Gelvin SB, Goodner BW, Orser CS, Siemieniak D, Slightom JL. Nucleotide sequence of a mutation in the proB gene of Escherichia coli that confers proline overproduction and enhanced tolerance to osmotic stress. Gene 64: 199-205 (1988).

Csonka LN, Hanson AD. Prokaryotic osmoregulation - genetics and physiology. Annu. Rev. Microbiol. 45: 569-606 (1991).

Culham DE, Dalgado C, Gyles CL, Mamelak D, MacLellan S, Wood JM. Osmoregulatory transporter ProP influences colonization of the urinary tract by Escherichia coli. Microbiology 144: 91-102 (1998).

Culham DE, Emmerson KS, Lasby B, Mamelak D, Steer BA, Gyles CL, Villarejo M, Wood JM. Genes encoding osmoregulatory proline/glycine betaine transporters and the proline catabolic system are present and expressed in diverse clinical Escherichia coli isolates. Can. J. Microbiol. 40: 397-402 (1994).

Culham DE, Hillar A, Henderson J, Ly A, Vernikovska YI, Racher KI, Boggs JM, Wood JM. Creation of a fully functional cysteine-less variant of osmosensor and proton-osmoprotectant symporter ProP from Escherichia coli and its application to assess the transporter's membrane orientation. Biochemistry 42: 11815-11823 (2003).

Culham DE, Lasby B, Marangoni AG, Milner JL, Steer BA, van Nues RW, Wood JM. Isolation and sequencing of Escherichia coli gene proP reveals unusual structural features of the osmoregulatory proline/betaine transporter, ProP. J. Mol. Biol. 229: 268-276 (1993).

Cullin C, Baudin-Baillieu A, Guillemet E, Ozier-Kalogeropoulos O. Functional analysis of YCL09C: evidence for a role as the regulatory subunit of acetolactate synthase. Yeast 12: 1511-1518 (1996).

Cumino A, Ekeroth C, Salerno GL. Sucrose-phosphate phosphatase from Anabaena sp. strain PCC 7120: isolation of the protein and gene revealed significant structural differences from the higher-plant enzyme. Planta 214: 250-256 (2001).

Cummings SP, Williamson MP, Gilmour DJ. Turgor regulation in a novel Halomonas species. Arch. Microbiol. 160: 319-323 (1993).

Cunningham FX Jr, Gantt E. A study in scarlet: enzymes of ketocarotenoid biosynthesis in the flowers of Adonis aestivalis. Plant J. 41: 478-492 (2005).

Cunningham L, Guest JR. Transcription and transcript processing in the sdhCDAB-sucABCD operon of Escherichia coli. Microbiology 144: 2113-2123 (1998).

Cunningham-Rundles S, Maas WK. Isolation, characterization, and mapping of Escherichia coli mutants blocked in the synthesis of ornithine decarboxylase. J. Bacteriol. 124: 791-799 (1975).

Curatti L, Porchia AC, Herrera-Estrella L, Salerno GL. A prokaryotic sucrose synthase gene (susA) isolated from a filamentous nitrogen-fixing cyanobacterium encodes a protein similar to those of plants. Planta 211: 729-735 (2000).

Curien G, Dumas R, Ravanel S, Douce R. Characterization of an Arabidopsis thaliana cDNA encoding an S-adenosylmethionine-sensitive threonine synthase. Threonine synthase from higher plants. FEBS Lett. 390: 85-90 (1996).

Curien G, Job D, Douce R, Dumas R. Allosteric activation of Arabidopsis threonine synthase by S-adenosylmethionine. Biochemistry 37: 13212-13221 (1998).

Cussiol JR, Alves SV, de Oliveira MA, Netto LE. Organic hydroperoxide resistance gene encodes a thiol-dependent peroxidase. J. Biol. Chem. 278: 11570-11578 (2003).

Cvejic JH, Rohmer M. CO2 as main carbon source for isoprenoid biosynthesis via the mevalonate-independent methylerythritol 4-phosphate route in the marine diatoms Phaeodactylum tricornutum and Nitzschia ovalis. Phytochemistry 53: 21-28 (2000).

Cvitkovitch DG, Gutierrez JA, Bleiweis AS. Role of the citrate pathway in glutamate biosynthesis by Streptococcus mutans. J. Bacteriol. 179: 650-655 (1997).

D'Ari L, Rabinowitz JC. Purification, characterization, cloning, and amino acid sequence of the bifunctional enzyme 5,10-methylenetetrahydrofolate dehydrogenase/5,10-methenyltetrahydrofolate cyclohydrolase from Escherichia coli. J. Biol. Chem. 266: 23953-23958 (1991).

D'Auria JC, Chen F, Pichersky E. Characterization of an acyltransferase capable of synthesizing benzylbenzoate and other volatile esters in flowers and damaged leaves of Clarkia breweri. Plant Physiol. 130: 466-476 (2002).

Daabrowski S, Brillowska A, Kur J. Use of the green fluorescent protein variant (YFP) to monitor MetArg human proinsulin production in Escherichia coli. Protein Expr. Purif. 16: 315-323 (1999).

Dabizzi S, Ammannato S, Fani R. Expression of horizontally transferred gene clusters: activation by promoter-generating mutations. Res. Microbiol. 152: 539-549 (2001).

Dabrowski MJ, Dietze EC, Atkins WM. Engineering the aggregation properties of dodecameric glutamine synthetase: a single amino acid substitution controls 'salting out'. Protein Eng. 9: 291-298 (1996).

Dabrowski MJ, Yanchunas J Jr, Villafranca BC, Dietze EC, Schurke P, Atkins WM. Supramolecular self-assembly of glutamine synthetase: mutagenesis of a novel intermolecular metal binding site required for dodecamer stacking. Biochemistry 33: 14957-14964 (1994).

Dahiya P, Kardailsky IV, Brewin NJ. Immunolocalization of PsNLEC-1, a lectin-like glycoprotein expressed in developing pea nodules. Plant Physiol. 115: 1431-1442 (1997).

Dahlquist FW, Purich DL. Regulation of Escherichia coli glutamine synthetase. Evidence for the action of some feedback modifiers at the active site of the unadenylylated enzyme. Biochemistry 14: 1980-1989 (1975).

Dai M, Ziesman S, Ratcliffe T, Gill RT, Copley SD. Visualization of protoplast fusion and quantitation of recombination in fused protoplasts of auxotrophic strains of Escherichia coli. Metab. Eng. 7: 45-52 (2005).

Dall'osto L, Caffarri S, Bassi R. A mechanism of nonphotochemical energy dissipation, independent from PsbS, revealed by a conformational change in the antenna protein CP26. Plant Cell 17: 1217-1232 (2005).

Dall-Larsen T. Stopped flow kinetic studies of adenosine triphosphate phosphoribosyl transferase, the first enzyme in the histidine biosynthesis of Escherichia coli. Int. J. Biochem. 20: 811-815 (1988).

Dalton DA, Diaz del Castillo L, Kahn ML, Joyner SL, Chatfield JM. Heterologous expression and characterization of soybean cytosolic ascorbate peroxidase. Arch. Biochem. Biophys. 328: 1-8 (1996).

Dandekar AM, Uratsu SL. A single base pair change in proline biosynthesis genes causes osmotic stress tolerance. J. Bacteriol. 170: 5943-5945 (1988).

Danielsson H, Stenklo TK, Karlsson J, Nilsson T. A gene cluster for chlorate metabolism in Ideonella dechloratans. Appl. Environ. Microbiol. 69: 5585-5592 (2003).

Danishefsky AT, Onnufer JJ, Petsko GA, Ringe D. Activity and structure of the active-site mutants R386Y and R386F of Escherichia coli aspartate aminotransferase. Biochemistry 30: 1980-1985 (1991).

Darimont B, Stehlin C, Szadkowski H, Kirschner K. Mutational analysis of the active site of indoleglycerol phosphate synthase from Escherichia coli. Protein Sci. 7: 1221-1232 (1998).

Dartois V, Liu J, Hoch JA. Alterations in the flow of one-carbon units affect KinB-dependent sporulation in Bacillus subtilis. Mol. Microbiol. 25: 39-51 (1997).

Darwin AJ, Li J, Stewart V. Analysis of nitrate regulatory protein NarL-binding sites in the fdnG and narG operon control regions of Escherichia coli K-12. Mol. Microbiol. 20: 621-632 (1996).

Darwin AJ, Ziegelhoffer EC, Kiley PJ, Stewart V. Fnr, NarP, and NarL regulation of Escherichia coli K-12 napF (periplasmic nitrate reductase) operon transcription in vitro. J. Bacteriol. 180: 4192-4198 (1998).

Daschner K, Couee I, Binder S. The mitochondrial isovaleryl-coenzyme A dehydrogenase of Arabidopsis oxidizes intermediates of leucine and valine catabolism. Plant Physiol. 126: 601-612 (2001).

DasSarma S, Tischer E, Goodman HM. Plant glutamine synthetase complements a glnA mutation in Escherichia coli. Science 232: 1242-1244 (1986).

Datta S, Koutmos M, Pattridge KA, Ludwig ML, Matthews RG. A disulfide-stabilized conformer of methionine synthase reveals an unexpected role for the histidine ligand of the cobalamin cofactor. Proc. Natl. Acad. Sci. U.S.A. 105: 4115-4120 (2008).

Dattananda CS, Gowrishankar J. Osmoregulation in Escherichia coli: complementation analysis and gene-protein relationships in the proU locus. J. Bacteriol. 171: 1915-1922 (1989).

Daugherty M, Polanuyer B, Farrell M, Scholle M, Lykidis A, de Crecy-Lagard V, Osterman A. Complete reconstitution of the human coenzyme A biosynthetic pathway via comparative genomics. J. Biol. Chem. 277: 21431-21439 (2002).

Davidovich-Rikanati R, Lewinsohn E, Bar E, Iijima Y, Pichersky E, Sitrit Y. Overexpression of the lemon basil alpha-zingiberene synthase gene (ZIS) increases both mono- and sesquiterpene contents in tomato fruit. Plant J. 56: 228-238 (2008).

Davies C, Shin R, Liu W, Thomas MR, Schachtman DP. Transporters expressed during grape berry (Vitis vinifera L.) development are associated with an increase in berry size and berry potassium accumulation. J. Exp. Bot. 57: 3209-3216 (2006).

Davis EM, Ringer KL, McConkey ME, Croteau R. Monoterpene metabolism. Cloning, expression, and characterization of menthone reductases from peppermint. Plant Physiol. 137: 873-881 (2005).

Dayakar BV, Lin HJ, Chen CH, Ger MJ, Lee BH, Pai CH, Chow D, Huang HE, Hwang SY, Chung MC, Feng TY. Ferredoxin from sweet pepper (Capsicum annuum L.) intensifying harpin(pss)-mediated hypersensitive response shows an enhanced production of active oxygen species (AOS). Plant Mol. Biol. 51: 913-924 (2003).

De Anda R, Lara AR, Hernandez V, Hernandez-Montalvo V, Gosset G, Bolivar F, Ramirez OT. Replacement of the glucose phosphotransferase transport system by galactose permease reduces acetate accumulation and improves process performance of Escherichia coli for recombinant protein production without impairment of growth rate. Metab. Eng. 8: 281-290 (2006).

De Biase D, Simmaco M, Sweeney G, Barra D, Bossa F, John RA. Isolation and cloning of the gene from Escherichia coli encoding glutamate decarboxylase. Biotechnol. Appl. Biochem. 18: 139-142 (1993).

De Biase D, Tramonti A, Bossa F, Visca P. The response to stationary-phase stress conditions in Escherichia coli: role and regulation of the glutamic acid decarboxylase system. Mol. Microbiol. 32: 1198-1211 (1999).

De Biase D, Tramonti A, John RA, Bossa F. Isolation, overexpression, and biochemical characterization of the two isoforms of glutamic acid decarboxylase from Escherichia coli. Protein Expr. Purif. 8: 430-438 (1996).

De Jaeger G, Buys E, Eeckhout D, Bruyns AM, De Neve M, De Wilde C, Gerats T, Van Montagu M, Fischer R, Depicker A. Use of phage display for isolation and characterization of single-chain variable fragments against dihydroflavonol 4-reductase from Petunia hybrida. FEBS Lett. 403: 116-122 (1997).

de Kraker JW, Luck K, Textor S, Tokuhisa JG, Gershenzon J. Two Arabidopsis genes (IPMS1 and IPMS2) encode isopropylmalate synthase, the branchpoint step in the biosynthesis of leucine. Plant Physiol. 143: 970-986 (2007).

De La Fuente Van Bentem S, Vossen JH, Vermeer JE, De Vroomen MJ, Gadella TW Jr, Haring MA, Cornelissen BJ. The subcellular localization of plant protein phosphatase 5 isoforms is determined by alternative splicing. Plant Physiol. 133: 702-712 (2003).

de la Torre F, De Santis L, Suarez MF, Crespillo R, Canovas FM. Identification and functional analysis of a prokaryotic-type aspartate aminotransferase: implications for plant amino acid metabolism. Plant J. 46: 414-425 (2006).

de la Torre F, Suarez MF, Santis L, Canovas FM. The aspartate aminotransferase family in conifers: biochemical analysis of a prokaryotic-type enzyme from maritime pine. Tree Physiol. 27: 1283-1291 (2007).

De Luca V, Marineau C, Brisson N. Molecular cloning and analysis of cDNA encoding a plant tryptophan decarboxylase: comparison with animal dopa decarboxylases. Proc. Natl. Acad. Sci. U.S.A. 86: 2582-2586 (1989).

de Marco A, Vigh L, Diamant S, Goloubinoff P. Native folding of aggregation-prone recombinant proteins in Escherichia coli by osmolytes, plasmid- or benzyl alcohol-overexpressed molecular chaperones. Cell. Stress Chaperones 10: 329-339 (2005).

de Mel VS, Kamberov ES, Martin PD, Zhang J, Ninfa AJ, Edwards BF. Preliminary X-ray diffraction analysis of crystals of the PII protein from Escherichia coli. J. Mol. Biol. 243: 796-798 (1994).

de Pater S, Pham K, Memelink J, Kijne J. RAP-1 is an Arabidopsis MYC-like R protein homologue, that binds to G-box sequence motifs. Plant Mol. Biol. 34: 169-174 (1997).

de Paula RM, Wilson WA, Roach PJ, Terenzi HF, Bertolini MC. Biochemical characterization of Neurospora crassa glycogenin (GNN), the self-glucosylating initiator of glycogen synthesis. FEBS Lett. 579: 2208-2214 (2005).

De Rossi E, Leva R, Gusberti L, Manachini PL, Riccardi G. Cloning, sequencing and expression of the ilvBNC gene cluster from Streptomyces avermitilis. Gene 166: 127-132 (1995).

de Rudder KEE, Sohlenkamp C, Geiger O. Plant exuded choline is used for rhizobial membrane lipid biosynthesis by phosphatidylcholine synthase. J. Biol. Chem. 274: 20011-20016 (1999).

de Vienne D, Bost B, Fievet J, Zivy M, Dillmann C. Genetic variability of proteome expression and metabolic control. Plant Physiol. & Biochem. 39: 271-283 (2001).

De Vos D, Xu Y, Aerts T, Van Petegem F, Van Beeumen JJ. Crystal structure of Sulfolobus acidocaldarius aspartate carbamoyltransferase in complex with its allosteric activator CTP. Biochem. Biophys. Res. Commun. 372: 40-44 (2008).

de Wind N, de Jong M, Meijer M, Stuitje AR. Site-directed mutagenesis of the Escherichia coli chromosome near oriC: identification and characterization of asnC, a regulatory element in E. coli asparagine metabolism. Nucleic Acids Res. 13: 8797-8811 (1985).

de Zamaroczy M, Delorme F, Elmerich C. Characterization of three different nitrogen-regulated promoter regions for the expression of glnB and glnA in Azospirillum brasilense. Mol. Gen. Genet. 224: 421-430 (1990).

de Zelicourt A, Letousey P, Thoiron S, Campion C, Simoneau P, Elmorjani K, Marion D, Simier P, Delavault P. Ha-DEF1, a sunflower defensin, induces cell death in Orobanche parasitic plants. Planta 226: 591-600 (2007).

Dean AM. Fitness, flux and phantoms in temporally variable environments. Genetics 136: 1481-1495 (1994).

Deane SM, Rawlings DE. Cloning and sequencing of the gene for the Thiobacillus ferrooxidans ATCC33020 glutamate synthase (GOGAT) small subunit and complementation of an Escherichia coli gltD mutant. Gene 177: 261-263 (1996).

Decatur WA, Fournier MJ. rRNA modifications and ribosome function. Trends Biochem. Sci. 27: 344-351 (2002).

Decou R, Lhernould S, Laurans F, Sulpice E, Leple JC, Dejardin A, Pilate G, Costa G. Cloning and expression analysis of a wood-associated xylosidase gene (PtaBXL1) in poplar tension wood. Phytochemistry 70: 163-172 (2009).

Dehesh K, Edwards P, Hayes T, Cranmer AM, Fillatti J. Two novel thioesterases are key determinants of the bimodal distribution of acyl chain length of Cuphea palustris seed oil. Plant Physiol. 110: 203-210 (1996).

Deka RK, Anton IA, Dunbar B, Coggins JR. The characterisation of the shikimate pathway enzyme dehydroquinase from Pisum sativum. FEBS Lett. 349: 397-402 (1994).

Deka RK, Kleanthous C, Coggins JR. Identification of the essential histidine residue at the active site of Escherichia coli dehydroquinase. J. Biol. Chem. 267: 22237-22242 (1992).

Delaney KJ, Xu R, Zhang J, Li QQ, Yun KY, Falcone DL, Hunt AG. Calmodulin interacts with and regulates the RNA-binding activity of an Arabidopsis polyadenylation factor subunit. Plant Physiol. 140: 1507-1521 (2006).

Delannay S, Charlier D, Tricot C, Villeret V, Pierard A, Stalon V. Serine 948 and threonine 1042 are crucial residues for allosteric regulation of Escherichia coli carbamoylphosphate synthetase and illustrate coupling effects of activation and inhibition pathways. J. Mol. Biol. 286: 1217-1228 (1999).

Delauney AJ, Hu CA, Kishor PB, Verma DP. Cloning of ornithine delta-aminotransferase cDNA from Vigna aconitifolia by trans-complementation in Escherichia coli and regulation of proline biosynthesis. J. Biol. Chem. 268: 18673-18678 (1993).

Delgado IJ, Wang Z, de Rocher A, Keegstra K, Raikhel NV. Cloning and characterization of AtRGP1. A reversibly autoglycosylated Arabidopsis protein implicated in cell wall biosynthesis. Plant Physiol. 116: 1339-1350 (1998).

Delgado MJ, Bonnard N, Tresierra-Ayala A, Bedmar EJ, Muller P. The Bradyrhizobium japonicum napEDABC genes encoding the periplasmic nitrate reductase are essential for nitrate respiration. Microbiology (U.K.) 149: 3395-3403 (2003).

DeLisa MP, Li J, Rao G, Weigand WA, Bentley WE. Monitoring GFP-operon fusion protein expression during high cell density cultivation of Escherichia coli using an on-line optical sensor. Biotechnol. Bioeng. 65: 54-64 (1999).

Delle Fratte S, Iurescia S, Angelaccio S, Bossa F, Schirch V. The function of arginine 363 as the substrate carboxyl-binding site in Escherichia coli serine hydroxymethyltransferase. Eur. J. Biochem. 225: 395-401 (1994).

Delorme C, Ehrlich SD, Renault P. Regulation of expression of the Lactococcus lactis histidine operon. J. Bacteriol. 181: 2026-2037 (1999).

Delumeau O, Renard M, Montrichard F. Characterization and possible redox regulation of the purified calmodulin-dependent NAD+ kinase from Lycopersicon pimpinellifolium. Plant Cell Environ. 23: 1267-1273 (2000).

Demir V, Dincturk HB. Semi-anaerobic growth conditions are favoured by some Escherichia coli strains during heterologous expression of some archaeal proteins. Mol. Biol. Rep. 33: 59-63 (2006).

Demirci H, Gregory ST, Dahlberg AE, Jogl G. Multiple-site trimethylation of ribosomal protein L11 by the PrmA methyltransferase. Structure 16: 1059-1066 (2008).

DeMoss JA, Hsu PY. NarK enhances nitrate uptake and nitrite excretion in Escherichia coli. J. Bacteriol. 173: 3303-3310 (1991).

Deng MD, Severson DK, Grund AD, Wassink SL, Burlingame RP, Berry A, Running JA, Kunesh CA, Song L, Jerrell TA, Rosson RA. Metabolic engineering of Escherichia coli for industrial production of glucosamine and N-acetylglucosamine. Metab. Eng. 7: 201-214 (2005).

DeRidder BP, Dixon DP, Beussman DJ, Edwards R, Goldsbrough PB. Induction of glutathione S-transferases in Arabidopsis by herbicide safeners. Plant Physiol. 130: 1497-1505 (2002).

Desplats C, Beyly A, Cuine S, Bernard L, Cournac L, Peltier G. Modification of substrate specificity in single point mutants of Agrobacterium tumefaciens type II NADH dehydrogenase. FEBS Lett. 581: 4017-4022 (2007).

Detsch C, Stulke J. Ammonium utilization in Bacillus subtilis: transport and regulatory functions of NrgA and NrgB. Microbiology (U.K.) 149: 3289-3297 (2003).

Deutch AH, Rushlow KE, Smith CJ. Analysis of the Escherichia coli proBA locus by DNA and protein sequencing. Nucleic Acids Res. 12: 6337-6355 (1984).

Deutch CE. Oxidation of L-thiazolidine-4-carboxylate by L-proline dehydrogenase in Escherichia coli. J. Gen. Microbiol. 138: 1593-1598 (1992).

Deutch CE, Hasler JM, Houston RM, Sharma M, Stone VJ. Nonspecific inhibition of proline dehydrogenase synthesis in Escherichia coli during osmotic stress. Can. J. Microbiol. 35: 779-785 (1989).

Deutch CE, Klarstrom JL, Link CL, Ricciardi DL. Oxidation of L-thiazolidine-4-carboxylate by delta1-pyrroline-5-carboxylate reductase in Escherichia coli. Curr. Microbiol. 42: 442-446 (2001).

Deutch CE, O'Brien JM Jr, VanNieuwenhze MS. Identification of a trans-dominant mutation affecting proline dehydrogenase in Escherichia coli. Can. J. Microbiol. 31: 988-993 (1985).

Deutch CE, Soffer RL. Regulation of proline catabolism by leucyl,phenylalanyl-tRNA-protein transferase. Proc. Natl. Acad. Sci. U.S.A. 72: 405-408 (1975).

Dhankher OP, Rosen BP, McKinney EC, Meagher RB. Hyperaccumulation of arsenic in the shoots of Arabidopsis silenced for arsenate reductase (ACR2). Proc. Natl. Acad. Sci. U.S.A. 103: 5413-5418 (2006).

Dharmawardhana DP, Ellis BE, Carlson JE. cDNA cloning and heterologous expression of coniferin beta-glucosidase. Plant Mol. Biol. 40: 365-372 (1999).

Di Fraia R, Wilquet V, Ciardiello MA, Carratore V, Antignani A, Camardella L, Glansdorff N, Di Prisco G. NADP+-dependent glutamate dehydrogenase in the Antarctic psychrotolerant bacterium Psychrobacter sp. tad1. Characterization, protein and DNA sequence, and relationship to other glutamate dehydrogenases. Eur. J. Biochem. 267: 121-131 (2000).

di Salvo ML, Hunt S, Schirch V. Expression, purification, and kinetic constants for human and Escherichia coli pyridoxal kinases. Protein Expr. Purif. 36: 300-306 (2004).

Diamant S, Eliahu N, Rosenthal D, Goloubinoff P. Chemical chaperones regulate molecular chaperones in vitro and in cells under combined salt and heat stresses. J. Biol. Chem. 276: 39586-39591 (2001).

Diamant S, Rosenthal D, Azem A, Eliahu N, Ben-Zvi AP, Goloubinoff P. Dicarboxylic amino acids and glycine-betaine regulate chaperone-mediated protein-disaggregation under stress. Mol. Microbiol. 49: 401-410 (2003).

Dias JM, Than ME, Humm A, Huber R, Bourenkov GP, Bartunik HD, Bursakov S, Calvete J, Caldeira J, Carneiro C, Moura JJ, Moura I, Romao MJ. Crystal structure of the first dissimilatory nitrate reductase at 1.9 A solved by MAD methods. Structure 7: 65-79 (1999).

Diaz S, Perez-Pomares F, Pire C, Ferrer J, Bonete MJ. Gene cloning, heterologous overexpression and optimized refolding of the NAD-glutamate dehydrogenase from Haloferax mediterranei. Extremophiles 10: 105-115 (2006).

Dibrov P, Rimon A, Dzioba J, Winogrodzki A, Shalitin Y, Padan E. 2-Aminoperimidine, a specific inhibitor of bacterial NhaA Na(+)/H(+) antiporters. FEBS Lett. 579: 373-378 (2005).

Diebold R, Schuster J, Daschner K, Binder S. The branched-chain amino acid transaminase gene family in Arabidopsis encodes plastid and mitochondrial proteins. Plant Physiol. 129: 540-550 (2002).

Diepold A, Li G, Lennarz WJ, Nurnberger T, Brunner F. The Arabidopsis AtPNG1 gene encodes a peptide: N-glycanase. Plant J. 52: 94-104 (2007).

Diez B, Mellado E, Rodriguez M, Bernasconi E, Barredo JL. The NADP-dependent glutamate dehydrogenase gene from Penicillium chrysogenum and the construction of expression vectors for filamentous fungi. Appl. Microbiol. Biotechnol. 52: 196-207 (1999).

Dionisio G, Holm PB, Brinch-Pedersen H. Wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) multiple inositol polyphosphate phosphatases (MINPPs) are phytases expressed during grain filling and germination. Plant Biotechnol. J. 5: 325-338 (2007).

Dippe M, Ulbrich-Hofmann R. Substrate specificity in phospholipid transformations by plant phospholipase D isoenzymes. Phytochemistry 70: 361-365 (2009).

Dirk LM, Williams MA, Houtz RL. Eukaryotic peptide deformylases. Nuclear-encoded and chloroplast-targeted enzymes in Arabidopsis. Plant Physiol. 127: 97-107 (2001).

Dixon DP, Cole DJ, Edwards R. Dimerisation of maize glutathione transferases in recombinant bacteria. Plant Mol. Biol. 40: 997-1008 (1999).

Dixon DP, Edwards R. Selective binding of glutathione conjugates of fatty acid derivatives by plant glutathione transferases. J. Biol. Chem. 284: 21249-21256 (2009).

Dixon DP, Hawkins T, Hussey PJ, Edwards R. Enzyme activities and subcellular localization of members of the Arabidopsis glutathione transferase superfamily. J. Exp. Bot. 60: 1207-1218 (2009).

Do PM, Angerhofer A, Hrdy I, Bardonova L, Ingram LO, Shanmugam KT. Engineering Escherichia coli for fermentative dihydrogen production: potential role of NADH-ferredoxin oxidoreductase from the hydrogenosome of anaerobic protozoa. Appl. Biochem. Biotechnol. 153: 21-33 (2009).

Dobric N, Limsowtin GKY, Hillier AJ, Dudman NPB, Davidson BE. Identification and characterization of a cystathionine beta/gamma-lyase from Lactococcus lactis ssp. cremoris MG1363. FEMS Microbiol. Lett. 182: 249-254 (2000).

Doig P, de Jonge BL, Alm RA, Brown ED, Uria-Nickelsen M, Noonan B, Mills SD, Tummino P, Carmel G, Guild BC, Moir DT, Vovis GF, Trust TJ. Helicobacter pylori physiology predicted from genomic comparison of two strains. Microbiol. Mol. Biol. Rev. 63: 675-708 (1999).

Dolzan M, Johansson K, Roig-Zamboni V, Campanacci V, Tegoni M, Schneider G, Cambillau C. Crystal structure and reactivity of YbdL from Escherichia coli identify a methionine aminotransferase function. FEBS Lett. 571: 141-146 (2004).

Domach MM, Leung SK, Cahn RE, Cocks GG, Shuler ML. Computer model for glucose-limited growth of a single cell of Escherichia coli B/r-A. Biotechnol. Bioeng. 67: 827-840 (2000).

Dommelen A, De Mot R, Vanderleyden J. Ammonium transport: unifying concepts and unique aspects. Aust. J. Plant Physiol. 28: 959-967 (2001).

Donnelly MI, Cooper RA. Two succinic semialdehyde dehydrogenases are induced when Escherichia coli K-12 Is grown on gamma-aminobutyrate. J. Bacteriol. 145: 1425-1427 (1981).

Donnelly MI, Cooper RA. Succinic semialdehyde dehydrogenases of Escherichia coli: their role in the degradation of p-hydroxyphenylacetate and gamma-aminobutyrate. Eur. J. Biochem. 113: 555-561 (1981).

Doran-Peterson J, Cook DM, Brandon SK. Microbial conversion of sugars from plant biomass to lactic acid or ethanol. Plant J. 54: 582-592 (2008).

Dorion S, Matton DP, Rivoal J. Characterization of a cytosolic nucleoside diphosphate kinase associated with cell division and growth in potato. Planta 224: 108-124 (2006).

Dosselaere F, Lambrecht M, Vanderleyden J. Isolation and sequence analysis of the trpBA gene cluster, encoding tryptophan synthase, from Azospirillum brasilense. DNA Seq. 11: 287-293 (2000).

Dowhan W. Molecular basis for membrane phospholipid diversity: why are there so many lipids? Annu. Rev. Biochem. 66: 199-232 (1997).

Draborg H, Villadsen D, Nielsen TH. Cloning, characterization and expression of a bifunctional fructose-6-phosphate, 2-kinase/fructose-2,6-bisphosphatase from potato. Plant Mol. Biol. 39: 709-720 (1999).

Draczynska-Lusiak B, Brown OR. Asparagine synthetase: an oxidant-sensitive enzyme in Escherichia coli. Microbios 77: 141-152 (1994).

Drea SC, Mould RM, Hibberd JM, Gray JC, Kavanagh TA. Tissue-specific and developmental-specific expression of an Arabidopsis thaliana gene encoding the lipoamide dehydrogenase component of the plastid pyruvate dehydrogenase complex. Plant Mol. Biol. 46: 705-715 (2001).

Drennan CL, Huang S, Drummond JT, Matthews RG, Lidwig ML. How a protein binds B12: A 3.0 A X-ray structure of B12-binding domains of methionine synthase. Science 266: 1669-1674 (1994).

Drew DP, Lunde C, Lahnstein J, Fincher GB. Heterologous expression of cDNAs encoding monodehydroascorbate reductases from the moss, Physcomitrella patens and characterization of the expressed enzymes. Planta 225: 945-954 (2007).

Dridge EJ, Richardson DJ, Lewis RJ, Butler CS. Developing structure-based models to predict substrate specificity of D-group (type II) molybdenum enzymes: application to a molybdo-enzyme of unknown function from Archaeoglobus fulgidus. Biochem. Soc. Trans. 34: 118-121 (2006).

Drsata J. Tryptophan metabolism via transamination. In vitro aminotransferase assay using dinitrophenylhydrazine method. Adv. Exp. Med. Biol. 527: 511-517 (2003).

Drummond JT, Huang S, Blumenthal RM, Matthews RG. Assignment of enzymatic function to specific protein regions of cobalamin-dependent methionine synthase from Escherichia coli. Biochemistry 32: 9290-9295 (1993).

Drummond JT, Loo RR, Matthews RG. Electrospray mass spectrometric analysis of the domains of a large enzyme: observation of the occupied cobalamin-binding domain and redefinition of the carboxyl terminus of methionine synthase. Biochemistry 32: 9282-9289 (1993).

du Jardin P, Rojas-Beltran J, Gebhardt C, Brasseur R. Molecular cloning and characterization of a soluble inorganic pyrophosphatase in potato. Plant Physiol. 109: 853-860 (1995).

Duan X, Song Y, Yang A, Zhang J. The transgene pyramiding tobacco with betaine synthesis and heterologous expression of AtNHX1 is more tolerant to salt stress than either of the tobacco lines with betaine synthesis or AtNHX1. Physiol. Plant. 135: 281-295 (2009).

Dubourdieu M, DeMoss JA. The narJ gene product is required for biogenesis of respiratory nitrate reductase in Escherichia coli. J. Bacteriol. 174: 867-872 (1992).

Duhaze C, Gagneul D, Leport L, Larher FR, Bouchereau A. Uracil as one of the multiple sources of beta-alanine in Limonium latifolium, a halotolerant beta-alanine betaine accumulating Plumbaginaceae. Plant Physiol. Biochem. 41: 993-998 (2003).

Dukan S, Nystrom T. Bacterial senescence: stasis results in increased and differential oxidation of cytoplasmic proteins leading to developmental induction of the heat shock regulon. Genes Dev. 12: 3431-3441 (1998).

Dumas R, Biou V, Douce R. Purification and characterization of a fusion protein of plant acetohydroxy acid synthase and acetohydroxy acid isomeroreductase. FEBS Lett. 408: 156-160 (1997).

Dumas R, Job D, Ortholand JY, Emeric G, Greiner A, Douce R. Isolation and kinetic properties of acetohydroxy acid isomeroreductase from spinach (Spinacia oleracea) chloroplasts overexpressed in Escherichia coli. Biochem. J. 288: 865-874 (1992).

Dumas R, Lebrun M, Douce R. Isolation, characterization and sequence analysis of a full-length cDNA clone encoding acetohydroxy acid reductoisomerase from spinach chloroplasts. Biochem. J. 277: 469-475 (1991).

Duncan K, Coggins JR. The serC-aro A operon of Escherichia coli. A mixed function operon encoding enzymes from two different amino acid biosynthetic pathways. Biochem. J. 234: 49-57 (1986).

Duncan PA, White BA, Mackie RI. Purification and properties of NADP-dependent glutamate dehydrogenase from Ruminococcus flavefaciens FD-1. Appl. Environ. Microbiol. 58: 4032-4037 (1992).

Dunn MF, Aguilar V, Brzovic P, Drewe WF Jr, Houben KF, Leja CA, Roy M. The tryptophan synthase bienzyme complex transfers indole between the alpha- and beta-sites via a 25-30 A long tunnel. Biochemistry 29: 8598-8607 (1990).

Dupuy DL, Rial DV, Ceccarelli EA. Inhibition of pea ferredoxin-NADP(H) reductase by Zn-ferrocyanide. Eur. J. Biochem. 271: 4582-4593 (2004).

Durnin G, Clomburg J, Yeates Z, Alvarez PJ, Zygourakis K, Campbell P, Gonzalez R. Understanding and harnessing the microaerobic metabolism of glycerol in Escherichia coli. Biotechnol. Bioeng. 103: 148-161 (2009).

Dusch N, P hler A, Kalinowski J. Expression of the Corynebacterium glutamicum panD gene encoding L-aspartate-alpha-decarboxylase leads to pantothenate overproduction in Escherichia coli. Appl. Environ. Microbiol. 65: 1530-1539 (1999).

Dutzler R. Structural basis for ion conduction and gating in ClC chloride channels. FEBS Lett. 564: 229-233 (2004).

Duval FD, Renard M, Jaquinod M, Biou V, Montrichard F, Macherel D. Differential expression and functional analysis of three calmodulin isoforms in germinating pea (Pisum sativum L.) seeds. Plant J. 32: 481-493 (2002).

Duwenig E, Steup M, Kossmann J. Induction of genes encoding plastidic phosphorylase from spinach (Spinacia oleracea L.) and potato (Solanum tuberosum L.) by exogenously supplied carbohydrates in excised leaf discs. Planta 203: 111-120 (1997).

Dyer WE, Weaver LM, Zhao JM, Kuhn DN, Weller SC, Herrmann KM. A cDNA encoding 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Solanum tuberosum L. J. Biol. Chem. 265: 1608-1614 (1990).

Dykema PE, Sipes PR, Marie A, Biermann BJ, Crowell DN, Randall SK. A new class of proteins capable of binding transition metals. Plant Mol. Biol. 41: 139-150 (1999).

Eastmond PJ. Glycerol-insensitive Arabidopsis mutants: gli1 seedlings lack glycerol kinase, accumulate glycerol and are more resistant to abiotic stress. Plant J. 37: 617-625 (2004).

Eaves DJ, Grove J, Staudenmann W, James P, Poole RK, White SA, Griffiths I, Cole JA. Involvement of products of the nrfEFG genes in the covalent attachment of haem c to a novel cysteine-lysine motif in the cytochrome c552 nitrite reductase from Escherichia coli. Mol. Microbiol. 28: 205-216 (1998).

Eaves DJ, Palmer T, Boxer DH. The product of the molybdenum cofactor gene mobB of Escherichia coli is a GTP-binding protein. Eur. J. Biochem. 246: 690-697 (1997).

Eberhard J, Bischoff M, Raesecke HR, Amrhein N, Schmid J. Isolation of a cDNA from tomato coding for an unregulated, cytosolic chorismate mutase. Plant Mol. Biol. 31: 917-922 (1996).

Eberhard J, Ehrler TT, Epple P, Felix G, Raesecke HR, Amrhein N, Schmid J. Cytosolic and plastidic chorismate mutase isozymes from Arabidopsis thaliana: molecular characterization and enzymatic properties. Plant J. 10: 815-821 (1996).

Ebmeier A, Allison L, Cerutti H, Clemente T. Evaluation of the Escherichia coli threonine deaminase gene as a selectable marker for plant transformation. Planta 218: 751-758 (2004).

Eckardt NA. Viral defense and counterdefense: a role for adenosine kinase in innate defense and RNA silencing. Plant Cell 15: 2758-2762 (2003).

Eckardt NA. Photorespiration revisited. Plant Cell 17: 2139-2141 (2005).

Eckermann C, Eichel J, Schroder J. Plant methionine synthase: new insights into properties and expression. Biol. Chem. 381: 695-703 (2000).

Edman JC, Goldstein AL, Erbe JG. Para-aminobenzoate synthase gene of Saccharomyces cerevisiae encodes a bifunctional enzyme. Yeast 9: 669-675 (1993).

Edwards A, Marshall J, Denyer K, Sidebottom C, Visser RG, Martin C, Smith AM. Evidence that a 77-kilodalton protein from the starch of pea embryos is an isoform of starch synthase that is both soluble and granule bound. Plant Physiol. 112: 89-97 (1996).

Edwards JS, Covert MW, Palsson BO. Metabolic modelling of microbes: the flux-balance approach. Environ. Microbiol. 4: 133-140 (2002).

Edwards JS, Ibarra RU, Palsson BO. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat. Biotechnol. 19: 125-130 (2001).

Edwards JS, Palsson BO. The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities. Proc. Natl. Acad. Sci. U.S.A. 97: 5528-5533 (2000).

Edwards JS, Palsson BO. Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. BMC Bioinformatics 1: 1-10 (2000).

Edwards JS, Palsson BO. Robustness analysis of the Escherichia coli metabolic network. Biotechnol. Prog. 16: 927-939 (2000).

Edwards JS, Ramakrishna R, Palsson BO. Characterizing the metabolic phenotype: a phenotype phase plane analysis. Biotechnol. Bioeng. 77: 27-36 (2002).

Edwards R, Merrick M. The role of uridylyltransferase in the control of Klebsiella pneumoniae nif gene regulation. Mol. Gen. Genet. 247: 189-198 (1995).

Egan SM, Stewart V. Nitrate regulation of anaerobic respiratory gene expression in narX deletion mutants of Escherichia coli K-12. J. Bacteriol. 172: 5020-5029 (1990).

Ehlers C, Grabbe R, Veit K, Schmitz RA. Characterization of GlnK(1) from Methanosarcina mazei strain Go1: Complementation of an Escherichia coli glnK mutant strain by GlnK(1). J. Bacteriol. 184: 1028-1040 (2002).

Ehsani P, Meunier A, Nato F, Jafari A, Nato A, Lafaye P. Expression of anti human IL-4 and IL-6 scFvs in transgenic tobacco plants. Plant Mol. Biol. 52: 17-29 (2003).

Eichel J, Gonzalez JC, Hotze M, Matthews RG, Schroder J. Vitamin-B12-independent methionine synthase from a higher plant (Catharanthus roseus). Molecular characterization, regulation, heterologous expression, and enzyme properties. Eur. J. Biochem. 230: 1053-1058 (1995).

Eikmanns BJ, Metzger M, Reinscheid D, Kircher M, Sahm H. Amplification of three threonine biosynthesis genes in Corynebacterium glutamicum and its influence on carbon flux in different strains. Appl. Microbiol. Biotechnol. 34: 617-622 (1991).

El Malki F, Frankard V, Jacobs M. Molecular cloning and expression of a cDNA sequence encoding histidinol phosphate aminotransferase from Nicotiana tabacum. Plant Mol. Biol. 37: 1013-1022 (1998).

el-Mansi EM, Dawson GC, Bryce CF. Steady-state modelling of metabolic flux between the tricarboxylic acid cycle and the glyoxylate bypass in Escherichia coli. Comput. Appl. Biosci. 10: 295-299 (1994).

Elischewski F, Puhler A, Kalinowski J. Pantothenate production in Escherichia coli K12 by enhanced expression of the panE gene encoding ketopantoate reductase. J. Biotechnol. 75: 135-146 (1999).

Elliott SJ, Hoke KR, Heffron K, Palak M, Rothery RA, Weiner JH, Armstrong FA. Voltammetric studies of the catalytic mechanism of the respiratory nitrate reductase from Escherichia coli: How nitrate reduction and inhibition depend on the oxidation state of the active site. Biochemistry 43: 799-807 (2004).

Elmansi EMT, MacKintosh C, Duncan K, Holms WH, Nimmo HG. Molecular cloning and over-expression of the glyoxylate bypass operon from Escherichia coli ML308. Biochem. J. 242: 661-665 (1987).

Elumalai RP, Nagpal P, Reed JW. A mutation in the Arabidopsis KT2/KUP2 potassium transporter gene affects shoot cell expansion. Plant Cell 14: 119-131 (2002).

Ely B, Amarasinghe AB, Bender RA. Ammonia assimilation and glutamate formation in Caulobacter crescentus. J. Bacteriol. 133: 225-230 (1978).

Emmerling M, Bailey JE, Sauer U. Glucose catabolism of Escherichia coli strains with increased activity and altered regulation of key glycolytic enzymes. Metab. Eng. 1: 117-127 (1999).

Emmerling M, Bailey JE, Sauer U. Altered regulation of pyruvate kinase or co-overexpression of phosphofructokinase increases glycolytic fluxes in resting Escherichia coli. Biotechnol. Bioeng. 67: 623-627 (2000).

Emmerling M, Dauner M, Ponti A, Fiaux J, Hochuli M, Szyperski T, Wuthrich K, Bailey JE, Sauer U. Metabolic flux responses to pyruvate kinase knockout in Escherichia coli. J. Bacteriol. 184: 152-164 (2002).

Encinas MV, Gonzalez-Nilo FD, Goldie H, Cardemil E. Ligand interactions and protein conformational changes of phosphopyridoxyl-labeled Escherichia coli phosphoenolpyruvate carboxykinase determined by fluorescence spectroscopy. Eur. J. Biochem. 269: 4960-4968 (2002).

Endo T, Mihara Y, Furumoto T, Matsumura H, Kai Y, Izui K. Maize C4-form phosphoenolpyruvate carboxylase engineered to be functional in C3 plants: mutations for diminished sensitivity to feedback inhibitors and for increased substrate affinity. J. Exp. Bot. 59: 1811-1818 (2008).

Endy D. Foundations for engineering biology. Nature 438: 449-453 (2005).

Engel S, Vyazmensky M, Geresh S, Barak Z, Chipman DM. Acetohydroxyacid synthase: A new enzyme for chiral synthesis of R-phenylacetylcarbinol. Biotechnol. Bioeng. 83: 833-840 (2003).

Engemann C, Elssner T, Pfeifer S, Krumbholz C, Maier T, Kleber HP. Identification and functional characterisation of genes and corresponding enzymes involved in carnitine metabolism of Proteus sp. Arch. Microbiol. 183: 176-189 (2005).

Entus R, Poling M, Herrmann KM. Redox regulation of Arabidopsis 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase. Plant Physiol. 129: 1866-1871 (2002).

Eom SJ, Ahn HJ, Kim HW, Baek SH, Suh SW. Crystallization and preliminary X-ray crystallographic studies of phosphopantetheine adenylyltransferase from Helicobacter pylori. Acta Crystallogr. D. Biol. Crystallogr. 59: 561-562 (2003).

Epelbaum S, McDevitt R, Falco SC. Lysine-ketoglutarate reductase and saccharopine dehydrogenase from Arabidopsis thaliana: nucleotide sequence and characterization. Plant Mol. Biol. 35: 735-748 (1997).

Eppler T, Postma P, Schutz A, Volker U, Boos W. Glycerol-3-phosphate-induced catabolite repression in Escherichia coli. J. Bacteriol. 184: 3044-3052 (2002).

Erasto P, Bojase-Moleta G, Majinda RR. Antimicrobial and antioxidant flavonoids from the root wood of Bolusanthus speciosus. Phytochemistry 65: 875-880 (2004).

Erbeznik M, Strobel HJ, Dawson KA. Organization and sequence of histidine biosynthesis genes hisH, -A, -F, and -IE in Thermoanaerobacter ethanolicus. Curr. Microbiol. 40: 140-142 (2000).

Erikson O, Hertzberg M, Nasholm T. A conditional marker gene allowing both positive and negative selection in plants. Nat. Biotechnol. 22: 455-458 (2004).

Erikson O, Hertzberg M, Nasholm T. The dsdA gene from Escherichia coli provides a novel selectable marker for plant transformation. Plant Mol. Biol. 57: 425-433 (2005).

Ernsting BR, Atkinson MR, Ninfa AJ, Matthews RG. Characterization of the regulon controlled by the leucine-responsive regulatory protein in Escherichia coli. J. Bacteriol. 174: 1109-1118 (1992).

Ernsting BR, Denninger JW, Blumenthal RM, Matthews RG. Regulation of the gltBDF operon of Escherichia coli: how is a leucine-insensitive operon regulated by the leucine-responsive regulatory protein? J. Bacteriol. 175: 7160-7169 (1993).

Eschenburg S, Healy ML, Priestman MA, Lushington GH, Schonbrunn E. How the mutation glycine96 to alanine confers glyphosate insensitivity to 5-enolpyruvyl shikimate-3-phosphate synthase from Escherichia coli. Planta 216: 129-135 (2002).

Escobar-Paramo P, Clermont O, Blanc-Potard AB, Bui H, Le Bouguenec C, Denamur E. A specific genetic background is required for acquisition and expression of virulence factors in Escherichia coli. Mol. Biol. Evol. 21: 1085-1094 (2004).

Eshoo MW. lac fusion analysis of the bet genes of Escherichia coli: regulation by osmolarity, temperature, oxygen, choline, and glycine betaine. J. Bacteriol. 170: 5208-5215 (1988).

Espinosa-Ruiz A, Belles JM, Serrano R, Culianez-MacIa FA. Arabidopsis thaliana AtHAL3: a flavoprotein related to salt and osmotic tolerance and plant growth. Plant J. 20: 529-539 (1999).

Essar DW, Eberly L, Hadero A, Crawford IP. Identification and characterization of genes for a second anthranilate synthase in Pseudomonas aeruginosa: interchangeability of the two anthranilate synthases and evolutionary implications. J. Bacteriol. 172: 884-900 (1990).

Essenberg RC, Sharma YK. Cloning of genes for proline and leucine biosynthesis from Brucella abortus by functional complementation in Escherichia coli. J. Gen. Microbiol. 139: 87-93 (1993).

Essigmann B, Hespenheide BM, Kuhn LA, Benning C. Prediction of the active-site structure and NAD(+) binding in SQD1, a protein essential for sulfolipid biosynthesis in Arabidopsis. Arch. Biochem. Biophys. 369: 30-41 (1999).

Estelle M. Proteases and cellular regulation in plants. Curr. Opin. Plant Biol. 4: 254-260 (2001).

Estrada AF, Maier D, Scherzinger D, Avalos J, Al-Babili S. Novel apocarotenoid intermediates in Neurospora crassa mutants imply a new biosynthetic reaction sequence leading to neurosporaxanthin formation. Fungal Genet. Biol. 45: 1497-1505 (2008).

Eudes A, Mouille G, Thevenin J, Minic Z, Jouanin L. Purification, cloning and functional characterization of an endogenous beta-glucuronidase in Arabidopsis thaliana. Plant Cell Physiol. 49: 1331-1341 (2008).

Evans JD, Al-Khaldi SF, Martin SA. Cloning of the O-acetylserine lyase gene from the ruminal bacterium Selenomonas ruminantium HD4. Curr. Microbiol. 44: 161-166 (2002).

Everard JD, Cantini C, Grumet R, Plummer J, Loescher WH. Molecular cloning of mannose-6-phosphate reductase and its developmental expression in celery. Plant Physiol. 113: 1427-1435 (1997).

Evstigneeva ZG, Solov'eva NA, Sidel'nikova LI. Methionine sulfoximine and phosphinothrycin: A review of their herbicidal activity and effects on glutamine synthetase . Appl. Biochem. Microbiol. 39: 539-543 (2003).

Exley GE, Colandene JD, Garrett RH. Molecular cloning, characterization, and nucleotide sequence of nit-6, the structural gene for nitrite reductase in Neurospora crassa. J. Bacteriol. 175: 2379-2392 (1993).

Faatz E, Middendorf A, Bremer E. Cloned structural genes for the osmotically regulated binding-protein-dependent glycine betaine transport system (ProU) of Escherichia coli K-12. Mol. Microbiol. 2: 265-279 (1988).

Facchini PJ, De Luca V. Expression in Escherichia coli and partial characterization of two tyrosine/dopa decarboxylases from opium poppy. Phytochemistry 38: 1119-1126 (1995).

Facchini PJ, De Luca V. Differential and tissue-specific expression of a gene family for tyrosine/dopa decarboxylase in opium poppy. J. Biol. Chem. 269: 26684-26690 (1994).

Fairbairn DJ, Liu W, Schachtman DP, Gomez-Gallego S, Day SR, Teasdale RD. Characterisation of two distinct HKT1-like potassium transporters from Eucalyptus camaldulensis. Plant Mol. Biol. 43: 515-525 (2000).

Faldt J, Arimura G, Gershenzon J, Takabayashi J, Bohlmann J. Functional identification of AtTPS03 as ( E)-beta-ocimene synthase: a monoterpene synthase catalyzing jasmonate- and wound-induced volatile formation in Arabidopsis thaliana. Planta 216: 745-751 (2003).

Falkenberg P, Strom AR. Purification and characterization of osmoregulatory betaine aldehyde dehydrogenase of Escherichia coli. Biochim. Biophys. Acta 1034: 253-259 (1990).

Fan F, Ghanem M, Gadda G. Cloning, sequence analysis, and purification of choline oxidase from Arthrobacter globiformis: a bacterial enzyme involved in osmotic stress tolerance. Arch. Biochem. Biophys. 421: 149-158 (2004).

Fan W, Zhang Z, Zhang Y. Cloning and molecular characterization of fructose-1,6-bisphosphate aldolase gene regulated by high-salinity and drought in Sesuvium portulacastrum. Plant Cell Rep. 28: 975-984 (2009).

Fan X, Pericone CD, Lysenko E, Goldfine H, Weiser JN. Multiple mechanisms for choline transport and utilization in Haemophilus influenzae. Mol. Microbiol. 50: 537-548 (2003).

Fan Z, Yuan L, Chatterjee R. Increased hydrogen production by genetic engineering of Escherichia coli. PLoS One 4: e4432 (2009).

Fang Y, Kolmakova-Partensky L, Miller C. A bacterial arginine-agmatine exchange-transporter involved in extreme acid resistance. J. Biol. Chem. 282: 176-182 (2007).

Fani R, Brilli M, Fondi M, Lio P. The role of gene fusions in the evolution of metabolic pathways: the histidine biosynthesis case. BMC Evol. Biol. 7 Suppl. 2: S4 (2007).

Fani R, Lio P, Chiarelli I, Bazzicalupo M. The evolution of the histidine biosynthetic genes in prokaryotes: a common ancestor for the hisA and hisF genes. J. Mol. Evol. 38: 489-495 (1994).

Fani R, Mori E, Tamburini E, Lazcano A. Evolution of the structure and chromosomal distribution of histidine biosynthetic genes. Orig. Life Evol. Biosph. 28: 555-570 (1998).

Fani R, Tamburini E, Mori E, Lazcano A, Lio P, Barberio C, Casalone E, Cavalieri D, Perito B, Polsinelli M. Paralogous histidine biosynthetic genes: evolutionary analysis of the Saccharomyces cerevisiae HIS6 and HIS7 genes. Gene 197: 9-17 (1997).

Farmer MJ, Czernic P, Michael A, Negrel J. Identification and characterization of cDNA clones encoding hydroxycinnamoyl-CoA:tyramine N-hydroxycinnamoyltransferase from tobacco. Eur. J. Biochem. 263: 686-694 (1999).

Farmer WR, Liao JC. Precursor balancing for metabolic engineering of lycopene production in Escherichia coli. Biotechnol. Prog. 17: 57-61 (2001).

Farmer WR, Liao JC. Reduction of aerobic acetate production by Escherichia coli. Appl. Environ. Microbiol. 63: 3205-3210 (1997).

Farmer WR, Liao JC. Improving lycopene production in Escherichia coli by engineering metabolic control. Nat. Biotechnol. 18: 533-537 (2000).

Farre EM, Bachmann A, Willmitzer L, Trethewey RN. Acceleration of potato tuber sprouting by the expression of a bacterial pyrophosphatase. Nat. Biotechnol. 19: 268-272 (2001).

Farrington GK, Kumar A, Shames SL, Ewaskiewicz JI, Ash DE, Wedler FC. Threonine synthase of Escherichia coli: inhibition by classical and slow-binding analogues of homoserine phosphate. Arch. Biochem. Biophys. 307: 165-174 (1993).

Faure M, Bourguignon J, Neuburger M, MacHerel D, Sieker L, Ober R, Kahn R, Cohen-Addad C, Douce R. Interaction between the lipoamide-containing H-protein and the lipoamide dehydrogenase (L-protein) of the glycine decarboxylase multienzyme system. 2. Crystal structures of H- and L-proteins. Eur. J. Biochem. 267: 2890-2898 (2000).

Fazel A, Guillou Y, Cohen GN. A hybrid proteolytic fragment of Escherichia coli aspartokinase I-homoserine dehydrogenase I. Structure, inhibition pattern, dissociation properties, and generation of two homodimers. J. Biol. Chem. 258: 13570-13574 (1983).

Fazel A, Muller K, Le Bras G, Garel JR, Veron M, Cohen GN. A triglobular model for the polypeptide chain of aspartokinase I-homoserine dehydrogenase I of Escherichia coli. Biochemistry 22: 158-165 (1983).

Federici MM, Stadtman ER. Interaction of Cibacron Blue F3GA with glutamine synthetase: use of the dye as a conformational probe. 2. Studies using isolated dye fractions. Biochemistry 24: 661-666 (1985).

Feild MJ, Nguyen DC, Armstrong FB. Amino acid sequence of Salmonella typhimurium branched-chain amino acid aminotransferase. Biochemistry 28: 5306-5310 (1989).

Feist AM, Palsson BO. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat. Biotechnol. 26: 659-667 (2008).

Fell DA, Chassagnole C, Mazat JP. Building a computer simulation of threonine synthesis in Escherichia coli. ICSB 2nd International Conference on Systems Biology, "The Future of Biology in the 21st Century", November 4-7, 2001, California Institute of Technology (2001).

Fell DA, Wagner A. The small world of metabolism. Nat. Biotechnol. 18: 1121-1122 (2000).

Feltkamp D, Masterson R, Starke J, Rosahl S. Analysis of the involvement of ocs-like bZip-binding elements in the differential strength of the bidirectional mas1'2' promoter. Plant Physiol. 105: 259-268 (1994).

Feng J, Atkinson MR, McCleary W, Stock JB, Wanner BL, Ninfa AJ. Role of phosphorylated metabolic intermediates in the regulation of glutamine synthetase synthesis in Escherichia coli. J. Bacteriol. 174: 6061-6070 (1992).

Feng J, Goss TJ, Bender RA, Ninfa AJ. Activation of transcription initiation from the nac promoter of Klebsiella aerogenes. J. Bacteriol. 177: 5523-5534 (1995).

Feng L, Prestwich GD. Expression and characterization of a lepidopteran general odorant binding protein. Insect Biochem. Mol. Biol. 27: 405-412 (1997).

Feniouk BA, Suzuki T, Yoshida M. Regulatory interplay between proton motive force, ADP, phosphate, and subunit epsilon in bacterial ATP synthase. J. Biol. Chem. 282: 764-772 (2007).

Fernandez M, Cuadrado Y, Recio E, Aparicio JF, Martin JF. Characterization of the hom-thrC-thrB cluster in aminoethoxyvinylglycine-producing Streptomyces sp NRRL 5331. Microbiology 148: 1413-1420 (2002).

Fernandez M, Kleerebezem M, Kuipers OP, Siezen RJ, van Kranenburg R. Regulation of the metC-cysK operon, involved in sulfur metabolism in Lactococcus lactis. J. Bacteriol. 184: 82-90 (2002).

Fernandez M, van Doesburg W, Rutten GAM, Marugg JD, Alting AC, van Kranenburg R, Kuipers OP. Molecular and functional analyses of the metC gene of Lactococcus lactis, encoding cystathionine beta-lyase. Appl. Environ. Microbiol. 66: 42-48 (2000).

Fernandez-Gonzalez C, Gil JA, Mateos LM, Schwarzer A, Schafer A, Kalinowski J, Puhler A, Martin JF. Construction of L-lysine-overproducing strains of Brevibacterium lactofermentum by targeted disruption of the hom and thrB genes. Appl. Microbiol. Biotechnol. 46: 554-548 (1996).

Ferrandez A, Prieto MA, Garcia JL, Diaz E. Molecular characterization of PadA, a phenylacetaldehyde dehydrogenase from Escherichia coli. FEBS Lett. 406: 23-27 (1997).

Ferrara P, Duchange N, Zakin MM, Cohen GN. Internal homologies in the two aspartokinase-homoserine dehydrogenases of Escherichia coli K-12. Proc. Natl. Acad. Sci. U.S.A. 81: 3019-3023 (1984).

Fiehn O. Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks. Comparative & Functional Genomics 2: 155-168 (2001).

Field B, Cardon G, Traka M, Botterman J, Vancanneyt G, Mithen R. Glucosinolate and amino acid biosynthesis in Arabidopsis. Plant Physiol. 135: 828-839 (2004).

Field SJ, Thorndycroft FH, Matorin AD, Richardson DJ, Watmough NJ. The respiratory nitric oxide reductase (NorBC) from Paracoccus denitrificans. Methods Enzymol. 437: 79-101 (2008).

Fierro-Monti IP, Reid SJ, Woods DR. Differential expression of a Clostridium acetobutylicum antisense RNA: implications for regulation of glutamine synthetase. J. Bacteriol. 174: 7642-7647 (1992).

Filetici P, Martegani MP, Valenzuela L, Gonzalez A, Ballario P. Sequence of the GLT1 gene from Saccharomyces cerevisiae reveals the domain structure of yeast glutamate synthase. Yeast 12: 1359-1366 (1996).

Finke JM, Onuchic JN. Equilibrium and kinetic folding pathways of a TIM barrel with a funneled energy landscape. Biophys. J. 89: 488-505 (2005).

Firestine SM, Misialek S, Toffaletti DL, Klem TJ, Perfect JR, Davisson VJ. Biochemical role of the Cryptococcus neoformans ADE2 protein in fungal de novo purine biosynthesis. Arch. Biochem. Biophys. 351: 123-134 (1998).

Fischer E, Sauer U. Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS. Eur. J. Biochem. 270: 880-891 (2003).

Fisher MT. Promotion of the in vitro renaturation of dodecameric glutamine synthetase from Escherichia coli in the presence of GroEL (chaperonin-60) and ATP. Biochemistry 31: 3955-3963 (1992).

Fisher MT. GroE chaperonin-assisted folding and assembly of dodecameric glutamine synthetase. Biochemistry (Mosc.) 63: 382-398 (1998).

Fisher MT, Stadtman ER. Oxidative modification of Escherichia coli glutamine synthetase. Decreases in the thermodynamic stability of protein structure and specific changes in the active site conformation. J. Biol. Chem. 267: 1872-1880 (1992).

Fisher R, Tuli R, Haselkorn R. A cloned cyanobacterial gene for glutamine synthetase functions in Escherichia coli, but the enzyme is not adenylylated. Proc. Natl. Acad. Sci. U.S.A. 78: 3393-3397 (1981).

Fisher SH. Glutamine synthesis in Streptomyces--a review. Gene 115: 13-17 (1992).

Fisher SH, Rosenkrantz MS, Sonenshein AL. Glutamine synthetase gene of Bacillus subtilis. Gene 32: 427-438 (1984).

Fitzgerald JR, Musser JM. Evolutionary genomics of pathogenic bacteria. Trends Microbiol. 9: 547-553 (2001).

Fleming GA, Hagedorn CH, Granger AS, Phang JM. Pyrroline-5-carboxylate in human plasma. Metabolism 33: 739-742 (1984).

Fletcher SA, Csonka LN. Characterization of the induction of increased thermotolerance by high osmolarity in Salmonella. Food Microbiol. 15: 307-317 (1998).

Fletcher SA, Rhodes D, Csonka LN. Analysis of the effects of osmoprotectants on the high osmolality-dependent induction of increased thermotolerance in Salmonella typhimurium. Food Microbiol. 18: 345-354 (2001).

Fliegmann J, Sandermann H Jr. Maize glutathione-dependent formaldehyde dehydrogenase cDNA: a novel plant gene of detoxification. Plant Mol. Biol. 34: 843-854 (1997).

Flint DH. Escherichia coli contains a protein that is homologous in function and N-terminal sequence to the protein encoded by the nifS gene of Azotobacter vinelandii and that can participate in the synthesis of the Fe-S cluster of dihydroxy-acid dehydratase. J. Biol. Chem. 271: 16068-16074 (1996).

Flint DH, Smyk-Randall E, Tuminello JF, Draczynska-Lusiak B, Brown OR. The inactivation of dihydroxy-acid dehydratase in Escherichia coli treated with hyperbaric oxygen occurs because of the destruction of its Fe-S cluster, but the enzyme remains in the cell in a form that can be reactivated. J. Biol. Chem. 268: 25547-25552 (1993).

Flint DH, Tuminello JF, Emptage MH. The inactivation of Fe-S cluster containing hydro-lyases by superoxide. J. Biol. Chem. 268: 22369-22376 (1993).

Flint DH, Tuminello JF, Miller TJ. Studies on the synthesis of the Fe-S cluster of dihydroxy-acid dehydratase in Escherichia coli crude extract. (contd) J. Biol. Chem. 271: 16053-16067 (1996).

Flores N, Flores S, Escalante A, de Anda R, Leal L, Malpica R, Georgellis D, Gosset G, Bolivar F. Adaptation for fast growth on glucose by differential expression of central carbon metabolism and gal regulon genes in an Escherichia coli strain lacking the phosphoenolpyruvate:carbohydrate phosphotransferase system. Metab. Eng. 7: 70-87 (2005).

Flores N, Xiao J, Berry A, Bolivar F, Valle F. Pathway engineering for the production of aromatic compounds in Escherichia coli. Nat. Biotechnol. 14: 620-623 (1996).

Flores S, Gosset G, Flores N, de Graaf AA, Bolivar F. Analysis of carbon metabolism in Escherichia coli strains with an inactive phosphotransferase system by (13)C labeling and NMR spectroscopy. Metab. Eng. 4: 124-137 (2002).

Follettie MT, Peoples OP, Agoropoulou C, Sinskey AJ. Gene structure and expression of the Corynebacterium flavum N13 ask-asd operon. J. Bacteriol. 175: 4096-4103 (1993).

Follstad BD, Stephanopoulos G. Effect of reversible reactions on isotope label redistribution--analysis of the pentose phosphate pathway. Eur. J. Biochem. 252: 360-371 (1998).

Fondi M, Brilli M, Fani R. On the origin and evolution of biosynthetic pathways: integrating microarray data with structure and organization of the Common Pathway genes. BMC Bioinformatics 8 Suppl. 1: S12 (2007).

Fong RN, Kim KS, Yoshihara C, Inwood WB, Kustu S. The W148L substitution in the Escherichia coli ammonium channel AmtB increases flux and indicates that the substrate is an ion. Proc. Natl. Acad. Sci. U.S.A. 104: 18706-18711 (2007).

Fong SS, Marciniak JY, Palsson BO. Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model. J. Bacteriol. 185: 6400-6408 (2003).

Fong SS, Nanchen A, Palsson BO, Sauer U. Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes. J. Biol. Chem. 281: 8024-8033 (2006).

Fong SS, Palsson BO. Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat. Genet. 36: 1056-1058 (2004).

Fons M, Cami B, Chippaux M. Possible involvement of a L-delta 1-pyrroline-5-carboxylate (P5C) reductase in the synthesis of proline in Desulfovibrio desulfuricans Norway. Biochem. Biophys. Res. Commun. 179: 1088-1094 (1991).

Forchhammer K, Hedler A. Phosphoprotein PII from cyanobacteria--analysis of functional conservation with the PII signal-transduction protein from Escherichia coli. Eur. J. Biochem. 244: 869-875 (1997).

Forchhammer K, Hedler A, Strobel H, Weiss V. Heterotrimerization of PII-like signalling proteins: implications for PII-mediated signal transduction systems. Mol. Microbiol. 33: 338-349 (1999).

Forchhammer K, Irmler A, Kloft N, Ruppert U. P-II signalling in unicellular cyanobacteria: analysis of redox-signals and energy charge. Physiol. Plant. 120: 51-56 (2004).

Forde BG. Nitrate transporters in plants: structure, function and regulation. Biochim. Biophys. Acta 1465: 219-235 (2000).

Forlani G, Scainelli D, Nielsen E. Delta(1)-pyrroline-5-carboxylate dehydrogenase from cultured cells of potato: purification and properties. Plant Physiol. 113: 1413-1418 (1997).

Forsberg J, Strom J, Kieselbach T, Larsson H, Alexciev K, Engstrom A, Akerlund HE. Protease activities in the chloroplast capable of cleaving an LHCII N-terminal peptide. Physiol. Plant. 123: 21-29 (2005).

Forster J, Famili I, Fu P, Palsson BO, Nielsen J. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 13: 244-253 (2003).

Foster JW, Moreno M. Inducible acid tolerance mechanisms in enteric bacteria. Novartis Found. Symp. 221: 55-69 (1999).

Foster R, Thorner J, Martin GS. Nucleotidylation, not phosphorylation, is the major source of the phosphotyrosine detected in enteric bacteria. J. Bacteriol. 171: 272-279 (1989).

Foster WB, Griffith MJ, Kingdon HS. Affinity labeling of the active site of Escherichia coli glutamine synthetase by 5'-p-fluorosulfonylbenzoyladenosine. J. Biol. Chem. 256: 882-886 (1981).

Fotheringham IG, Grinter N, Pantaleone DP, Senkpeil RF, Taylor PP. Engineering of a novel biochemical pathway for the biosynthesis of L-2-aminobutyric acid in Escherichia coli K12. Bioorg. Med. Chem. 7: 2209-2213 (1999).

Fouad WM, Altpeter F. Transplastomic expression of bacterial L-aspartate-alpha-decarboxylase enhances photosynthesis and biomass production in response to high temperature stress. Transgenic Res. 18: 707-718 (2009).

Fouad WM, Rathinasabapathi B. Expression of bacterial L-aspartate-alpha-decarboxylase in tobacco increases beta-alanine and pantothenate levels and improves thermotolerance. Plant Mol. Biol. 60: 495-505 (2006).

Fougere F, Le Rudulier D. Glycine betaine biosynthesis and catabolism in bacteroids of Rhizobium meliloti - effect of salt stress. J. Gen. Microbiol. 136: 2503-2510 (1990).

Fox BA, Ristuccia JG, Bzik DJ. Genetic identification of essential indels and domains in carbamoyl phosphate synthetase II of Toxoplasma gondii. Int. J. Parasitol. 39: 533-539 (2009).

Fraissinet-Tachet L, Baltz R, Chong J, Kauffmann S, Fritig B, Saindrenan P. Two tobacco genes induced by infection, elicitor and salicylic acid encode glucosyltransferases acting on phenylpropanoids and benzoic acid derivatives, including salicylic acid. FEBS Lett. 437: 319-323 (1998).

Francklyn C, Adams J, Augustine J. Catalytic defects in mutants of class II histidyl-tRNA synthetase from Salmonella typhimurium previously linked to decreased control of histidine biosynthesis regulation. J. Mol. Biol. 280: 847-858 (1998).

Frank L, Ranhand B. Proline metabolism in Escherichia coli. III. The proline catabolic pathway. Arch. Biochem. Biophys. 107: 323-331 (1964).

Frankard V, Vauterin M, Jacobs M. Molecular characterization of an Arabidopsis thaliana cDNA coding for a monofunctional aspartate kinase. Plant Mol. Biol. 34: 233-242 (1997).

Frasca V, Banerjee RV, Dunham WR, Sands RH, Matthews RG. Cobalamin-dependent methionine synthase from Escherichia coli B: electron paramagnetic resonance spectra of the inactive form and the active methylated form of the enzyme. Biochemistry 27: 8458-8465 (1988).

Frendo P, Jimenez MJ, Mathieu C, Duret L, Gallesi D, Van De Sype G, Herouart D, Puppo A. A Medicago truncatula homoglutathione synthetase is derived from glutathione synthetase by gene duplication. Plant Physiol. 126: 1706-1715 (2001).

Fresquet V, Mora P, Rochera L, Ramon-Maiques S, Rubio V, Cervera J. Site-directed mutagenesis of the regulatory domain of Escherichia coli carbamoyl phosphate synthetase identifies crucial residues for allosteric regulation and for transduction of the regulatory signals. J. Mol. Biol. 299: 979-991 (2000).

Frey AD, Fiaux J, Szyperski T, Wuthrich K, Bailey JE, Kallio PT. Dissection of central carbon metabolism of hemoglobin-expressing Escherichia coli by (13)C nuclear magnetic resonance flux distribution analysis in microaerobic bioprocesses. Appl. Environ. Microbiol. 67: 680-687 (2001).

Frey B, Janel G, Michelsen U, Kersten H. Mutations in the Escherichia coli fnr and tgt genes: control of molybdate reductase activity and the cytochrome d complex by fnr. J. Bacteriol. 171: 1524-1530 (1989).

Frey PA. Radical mechanisms of enzymatic catalysis. Annu. Rev. Biochem. 70: 121-148 (2001).

Fridman E, Wang J, Iijima Y, Froehlich JE, Gang DR, Ohlrogge J, Pichersky E. Metabolic, genomic, and biochemical analyses of glandular trichomes from the wild tomato species Lycopersicon hirsutum identify a key enzyme in the biosynthesis of methylketones. Plant Cell 17: 1252-1267 (2005).

Frisch DA, Tommey AM, Gengenbach BG, Somers DA. Direct genetic selection of a maize cDNA for dihydrodipicolinate synthase in an Escherichia coli dapA- auxotroph. Mol. Gen. Genet. 228: 287-293 (1991).

Frodyma ME, Downs D. The panE gene, encoding ketopantoate reductase, maps at 10 minutes and is allelic to apbA in Salmonella typhimurium. J. Bacteriol. 180: 4757-4759 (1998).

Froman BE, Edwards PC, Bursch AG, Dehesh K. ACX3, a novel medium-chain acyl-coenzyme A oxidase from Arabidopsis. Plant Physiol. 123: 733-742 (2000).

Frommer WB, Kwart M, Hirner B, Fischer WN, Hummel S, Ninnemann O. Transporters for nitrogenous compounds in plants. Plant Mol. Biol. 26: 1651-1670 (1994).

Frost JW, Draths KM. Biocatalytic syntheses of aromatics from D-glucose: renewable microbial sources of aromatic-compounds. Annu. Rev. Microbiol. 49: 557-579 (1995).

Frueauf JB, Ballicora MA, Preiss J. ADP-glucose pyrophosphorylase from potato tuber: site-directed mutagenesis of homologous aspartic acid residues in the small and large subunits. Plant J. 33: 503-511 (2003).

Fry B, Zhu T, Domach MM, Koepsel RR, Phalakornkule C, Ataai MM. Characterization of growth and acid formation in a Bacillus subtilis pyruvate kinase mutant. Appl. Environ. Microbiol. 66: 4045-4049 (2000).

Fu TF, Boja ES, Safo MK, Schirch V. Role of proline residues in the folding of serine hydroxymethyltransferase. J. Biol. Chem. 278: 31088-31094 (2003).

Fu Y, Ballicora MA, Preiss J. Mutagenesis of the glucose-1-phosphate-binding site of potato tuber ADP-glucose pyrophosphorylase. Plant Physiol. 117: 989-996 (1998).

Fu YH, Marzluf GA. Site-directed mutagenesis of the 'zinc finger' DNA-binding domain of the nitrogen-regulatory protein NIT2 of Neurospora. Mol. Microbiol. 4: 1847-1852 (1990).

Fuchs RL, Madonna MJ, Brenchley JE. Identification of the structural genes for glutamate synthase and genetic characterization of this region of the Salmonella typhimurium chromosome. J. Bacteriol. 149: 906-915 (1982).

Fuchs TM, Schneider B, Krumbach K, Eggeling L, Gross R. Characterization of a Bordetella pertussis diaminopimelate (DAP) biosynthesis locus identifies dapC, a novel gene coding for an N-succinyl-L,L-DAP aminotransferase. J. Bacteriol. 182: 3626-3631 (2000).

Fuhrmann M, Oertel W, Hegemann P. A synthetic gene coding for the green fluorescent protein (GFP) is a versatile reporter in Chlamydomonas reinhardtii. Plant J. 19: 353-361 (1999).

Fujii T, Mukaihara M, Agematu H, Tsunekawa H. Biotransformation of L-lysine to L-pipecolic acid catalyzed by L-lysine 6-aminotransferase and pyrroline-5-carboxylate reductase. Biosci. Biotechnol. Biochem. 66: 622-627 (2002).

Fujii T, Narita T, Agematu H, Agata N, Isshiki K. Characterization of L-lysine 6-aminotransferase and its structural gene from Flavobacterium lutescens IFO3084. J. Biochem. (Tokyo) 128: 391-397 (2000).

Fujimori K, Ohta D. Isolation and characterization of a histidine biosynthetic gene in Arabidopsis encoding a polypeptide with two separate domains for phosphoribosyl-ATP pyrophosphohydrolase and phosphoribosyl-AMP cyclohydrolase. Plant Physiol. 118: 275-283 (1998).

Fujio T, Maruyama A. Enzymatic production of pyrimidine nucleotides using Corynebacterium ammoniagenes cells and recombinant Escherichia coli cells: enzymatic production of CDP-choline from orotic acid and choline chloride (Part I). Biosci. Biotechnol. Biochem. 61: 956-959 (1997).

Fujio T, Teshiba S, Maruyama A. Construction of a plasmid carrying both CTP synthetase and a fused gene formed from cholinephosphate cytidylyltransferase and choline kinase genes and its application to industrial CDP-choline production… Biosci. Biotechnol. Biochem. 61: 960-964 (1997).

Fujita S, Ohnishi T, Watanabe B, Yokota T, Takatsuto S, Fujioka S, Yoshida S, Sakata K, Mizutani M. Arabidopsis CYP90B1 catalyses the early C-22 hydroxylation of C27, C28 and C29 sterols. Plant J. 45: 765-774 (2006).

Fujitani Y, Nakajima N, Ishihara K, Oikawa T, Ito K, Sugimoto M. Molecular and biochemical characterization of a serine racemase from Arabidopsis thaliana. Phytochemistry 67: 668-674 (2006).

Fujiwara H, Tanaka Y, Yonekura-Sakakibara K, Fukuchi-Mizutani M, Nakao M, Fukui Y, Yamaguchi M, Ashikari T, Kusumi T. cDNA cloning, gene expression and subcellular localization of anthocyanin 5-aromatic acyltransferase from Gentiana triflora. Plant J. 16: 421-431 (1998).

Fujiwara T, Hori K, Ozaki K, Yokota Y, Mitsuya S, Ichiyanagi T, Hattori T, Takabe T. Enzymatic characterization of peroxisomal and cytosolic betaine aldehyde dehydrogenases in barley. Physiol. Plant. 134: 22-30 (2008).

Fukuda A, Okada Y, Suzui N, Fujiwara T, Yoneyama T, Hayashi H. Cloning and characterization of the gene for a phloem-specific glutathione S-transferase from rice leaves. Physiol. Plant. 120: 595-602 (2004).

Funanage VL, Brenchley JE. Characterization of Salmonella typhimurium mutants with altered glutamine synthetase activity. Genetics 86: 513-526 (1977).

Fung E, Wong WW, Suen JK, Bulter T, Lee SG, Liao JC. A synthetic gene-metabolic oscillator. Nature 435: 118-122 (2005).

Funke T, Yang Y, Han H, Healy-Fried ML, Olesen S, Becker A, Schonbrunn E. Structural basis of glyphosate tolerance resulting from the double mutation Thr97Ala and Pro101Ser in 5-enolpyruvyl-shikimate-3-phosphate synthase from Escherichia coli. J. Biol. Chem. 284: 9854-9860 (2009).

Furano AV, Wittel FP. Effect of the relA gene on derepression of amino acid biosynthetic enzymes in growing Escherichia coli depends on the pathway being derepressed. J. Bacteriol. 132: 352-355 (1977).

Furumoto T, Hata S, Izui K. cDNA cloning and characterization of maize phosphoenolpyruvate carboxykinase, a bundle sheath cell-specific enzyme. Plant Mol. Biol. 41: 301-311 (1999).

Gabrielsen M, Bond CS, Hallyburton I, Hecht S, Bacher A, Eisenreich W, Rohdich F, Hunter WN. Hexameric assembly of the bifunctional IspDF and protein-protein associations in the deoxy-xylulose dependent pathway of isoprenoid precursor biosynthesis. J. Biol. Chem. 279: 52753-52761 (2004).

Gaille C, Kast P, Haas D. Salicylate biosynthesis in Pseudomonas aeruginosa. Purification and characterization of PchB, a novel bifunctional enzyme displaying isochorismate pyruvate-lyase and chorismate mutase activities. J. Biol. Chem. 277: 21768-21775 (2002).

Gakiere B, Denis L, Droux M, Job D. Over-expression of cystathionine gamma-synthase in Arabidopsis thaliana leads to increased levels of methionine and S- methylmethionine. Plant Physiol. Biochem. 40: 119-126 (2002).

Galili S, Guenoune D, Wininger S, Hana B, Schupper A, Ben-Dor B, Kapulnik Y. Enhanced levels of free and protein-bound threonine in transgenic alfalfa (Medicago sativa L.) expressing a bacterial feedback-insensitive aspartate kinase gene. Transgenic Res. 9: 137-144 (2000).

Gall S, Lynch MD, Sandoval N, Gill RT. Parallel mapping of genotypes to phenotypes contributing to overall biological fitness. Metab. Eng. 10: 382-393 (2008).

Gallagher DT, Eisenstein E, Fisher KE, Zondlo J, Chinchilla D, Yu HD, Dill J, Winborne E, Ducote K, Xiao G, Gilliland GL. Polymorphous crystallization and diffraction of threonine deaminase from Escherichia coli. Acta Crystallogr. D. Biol. Crystallogr. 54: 467-469 (1998).

Gallagher DT, Gilliland GL, Xiao G, Zondlo J, Fisher KE, Chinchilla D, Eisenstein E. Structure and control of pyridoxal phosphate dependent allosteric threonine deaminase. Structure 6: 465-475 (1998).

Gallego ME, Sirand-Pugnet P, White CI. Positive-negative selection and T-DNA stability in Arabidopsis transformation. Plant Mol. Biol. 39: 83-93 (1999).

Galloway GL, Malmberg RL, Price RA. Phylogenetic utility of the nuclear gene arginine decarboxylase: An example from Brassicaceae. Mol. Biol. Evol. 15: 1312-1320 (1998).

Galperin MY, Grishin NV. The synthetase domains of cobalamin biosynthesis amidotransferases CobB and CobQ belong to a new family of ATP-dependent amidoligases, related to dethiobiotin synthetase. Proteins 41: 238-247 (2000).

Gamper H, Moses V. Enzyme organization in the proline biosynthetic pathway of Escherichia coli. Biochim. Biophys. Acta 354: 75-87 (1974).

Gang DR, Kasahara H, Xia ZQ, Vander Mijnsbrugge K, Bauw G, Boerjan W, Van Montagu M, Davin LB, Lewis NG. Evolution of plant defense mechanisms. Relationships of phenylcoumaran benzylic ether reductases to pinoresinol-lariciresinol and isoflavone reductases. J. Biol. Chem. 274: 7516-7527 (1999).

Gang DR, Lavid N, Zubieta C, Chen F, Beuerle T, Lewinsohn E, Noel JP, Pichersky E. Characterization of phenylpropene O-methyltransferases from sweet basil: facile change of substrate specificity and convergent evolution within a plant O-methyltransferase family. Plant Cell 14: 505-519 (2002).

Gao Y, Schofield OM, Leustek T. Characterization of sulfate assimilation in marine algae focusing on the enzyme 5'-adenylylsulfate reductase. Plant Physiol. 123: 1087-1096 (2000).

Garcia E, Bancroft S, Rhee SG, Kustu S. The product of a newly identified gene, glnF, is required for synthesis of glutamine synthetase in Salmonella. Proc. Natl. Acad. Sci. U.S.A. 74: 1662-1666 (1977).

Garcia E, Rhee SG. Cascade control of Escherichia coli glutamine synthetase. Purification and properties of PII uridylyltransferase and uridylyl-removing enzyme. J. Biol. Chem. 258: 2246-2253 (1983).

Garcia I, Rodgers M, Pepin R, Hsieh TF, Matringe M. Characterization and subcellular compartmentation of recombinant 4-hydroxyphenylpyruvate dioxygenase from Arabidopsis in transgenic tobacco. Plant Physiol. 119: 1507-1516 (1999).

Garcia JL, Gonzalez de Buitrago G, Barbero JL. Hyperproduction of L-proline in Escherichia coli. Microbiologia 1: 43-51 (1985).

Garcia-Alles LF, Navdaeva V, Haenni S, Erni B. The glucose-specific carrier of the Escherichia coli phosphotransferase system. Eur. J. Biochem. 269: 4969-4980 (2002).

Garcia-Dominguez M, Florencio FJ. Nitrogen availability and electron transport control the expression of glnB gene (encoding PII protein) in the cyanobacterium Synechocystis sp. PCC 6803. Plant Mol. Biol. 35: 723-734 (1997).

Garcia-Dominguez M, Reyes JC, Florencio FJ. Glutamine synthetase inactivation by protein-protein interaction. Proc. Natl. Acad. Sci. U.S.A. 96: 7161-7166 (1999).

Garcia-Dominguez M, Reyes JC, Florencio FJ. Purification and characterization of a new type of glutamine synthetase from cyanobacteria. Eur. J. Biochem. 244: 258-264 (1997).

Garcia-Gonzalez V, Govantes F, Shaw LJ, Burns RG, Santero E. Nitrogen control of atrazine utilization in Pseudomonas sp strain ADP. Appl. Environ. Microbiol. 69: 6987-6993 (2003).

Garcia-Ojalvo J, Elowitz MB, Strogatz SH. Modeling a synthetic multicellular clock: repressilators coupled by quorum sensing. Proc. Natl. Acad. Sci. U.S.A. 101: 10955-10960 (2004).

Garcia-Ortiz MV, Ariza RR, Hoffman PD, Hays JB, Roldan-Arjona T. Arabidopsis thaliana AtPOLK encodes a DinB-like DNA polymerase that extends mispaired primer termini and is highly expressed in a variety of tissues. Plant J. 39: 84-97 (2004).

Garcia-Ortiz MV, Ariza RR, Roldan-Arjona T. An OGG1 orthologue encoding a functional 8-oxoguanine DNA glycosylase/lyase in Arabidopsis thaliana. Plant Mol. Biol. 47: 795-804 (2001).

Garcia-Rios M, Fujita T, LaRosa PC, Locy RD, Clithero JM, Bressan RA, Csonka LN. Cloning of a polycistronic cDNA from tomato encoding gamma-glutamyl kinase and gamma-glutamyl phosphate reductase. Proc. Natl. Acad. Sci. U.S.A. 94: 8249-8254 (1997).

Garcia-Rodriguez FM, Zekri S, Toro N. Characterization of the Sinorhizobium meliloti genes encoding a functional dihydrodipicolinate synthase (dapA) and dihydrodipicolinate reductase (dapB). Arch. Microbiol. 173: 438-444 (2000).

Garciadeblas B, Benito B, Rodriguez-Navarro A. Molecular cloning and functional expression in bacteria of the potassium transporters CnHAK1 and CnHAK2 of the seagrass Cymodocea nodosa. Plant Mol. Biol. 50: 623-633 (2002).

Garciadeblas B, Haro R, Benito B. Cloning of two SOS1 transporters from the seagrass Cymodocea nodosa. SOS1 transporters from Cymodocea and Arabidopsis mediate potassium uptake in bacteria. Plant Mol. Biol. 63: 479-490 (2007).

Gardner TS, Cantor CR, Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature 403: 339-342 (2000).

Gardner TS, di Bernardo D, Lorenz D, Collins JJ. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301: 102-105 (2003).

Garg AK, Kim JK, Owens TG, Ranwala AP, Choi YD, Kochian LV, Wu RJ. Trehalose accumulation in rice plants confers high tolerance levels to different abiotic stresses. Proc. Natl. Acad. Sci. U.S.A. 99: 15898-15903 (2002).

Garner RM, Fulkerson J Jr, Mobley HL. Helicobacter pylori glutamine synthetase lacks features associated with transcriptional and posttranslational regulation. Infect. Immun. 66: 1839-1847 (1998).

Garrido-Franco M, Ehlert S, Messerschmidt A, Marinkovic S, Huber R, Laber B, Bourenkov GP, Clausen T. Structure and function of threonine synthase from yeast. J. Biol. Chem. 277: 12396-12405 (2002).

Garrity LF, Schiel SL, Merrill R, Reizer J, Saier MH Jr, Ordal GW. Unique regulation of carbohydrate chemotaxis in Bacillus subtilis by the phosphoenolpyruvate-dependent phosphotransferase system and the methyl-accepting chemotaxis protein McpC. J. Bacteriol. 180: 4475-4480 (1998).

Garrow TA. Purification, kinetic properties, and cDNA cloning of mammalian betaine-homocysteine methyltransferase. J. Biol. Chem. 271: 22831-22838 (1996).

Garrow TA, Brenner AA, Whitehead VM, Chen XN, Duncan RG, Korenberg JR, Shane B. Cloning of human cDNAs encoding mitochondrial and cytosolic serine hydroxymethyltransferases and chromosomal localization. J. Biol. Chem. 268: 11910-11916 (1993).

Garwe D, Thomson JA, Mundree SG. Molecular characterization of XVSAP1, a stress-responsive gene from the resurrection plant Xerophyta viscosa Baker. J. Exp. Bot. 54: 191-201 (2003).

Garzon A, Li J, Flores A, Casadesus J, Stewart V. Molybdenum cofactor (chlorate-resistant) mutants of Klebsiella pneumoniae M5al can use hypoxanthine as the sole nitrogen source. J. Bacteriol. 174: 6298-6302 (1992).

Gates AJ, Hughes RO, Sharp SR, Millington PD, Nilavongse A, Cole JA, Leach ER, Jepson B, Richardson DJ, Butler CS. Properties of the periplasmic nitrate reductases from Paracoccus pantotrophus and Escherichia coli after growth in tungsten-supplemented media. FEMS Microbiol. Lett. 220: 261-269 (2003).

Gatti DL, Tzagoloff A. Structure and evolution of a group of related aminoacyl-tRNA synthetases. J. Mol. Biol. 218: 557-568 (1991).

Gaulin E, Drame N, Lafitte C, Torto-Alalibo T, Martinez Y, Ameline-Torregrosa C, Khatib M, Mazarguil H, Villalba-Mateos F, Kamoun S, Mazars C, Dumas B, Bottin A, Esquerre-Tugaye MT, Rickauer M. Cellulose binding domains of a Phytophthora cell wall protein are novel pathogen-associated molecular patterns. Plant Cell 18: 1766-1777 (2006).

Gauthier MJ, Flatau GN, Le Rudulier D, Clement RL, Combarro Combarro MP. Intracellular accumulation of potassium and glutamate specifically enhances survival of Escherichia coli in seawater. Appl. Environ. Microbiol. 57: 272-276 (1991).

Gavidia I, Perez-Bermudez P, Seitz HU. Cloning and expression of two novel aldo-keto reductases from Digitalis purpurea leaves. Eur. J. Biochem. 269: 2842-2850 (2002).

Gavira M, Roldan MD, Castillo F, Moreno-Vivian C. Regulation of nap gene expression and periplasmic nitrate reductase activity in the phototrophic bacterium Rhodobacter sphaeroides DSM158. J. Bacteriol. 184: 1693-1702 (2002).

Gawronski JD, Benson DR. Microtiter assay for glutamine synthetase biosynthetic activity using inorganic phosphate detection. Anal. Biochem. 327: 114-118 (2004).

Ge X, Wang H, Cao K. Transformation by T-DNA integration causes highly sterile phenotype independent of transgenes in Arabidopsis thaliana. Plant Cell Rep. 27: 1341-1348 (2008).

Gebhardt JS, Wadsworth GJ, Matthews BF. Characterization of a single soybean cDNA encoding cytosolic and glyoxysomal isozymes of aspartate aminotransferase. Plant Mol. Biol. 37: 99-108 (1998).

Geck MK, Kirsch JF. A novel, definitive test for substrate channeling illustrated with the aspartate aminotransferase/malate dehydrogenase system. Biochemistry 38: 8032-8037 (1999).

Gee R, Goyal A, Byerrum RU, Tolbert NE. Two isoforms of dihydroxyacetone phosphate reductase from the chloroplasts of Dunaliella tertiolecta. Plant Physiol. 103: 243-249 (1993).

Geerlof A, Lewendon A, Shaw WV. Purification and characterization of phosphopantetheine adenylyltransferase from Escherichia coli. J. Biol. Chem. 274: 27105-27111 (1999).

Geerts A, Feltkamp D, Rosahl S. Expression of lipoxygenase in wounded tubers of Solanum tuberosum L. Plant Physiol. 105: 269-277 (1994).

Geigenberger P, Hajirezaei M, Geiger M, Deiting U, Sonnewald U, Stitt M. Overexpression of pyrophosphatase leads to increased sucrose degradation and starch synthesis, increased activities of enzymes for sucrose-starch interconversions, and increased levels of nucleotides in growing potato tubers. Planta 205: 428-437 (1998).

Geiger LE, Morris DR. Stimulation of deoxyribonucleic acid replication fork movement by spermidine analogs in polyamine-deficient Escherichia coli. J. Bacteriol. 141: 1192-1198 (1980).

Ger YM, Chen SL, Chiang HJ, Shiuan D. A single Ser-180 mutation desensitizes feedback inhibition of the phenylalanine-sensitive 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthetase in Escherichia coli. J. Biochem. (Tokyo) 116: 986-990 (1994).

Gerasimenko I, Sheludko Y, Ma X, Stockigt J. Heterologous expression of a Rauvolfia cDNA encoding strictosidine glucosidase, a biosynthetic key to over 2000 monoterpenoid indole alkaloids. Eur. J. Biochem. 269: 2204-2213 (2002).

Gerdes HH, Kindl H. Gene response upon illumination in forming mRNA encoding peroxisomal glycollate oxidase. Biochim. Biophys. Acta 949: 195-205 (1988).

Gerdes SY, Kurnasov OV, Shatalin K, Polanuyer B, Sloutsky R, Vonstein V, Overbeek R, Osterman AL. Comparative genomics of NAD biosynthesis in cyanobacteria. J. Bacteriol. 188: 3012-3023 (2006).

Gerdes SY, Scholle MD, D'Souza M, Bernal A, Baev MV, Farrell M, Kurnasov OV, Daugherty MD, Mseeh F, Polanuyer BM, Campbell JW, Anantha S, Shatalin KY, Chowdhury SA, Fonstein MY, Osterman AL. From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways. J. Bacteriol. 184: 4555-4572 (2002).

Gerhardt S, Echt S, Busch M, Freigang J, Auerbach G, Bader G, Martin WF, Bacher A, Huber R, Fischer M. Structure and properties of an engineered transketolase from maize. Plant Physiol. 132: 1941-1949 (2003).

Gething MJ, Davidson BE. Chorismate mutase/prephenate dehydratase from Escherichia coli K12. 2. Evidence for identical subunits catalysing the two activities. Eur. J. Biochem. 71: 327-336 (1976).

Geuting V, Kobbe D, Hartung F, Dürr J, Focke M, Puchta H. Two distinct MUS81-EME1 complexes from Arabidopsis process Holliday junctions. Plant Physiol. 150: 1062-1071 (2009).

Ghanem M, Fan F, Francis K, Gadda G. Spectroscopic and kinetic properties of recombinant choline oxidase from Arthrobacter globiform. Biochemistry 42: 15179-15188 (2003).

Ghim CM, Goh KI, Kahng B. Lethality and synthetic lethality in the genome-wide metabolic network of Escherichia coli. J. Theor. Biol. 237: 401-411 (2005).

Ghislain M, Frankard V, Jacobs M. A dinucleotide mutation in dihydrodipicolinate synthase of Nicotiana sylvestris leads to lysine overproduction. Plant J. 8: 733-743 (1995).

Ghislain M, Frankard V, Vandenbossche D, Matthews BF, Jacobs M. Molecular analysis of the aspartate kinase-homoserine dehydrogenase gene from Arabidopsis thaliana. Plant Mol. Biol. 24: 835-851 (1994).

Ghosh R, Biswas S, Roy S. An apyrase from Mimosa pudica contains N5,N10-methenyl tetrahydrofolate and is stimulated by light. Eur. J. Biochem. 258: 1009-1013 (1998).

Ghrist AC, Stauffer GV. The Escherichia coli glycine transport system and its role in the regulation of the glycine cleavage enzyme system. Microbiology 141: 133-140 (1995).

Giaever HM, Styrvold OB, Kaasen I, Strom AR. Biochemical and genetic characterization of osmoregulatory trehalose synthesis in Escherichia coli. J. Bacteriol. 170: 2841-2849 (1988).

Giddings G, Allison G, Brooks D, Carter A. Transgenic plants as factories for biopharmaceuticals. Nat. Biotechnol. 18: 1151-1155 (2000).

Giermann N, Schroder M, Ritter T, Zrenner R. Molecular analysis of de novo pyrimidine synthesis in solanaceous species. Plant Mol. Biol. 50: 393-403 (2002).

Gilberthorpe NJ, Poole RK. Nitric oxide homeostasis in Salmonella typhimurium: roles of respiratory nitrate reductase and flavohemoglobin. J. Biol. Chem. 283: 11146-11154 (2008).

Gill RT, Valdes JJ, Bentley WE. A comparative study of global stress gene regulation in response to overexpression of recombinant proteins in Escherichia coli. Metab. Eng. 2: 178-189 (2000).

Gilmour SJ, Lin C, Thomashow MF. Purification and properties of Arabidopsis thaliana COR (cold-regulated) gene polypeptides COR15am and COR6.6 expressed in Escherichia coli. Plant Physiol. 111: 293-299 (1996).

Ginsburg A, Gorman EG, Neece SH, Blackburn MB. Thermodynamics of active-site ligand binding to Escherichia coli glutamine synthetase. Biochemistry 26: 5989-5996 (1987).

Ginsburg A, Zolkiewski M. Differential scanning calorimetry study of reversible, partial unfolding transitions in dodecameric glutamine synthetase from Escherichia coli. Biochemistry 30: 9421-9429 (1991).

Giordani R, Buc J. Evidence for two different electron transfer pathways in the same enzyme, nitrate reductase A from Escherichia coli. Eur. J. Biochem. 271: 2400-2407 (2004).

Giordano G, Boxer DH, Pommier J. Molybdenum cofactor requirement for in vitro activation of apo-molybdoenzymes of Escherichia coli. Mol. Microbiol. 4: 645-650 (1990).

Giordano G, Violet M, Medani CL, Pommier J. A common pathway for the activation of several molybdoenzymes in Escherichia coli K12. Biochim. Biophys. Acta 798: 216-225 (1984).

Gisselmann G, Klausmeier P, Schwenn JD. The ferredoxin:sulphite reductase gene from Synechococcus PCC7942. Biochim. Biophys. Acta 1144: 102-106 (1993).

Giulivi C, Traaseth NJ, Davies KJA. Tyrosine oxidation products: analysis and biological relevance. Amino Acids 25: 227-232 (2003).

Glaser P, Danchin A, Kunst F, Zuber P, Nakano MM. Identification and isolation of a gene required for nitrate assimilation and anaerobic growth of Bacillus subtilis. J. Bacteriol. 177: 1112-1115 (1995).

Gleason FK, Holmgren A. Thioredoxin and related proteins in procaryotes. FEMS Microbiol. Rev. 4: 271-297 (1988).

Goda S, Kojima M, Nishikawa Y, Kujo C, Kawakami R, Kuramitsu S, Sakuraba H, Hiragi Y, Ohshima T. Intersubunit interaction induced by subunit rearrangement is essential for the catalytic activity of the hyperthermophilic glutamate dehydrogenase from Pyrobaculum islandicum. Biochemistry 44: 15304-15313 (2005).

Godard KA, Byun-McKay A, Levasseur C, Plant A, Seguin A, Bohlmann J. Testing of a heterologous, wound- and insect-inducible promoter for functional genomics studies in conifer defense. Plant Cell Rep. 26: 2083-2090 (2007).

Goddijn OJ, Verwoerd TC, Voogd E, Krutwagen RW, de Graaf PT, van Dun K, Poels J, Ponstein AS, Damm B, Pen J. Inhibition of trehalase activity enhances trehalose accumulation in transgenic plants. Plant Physiol. 113: 181-190 (1997).

Goepfert S, Vidoudez C, Rezzonico E, Hiltunen JK, Poirier Y. Molecular identification and characterization of the Arabidopsis delta(3,5),delta(2,4)-dienoyl-coenzyme A isomerase, a peroxisomal enzyme participating in the {beta}-oxidation cycle of unsaturated fatty acids. Plant Physiol. 138: 1947-1956 (2005).

Goerke AR, Loening AM, Gambhir SS, Swartz JR. Cell-free metabolic engineering promotes high-level production of bioactive Gaussia princeps luciferase. Metab. Eng. 10: 187-200 (2008).

Goffner D, Van Doorsselaere J, Yahiaoui N, Samaj J, Grima-Pettenati J, Boudet AM. A novel aromatic alcohol dehydrogenase in higher plants: molecular cloning and expression. Plant Mol. Biol. 36: 755-765 (1998).

Gogami Y, Ito K, Kamitani Y, Matsushima Y, Oikawa T. Occurrence of D-serine in rice and characterization of rice serine racemase. Phytochemistry 70: 380-387 (2009).

Gokarn RR, Eiteman MA, Altman E. Metabolic analysis of Escherichia coli in the presence and absence of the carboxylating enzymes phosphoenolpyruvate carboxylase and pyruvate carboxylase. Appl. Environ. Microbiol. 66: 1844-1850 (2000).

Goldemberg SH, Algranati ID. Polyamines and protein synthesis: studies in various polyamine-requiring mutants of Escherichia coli. Mol. Cell Biochem. 16: 71-77 (1977).

Golovko A, Sitbon F, Tillberg E, Nicander B. Identification of a tRNA isopentenyltransferase gene from Arabidopsis thaliana. Plant Mol. Biol. 49: 161-169 (2002).

Golovleva L, Golovlev E. Microbial cellular biology and current problems of metabolic engineering. J. Molecular Catalysis B-Enzymatic 10: 5-21 (2000).

Gomez-Baena G, Diez J, Garcia-Fernandez JM, El Alaoui S, Humanes L. Regulation of glutamine synthetase by metal-catalyzed oxidative modification in the marine oxyphotobacterium Prochlorococcus. Biochim. Biophys. Acta 1568: 237-244 (2001).

Gomi K, Yamamato H, Akimitsu K. Epoxide hydrolase: a mRNA induced by the fungal pathogen Alternaria alternata on rough lemon (Citrus jambhiri Lush). Plant Mol. Biol. 53: 189-199 (2003).

Gomord V, Faye L. Posttranslational modification of therapeutic proteins in plants. Curr. Opin. Plant Biol. 7: 171-181 (2004).

Gong D, Gong Z, Guo Y, Zhu JK. Expression, activation, and biochemical properties of a novel Arabidopsis protein kinase. Plant Physiol. 129: 225-234 (2002).

Gong D, Guo Y, Jagendorf AT, Zhu JK. Biochemical characterization of the Arabidopsis protein kinase SOS2 that functions in salt tolerance. Plant Physiol. 130: 256-264 (2002).

Gonzalez C, Brito N, Marzluf GA. Functional analysis by site-directed mutagenesis of individual amino acid residues in the flavin domain of Neurospora crassa nitrate reductase. Mol. Gen. Genet. 249: 456-464 (1995).

Gonzalez CF, Proudfoot M, Brown G, Korniyenko Y, Mori H, Savchenko AV, Yakunin AF. Molecular basis of formaldehyde detoxification: characterization of two S-formylglutathione hydrolases from Escherichia coli, FrmB and YeiG. J. Biol. Chem. 281: 14514-14522 (2006).

Gonzalez JC, Banerjee RV, Huang S, Sumner JS, Matthews RG. Comparison of cobalamin-independent and cobalamin-dependent methionine synthases from Escherichia coli: two solutions to the same chemical problem. Biochemistry 31: 6045-6056 (1992).

Gonzalez JC, Peariso K, Penner-Hahn JE, Matthews RG. Cobalamin-independent methionine synthase from Escherichia coli: a zinc metalloenzyme. Biochemistry 35: 12228-12234 (1996).

Gonzalez R, Murarka A, Dharmadi Y, Yazdani SS. A new model for the anaerobic fermentation of glycerol in enteric bacteria: trunk and auxiliary pathways in Escherichia coli. Metab. Eng. 10: 234-245 (2008).

Gonzalez R, Tao H, Purvis JE, York SW, Shanmugam KT, Ingram LO. Gene array-based identification of changes that contribute to ethanol tolerance in ethanologenic Escherichia coli: comparison of KO11 (parent) to LY01 (resistant mutant). Biotechnol. Prog. 19: 612-623 (2003).

Gonzalez R, Tao H, Shanmugam KT, York SW, Ingram LO. Global gene expression differences associated with changes in glycolytic flux and growth rate in Escherichia coli during the fermentation of glucose and xylose. Biotechnol. Prog. 18: 6-20 (2002).

Gonzalez-Lergier J, Broadbelt LJ, Hatzimanikatis V. Anlysis of the maximum theoretical yield for the synthesis of erythromycin precursors in Escherichia coli. Biotechnol. Bioeng. 95: 638-644 (2006).

Gonzalez-Segura L, Velasco-Garcia R, Rudino-Pinera E, Mujica-Jimenez C, Munoz-Clares RA. Site-directed mutagenesis and homology modeling indicate an important role of cysteine 439 in the stability of betaine aldehyde dehydrogenase from Pseudomonas aeruginosa. Biochimie 87: 1056-1064 (2005).

Goodacre R, Neal MJ, Kell DB. Rapid and quantitative analysis of the pyrolysis mass spectra of complex binary and tertiary mixtures using multivariate calibration and artificial neural networks. Anal. Chem. 66: 1070-1085 (1994).

Goodacre R, Neal MJ, Kell DB. Quantitative analysis of multivariate data using artificial neural networks: a tutorial review and applications to the deconvolution of pyrolysis mass spectra. Zentralbl. Bakteriol. 284: 516-539 (1996).

Goodman HJ, Woods DR. Cloning and nucleotide sequence of the Butyrivibrio fibrisolvens gene encoding a type III glutamine synthetase. J. Gen. Microbiol. 139: 1487-1493 (1993).

Goss TJ, Perez-Matos A, Bender RA. Roles of glutamate synthase, gltBD, and gltF in nitrogen metabolism of Escherichia coli and Klebsiella aerogenes. J. Bacteriol. 183: 6607-6619 (2001).

Goude R, Renaud S, Bonnassie S, Bernard T, Blanco C. Glutamine, glutamate, and alpha-glucosylglycerate are the major osmotic solutes accumulated by Erwinia chrysanthemi strain 3937. Appl. Environ. Microbiol. 70: 6535-6541 (2004).

Gouesbet G, Abaibou H, Wu LF, Mandrand-Berthelot MA, Blanco C. Osmotic repression of anaerobic metabolic systems in Escherichia coli. J. Bacteriol. 175: 214-221 (1993).

Gouesbet G, Jebbar M, Talibart R, Bernard T, Blanco C. Pipecolic acid is an osmoprotectant for Escherichia coli taken up by the general osmoporters ProU and ProP. Microbiology 140: 2415-2422 (1994).

Gouesbet G, Trautwetter A, Bonnassie S, Wu LF, Blanco C. Characterization of the Erwinia chrysanthemi osmoprotectant transporter gene ousA. J. Bacteriol. 178: 447-455 (1996).

Gouffi K, Pica N, Pichereau V, Blanco C. Disaccharides as a new class of nonaccumulated osmoprotectants for Sinorhizobium meliloti. Appl. Environ. Microbiol. 65: 1491-1500 (1999).

Goulding CW, Matthews RG. Cobalamin-dependent methionine synthase from Escherichia coli: involvement of zinc in homocysteine activation. Biochemistry 36: 15749-15757 (1997).

Gowrishankar J. Nucleotide sequence of the osmoregulatory proU operon of Escherichia coli. J. Bacteriol. 171: 1923-1931 (1989).

Gowrishankar J, Jayashree P, Rajkumari K. Molecular cloning of an osmoregulatory locus in Escherichia coli: increased proU gene dosage results in enhanced osmotolerance. J. Bacteriol. 168: 1197-1204 (1986).

Gowrishankar J, Manna D. How is osmotic regulation of transcription of the Escherichia coli proU operon achieved? A review and a model. Genetica 97: 363-378 (1996).

Goyer A, Collakova E, Shachar-Hill Y, Hanson AD. Functional characterization of a methionine gamma-lyase in Arabidopsis and its implication in an alternative to the reverse trans-sulfuration pathway. Plant Cell Physiol. 48: 232-242 (2007).

Goyer A, Illarionova V, Roje S, Fischer M, Bacher A, Hanson AD. Folate biosynthesis in higher plants. cDNA cloning, heterologous expression, and characterization of dihydroneopterin aldolases. Plant Physiol. 135: 103-111 (2004).

Goyer A, Johnson TL, Olsen LJ, Collakova E, Shachar-Hill Y, Rhodes D, Hanson AD. Characterization and metabolic function of a peroxisomal sarcosine and pipecolate oxidase from Arabidopsis. J. Biol. Chem. 279: 16947-16953 (2004).

Grabbe R, Kuhn A, Schmitz RA. Cloning, sequencing and characterization of Fnr from Klebsiella pneumoniae. Antonie Van Leeuwenhoek 79: 319-326 (2001).

Grabbe R, Schmitz RA. Oxygen control of nif gene expression in Klebsiella pneumoniae depends on NifL reduction at the cytoplasmic membrane by electrons derived from the reduced quinone pool. Eur. J. Biochem. 270: 1555-1566 (2003).

Graber R, Kasper P, Malashkevich VN, Strop P, Gehring H, Jansonius JN, Christen P. Conversion of aspartate aminotransferase into an L-aspartate beta-decarboxylase by a triple active-site mutation. J. Biol. Chem. 274: 31203-31208 (1999).

Graciet E, Lebreton S, Camadro JM, Gontero B. Characterization of native and recombinant A4 glyceraldehyde 3-phosphate dehydrogenase. Kinetic evidence for confromation changes upon association with the small protein CP12. Eur. J. Biochem. 270: 129-136 (2003).

Graeme-Cook KA. The regulation of porin expression in Escherichia coli: effect of turgor stress. FEMS Microbiol. Lett. 63: 219-223 (1991).

Graham JE, Bryant DA. The biosynthetic pathway for myxol-2' fucoside (myxoxanthophyll) in the cyanobacterium Synechococcus sp. strain PCC 7002. J. Bacteriol. 191: 3292-3300 (2009).

Graham SB, Stephenson JT, Wood JM. Proline dehydrogenase from Escherichia coli K12. Reconstitution of a functional membrane association. J. Biol. Chem. 259: 2656-2661 (1984).

Grant MM, Brown AS, Corwin LM, Troxler RF, Franzblau C. Effect of L-azetidine 2-carboxylic acid on growth and proline metabolism in Escherichia coli. Biochim. Biophys. Acta 404: 180-187 (1975).

Grassl G, Bufe B, Muller B, Rosel M, Kleiner D. Characterization of the gltF gene product of Escherichia coli. FEMS Microbiol. Lett. 179: 79-84 (1999).

Gray JV, Golinelli-Pimpaneau B, Knowles JR. Monofunctional chorismate mutase from Bacillus subtilis: purification of the protein, molecular cloning of the gene, and overexpression of the gene product in Escherichia coli. Biochemistry 29: 376-383 (1990).

Greene RC, Smith AA. Insertion mutagenesis of the metJBLF gene cluster of Escherichia coli K-12:evidence for an metBL operon. J. Bacteriol. 159: 767-769 (1984).

Greenler JM, Sloan JS, Schwartz BW, Becker WM. Isolation, characterization and sequence analysis of a full-length cDNA clone encoding NADH-dependent hydroxypyruvate reductase from cucumber. Plant Mol. Biol. 13: 139-150 (1989).

Greenshields DL, Liu G, Selvaraj G, Wei Y. Differential regulation of wheat quinone reductases in response to powdery mildew infection. Planta 222: 867-875 (2005).

Gregerson RG, Miller SS, Twary SN, Gantt JS, Vance CP. Molecular characterization of NADH-dependent glutamate synthase from alfalfa nodules. Plant Cell 5: 215-226 (1993).

Griesser M, Vitzthum F, Fink B, Bellido ML, Raasch C, Munoz-Blanco J, Schwab W. Multi-substrate flavonol O-glucosyltransferases from strawberry (Fragaria x ananassa) achene and receptacle. J. Exp. Bot. 59: 2611-2625 (2008).

Griessler R, Schwarz A, Mucha J, Nidetzky B. Tracking interactions that stabilize the dimer structure of starch phosphorylase from Corynebacterium callunae. Eur. J. Biochem. 270: 2126-2136 (2003).

Griffin HG, Gasson MJ. The gene (aroK) encoding shikimate kinase I from Escherichia coli. DNA Seq. 5: 195-197 (1995).

Griffin HG, Griffin AM. Cloning and DNA sequence analysis of the serC-aroA operon from Salmonella gallinarum; evolutionary relationships between the prokaryotic and eukaryotic aroA-encoded enzymes. J. Gen. Microbiol. 137: 113-121 (1991).

Griffiths L, Cole JA. Lack of redox control of the anaerobically-induced nirB+ gene of Escherichia coli K-12. Arch. Microbiol. 147: 364-369 (1987).

Grimm B. Primary structure of a key enzyme in plant tetrapyrrole synthesis: glutamate 1-semialdehyde aminotransferase. Proc. Natl. Acad. Sci. U.S.A. 87: 4169-4173 (1990).

Grimm B, Smith AJ, Kannangara CG, Smith M. Gabaculine-resistant glutamate 1-semialdehyde aminotransferase of Synechococcus. Deletion of a tripeptide close to the NH2 terminus and internal amino acid substitution. J. Biol. Chem. 266: 12495-12501 (1991).

Gross F, Luniak N, Perlova O, Gaitatzis N, Jenke-Kodama H, Gerth K, Gottschalk D, Dittmann E, Muller R. Bacterial type III polyketide synthases: phylogenetic analysis and potential for the production of novel secondary metabolites by heterologous expression in pseudomonads. Arch. Microbiol. 185: 28-38 (2006).

Gross R, Pisa R, Sanger M, Lancaster CRD, Simon J. Characterization of the menaquinone reduction site in the diheme cytochrome b membrane anchor of Wolinella succinogenes NiFe-hydrogenase. J. Biol. Chem. 279: 274-281 (2004).

Grossmann K, Herbster K, Mack M. Rapid cloning of metK encoding methionine adenosyltransferase from Corynebacterium glutamicum by screening a genomic library on a high density colony-array. FEMS Microbiol. Lett. 193: 99-103 (2000).

Grothe S, Krogsrud RL, McClellan DJ, Milner JL, Wood JM. Proline transport and osmotic stress response in Escherichia coli K-12. J. Bacteriol. 166: 253-259 (1986).

Gruez A, Roig-Zamboni V, Grisel S, Salomoni A, Valencia C, Campanacci V, Tegoni M, Cambillau C. Crystal structure and kinetics identify Escherichia coli YdcW gene product as a medium-chain aldehyde dehydrogenase. J. Mol. Biol. 343: 29-41 (2004).

Gruys KJ, Walker MC, Sikorski JA. Substrate synergism and the steady-state kinetic reaction mechanism for EPSP synthase from Escherichia coli. Biochemistry 31: 5534-5544 (1992).

Gu L, Lajoie C, Kelly C. Expression of a Phanerochaete chrysosporium manganese peroxidase gene in the yeast Pichia pastoris. Biotechnol. Prog. 19: 1403-1409 (2003).

Gu YQ, Walling LL. Identification of residues critical for activity of the wound-induced leucine aminopeptidase (LAP-A) of tomato. Eur. J. Biochem. 269: 1630-1640 (2002).

Gu ZJ, Wang L, Le Rudulier D, Zhang B, Yang SS. Characterization of the glycine betainebiosynthetic genes in the moderately halophilic bacterium Halobacillus dabanensis D-8(T). Curr. Microbiol. 57: 306-311 (2008).

Guan HP, Baba T, Preiss J. Expression of branching enzyme I of maize endosperm in Escherichia coli. Plant Physiol. 104: 1449-1453 (1994).

Guan Y, Ramalingam S, Nagegowda D, Taylor PW, Chye ML. Brassica juncea chitinase BjCHI1 inhibits growth of fungal phytopathogens and agglutinates Gram-negative bacteria. J. Exp. Bot. 59: 3475-3484 (2008).

Guedon E, Moore CM, Que Q, Wang T, Ye RW, Helmann JD. The global transcriptional response of Bacillus subtilis to manganese involves the MntR, Fur, TnrA and sigma(B) regulons. Mol. Microbiol. 49: 1477-1491 (2003).

Guerreiro P, Barreiros T, Soares H, Cyrne L, Maia e Silva A, Rodrigues-Pousada C. Sequencing of a 17.6 kb segment on the right arm of yeast chromosome VII reveals 12 ORFs, including CCT, ADE3 and TR-I genes, homologues of the yeast PMT and EF1G genes, of the human and bacterial … Yeast 12: 273-280 (1996).

Guet CC, Elowitz MB, Hsing W, Leibler S. Combinatorial synthesis of genetic networks. Science 296: 1466-1470 (2002).

Guigliarelli B, Magalon A, Asso M, Bertrand P, Frixon C, Giordano G, Blasco F. Complete coordination of the four Fe-S centers of the beta subunit from Escherichia coli nitrate reductase. Physiological, biochemical, and EPR characterization of site-directed mutants lacking the highest or lowest potential [4Fe-4S] clusters. Biochemistry 35: 4828-4836 (1996).

Guignard L, Ozawa K, Pursglove SE, Otting G, Dixon NE. NMR analysis of in vitro-synthesized proteins without purification: a high-throughput approach. FEBS Lett. 524: 159-162 (2002).

Guillouet S, Rodal AA, An G, Lessard PA, Sinskey AJ. Expression of the Escherichia coli catabolic threonine dehydratase in Corynebacterium glutamicum and its effect on isoleucine production. Appl. Environ. Microbiol. 65: 3100-3107 (1999).

Gunasekera TS, Csonka LN, Paliy O. Genome-wide transcriptional responses of Escherichia coli K-12 to continuous osmotic and heat stresses. J. Bacteriol. 190: 3712-3720 (2008).

Guo N, Puhlev I, Brown DR, Mansbridge J, Levine F. Trehalose expression confers desiccation tolerance on human cells. Nat. Biotechnol. 18: 168-171 (2000).

Guranowski A, de Diego A, Sillero A, Gunther Sillero MA. Uridine 5'-polyphosphates (p4U and p5U) and uridine(5')polyphospho(5')nucleosides (Up(n)Ns) can be synthesized by UTP:glucose-1-phosphate uridylyltransferase from Saccharomyces cerevisiae. FEBS Lett. 561: 83-88 (2004).

Guterman I, Shalit M, Menda N, Piestun D, Dafny-Yelin M, Shalev G, Bar E, Davydov O, Ovadis M, Emanuel M, Wang J, Adam Z, Pichersky E, Lewinsohn E, Zamir D, Vainstein A, Weiss D. Rose scent: genomics approach to discovering novel floral fragrance-related genes. Plant Cell 14: 2325-2338 (2002).

Gutheil WG, Holmquist B, Vallee BL. Purification, characterization, and partial sequence of the glutathione-dependent formaldehyde dehydrogenase from Escherichia coli: a class III alcohol dehydrogenase. Biochemistry 31: 475-481 (1992).

Guthrie TA, Apgar GA, Griswold KE, Lindemann MD, Radcliffe JS, Jacobson BN. Nutritional value of a corn containing a glutamate dehydrogenase gene for growing pigs. J. Anim. Sci. 82: 1693-1698 (2004).

Gutierrez JA, Crowder T, Rinaldo-Matthis A, Ho MC, Almo SC, Schramm VL. Transition state analogs of 5'-methylthioadenosine nucleosidase disrupt quorum sensing. Nat. Chem. Biol. 5: 251-257 (2009).

Gutierrez JA, Crowley PJ, Cvitkovitch DG, Brady LJ, Hamilton IR, Hillman JD, Bleiweis AS. Streptococcus mutans ffh, a gene encoding a homologue of the 54 kDa subunit of the signal recognition particle, is involved in resistance to acid stress. Microbiology 145: 357-366 (1999).

Gutierrez JA, Csonka LN. Isolation and characterization of adenylate kinase (adk) mutations in Salmonella typhimurium which block the ability of glycine betaine to function as an osmoprotectant. J. Bacteriol. 177: 390-400 (1995).

Gutierrez-Marcos JF, Roberts MA, Campbell EI, Wray JL. Three members of a novel small gene-family from Arabidopsis thaliana able to complement functionally an Escherichia coli mutant defective in PAPS reductase activity encode proteins with a thioredoxin-like domain and "APS reductase" activity. Proc. Natl. Acad. Sci. U.S.A. 93: 13377-13382 (1996).

Gwyer JD, Zhang J, Butt JN, Ulstrup J. Voltammetry and in situ scanning tunnelling microscopy of cytochrome c nitrite reductase on Au(111)-electrodes. Biophys. J. 91: 3897-3906 (2006).

Ha SB, Smith AP, Howden R, Dietrich WM, Bugg S, O'Connell MJ, Goldsbrough PB, Cobbett CS. Phytochelatin synthase genes from Arabidopsis and the yeast Schizosaccharomyces pombe. Plant Cell 11: 1153-1164 (1999).

Haardt M, Bremer E. Use of phoA and lacZ fusions to study the membrane topology of ProW, a component of the osmoregulated ProU transport system of Escherichia coli. J. Bacteriol. 178: 5370-5381 (1996).

Haardt M, Kempf B, Faatz E, Bremer E. The osmoprotectant proline betaine is a major substrate for the binding-protein-dependent transport system ProU of Escherichia coli K-12. Mol. Gen. Genet. 246: 783-786 (1995).

Hacham Y, Avraham T, Amir R. The N-terminal region of Arabidopsis cystathionine gamma-synthase plays an important regulatory role in methionine metabolism. Plant Physiol. 128: 454-462 (2002).

Hadfield A, Kryger G, Ouyang J, Petsko GA, Ringe D, Viola R. Structure of aspartate-beta-semialdehyde dehydrogenase from Escherichia coli, a key enzyme in the aspartate family of amino acid biosynthesis. J. Mol. Biol. 289: 991-1002 (1999).

Hadlich F, Noack S, Wiechert W. Translating biochemical network models between different kinetic formats. Metab. Eng. 11: 87-100 (2009).

Haenzelmann P, Hernandez HL, Menzel C, Garcia-Serres R, Huynh BH, Johnson MK, Mendel RR, Schindelin H. Characterization of MOCS1A, an oxygen-sensitive iron-sulfur protein involved in human molybdenum cofactor biosynthesis. J. Biol. Chem. 279: 34721-34732 (2004).

Hafner EW, Tabor CW, Tabor H. Mutants of Escherichia coli that do not contain 1,4-diaminobutane (putrescine) or spermidine. J. Biol. Chem. 254: 12419-12426 (1979).

Hafner EW, Tabor CW, Tabor H. Isolation of a metK mutant with a temperature-sensitive S-adenosylmethionine synthetase. J. Bacteriol. 132: 832-840 (1977).

Hagemann M, Schoor A, Jeanjean R, Zuther E, Joset F. The stpA gene form Synechocystis sp. strain PCC 6803 encodes the glucosylglycerol-phosphate phosphatase involved in cyanobacterial osmotic response to salt shock. J. Bacteriol. 179: 1727-1733 (1997).

Haghani K, Hatef Salmanian A, Ranjbar B, Zakikhan-Alang K, Khajeh K. Comparative studies of wild type Escherichia coli 5-enolpyruvylshikimate 3-phosphate synthase with three glyphosate-insensitive mutated forms: Activity, stability and structural characterization. Biochim. Biophys. Acta 1784: 1167-1175 (2008).

Hagishita T, Yoshida T, Izumi Y, Mitsunaga T. Cloning and expression of the gene for serine-glyoxylate aminotransferase from an obligate methylotroph Hyphomicrobium methylovorum GM2. Eur. J. Biochem. 241: 1-5 (1996).

Hahn FM, Hurlburt AP, Poulter CD. Escherichia coli open reading frame 696 is idi, a nonessential gene encoding isopentenyl diphosphate isomerase. J. Bacteriol. 181: 4499-4504 (1999).

Hall DA, Jordan-Starck TC, Loo RO, Ludwig ML, Matthews RG. Interaction of flavodoxin with cobalamin-dependent methionine synthase. Biochemistry 39: 10711-10719 (2000).

Hall DA, Vander Kooi CW, Stasik CN, Stevens SY, Zuiderweg ER, Matthews RG. Mapping the interactions between flavodoxin and its physiological partners flavodoxin reductase and cobalamin-dependent methionine synthase. Proc. Natl. Acad. Sci. U.S.A. 98: 9521-9526 (2001).

Halsall DM. Overproduction of lysine by mutant strains of Escherichia coli with defective lysine transport systems. Biochem. Genet. 13: 109-124 (1975).

Hama H, Kayahara T, Tsuda M, Tsuchiya T. Inhibition of homoserine dehydrogenase I by L-serine in Escherichia coli. J. Biochem. (Tokyo) 109: 604-608 (1991).

Hama H, Sumita Y, Kakutani Y, Tsuda M, Tsuchiya T. Target of serine inhibition in Escherichia coli. Biochem. Biophys. Res. Commun. 168: 1211-1216 (1990).

Hamada A, Hibino T, Nakamura T, Takabe T. Na(+)/H(+) antiporter from Synechocystis species PCC 6803, homologous to SOS1, contains an aspartic residue and long C-terminal tail important for the carrier activity. Plant Physiol. 125: 437-446 (2001).

Hammarstrom A, Soliman A, Nordlund S. Low- and high-activity forms of glutamine synthetase from Rhodospirillum rubrum: sensitivity to feed-back effectors and activation of the low-activity form. Biochim. Biophys. Acta 1080: 259-263 (1991).

Han KY, Park JS, Seo HS, Ahn KY, Lee J. Multiple stressor-induced proteome responses of Escherichia coli BL21(DE3). J. Proteome Res. 7: 1891-1903 (2008).

Han SJ, Chang HN, Lee J. Characterization of an oxygen-dependent inducible promoter, the nar promoter of Escherichia coli, to utilize in metabolic engineering. Biotechnol. Bioeng. 72: 573-576 (2001).

Handrick R, Reinhardt S, Schultheiss D, Reichart T, Schuler D, Jendrossek V, Jendrossek D. Unraveling the function of the Rhodospirillum rubrum activator of polyhydroxybutyrate (PHB) degradation: the activator is a PHB-granule-bound protein (phasin). J. Bacteriol. 186: 2466-2475 (2004).

Hanlon MH, Ferone R, Weaver K, Ray P. Enzymatic synthesis of folate and antifolate polyglutamates with Escherichia coli folylpolyglutamate synthetase. Anal. Biochem. 216: 345-351 (1994).

Hanlon SP, Hill TK, Flavell MA, Stringfellow JM, Cooper RA. 2-phenylethylamine catabolism by Escherichia coli K-12: gene organization and expression. Microbiology 143: 513-518 (1997).

Hannaert V, Albert MA, Rigden DJ, da Silva Giotto MT, Thiemann O, Garratt RC, Van Roy J, Opperdoes FR, Michels PA. Kinetic characterization, structure modelling studies and crystallization of Trypanosoma brucei enolase. Eur. J. Biochem. 270: 3205-3213 (2003).

Hans J, Hause B, Strack D, Walter MH. Cloning, characterization, and immunolocalization of a mycorrhiza-inducible 1-deoxy-d-xylulose 5-phosphate reductoisomerase in arbuscule-containing cells of maize. Plant Physiol. 134: 614-624 (2004).

Hansen CH, Du L, Naur P, Olsen CE, Axelsen KB, Hick AJ, Pickett JA, Halkier BA. CYP83b1 is the oxime-metabolizing enzyme in the glucosinolate pathway in Arabidopsis. J. Biol. Chem. 276: 24790-24796 (2001).

Hansen CH, Wittstock U, Olsen CE, Hick AJ, Pickett JA, Halkier BA. Cytochrome P450 CYP79F1 from Arabidopsis catalyzes the conversion of dihomomethionine and trihomomethionine to the corresponding aldoximes in the biosynthesis of aliphatic glucosinolates. J. Biol. Chem. 276: 11078-11085 (2001).

Hansen J, Johannesen PF. Cysteine is essential for transcriptional regulation of the sulfur assimilation genes in Saccharomyces cerevisiae. Mol. Gen. Genet. 263: 535-542 (2000).

Hanson AD, Rathinasabapathi B, Chamberlin B, Gage DA. Comparative physiological evidence that beta-alanine betaine and choline-O-sulfate act as compatible osmolytes in halophytic Limonium species. Plant Physiol. 97: 1199-1205 (1991).

Hansson M, Gough SP, Kannangara CG, vonWettstein D. Analysis of RNA and enzymes of potential importance for regulation of 5-aminolevulinic acid synthesis in the protochlorophyllide accumulating barley mutant tigrina-d(12). Plant Physiol. Biochem. 35: 827-836 (1997).

Hantke K. Is the bacterial ferrous iron transporter FeoB a living fossil? Trends Microbiol. 11: 192-195 (2003).

Hanzawa Y, Takahashi T, Michael AJ, Burtin D, Long D, Pineiro M, Coupland G, Komeda Y. ACAULIS5, an Arabidopsis gene required for stem elongation, encodes a spermine synthase. EMBO J. 19: 4248-4256 (2000).

Hao R, Schmit JC. Cloning of the gene for glutamate decarboxylase and its expression during conidiation in Neurospora crassa. Biochem. J. 293: 735-738 (1993).

Hara KY, Shimodate N, Ito M, Baba T, Mori H, Mori H. Systematic genome-wide scanning for genes involved in ATP generation in Escherichia coli. Metab. Eng. 11: 1-7 (2009).

Hara M, Terashima S, Fukaya T, Kuboi T. Enhancement of cold tolerance and inhibition of lipid peroxidation by citrus dehydrin in transgenic tobacco. Planta 217: 290-298 (2003).

Harada H, Yu F, Okamoto S, Kuzuyama T, Utsumi R, Misawa N. Efficient synthesis of functional isoprenoids from acetoacetate through metabolic pathway-engineered Escherichia coli. Appl. Microbiol. Biotechnol. 81: 915-925 (2009).

Harborne NR, Griffiths L, Busby SJ, Cole JA. Transcriptional control, translation and function of the products of the five open reading frames of the Escherichia coli nir operon. Mol. Microbiol. 6: 2805-2813 (1992).

Hardin A, Villalta CF, Doan M, Jabri M, Chockalingham V, White SJ, Fowler RG. A molecular characterization of spontaneous frameshift mutagenesis within the trpA gene of Escherichia coli. DNA Repair (Amst.) 6: 177-189 (2007).

Hardin SC, Duncan KA, Huber SC. Determination of structural requirements and probable regulatory effectors for membrane association of maize sucrose synthase 1. Plant Physiol. 141: 1106-1119 (2006).

Harker M, Bramley PM. Expression of prokaryotic 1-deoxy-D-xylulose-5-phosphatases in Escherichia coli increases carotenoid and ubiquinone biosynthesis. FEBS Lett. 448: 115-119 (1999).

Harms K, von Ballmoos P, Brunold C, Hofgen R, Hesse H. Expression of a bacterial serine acetyltransferase in transgenic potato plants leads to increased levels of cysteine and glutathione. Plant J. 22: 335-343 (2000).

Harms N, Ras J, Reijnders WN, van Spanning RJ, Stouthamer AH. S-formylglutathione hydrolase of Paracoccus denitrificans is homologous to human esterase D: a universal pathway for formaldehyde detoxification? J. Bacteriol. 178: 6296-6299 (1996).

Harn C, Knight M, Ramakrishnan A, Guan H, Keeling PL, Wasserman BP. Isolation and characterization of the zSSIIa and zSSIIb starch synthase cDNA clones from maize endosperm. Plant Mol. Biol. 37: 639-649 (1998).

Harper AD, Bar-Peled M. Biosynthesis of UDP-xylose. Cloning and characterization of a novel Arabidopsis gene family, UXS, encoding soluble and putative membrane-bound UDP-glucuronic acid decarboxylase isoforms. Plant Physiol. 130: 2188-2198 (2002).

Harris LM, Blank L, Desai RP, Welker NE, Papoutsakis ET. Fermentation characterization and flux analysis of recombinant strains of Clostridium acetobutylicum with an inactivated solR gene. J. Ind. Microbiol. Biotechnol. 27: 322-328 (2001).

Harris RL, Eady RR, Samar Hasnain S, Gary Sawers R. Coordinate synthesis of azurin I and copper nitrite reductase in Alcaligenes xylosoxidans during denitrification. Arch. Microbiol. 186: 241-249 (2006).

Harrod AC, Yang X, Junker M, Reitzer L. Evidence for a second interaction between the regulatory amino-terminal and central output domains of the response regulator NtrC (nitrogen regulator I) in Escherichia coli. J. Biol. Chem. 279: 2350-2359 (2004).

Hart EJ, Powers-Lee SG. Role of Cys-1327 and Cys-1337 in redox sensitivity and allosteric monitoring in human carbamoyl phosphate synthetase. J. Biol. Chem. 284: 5977-5985 (2009).

Hart EJ, Powers-Lee SG. Mutation analysis of carbamoyl phosphate synthetase: does the structurally conserved glutamine amidotransferase triad act as a functional dyad? Protein Sci. 17: 1120-1128 (2008).

Harth G, Horwitz MA. Expression and efficient export of enzymatically active Mycobacterium tuberculosis glutamine synthetase in Mycobacterium smegmatis and evidence that the information for export is contained within the protein. J. Biol. Chem. 272: 22728-22735 (1997).

Hartig E, Schiek U, Vollack KU, Zumft WG. Nitrate and nitrite control of respiratory nitrate reduction in denitrifying Pseudomonas stutzeri by a two-component regulatory system homologous to NarXL of Escherichia coli. J. Bacteriol. 181: 3658-3665 (1999).

Hashiguchi K, Matsui H, Kurahashi O. Effects of a feedback-resistant aspartokinase III gene on L-isoleucine production in Escherichia coli K-12. Biosci. Biotechnol. Biochem. 63: 2023-2024 (1999).

Hashiguchi K, Takesada H, Suzuki E, Matsui H. Construction of an L-isoleucine overproducing strain of Escherichia coli K-12. Biosci. Biotechnol. Biochem. 63: 672-679 (1999).

Hashimoto T, Shoji T, Mihara T, Oguri H, Tamaki K, Suzuki K, Yamada Y. Intraspecific variability of the tandem repeats in Nicotiana putrescine N-methyltransferases Plant Mol. Biol. 37: 25-37 (1998).

Haslekas C, Viken MK, Grini PE, Nygaard V, Nordgard SH, Meza TJ, Aalen RB. Seed 1-cysteine peroxiredoxin antioxidants are not involved in dormancy, but contribute to inhibition of germination during stress. Plant Physiol. 133: 1148-1157 (2003).

Hasona A, Ray RM, Shanmugam KT. Physiological and genetic analyses leading to identification of a biochemical role for the moeA (molybdate metabolism) gene product in Escherichia coli. J. Bacteriol. 180: 1466-1472 (1998).

Hasona A, Self WT, Shanmugam KT. Transcriptional regulation of the moe (molybdate metabolism) operon of Escherichia coli. Arch. Microbiol. 175: 178-188 (2001).

Hasslacher M, Schall M, Hayn M, Griengl H, Kohlwein SD, Schwab H. Molecular cloning of the full-length cDNA of (S)-hydroxynitrile lyase from Hevea brasiliensis. Functional expression in Escherichia coli and Saccharomyces cerevisiae and identification of an active site residue. J. Biol. Chem. 271: 5884-5891 (1996).

Hatten LA, Schweizer HP, Averill N, Wang L, Schryvers AB. Cloning and characterization of the Neisseria meningitidis asd gene. Gene 129: 123-128 (1993).

Hatzfeld Y, Lee S, Lee M, Leustek T, Saito K. Functional characterization of a gene encoding a fourth ATP sulfurylase isoform from Arabidopsis thaliana. Gene 248: 51-58 (2000).

Hatzimanikatis V, Emmerling M, Sauer U, Bailey JE. Application of mathematical tools for metabolic design of microbial ethanol production. Biotechnol. Bioeng. 58: 154-161 (1998).

Hause B, Meyer K, Viitanen PV, Chapple C, Strack D. Immunolocalization of 1-O-sinapoylglucose:malate sinapoyltransferase in Arabidopsis thaliana. Planta 215: 26-32 (2002).

Haverkamp T, Schwenn JD. Structure and function of a cysBJIH gene cluster in the purple sulphur bacterium Thiocapsa roseopersicina. Microbiology 145: 115-125 (1999).

Hawkes TR, Thomas PG, Edwards LS, Rayner SJ, Wilkinson KW, Rice DW. Purification and characterization of the imidazoleglycerol-phosphate dehydratase of Saccharomyces cerevisiae from recombinant Escherichia coli. Biochem. J. 306: 385-397 (1995).

Hayashi M, De Bellis L, Alpi A, Nishimura M. Cytosolic aconitase participates in the glyoxylate cycle in etiolated pumpkin cotyledons. Plant Cell Physiol. 36: 669-680 (1995).

Hayzer DJ. Sub-cloning of the wild-type proAB region of the Escherichia coli genome. J. Gen. Microbiol. 129: 3215-3225 (1983).

Hayzer DJ, Leisinger T. Proline biosynthesis in Escherichia coli. Stoichiometry and end-product identification of the reaction catalysed by glutamate semialdehyde dehydrogenase. Biochem. J. 197: 269-274 (1981).

Hayzer DJ, Leisinger T. Proline biosynthesis in Escherichia coli: Purification and characterisation of glutamate-semialdehyde dehydrogenase. Eur. J. Biochem. 121: 561-565 (1982).

Hayzer DJ, Leisinger T. The gene-enzyme relationships of proline biosynthesis in Escherichia coli. J. Gen. Microbiol. 118: 287-293 (1980).

Hayzer DJ, Moses V. The enzymes of proline biosynthesis in Escherichia coli. Their molecular weights and the problem of enzyme aggregation. Biochem. J. 173: 219-228 (1978).

Hayzer DJ, Moses V. Proline biosynthesis by cell-free extracts of Escherichia coli and potential errors arising from the use of a bioradiological assay procedure. Biochem. J. 173: 207-217 (1978).

Haziza C, Stragier P, Patte JC. Nucleotide sequence of the asd gene of Escherichia coli: absence of a typical attenuation signal. EMBO J. 1: 379-384 (1982).

He L, Soupene E, Kustu S. NtrC is required for control of Klebsiella pneumoniae NifL activity. J. Bacteriol. 179: 7446-7455 (1997).

He XZ, Reddy JT, Dixon RA. Stress responses in alfalfa (Medicago sativa L). XXII. cDNA cloning and characterization of an elicitor-inducible isoflavone 7-O-methyltransferase. Plant Mol. Biol. 36: 43-54 (1998).

He Y, Gan S. A gene encoding an acyl hydrolase is involved in leaf senescence in Arabidopsis. Plant Cell 14: 805-815 (2002).

He Z, Nadeau LJ, Spain JC. Characterization of hydroxylaminobenzene mutase from pNBZ139 cloned from Pseudomonas pseudoalcaligenes JS45 a highly associated SDS-stable enzyme catalyzing an intramolecular transfer of hydroxy groups. Eur. J. Biochem. 267: 1110-1116 (2000).

Heck IS, Ninnemann H. Molybdenum cofactor biosynthesis in Neurospora crassa: biochemical characterization of pleiotropic molybdoenzyme mutants nit-7, nit-8, nit-9A, B and C. Photochem. Photobiol. 61: 54-60 (1995).

Heeb S, Kuehne SA, Bycroft M, Crivii S, Allen MD, Haas D, Camara M, Williams P. Functional analysis of the post-transcriptional regulator RsmA reveals a novel RNA-binding site. J. Mol. Biol. 355: 1026-1036 (2006).

Heermann R, Jung K. Structural features and mechanisms for sensing high osmolarity in microorganisms. Curr. Opin. Microbiol. 7: 168-174 (2004).

Heilbronn J, Wilson J, Berger BJ. Tyrosine aminotransferase catalyzes the final step of methionine recycling in Klebsiella pneumoniae. J. Bacteriol. 181: 1739-1747 (1999).

Helfert C, Gotsche S, Dahl MK. Cleavage of trehalose-phosphate in Bacillus subtilis is catalysed by a phospho-alpha-(1-1)-glucosidase encoded by the treA gene. Mol. Microbiol. 16: 111-120 (1995).

Hell R. Molecular physiology of plant sulfur metabolism. Planta 202: 138-148 (1997).

Helleboid S, Chapman A, Hendriks T, Inze D, Vasseur J, Hilbert JL. Cloning of beta-1,3-glucanases expressed during Cichorium somatic embryogenesis. Plant Mol. Biol. 42: 377-386 (2000).

Hellens RP, Edwards EA, Leyland NR, Bean S, Mullineaux PM. pGreen: a versatile and flexible binary Ti vector for Agrobacterium-mediated plant transformation. Plant Mol. Biol. 42: 819-832 (2000).

Heller JS, Rostomily R, Kyriakidis DA, Canellakis ES. Regulation of polyamine biosynthesis in Escherichia coli by basic proteins. Proc. Natl. Acad. Sci. U.S.A. 80: 5181-5184 (1983).

Helling RB. Pathway choice in glutamate synthesis in Escherichia coli. J. Bacteriol. 180: 4571-4575 (1998).

Helling RB. Speed versus efficiency in microbial growth and the role of parallel pathways. J. Bacteriol. 184: 1041-1045 (2002).

Helling RB. Why does Escherichia coli have two primary pathways for synthesis of glutamate? J. Bacteriol. 176: 4664-4668 (1994).

Hellmer J, Patzold R, Zeilinger C. Identification of a pH regulated Na+/H+ antiporter of Methanococcus jannaschii. FEBS Lett. 527: 245-249 (2002).

Helmstaedt K, Krappmann S, Braus GH. Allosteric regulation of catalytic activity: Escherichia coli aspartate transcarbamoylase versus yeast chorismate mutase. Microbiol. Mol. Biol. Rev. 65: 404-421 (2001).

Hemschemeier S, Grund M, Keuntje B, Eichenlaub R. Isolation of Escherichia coli mutants defective in uptake of molybdate. J. Bacteriol. 173: 6499-6506 (1991).

Henne A, Daniel R, Schmitz RA, Gottschalk G. Construction of environmental DNA libraries in Escherichia coli and screening for the presence of genes conferring utilization of 4-hydroxybutyrate. Appl. Environ. Microbiol. 65: 3901-3907 (1999).

Herbette S, Lenne C, Leblanc N, Julien JL, Drevet JR, Roeckel-Drevet P. Two GPX-like proteins from Lycopersicon esculentum and Helianthus annuus are antioxidant enzymes with phospholipid hydroperoxide glutathione peroxidase and thioredoxin peroxidase activities. Eur. J. Biochem. 269: 2414-2420 (2002).

Herd S, Christensen MJ, Saunders K, Scott DB, Schmid J. Quantitative assessment of in planta distribution of metabolic activity and gene expression of an endophytic fungus. Microbiology 143: 267-275 (1997).

Herl V, Fischer G, Muller-Uri F, Kreis W. Molecular cloning and heterologous expression of progesterone 5beta-reductase from Digitalis lanata Ehrh. Phytochemistry 67: 225-231 (2006).

Hernandez-Montalvo V, Martinez A, Hernandez-Chavez G, Bolivar F, Valle F, Gosset G. Expression of galP and glk in a Escherichia coli PTS mutant restores glucose transport and increases glycolytic flux to fermentation products. Biotechnol. Bioeng. 83: 687-694 (2003).

Hernando-Rico V, Martin JF, Santamarta I, Liras P. Structure of the ask-asd operon and formation of aspartokinase subunits in the cephamycin producer 'Amycolatopsis lactamdurans'. Microbiology 147: 1547-1555 (2001).

Herrgard MJ, Covert MW, Palsson BO. Reconciling gene expression data with known genome-scale regulatory network structures. Genome Res. 13: 2423-2434 (2003).

Herring PA, McKnight BL, Jackson JH. Channeling behavior and activity models for Escherichia coli K-12 acetohydroxy acid synthases at physiological substrate levels. Biochem. Biophys. Res. Commun. 207: 48-54 (1995).

Herrington MB, MacRae TJ, Panagopoulos D, Wong SH. A mutation in the folA promoter delays adaptation to minimal medium by Escherichia coli K-12. J. Basic Microbiol. 42: 172-180 (2002).

Hersh BM, Farooq FT, Barstad DN, Blankenhorn DL, Slonczewski JL. A glutamate-dependent acid resistance gene in Escherichia coli. J. Bacteriol. 178: 3978-3981 (1996).

Hershey HP, Schwartz LJ, Gale JP, Abell LM. Cloning and functional expression of the small subunit of acetolactate synthase from Nicotiana plumbaginifolia. Plant Mol. Biol. 40: 795-806 (1999).

Hertweck C, Jarvis AP, Xiang LK, Moore BS, Oldham NJ. A mechanism of benzoic acid biosynthesis in plants and bacteria that mirrors fatty acid beta-oxidation. Chembiochem. 2: 784-787 (2001).

Hess WR, Steglich C, Lichtle C, Partensky F. Phycoerythrins of the oxyphotobacterium Prochlorococcus marinus are associated to the thylakoid membrane and are encoded by a single large gene cluster. Plant Mol. Biol. 40: 507-521 (1999).

Hesslinger C, Fairhurst SA, Sawers G. Novel keto acid formate-lyase and propionate kinase enzymes are components of an anaerobic pathway in Escherichia coli that degrades L-threonine to propionate. Mol. Microbiol. 27: 477-492 (1998).

Hester G, Stark W, Moser M, Kallen J, Markovic-Housley Z, Jansonius JN. Crystal structure of phosphoserine aminotransferase from Escherichia coli at 2.3 A resolution: comparison of the unligated enzyme and a complex with alpha-methyl-L-glutamate. J. Mol. Biol. 286: 829-850 (1999).

Hettwer S, Sterner R. A novel tryptophan synthase beta-subunit from the hyperthermophile Thermotoga maritima - Quaternary structure, steady-state kinetics, and putative physiological role. J. Biol. Chem. 277: 8194-8201 (2002).

Hewagama A, Guy HI, Chaparian M, Evans DR. The function of Glu338 in the catalytic triad of the carbamoyl phosphate synthetase amidotransferase domain. Biochim. Biophys. Acta 1388: 489-499 (1998).

Hewagama A, Guy HI, Vickrey JF, Evans DR. Functional linkage between the glutaminase and synthetase domains of carbamoyl-phosphate synthetase. Role of serine 44 in carbamoyl-phosphate synthetase-aspartate carbamoyltransferase-dihydroorotase (cad). J. Biol. Chem. 274: 28240-28245 (1999).

Hey TD, Hartley M, Walsh TA. Maize ribosome-inactivating protein (b-32). Homologs in related species, effects on maize ribosomes, and modulation of activity by pro-peptide deletions. Plant Physiol. 107: 1323-1332 (1995).

Hibi N, Higashiguchi S, Hashimoto T, Yamada Y. Gene expression in tobacco low-nicotine mutants. Plant Cell 6: 723-735 (1994).

Hibi T, Nii H, Nakatsu T, Kimura A, Kato H, Hiratake J, Oda J. Crystal structure of gamma-glutamylcysteine synthetase: insights into the mechanism of catalysis by a key enzyme for glutathione homeostasis. Proc. Natl. Acad. Sci. U.S.A. 101: 15052-15057 (2004).

Hibino T, Kaku N, Yoshikawa H, Takabe T, Takabe T. Molecular characterization of DnaK from the halotolerant cyanobacterium Aphanothece halophytica for ATPase, protein folding, and copper binding under various salinity conditions. Plant Mol. Biol. 40: 409-418 (1999).

Hibino T, Meng YL, Kawamitsu Y, Uehara N, Matsuda N, Tanaka Y, Ishikawa H, Baba S, Takabe T, Wada K, Ishii T, Takabe T. Molecular cloning and functional characterization of two kinds of betaine-aldehyde dehydrogenase in betaine-accumulating mangrove Avicennia marina (Forsk.) Vierh. Plant Mol. Biol. 45: 353-363 (2001).

Hicks MG, de Leeuw E, Porcelli I, Buchanan G, Berks BC, Palmer T. The Escherichia coli twin-arginine translocase: conserved residues of TatA and TatB family components involved in protein transport. FEBS Lett. 539: 61-67 (2003).

Hieber AD, Bugos RC, Verhoeven AS, Yamamoto HY. Overexpression of violaxanthin de-epoxidase: properties of C-terminal deletions on activity and pH-dependent lipid binding. Planta 214: 476-483 (2002).

Higo K, Higo H. Cloning and characterization of the rice CatA catalase gene, a homologue of the maize Cat3 gene. Plant Mol. Biol. 30: 505-521 (1996).

Higuchi K, Suzuki K, Nakanishi H, Yamaguchi H, Nishizawa NK, Mori S. Cloning of nicotianamine synthase genes, novel genes involved in the biosynthesis of phytosiderophores. Plant Physiol. 119: 471-480 (1999).

Hill CM, Duggleby RG. Mutagenesis of Escherichia coli acetohydroxyacid synthase isoenzyme II and characterization of three herbicide-insensitive forms. Biochem. J. 335: 653-661 (1998).

Hill CM, Duggleby RG. Purified recombinant Escherichia coli ketol-acid reductoisomerase is unsuitable for use in a coupled assay of acetohydroxyacid synthase activity due to an unexpected side reaction. Protein Expr. Purif. 15: 57-61 (1999).

Hill CM, Pang SS, Duggleby RG. Purification of Escherichia coli acetohydroxyacid synthase isoenzyme II and reconstitution of active enzyme from its individual pure subunits. Biochem. J. 327: 891-898 (1997).

Hillar A, Culham DE, Vernikovska YI, Wood JM, Boggs JM. Formation of an antiparallel, intermolecular coiled coil is associated with in vivo dimerization of osmosensor and osmoprotectant transporter ProP in Escherichia coli. Biochemistry 44: 10170-10180 (2005).

Hillar A, Culham DE, Vernikovska YI, Wood JM, Boggs JM. Formation of an antiparallel, intermolecular coiled coil is associated with in vivo dimerization of osmosensor and osmoprotectant transporter ProP in Escherichia coli. Biochemistry 44: 15636 (2005).

Hiltonen T, Bjorkbacka H, Forsman C, Clarke AK, Samuelsson G. Intracellular beta-carbonic anhydrase of the unicellular green alga Coccomyxa. Cloning of the cDNA and characterization of the functional enzyme overexpressed in Escherichia coli. Plant Physiol. 117: 1341-1349 (1998).

Hinchman SK, Henikoff S, Schuster SM. A relationship between asparagine synthetase A and aspartyl tRNA synthetase. J. Biol. Chem. 267: 144-149 (1992).

Hinchman SK, Schuster SM. Overproduction, preparation of monoclonal antibodies and purification of E. coli asparagine synthetase A. Protein Eng. 5: 279-283 (1992).

Hinshelwood S, Stoker NG. Cloning of mycobacterial histidine synthesis genes by complementation of a Mycobacterium smegmatis auxotroph. Mol. Microbiol. 6: 2887-2895 (1992).

Hiraga K, Yamagishi A, Oshima T. Mapping of unit boundaries of a protein: exhaustive search for permissive sites for duplication by complementation analysis of random fragment libraries of tryptophan synthase alpha subunit. J. Mol. Biol. 335: 1093-1104 (2004).

Hirani TA, Suzuki I, Murata N, Hayashi H, Eaton-Rye JJ. Characterization of a two-component signal transduction system involved in the induction of alkaline phosphatase under phosphate-limiting conditions in Synechocystis sp. PCC 6803. Plant Mol. Biol. 45: 133-144 (2001).

Hirano N, Sawasaki T, Tozawa Y, Endo Y, Takai K. Tolerance for random recombination of domains in prokaryotic and eukaryotic translation systems: limited interdomain misfolding in a eukaryotic translation system. Proteins 64: 343-354 (2006).

Hirasawa T, Wachi M, Nagai K. A mutation in the Corynebacterium glutamicum itsA gene causes susceptibility to lysozyme, temperature-sensitive growth, and L-glutamate production. J. Bacteriol. 182: 2696-2701 (2000).

Hirayama T, Ohto C, Mizoguchi T, Shinozaki K. A gene encoding a phosphatidylinositol-specific phospholipase C is induced by dehydration and salt stress in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A. 92: 3903-3907 (1995).

Hirner AA, Seitz HU. Isoforms of chalcone synthase in Daucus carota L. and their differential expression in organs from the European wild carrot and in ultraviolet-A-irradiated cell cultures. Planta 210: 993-998 (2000).

Hirotani M, Kuroda R, Suzuki H, Yoshikawa T. Cloning and expression of UDP-glucose:flavonoid 7-O-glucosyltransferase from hairy root cultures of Scutellaria baicalensis. Planta 210: 1006-1013 (2000).

Hirschberg J. Carotenoid biosynthesis in flowering plants. Curr. Opin. Plant Biol. 4: 210-218 (2001).

Hmida-Sayari A, Gargouri-Bouzid R, Bidani A, Jaoua L, Savoure A, Jaoua S. Overexpression of Delta(1)-pyrroline-5-carboxylate synthetase increases proline production and confers salt tolerance in transgenic potato plants. Plant Sci. 169: 746-752 (2005).

Ho CL, Noji M, Saito K. Plastidic pathway of serine biosynthesis. Molecular cloning and expression of 3-phosphoserine phosphatase from Arabidopsis thaliana. J. Biol. Chem. 274: 11007-11012 (1999).

Ho CL, Noji M, Saito M, Saito K. Regulation of serine biosynthesis in Arabidopsis. Crucial role of plastidic 3-phosphoglycerate dehydrogenase in non-photosynthetic tissues. J. Biol. Chem. 274: 397-402 (1999).

Ho CL, Saito K. Molecular biology of the plastidic phosphorylated serine biosynthetic pathway in Arabidopsis thaliana. Amino Acids 20: 243-259 (2001).

Hoang TT, Schweizer HP. Identification and genetic characterization of the Pseudomonas aeruginosa leuB gene encoding 3-isopropylmalate dehydrogenase. Mol. Gen. Genet. 254: 166-170 (1997).

Hoang TT, Williams S, Schweizer HP, Lam JS. Molecular genetic analysis of the region containing the essential Pseudomonas aeruginosa asd gene encoding aspartate-beta-semialdehyde dehydrogenase. Microbiology 143: 899-907 (1997).

Hochuli M, Szyperski T, Wuthrich K. Deuterium isotope effects on the central carbon metabolism of Escherichia coli cells grown on a D2O-containing minimal medium. J. Biomol. NMR 17: 33-42 (2000).

Hocker B, Beismann-Driemeyer S, Hettwer S, Lustig A, Sterner R. Dissection of a (beta alpha)(8)-barrel enzyme into two folded halves. Nat. Struct. Biol. 8: 32-36 (2001).

Hoelscher DJ, Williams DC, Wildung MR, Croteau R. A cDNA clone for 3-carene synthase from Salvia stenophylla( small star, filled ). Phytochemistry 62: 1081-1086 (2003).

Hoff T, Schnorr KM, Meyer C, Caboche M. Isolation of two Arabidopsis cDNAs involved in early steps of molybdenum cofactor biosynthesis by functional complementation of Escherichia coli mutants. J. Biol. Chem. 270: 6100-6107 (1995).

Hohn MJ, Park HS, O'donoghue P, Schnitzbauer M, Soll D. Emergence of the universal genetic code imprinted in an RNA record. Proc. Natl. Acad. Sci. U.S.A. 103: 18095-18100 (2006).

Holden C. CELL BIOLOGY: Alliance launched to model E. coli. Science 297: 1459-1460 (2002).

Holms H. Flux analysis: a basic tool of microbial physiology. Adv. Microb. Physiol. 45: 271-340 (2001).

Holms H. Flux analysis and control of the central metabolic pathways in Escherichia coli. FEMS Microbiol. Rev. 19: 85-116 (1996).

Holmstrom KO, Somersalo S, Mandal A, Palva TE, Welin B. Improved tolerance to salinity and low temperature in transgenic tobacco producing glycine betaine. J. Exp. Bot. 51: 177-185 (2000).

Holmstrom KO, Welin B, Mandal A, Kristiansdottir I, Teeri TH, Lamark T, Strom AR, Palva ET. Production of the Escherichia coli betaine-aldehyde dehydrogenase, an enzyme required for the synthesis of the osmoprotectant glycine betaine, in transgenic plants. Plant J. 6: 749-758 (1994).

Holtmann G, Bremer E. Thermoprotection of Bacillus subtilis by exogenously provided glycine betaine and structurally related compatible solutes: Involvement of Opu transporters. J. Bacteriol. 186: 1683-1693 (2004).

Hong MC, Wu ML, Chang MC. Cloning and complete nucleotide sequence of Acinetobacter radioresistens CMC-1 AglyA gene encoding serine hydroxymethyltransferase. FEMS Microbiol. Lett. 170: 413-418 (1999).

Hong NN, Yang G, Li J, Zhang YP, Li JL. Rapid determination of L-glutamine using engineered Escherichia coli overexpressing glutamine synthetase. Appl. Biochem. Biotechnol. 158: 398-407 (2009).

Hong SH, Lee SY. Metabolic flux distribution in a metabolically engineered Escherichia coli strain producing succinic acid. J. Microbiol. Biotechnol. 10: 496-501 (2000).

Hong SH, Lee SY. Metabolic flux analysis for succinic acid production by recombinant Escherichia coli with amplified malic enzyme activity. Biotechnol. Bioeng. 74: 89-95 (2001).

Hong SH, Park SJ, Moon SY, Park JP, Lee SY. In silico prediction and validation of the importance of the Entner-Doudoroff pathway in poly(3-hydroxybutyrate) production by metabolically engineered Escherichia coli. Biotechnol. Bioeng. 83: 854-863 (2003).

Hoover DM, Jarrett JT, Sands RH, Dunham WR, Ludwig ML, Matthews RG. Interaction of Escherichia coli cobalamin-dependent methionine synthase and its physiological partner flavodoxin: binding of flavodoxin leads to axial ligand dissociation from the cobalamin cofactor. Biochemistry 36: 127-138 (1997).

Hopkins L, Parmar S, Blaszczyk A, Hesse H, Hoefgen R, Hawkesford MJ. O-Acetylserine and the regulation of expression of genes encoding components for sulfate uptake and assimilation in potato. Plant Physiol. 138: 433-440 (2005).

Hopkins S, Schirch V. Properties of a serine hydroxymethyltransferase in which an active site histidine has been changed to an asparagine by site-directed mutagenesis. J. Biol. Chem. 261: 3363-3369 (1986).

Hopkins S, Schirch V. Properties of a serine hydroxymethyltransferase in which an active site histidine has been changed to an asparagine by site-directed mutagenesis. J. Biol. Chem. 261: 3363-3369 (1986).

Horlacher R, Boos W. Characterization of TreR, the major regulator of the Escherichia coli trehalose system. J. Biol. Chem. 272: 13026-13032 (1997).

Horlacher R, Peist R, Boos W. Improved method for the preparative synthesis of labeled trehalose of high specific activity by Escherichia coli. Appl. Environ. Microbiol. 62: 3861-3863 (1996).

Horlacher R, Uhland K, Klein W, Ehrmann M, Boos W. Characterization of a cytoplasmic trehalase of Escherichia coli. J. Bacteriol. 178: 6250-6257 (1996).

Horling F, Lamkemeyer P, Konig J, Finkemeier I, Kandlbinder A, Baier M, Dietz KJ. Divergent light-, ascorbate-, and oxidative stress-dependent regulation of expression of the peroxiredoxin gene family in Arabidopsis. Plant Physiol. 131: 317-325 (2003).

Horn C, Bremer E, Schmitt L. Nucleotide dependent monomer/dimer equilibrium of OpuAA, the nucleotide- binding protein of the osmotically regulated ABC transporter OpuA from Bacillus subtilis. J. Mol. Biol. 334: 403-419 (2003).

Horvath MM, Grishin NV. The C-terminal domain of HPII catalase is a member of the type I glutamine amidotransferase superfamily. Proteins 42: 230-236 (2001).

Hoshino T, Kosuge T, Hidaka Y, Tabata K, Nakahara T. Molecular cloning and sequence analysis of the proC gene encoding delta 1-pyrroline-5-carboxylate reductase from an extremely thermophilic eubacterium Thermus thermophilus. Biochem. Biophys. Res. Commun. 199: 410-417 (1994).

Hosted TJ, Rochefort DA, Benson DR. Close linkage of genes encoding glutamine synthetases I and II in Frankia alni CpI1. J. Bacteriol. 175: 3679-3684 (1993).

Houben E, de Gier JW, van Wijk KJ. Insertion of leader peptidase into the thylakoid membrane during synthesis in a chloroplast translation system. Plant Cell 11: 1553-1564 (1999).

Houde M, Dhindsa RS, Sarhan F. A molecular marker to select for freezing tolerance in Gramineae. Mol. Gen. Genet. 234: 43-48 (1992).

Houssin C, Eynard N, Shechter E, Ghazi A. Effect of osmotic pressure on membrane energy-linked functions in Escherichia coli. Biochim. Biophys. Acta 1056: 76-84 (1991).

Howe GA, Lee GI, Itoh A, Li L, DeRocher AE. Cytochrome P450-dependent metabolism of oxylipins in tomato. Cloning and expression of allene oxide synthase and fatty acid hydroperoxide lyase. Plant Physiol. 123: 711-724 (2000).

Howell DM, Graupner M, Xu H, White RH. Identification of enzymes homologous to isocitrate dehydrogenase that are involved in coenzyme B and leucine biosynthesis in methanoarchaea. J. Bacteriol. 182: 5013-5016 (2000).

Hsieh MH, Goodman HM. The Arabidopsis IspH homolog is involved in the plastid nonmevalonate pathway of isoprenoid biosynthesis. Plant Physiol. 138: 641-653 (2005).

Hsieh MH, Goodman HM. Functional evidence for the involvement of Arabidopsis IspF homolog in the nonmevalonate pathway of plastid isoprenoid biosynthesis. Planta 223: 779-784 (2006).

Hsieh MH, Lam HM, van de Loo FJ, Coruzzi G. A PII-like protein in Arabidopsis: putative role in nitrogen sensing. Proc. Natl. Acad. Sci. U.S.A. 95: 13965-13970 (1998).

Hsing YC, Tsou CH, Hsu TF, Chen ZY, Hsieh KL, Hsieh JS, Chow TY. Tissue- and stage-specific expression of a soybean (Glycine max L.) seed-maturation, biotinylated protein. Plant Mol. Biol. 38: 481-490 (1998).

Hu CA, Delauney AJ, Verma DP. A bifunctional enzyme (delta 1-pyrroline-5-carboxylate synthetase) catalyzes the first two steps in proline biosynthesis in plants. Proc. Natl. Acad. Sci. U.S.A. 89: 9354-9358 (1992).

Hu CA, Lin WW, Valle D. Cloning, characterization, and expression of cDNAs encoding human delta 1-pyrroline-5-carboxylate dehydrogenase. J. Biol. Chem. 271: 9795-9800 (1996).

Hu L, Lu H, Liu Q, Chen X, Jiang X. Overexpression of mtlD gene in transgenic Populus tomentosa improves salt tolerance through accumulation of mannitol. Tree Physiol. 25: 1273-1281 (2005).

Hu LA, King SC. Identification of the amine-polyamine-choline transporter superfamily 'consensus amphipathic region' as the target for inactivation of the Escherichia coli GABA transporter GabP by thiol modification reagents. Biochem. J. 339: 649-655 (1999).

Hu WJ, Kawaoka A, Tsai CJ, Lung J, Osakabe K, Ebinuma H, Chiang VL. Compartmentalized expression of two structurally and functionally distinct 4-coumarate:CoA ligase genes in aspen (Populus tremuloides). Proc. Natl. Acad. Sci. U.S.A. 95: 5407-5412 (1998).

Hu X, Reddy AS. Cloning and expression of a PR5-like protein from Arabidopsis: inhibition of fungal growth by bacterially expressed protein. Plant Mol. Biol. 34: 949-959 (1997).

Hua Q, Joyce AR, Fong SS, Palsson BO. Metabolic analysis of adaptive evolution for in silico designed lactate-producing strains. Biotechnol. Bioeng. 95: 992-1002 (2006).

Hua Q, Yang C, Oshima T, Mori H, Shimizu K. Analysis of gene expression in Escherichia coli in response to changes of growth-limiting nutrient in chemostat cultures. Appl. Environ. Microbiol. 70: 2354-2366 (2004).

Huang DJ, Chen HJ, Hou WC, Chen TE, Hsu WY, Lin YH. Expression and function of a cysteine proteinase cDNA from sweet potato (Ipomoea batatas [L.] Lam 'Tainong 57') storage roots. Plant Sci. 169: 423-431 (2005).

Huang FC, Horvath G, Molnar P, Turcsi E, Deli J, Schrader J, Sandmann G, Schmidt H, Schwab W. Substrate promiscuity of RdCCD1, a carotenoid cleavage oxygenase from Rosa damascena. Phytochemistry 70: 457-464 (2009).

Huang KJ, Hseu TH. Effects of lysine-sensitive aspartokinase III on lysine biosynthesis in Escherichia coli K-12. Proc. Natl. Sci. Counc. Repub. China. B. 17: 91-97 (1993).

Huang KX, Huang QL, Wildung MR, Croteau R, Scott AI. Overproduction, in Escherichia coli, of soluble taxadiene synthase, a key enzyme in the Taxol biosynthetic pathway. Protein Expr. Purif. 13: 90-96 (1998).

Huang SC, Panagiotidis CA, Canellakis ES. Transcriptional effects of polyamines on ribosomal proteins and on polyamine-synthesizing enzymes in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 87: 3464-3468 (1990).

Huang T, Duman JG. Cloning and characterization of a thermal hysteresis (antifreeze) protein with DNA-binding activity from winter bittersweet nightshade, Solanum dulcamara. Plant Mol. Biol. 48: 339-350 (2002).

Huang TC, Huang YW, Hung HJ, Ho CT, Wu ML. Delta1-pyrroline-5-carboxylic acid formed by proline dehydrogenase from the Bacillus subtilis ssp natto expressed in Escherichia coli as a precursor for 2-acetyl-1-pyrroline. J. Agric. Food Chem. 55: 5097-5102 (2007).

Huang W, Jia J, Edwards P, Dehesh K, Schneider G, Lindqvist Y. Crystal structure of beta-ketoacyl-acyl carrier protein synthase II from E.coli reveals the molecular architecture of condensing enzymes. EMBO J. 17: 1183-1191 (1998).

Huang X, Raushel FM. Role of the hinge loop linking the N- and C-terminal domains of the amidotransferase subunit of carbamoyl phosphate synthetase. Arch. Biochem. Biophys. 380: 174-180 (2000).

Huang X, Raushel FM. An engineered blockage within the ammonia tunnel of carbamoyl phosphate synthetase prevents the use of glutamine as a substrate but not ammonia. Biochemistry 39: 3240-3247 (2000).

Huang X, Raushel FM. Deconstruction of the catalytic array within the amidotransferase subunit of carbamoyl phosphate synthetase. Biochemistry 38: 15909-15914 (1999).

Huang X, Raushel FM. Restricted passage of reaction intermediates through the ammonia tunnel of carbamoyl phosphate synthetase. J. Biol. Chem. 275: 26233-26240 (2000).

Huang Y, Baxter R, Smith BS, Partch CL, Colbert CL, Deisenhofer J. Crystal structure of cryptochrome 3 from Arabidopsis thaliana and its implications for photolyase activity. Proc. Natl. Acad. Sci. U.S.A. 103: 17701-17706 (2006).

Huang Y, Lemieux MJ, Song J, Auer M, Wang DN. Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli. Science 301: 616-620 (2003).

Hudson AO, Singh BK, Leustek T, Gilvarg C. An L,L-diaminopimelate aminotransferase defines a novel variant of the lysine biosynthesis pathway in plants. Plant Physiol. 140: 292-301 (2006).

Hughes CA, Beard HS, Matthews BF. Molecular cloning and expression of two cDNAs encoding asparagine synthetase in soybean. Plant Mol. Biol. 33: 301-311 (1997).

Hughes CA, Gebhardt JS, Reuss A, Matthews BF. Identification and expression of a cDNA encoding cystathionine gamma-synthase in soybean. Plant Sci. 146: 69-79 (1999).

Hugo AA, De Antoni GL, Perez PF. Lactobacillus delbrueckii subsp lactis strain CIDCA 133 inhibits nitrate reductase activity of Escherichia coli. Int. J. Food Microbiol. 111: 191-196 (2006).

Hunter BK, Nicholls KM, Sanders JK. Formaldehyde metabolism by Escherichia coli. In vivo carbon, deuterium, and two-dimensional NMR observations of multiple detoxifying pathways. Biochemistry 23: 508-514 (1984).

Hunter BK, Nicholls KM, Sanders JK. Formaldehyde metabolism by Escherichia coli. Carbon and solvent deuterium incorporation into glycerol, 1,2-propanediol, and 1,3-propanediol. Biochemistry 24: 4148-4155 (1985).

Hunter DA, Dong Yoo S, Butcher SM, McManus MT. Expression of 1-aminocyclopropane-1-carboxylate oxidase during leaf ontogeny in white clover. Plant Physiol. 120: 131-142 (1999).

Hunter T, Bannister JV, Hunter GJ. Thermostability of manganese- and iron-superoxide dismutases from Escherichia coli is determined by the characteristic position of a glutamine residue. Eur. J. Biochem. 269: 5137-5148 (2002).

Huo X, Viola RE. Functional group characterization of homoserine kinase from Escherichia coli. Arch. Biochem. Biophys. 330: 373-379 (1996).

Huo X, Viola RE. Substrate specificity and identification of functional groups of homoserine kinase from Escherichia coli. Biochemistry 35: 16180-16185 (1996).

Huo YX, Nan BY, You CH, Tian ZX, Kolb A, Wang YP. FIS activates glnAp2 in Escherichia coli: role of a DNA bend centered at -55, upstream of the transcription start site. FEMS Microbiol. Lett. 257: 99-105 (2006).

Hurle MR, Tweedy NB, Matthews CR. Synergism in folding of a double mutant of the alpha subunit of tryptophan synthase. Biochemistry 25: 6356-6360 (1986).

Hurley JH, Chen R, Dean AM. Determinants of cofactor specificity in isocitrate dehydrogenase: structure of an engineered NADP+ --> NAD+ specificity-reversal mutant. Biochemistry 35: 5670-5678 (1996).

Hussain H, Grove J, Griffiths L, Busby S, Cole J. A seven-gene operon essential for formate-dependent nitrite reduction to ammonia by enteric bacteria. Mol. Microbiol. 12: 153-163 (1994).

Hussain H, Mant A, Seale R, Zeeman S, Hinchliffe E, Edwards A, Hylton C, Bornemann S, Smith AM, Martin C, Bustos R. Three isoforms of isoamylase contribute different catalytic properties for the debranching of potato glucans. Plant Cell 15: 133-149 (2003).

Hutson SM, Bledsoe RK, Hall TR, Dawson PA. Cloning and expression of the mammalian cytosolic branched chain aminotransferase isoenzyme. J. Biol. Chem. 270: 30344-30352 (1995).

Huxtable S, Zhou H, Wong S, Li N. Renaturation of 1-aminocyclopropane-1-carboxylate synthase expressed in Escherichia coli in the form of inclusion bodies into a dimeric and catalytically active enzyme. Protein Expr. Purif. 12: 305-314 (1998).

Huynh QK. Inactivation of 5-enolpyruvylshikimate 3-phosphate synthase by its substrate analogue pyruvate in the presence of sodium cyanoborohydride. Biochem. Biophys. Res. Commun. 185: 317-322 (1992).

Huynh QK. Photo-oxidation of 5-enolpyruvoylshikimate-3-phosphate synthase from Escherichia coli: evidence for a reactive imidazole group (His385) at the herbicide glyphosate-binding site. Biochem. J. 290: 525-530 (1993).

Hwang BJ, Kim Y, Kim HB, Hwang HJ, Kim JH, Lee HS. Analysis of Corynebacterium glutamicum methionine biosynthetic pathway: isolation and analysis of metB encoding cystathionine gamma-synthase. Mol. Cells 9: 300-308 (1999).

Hwang BJ, Yeom HJ, Kim Y, Lee HS. Corynebacterium glutamicum utilizes both transsulfuration and direct sulfhydrylation pathways for methionine biosynthesis. J. Bacteriol. 184: 1277-1286 (2002).

Hyde GE, Campbell WH. High-level expression in Escherichia coli of the catalytically active flavin domain of corn leaf NADH:nitrate reductase and its comparison to human NADH:cytochrome B5 reductase. Biochem. Biophys. Res. Commun. 168: 1285-1291 (1990).

Ibarra RU, Edwards JS, Palsson BO. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420: 186-189 (2002).

Ibdah M, Azulay Y, Portnoy V, Wasserman B, Bar E, Meir A, Burger Y, Hirschberg J, Schaffer AA, Katzir N, Tadmor Y, Lewinsohn E. Functional characterization of CmCCD1, a carotenoid cleavage dioxygenase from melon. Phytochemistry 67: 1579-1589 (2006).

Ibdah M, Bar-Ilan A, Livnah O, Schloss JV, Barak Z, Chipman DM. Homology modeling of the structure of bacterial acetohydroxy acid synthase and examination of the active site by site-directed mutagenesis. Biochemistry 35: 16282-16291 (1996).

Ibdah M, Chen YT, Wilkerson CG, Pichersky E. An aldehyde oxidase in developing seeds of Arabidopsis converts benzaldehyde to benzoic acid. Plant Physiol. 150: 416-423 (2009).

Igamberdiev AU, Bykova NV, Hill RD. Nitric oxide scavenging by barley hemoglobin is facilitated by a monodehydroascorbate reductase-mediated ascorbate reduction of methemoglobin. Planta 223: 1033-1040 (2006).

Igamberdiev AU, Seregelyes C, Manac'h N, Hill RD. NADH-dependent metabolism of nitric oxide in alfalfa root cultures expressing barley hemoglobin. Planta 219: 95-102 (2004).

Iglesias AA, Charng YY, Ball S, Preiss J. Characterization of the kinetic, regulatory, and structural properties of ADP-glucose pyrophosphorylase from Chlamydomonas reinhardtii. Plant Physiol. 104: 1287-1294 (1994).

Ignatova Z, Gierasch LM. Inhibition of protein aggregation in vitro and in vivo by a natural osmoprotectant. Proc. Natl. Acad. Sci. U.S.A. 103: 13357-13361 (2006).

Igo MM, Ninfa AJ, Silhavy TJ. A bacterial environmental sensor that functions as a protein kinase and stimulates transcriptional activation. Genes Dev. 3: 598-605 (1989).

Igoshin OA, Goldbeter A, Kaiser D, Oster G. A biochemical oscillator explains several aspects of Myxococcus xanthus behavior during development. Proc. Natl. Acad. Sci. U.S.A. 101: 15760-15765 (2004).

Iijima Y, Davidovich-Rikanati R, Fridman E, Gang DR, Bar E, Lewinsohn E, Pichersky E. The biochemical and molecular basis for the divergent patterns in the biosynthesis of terpenes and phenylpropenes in the peltate glands of three cultivars of basil. Plant Physiol. 136: 3724-3736 (2004).

Iijima Y, Gang DR, Fridman E, Lewinsohn E, Pichersky E. Characterization of geraniol synthase from the peltate glands of sweet basil. Plant Physiol. 134: 370-379 (2004).

Ikai H, Yamamoto S. Two genes involved in the 1,3-diaminopropane production pathway in Haemophilus influenzae. Biol. Pharm. Bull. 21: 170-173 (1998).

Ikai H, Yamamoto S. Identification and analysis of a gene encoding L-2,4-diaminobutyrate:2-ketoglutarate 4-aminotransferase involved in the 1,3-diaminopropane production pathway in Acinetobacter baumannii. J. Bacteriol. 179: 5118-5125 (1997).

Ikeda Y, Koizumi N, Kusano T, Sano H. Sucrose and cytokinin modulation of WPK4, a gene encoding a SNF1-related protein kinase from wheat. Plant Physiol. 121: 813-820 (1999).

Ilbert M, Mejean V, Giudici-Orticoni MT, Samama JP, Iobbi-Nivol C. Involvement of a mate chaperone (TorD) in the maturation pathway of molybdoenzyme TorA. J. Biol. Chem. 278: 28787-28792 (2003).

Imamura A, Hanaki N, Umeda H, Nakamura A, Suzuki T, Ueguchi C, Mizuno T. Response regulators implicated in His-to-Asp phosphotransfer signaling in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 95: 2691-2696 (1998).

Imielinski M, Belta C, Rubin H, Halasz A. Systematic analysis of conservation relations in Escherichia coli genome-scale metabolic network reveals novel growth media. Biophys. J. 90: 2659-2672 (2006).

Imsande J. Iron-sulfur clusters: Formation, perturbation, and physiological functions. Plant Physiol. Biochem. 37: 87-97 (1999).

In O, Berberich T, Romdhane S, Feierabend J. Changes in gene expression during dehardening of cold-hardened winter rye (Secale cereale L.) leaves and potential role of a peptide methionine sulfoxide reductase in cold-acclimation. Planta 220: 941-950 (2005).

Incharoensakdi A, Hibino T, Takabe T. Glu 103 gln site-directed mutation causes an alteration in physical properties of spinach betaine aldehyde dehydrogenase. J. Biochem. Mol. Biol. Biophys. 6: 243-248 (2002).

Incharoensakdi A, Matsuda N, Hibino T, Meng YL, Ishikawa H, Hara A, Funaguma T, Takabe T, Takabe T. Overproduction of spinach betaine aldehyde dehydrogenase in Escherichia coli. Structural and functional properties of wild-type, mutants and E. coli enzymes. Eur. J. Biochem. 267: 7015-7023 (2000).

Ingram LO, Gomez PF, Lai X, Moniruzzaman M, Wood BE, Yomano LP, York SW. Metabolic engineering of bacteria for ethanol production. Biotechnol. Bioeng. 58: 204-214 (1998).

Inoue H, Inagaki K, Sugimoto M, Esaki N, Soda K, Tanaka H. Structural analysis of the L-methionine gamma-lyase gene from Pseudomonas putida. J. Biochem. (Tokyo) 117: 1120-1125 (1995).

Inoue K, Kuramitsu S, Aki K, Watanabe Y, Takagi T, Nishigai M, Ikai A, Kagamiyama H. Branched-chain amino acid aminotransferase of Escherichia coli: overproduction and properties. J. Biochem. (Tokyo) 104: 777-784 (1988).

Inoue K, Kuramitsu S, Okamoto A, Hirotsu K, Higuchi T, Morino Y, Kagamiyama H. Tyr225 in aspartate aminotransferase: contribution of the hydrogen bond between Tyr225 and coenzyme to the catalytic reaction. J. Biochem. (Tokyo) 109: 570-576 (1991).

Inoue K, Noji M, Saito K. Determination of the sites required for the allosteric inhibition of serine acetyltransferase by L-cysteine in plants. Eur. J. Biochem. 266: 220-227 (1999).

Inoue K, Sewalt VJ, Murray GB, Ni W, Sturzer C, Dixon RA. Developmental expression and substrate specificities of alfalfa caffeic acid 3-O-methyltransferase and caffeoyl coenzyme A 3-O-methyltransferase in relation to lignification. Plant Physiol. 117: 761-770 (1998).

Iobbi-Nivol C, Santini CL, Blasco F, Giordano G. Purification and further characterization of the second nitrate reductase of Escherichia coli K12. Eur. J. Biochem. 188: 679-687 (1990).

Isaacson T, Ohad I, Beyer P, Hirschberg J. Analysis in vitro of the enzyme CRTISO establishes a poly-cis-carotenoid biosynthesis pathway in plants. Plant Physiol. 136: 4246-4255 (2004).

Isayenkova J, Wray V, Nimtz M, Strack D, Vogt T. Cloning and functional characterisation of two regioselective flavonoid glucosyltransferases from Beta vulgaris. Phytochemistry 67: 1598-1612 (2006).

Ishida H, Anzawa D, Kokubun N, Makino A, Mae T. Direct evidence for non-enzymatic fragmentation of chloroplastic glutamine synthetase by a reactive oxygen species. Plant Cell Environ. 25: 625-631 (2002).

Ishii K, Nakamura S, Morohashi M, Sugimoto M, Ohashi Y, Kikuchi S, Tomita M. Comparison of metabolite production capability indices generated by network analysis methods. Biosystems 91: 166-170 (2008).

Ishikawa K, Gunji Y, Yasueda H, Asano K. Improvement of L-lysine production by Methylophilus methylotrophus from methanol via the Entner-Doudoroff pathway, originating in Escherichia coli. Biosci. Biotechnol. Biochem. 72: 2535-2542 (2008).

Ishikawa T, Yoshimura K, Sakai K, Tamoi M, Takeda T, Shigeoka S. Molecular characterization and physiological role of a glyoxysome-bound ascorbate peroxidase from spinach. Plant Cell Physiol. 39: 23-34 (1998).

Ishino Y, Morgenthaler P, Hottinger H, Soll D. Organization and nucleotide sequence of the glutamine synthetase (glnA) gene from Lactobacillus delbrueckii subsp. bulgaricus. Appl. Environ. Microbiol. 58: 3165-3169 (1992).

Ishitani M, Nakamura T, Han SY, Takabe T. Expression of the betaine aldehyde dehydrogenase gene in barley in response to osmotic stress and abscisic acid. Plant Mol. Biol. 27: 307-315 (1995).

Ishiwata K, Fukuhara N, Shimada M, Makiguchi N, Soda K. Enzymatic production of L-tryptophan from DL-serine and indole by a coupled reaction of tryptophan synthase and amino acid racemase. Biotechnol. Appl. Biochem. 12: 141-149 (1990).

Ishiwatari Y, Honda C, Kawashima I, Nakamura S, Hirano H, Mori S, Fujiwara T, Hayashi H, Chino M. Thioredoxin h is one of the major proteins in rice phloem sap. Planta 195: 456-463 (1995).

Ismail W, El-Said Mohamed M, Wanner BL, Datsenko KA, Eisenreich W, Rohdich F, Bacher A, Fuchs G. Functional genomics by NMR spectroscopy. Phenylacetate catabolism in Escherichia coli. Eur. J. Biochem. 270: 3047-3054 (2003).

Isono K, Niwa Y, Satoh K, Kobayashi H. Evidence for transcriptional regulation of plastid photosynthesis genes in Arabidopsis thaliana roots. Plant Physiol. 114: 623-630 (1997).

Ito M, Baba T, Mori H, Mori H. Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7: 318-327 (2005).

Ito Y, Suzuki M, Husimi Y. A novel mutant of green fluorescent protein with enhanced sensitivity for microanalysis at 488 nm excitation. Biochem. Biophys. Res. Commun. 264: 556-560 (1999).

Itoh N, Matsuda M, Mabuchi M, Dairi T, Wang J. Chiral alcohol production by NADH-dependent phenylacetaldehyde reductase coupled with in situ regeneration of NADH. Eur. J. Biochem. 269: 2394-2402 (2002).

Itoh N, Toda H, Matsuda M, Negishi T, Taniguchi T, Ohsawa N. Involvement of S-adenosylmethionine-dependent halide/thiol methyltransferase (HTMT) in methyl halide emissions from agricultural plants: isolation and characterization of an HTMT-coding gene from Raphanus sativus (daikon radish). BMC Plant Biol. 9: 116 (2009).

Itoh R, Takano H, Ohta N, Miyagishima S, Kuroiwa H, Kuroiwa T. Two ftsH-family genes encoded in the nuclear and chloroplast genomes of the primitive red alga Cyanidioschyzon merolae. Plant Mol. Biol. 41: 321-337 (1999).

Iuchi S, Cameron DC, Lin EC. A second global regulator gene (arcB) mediating repression of enzymes in aerobic pathways of Escherichia coli. J. Bacteriol. 171: 868-873 (1989).

Iuchi S, Cole ST, Lin EC. Multiple regulatory elements for the glpA operon encoding anaerobic glycerol-3-phosphate dehydrogenase and the glpD operon encoding aerobic glycerol-3-phosphate dehydrogenase in Escherichia coli: further characterization of respiratory control. J. Bacteriol. 172: 179-184 (1990).

Iuchi S, Lin EC. arcA (dye), a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways. Proc. Natl. Acad. Sci. U.S.A. 85: 1888-1892 (1988).

Iuchi S, Matsuda Z, Fujiwara T, Lin EC. The arcB gene of Escherichia coli encodes a sensor-regulator protein for anaerobic repression of the arc modulon. Mol. Microbiol. 4: 715-727 (1990).

Iverson TM, Luna-Chavez C, Cecchini G, Rees DC. Structure of the Escherichia coli fumarate reductase respiratory complex. Science 284: 1961-1966 (1999).

Ivey RA 3rd, Subramanian C, Bruce BD. Identification of a Hsp70 recognition domain within the Rubisco small subunit transit peptide. Plant Physiol. 122: 1289-1300 (2000).

Iwatani S, Van Dien S, Shimbo K, Kubota K, Kageyama N, Iwahata D, Miyano H, Hirayama K, Usuda Y, Shimizu K, Matsui K. Determination of metabolic flux changes during fed-batch cultivation from measurements of intracellular amino acids by LC-MS/MS. J. Biotechnol. 128: 93-111 (2007).

Iyer RK, Kim HK, Tsoa RW, Grody WW, Cederbaum SD. Cloning and characterization of human agmatinase. Mol. Genet. Metab. 75: 209-218 (2002).

Izard T. The crystal structures of phosphopantetheine adenylyltransferase with bound substrates reveal the enzyme's catalytic mechanism. J. Mol. Biol. 315: 487-495 (2002).

Izard T, Geerlof A. The crystal structure of a novel bacterial adenylyltransferase reveals half of sites reactivity. EMBO J. 18: 2021-2030 (1999).

Izard T, Geerlof A, Lewendon A, Barker JJ. Cubic crystals of phosphopantetheine adenylyltransferase from Escherichia coli. Acta Crystallogr. D. Biol. Crystallogr. 55: 1226-1228 (1999).

Jackowski S, Rock CO. Metabolism of 4'-phosphopantetheine in Escherichia coli. J. Bacteriol. 158: 115-120 (1984).

Jackowski S, Rock CO. Regulation of coenzyme A biosynthesis. J. Bacteriol. 148: 926-932 (1981).

Jackowski S, Rock CO. Consequences of reduced intracellular coenzyme A content in Escherichia coli. J. Bacteriol. 166: 866-871 (1986).

Jackowski S, Rock CO. Ratio of active to inactive forms of acyl carrier protein in Escherichia coli. J. Biol. Chem. 258: 15186-15191 (1983).

Jackson RH, Cole JA, Cornish-Bowden A. The steady-state kinetics of the NADH-dependent nitrite reductase from Escherichia coli K 12. Nitrite and hydroxylamine reduction. Biochem. J. 199: 171-178 (1981).

Jackson RH, Cole JA, Cornish-Bowden A. The steady state kinetics of the NADH-dependent nitrite reductase from Escherichia coli K12. The reduction of single-electron acceptors. Biochem. J. 203: 505-510 (1982).

Jacobs JM, Jacobs NJ. Porphyrin accumulation and export by isolated barley (Hordeum vulgare) plastids. Effect of diphenyl ether herbicides. Plant Physiol. 101: 1181-1187 (1993).

Jacquot JP, Rivera-Madrid R, Marinho P, Kollarova M, Le Marechal P, Miginiac-Maslow M, Meyer Y. Arabidopsis thaliana NAPHP thioredoxin reductase. cDNA characterization and expression of the recombinant protein in Escherichia coli. J. Mol. Biol. 235: 1357-1363 (1994).

Jadaho SB, Yang RZ, Lin Q, Hu H, Anania FA, Shuldiner AR, Gong DW. Murine alanine aminotransferase: cDNA cloning, functional expression, and differential gene regulation in mouse fatty liver. Hepatology 39: 1297-1302 (2004).

Jagath-Reddy J, Ganesan K, Savithri HS, Datta A, Rao NA. cDNA cloning, overexpression in Escherichia coli, purification and characterization of sheep liver cytosolic serine hydroxymethyltransferase. Eur. J. Biochem. 230: 533-537 (1995).

Jaggi R, van Heeswijk WC, Westerhoff HV, Ollis DL, Vasudevan SG. The two opposing activities of adenylyl transferase reside in distinct homologous domains, with intramolecular signal transduction. EMBO J. 16: 5562-5571 (1997).

Jaggi R, Ybarlucea W, Cheah E, Carr PD, Edwards KJ, Ollis DL, Vasudevan SG. The role of the T-loop of the signal transducing protein PII from Escherichia coli. FEBS Lett. 391: 223-228 (1996).

Jagusztyn-Krynicka EK, Malaszewska-Keough A, Kauc B. Cloning and expression of Thiobacillus versutus aspartate-semialdehyde dehydrogenase gene in Escherichia coli. FEMS Microbiol. Lett. 50: 21-25 (1989).

Jagusztyn-Krynicka EK, Smorawinska M, Curtiss R 3d. Expression of Streptococcus mutans aspartate-semialdehyde dehydrogenase gene cloned into plasmid pBR322. J. Gen. Microbiol. 128: 1135-1145 (1982).

Jain A, Ziegler J, Liscombe DK, Facchini PJ, Tucker PA, Panjikar S. Purification, crystallization and X-ray diffraction analysis of pavine N-methyltransferase from Thalictrum flavum. Acta Crystallogr. Sect. F. Struct. Biol. Cryst. Commun. 64: 1066-1069 (2008).

Jaindl M, Popp M. Cyclitols protect glutamine synthetase and malate dehydrogenase against heat induced deactivation and thermal denaturation. Biochem. Biophys. Res. Commun. 345: 761-765 (2006).

Jakab G, Manrique A, Zimmerli L, Metraux JP, Mauch-Mani B. Molecular characterization of a novel lipase-like pathogen-inducible gene family of Arabidopsis. Plant Physiol. 132: 2230-2239 (2003).

Jakoby M, Kramer R, Burkovski A. Nitrogen regulation in Corynebacterium glutamicum: isolation of genes involved and biochemical characterization of corresponding proteins. FEMS Microbiol. Lett. 173: 303-310 (1999).

Jambunathan N, Mahalingam R. Analysis of Arabidopsis growth factor gene 1 (GFG1) encoding a nudix hydrolase during oxidative signaling. Planta 224: 1-11 (2006).

James TY, Boulianne RP, Bottoli APF, Granado JD, Aebi M, Kues U. The pab1 gene of Coprinus cinereus encodes a bifunctional protein for para-aminobenzoic acid (PABA) synthesis: implications for the evolution of fused PABA synthases. J. Basic Microbiol. 42: 91-103 (2002).

Jameson GN, Cosper MM, Hernandez HL, Johnson MK, Huynh BH. Role of the [2Fe-2S] cluster in recombinant Escherichia coli biotin synthase. Biochemistry 43: 2022-2031 (2004).

Jan A, Kitano H, Matsumoto H, Komatsu S. The rice OsGAE1 is a novel gibberellin-regulated gene and involved in rice growth. Plant Mol. Biol. 62: 439-452 (2006).

Janes BK, Bender RA. Alanine catabolism in Klebsiella aerogenes: molecular characterization of the dadAB operon and its regulation by the nitrogen assimilation control protein. J. Bacteriol. 180: 563-570 (1998).

Jang HJ, Pih KT, Kang SG, Lim JH, Jin JB, Piao HL, Hwang I. Molecular cloning of a novel Ca2+-binding protein that is induced by NaCl stress. Plant Mol. Biol. 37: 839-847 (1998).

Jang IC, Oh SJ, Seo JS, Choi WB, Song SI, Kim CH, Kim YS, Seo HS, Choi YD, Nahm BH, Kim JK. Expression of a bifunctional fusion of the Escherichia coli genes for trehalose-6-phosphate synthase and trehalose-6-phosphate phosphatase in transgenic rice plants increases trehalose accumulation and abiotic stress tolerance without stunting growth. Plant Physiol. 131: 516-524 (2003).

Jang S, Imlay JA. Micromolar intracellular hydrogen peroxide disrupts metabolism by damaging iron-sulfur enzymes. J. Biol. Chem. 282: 929-937 (2007).

Janiyani KL, Ray MK. Cloning, sequencing, and expression of the cold-inducible hutU gene from the antarctic psychrotrophic bacterium Pseudomonas syringae. Appl. Environ. Microbiol. 68: 1-10 (2002).

Janosik M, Meier M, Kery V, Oliveriusova J, Burkhard P, Kraus JP. Crystallization and preliminary X-ray diffraction analysis of the active core of human recombinant cystathionine beta-synthase: an enzyme involved in vascular disease. Acta Crystallogr. Sect. D. Biol. Crystallogr. 57: 289-291 (2001).

Janson CA, Kayne PS, Almassy RJ, Grunstein M, Eisenberg D. Sequence of glutamine synthetase from Salmonella typhimurium and implications for the protein structure. Gene 46: 297-300 (1986).

Janssen PJ, Jones DT, Woods DR. Studies on Clostridium acetobutylicum glnA promoters and antisense RNA. Mol. Microbiol. 4: 1575-1583 (1990).

Jarrett JT, Wan JT. Thermal inactivation of reduced ferredoxin (flavodoxin): NADP(+) oxidoreductase from Escherichia coli. FEBS Lett. 529: 237-242 (2002).

Javelle A, Lupo D, Zheng L, Li XD, Winkler FK, Merrick M. An unusual twin-His arrangement in the pore of ammonia channels is essential for substrate conductance. J. Biol. Chem. 281: 39492-39498 (2006).

Javelle A, Severi E, Thornton J, Merrick M. Ammonium sensing in Escherichia coli: role of the ammonium transporter AmtB and AmtB-GlnK complex formation. J. Biol. Chem. 279: 8530-8538 (2004).

Javelle A, Thomas G, Marini AM, Kramer R, Merrick M. In vivo functional characterisation of the Escherichia coli ammonium channel AmtB: evidence for metabolic coupling of AmtB to glutamine synthetase. Biochem. J. 390: 215-222 (2005).

Javid-Majd F, Mullins LS, Raushel FM, Stapleton MA. The differentially conserved residues of carbamoyl-phosphate synthetase. J. Biol. Chem. 275: 5073-5080 (2000).

Jayaraman PS, Cole JA, Busby SJ. Mutational analysis of the nucleotide sequence at the FNR-dependent nirB promoter in Escherichia coli. Nucleic Acids Res. 17: 135-145 (1989).

Jayaraman PS, Gaston KL, Cole JA, Busby SJ. The nirB promoter of Escherichia coli: location of nucleotide sequences essential for regulation by oxygen, the FNR protein and nitrite. Mol. Microbiol. 2: 527-530 (1988).

Jayaraman PS, Peakman TC, Busby SJ, Quincey RV, Cole JA. Location and sequence of the promoter of the gene for the NADH-dependent nitrite reductase of Escherichia coli and its regulation by oxygen, the Fnr protein and nitrite. J. Mol. Biol. 196: 781-788 (1987).

Jebbar M, Talibart R, Gloux K, Bernard T, Blanco C. Osmoprotection of Escherichia coli by ectoine: uptake and accumulation characteristics. J. Bacteriol. 174: 5027-5035 (1992).

Jeffery CJ, Barry T, Doonan S, Petsko GA, Ringe D. Crystal structure of Saccharomyces cerevisiae cytosolic aspartate aminotransferase. Protein Sci. 7: 1380-1387 (1998).

Jeffery CJ, M Gloss L, A Petsko G, Ringe D. The role of residues outside the active site: structural basis for function of C191 mutants of Escherichia coli aspartate aminotransferase. Protein Eng. 13: 105-112 (2000).

Jeong J, Suh S, Guan C, Tsay YF, Moran N, Oh CJ, An CS, Demchenko KN, Pawlowski K, Lee Y. A nodule-specific dicarboxylate transporter from alder is a member of the peptide transporter family. Plant Physiol. 134: 969-978 (2004).

Jeong MS, Jang SB. Crystallization and X-ray crystallographic studies of wild-type and mutant tryptophan synthase alpha-subunits from Escherichia coli. Mol. Cells 19: 219-222 (2005).

Jeong MS, Jeong JK, Lim WK, Jang SB. Structures of wild-type and P28L/Y173F tryptophan synthase alpha-subunits from Escherichia coli. Biochem. Biophys. Res. Commun. 323: 1257-1264 (2004).

Jeong MS, Jeong JK, Park KS, Kim HT, Lee KM, Lim WK, Jang SB. Crystallization and preliminary X-ray analysis of tryptophan synthase alpha-subunits from Escherichia coli. Acta Crystallogr. D. Biol. Crystallogr. 60: 132-134 (2004).

Jepson BJ, Mohan S, Clarke TA, Gates AJ, Cole JA, Butler CS, Butt JN, Hemmings AM, Richardson DJ. Spectropotentiometric and structural analysis of the periplasmic nitrate reductase from Escherichia coli. J. Biol. Chem. 282: 6425-6437 (2007).

Jewett MC, Calhoun KA, Voloshin A, Wuu JJ, Swartz JR. An integrated cell-free metabolic platform for protein production and synthetic biology. Mol. Syst. Biol. 4: 220 (2008).

Jewett MC, Miller ML, Chen Y, Swartz JR. Continued protein synthesis at low [ATP] and [GTP] enables cell adaptation during energy limitation. J. Bacteriol. 191: 1083-1091 (2009).

Jhee KH, McPhie P, Miles EW. Yeast cystathionine beta-synthase is a pyridoxal phosphate enzyme but, unlike the human enzyme, is not a heme protein. J. Biol. Chem. 275: 11541-11544 (2000).

Jhee KH, Niks D, McPhie P, Dunn MF, Miles EW. The reaction of yeast cystathionine beta-synthase is rate-limited by the conversion of aminoacrylate to cystathionine. Biochemistry 40: 1087-10880 (2001).

Jhee KH, Yoshimura T, Miles EW, Takeda S, Miyahara I, Hirotsu K, Soda K, Kawata Y, Esaki N. Stereochemistry of the transamination reaction catalyzed by aminodeoxychorismate lyase from Escherichia coli: close relationship between fold type and stereochemistry. J. Biochem. (Tokyo) 128: 679-686 (2000).

Jhon DY, Kim K, Byun SM. The sites of cleavage on Escherichia coli glutamine synthetase by dithiothreitol, Fe(III) and O2. Biofactors 3: 121-125 (1991).

Jiang C, Schommer CK, Kim SY, Suh DY. Cloning and characterization of chalcone synthase from the moss, Physcomitrella patens. Phytochemistry 67: 2531-2540 (2006).

Jiang C, Xu J, Zhang H, Zhang X, Shi J, Li M, Ming F. A cytosolic class I small heat shock protein, RcHSP17.8, of Rosa chinensis confers resistance to a variety of stresses to Escherichia coli, yeast and Arabidopsis thaliana. Plant Cell Environ. Apr 22 [Epub ahead of print] (2009).

Jiang H, Dian W, Liu F, Wu P. Molecular cloning and expression analysis of three genes encoding starch synthase II in rice. Planta 218: 1062-1070 (2004).

Jiang P, Atkinson MR, Srisawat C, Sun Q, Ninfa AJ. Functional dissection of the dimerization and enzymatic activities of Escherichia coli nitrogen regulator II and their regulation by the PII protein. Biochemistry 39: 13433-13449 (2000).

Jiang P, Mayo AE, Ninfa AJ. Escherichia coli glutamine synthetase adenylyltransferase (ATase, EC kinetic characterization of regulation by PII, PII-UMP, glutamine, and alpha-ketoglutarate. Biochemistry 46: 4133-4146 (2007).

Jiang P, Ninfa AJ. Regulation of autophosphorylation of Escherichia coli nitrogen regulator II by the PII signal transduction protein. J. Bacteriol. 181: 1906-1911 (1999).

Jiang P, Ninfa AJ. Escherichia coli PII signal transduction protein controlling nitrogen assimilation acts as a sensor of adenylate energy charge in vitro. Biochemistry 46: 12979-12996 (2007).

Jiang P, Ninfa AJ. Reconstitution of Escherichia coli glutamine synthetase adenylyltransferase from N-terminal and C-terminal fragments of the enzyme. Biochemistry 48: 415-423 (2009).

Jiang P, Peliska JA, Ninfa AJ. The regulation of Escherichia coli glutamine synthetase revisited: role of 2-ketoglutarate in the regulation of glutamine synthetase adenylylation state. Biochemistry 37: 12802-12810 (1998).

Jiang P, Peliska JA, Ninfa AJ. Reconstitution of the signal-transduction bicyclic cascade responsible for the regulation of Ntr gene transcription in Escherichia coli. Biochemistry 37: 12795-12801 (1998).

Jiang P, Peliska JA, Ninfa AJ. Asymmetry in the autophosphorylation of the two-component regulatory system transmitter protein nitrogen regulator II of Escherichia coli. Biochemistry 39: 5057-5065 (2000).

Jiang P, Peliska JA, Ninfa AJ. Enzymological characterization of the signal-transducing uridylyltransferase/uridylyl-removing enzyme (EC of Escherichia coli and its interaction with the PII protein. Biochemistry 37: 12782-12794 (1998).

Jiang P, Pioszak AA, Ninfa AJ. Structure-function analysis of glutamine synthetase adenylyltransferase (ATase, EC of Escherichia coli. Biochemistry 46: 4117-4132 (2007).

Jiang P, Zucker P, Atkinson MR, Kamberov ES, Tirasophon W, Chandran P, Schefke BR, Ninfa AJ. Structure/function analysis of the PII signal transduction protein of Escherichia coli: genetic separation of interactions with protein receptors. J. Bacteriol. 179: 4342-4353 (1997).

Jiang P, Zucker P, Ninfa AJ. Probing interactions of the homotrimeric PII signal transduction protein with its receptors by use of PII heterotrimers formed in vitro from wild-type and mutant subunits. J. Bacteriol. 179: 4354-4360 (1997).

Jiang PL, Jauh GY, Wang CS, Tzen JT. A unique caleosin in oil bodies of lily pollen. Plant Cell Physiol. 49: 1390-1395 (2008).

Jiao JA, Podesta FE, Chollet R, OLeary MH, Andreo CS. Isolation and sequence of an active site peptide from maize leaf phosphoenolpyruvate carboxylase inactivated by pyridoxal 5'-phosphate. Biochim. Biophys. Acta 1041: 291-295 (1990).

Jimenez JA, Rodriguez D, Calvo AP, Mortensen LC, Nicolas G, Nicolas C. Expression of a transcription factor (FsERF1) involved in ethylene signalling during the breaking of dormancy in Fagus sylvatica seeds. Physiol. Plant. 125: 373-380 (2005).

Jin L, Stec B, Kantrowitz ER. A cis-proline to alanine mutant of E. coli aspartate transcarbamoylase: kinetic studies and three-dimensional crystal structures. Biochemistry 39: 8058-8066 (2000).

Jin YS, Stephanopoulos G. Multi-dimensional gene target search for improving lycopene biosynthesis in Escherichia coli. Metab. Eng. 9: 337-347 (2007).

Jindaprasert A, Springob K, Schmidt J, De-Eknamkul W, Kutchan TM. Pyrone polyketides synthesized by a type III polyketide synthase from Drosophyllum lusitanicum. Phytochemistry 69: 3043-3053 (2008).

Job V, Molla G, Pilone MS, Pollegioni L. Overexpression of a recombinant wild-type and His-tagged Bacillus subtilis glycine oxidase in Escherichia coli. Eur. J. Biochem. 269: 1456-1463 (2002).

Jobling SA, Schwall GP, Westcott RJ, Sidebottom CM, Debet M, Gidley MJ, Jeffcoat R, Safford R. A minor form of starch branching enzyme in potato (Solanum tuberosum L.) tubers has a major effect on starch structure: cloning and characterisation of multiple forms of SBE A. Plant J. 18: 163-171 (1999).

Jofre A, Molinas M, Pla M. A 10-kDa class-CI sHsp protects E. coli from oxidative and high-temperature stress. Planta 217: 813-819 (2003).

Johansson M, Nordlund S. Purification of P(II) and P(II)-UMP and in vitro studies of regulation of glutamine synthetase in Rhodospirillum rubrum. J. Bacteriol. 181: 6524-6529 (1999).

Johnson ET, Schmidt-Dannert C. Light-energy conversion in engineered microorganisms. Trends Biotechnol. 26: 682-689 (2008).

Johnson JL, Wuebbens MM, Mandell R, Shih VE. Molybdenum cofactor biosynthesis in humans. Identification of two complementation groups of cofactor-deficient patients and preliminary characterization of a diffusible molybdopterin precursor. J. Clin. Invest. 83: 897-903 (1989).

Jonczyk R, Genschel U. Molecular adaptation and allostery in plant pantothenate synthetases. J. Biol. Chem. 281: 37435-37446 (2006).

Jones AL, Gane AM, Herbert D, Willey DL, Rutter AJ, Kille P, Dancer JE, Harwood JL. beta-Ketoacyl-acyl carrier protein synthase III from pea (Pisum sativum L.): properties, inhibition by a novel thiolactomycin analogue and isolation of a cDNA clone encoding the enzyme. Planta 216: 752-761 (2003).

Jones CE, Brook JM, Buck D, Abell C, Smith AG. Cloning and sequencing of the Escherichia coli panB gene, which encodes ketopantoate hydroxymethyltransferase, and overexpression of the enzyme. J. Bacteriol. 175: 2125-2130 (1993).

Jones KL, Kim SW, Keasling JD. Low-copy plasmids can perform as well as or better than high-copy plasmids for metabolic engineering of bacteria. Metab. Eng. 2: 328-338 (2000).

Jones MA, Raymond MJ, Smirnoff N. Analysis of the root-hair morphogenesis transcriptome reveals the molecular identity of six genes with roles in root-hair development in Arabidopsis. Plant J. 45: 83-100 (2006).

Jones PL, Willey DL, Gacesa P, Harwood JL. Isolation, characterisation and expression of a cDNA for pea cholinephosphate cytidylyltransferase. Plant Mol. Biol. 37: 179-185 (1998).

Jongsareejit B, Rahman RN, Fujiwara S, Imanaka T. Gene cloning, sequencing and enzymatic properties of glutamate synthase from the hyperthermophilic archaeon Pyrococcus sp. KOD1. Mol. Gen. Genet. 254: 635-642 (1997).

Jonsson A, Nordlund S. In vitro studies of the uridylylation of the three PII protein paralogs from Rhodospirillum rubrum: the transferase activity of R. rubrum GlnD is regulated by alpha-ketoglutarate and divalent cations but not by glutamine. J. Bacteriol. 189: 3471-3478 (2007).

Jonsson A, Teixeira PF, Nordlund S. The activity of adenylyltransferase in Rhodospirillum rubrum is only affected by alpha-ketoglutarate and unmodified PII proteins, but not by glutamine, in vitro. FEBS J. 274: 2449-2460 (2007).

Jordan A, Reichard P. Ribonucleotide reductases. Annu. Rev. Biochem. 67: 71-98 (1998).

Jormakka M, Byrne B, Iwata S. Formate dehydrogenase - a versatile enzyme in changing environments. Curr. Opin. Struct. Biol. 13: 418-423 (2003).

Joshi S, Singh AR, Kumar A, Misra PC, Siddiqi MI, Saxena JK. Molecular cloning and characterization of Plasmodium falciparum transketolase. Mol. Biochem. Parasitol. 160: 32-41 (2008).

Josse EM, Simkin AJ, Gaffe J, Laboure AM, Kuntz M, Carol P. A plastid terminal oxidase associated with carotenoid desaturation during chromoplast differentiation. Plant Physiol. 123: 1427-1436 (2000).

Jost R, Berkowitz O, Wirtz M, Hopkins L, Hawkesford MJ, Hell R. Genomic and functional characterization of the oas gene family encoding O-acetylserine (thiol) lyases, enzymes catalyzing the final step in cysteine biosynthesis in Arabidopsis thaliana. Gene 253: 237-247 (2000).

Jovanovich SB, Martinell M, Record MT Jr, Burgess RR. Rapid response to osmotic upshift by osmoregulated genes in Escherichia coli and Salmonella typhimurium. J. Bacteriol. 170: 534-539 (1988).

Joyce MA, Fraser ME, James MN, Bridger WA, Wolodko WT. ADP-binding site of Escherichia coli succinyl-CoA synthetase revealed by X-ray crystallography. Biochemistry 39: 17-25 (2000).

Jude DA, Ewart CD, Thain JL, Davies GM, Nichols WW. Transport of the antibacterial agent (6S)-6-fluoroshikimate and other shikimate analogues by the shikimate transport system of Escherichia coli. Biochim. Biophys. Acta 1279: 125-129 (1996).

Jullien M, Baudet S, Rodier F, Le Bras G. Allosteric transition of aspartokinase I-homoserine dehydrogenase I studied by time-resolved fluorescence. Biochimie 70: 1807-1814 (1988).

Jung B, Florchinger M, Kunz HH, Traub M, Wartenberg R, Jeblick W, Neuhaus HE, Mohlmann T. Uridine-ribohydrolase is a key regulator in the uridine degradation pathway of Arabidopsis. Plant Cell 21: 876-891 (2009).

Jung H. The sodium/substrate symporter family: structural and functional features. FEBS Lett. 529: 73-77 (2002).

Jung H, Buchholz M, Clausen J, Nietschke M, Revermann A, Schmid R, Jung K. CaiT of Escherichia coli: a new transporter catalyzing L-carnitine/gamma-butyrobetaine exchange. J. Biol. Chem. 277: 39251-39258 (2002).

Jung H, Jung K, Kleber H-P. L-Carnitine metabolization and osmotic stress response in Escherichia coli. J. Basic Microbiol. 30: 409-413 (1990).

Jung H, Jung K, Kleber HP. L-Carnitine uptake by Escherichia coli. J. Basic Microbiol. 30: 507-514 (1990).

Jung H, Kleber H-P. Metabolism of D(+)-carnitine by Escherichia coli. Appl. Microbiol. Biotechnol. 35: 393-395 (1991).

Jung SI, Han MS, Kwon JH, Cheon CI, Min KH, Lee MS. Cloning of the histidine biosynthetic genes of Corynebacterium glutamicum: organization and sequencing analysis of the hisA, impA, and hisF gene cluster. Biochem. Biophys. Res. Commun. 247: 741-745 (1998).

Justin AM, Kader JC, Collin S. Synthetic capacity of Arabidopsis phosphatidylinositol synthase 1 expressed in Escherichia coli. Biochim. Biophys. Acta 1634: 52-60 (2003).

Justin AM, Kader JC, Collin S. Phosphatidylinositol synthesis and exchange of the inositol head are catalysed by the single phosphatidylinositol synthase 1 from Arabidopsis. Eur. J. Biochem. 269: 2347-2352 (2002).

Justino MC, Vicente JB, Teixeira M, Saraiva LM. New genes implicated in the protection of anaerobically grown Escherichia coli against nitric oxide. J. Biol. Chem. 280: 2636-2643 (2005).

Juty NS, Spence HD, Hotz HR, Tang H, Goryanin I, Hodgman TC. Simultaneous modelling of metabolic, genetic and product-interaction networks. Brief Bioinform. 2: 223-232 (2001).

Kacprzak MM, Lewandowska I, Matthews RG, Paszewski A. Transcriptional regulation of methionine synthase by hornocysteine and choline in Aspergillus nidulans. Biochem. J. 376: 517-524 (2003).

Kaczor CM, Smith MW, Sangwan I, O'Brian MR. Plant delta-aminolevulinic acid dehydratase. Expression in soybean root nodules and evidence for a bacterial lineage of the Alad gene. Plant Physiol. 104: 1411-1417 (1994).

Kaczorowski T, Sektas M, Skowron P, Podhajska AJ. The FokI methyltransferase from Flavobacterium okeanokoites. Purification and characterization of the enzyme and its truncated derivatives. Mol. Biotechnol. 13: 1-15 (1999).

Kadaba NS, Kaiser JT, Johnson E, Lee A, Rees DC. The high-affinity E. coli methionine ABC transporter: structure and allosteric regulation. Science 321: 250-253 (2008).

Kadokura H, Katzen F, Beckwith J. Protein disulfide bond formation in prokaryotes. Annu. Rev. Biochem. 72: 111-135 (2003).

Kafala B, Sasarman A. Isolation of the Staphylococcus aureus hemCDBL gene cluster coding for early steps in heme biosynthesis. Gene 199: 231-239 (1997).

Kakinuma K, Fukushima M, Kawaguchi R. Detection and identification of Escherichia coli, Shigella, and Salmonella by microarrays using the gyrB gene. Biotechnol. Bioeng. 83: 721-728 (2003).

Kalinowski J, Bachmann B, Thierbach G, Puhler A. Aspartokinase genes lysC alpha and lysC beta overlap and are adjacent to the aspartate beta-semialdehyde dehydrogenase gene asd in Corynebacterium glutamicum. Mol. Gen. Genet. 224: 317-324 (1990).

Kalman LV, Gunsalus RP. Nitrate- and molybdenum-independent signal transduction mutations in narX that alter regulation of anaerobic respiratory genes in Escherichia coli. J. Bacteriol. 172: 7049-7056 (1990).

Kaltenbach M, Schroder G, Schmelzer E, Lutz V, Schroder J. Flavonoid hydroxylase from Catharanthus roseus: cDNA, heterologous expression, enzyme properties and cell-type specific expression in plants. Plant J. 19: 183-193 (1999).

Kamarthapu V, Rao KV, Srinivas PN, Reddy GB, Reddy VD. Structural and kinetic properties of Bacillus subtilis S-adenosylmethionine synthetase expressed in Escherichia coli. Biochim. Biophys. Acta 1784: 1949-1958 (2008).

Kamberov ES, Atkinson MR, Chandran P, Ninfa AJ. Effect of mutations in Escherichia coli glnL (ntrB), encoding nitrogen regulator II (NRII or NtrB), on the phosphatase activity involved in bacterial nitrogen regulation. J. Biol. Chem. 269: 28294-28299 (1994).

Kamberov ES, Atkinson MR, Ninfa AJ. The Escherichia coli PII signal transduction protein is activated upon binding 2-ketoglutarate and ATP. J. Biol. Chem. 270: 17797-17807 (1995).

Kamps A, Achebach S, Fedtke I, Unden G, Gotz F. Staphylococcal NreB: an O2-sensing histidine protein kinase with an O-2- labile iron-sulphur cluster of the FNR type. Mol. Microbiol. 52: 713-723 (2004).

Kanao T, Fukui T, Atomi H, Imanaka T. Kinetic and biochemical analyses on the reaction mechanism of a bacterial ATP-citrate lyase. Eur. J. Biochem. 269: 3409-3416 (2002).

Kaneko T, Hashimoto T, Kumpaisal R, Yamada Y. Molecular cloning of wheat dihydrodipicolinate synthase. J. Biol. Chem. 265: 17451-17455 (1990).

Kang HG, Jun SH, Kim J, Kawaide H, Kamiya Y, An G. Cloning and molecular analyses of a gibberellin 20-oxidase gene expressed specifically in developing seeds of watermelon. Plant Physiol. 121: 373-382 (1999).

Kang K, Back K. Production of phenylpropanoid amides in recombinant Escherichia coli. Metab. Eng. 11: 64-68 (2009).

Kang Z, Wang Q, Zhang H, Qi Q. Construction of a stress-induced system in Escherichia coli for efficient polyhydroxyalkanoates production. Appl. Microbiol. Biotechnol. 79: 203-208 (2008).

Kao KC, Tran LM, Liao JC. A global regulatory role of gluconeogenic genes in Escherichia coli revealed by transcriptome network analysis. J. Biol. Chem. 280: 36079-36087 (2005).

Kappler U, Bennett B, Rethmeier J, Schwarz G, Deutzmann R, McEwan AG, Dahl C. Sulfite:cytochrome c oxidoreductase from Thiobacillus novellus: purification, characterization, and molecular biology of a heterodimeric member of the sulfite oxidase family. J. Biol. Chem. 275: 13202-13212 (2000).

Karim S, Lundh D, Holmstrom KO, Mandal A, Pirhonen M. Structural and functional characterization of AtPTR3, a stress-induced peptide transporter of Arabidopsis. J. Mol. Model. 11: 226-236 (2005).

Karita M, Etterbeek ML, Forsyth MH, Tummuru MK, Blaser MJ. Characterization of Helicobacter pylori dapE and construction of a conditionally lethal dapE mutant. Infect. Immun. 65: 4158-4164 (1997).

Karp PD. Pathway databases: a case study in computational symbolic theories. Science 293: 2040-2044 (2001).

Karp PD, Riley M, Paley SM, Pelligrini-Toole A. EcoCyc: an encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res. 24: 32-39 (1996).

Karr DB, Emerich DW. Bradyrhizobium japonicum isocitrate dehydrogenase exhibits calcium-dependent hysteresis. Arch. Biochem. Biophys. 376: 101-108 (2000).

Karsten WE. Dihydrodipicolinate synthase from Escherichia coli: pH dependent changes in the kinetic mechanism and kinetic mechanism of allosteric inhibition by L-lysine. Biochemistry 36: 1730-1739 (1997).

Karsten WE, Hunsley JR, Viola RE. Purification of aspartase and aspartokinase-homoserine dehydrogenase I from Escherichia coli by dye-ligand chromatography. Anal. Biochem. 147: 336-341 (1985).

Karsten WE, Viola RE. Chemical and kinetic mechanisms of aspartate-beta-semialdehyde dehydrogenase from Escherichia coli. Biochim. Biophys. Acta 1077: 209-219 (1991).

Karsten WE, Viola RE. Identification of an essential cysteine in the reaction catalyzed by aspartate-beta-semialdehyde dehydrogenase from Escherichia coli. Biochim. Biophys. Acta 1121: 234-238 (1992).

Kasahara H, Jiao Y, Bedgar DL, Kim SJ, Patten AM, Xia ZQ, Davin LB, Lewis NG. Pinus taeda phenylpropenal double-bond reductase: purification, cDNA cloning, heterologous expression in Escherichia coli, and subcellular localization in P. taeda. Phytochemistry 67: 1765-1780 (2006).

Kasahara M, Swartz TE, Olney MA, Onodera A, Mochizuki N, Fukuzawa H, Asamizu E, Tabata S, Kanegae H, Takano M, Christie JM, Nagatani A, Briggs WR. Photochemical properties of the flavin mononucleotide-binding domains of the phototropins from Arabidopsis, rice, and Chlamydomonas reinhardtii. Plant Physiol. 129: 762-773 (2002).

Kashiwagi A, Sakurai T, Tsuru S, Ying BW, Mori K, Yomo T. Construction of Escherichia coli gene expression level perturbation collection. Metab. Eng. 11: 56-63 (2009).

Kashiwagi K. Polyamine transport in Escherichia coli and eukaryotic cells. Yakugaku Zasshi 116: 175-191 (1996).

Kashiwagi K, Hosokawa N, Furuchi T, Kobayashi H, Sasakawa C, Yoshikawa M, Igarashi K. Isolation of polyamine transport-deficient mutants of Escherichia coli and cloning of the genes for polyamine transport proteins. J. Biol. Chem. 265: 20893-20897 (1990).

Kashiwagi K, Igarashi K. Adjustment of polyamine contents in Escherichia coli. J. Bacteriol. 170: 3131-3135 (1988).

Kashiwagi K, Kobayashi H, Igarashi K. Apparently unidirectional polyamine transport by proton motive force in polyamine-deficient Escherichia coli. J. Bacteriol. 165: 972-977 (1986).

Kast P, Asif-Ullah M, Jiang N, Hilvert D. Exploring the active site of chorismate mutase by combinatorial mutagenesis and selection: the importance of electrostatic catalysis. Proc. Natl. Acad. Sci. U.S.A. 93: 5043-5048 (1996).

Kasunic DA, Kushner SR. Expression of the HIS3 gene of Saccharomyces cerevisiae in polynucleotide phosphorylase-deficient strains of Escherichia coli K-12. Gene 12: 1-10 (1980).

Katinka M, Cossart P, Sibilli L, Saint-Girons I, Chalvignac MA, Le Bras G, Cohen GN, Yaniv M. Nucleotide sequence of the thrA gene of Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 77: 5730-5733 (1980).

Katoh A, Shoji T, Hashimoto T. Molecular cloning of N-methylputrescine oxidase from tobacco. Plant Cell Physiol. 48: 550-554 (2007).

Katoh A, Uenohara K, Akita M, Hashimoto T. Early steps in the biosynthesis of NAD in Arabidopsis start with aspartate and occur in the plastid. Plant Physiol. 141: 851-857 (2006).

Katsuyama Y, Matsuzawa M, Funa N, Horinouchi S. Production of curcuminoids by Escherichia coli carrying an artificial biosynthesis pathway. Microbiology 154: 2620-2628 (2008).

Kawaguchi H, Inagaki K, Tanaka H. Regulatory region of expression of Thiobacillus ferrooxidans leuB gene in Escherichia coli. Biosci. Biotechnol. Biochem. 61: 2119-2121 (1997).

Kawalleck P, Keller H, Hahlbrock K, Scheel D, Somssich IE. A pathogen-responsive gene of parsley encodes tyrosine decarboxylase. J. Biol. Chem. 268: 2189-2194 (1993).

Kawalleck P, Plesch G, Hahlbrock K, Somssich IE. Induction by fungal elicitor of S-adenosyl-L-methionine synthetase and S-adenosyl-L-homocysteine hydrolase mRNAs in cultured cells and leaves of Petroselinum crispum. Proc. Natl. Acad. Sci. U.S.A. 89: 4713-4717 (1992).

Kawashima CG, Berkowitz O, Hell R, Noji M, Saito K. Characterization and expression analysis of a serine acetyltransferase gene family involved in a key step of the sulfur assimilation pathway in Arabidopsis. Plant Physiol. 137: 220-230 (2005).

Kaya-Celiker H, Angardi V, Calik P. Regulatory effects of oxygen transfer on overexpression of recombinant benzaldehyde lyase production by Escherichia coli BL21 (DE3). Biotechnol J. 4: 1066-1076 (2009).

Kayser A, Weber J, Hecht V, Rinas U. Metabolic flux analysis of Escherichia coli in glucose-limited continuous culture. I. Growth-rate-dependent metabolic efficiency at steady state. Microbiology 151: 693-706 (2005).

Keasling JD, Van Dien SJ, Pramanik J. Engineering polyphosphate metabolism in Escherichia coli: implications for bioremediation of inorganic contaminants. Biotechnol. Bioeng. 58: 231-239 (1998).

Keating DH, Carey MR, Cronan JE Jr. The unmodified (apo) form of Escherichia coli acyl carrier protein is a potent inhibitor of cell growth. J. Biol. Chem. 270: 22229-22235 (1995).

Keating DH, Zhang Y, Cronan JE Jr. The apparent coupling between synthesis and posttranslational modification of Escherichia coli acyl carrier protein is due to inhibition of amino acid biosynthesis. J. Bacteriol. 178: 2662-2667 (1996).

Kebeish R, Niessen M, Thiruveedhi K, Bari R, Hirsch HJ, Rosenkranz R, Stabler N, Schonfeld B, Kreuzaler F, Peterhansel C. Chloroplastic photorespiratory bypass increases photosynthesis and biomass production in Arabidopsis thaliana. Nat. Biotechnol. 25: 593-599 (2007).

Keeler SJ, Maloney CL, Webber PY, Patterson C, Hirata LT, Falco SC, Rice JA. Expression of de novo high-lysine alpha-helical coiled-coil proteins may significantly increase the accumulated levels of lysine in mature seeds of transgenic tobacco plants. Plant Mol. Biol. 34: 15-29 (1997).

Keiner R, Kaiser H, Nakajima K, Hashimoto T, Drager B. Molecular cloning, expression and characterization of tropinone reductase II, an enzyme of the SDR family in Solanum tuberosum (L.). Plant Mol. Biol. 48: 299-308 (2002).

Kelly BS, Antholine WE, Griffith OW. Escherichia coli gamma-glutamylcysteine synthetase. Two active site metal ions affect substrate and inhibitor binding. J. Biol. Chem. 277: 50-58 (2002).

Kelo E, Noronkoski T, Stoineva IB, Petkov DD, Mononen I. Beta-aspartylpeptides as substrates of L-asparaginases from Escherichia coli and Erwinia chrysanthemi. FEBS Lett. 528: 130-132 (2002).

Kempf B, Bremer E. OpuA, an osmotically regulated binding protein-dependent transport system for the osmoprotectant glycine betaine in Bacillus subtilis. J. Biol. Chem. 270: 16701-16713 (1995).

Kempf B, Bremer E. Uptake and synthesis of compatible solutes as microbial stress responses to high-osmolality environments. Arch. Microbiol. 170: 319-330 (1998).

Kempf B, Gade J, Bremer E. Lipoprotein from the osmoregulated ABC transport system OpuA of Bacillus subtilis: purification of the glycine betaine binding protein and characterization of a functional lipidless mutant. J. Bacteriol. 179: 6213-6220 (1997).

Keng YF, Viola RE. Specificity of aspartokinase III from Escherichia coli and an examination of important catalytic residues. Arch. Biochem. Biophys. 335: 73-81 (1996).

Kengen SW, van der Oost J, de Vos WM. Molecular characterization of H2O2-forming NADH oxidases from Archaeoglobus fulgidus. Eur. J. Biochem. 270: 2885-2894 (2003).

Kenklies J, Ziehn R, Fritsche K, Pich A, Andreesen JR. Proline biosynthesis from L-ornithine in Clostridium sticklandii: purification of delta1-pyrroline-5-carboxylate reductase, and sequence and expression of the encoding gene, proC. Microbiology 145: 819-826 (1999).

Kerbarh O, Ciulli A, Howard NI, Abell C. Salicylate biosynthesis: overexpression, purification, and characterization of Irp9, a bifunctional salicylate synthase from Yersinia enterocolitica. J. Bacteriol. 187: 5061-5066 (2005).

Kerk D, Bulgrien J, Smith DW, Gribskov M. Arabidopsis proteins containing similarity to the universal stress protein domain of bacteria. Plant Physiol. 131: 1209-1219 (2003).

Kershaw NJ, McNaughton HJ, Hewitson KS, Hernandez H, Griffin J, Hughes C, Greaves P, Barton B, Robinson CV, Schofield CJ. ORF6 from the clavulanic acid gene cluster of Streptomyces clavuligerus has ornithine acetyltransferase activity. Eur. J. Biochem. 269: 2052-2059 (2002).

Kersten B, Feilner T, Kramer A, Wehrmeyer S, Possling A, Witt I, Zanor MI, Stracke R, Lueking A, Kreutzberger J, Lehrach H, Cahilll DJ. Generation of Arabidopsis protein chips for antibody and serum screening. Plant Mol. Biol. 52: 999-1010 (2003).

Keuntje B, Masepohl B, Klipp W. Expression of the putA gene encoding proline dehydrogenase from Rhodobacter capsulatus is independent of NtrC regulation but requires an Lrp-like activator protein. J. Bacteriol. 177: 6432-6439 (1995).

Khan MI, Ito K, Kim H, Ashida H, Ishikawa T, Shibata H, Sawa Y. Molecular properties and enhancement of thermostability by random mutagenesis of glutamate dehydrogenase from Bacillus subtilis. Biosci. Biotechnol. Biochem. 69: 1861-170 (2005).

Khristoforov RR, Sukhareva BS, Dixon HB, Sparkes MJ, Krasnov VP, Bukrina IM. The interaction of glutamate decarboxylase from Escherichia coli with substrate analogues modified at C-3 and C-4. Biochem. Mol. Biol. Int. 36: 77-85 (1995).

Kiefer P, Nicolas C, Letisse F, Portais JC. Determination of carbon labeling distribution of intracellular metabolites from single fragment ions by ion chromatography tandem mass spectrometry. Anal. Biochem. 360: 182-188 (2007).

Kiene RP, Williams LPH. Glycine betaine uptake, retention, and degradation by microorganisms in seawater. Limnol. Oceanog. 43: 1592-1603 (1998).

Kiene RP, Williams LPH, Walker JE. Seawater microorganisms have a high affinity glycine betaine uptake system which also recognizes dimethylsulfoniopropionate. Aquat. Microbial Ecol. 15: 39-51 (1998).

Kikuchi Y, Kojima H, Tanaka T. Mutational analysis of the feedback sites of lysine-sensitive aspartokinase of Escherichia coli. FEMS Microbiol. Lett. 173: 211-215 (1999).

Kikuchi Y, Tsujimoto K, Kurahashi O. Mutational analysis of the feedback sites of phenylalanine-sensitive 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase of Escherichia coli. Appl. Environ. Microbiol. 63: 761-762 (1997).

Kiley PJ, Reznikoff WS. Fnr mutants that activate gene expression in the presence of oxygen. J. Bacteriol. 173: 16-22 (1991).

Kim AD, Graham DE, Seeholzer SH, Markham GD. S-Adenosylmethionine decarboxylase from the archaeon Methanococcus jannaschii: identification of a novel family of pyruvoyl enzymes. J. Bacteriol. 182: 6667-6672 (2000).

Kim BG, Lee Y, Hur HG, Lim Y, Ahn JH. Flavonoid 3'-O-methyltransferase from rice: cDNA cloning, characterization and functional expression. Phytochemistry 67: 387-394 (2006).

Kim CH, Hollocher TC. 13N isotope studies on the pathway of ammonia assimilation in Bacillus megaterium and Escherichia coli. J. Bacteriol. 151: 358-366 (1982).

Kim EJ, Kwak JM, Uozumi N, Schroeder JI. AtKUP1: an Arabidopsis gene encoding high-affinity potassium transport activity. Plant Cell 10: 51-62 (1998).

Kim ES, Choi E, Kim Y, Cho K, Lee A, Shim J, Rakwal R, Agrawal GK, Han O. Dual positional specificity and expression of non-traditional lipoxygenase induced by wounding and methyl jasmonate in maize seedlings. Plant Mol. Biol. 52: 1203-1213 (2003).

Kim HU, van Oostende C, Basset GJ, Browse J. The AAE14 gene encodes the Arabidopsis O-succinylbenzoyl-CoA ligase that is essential for phylloquinone synthesis and photosystem-I function. Plant J. 54: 272-283 (2008).

Kim IH, Kwak SJ, Kang J, Park SC. Transcriptional control of the glnD gene is not dependent on nitrogen availability in Escherichia coli. Mol. Cells 8: 483-490 (1998).

Kim J, Leustek T. Cloning and analysis of the gene for cystathionine gamma-synthase from Arabidopsis thaliana. Plant Mol. Biol. 32: 1117-1124 (1996).

Kim J, Malashkevich V, Roday S, Lisbin M, Schramm VL, Almo SC. Structural and kinetic characterization of Escherichia coli TadA, the wobble-specific tRNA deaminase. Biochemistry 45: 6407-6416 (2006).

Kim JH, Krahn JM, Tomchick DR, Smith JL, Zalkin H. Structure and function of the glutamine phosphoribosylpyrophosphate amidotransferase glutamine site and communication with the phosphoribosylpyrophosphate site. J. Biol. Chem. 271: 15549-15557 (1996).

Kim JJ, Sundin GW. Regulation of the rulAB mutagenic DNA repair operon of Pseudomonas syringae by UV-B (290 to 320 nanometers) radiation and analysis of rulAB-mediated mutability in vitro and in planta. J. Bacteriol. 182: 6137-6144 (2000).

Kim JS, Kim KA, Oh TR, Park CM, Kang H. Functional characterization of DEAD-box RNA helicases in Arabidopsis thaliana under abiotic stress conditions. Plant Cell Physiol. 49: 1563-1571 (2008).

Kim JS, Lowe KE, Shane B. Regulation of folate and one-carbon metabolism in mammalian cells. IV. Role of folylpoly-gamma-glutamate synthetase in methotrexate metabolism and cytotoxicity. J. Biol. Chem. 268: 21680-21685 (1993).

Kim JW, Kim EY, Park HH, Jung JE, Kim HD, Shin HJ, Lim WK. Homodimers of mutant tryptophan synthase alpha-subunits in Escherichia coli. Biochem. Biophys. Res. Commun. 289: 568-572 (2001).

Kim JY, Cha HJ. Down-regulation of acetate pathway through antisense strategy in Escherichia coli: Improved foreign protein production. Biotechnol. Bioeng. 83: 841-853 (2003).

Kim JY, Park SJ, Jang B, Jung CH, Ahn SJ, Goh CH, Cho K, Han O, Kang H. Functional characterization of a glycine-rich RNA-binding protein 2 in Arabidopsis thaliana under abiotic stress conditions. Plant J. 50: 439-451 (2007).

Kim KH, Janiak V, Petersen M. Purification, cloning and functional expression of hydroxyphenylpyruvate reductase involved in rosmarinic acid biosynthesis in cell cultures of Coleus blumei. Plant Mol. Biol. 54: 311-323 (2004).

Kim MC, Lee SH, Kim JK, Chun HJ, Choi MS, Chung WS, Moon BC, Kang CH, Park CY, Yoo JH, Kang YH, Koo SC, Koo YD, Jung JC, Kim ST, Schulze-Lefert P, Lee SY, Cho MJ. Mlo, a modulator of plant defense and cell death, is a novel calmodulin-binding protein - Isolation and characterization of a rice Mlo homologue. J. Biol. Chem. 277: 19304-19314 (2002).

Kim PJ, Lee DY, Kim TY, Lee KH, Jeong H, Lee SY, Park S. Metabolite essentiality elucidates robustness of Escherichia coli metabolism. Proc. Natl. Acad. Sci. U.S.A. 104: 13638-13642 (2007).

Kim SM, Kim YB, Kuzuyama T, Kim SU. Two copies of 4-(cytidine 5'-diphospho)-2-C-methyl-D: -erythritol kinase (CMK) gene in Ginkgo biloba: molecular cloning and functional characterization. Planta 228: 941-950 (2008).

Kim SM, Kuzuyama T, Chang YJ, Kwon HJ, Kim SU. Cloning and functional characterization of 2-C-methyl-d-erythritol 4-phosphate cytidyltransferase (GbMECT) gene from Ginkgo biloba. Phytochemistry 67: 1435-1441 (2006).

Kim SW, Keasling JD. Metabolic engineering of the nonmevalonate isopentenyl diphosphate synthesis pathway in Escherichia coli enhances lycopene production. Biotechnol. Bioeng. 72: 408-415 (2001).

Kim TG, Baek MY, Lee EK, Kwon TH, Yang MS. Expression of human growth hormone in transgenic rice cell suspension culture. Plant Cell Rep. 27: 885-891 (2008).

Kim WS, Kim J, Krishnan HB, Nahm BH. Expression of Escherichia coli branching enzyme in caryopses of transgenic rice results in amylopectin with an increased degree of branching. Planta 220: 689-695 (2005).

Kim YO, Kim JS, Kang H. Cold-inducible zinc finger-containing glycine-rich RNA-binding protein contributes to the enhancement of freezing tolerance in Arabidopsis thaliana. Plant J. 42: 890-900 (2005).

Kim YS, Nosaka K, Downs DM, Kwak JM, Park D, Chung IK, Nam HG. A Brassica cDNA clone encoding a bifunctional hydroxymethylpyrimidine kinase/thiamin-phosphate pyrophosphorylase involved in thiamin biosynthesis. Plant Mol. Biol. 37: 955-966 (1998).

Kim YT, Song YH, Churchich JE. Recombinant brain 4-aminobutyrate aminotransferases overexpression, purification, and identification of Lys-330 at the active site. Biochim. Biophys. Acta 1337: 248-256 (1997).

Kim YW, Park DS, Park SC, Kim SH, Cheong GW, Hwang I. Arabidopsis dynamin-like 2 that binds specifically to phosphatidylinositol 4-phosphate assembles into a high-molecular weight complex in vivo and in vitro. Plant Physiol. 127: 1243-1255 (2001).

Kimura K, Sugano S, Funae A, Nakano Y. Characterization of Bacillus subtilis glutamine synthetase by limited proteolysis. J. Biochem. (Tokyo) 110: 526-531 (1991).

Kimura K, Yagi K, Matsuoka K. Regulation of Mycobacterium smegmatis glutamine synthetase by adenylylation. J. Biochem. (Tokyo) 95: 1559-1567 (1984).

Kimura S, Hayatsu H, Arimoto-Kobayashi S. Glycine betaine in beer as an antimutagenic substance against 2-chloro-4-methylthiobutanoic acid, the sanma-fish mutagen. Mut. Res. 439: 267-276 (1999).

Kimura S, Laosinchai W, Itoh T, Cui X, Linder CR, Brown RM Jr. Immunogold labeling of rosette terminal cellulose-synthesizing complexes in the vascular plant Vigna angularis. Plant Cell 11: 2075-2086 (1999).

Kimura S, Ueda T, Hatanaka M, Takenouchi M, Hashimoto J, Sakaguchi K. Plant homologue of flap endonuclease-1: molecular cloning, characterization, and evidence of expression in meristematic tissues. Plant Mol. Biol. 42: 415-427 (2000).

King T, Ferenci T. Divergent roles of RpoS in Escherichia coli under aerobic and anaerobic conditions. FEMS Microbiol. Lett. 244: 323-327 (2005).

Kinnaird JH, Fincham JR. The complete nucleotide sequence of the Neurospora crassa am (NADP-specific glutamate dehydrogenase) gene. Gene 26: 253-260 (1983).

Kinoshita T, Emi T, Tominaga M, Sakamoto K, Shigenaga A, Doi M, Shimazaki K. Blue-light- and phosphorylation-dependent binding of a 14-3-3 protein to phototropins in stomatal guard cells of broad bean. Plant Physiol. 133: 1453-1463 (2003).

Kirksey TJ, Appling DR. Site-directed mutagenesis of a highly conserved aspartate in the putative 10-formyl-tetrahydrofolate binding site of yeast C1-tetrahydrofolate synthase. Arch. Biochem. Biophys. 333: 251-259 (1996).

Kitano H. International alliances for quantitative modeling in systems biology. Mol. Syst. Biol. 1: 2005.0007 (2005).

Kitaoka S, Wada K, Hasegawa Y, Minami Y, Fukuyama K, Takahashi Y. Crystal structure of Escherichia coli SufC, an ABC-type ATPase component of the SUF iron-sulfur cluster assembly machinery. FEBS Lett. 580: 137-143 (2006).

Kitazume T, Tanaka A, Takaya N, Nakamura A, Matsuyama S, Suzuki T, Shoun H. Kinetic analysis of hydroxylation of saturated fatty acids by recombinant P450foxy produced by an Escherichia coli expression system. Eur. J. Biochem. 269: 2075-2082 (2002).

Kizer L, Pitera DJ, Pfleger BF, Keasling JD. Application of functional genomics to pathway optimization for increased isoprenoid production. Appl. Environ. Microbiol. 74: 3229-3241 (2008).

Klamt S, Schuster S, Gilles ED. Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria. Biotechnol. Bioeng. 77: 734-751 (2002).

Klamt S, Stelling J. Combinatorial complexity of pathway analysis in metabolic networks. Mol. Biol. Rep. 29: 233-236 (2002).

Klaus SM, Kunji ER, Bozzo GG, Noiriel A, de la Garza RD, Basset GJ, Ravanel S, Rebeille F, Gregory JF 3rd, Hanson AD. Higher plant plastids and cyanobacteria have folate carriers related to those of trypanosomatids. J. Biol. Chem. 280: 38457-38463 (2005).

Klaus SM, Wegkamp A, Sybesma W, Hugenholtz J, Gregory JF 3rd, Hanson AD. A nudix enzyme removes pyrophosphate from dihydroneopterin triphosphate in the folate synthesis pathway of bacteria and plants. J. Biol. Chem. 280: 5274-5280 (2005).

Kleijn RJ, van Winden WA, van Gulik WM, Heijnen JJ. Revisiting the 13C-label distribution of the non-oxidative branch of the pentose phosphate pathway based upon kinetic and genetic evidence. FEBS J. 272: 4970-4982 (2005).

Klein M, Papenbrock J. Kinetics and substrate specificities of desulfo-glucosinolate sulfotransferases in Arabidopsis thaliana. Physiol. Plant. 135: 140-149 (2009).

Klein RD, Geary TG, Gibson AS, Favreau MA, Winterrowd CA, Upton SJ, Keithly JS, Zhu G, Malmberg RL, Martinez MP, Yarlett N. Reconstitution of a bacterial/plant polyamine biosynthesis pathway in Saccharomyces cerevisiae. Microbiology 145: 301-307 (1999).

Klein W, Ehmann U, Boos W. The repression of trehalose transport and metabolism in Escherichia coli by high osmolarity is mediated by trehalose-6-phosphate phosphatase. Res. Microbiol. 142: 359-371 (1991).

Klein W, Horlacher R, Boos W. Molecular analysis of treB encoding the Escherichia coli enzyme II specific for trehalose. J. Bacteriol. 177: 4043-4052 (1995).

Kleiner O, Butenandt J, Carell T, Batschauer A. Class II DNA photolyase from Arabidopsis thaliana contains FAD as a cofactor. Eur. J. Biochem. 264: 161-167 (1999).

Kliebenstein DJ, Lambrix VM, Reichelt M, Gershenzon J, Mitchell-Olds T. Gene duplication in the diversification of secondary metabolism. Tandem 2-oxoglutarate-dependent dioxygenases control glucosinolate biosynthesis in Arabidopsis. Plant Cell 13: 681-693 (2001).

Klimczak LJ, Farini D, Lin C, Ponti D, Cashmore AR, Giuliano G. Multiple isoforms of Arabidopsis casein kinase I combine conserved catalytic domains with variable carboxyl-terminal extensions. Plant Physiol. 109: 687-696 (1995).

Klotz KL, Liu TT, Liu L, Lagrimini LM. Expression of the tobacco anionic peroxidase gene is tissue-specific and developmentally regulated. Plant Mol. Biol. 36: 509-520 (1998).

Knaggs AR. The biosynthesis of shikimate metabolites. Nat. Prod. Rep. 18: 334-355 (2001).

Knapp KG, Swartz JR. Cell-free production of active E. coli thioredoxin reductase and glutathione reductase. FEBS Lett. 559: 66-70 (2004).

Knappe J, Sawers G. A radical-chemical route to acetyl-CoA: the anaerobically induced pyruvate formate-lyase system of Escherichia coli. FEMS Microbiol. Rev. 6: 383-398 (1990).

Knutzon DS, Lardizabal KD, Nelsen JS, Bleibaum JL, Davies HM, Metz JG. Cloning of a coconut endosperm cDNA encoding a 1-acyl-sn-glycerol-3-phosphate acyltransferase that accepts medium-chain-length substrates. Plant Physiol. 109: 999-1006 (1995).

Ko R, Smith LT. Identification of an ATP-driven, osmoregulated glycine betaine transport system in Listeria monocytogenes. Appl. Environ. Microbiol. 65: 4040-4048 (1999).

Ko TP, Wu SP, Yang WZ, Tsai H, Yuan HS. Crystallization and preliminary crystallographic analysis of the Escherichia coli tyrosine aminotransferase. Acta Crystallogr. D. Biol. Crystallogr. 55: 1474-1477 (1999).

Kobayashi M, Izui H, Nagasawa T, Yamada H. Nitrilase in biosynthesis of the plant hormone indole-3-acetic acid from indole-3-acetonitrile: cloning of the Alcaligenes gene and site-directed mutagenesis of cysteine residues. Proc. Natl. Acad. Sci. U.S.A. 90: 247-251 (1993).

Kodumal SJ, Patel KG, Reid R, Menzella HG, Welch M, Santi DV. Total synthesis of long DNA sequences: synthesis of a contiguous 32-kb polyketide synthase gene cluster. Proc. Natl. Acad. Sci. U.S.A. 101: 15573-15578 (2004).

Koh BT, Tan RB, Yap MG. Genetically structured mathematical modeling of trp attenuator mechanism. Biotechnol. Bioeng. 58: 502-509 (1998).

Kohl S, Bock R. Transposition of a bacterial insertion sequence in chloroplasts. Plant J. 58: 423-436 (2009).

Koistinen KM, Kokko HI, Hassinen VH, Tervahauta AI, Auriola S, Karenlampi SO. Stress-related RNase PR-10c is post-translationally modified by glutathione in birch. Plant Cell Environ. 25: 707-715 (2002).

Kolesnikow T, Schroder I, Gunsalus RP. Regulation of narK gene expression in Escherichia coli in response to anaerobiosis, nitrate, iron, and molybdenum. J. Bacteriol. 174: 7104-7111 (1992).

Kolko MM, Kapetanovich LA, Lawrence JG. Alternative pathways for siroheme synthesis in Klebsiella aerogenes. J. Bacteriol. 183: 328-835 (2001).

Kolling R, Lother H. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli. J. Bacteriol. 164: 310-315 (1985).

Kollmann M, Lovdok L, Bartholome K, Timmer J, Sourjik V. Design principles of a bacterial signalling network. Nature 438: 504-507 (2005).

Komatsu M, Tsuda M, Omura S, Oikawa H, Ikeda H. Identification and functional analysis of genes controlling biosynthesis of 2-methylisoborneol. Proc. Natl. Acad. Sci. U.S.A. 105: 7422-7427 (2008).

Komoto J, Yamada T, Takata Y, Markham GD, Takusagawa F. Crystal structure of the S-adenosylmethionine synthetase ternary complex: a novel catalytic mechanism of S-adenosylmethionine synthesis from ATP and Met. Biochemistry 43: 1821-1831 (2004).

Kondo K, Wakabayashi S, Kagamiyama H. Structural studies on aspartate aminotransferase from Escherichia coli. Covalent structure. J. Biol. Chem. 262: 8648-8657 (1987).

Kondo K, Wakabayashi S, Yagi T, Kagamiyama H. The complete amino acid sequence of aspartate aminotransferase from Escherichia coli: sequence comparison with pig isoenzymes. Biochem. Biophys. Res. Commun. 122: 62-67 (1984).

Kontur WS, Saecker RM, Davis CA, Capp MW, Record MT Jr. Solute probes of conformational changes in open complex (RPo) formation by Escherichia coli RNA polymerase at the lambdaPR promoter: evidence for unmasking of the active site in the isomerization step and for large-scale coupled folding … Biochemistry 45: 2161-2177 (2006).

Koo YJ, Kim MA, Kim EH, Song JT, Jung C, Moon JK, Kim JH, Seo HS, Song SI, Kim JK, Lee JS, Cheong JJ, Choi YD. Overexpression of salicylic acid carboxyl methyltransferase reduces salicylic acid-mediated pathogen resistance in Arabidopsis thaliana. Plant Mol. Biol. 64: 1-15 (2007).

Koonin EV, Mushegian AR, Galperin MY, Walker DR. Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea. Mol. Microbiol. 25: 619-637 (1997).

Koop HU, Steinmuller K, Wagner H, Rossler C, Eibl C, Sacher L. Integration of foreign sequences into the tobacco plastome via polyethylene glycol-mediated protoplast transformation. Planta 199: 193-201 (1996).

Kopka J, Ludewig M, Muller-Rober B. Complementary DNAs encoding eukaryotic-type cytidine-5'-diphosphate-diacylglycerol synthases of two plant species. Plant Physiol. 113: 997-1002 (1997).

Kopke D, Schroder R, Fischer HM, Gershenzon J, Hilker M, Schmidt A. Does egg deposition by herbivorous pine sawflies affect transcription of sesquiterpene synthases in pine? Planta 228: 427-438 (2008).

Kopriva S, Buchert T, Fritz G, Suter M, Weber M, Benda R, Schaller J, Feller U, Schurmann P, Schunemann V, Trautwein AX, Kroneck PM, Brunold C. Plant adenosine 5'-phosphosulfate reductase is a novel iron-sulfur protein. J. Biol. Chem. 276: 42881-42886 (2001).

Kopriva S, Turner SR, Rawsthorne S, Bauwe H. T-protein of the glycine decarboxylase multienzyme complex: evidence for partial similarity to formyltetrahydrofolate synthetase. Plant Mol. Biol. 27: 1215-1220 (1995).

Kordic S, Cummins I, Edwards R. Cloning and characterization of an S-formylglutathione hydrolase from Arabidopsis thaliana. Arch. Biochem. Biophys. 399: 232-238 (2002).

Kornberg A, Rao NN, Ault-Riche D. Inorganic polyphosphate: a molecule of many functions. Annu. Rev. Biochem. 68: 89-125 (1999).

Kort R, Liebl W, Labedan B, Forterre P, Eggen RI, de Vos WM. Glutamate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima: molecular characterization and phylogenetic implications. Extremophiles 1: 52-60 (1997).

Koschutzki D, Schwobbermeyer H, Schreiber F. Ranking of network elements based on functional substructures. J. Theor. Biol. 248: 471-479 (2007).

Kosuge T, Hoshino T. Construction of a proline-producing mutant of the extremely thermophilic eubacterium Thermus thermophilus HB27. Appl. Environ. Microbiol. 64: 4328-4332 (1998).

Kota P, Guo D, Zubieta C, Noel J, Dixon RA. O-Methylation of benzaldehyde derivatives by "lignin specific" caffeic acid 3-O-methyltransferase. Phytochemistry 65: 837-846 (2004).

Kouri ED, Labrou NE, Garbis SD, Kalliampakou KI, Stedel C, Dimou M, Udvardi MK, Katinakis P, Flemetakis E. Molecular and biochemical characterization of the parvulin-type PPIases in Lotus japonicus. Plant Physiol. 150: 1160-1173 (2009).

Koussevitzky S, Stanne TM, Peto CA, Giap T, Sjogren LL, Zhao Y, Clarke AK, Chory J. An Arabidopsis thaliana virescent mutant reveals a role for ClpR1 in plastid development. Plant Mol. Biol. 63: 85-96 (2007).

Kovalchuk I, Filkowski J, Smith K, Kovalchuk O. Reactive oxygen species stimulate homologous recombination in plants. Plant Cell Environ. 26: 1531-1539 (2003).

Kozlov IuI, Kochetova LP, Livshits VA, Mashko SV, Moshentseva VN. Cloning of threonine operon genes in Escherichia coli cells. Genetika 16: 66-77 (1980).

Krafft T, Bowen A, Theis F, Macy JM. Cloning and sequencing of the genes encoding the periplasmic-cytochrome B-containing selenate reductase of Thauera selenatis. DNA Seq. 10: 365-377 (2000).

Kraft E, Stone SL, Ma L, Su N, Gao Y, Lau OS, Deng XW, Callis J. Genome analysis and functional characterization of the E2 and RING-type E3 ligase ubiquitination enzymes of Arabidopsis. Plant Physiol. 139: 1597-1611 (2005).

Kramer M, Bongaerts J, Bovenberg R, Kremer S, Muller U, Orf S, Wubbolts M, Raeven L. Metabolic engineering for microbial production of shikimic acid. Metab. Eng. 5: 277-283 (2003).

Krath BN, Hove-Jensen B. Organellar and cytosolic localization of four phosphoribosyl diphosphate synthase isozymes in spinach. Plant Physiol. 119: 497-506 (1999).

Krause T, Luersen K, Wrenger C, Gilberger TW, Muller S, Walter RD. The ornithine decarboxylase domain of the bifunctional ornithine decarboxylase/S-adenosylmethionine decarboxylase of Plasmodium falciparum: recombinant expression and catalytic properties of two different constructs. Biochem. J. 352: 287-292 (2000).

Kreimeyer A, Perret A, Lechaplais C, Vallenet D, Médigue C, Salanoubat M, Weissenbach J. Identification of the last unknown genes in the fermentation pathway of lysine. J. Biol. Chem. 282: 7191-7197 (2007).

Kremer A, Westrich L, Li SM. A 7-dimethylallyltryptophan synthase from Aspergillus fumigatus: overproduction, purification and biochemical characterization. Microbiology 153: 3409-3416 (2007).

Kremling A, Bettenbrock K, Laube B, Jahreis K, Lengeler JW, Gilles ED. The organization of metabolic reaction networks. Metab. Eng. 3: 362-379 (2001).

Kremling A, Gilles ED. The organization of metabolic reaction networks II. Signal processing in hierarchical structured functional units. Metab. Eng. 3: 138-150 (2001).

Kremling A, Jahreis K, Lengeler JW, Gilles ED. The organization of metabolic reaction networks: a signal-oriented approach to cellular models. Metab. Eng. 2: 190-200 (2000).

Kreuzer-Martin HW, Ehleringer JR, Hegg EL. Oxygen isotopes indicate most intracellular water in log-phase Escherichia coli is derived from metabolism. Proc. Natl. Acad. Sci. U. S. A. 102: 17337-17341 (2005).

Kreuzwieser J, Schnitzler JP, Steinbrecher R. Biosynthesis of organic compounds emitted by plants. Plant Biol. 1: 149-159 (1999).

Kriete G, Niehaus K, Perlick AM, Puhler A, Broer I. Male sterility in transgenic tobacco plants induced by tapetum-specific deacetylation of the externally applied non-toxic compound N-acetyl-L-phosphinothricin. Plant J. 9: 809-818 (1996).

Krishnan IS, Singhal RK, Dua RD. Purification and characterization of glutamine synthetase from Clostridium pasteurianum. Biochemistry 25: 1589-1599 (1986).

Kromer JO, Wittmann C, Schroder H, Heinzle E. Metabolic pathway analysis for rational design of L-methionine production by Escherichia coli and Corynebacterium glutamicum. Metab. Eng. 8: 353-369 (2006).

Krone FA, Westphal G, Meyer HE, Schwenn JD. PAPS-reductase of Escherichia coli. Correlating the N-terminal amino acid sequence with the DNA of gene cys H. FEBS Lett. 260: 6-9 (1990).

Krone FA, Westphal G, Schwenn JD. Characterisation of the gene cysH and of its product phospho-adenylylsulphate reductase from Escherichia coli. Mol. Gen. Genet. 225: 314-319 (1991).

Krueger RJ, Siegel LM. Spinach siroheme enzymes: isolation and characterization of ferredoxin-sulfite reductase and comparison of properties with ferredoxin-nitrite reductase. Biochemistry 21: 2892-2904 (1982).

Kruse E, Mock HP, Grimm B. Coproporphyrinogen III oxidase from barley and tobacco--sequence analysis and initial expression studies. Planta 196: 796-803 (1995).

Kryger G, Petsko GA, Ouyang J, Viola RE. Crystallization and preliminary crystallographic analysis of aspartate-beta-semialdehyde dehydrogenase from Escherichia coli. J. Mol. Biol. 228: 300-301 (1992).

Kubigsteltig II, Weiler EW. Arabidopsis mutants affected in the transcriptional control of allene oxide synthase, the enzyme catalyzing the entrance step in octadecanoid biosynthesis. Planta 217: 748-757 (2003).

Kujo C, Sakuraba H, Nunoura N, Ohshima T. The NAD-dependent glutamate dehydrogenase from the hyperthermophilic archaeon Pyrobaculum islandicum: cloning, sequencing, and expression of the enzyme gene. Biochim. Biophys. Acta 1434: 365-371 (1999).

Kukimoto M, Nishiyama M, Murphy ME, Turley S, Adman ET, Horinouchi S, Beppu T. X-ray structure and site-directed mutagenesis of a nitrite reductase from Alcaligenes faecalis S-6: roles of two copper atoms in nitrite reduction. Biochemistry 33: 5246-5252 (1994).

Kumada Y, Takano E, Nagaoka K, Thompson CJ. Streptomyces hygroscopicus has two glutamine synthetase genes. J. Bacteriol. 172: 5343-5351 (1990).

Kumar AM, Soll D. Arabidopsis alternative oxidase sustains Escherichia coli respiration. Proc. Natl. Acad. Sci. U.S.A. 89: 10842-10846 (1992).

Kumar R, Raclaru M, Schusseler T, Gruber J, Sadre R, Luhs W, Zarhloul KM, Friedt W, Enders D, Frentzen M, Weier D. Characterisation of plant tocopherol cyclases and their overexpression in transgenic Brassica napus seeds. FEBS Lett. 579: 1357-1364 (2005).

Kumar VS, Maranas CD. GrowMatch: an automated method for reconciling in silico/in vivo growth predictions. PLoS Comput. Biol. 5: e1000308 (2009).

Kummel A, Panke S, Heinemann M. Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data. Mol. Syst. Biol. 2: 2006.0034 (2006).

Kunin CM, Hua TH, Van Arsdale White L, Villarejo M. Growth of Escherichia coli in human urine: role of salt tolerance and accumulation of glycine betaine. J. Infect. Dis. 166: 1311-1315 (1992).

Kunin CM, Rudy J. Effect of NaCl-induced osmotic stress on intracellular concentrations of glycine betaine and potassium in Escherichia coli, Enterococcus faecalis, and staphylococci. J. Lab. Clin. Med. 118: 217-224 (1991).

Kunin CM, Tong HH, Miller DD, Abdel-Ghany Y, Poggi MC, LeRudulier D. Effect of novel compound, 1-methyl-1-piperidino methane sulfonate (MPMS), on the osmoprotectant activity of glycine betaine, choline and L-proline in Escherichia coli. Arch. Microbiol. 160: 81-86 (1993).

Kunte HJ, Galinski EA. Transposon mutagenesis in halophilic eubacteria: conjugal transfer and insertion of transposon Tn5 and Tn1732 in Halomonas elongata. FEMS Microbiol. Lett. 128: 293-299 (1995).

Kunze G, Zipfel C, Robatzek S, Niehaus K, Boller T, Felix G. The N terminus of bacterial elongation factor Tu elicits innate immunity in Arabidopsis plants. Plant Cell 16: 3496-3507 (2004).

Kunzler M, Paravicini G, Egli CM, Irniger S, Braus GH. Cloning, primary structure and regulation of the ARO4 gene, encoding the tyrosine-inhibited 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Saccharomyces cerevisiae. Gene 113: 67-74 (1992).

Kuo LC, Miller AW, Lee S, Kozuma C. Site-directed mutagenesis of Escherichia coli ornithine transcarbamoylase: role of arginine-57 in substrate binding and catalysis. Biochemistry 27: 8823-8832 (1988).

Kuo WN, Kocis JM, Webb J. Protein denitration/modification by Escherichia coli nitrate reductase and mammalian cytochrome P-450 reductase. Front. Biosci. 7: A9-A14 (2002).

Kuper J, Palmer T, Mendel RR, Schwarz G. Mutations in the molybdenum cofactor biosynthetic protein Cnx1G from Arabidopsis thaliana define functions for molybdopterin binding, molybdenum insertion, and molybdenum cofactor stabilization. Proc. Natl. Acad. Sci. U.S.A. 97: 6475-6480 (2000).

Kupke T. Molecular characterization of the 4'-phosphopantothenoylcysteine decarboxylase domain of bacterial Dfp flavoproteins. J. Biol. Chem. 276: 27597-27604 (2001).

Kupke T, Uebele M, Schmid D, Jung G, Blaesse M, Steinbacher S. Molecular characterization of lantibiotic-synthesizing enzyme EpiD reveals a function for bacterial Dfp proteins in coenzyme A biosynthesis. J. Biol. Chem. 275: 31838-31846 (2000).

Kuramitsu S, Inoue K, Ogawa T, Ogawa H, Kagamiyama H. Aromatic amino acid aminotransferase of Escherichia coli: nucleotide sequence of the tyrB gene. Biochem. Biophys. Res. Commun. 133: 134-139 (1985).

Kuramitsu S, Ogawa T, Ogawa H, Kagamiyama H. Branched-chain amino acid aminotransferase of Escherichia coli: nucleotide sequence of the ilvE gene and the deduced amino acid sequence. J. Biochem. (Tokyo) 97: 993-999 (1985).

Kuramitsu S, Okuno S, Ogawa T, Ogawa H, Kagamiyama H. Aspartate aminotransferase of Escherichia coli: nucleotide sequence of the aspC gene. J. Biochem. (Tokyo) 97: 1259-1262 (1985).

Kurihara S, Oda S, Tsuboi Y, Kim HG, Oshida M, Kumagai H, Suzuki H. gamma-Glutamylputrescine synthetase in the putrescine utilization pathway of Escherichia coli K-12. J. Biol. Chem. 283: 19981-19990 (2008).

Kurtov D, Kinghorn JR, Unkles SE. The Aspergillus nidulans panB gene encodes ketopantoate hydroxymethyltransferase, required for biosynthesis of pantothenate and Coenzyme A. Mol. Gen. Genet. 262: 115-120 (1999).

Kurys G, Shah PC, Kikonygo A, Reed D, Ambroziak W, Pietruszko R. Human aldehyde dehydrogenase. cDNA cloning and primary structure of the enzyme that catalyzes dehydrogenation of 4-aminobutyraldehyde. Eur. J. Biochem. 218: 311-320 (1993).

Kutchan TM. Expression of enzymatically active cloned strictosidine synthase from the higher plant Rauvolfia serpentina in Escherichia coli. FEBS Lett. 257: 127-130 (1989).

Kutukova EA, Livshits VA, Altman IP, Ptitsyn LR, Zyiatdinov MH, Tokmakova IL, Zakataeva NP. The yeaS (leuE) gene of Escherichia coli encodes an exporter of leucine, and the Lrp protein regulates its expression. FEBS Lett. 579: 4629-4634 (2005).

Kuznetsova E, Proudfoot M, Gonzalez CF, Brown G, Omelchenko MV, Borozan I, Carmel L, Wolf YI, Mori H, Savchenko AV, Arrowsmith CH, Koonin EV, Edwards AM, Yakunin AF. Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family. J. Biol. Chem. 281: 36149-36161 (2006).

Kuzuyama T, Takahashi S, Seto H. Construction and characterization of Escherichia coli disruptants defective in the yaeM gene. Biosci. Biotechnol. Biochem. 63: 776-778 (1999).

Kwon AR, Lee BI, Han BW, Ahn HJ, Yang JK, Yoon HJ, Suh SW. Crystallization and preliminary X-ray crystallographic analysis of aspartate 1-decarboxylase from Helicobacter pylori. Acta Crystallogr. D. Biol. Crystallogr. 58: 861-863 (2002).

Kwon HB, Park SC, Peng HP, Goodman HM, Dewdney J, Shih MC. Identification of a light-responsive region of the nuclear gene encoding the B subunit of chloroplast glyceraldehyde 3-phosphate dehydrogenase from Arabidopsis thaliana. Plant Physiol. 105: 357-367 (1994).

Kyriakidis DA, Heller JS, Canellakis ES. Modulation of ornithine decarboxylase activity in Escherichia coli by positive and negative effectors. Proc. Natl. Acad. Sci. U.S.A. 75: 4699-4703 (1978).

L'vov NP, Nosikov AN, Antipov AN. Tungsten-containing enzymes. Biochem. (Moscow) 67: 196-200 (2002).

Laber B, Gerbling KP, Harde C, Neff KH, Nordhoff E, Pohlenz HD. Mechanisms of interaction of Escherichia coli threonine synthase with substrates and inhibitors. Biochemistry 33: 3413-3423 (1994).

Laber B, Gomis-Ruth FX, Romao MJ, Huber R. Escherichia coli dihydrodipicolinate synthase. Identification of the active site and crystallization. Biochem. J. 288: 691-695 (1992).

Laber B, Lindell SD, Pohlenz HD. Inactivation of Escherichia coli threonine synthase by DL-Z-2-amino-5-phosphono-3-pentenoic acid. Arch. Microbiol. 161: 400-403 (1994).

Laber B, Maurer W, Hanke C, Grafe S, Ehlert S, Messerschmidt A, Clausen T. Characterization of recombinant Arabidopsis thaliana threonine synthase. Eur. J. Biochem. 263: 212-221 (1999).

Lacombe E, Hawkins S, Van Doorsselaere J, Piquemal J, Goffner D, Poeydomenge O, Boudet AM, Grima-Pettenati J. Cinnamoyl CoA reductase, the first committed enzyme of the lignin branch biosynthetic pathway: cloning, expression and phylogenetic relationships. Plant J. 11: 429-441 (1997).

Laflamme P, St-Pierre B, De Luca V. Molecular and biochemical analysis of a Madagascar periwinkle root-specific minovincinine-19-hydroxy-O-acetyltransferase. Plant Physiol. 125: 189-198 (2001).

Lagerstedt JO, Voss JC, Wieslander A, Persson BL. Structural modeling of dual-affinity purified Pho84 phosphate transporter. FEBS Lett. 578: 262-268 (2004).

Laing WA, Bulley S, Wright M, Cooney J, Jensen D, Barraclough D, Macrae E. A highly specific L-galactose-1-phosphate phosphatase on the path to ascorbate biosynthesis. Proc. Natl. Acad. Sci. U.S.A. 101: 16976-16981 (2004).

Lakaye B, Wirtzfeld B, Wins P, Grisar T, Bettendorff L. Thiamine triphosphate, a new signal required for optimal growth of Escherichia coli during amino acid starvation. J. Biol. Chem. 279: 17142-17147 (2004).

Laksanalamai P, Maeder DL, Robb FT. Regulation and mechanism of action of the small heat shock protein from the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol. 183: 5198-5202 (2001).

Lalle M, Visconti S, Marra M, Camoni L, Velasco R, Aducci P. ZmMPK6, a novel maize MAP kinase that interacts with 14-3-3 proteins. Plant Mol. Biol. 59: 713-722 (2005).

Lamark T, Kaasen I, Eshoo MW, Falkenberg P, McDougall J, Strom AR. DNA sequence and analysis of the bet genes encoding the osmoregulatory choline-glycine betaine pathway of Escherichia coli. Mol. Microbiol. 5: 1049-1064 (1991).

Lamark T, Rokenes TP, McDougall J, Strom AR. The complex bet promoters of Escherichia coli: regulation by oxygen (ArcA), choline (BetI), and osmotic stress. J. Bacteriol. 178: 1655-1662 (1996).

Lamark T, Styrvold OB, Strom AR. Efflux of choline and glycine betaine from osmoregulating cells of Escherichia coli. FEMS Microbiol. Lett. 75: 149-154 (1992).

Lamb HK, Dodds AL, Swatman DR, Cairns E, Hawkins AR. Deletion of the N-terminal region of the AREA protein is correlated with a derepressed phenotype with respect to nitrogen metabolite repression. J. Bacteriol. 179: 6649-6656 (1997).

Lamberg KE, Kiley PJ. FNR-dependent activation of the class II dmsA and narG promoters of Escherichia coli requires FNR-activating regions 1 and 3. Mol. Microbiol. 38: 817-827 (2000).

Landfald B, Strom AR. Choline-glycine betaine pathway confers a high level of osmotic tolerance in Escherichia coli. J. Bacteriol. 165: 849-855 (1986).

Landgraf JR, Boxer JA, Calvo JM. Escherichia coli Lrp (leucine-responsive regulatory protein) does not directly regulate expression of the leu operon promoter. J. Bacteriol. 181: 6547-6551 (1999).

Landis L, Xu JM, Johnson RC. The cAMP receptor protein CRP can function as an osmoregulator of transcription in Escherichia coli. Genes & Dev. 13: 3081-3091 (1999).

Lane M, Meade J, Manian SS, O'Gara F. Expression and regulation of the Escherichia coli glutamate dehydrogenase gene (gdh) in Rhizobium japonicum. Arch. Microbiol. 144: 29-34 (1986).

Lange BM, Croteau R. Isoprenoid biosynthesis via a mevalonate-independent pathway in plants: cloning and heterologous expression of 1-deoxy-D-xylulose-5-phosphate reductoisomerase from peppermint. Arch. Biochem. Biophys. 365: 170-174 (1999).

Lange BM, Wildung MR, McCaskill D, Croteau R. A family of transketolases that directs isoprenoid biosynthesis via a mevalonate-independent pathway. Proc. Natl. Acad. Sci. U.S.A. 95: 2100-2104 (1998).

Lange BM, Wildung MR, Stauber EJ, Sanchez C, Pouchnik D, Croteau R. Probing essential oil biosynthesis and secretion by functional evaluation of expressed sequence tags from mint glandular trichomes. Proc. Natl. Acad. Sci. U.S.A. 97: 2934-2939 (2000).

Langer K, Ache P, Geiger D, Stinzing A, Arend M, Wind C, Regan S, Fromm J, Hedrich R. Poplar potassium transporters capable of controlling K+ homeostasis and K+-dependent xylogenesis. Plant J. 32: 997-1009 (2002).

Langer K, Levchenko V, Fromm J, Geiger D, Steinmeyer R, Lautner S, Ache P, Hedrich R. The poplar K+ channel KPT1 is associated with K+ uptake during stomatal opening and bud development. Plant J. 37: 828-838 (2004).

Langeveld SM, Vennik M, Kottenhagen M, Van Wijk R, Buijk A, Kijne JW, De Pater S. Glucosylation activity and complex formation of two classes of reversibly glycosylated polypeptides. Plant Physiol. 129: 278-289 (2002).

Lannenpaa M, Janonen I, Holtta-Vuori M, Gardemeister M, Porali I, Sopanen T. A new SBP-box gene BpSPL1 in silver birch (Betula pendula). Physiol. Plant. 120: 491-500 (2004).

Large PJ. Enzymes and pathways of polyamine breakdown in microorganisms. FEMS Microbiol. Rev. 88: 249-262 (1992).

Larsen PI, Sydnes LK, Landfald B, Strom AR. Osmoregulation in Escherichia coli by accumulation of organic osmolytes: betaines, glutamic acid, and trehalose. Arch. Microbiol. 147: 1-7 (1987).

Larsen TM, Boehlein SK, Schuster SM, Richards NG, Thoden JB, Holden HM, Rayment I. Three-dimensional structure of Escherichia coli asparagine synthetase B: a short journey from substrate to product. Biochemistry 38: 16146-16157 (1999).

Larsson J, Rasmuson-Lestander A. Molecular-cloning of the S-adenosylmethionine synthetase gene in Drosophila melanogaster. FEBS Lett. 342: 329-333 (1994).

Larsson KA, Zetterlund I, Delp G, Jonsson LM. N-Methyltransferase involved in gramine biosynthesis in barley: cloning and characterization. Phytochemistry 67: 2002-2008 (2006).

Larsson S, Bjorkbacka H, Forsman C, Samuelsson G, Olsson O. Molecular cloning and biochemical characterization of carbonic anhydrase from Populus tremula x tremuloides. Plant Mol. Biol. 34: 583-592 (1997).

Laskowski MJ, Dreher KA, Gehring MA, Abel S, Gensler AL, Sussex IM. FQR1, a novel primary auxin-response gene, encodes a flavin mononucleotide-binding quinone reductase. Plant Physiol. 128: 578-590 (2002).

Laville J, Blumer C, Von Schroetter C, Gaia V, Defago G, Keel C, Haas D. Characterization of the hcnABC gene cluster encoding hydrogen cyanide synthase and anaerobic regulation by ANR in the strictly aerobic biocontrol agent Pseudomonas fluorescens CHA0. J. Bacteriol. 180: 3187-3196 (1998).

Lawit SJ, Miller PW, Dunn WI, Mirabile JS, Schmidt RR. Heterologous expression of cDNAs encoding Chlorella sorokiniana NADP-specific glutamate dehydrogenase wild-type and mutant subunits in Escherichia coli cells and comparison of kinetic and thermal stability properties of their homohexamers. Plant Mol. Biol. 52: 605-616 (2003).

Lawley B, Pittard AJ. Regulation of aroL expression by TyrR protein and Trp repressor in Escherichia coli K-12. J. Bacteriol. 176: 6921-6930 (1994).

Lawrence SD, Greenwood JS, Korhnak TE, Davis JM. A vegetative storage protein homolog is expressed in the growing shoot apex of hybrid poplar. Planta 203: 237-244 (1997).

Lawton JM, Doonan S. Thermal inactivation and chaperonin-mediated renaturation of mitochondrial aspartate aminotransferase. Biochem. J. 334: 219-224 (1998).

Lay VJ, Prescott AG, Thomas PG, John P. Heterologous expression and site-directed mutagenesis of the 1-aminocyclopropane-1-carboxylate oxidase from kiwi fruit. Eur. J. Biochem. 242: 228-234 (1996).

Le Coq D, Fillinger S, Aymerich S. Histidinol phosphate phosphatase, catalyzing the penultimate step of the histidine biosynthesis pathway, is encoded by ytvP (hisJ) in Bacillus subtilis. J. Bacteriol. 181: 3277-3280 (1999).

Le Guen L, Santos R, Camadro JM. Functional analysis of the hemK gene product involvement in protoporphyrinogen oxidase activity in yeast. FEMS Microbiol. Lett. 173: 175-182 (1999).

Le Rudulier D, Bouillard L. Glycine betaine, an osmotic effector in Klebsiella pneumoniae and other members of the Enterobacteriaceae. Appl. Environ. Microbiol. 46: 152-159 (1983).

Le Rudulier D, Strom AR, Dandekar AM, Smith LT, Valentine RC. Molecular biology of osmoregulation. Science 224: 1064-1068 (1984).

Le Y, He J, Vining LC. Streptomyces akiyoshiensis differs from other gram-positive bacteria in the organization of a core biosynthetic pathway gene for aspartate family amino acids. Microbiology 142: 791-798 (1996).

Lea PJ, Chen ZH, Leegood RC, Walker RP. Does phosphoenolpyruvate carboxykinase have a role in both amino acid and carbohydrate metabolism? Amino Acids 20: 225-241 (2001).

Lebbink JH, Knapp S, van der Oost J, Rice D, Ladenstein R, de Vos WM. Engineering activity and stability of Thermotoga maritima glutamate dehydrogenase. I. Introduction of a six-residue ion-pair network in the hinge region. J. Mol. Biol. 280: 287-296 (1998).

Leblanc N, Roux C, Pradier JM, Perrot-Rechenmann C. Characterization of two cDNAs encoding auxin-binding proteins in Nicotiana tabacum. Plant Mol. Biol. 33: 679-689 (1997).

Lee B, Yen J, Yang L, Liao JC. Incorporating qualitative knowledge in enzyme kinetic models using fuzzy logic. Biotechnol. Bioeng. 62: 722-729 (1999).

Lee BH, Hibino T, Jo J, Viale AM, Takabe T. Isolation and characterization of a dnaK genomic locus in a halotolerant cyanobacterium Aphanothece halophytica. Plant Mol. Biol. 35: 763-775 (1997).

Lee DS, Rieger H. Comparative study of the transcriptional regulatory networks of E. coli and yeast: structural characteristics leading to marginal dynamic stability. J. Theor. Biol. 248: 618-626 (2007).

Lee DY, Fan LT, Park S, Lee SY, Shafie S, Bertok B, Friedler F. Complementary identification of multiple flux distributions and multiple metabolic pathways. Metab. Eng. 7: 182-200 (2005).

Lee EC, Walker RI, Guerry P. Expression of Campylobacter genes for proline biosynthesis in Escherichia coli. Can. J. Microbiol. 31: 1064-1067 (1985).

Lee EY, Huh JW, Yang SJ, Choi SY, Cho SW, Choi HJ. Histidine 454 plays an important role in polymerization of human glutamate dehydrogenase. FEBS Lett. 540: 163-166 (2003).

Lee GJ, Vierling E. A small heat shock protein cooperates with heat shock protein 70 systems to reactivate a heat-denatured protein. Plant Physiol. 122: 189-198 (2000).

Lee HC, Kim JH, Kim JS, Jang W, Kim SY. Fermentative production of thymidine by a metabolically engineered Escherichia coli strain. Appl. Environ. Microbiol. 75: 2423-2432 (2009).

Lee IS, Muragaki Y, Ideguchi T, Hase T, Tsuji M, Ooshima A, Okuno E, Kido R. Molecular cloning and sequencing of a cDNA encoding alanine-glyoxylate aminotransferase 2 from rat kidney. J. Biochem. (Tokyo) 117: 856-862 (1995).

Lee J, Bae H, Jeong J, Lee JY, Yang YY, Hwang I, Martinoia E, Lee Y. Functional expression of a bacterial heavy metal transporter in Arabidopsis enhances resistance to and decreases uptake of heavy metals. Plant Physiol. 133: 589-596 (2003).

Lee J, Sperandio V, Frantz DE, Longgood J, Camilli A, Phillips MA, Michael AJ. An alternative polyamine biosynthetic pathway is widespread in bacteria and essential for biofilm formation in Vibrio cholerae. J. Biol. Chem. 284: 9899-9907 (2009).

Lee JH, Sung BH, Kim MS, Blattner FR, Yoon BH, Kim JH, Kim SC. Metabolic engineering of a reduced-genome strain of Escherichia coli for L-threonine production. Microb. Cell Fact. 8: 2 (2009).

Lee JH, Wendt JC, Shanmugam KT. Identification of a new gene, molR, essential for utilization of molybdate by Escherichia coli. J. Bacteriol. 172: 2079-2087 (1990).

Lee KH, Cho MH, Chung T, Chang HN, Lim SH, Lee J. Characterization of an oxygen-dependent inducible promoter, the Escherichia coli nar promoter, in gram-negative host strains. Biotechnol. Bioeng. 82: 271-277 (2003).

Lee KM, Rhee CH, Kang CK, Kim JH. Statistical medium formulation and process modeling by mixture design of experiment for peptide overexpression in recombinant Escherichia coli. Appl. Biochem. Biotechnol. 135: 81-110 (2006).

Lee M, Leustek T. Identification of the gene encoding homoserine kinase from Arabidopsis thaliana and characterization of the recombinant enzyme derived from the gene. Arch. Biochem. Biophys. 372: 135-142 (1999).

Lee M, Martin MN, Hudson AO, Lee J, Muhitch MJ, Leustek T. Methionine and threonine synthesis are limited by homoserine availability and not the activity of homoserine kinase in Arabidopsis thaliana. Plant J. 41: 685-696 (2005).

Lee MK, Gonzalez JM, Robb FT. Extremely thermostable glutamate dehydrogenase (GDH) from the freshwater archaeon Thermococcus waiotapuensis: cloning and comparison with two marine hyperthermophilic GDHs. Extremophiles 6: 151-159 (2002).

Lee PC, Petri R, Mijts BN, Watts KT, Schmidt-Dannert C. Directed evolution of Escherichia coli farnesyl diphosphate synthase (IspA) reveals novel structural determinants of chain length specificity. Metab. Eng. 7: 18-26 (2005).

Lee SB, Bailey JE. Analysis of growth rate effects on productivity of recombinant Escherichia coli populations using molecular mechanism models. Biotechnol. Bioeng. 67: 805-812 (2000).

Lee SG, Choi TJ, Kim YT. High level expression and purification of recombinant 4-aminobutyrate aminotransferases in Escherichia coli. J. Microbiol. Biotechnol. 6: 162-166 (1996).

Lee SG, Liao JC. Control of acetate production rate in Escherichia coli by regulating expression of single-copy pta using lacI(Q) in multicopy plasmid. J. Microbiol. Biotechnol. 18: 334-337 (2008).

Lee SJ, Lee DY, Kim TY, Kim BH, Lee J, Lee SY. Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation. Appl. Environ. Microbiol. 71: 7880-7887 (2005).

Lee SY, Kim HU, Park JH, Park JM, Kim TY. Metabolic engineering of microorganisms: general strategies and drug production. Drug Discov. Today 14: 78-88 (2009).

Lee SY, Lee DY, Hong SH, Kim TY, Yun H, Oh YG, Park S. MetaFluxNet, a program package for metabolic pathway construction and analysis, and its use in large-scale metabolic flux analysis of Escherichia coli. Genome Inform. Ser. Workshop Genome Inform. 14: 23-33 (2003).

Lee W, Dasilva NA. Application of sequential integration for metabolic engineering of 1,2-propanediol production in yeast. Metab. Eng. 8: 58-65 (2006).

Lee WL, Gold B, Darby C, Brot N, Jiang X, de Carvalho LP, Wellner D, St John G, Jacobs WR Jr, Nathan C. Mycobacterium tuberculosis expresses methionine sulphoxide reductases A and B that protect from killing by nitrite and hypochlorite. Mol. Microbiol. 71: 583-593 (2009).

Lee Y, Choi YA, Hwang ID, Kim SG, Kwon YM. cDNA cloning of two isoforms of ornithine carbamoyltransferase from Canavalia lineata leaves and the effect of site-directed mutagenesis of the carbamoyl phosphate binding site. Plant Mol. Biol. 46: 651-660 (2001).

Lee YS, Cho YD. Identification of essential active-site residues in ornithine decarboxylase of Nicotiana glutinosa decarboxylating both L-ornithine and L-lysine. Biochem. J. 360: 657-665 (2001).

Lee YS, Park SC, Goldberg AL, Chung CH. Protease So from Escherichia coli preferentially degrades oxidatively damaged glutamine synthetase. J. Biol. Chem. 263: 6643-6646 (1988).

Lee YY, Shearer N, Spiro S. Transcription factor NNR from Paracoccus denitrificans is a sensor of both nitric oxide and oxygen: isolation of nnr* alleles encoding effector-independent proteins and evidence for a haem-based sensing mechanism. Microbiology 152: 1461-14670 (2006).

Leech AP, Boetzel R, McDonald C, Shrive AK, Moore GR, Coggins JR, Sawyer L, Kleanthous C. Re-evaluating the role of His-143 in the mechanism of type I dehydroquinase from Escherichia coli using two-dimensional 1H,13C NMR. J. Biol. Chem. 273: 9602-9607 (1998).

Lehfeldt C, Shirley AM, Meyer K, Ruegger MO, Cusumano JC, Viitanen PV, Strack D, Chapple C. Cloning of the SNG1 gene of Arabidopsis reveals a role for a serine carboxypeptidase-like protein as an acyltransferase in secondary metabolism. Plant Cell 12: 1295-1306 (2000).

Lei M, Aebi U, Heidner EG, Eisenberg D. Limited proteolysis of glutamine synthetase is inhibited by glutamate and by feedback inhibitors. J. Biol. Chem. 254: 3129-3134 (1979).

Leimkuhler S, Klipp W. The molybdenum cofactor biosynthesis protein MobA from Rhodobacter capsulatus is required for the activity of molybdenum enzymes containing MGD, but not for xanthine dehydrogenase harboring the MPT cofactor. FEMS Microbiol. Lett. 174: 239-246 (1999).

Lemaire SD, Collin V, Keryer E, Quesada A, Miginiac-Maslow M. Characterization of thioredoxin y, a new type of thioredoxin identified in the genome of Chlamydomonas reinhardtii. FEBS Lett. 543: 87-92 (2003).

Lemuth K, Hardiman T, Winter S, Pfeiffer D, Keller MA, Lange S, Reuss M, Schmid RD, Siemann-Herzberg M. Global transcription and metabolic flux analysis of Escherichia coli in glucose-limited fed-batch cultivations. Appl. Environ. Microbiol. 74: 7002-7015 (2008).

Lengeler JW. Metabolic networks: a signal-oriented approach to cellular models. Biol. Chem. 381: 911-920 (2000).

Leon S, Touraine B, Briat JF, Lobreaux S. Mitochondrial localization of Arabidopsis thaliana Isu Fe-S scaffold proteins. FEBS Lett. 579: 1930-1934 (2005).

Leon-Kloosterziel KM, Verhagen BW, Keurentjes JJ, Van Pelt JA, Rep M, Van Loon LC, Pieterse CM. Colonization of the Arabidopsis rhizosphere by fluorescent Pseudomonas spp. activates a root-specific, ethylene-responsive PR-5 gene in the vascular bundle. Plant Mol. Biol. 57: 731-748 (2005).

Leonard E, Yan Y, Fowler ZL, Li Z, Lim CG, Lim KH, Koffas MA. Strain improvement of recombinant Escherichia coli for efficient production of plant flavonoids. Mol. Pharm. 5: 257-265 (2008).

Leonard E, Yan Y, Koffas MA. Functional expression of a P450 flavonoid hydroxylase for the biosynthesis of plant-specific hydroxylated flavonols in Escherichia coli. Metab. Eng. 8: 172-181 (2006).

Leonardi R, Fairhurst SA, Kriek M, Lowe DJ, Roach PL. Thiamine biosynthesis in Escherichia coli: isolation and initial characterisation of the ThiGH complex. FEBS Lett. 539: 95-99 (2003).

Leonardi R, Roach PL. Thiamine biosynthesis in Escherichia coli: in vitro reconstitution of the thiazole synthase activity. J. Biol. Chem. 279: 17054-17062 (2004).

Leonhartsberger S, Korsa I, Bock A. The molecular biology of formate metabolism in enterobacteria. J. Mol. Microbiol. Biotechnol. 4: 269-276 (2002).

Lepo JE, Stacey G, Wyss O, Tabita FR. The purification of glutamine synthetase from Azotobacter and other procaryotes by blue sepharose chromatography. Biochim. Biophys. Acta 568: 428-436 (1979).

Leppanen VM, Merckel MC, Ollis DL, Wong KK, Kozarich JW, Goldman A. Pyruvate formate lyase is structurally homologous to type I ribonucleotide reductase. Structure Fold. Des. 7: 733-744 (1999).

Leppanen VM, Parast CV, Wong KK, Kozarich JW, Goldman A. Purification and crystallization of a proteolytic fragment of Escherichia coli pyruvate formate-lyase. Acta Crystallogr. D. Biol. Crystallogr. 55: 531-533 (1999).

Leranoz AM, Fuste MC, Vinas M, Hull RA, Williams RP. Cloning and expression in Escherichia coli of a gene encoding proline oxidase of Serratia marcescens. Microbios 67: 87-94 (1991).

Lerchl J, Geigenberger P, Stitt M, Sonnewald U. Impaired photoassimilate partitioning caused by phloem-specific removal of pyrophosphate can be complemented by a phloem-specific cytosolic yeast-derived invertase in transgenic plants. Plant Cell 7: 259-270 (1995).

Lerondel G, Doan T, Zamboni N, Sauer U, Aymerich S. YtsJ has the major physiological role of the four paralogous malic enzyme isoforms in Bacillus subtilis. J. Bacteriol. 188: 4727-4736 (2006).

Lester DR, Ross JJ, Smith JJ, Elliott RC, Reid JB. Gibberellin 2-oxidation and the SLN gene of Pisum sativum. Plant J. 19: 65-73 (1999).

Leustek T, Saito K. Sulfate transport and assimilation in plants. Plant Physiol. 120: 637-644 (1999).

Leustek T, Smith M, Murillo M, Singh DP, Smith AG, Woodcock SC, Awan SJ, Warren MJ. Siroheme biosynthesis in higher plants. Analysis of an S-adenosyl-L-methionine-dependent uroporphyrinogen III methyltransferase from Arabidopsis thaliana. J. Biol. Chem. 272: 2744-2752 (1997).

Levine RL. Oxidative modification of glutamine synthetase. I. Inactivation is due to loss of one histidine residue. J. Biol. Chem. 258: 11823-11827 (1983).

Levine RL. Carbonyl modified proteins in cellular regulation, aging, and disease. Free Radic. Biol. Med. 32: 790-796 (2002).

Levine RL, Berlett BS, Moskovitz J, Mosoni L, Stadtman ER. Methionine residues may protect proteins from critical oxidative damage. Mech. Ageing Dev. 107: 323-332 (1999).

Levine RL, Mosoni L, Berlett BS, Stadtman ER. Methionine residues as endogenous antioxidants in proteins. Proc. Natl. Acad. Sci. U.S.A. 93: 15036-15040 (1996).

Levy S, Danchin A. Phylogeny of metabolic pathways: O-acetylserine sulphydrylase A is homologous to the tryptophan synthase beta subunit. Mol. Microbiol. 2: 777-783 (1988).

Levy-Rimler G, Bell RE, Ben-Tal N, Azem A. Type I chaperonins: not all are created equal. FEBS Lett. 529: 1-5 (2002).

Li AD, Anderson LE. Expression and characterization of pea chloroplastic glyceraldehyde-3-phosphate dehydrogenase composed of only the B-subunit. Plant Physiol. 115: 1201-1209 (1997).

Li C, Peck HD Jr, Przybyla AE. Cloning of the 3'-phosphoadenylyl sulfate reductase and sulfite reductase genes from Escherichia coli K-12. Gene 53: 227-234 (1987).

Li D, Liu H, Zhang H, Wang X, Song F. OsBIRH1, a DEAD-box RNA helicase with functions in modulating defence responses against pathogen infection and oxidative stress. J. Exp. Bot. 59: 2133-2146 (2008).

Li J, Zhao J, Rose AB, Schmidt R, Last RL. Arabidopsis phosphoribosylanthranilate isomerase: molecular genetic analysis of triplicate tryptophan pathway genes. Plant Cell 7: 447-461 (1995).

Li JF, Qu LH, Li N. Tyr152 plays a central role in the catalysis of 1-aminocyclopropane-1-carboxylate synthase. J. Exp. Bot. 56: 2203-2210 (2005).

Li L, Lin K, Correia JJ, Pilkis SJ. Lysine 356 is a critical residue for binding the C-6 phospho group of fructose 2,6-bisphosphate to the fructose-2,6-bisphosphatase domain of rat liver 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase. J. Biol. Chem. 267: 16669-16675 (1992).

Li L, Ling S, Wu Cl, Yao W, Xu G. Separate bisphosphatase domain of chicken liver 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase: the role of the C-terminal tail in modulating enzyme activity. Biochem. J. 328: 751-756 (1997).

Li L, Osakabe Y, Joshi CP, Chiang VL. Secondary xylem-specific expression of caffeoyl-coenzyme A 3-O-methyltransferase plays an important role in the methylation pathway associated with lignin biosynthesis in loblolly pine. Plant Mol. Biol. 40: 555-565 (1999).

Li M, Ho PY, Yao S, Shimizu K. Effect of lpdA gene knockout on the metabolism in Escherichia coli based on enzyme activities, intracellular metabolite concentrations and metabolic flux analysis by (13)C-labeling experiments. J. Biotechnol. 122: 254-266 (2006).

Li M, Huang W, Yang Q, Liu X, Wu Q. Expression and oxidative stress tolerance studies of glutaredoxin from cyanobacterium Synechocystis sp. PCC 6803 in Escherichia coli. Protein Expr. Purif. 42: 85-91 (2005).

Li N, Jiang XN, Cai GP, Yang SF. A novel bifunctional fusion enzyme catalyzing ethylene synthesis via 1-aminocyclopropane1-carboxylic acid. J. Biol. Chem. 271: 25738-25741 (1996).

Li N, Lv J, Niu DK. Low contents of carbon and nitrogen in highly abundant proteins: evidence of selection for the economy of atomic composition. J. Mol. Evol. 68: 248-255 (2009).

Li R, Haile JD, Kennelly PJ. An arsenate reductase from Synechocystis sp. strain PCC 6803 exhibits a novel combination of catalytic characteristics. J. Bacteriol. 185: 6780-6789 (2003).

Li SM. Evolution of aromatic prenyltransferases in the biosynthesis of indole derivatives. Phytochemistry Apr 25 [Epub ahead of print] (2009).

Li W, Brandriss MC. Proline biosynthesis in Saccharomyces cerevisiae: molecular analysis of the PRO1 gene, which encodes gamma-glutamyl kinase. J. Bacteriol. 174: 4148-4156 (1992).

Li Y, de Ridder D, de Groot MJ, Reinders MJ. Metabolic pathway alignment between species using a comprehensive and flexible similarity measure. BMC Syst. Biol. 2: 111 (2008).

Li Y, Dhankher OP, Carreira L, Lee D, Chen A, Schroeder JI, Balish RS, Meagher RB. Overexpression of phytochelatin synthase in Arabidopsis leads to enhanced arsenic tolerance and cadmium hypersensitivity. Plant Cell Physiol. 45: 1787-1797 (2004).

Li Y, Yang G, Huang X, Ye B, Liu M, Lin Z, Li C, Cao ZA. Recombinant glutamine synthetase (GS) from C. glutamicum existed as both hexamers & dedocamers and C-terminal His-tag enhanced inclusion bodies formation in E. coli. Appl. Biochem. Biotechnol. Jan 16 [Epub ahead of print] (2009).

Li YF, Hess S, Pannell LK, White Tabor C, Tabor H. In vivo mechanism-based inactivation of S-adenosylmethionine decarboxylases from Escherichia coli, Salmonella typhimurium, and Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 98: 10578-10583 (2001).

Liang A, Houghton RL. Coregulation of oxidized nicotinamide adenine dinucleotide (phosphate) transhydrogenase and glutamate dehydrogenase activities in enteric bacteria during nitrogen limitation. J. Bacteriol. 146: 997-1002 (1981).

Liang X, Abel S, Keller JA, Shen NF, Theologis A. The 1-aminocyclopropane-1-carboxylate synthase gene family of Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A. 89: 11046-11050 (1992).

Liang Zhu Y, Pilon-Smits EA, Jouanin L, Terry N. Overexpression of glutathione synthetase in indian mustard enhances cadmium accumulation and tolerance. Plant Physiol. 119: 73-80 (1999).

Liao HH, Hseu TH. Analysis of the regulatory region of the lysC gene of Escherichia coli. FEMS Microbiol. Lett. 168: 31-36 (1998).

Liao JC. Inverse flux analysis. J. Biotechnol. 71: 259-262 (1999).

Liao JC, Hou SY, Chao YP. Pathway analysis, engineering, and physiological considerations for redirecting central metabolism. Biotechnol. Bioeng. 52: 129-140 (1996).

Liao XY, Shen W, Chen J, Li Y, Du GC. Improved glutathione production by gene expression in Escherichia coli. Lett. Appl. Microbiol. 43: 211-214 (2006).

Liaw SH, Villafranca JJ, Eisenberg D. A model for oxidative modification of glutamine synthetase, based on crystal structures of mutant H269N and the oxidized enzyme. Biochemistry 32: 7999-8003 (1993).

Liepman AH, Olsen LI. Genomic analysis of aminotransferases in Arabidopsis thaliana. Crit. Rev. Plant Sci. 23: 73-89 (2004).

Liepman AH, Olsen LJ. Peroxisomal alanine:glyoxylate aminotransferase (AGT1) is a photorespiratory enzyme with multiple substrates in Arabidopsis thaliana. Plant J. 25: 487-498 (2001).

Liepman AH, Olsen LJ. Alanine aminotransferase homologs catalyze the glutamate:glyoxylate aminotransferase reaction in peroxisomes of Arabidopsis. Plant Physiol. 131: 215-227 (2003).

Lightfoot DA, Baron AJ, Cock JM, Wootton JC. A nitrate reductase gene of the cyanobacterium Synechococcus PCC6301 inferred by heterologous hybridization, cloning and targeted mutagenesis. Genetica 85: 107-117 (1992).

Lillig CH, Prior A, Schwenn JD, Aslund F, Ritz D, Vlamis-Gardikas A, Holmgren A. New thioredoxins and glutaredoxins as electron donors of 3'-phosphoadenylylsulfate reductase. J. Biol. Chem. 274: 7695-7698 (1999).

Lim WK, Sarkar SK, Hardman JK. Enzymatic properties of mutant Escherichia coli tryptophan synthase alpha-subunits. J. Biol. Chem. 266: 20205-20212 (1991).

Lim WK, Shin HJ, Milton DL, Hardman JK. Relative activities and stabilities of mutant Escherichia coli tryptophan synthase alpha subunits. J. Bacteriol. 173: 1886-1893 (1991).

Limauro D, Falciatore A, Basso AL, Forlani G, DeFelice M. Proline biosynthesis in Streptococcus thermophilus: Characterization of the proBA operon and its products. Microbiology 142: 3275-3282 (1996).

Lin BF, Huang RF, Shane B. Regulation of folate and one-carbon metabolism in mammalian cells. III. Role of mitochondrial folylpoly-gamma-glutamate synthetase. J. Biol. Chem. 268: 21674-21679 (1993).

Lin BF, Shane B. Expression of Escherichia coli folylpolyglutamate synthetase in the Chinese hamster ovary cell mitochondrion. J. Biol. Chem. 269: 9705-9713 (1994).

Lin C, Paradkar AS, Vining LC. Regulation of an anthranilate synthase gene in Streptomyces venezuelae by a trp attenuator. Microbiology 144: 1971-1980 (1998).

Lin H, Bennett GN, San KY. Chemostat culture characterization of Escherichia coli mutant strains metabolically engineered for aerobic succinate production: a study of the modified metabolic network based on metabolite profile, enzyme activity, and gene expression profile. Metab. Eng. 7: 337-352 (2005).

Lin H, Bennett GN, San KY. Metabolic engineering of aerobic succinate production systems in Escherichia coli to improve process productivity and achieve the maximum theoretical succinate yield. Metab. Eng. 7: 116-127 (2005).

Lin JW, Yu KY, Chen HY, Weng SF. Regulatory region with putA gene of proline dehydrogenase that links to the lum and the lux operons in Photobacterium leiognathi. Biochem. Biophys. Res. Commun. 219: 868-875 (1996).

Lin LJ, Tai SS, Peng CC, Tzen JT. Steroleosin, a sterol-binding dehydrogenase in seed oil bodies. Plant Physiol. 128: 1200-1211 (2002).

Lin PH, Su SC, Tsai YC, Lee CY. Identification and characterization of a new gene from Variovorax paradoxus Iso1 encoding N-acyl-D-amino acid amidohydrolase responsible for D-amino acid production. Eur. J. Biochem. 269: 4868-4878 (2002).

Lin WY, Dombrosky P, Atkins WM, Villafranca JJ. Terbium(III) luminescence study of tyrosine emission from Escherichia coli glutamine synthetase. Biochemistry 30: 3427-3431 (1991).

Lin WY, Eads CD, Villafranca JJ. Fluorescent probes for measuring the binding constants and distances between the metal ions bound to Escherichia coli glutamine synthetase. Biochemistry 30: 3421-3426 (1991).

Lin Y, Hansen JN. Characterization of a chimeric proU operon in a subtilin-producing mutant of Bacillus subtilis 168. J. Bacteriol. 177: 6874-6880 (1995).

Lin Y, Ulanov AV, Lozovaya V, Widholm J, Zhang G, Guo J, Goodman HM. Genetic and transgenic perturbations of carbon reserve production in Arabidopsis seeds reveal metabolic interactions of biochemical pathways. Planta 225: 153-164 (2006).

Lin YF, Walmsley AR, Rosen BP. An arsenic metallochaperone for an arsenic detoxification pump. Proc. Natl. Acad. Sci. U.S.A. 103: 15617-15622 (2006).

Lin YK, Myhrman R, Schrag ML, Gelb MH. Bacterial N-succinyl-L-diaminopimelic acid desuccinylase. Purification, partial characterization, and substrate specificity. J. Biol. Chem. 263: 1622-1627 (1988).

Linde K, Grobner G, Rilfors L. Lipid dependence and activity control of phosphatidylserine synthase from Escherichia coli. FEBS Lett. 575: 77-80 (2004).

Lindermayr C, Mollers B, Fliegmann J, Uhlmann A, Lottspeich F, Meimberg H, Ebel J. Divergent members of a soybean (Glycine max L.) 4-coumarate:coenzyme A ligase gene family. Eur. J. Biochem. 269: 1304-1315 (2002).

Ling M, Allen SW, Wood JM. Sequence analysis identifies the proline dehydrogenase and delta 1-pyrroline-5-carboxylate dehydrogenase domains of the multifunctional Escherichia coli PutA protein. J. Mol. Biol. 243: 950-956 (1994).

Linley PJ, Landsberger M, Kohchi T, Cooper JB, Terry MJ. The molecular basis of heme oxygenase deficiency in the pcd1 mutant of pea. FEBS J. 273: 2594-2606 (2006).

Lisse T, Bartels D, Kalbitzer HR, Jaenicke R. The recombinant dehydrin-like desiccation stress protein from the resurrection plant Craterostigma plantagineum displays no defined three-dimensional structure in its native state. Biol. Chem. 377: 555-561 (1996).

Liszewska F, Blaszczyk A, Sirko A. Modification of non-protein thiols contents in transgenic tobacco plants producing bacterial enzymes of cysteine biosynthesis pathway. Acta Biochim. Pol. 48: 647-656 (2001).

Little R, Colombo V, Leech A, Dixon R. Direct interaction of the NifL regulatory protein with the GlnK signal transducer enables the Azotobacter vinelandii NifL-NifA regulatory system to respond to conditions replete for nitrogen. J. Biol. Chem. 277: 15472-15481 (2002).

Little S, Hyde S, Campbell CJ, Lilley RJ, Robinson MK. Translational coupling in the threonine operon of Escherichia coli K-12. J. Bacteriol. 171: 3518-3522 (1989).

Liu J, Magasanik B. The glnB region of the Escherichia coli chromosome. J. Bacteriol. 175: 7441-7449 (1993).

Liu J, Magasanik B. Activation of the dephosphorylation of nitrogen regulator I-phosphate of Escherichia coli. J. Bacteriol. 177: 926-931 (1995).

Liu JQ, Nagata S, Dairi T, Misono H, Shimizu S, Yamada H. The GLY1 gene of Saccharomyces cerevisiae encodes a low-specific L-threonine aldolase that catalyzes cleavage of L-allo-threonine and L-threonine to glycine. Eur. J. Biochem. 245: 289-293 (1997).

Liu JQ, Odani M, Dairi T, Itoh N, Shimizu S, Yamada H. A new route to L-threo-3-[4-(methylthio)phenylserine], a key intermediate for the synthesis of antibiotics: recombinant low-specificity D-threonine aldolase-catalyzed stereospecific resolution. Appl. Microbiol. Biotechnol. 51: 586-591 (1999).

Liu JY, Le Y, Ye B, Zhen Y, Zhu CM, Shen J, Zhang RQ. Tabtoxin-resistant protein: Overexpression, purification, and characterization. Protein Expr. Purif. 24: 439-444 (2002).

Liu LJ, Iwata K, Yohda M, Miki K. Structural insight into gene duplication, gene fusion and domain swapping in the evolution of PLP-independent amino acid racemases. FEBS Lett. 528: 114-118 (2002).

Liu MT, Wuebbens MM, Rajagopalan KV, Schindelin H. Crystal structure of the gephyrin-related molybdenum cofactor biosynthesis protein MogA from Escherichia coli. J. Biol. Chem. 275: 1814-1822 (2000).

Liu T, Nakashima S, Hirose K, Uemura Y, Shibasaka M, Katsuhara M, Kasamo K. A metallothionein and CPx-ATPase handle heavy-metal tolerance in the filamentous cyanobacterium Oscillatoria brevis. FEBS Lett. 542: 159-163 (2003).

Liu W, Xu ZH, Luo D, Xue HW. Roles of OsCKI1, a rice casein kinase I, in root development and plant hormone sensitivity. Plant J. 36: 189-202 (2003).

Liu X, DeMoss JA. Characterization of NarJ, a system-specific chaperone required for nitrate reductase biogenesis in Escherichia coli. J. Biol. Chem. 272: 24266-24271 (1997).

Liu Y, Dammann C, Bhattacharyya MK. The matrix metalloproteinase gene GmMMP2 is activated in response to pathogenic infections in soybean. Plant Physiol. 127: 1788-1797 (2001).

Liu YJ, Li PP, Zhao KX, Wang BJ, Jiang CY, Drake HL, Liu SJ. Corynebacterium glutamicum contains 3-deoxy-D-arabino-heptulosonate 7-phosphate synthases that display novel biochemical features. Appl. Environ. Microbiol. 74: 5497-5503 (2008).

Liu Z, Xia M, Poovaiah BW. Chimeric calcium/calmodulin-dependent protein kinase in tobacco: differential regulation by calmodulin isoforms. Plant Mol. Biol. 38: 889-897 (1998).

Llacer JL, Polo LM, Tavarez S, Alarcon B, Hilario R, Rubio V. The gene cluster for agmatine catabolism of Enterococcus faecalis: study of recombinant putrescine transcarbamylase and agmatine deiminase and a snapshot of agmatine deiminase catalyzing its reaction J. Bacteriol. 189: 1254-1265 (2007).

Llama-Palacios A, Lopez-Solanilla E, Poza-Carrion C, Garcia-Olmedo F, Rodriguez-Palenzuela P. The Erwinia chrysanthemi phoP-phoQ operon plays an important role in growth at low pH, virulence and bacterial survival in plant tissue. Mol. Microbiol. 49: 347-357 (2003).

Llamas A, Igeno MI, Galvan A, Fernandez E. Nitrate signalling on the nitrate reductase gene promoter depends directly on the activity of the nitrate transport systems in Chlamydomonas. Plant J. 30: 261-271 (2002).

Llamas A, Tejada-Jimenez M, Gonzalez-Ballester D, Higuera JJ, Schwarz G, Galvan A, Fernandez E. Chlamydomonas reinhardtii CNX1E reconstitutes molybdenum cofactor biosynthesis in Escherichia coli mutants. Eukaryot. Cell 6: 1063-1067 (2007).

Lloyd JR, Blennow A, Burhenne K, Kossmann J. Repression of a novel isoform of disproportionating enzyme (stDPE2) in potato leads to inhibition of starch degradation in leaves but not tubers stored at low temperature. Plant Physiol. 134: 1347-1354 (2004).

Lo M, Taylor C, Wang L, Nowack L, Wang TW, Thompson J. Characterization of an ultraviolet B-induced lipase in Arabidopsis. Plant Physiol. 135: 947-958 (2004).

Lobley CM, Schmitzberger F, Kilkenny ML, Whitney H, Ottenhof HH, Chakauya E, Webb ME, Birch LM, Tuck KL, Abell C, Smith AG, Blundell TL. Structural insights into the evolution of the pantothenate-biosynthesis pathway. Biochem. Soc. Trans. 31: 563-571 (2003).

Lodwig E, Kumar S, Allaway D, Bourdes A, Prell J, Priefer U, Poole P. Regulation of L-alanine dehydrogenase in Rhizobium leguminosarum bv. viciae and its role in pea nodules. J. Bacteriol. 186: 842-849 (2004).

Logusch EW, Walker DM, McDonald JF, Franz JE, Villafranca JJ, DiIanni CL, Colanduoni JA, Li B, Schineller JB. Inhibition of Escherichia coli glutamine synthetase by alpha- and gamma-substituted phosphinothricins. Biochemistry 29: 366-372 (1990).

Loh YT, Martin GB. The Pto bacterial resistance gene and the Fen insecticide sensitivity gene encode functional protein kinases with serine/threonine specificity. Plant Physiol. 108: 1735-1739 (1995).

Lohman TM, Bjornson KP. Mechanisms of helicase-catalyzed DNA unwinding. Annu. Rev. Biochem. 65: 169-214 (1996).

Lois LM, Campos N, Putra SR, Danielsen K, Rohmer M, Boronat A. Cloning and characterization of a gene from Escherichia coli encoding a transketolase-like enzyme that catalyzes the synthesis of D-1-deoxyxylulose 5-phosphate, a common precursor for isoprenoid, thiamin, and pyridoxol biosynthesis. Proc. Natl. Acad. Sci. U.S.A. 95: 2105-2110 (1998).

London RE, Allen DL, Gabel SA, DeRose EF. Carbon-13 nuclear magnetic resonance study of metabolism of propionate by Escherichia coli. J. Bacteriol. 181: 3562-3570 (1999).

Lopes-Lutz D, Alviano DS, Alviano CS, Kolodziejczyk PP. Screening of chemical composition, antimicrobial and antioxidant activities of Artemisia essential oils. Phytochemistry 69: 1732-1738 (2008).

Lopez Jaramillo J, Chueca A, Jacquot JP, Hermoso R, Lazaro JJ, Sahrawy M, Lopez Gorge J. High-yield expression of pea thioredoxin m and assessment of its efficiency in chloroplast fructose-1,6-bisphosphatase activation. Plant Physiol. 114: 1169-1175 (1997).

Lopez-Meyer M, Nessler CL. Tryptophan decarboxylase is encoded by two autonomously regulated genes in Camptotheca acuminata which are differentially expressed during development and stress. Plant J. 11: 1167-1175 (1997).

Lorenzo O, Nicolas C, Nicolas G, Rodriguez D. GA(3)-induced expression of a new functional AAA-ATPase (FsA1) is correlated with the onset of germination in Fagus sylvatica L. seeds (beechnuts). Plant Cell Physiol. 43: 27-34 (2002).

Louis P, Galinski EA. Characterization of genes for the biosynthesis of the compatible solute ectoine from Marinococcus halophilus and osmoregulated expression in Escherichia coli. Microbiology 143: 1141-1149 (1997).

Loulakakis KA, Primikirios NI, Nikolantonakis MA, Roubelakis-Angelakis KA. Immunocharacterization of Vitis vinifera L. ferredoxin-dependent glutamate synthase, and its spatial and temporal changes during leaf development. Planta 215: 630-638 (2002).

Lowe KE, Osborne CB, Lin BF, Kim JS, Hsu JC, Shane B. Regulation of folate and one-carbon metabolism in mammalian cells. II. Effect of f-g-g synthetase substrate specificity and level on folate metabolism and f-g-gl specificity of metabolic cycles of one-carbon metabolism. J. Biol. Chem. 268: 21665-21673 (1993).

Lozada-Ramirez JD, Martinez-Martinez I, Sanchez-Ferrer A, Garcia-Carmona F. S-Adenosylhomocysteine hydrolase from Corynebacterium glutamicum: cloning, overexpression, purification, and biochemical characterization. J. Mol. Microbiol. Biotechnol. 15: 277-286 (2008).

Lu C, Bentley WE, Rao G. Comparisons of oxidative stress response genes in aerobic Escherichia coli fermentations. Biotechnol. Bioeng. 83: 864-870 (2003).

Lu G, Campbell W, Lindqvist Y, Schneider G. Crystallization and preliminary crystallographic studies of the FAD domain of corn NADH: nitrate reductase. J. Mol. Biol. 224: 277-279 (1992).

Lu G, Sehnke PC, Ferl RJ. Phosphorylation and calcium binding properties of an Arabidopsis GF14 brain protein homolog. Plant Cell 6: 501-510 (1994).

Lu JH, Liao CC. Site-directed mutagenesis of the aspartokinase gene lysC and its characterization in Brevibacterium flavum. Lett. Appl. Microbiol. 24: 211-213 (1997).

Lu M, Fu D. Structure of the zinc transporter YiiP. Science 317: 1746-1748 (2007).

Lu T, Wu Y, Song H. Nucleotide sequence of gltB gene encoding the large subunit of Rhodobacter sphaeroides glutamate synthase. Wei Sheng Wu Hsueh Pao 37: 87-94 (1997).

Lu W, Zhao B, Feng D, Yang S. Cloning and characterization of the Halobacillus trueperi betH gene, encoding the transport system for the compatible solute glycine betaine. FEMS Microbiol. Lett. 235: 393-399 (2004).

Lu WD, Chi ZM, Su CD. Identification of glycine betaine as compatible solute in Synechococcus sp. WH8102 and characterization of its N-methyltransferase genes involved in betaine synthesis. Arch. Microbiol. 186: 495-506 (2006).

Lu Y, Sharkey TD. The role of amylomaltase in maltose metabolism in the cytosol of photosynthetic cells. Planta 218: 466-473 (2004).

Lu Y, Steichen JM, Yao J, Sharkey TD. The role of cytosolic {alpha}-glucan phosphorylase in maltose metabolism and the comparison of amylomaltase in Arabidopsis and Escherichia coli. Plant Physiol. 142: 878-889 (2006).

Lubitz SP, Weiner JH. The Escherichia coli ynfEFGHI operon encodes polypeptides which are paralogues of dimethyl sulfoxide reductase (DmsABC). Arch. Biochem. Biophys. 418: 205-216 (2003).

Lucht JM, Bremer E. Adaptation of Escherichia coli to high osmolarity environments: osmoregulation of the high-affinity glycine betaine transport system proU. FEMS Microbiol. Rev. 14: 3-20 (1994).

Lucht JM, Bremer E. Characterization of mutations affecting the osmoregulated proU promoter of Escherichia coli and identification of 5' sequences required for high-level expression. J. Bacteriol. 173: 801-809 (1991).

Lucker J, El Tamer MK, Schwab W, Verstappen FW, van der Plas LH, Bouwmeester HJ, Verhoeven HA. Monoterpene biosynthesis in lemon (Citrus limon). cDNA isolation and functional analysis of four monoterpene synthases. Eur. J. Biochem. 269: 3160-3171 (2002).

Luka Z, Ham AJ, Norris JL, Yeo EJ, Yermalitsky V, Glenn B, Caprioli RM, Liebler DC, Wagner C. Identification of phosphorylation sites in glycine N-methyltransferase from rat liver. Protein Sci. 15: 785-794 (2006).

Luka Z, Wagner C. Expression and purification of glycine N-methyltransferases in Escherichia coli. Protein Expr. Purif. 28: 280-286 (2003).

Luka Z, Wagner C. Effect of naturally occurring mutations in human glycine N-methyltransferase on activity and conformation. Biochem. Biophys. Res. Commun. 312: 1067-1072 (2003).

Lukacin R, Groning I, Schiltz E, Britsch L, Matern U. Purification of recombinant flavanone 3beta-hydroxylase from petunia hybrida and assignment of the primary site of proteolytic degradation. Arch. Biochem. Biophys. 375: 364-370 (2000).

Lukacin R, Matern U, Specker S, Vogt T. Cations modulate the substrate specificity of bifunctional class I O-methyltransferase from Ammi majus. FEBS Lett. 577: 367-370 (2004).

Lukacin R, Wellmann F, Britsch L, Martens S, Matern U. Flavonol synthase from Citrus unshiu is a bifunctional dioxygenase. Phytochemistry 62: 287-292 (2003).

Lundrigan MD, De Veaux LC, Mann BJ, Kadner RJ. Separate regulatory systems for the repression of metE and btuB by vitamin B12 in Escherichia coli. Mol. Gen. Genet. 206: 401-407 (1987).

Lunn FA, Macleod TJ, Bearne SL. Mutational analysis of conserved glycine residues 142, 143 and 146 reveals Gly(142) is critical for tetramerization of CTP synthase from Escherichia coli. Biochem. J. 412: 113-121 (2008).

Lunn JE. Evolution of sucrose synthesis. Plant Physiol. 128: 1490-1500 (2002).

Lunn JE, Ashton AR, Hatch MD, Heldt HW. Purification, molecular cloning, and sequence analysis of sucrose-6F-phosphate phosphohydrolase from plants. Proc. Natl. Acad. Sci. U.S.A. 97: 12914-12919 (2000).

Lunn JE, Price GD, Furbank RT. Cloning and expression of a prokaryotic sucrose-phosphate synthase gene from the cyanobacterium Synechocystis sp. PCC 6803. Plant Mol. Biol. 40: 297-305 (1999).

Lunzer M, Miller SP, Felsheim R, Dean AM. The biochemical architecture of an ancient adaptive landscape. Science 310: 499-501 (2005).

Luo M, Weinstein JD, Walker CJ. Magnesium chelatase subunit D from pea: characterization of the cDNA, heterologous expression of an enzymatically active protein and immunoassay of the native protein. Plant Mol. Biol. 41: 721-731 (1999).

Luo S, Levine RL. Methionine in proteins defends against oxidative stress. FASEB J. 23: 464-472 (2009).

Luo YE, Fan DD, Shang LA, Shi HJ, Ma XX, Mi Y, Zhao GF. Analysis of metabolic flux in Escherichia coli expressing human-like collagen in fed-batch culture. Biotechnol. Lett. 30: 637-643 (2008).

Luong TN, Kirsch JF. A continuous coupled spectrophotometric assay for tyrosine aminotransferase activity with aromatic and other nonpolar amino acids. Anal. Biochem. 253: 46-49 (1997).

Lupold DS, Caoile AG, Stern DB. Polyadenylation occurs at multiple sites in maize mitochondrial cox2 mRNA and is independent of editing status. Plant Cell 11: 1565-1578 (1999).

Lutke-Eversloh T, Steinbuchel A. Biochemical and molecular characterization of a succinate semialdehyde dehydrogenase involved in the catabolism of 4-hydroxybutyric acid in Ralstonia eutropha. FEMS Microbiol. Lett. 181: 63-71 (1999).

Lutkenhaus J. Assembly dynamics of the bacterial MinCDE system and spatial regulation of the Z ring. Annu. Rev. Biochem. 76: 539-562 (2007).

Lutz KA, Knapp JE, Maliga P. Expression of bar in the plastid genome confers herbicide resistance. Plant Physiol. 125: 1585-1590 (2001).

Ly A, Henderson J, Lu A, Culham DE, Wood JM. Osmoregulatory systems of Escherichia coli: Identification of betaine- carnitine-choline transporter family member BetU and distributions of betU and trkG among pathogenic and nonpathogenic isolates. J. Bacteriol. 186: 296-306 (2004).

Lyi SM, Heller LI, Rutzke M, Welch RM, Kochian LV, Li L. Molecular and biochemical characterization of the selenocysteine Se-methyltransferase gene and Se-methylselenocysteine synthesis in broccoli. Plant Physiol. 138: 409-420 (2005).

Lyngstadaas A, Lobner-Olesen A, Boye E. Characterization of three genes in the dam-containing operon of Escherichia coli. Mol. Gen. Genet. 247: 546-554 (1995).

Lynn SP, Bauer CE, Chapman K, Gardner JF. Identification and characterization of mutants affecting transcription termination at the threonine operon attenuator. J. Mol. Biol. 183: 529-541 (1985).

Lytovchenko A, Hajirezaei M, Eickmeier I, Mittendorf V, Sonnewald U, Willmitzer L, Fernie AR. Expression of an Escherichia coli phosphoglucomutase in potato (Solanum tuberosum L.) results in minor changes in tuber metabolism and a considerable delay in tuber sprouting. Planta 221: 915-927 (2005).

Ma LQ, Pang XB, Shen HY, Pu GB, Wang HH, Lei CY, Wang H, Li GF, Liu BY, Ye HC. A novel type III polyketide synthase encoded by a three-intron gene from Polygonum cuspidatum. Planta 229: 457-469 (2009).

Maaheimo H, Fiaux J, Cakar ZP, Bailey JE, Sauer U, Szyperski T. Central carbon metabolism of Saccharomyces cerevisiae explored by biosynthetic fractional C-13 labeling of common amino acids. Eur. J. Biochem. 268: 2464-2479 (2001).

Mabood F, Smith DL. Pre-incubation of Bradyrhizobium japonicum with jasmonates accelerates nodulation and nitrogen fixation in soybean (Glycine max) at optimal and suboptimal root zone temperatures. Physiol. Plant. 125: 311-323 (2005).

MacDonald H, Cole J. Molecular cloning and functional analysis of the cysG and nirB genes of Escherichia coli K12, two closely-linked genes required for NADH-dependent nitrite reductase activity. Mol. Gen. Genet. 200: 328-334 (1985).

MacDonald H, Pope NR, Cole JA. Isolation, characterization and complementation analysis of nirB mutants of Escherichia coli deficient only in NADH-dependent nitrite reductase activity. J. Gen. Microbiol. 131: 2771-2782 (1985).

Macherel D, Bourguignon J, Forest E, Faure M, Cohen-Addad C, Douce R. Expression, lipoylation and structure determination of recombinant pea H-protein in Escherichia coli. Eur. J. Biochem. 236: 27-33 (1996).

MacKintosh C, Nimmo HG. Purification and properties of Escherichia coli isocitrate lyase. Biochem. Soc. Trans. 14: 320-321 (1986).

MacKintosh C, Nimmo HG. Purification and regulatory properties of isocitrate lyase from Escherichia coli ML308. Biochem. J. 250: 25-31 (1988).

MacMillan J, Ward DA, Phillips AL, Sanchez-Beltran MJ, Gaskin P, Lange T, Hedden P. Gibberellin biosynthesis from gibberellin A12-aldehyde in endosperm and embryos of Marah macrocarpus. Plant Physiol. 113: 1369-1377 (1997).

MacMillan SV, Alexander DA, Culham DE, Kunte HJ, Marshall EV, Rochon D, Wood JM. The ion coupling and organic substrate specificities of osmoregulatory transporter ProP in Escherichia coli. Biochim. Biophys. Acta 1420: 30-44 (1999).

Macol C, Dutta M, Stec B, Tsuruta H, Kantrowitz ER. The 80s loop of the catalytic chain of Escherichia coli aspartate transcarbamoylase is critical for catalysis and homotropic cooperativity. Protein Sci. 8: 1305-1313 (1999).

Macrae M, Coffino P. Complementation of a polyamine-deficient Escherichia coli mutant by expression of mouse ornithine decarboxylase. Mol. Cell Biol. 7: 564-567 (1987).

Maddula S, Blank LM, Schmid A, Baumbach JI. Detection of volatile metabolites of Escherichia coli by multi capillary column coupled ion mobility spectrometry. Anal. Bioanal. Chem. 394: 791-800 (2009).

Maeda K, Finnie C, OStergaard O, Svensson B. Identification, cloning and characterization of two thioredoxin h isoforms, HvTrxh1 and HvTrxh2, from the barley seed proteome. Eur. J. Biochem. 270: 2633-2643 (2003).

Magalhaes M, Pereira C, Basso L, Santos D. Cloning and expression of functional shikimate dehydrogenase (EC from Mycobacterium tuberculosis H37Rv. Protein Expr. Purif. 26: 59-64 (2002).

Magalon A, Asso M, Guigliarelli B, Rothery RA, Bertrand P, Giordano G, Blasco F. Molybdenum cofactor properties and [Fe-S] cluster coordination in Escherichia coli nitrate reductase A: investigation by site-directed mutagenesis of the conserved his-50 residue in the NarG subunit. Biochemistry 37: 7363-7370 (1998).

Magalon A, Rothery RA, Lemesle-Meunier D, Frixon C, Weiner JH, Blasco F. Inhibitor binding within the NarI subunit (cytochrome bnr) of Escherichia coli nitrate reductase A. J. Biol. Chem. 273: 10851-10856 (1998).

Magasanik B, Bueno R. The role of uridylyltransferase and PII in the regulation of the synthesis of glutamine synthetase in Escherichia coli. Curr. Top. Cell Regul. 27: 215-220 (1985).

Mahadevan R, Bond DR, Butler JE, Esteve-Nunez A, Coppi MV, Palsson BO, Schilling CH, Lovley DR. Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling. Appl. Environ. Microbiol. 72: 1558-1568 (2006).

Mahadevan R, Edwards JS, Doyle FJ 3rd. Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophys. J. 83: 1331-1340 (2002).

Mahan MJ, Csonka LN. Genetic analysis of the proBA genes of Salmonella typhimurium: physical and genetic analyses of the cloned proB+ A+ genes of Escherichia coli and of a mutant allele that confers proline overproduction and enhanced osmotolerance. J. Bacteriol. 156: 1249-1262 (1983).

Maiti MK, Krishnasamy S, Owen HA, Makaroff CA. Molecular characterization of glyoxalase II from Arabidopsis thaliana. Plant Mol. Biol. 35: 471-481 (1997).

Makino T, Harada H, Ikenaga H, Matsuda S, Takaichi S, Shindo K, Sandmann G, Ogata T, Misawa N. Characterization of cyanobacterial carotenoid ketolase CrtW and hydroxylase CrtR by complementation analysis in Escherichia coli. Plant Cell Physiol. 49: 1867-1878 (2008).

Maklashina E, Berthold DA, Cecchini G. Anaerobic expression of Escherichia coli succinate dehydrogenase: functional replacement of fumarate reductase in the respiratory chain during anaerobic growth. J. Bacteriol. 180: 5989-5996 (1998).

Malashkevich VN, De Biase D, Markovic-Housley Z, Schlunegger MP, Bossa F, Jansonius JN. Crystallization and preliminary X-ray analysis of the beta-isoform of glutamate decarboxylase from Escherichia coli. Acta Crystallogr. D. Biol. Crystallogr. 54: 1020-1022 (1998).

Malashkevich VN, Jager J, Ziak M, Sauder U, Gehring H, Christen P, Jansonius JN. Structural basis for the catalytic activity of aspartate aminotransferase K258H lacking the pyridoxal 5'-phosphate-binding lysine residue. Biochemistry 34: 405-414 (1995).

Maldonado-Mendoza IE, Lopez-Meyer M, Galef JR, Burnett RJ, Nessler CL. Molecular analysis of a new member of the opium poppy tyrosine/3,4-dihydroxyphenylalanine decarboxylase gene family. Plant Physiol. 110: 43-49 (1996).

Malmberg RL, Smith KE, Bell E, Cellino ML. Arginine decarboxylase of oats is clipped from a precursor into two polypeptides found in the soluble enzyme. Plant Physiol. 100: 146-152 (1992).

Malmberg RL, Watson MB, Galloway GL, Yu W. Molecular genetic analyses of plant polyamines. Crit. Rev. Plant Sci. 17: 199-224 (1998).

Malone AS, Chung YK, Yousef AE. Genes of Escherichia coli O157:H7 that are involved in high-pressure resistance. Appl. Environ. Microbiol. 72: 2661-2671 (2006).

Malumbres M, Mateos LM, Guerrero C, Martin JF. Molecular cloning of the hom-thrC-thrB cluster from Bacillus sp. ULM1: expression of the thrC gene in Escherichia coli and corynebacteria, and evolutionary relationships of the threonine genes. Folia Microbiol. (Praha) 40: 595-606 (1995).

Malumbres M, Mateos LM, Lumbreras MA, Guerrero C, Martin JF. Analysis and expression of the thrC gene of Brevibacterium lactofermentum and characterization of the encoded threonine synthase. Appl. Environ. Microbiol. 60: 2209-2219 (1994).

Manabe T, Hasumi A, Sugiyama M, Yamazaki M, Saito K. Alliinase [S-alk(en)yl-L-cysteine sulfoxide lyase] from Allium tuberosum (Chinese chive). Purification, localization, cDNA cloning and heterologous functional expression. Eur. J. Biochem. 257: 21-30 (1998).

Mandon K, Osteras M, Boncompagni E, Trinchant JC, Spennato G, Poggi MC, Le Rudulier D. The Sinorhizobium meliloti glycine betaine biosynthetic genes (betlCBA) are induced by choline and highly expressed in bacteroids. Mol. Plant Microbe Interact. 16: 709-719 (2003).

Mansilla MC, Albanesi D, de Mendoza D. Transcriptional control of the sulfur-regulated cysH operon, containing genes involved in L-cysteine biosynthesis in Bacillus subtilis. J. Bacteriol. 182: 5885-5892 (2000).

Mantzaris NV, Liou J-J, Daoutidis P, Srienc F. Numerical solution of a mass structured cell population balance model in an environment of changing substrate concentration. J. Biotechnol. 71: 157-174 (1999).

Manucharian KG, Gening LV, Gusiatiner MM, Gazarian KG. Design of a gene coding encoding a polypeptide, mixing the enzyme activity of Escherichia coli homoserine kinase and threonine synthetase. Mol. Gen. Mikrobiol. Virusol. 2: 12-15 (1991).

Mao XJ, Huo YX, Buck M, Kolb A, Wang YP. Interplay between CRP-cAMP and PII-Ntr systems forms novel regulatory network between carbon metabolism and nitrogen assimilation in Escherichia coli. Nucleic Acids Res. 35: 1432-1440 (2007).

Mao Z, Shin HD, Chen R. A recombinant E. coli bioprocess for hyaluronan synthesis. Appl. Microbiol. Biotechnol. 84: 63-69 (2009).

Marais S, Thomson JA, Farrant JM, Mundree SG. XvVHA-c''1 - a novel stress-responsive V-ATPase subunit c'' homologue isolated from the resurrection plant Xerophyta viscosa. Physiol. Plant. 122: 54-61 (2004).

Maranas CD, Burgard AP. Web site review: review of EcoCyc and MetaCyc databases. Metab. Eng. 3: 98-99 (2001).

Maras B, Sweeney G, Barra D, Bossa F, John RA. The amino acid sequence of glutamate decarboxylase from Escherichia coli. Evolutionary relationship between mammalian and bacterial enzymes. Eur. J. Biochem. 204: 93-98 (1992).

Marasco EK, Vay K, Schmidt-Dannert C. Identification of carotenoid cleavage dioxygenases from Nostoc sp. PCC 7120 with different cleavage activities. J. Biol. Chem. 281: 31583-31593 (2006).

Marczak JE, Brandriss MC. Isolation of constitutive mutations affecting the proline utilization pathway in Saccharomyces cerevisiae and molecular analysis of the PUT3 transcriptional activator. Mol. Cell Biol. 9: 4696-4705 (1989).

Marechal LR. Transport and metabolism of trehalose in Escherichia coli and Salmonella typhimurium. Arch. Microbiol. 137: 70-73 (1984).

Marek LE, Henson JM. Cloning and expression of the Escherichia coli K-12 sad gene. J. Bacteriol. 170: 991-994 (1988).

Marelja Z, Stocklein W, Nimtz M, Leimkuhler S. A novel role for human Nfs1 in the cytoplasm: Nfs1 acts as a sulfur donor for MOCS3, a protein involved in molybdenum cofactor biosynthesis. J. Biol. Chem. 283: 25178-25185 (2008).

Marillia EF, MacPherson JM, Tsang EWT, Van Audenhove K, Keller WA, GrootWassink JWD. Molecular cloning of a Brassica napus thiohydroximate S-glucosyltransferase gene and its expression in Escherichia coli. Physiol. Plant. 113: 176-184 (2001).

Marin K, Zuther E, Kerstan T, Kunert A, Hagemann M. The ggpS gene from Synechocystis sp. strain PCC 6803 encoding glucosyl-glycerol-phosphate synthase is involved in osmolyte synthesis. J. Bacteriol. 180: 4843-4849 (1998).

Mariscal V, Rexach J, Fernandez E, Galvan A. The plastidic nitrite transporter NAR1;1 improves nitrate use efficiency for growth in Chlamydomonas. Plant Cell Environ. 27: 1321-1328 (2004).

Markham GD, Hafner EW, Tabor CW, Tabor H. S-Adenosylmethionine synthetase from Escherichia coli. J. Biol. Chem. 255: 9082-9092 (1980).

Markham JE, Kruger NJ. Kinetic properties of bifunctional 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase from spinach leaves. Eur. J. Biochem. 269: 1267-1277 (2002).

Marquardt JL, Siegele DA, Kolter R, Walsh CT. Cloning and sequencing of Escherichia coli murZ and purification of its product, a UDP-N-acetylglucosamine enolpyruvyl transferase. J. Bacteriol. 174: 5748-5752 (1992).

Marquez G, Sousa JM, Sanchez F. Cloning and expression in Escherichia coli of genes involved in the lysine pathway of Brevibacterium lactofermentum. J. Bacteriol. 164: 379-383 (1985).

Marrs KA, Alfenito MR, Lloyd AM, Walbot V. A glutathione S-transferase involved in vacuolar transfer encoded by the maize gene Bronze-2. Nature 375: 397-400 (1995).

Marsolier MC, Debrosses G, Hirel B. Identification of several soybean cytosolic glutamine synthetase transcripts highly or specifically expressed in nodules: expression studies using one of the corresponding genes in transgenic Lotus corniculatus. Plant Mol. Biol. 27: 1-15 (1995).

Martelli C, De Martino A, Marinari E, Marsili M, Castillo IP. Identifying essential genes in Escherichia coli from a metabolic optimization principle. Proc. Natl. Acad. Sci. U.S.A. 106: 2607-2611 (2009).

Martens S, Teeri T, Forkmann G. Heterologous expression of dihydroflavonol 4-reductases from various plants. FEBS Lett. 531: 453-458 (2002).

Martin DD, Ciulla RA, Roberts MF. Osmoadaptation in archaea. Appl. Environ. Microbiol. 65: 1815-1825 (1999).

Martin DE, Reinhold-Hurek B. Distinct roles of PII-like signal transmitter proteins and amtB in regulation of nif gene expression, nitrogenase activity, and posttranslational modification of NifH in Azoarcus sp strain BH72. J. Bacteriol. 184: 2251-2259 (2002).

Martin DM, Bohlmann J. Identification of Vitis vinifera (-)-alpha-terpineol synthase by in silico screening of full-length cDNA ESTs and functional characterization of recombinant terpene synthase. Phytochemistry 65: 1223-1229 (2004).

Martin DN, Proebsting WM, Parks TD, Dougherty WG, Lange T, Lewis MJ, Gaskin P, Hedden P. Feed-back regulation of gibberellin biosynthesis and gene expression in Pisum sativum L. Planta 200: 159-166 (1996).

Martin G, Haehnel W, Boger P. Oxidative inactivation of glutamine synthetase from the cyanobacterium Anabaena variabilis. J. Bacteriol. 179: 730-734 (1997).

Martin T, Sharma R, Sippel C, Waegemann K, Soll J, Vothknecht UC. A protein kinase family in Arabidopsis phosphorylates chloroplast precursor proteins. J. Biol. Chem. 281: 40216-40223 (2006).

Martinez I, Zhu J, Lin H, Bennett GN, San KY. Replacing Escherichia coli NAD-dependent glyceraldehyde 3-phosphate dehydrogenase (GAPDH) with a NADP-dependent enzyme from Clostridium acetobutylicum facilitates NADPH dependent pathways. Metab. Eng. 10: 352-359 (2008).

Martinez MB, Flickinger MC, Nelsestuen GL. Steady-state enzyme kinetics in the Escherichia coli periplasm: a model of whole cell biocatalyst. J. Biotechnol. 71: 59-66 (1999).

Martinez-Torres D, Buades C, Latorre A, Moya A. Molecular systematics of aphids and their primary endosymbionts. Mol. Phylogenet. Evol. 20: 437-449 (2001).

Martini F, Angelaccio S, Pascarella S, Barra D, Bossa F, Schirch V. The primary structure of rabbit liver cytosolic serine hydroxymethyltransferase. J. Biol. Chem. 262: 5499-5509 (1987).

Martini F, Maras B, Tanci P, Angelaccio S, Pascarella S, Barra D, Bossa F, Schirch V. The primary structure of rabbit liver mitochondrial serine hydroxymethyltransferase. J. Biol. Chem. 264: 8509-8519 (1989).

Marvin ME, Williams PH, Cashmore AM. The isolation and characterisation of a Saccharomyces cerevisiae gene (LIP2) involved in the attachment of lipoic acid groups to mitochondrial enzymes. FEMS Microbiol. Lett. 199: 131-136 (2001).

Mason RP, Sanders JK, Crawford A, Hunter BK. Formaldehyde metabolism by Escherichia coli. Detection by in vivo 13C NMR spectroscopy of S-(hydroxymethyl)glutathione as a transient intracellular intermediate. Biochemistry 25: 4504-4507 (1986).

Massarelli I, Forlani G, Ricca E, De Felice M. Enhanced and feedback-resistant gamma-glutamyl kinase activity of an Escherichia coli transformant carrying a mutated proB gene of Streptococcus thermophilus. FEMS Microbiol. Lett. 182: 143-147 (2000).

Massiah AJ, Hartley MR. Wheat ribosome-inactivating proteins: seed and leaf forms with different specificities and cofactor requirements. Planta 197: 633-640 (1995).

Massonneau A, Condamine P, Wisniewski JP, Zivy M, Rogowsky PM. Maize cystatins respond to developmental cues, cold stress and drought. Biochim. Biophys. Acta 1729: 186-199 (2005).

Massou S, Nicolas C, Letisse F, Portais JC. Application of 2D-TOCSY NMR to the measurement of specific 13C-enrichments in complex mixtures of 13C-labeled metabolites. Metab. Eng. 9: 252-257 (2007).

Matak-Vinkovic D, Vinkovic M, Saldanha SA, Ashurst JL, von Delft F, Inoue T, Miguel RN, Smith AG, Blundell TL, Abell C. Crystal structure of Escherichia coli ketopantoate reductase at 1.7 A resolution and insight into the enzyme mechanism. Biochemistry 40: 14493-14500 (2001).

Matchett WH, Lacy AM, DeMoss JA. Orientation of enzymic domains in tryptophan synthase of Neurospora crassa: an immunoblot analysis of TRP3 mutant products. Mol. Gen. Genet. 208: 398-407 (1987).

Mateos LM, Pisabarro A, Patek M, Malumbres M, Guerrero C, Eikmanns BJ, Sahm H, Martin JF. Transcriptional analysis and regulatory signals of the hom-thrB cluster of Brevibacterium lactofermentum. J. Bacteriol. 176: 7362-7371 (1994).

Matsuda N, Kobayashi H, Katoh H, Ogawa T, Futatsugi L, Nakamura T, Bakker EP, Uozumi N. Na+-dependent K+ uptake Ktr system from the cyanobacterium Synechocystis sp. PCC 6803 and its role in the early phases of cell adaptation to hyperosmotic shock. J. Biol. Chem. 279: 54952-54962 (2004).

Matsumura T, Kimata-Ariga Y, Sakakibara H, Sugiyama T, Murata H, Takao T, Shimonishi Y, Hase T. Complementary DNA cloning and characterization of ferredoxin localized in bundle-sheath cells of maize leaves. Plant Physiol. 119: 481-488 (1999).

Matsunami H, Kawaguchi H, Inagaki K, Eguchi T, Kakinuma K, Tanaka H. Overproduction and substrate specificity of 3-isopropylmalate dehydrogenase from Thiobacillus ferrooxidans. Biosci. Biotechnol. Biochem. 62: 372-373 (1998).

Matsushika A, Mizuno T. The structure and function of the histidine-containing phosphotransfer (HPt) signaling domain of the Escherichia coli ArcB sensor. J. Biochem. (Tokyo) 124: 440-445 (1998).

Mattanovich D, Kramer W, Luttich C, Weik R, Bayer K, Katinger H. Rational design of an improved induction scheme for recombinant Escherichia coli. Biotechnol. Bioeng. 58: 296-298 (1998).

Mattei P, Kast P, Hilvert D. Bacillus subtilis chorismate mutase is partially diffusion-controlled. Eur. J. Biochem. 261: 25-32 (1999).

Matthews PD, Wurtzel ET. Metabolic engineering of carotenoid accumulation in Escherichia coli by modulation of the isoprenoid precursor pool with expression of deoxyxylulose phosphate synthase. Appl. Microbiol. Biotechnol. 53: 396-400 (2000).

Matthews RG, Smith AE, Zhou ZHS, Taurog RE, Bandarian V, Evans JC, Ludwig M. Cobalamin-dependent and cobalamin-independent methionine synthases: are there two solutions to the same chemical problem? Helv. Chim. Acta 86: 3939-3954 (2003).

Maurizi MR, Ginsburg A. Active site ligand stabilization of quaternary structures of glutamine synthetase from Escherichia coli. J. Biol. Chem. 257: 7246-7251 (1982).

Maurizi MR, Ginsburg A. Reactivation of glutamine synthetase from Escherichia coli after auto-inactivation with L-methionine-S-sulfoximine, ATP, and Mn2+. J. Biol. Chem. 257: 4271-4278 (1982).

Maurizi MR, Ginsburg A. Adenosine 5'-triphosphate analogues as structural probes for Escherichia coli glutamine synthetase. Biochemistry 25: 131-140 (1986).

Maurizi MR, Rasulova F. Degradation of L-glutamate dehydrogenase from Escherichia coli: Allosteric regulation of enzyme stability. Arch. Biochem. Biophys. 397: 206-216 (2002).

Maury S, Geoffroy P, Legrand M. Tobacco O-methyltransferases involved in phenylpropanoid metabolism. The … Plant Physiol. 121: 215-224 (1999).

Maxon ME, Redfield B, Cai XY, Shoeman R, Fujita K, Fisher W, Stauffer G,. Regulation of methionine synthesis in Escherichia coli: effect of the MetR protein on the expression of the metE and metR genes. Proc. Natl. Acad. Sci. U.S.A. 86: 85-89 (1989).

May G, Faatz E, Lucht JM, Haardt M, Bolliger M, Bremer E. Characterization of the osmoregulated Escherichia coli proU promoter and identification of ProV as a membrane-associated protein. Mol. Microbiol. 3: 1521-1531 (1989).

May G, Faatz E, Villarejo M, Bremer E. Binding protein dependent transport of glycine betaine and its osmotic regulation in Escherichia coli K12. Mol. Gen. Genet. 205: 225-233 (1986).

May MJ, Leaver CJ. Arabidopsis thaliana gamma-glutamylcysteine synthetase is structurally unrelated to mammalian, yeast, and Escherichia coli homologs. Proc. Natl. Acad. Sci. U.S.A. 91: 10059-10063 (1994).

Mayer G, Launhardt H, Munder T. Application of the green fluorescent protein as a reporter for Ace1-based, two-hybrid studies. Biotechniques 27: 92-94 (1999).

Mazoch J, Kunak M, Kucera I, van Spanning RJM. Fine-tuned regulation by oxygen and nitric oxide of the activity of a semi- synthetic FNR-dependent promoter and expression of denitrification enzymes in Paracoccus denitrificans. Microbiology (U.K.) 149: 3405-3412 (2003).

McAlister FM, Lewis-Henderson WR, Jenkins CLD, Watson JM. Isolation and expression of a cinnamyl alcohol dehydrogenase cDNA from perennial ryegrass (Lolium perenne). Aust. J. Plant Physiol. 28: 1085-1094 (2001).

McCoy AJ, Adams NE, Hudson AO, Gilvarg C, Leustek T, Maurelli AT. L,L-Diaminopimelate aminotransferase, a trans-kingdom enzyme shared by Chlamydia and plants for synthesis of diaminopimelate/lysine. Proc. Natl. Acad. Sci. U.S.A. 103: 17909-17914 (2006).

McCoy JG, Arabshahi A, Bitto E, Bingman CA, Ruzicka FJ, Frey PA, Phillips GN Jr. Structure and mechanism of an ADP-glucose phosphorylase from Arabidopsis thaliana. Biochemistry 45: 3154-3162 (2006).

McDevitt CA, Hanson GR, Noble CJ, Cheesman MR, McEwan AG. Characterization of the redox centers in dimethyl sulfide dehydrogenase from Rhodovulum sulfidophilum. Biochemistry 41: 15234-15244 (2002).

McDougall J, Kaasen I, Strom AR. A yeast gene for trehalose-6-phosphate synthase and its complementation of an Escherichia coli otsA mutant. FEMS Microbiol. Lett. 107: 25-30 (1993).

McFarland N, McCarter L, Artz S, Kustu S. Nitrogen regulatory locus "glnR" of enteric bacteria is composed of cistrons ntrB and ntrC: identification of their protein products. Proc. Natl. Acad. Sci. U.S.A. 78: 2135-2139 (1981).

McKay SA, Hunter WL, Godard KA, Wang SX, Martin DM, Bohlmann J, Plant AL. Insect attack and wounding induce traumatic resin duct development and gene expression of (-)-pinene synthase in sitka spruce. Plant Physiol. 133: 368-378 (2003).

McKie AE, Edlind T, Walker J, Mottram JC, Coombs GH. The primitive protozoon Trichomonas vaginalis contains two methionine gamma-lyase genes that encode members of the gamma-family of pyridoxal 5'-phosphate-dependent enzymes. J. Biol. Chem. 273: 5549-5556 (1998).

McLaggan D, Epstein W. Escherichia coli accumulates the eukaryotic osmolyte taurine at high osmolarity. FEMS Microbiol. Lett. 65: 209-213 (1991).

McLaggan D, Jones MA, Gouesbet G, Levina N, Lindey S, Epstein W, Booth IR. Analysis of the kefA2 mutation suggests that KefA is a cation-specific channel involved in osmotic adaptation in Escherichia coli. Mol. Microbiol. 43: 521-536 (2002).

McLeod SM, Xu JM, Cramton SE, Gaal T, Gourse RL, Johnson RC. Localization of amino acids required for Fis to function as a class II transcriptional activator at the RpoS-dependent proP P2 promoter. J. Mol. Biol. 294: 333-346 (1999).

McNeil JB, Flynn J, Tsao N, Monschau N, Stahmann K, Haynes RH, McIntosh EM, Pearlman RE. Glycine metabolism in Candida albicans: characterization of the serine hydroxymethyltransferase (SHM1, SHM2) and threonine aldolase (GLY1) genes. Yeast 16: 167-175 (2000).

McNicholas PM, Gunsalus RP. The molybdate-responsive Escherichia coli ModE transcriptional regulator coordinates periplasmic nitrate reductase (napFDAGHBC) operon expression with nitrate and molybdate availability. J. Bacteriol. 184: 3253-3259 (2002).

McPherson MJ, Wootton JC. Complete nucleotide sequence of the Escherichia coli gdhA gene. Nucleic Acids Res. 11: 5257-5266 (1983).

McQualter RB, Chong BF, Meyer K, Van Dyk DE, O'Shea MG, Walton NJ, Viitanen PV, Brumbley SM. Initial evaluation of sugarcane as a production platform for p-hydroxybenzoic acid. Plant Biotechnol. J. 3: 29-41 (2005).

McQueney MS, Anderson KS, Markham GD. Energetics of S-adenosylmethionine synthetase catalysis. Biochemistry 39: 4443-4454 (2000).

Mee B, Kelleher D, Frias J, Malone R, Tipton KF, Henehan GT, Windle HJ. Characterization of cinnamyl alcohol dehydrogenase of Helicobacter pylori. An aldehyde dismutating enzyme. FEBS J. 272: 1255-1264 (2005).

Meganathan R. Ubiquinone biosynthesis in microorganisms. FEMS Microbiol. Lett. 203: 131-139 (2001).

Mehta BD, Jog SP, Johnson SC, Murthy PP. Lily pollen alkaline phytase is a histidine phosphatase similar to mammalian multiple inositol polyphosphate phosphatase (MINPP). Phytochemistry 67: 1874-1886 (2006).

Mehta PK, Hale TI, Christen P. Evolutionary relationships among aminotransferases. Tyrosine aminotransferase, histidinol-phosphate aminotransferase, and aspartate aminotransferase are homologous proteins. Eur. J. Biochem. 186: 249-253 (1989).

Mehta R, Pearson JT, Mahajan S, Nath A, Hickey MJ, Sherman DR, Atkins WM. Adenylylation and catalytic properties of Mycobacterium tuberculosis glutamine synthetase expressed in Escherichia coli versus mycobacteria. J. Biol. Chem. 279: 22477-22482 (2004).

Meijer AH, Lopes Cardoso MI, Voskuilen JT, de Waal A, Verpoorte R, Hoge JH. Isolation and characterization of a cDNA clone from Catharanthus roseus encoding NADPH:cytochrome P-450 reductase, an enzyme essential for reactions catalysed by cytochrome P-450 mono-oxygenases in plants. Plant J. 4: 47-60 (1993).

Meinhardt SW, Cheng W, Kwon CY, Donohue CM, Rasmussen JB. Role of the arginyl-glycyl-aspartic motif in the action of Ptr ToxA produced by Pyrenophora tritici-repentis. Plant Physiol. 130: 1545-1551 (2002).

Mellies J, Brems R, Villarejo M. The Escherichia coli proU promoter element and its contribution to osmotically signaled transcription activation. J. Bacteriol. 176: 3638-3645 (1994).

Mellies J, Wise A, Villarejo M. Two different Escherichia coli proP promoters respond to osmotic and growth phase signals. J. Bacteriol. 177: 144-151 (1995).

Mendel RR, Schwarz G. Biosynthesis and molecular biology of the molybdenum cofactor (Moco). Met. Ions Biol. Syst. 39: 317-368 (2002).

Menzella HG, Ceccarelli EA, Gramajo HC. Novel Escherichia coli strain allows efficient recombinant protein production using lactose as inducer. Biotechnol. Bioeng. 82: 809-817 (2003).

Merabet EK, Walker MC, Yuen HK, Sikorski JA. Differential scanning calorimetric study of 5-enolpyruvoyl shikimate-3-phosphate synthase and its complexes with shikimate-3-phosphate and glyphosate: irreversible thermal transitions. Biochim. Biophys. Acta 1161: 272-278 (1993).

Merighi M, Majerczak DR, Stover EH, Coplin DL. The HrpX/HrpY two-component system activates hrpS expression, the first step in the regulatory cascade controlling the Hrp regulon in Pantoea stewartii subsp. stewartii. Mol. Plant Microbe Interact. 16: 238-248 (2003).

Merkamm M, Chassagnole C, Lindley ND, Guyonvarch A. Ketopantoate reductase activity is only encoded by ilvC in Corynebacterium glutamicum. J. Biotechnol. 104: 253-260 (2003).

Merkel WK, Nichols BP. Characterization and sequence of the Escherichia coli panBCD gene cluster. FEMS Microbiol. Lett. 143: 247-252 (1996).

Mesa S, Ucurum Z, Hennecke H, Fischer HM. Transcription activation in vitro by the Bradyrhizobium japonicum regulatory protein FixK2. J. Bacteriol. 187: 3329-3338 (2005).

Metcalf WW, Zhang JK, Shi X, Wolfe RS. Molecular, genetic, and biochemical characterization of the serC gene of Methanosarcina barkeri Fusaro. J. Bacteriol. 178: 5797-5802 (1996).

Metheringham R, Tyson KL, Crooke H, Missiakas D, Raina S, Cole JA. Effects of mutations in genes for proteins involved in disulphide bond formation in the periplasm on the activities of anaerobically induced electron transfer chains in Escherichia coli K12. Mol. Gen. Genet. 253: 95-102 (1996).

Metz JG, Kuner J, Rosenzweig B, Lippmeier JC, Roessler P, Zirkle R. Biochemical characterization of polyunsaturated fatty acid synthesis in Schizochytrium: release of the products as free fatty acids. Plant Physiol. Biochem. 47: 472-478 (2009).

Metz JG, Pollard MR, Anderson L, Hayes TR, Lassner MW. Purification of a jojoba embryo fatty acyl-coenzyme A reductase and expression of its cDNA in high erucic acid rapeseed. Plant Physiol. 122: 635-644 (2000).

Metzer E, Halpern YS. In vivo cloning and characterization of the gabCTDP gene cluster of Escherichia coli K-12. J. Bacteriol. 172: 3250-3256 (1990).

Metzer E, Levitz R, Halpern YS. Isolation and properties of Escherichia coli K-12 mutants impaired in the utilization of gamma-aminobutyrate. J. Bacteriol. 137: 1111-1118 (1979).

Meury J. Immediate and transient inhibition of the respiration of Escherichia coli under hyperosmotic shock. FEMS Microbiol. Lett. 121: 281-286 (1994).

Meury J. Glycine betaine reverses the effects of osmotic stress on DNA replication and cellular division in Escherichia coli. Arch. Microbiol. 149: 232-239 (1988).

Meury J, Bahloul A, Kohiyama M. Impairment of nucleoid segregation and cell division at high osmolarity in a strain of Escherichia coli overproducing the chaperone DnaK. FEMS Microbiol. Lett. 113: 93-99 (1993).

Meyer A, Held M, Schmid A, Kohler HP, Witholt B. Synthesis of 3-tert-butylcatechol by an engineered monooxygenase. Biotechnol. Bioeng. 81: 518-524 (2003).

Meyer JM, Stadtman ER. Adenylylation state of glutamine synthetase and permeability properties of Pseudomonas fluorescens. Arch. Biochem. Biophys. 246: 622-632 (1986).

Meyer JM, Stadtman ER. Glutamine synthetase of pseudomonads: some biochemical and physicochemical properties. J. Bacteriol. 146: 705-712 (1981).

Meyer SE, Granett S, Jung JU, Villarejo MR. Osmotic regulation of PhoE porin synthesis in Escherichia coli. J. Bacteriol. 172: 5501-5502 (1990).

Meynial Salles I, Forchhammer N, Croux C, Girbal L, Soucaille P. Evolution of a Saccharomyces cerevisiae metabolic pathway in Escherichia coli. Metab. Eng. 9: 152-159 (2007).

Miao GH, Hirel B, Marsolier MC, Ridge RW, Verma DP. Ammonia-regulated expression of a soybean gene encoding cytosolic glutamine synthetase in transgenic Lotus corniculatus. Plant Cell 3: 11-22 (1991).

Michael AJ, Furze JM, Rhodes MJ, Burtin D. Molecular cloning and functional identification of a plant ornithine decarboxylase cDNA. Biochem. J. 314: 241-248 (1996).

Michel-Reydellet N, Calhoun K, Swartz J. Amino acid stabilization for cell-free protein synthesis by modification of the Escherichia coli genome. Metab. Eng. 6: 197-203 (2004).

Michels AK, Wedel N, Kroth PG. Diatom plastids possess a phosphoribulokinase with an altered regulation and no oxidative pentose phosphate pathway. Plant Physiol. 137: 911-920 (2005).

Miernyk JA, Hayman TG. ATPase activity and molecular chaperone function of the stress70 proteins. Plant Physiol. 110: 419-424 (1996).

Mihlan M, Homann V, Liu TW, Tudzynski B. AREA directly mediates nitrogen regulation of gibberellin biosynthesis in Gibberella fujikuroi, but its activity is not affected by NMR. Mol. Microbiol. 47: 975-991 (2003).

Mikkelsen MD, Hansen CH, Wittstock U, Halkier BA. Cytochrome P450 CYP79B2 from Arabidopsis catalyzes the conversion of tryptophan to indole-3-acetaldoxime, a precursor of indole glucosinolates and indole-3-acetic acid. J. Biol. Chem. 275: 33712-33717 (2000).

Mikkelsen MD, Naur P, Halkier BA. Arabidopsis mutants in the C-S lyase of glucosinolate biosynthesis establish a critical role for indole-3-acetaldoxime in auxin homeostasis. Plant J. 37: 770-777 (2004).

Milano A, De Rossi E, Zanaria E, Barbierato L, Ciferri O, Riccardi G. Molecular characterization of the genes encoding acetohydroxy acid synthase in the cyanobacterium Spirulina platensis. J. Gen. Microbiol. 138: 1399-1408 (1992).

Miles EW, Kawasaki H, Ahmed SA, Morita H, Morita H, Nagata S. The beta subunit of tryptophan synthase. Clarification of the roles of histidine 86, lysine 87, arginine 148, cysteine 170, and cysteine 230. J. Biol. Chem. 264: 6280-6287 (1989).

Miles EW, McPhie P, Yutani K. Evidence that glutamic acid 49 of tryptophan synthase alpha subunit is a catalytic residue. Inactive mutant proteins substituted at position 49 bind ligands and transmit ligand-dependent to the beta subunit. J. Biol. Chem. 263: 8611-8614 (1988).

Milkowski C, Baumert A, Strack D. Cloning and heterologous expression of a rape cDNA encoding UDP-glucose:sinapate glucosyltransferase. Planta 211: 883-886 (2000).

Mille Y, Beney L, Gervais P. Magnitude and kinetics of rehydration influence the viability of dehydrated E. coli K-12. Biotechnol. Bioeng. 83: 578-582 (2003).

Miller B, Heuser T, Zimmer W. A Synechococcus leopoliensis SAUG 1402-1 operon harboring the 1-deoxyxylulose 5-phosphate synthase gene and two additional open reading frames is functionally involved in the dimethylallyl diphosphate synthesis. FEBS Lett. 460: 485-490 (1999).

Miller B, Oschinski C, Zimmer W. First isolation of an isoprene synthase gene from poplar and successful expression of the gene in Escherichia coli. Planta 213: 483-487 (2001).

Miller ES, Brenchley JE. Cloning and characterization of gdhA, the structural gene for glutamate dehydrogenase of Salmonella typhimurium. J. Bacteriol. 157: 171-178 (1984).

Millevoi S, Pasquo A, Chiaraluce R, Consalvi V, Giangiacomo L, Britton KL, Stillman TJ, Rice DW, Engel PC. A monomeric mutant of Clostridium symbiosum glutamate dehydrogenase: comparison with a structured monomeric intermediate obtained during refolding. Protein Sci. 7: 966-974 (1998).

Millian NS, Garrow TA. Human betaine-homocysteine methyltransferase is a zinc metalloenzyme. Arch. Biochem. Biophys. 356: 93-98 (1998).

Mills RF, Krijger GC, Baccarini PJ, Hall JL, Williams LE. Functional expression of AtHMA4, a P1B-type ATPase of the Zn/Co/Cd/Pb subclass. Plant J. 35: 164-176 (2003).

Milner JL, McClellan DJ, Wood JM. Factors reducing and promoting the effectiveness of proline as an osmoprotectant in Escherichia coli K12. J. Gen. Microbiol. 133: 1851-1860 (1987).

Milner JL, Wood JM. Insertion proQ220::Tn5 alters regulation of proline porter II, a transporter of proline and glycine betaine in Escherichia coli. J. Bacteriol. 171: 947-951 (1989).

Milton DL, Napier ML, Myers RM, Hardman JK. In vitro mutagenesis and overexpression of the Escherichia coli trpA gene and the partial characterization of the resultant tryptophan synthase mutant alpha-subunits. J. Biol. Chem. 261: 16604-16615 (1986).

Mimura H, Nakanishi Y, Maeshima M. Disulfide-bond formation in the H+-pyrophosphatase of Streptomyces coelicolor and its implications for redox control and enzyme structure. FEBS Lett. 579: 3625-3631 (2005).

Min B, Kitabatake M, Polycarpo C, Pelaschier J, Raczniak G, Ruan B, Kobayashi H, Namgoong S, Soll D. Protein synthesis in Escherichia coli with mischarged tRNA. J. Bacteriol. 185: 3524-3526 (2003).

Minami H, Kim JS, Ikezawa N, Takemura T, Katayama T, Kumagai H, Sato F. Microbial production of plant benzylisoquinoline alkaloids. Proc. Natl. Acad. Sci. U.S.A. 105: 7393-7398 (2008).

Minami R, Uchiyama K, Murakami T, Kawai J, Mikami K, Yamada T, Yokoi D, Ito H, Matsui H, Honma M. Properties, sequence, and synthesis in Escherichia coli of 1-aminocyclopropane-1-carboxylate deaminase from Hansenula saturnus. J. Biochem. (Tokyo) 123: 1112-1118 (1998).

Mirete S, de Figueras CG, Gonzalez-Pastor JE. Novel nickel-resistance genes from the rhizosphere metagenome of acid mine drainage-adapted plants. Appl. Environ. Microbiol. 73: 6001-6011 (2007).

Mirwaldt C, Korndorfer I, Huber R. The crystal structure of dihydrodipicolinate synthase from Escherichia coli at 2.5 A resolution. J. Mol. Biol. 246: 227-239 (1995).

Misawa N, Shimada H. Metabolic engineering for the production of carotenoids in non-carotenogenic bacteria and yeasts. J. Biotechnol. 59: 169-181 (1997).

Misener SR, Walker VK. Extraordinarily high density of unrelated genes showing overlapping and intraintronic transcription units. Biochim. Biophys. Acta 1492: 269-270 (2000).

Mishra P, Park PK, Drueckhammer DG. Identification of yacE (coaE) as the structural gene for dephosphocoenzyme A kinase in Escherichia coli K-12. J. Bacteriol. 183: 2774-2778 (2001).

Misra HS, Khairnar NP, Barik A, Indira Priyadarsini K, Mohan H, Apte SK. Pyrroloquinoline-quinone: a reactive oxygen species scavenger in bacteria. FEBS Lett. 578: 26-30 (2004).

Misra N, Gupta AK. Effect of salt stress on proline metabolism in two high yielding genotypes of green gram. Plant Sci. 169: 331-339 (2005).

Mita G, Quarta A, Fasano P, De Paolis A, Di Sansebastiano GP, Perrotta C, Iannacone R, Belfield E, Hughes R, Tsesmetzis N, Casey R, Santino A. Molecular cloning and characterization of an almond 9-hydroperoxide lyase, a new CYP74 targeted to lipid bodies. J. Exp. Bot. 56: 2321-2333 (2005).

Mitani Y, Meng X, Kamagata Y, Tamura T. Characterization of LtsA from Rhodococcus erythropolis, an enzyme with glutamine amidotransferase activity. J. Bacteriol. 187: 2582-2591 (2005).

Mitra A, Sarma SP. Escherichia coli ilvN interacts with the FAD binding domain of ilvB and activates the AHAS I enzyme. Biochemistry 47: 1518-1531 (2008).

Mittl PR, Berry A, Scrutton NS, Perham RN, Schulz GE. Structural differences between wild-type NADP-dependent glutathione reductase from Escherichia coli and a redesigned NAD-dependent mutant. J. Mol. Biol. 231: 191-195 (1993).

Mittl PR, Berry A, Scrutton NS, Perham RN, Schulz GE. Anatomy of an engineered NAD-binding site. Protein Sci. 3: 1504-1514 (1994).

Miyamoto K, Katsuki H. Possible physiological roles of aspartase, NAD- and NADP-requiring glutamate dehydrogenases of Pseudomonas fluorescens. J. Biochem. (Tokyo) 112: 52-56 (1992).

Miyamoto S, Kashiwagi K, Ito K, Watanabe S, Igarashi K. Estimation of polyamine distribution and polyamine stimulation of protein synthesis in Escherichia coli. Arch. Biochem. Biophys. 300: 63-68 (1993).

Miyata A, Yoshida T, Yamaguchi K, Yokoyama C, Tanabe T, Toh H, Mitsunaga T, Izumi Y. Molecular cloning and expression of the gene for serine hydroxymethyltransferase from an obligate methylotroph Hyphomicrobium methylovorum GM2. Eur. J. Biochem. 212: 745-750 (1993).

Mizukami T, Hamu A, Ikeda M, Oka T, Katsumata R. Cloning of the ATP phosphoribosyl transferase gene of Corynebacterium glutamicum and application of the gene to L-histidine production. Biosci. Biotechnol. Biochem. 58: 635-638 (1994).

Mizutani M, Nakanishi H, Ema J, Ma SJ, Noguchi E, Inohara-Ochiai M, Fukuchi-Mizutani M, Nakao M, Sakata K. Cloning of beta-primeverosidase from tea leaves, a key enzyme in tea aroma formation. Plant Physiol. 130: 2164-2176 (2002).

Moberg P, Stahl A, Bhushan S, Wright SJ, Eriksson A, Bruce BD, Glaser E. Characterization of a novel zinc metalloprotease involved in degrading targeting peptides in mitochondria and chloroplasts. Plant J. 36: 616-628 (2003).

Moffatt BA, McWhinnie EA, Burkhart WE, Pasternak JJ, Rothstein SJ. A complete cDNA for adenine phosphoribosyltransferase from Arabidopsis thaliana. Plant Mol. Biol. 18: 653-662 (1992).

Moffatt BA, Wang L, Allen MS, Stevens YY, Qin W, Snider J, von Schwartzenberg K. Adenosine kinase of Arabidopsis. Kinetic properties and gene expression. Plant Physiol. 124: 1775-1785 (2000).

Moghaieb RE, Tanaka N, Saneoka H, Murooka Y, Ono H, Morikawa H, Nakamura A, Nguyen NT, Suwa R, Fujita K. Characterization of salt tolerance in ectoine-transformed tobacco plants (Nicotiana tabaccum): photosynthesis, osmotic adjustment, and nitrogen partitioning. Plant Cell Environ. 29: 173-182 (2006).

Mogi T, Yamamoto H, Nakao T, Yamato I, Anraku Y. Genetic and physical characterization of putP, the proline carrier gene of Escherichia coli K12. Mol. Gen. Genet. 202: 35-41 (1986).

Mohamed EA, Iwaki T, Munir I, Tamoi M, Shigeoka S, Wadano A. Overexpression of bacterial catalase in tomato leaf chloroplasts enhances photo-oxidative stress tolerance. Plant Cell Environ. 26: 2037-2046 (2003).

Mohammad A, Miranda-Rios J, Navarrete GE, Quinto C, Olivares JE, Garcia-Ponce B, Sanchez F. Nodulin 22 from Phaseolus vulgaris protects Escherichia coli cells from oxidative stress. Planta 219: 993-1002 (2004).

Molhoj M, Verma R, Reiter WD. The biosynthesis of the branched-chain sugar d-apiose in plants: functional cloning and characterization of a UDP-d-apiose/UDP-d-xylose synthase from Arabidopsis. Plant J. 35: 693-703 (2003).

Molina-Heredia FP, Houee-Levin C, Berthomieu C, Touati D, Tremey E, Favaudon V, Adam V, Niviere V. Detoxification of superoxide without production of H2O2: antioxidant activity of superoxide reductase complexed with ferrocyanide. Proc. Natl. Acad. Sci. U.S.A. 103: 14750-14755 (2006).

Monks DE, Goode JH, Dewey RE. Characterization of soybean choline kinase cDNAs and their expression in yeast and Escherichia coli. Plant Physiol. 110: 1197-1205 (1996).

Monroe DM, Noyes CM, Lundblad RL, Kingdon HS, Griffith MJ. Interaction of substrates with glutamine synthetase after limited proteolysis. Biochemistry 23: 4565-4572 (1984).

Monroe JD, Gough CM, Chandler LE, Loch CM, Ferrante JE, Wright PW. Structure, properties, and tissue localization of apoplastic alpha-glucosidase in crucifers. Plant Physiol. 119: 385-397 (1999).

Montesano M, Hyytiainen H, Wettstein R, Palva ET. A novel potato defence-related alcohol:NADP+ oxidoreductase induced in response to Erwinia carotovora. Plant Mol. Biol. 52: 177-189 (2003).

Montrichard F, Renard M, Alkhalfioui F, Duval FD, Macherel D. Identification and differential expression of two thioredoxin h isoforms in germinating seeds from pea. Plant Physiol. 132: 1707-1715 (2003).

Moon TS, Yoon SH, Lanza AM, Roy-Mayhew JD, Prather KL. Production of glucaric acid from a synthetic pathway in recombinant Escherichia coli. Appl. Environ. Microbiol. 75: 589-595 (2009).

Moore JB, Shiau SP, Reitzer LJ. Alterations of highly conserved residues in the regulatory domain of nitrogen regulator I (NtrC) of Escherichia coli. J. Bacteriol. 175: 2692-2701 (1993).

Moore JD, Hawkins AR. Overproduction of, and interaction within, bifunctional domains from the amino- and carboxy-termini of the pentafunctional AROM protein of Aspergillus nidulans. Mol. Gen. Genet. 240: 92-102 (1993).

Moorhead GB, Meek SE, Douglas P, Bridges D, Smith CS, Morrice N, MacKintosh C. Purification of a plant nucleotide pyrophosphatase as a protein that interferes with nitrate reductase and glutamine synthetase assays. Eur. J. Biochem. 270: 1356-1362 (2003).

Mootz HD, Finking R, Marahiel MA. 4'-Phosphopantetheine transfer in primary and secondary metabolism of Bacillus subtilis. J. Biol. Chem. 276: 37289-37298 (2001).

Mora P, Rubio V, Fresquet V, Cervera J. Localization of the site for the nucleotide effectors of Escherichia coli carbamoyl phosphate synthetase using site-directed mutagenesis. FEBS Lett. 446: 133-136 (1999).

Moraga AR, Nohales PF, Perez JA, Gomez-Gomez L. Glucosylation of the saffron apocarotenoid crocetin by a glucosyltransferase isolated from Crocus sativus stigmas. Planta 219: 955-966 (2004).

Moran JF, James EK, Rubio MC, Sarath G, Klucas RV, Becana M. Functional characterization and expression of a cytosolic iron-superoxide dismutase from cowpea root nodules. Plant Physiol. 133: 773-782 (2003).

Moran JF, Sun ZH, Sarath G, Arredondo-Peter R, James EK, Becana M, Klucas RV. Molecular cloning, functional characterization, and subcellular localization of soybean nodule dihydrolipoamide reductase. Plant Physiol. 128: 300-313 (2002).

Morbach S, Junger C, Sahm H, Eggeling L. Attenuation control of ilvBNC in Corynebacterium glutamicum: Evidence of leader peptide formation without the presence of a ribosome binding site. J. Biosci. Bioeng. 90: 501-507 (2000).

Morbach S, Kramer R. Impact of transport processes in the osmotic response of Corynebacterium glutamicum. J. Biotechnol. 104: 69-75 (2003).

Morehead TA, Gurnon JR, Adams B, Nickerson KW, Fitzgerald LA, Van Etten JL. Ornithine decarboxylase encoded by chlorella virus PBCV-1. Viorology 301: 165-175 (2002).

Morell MK, Paul K, O'Shea NJ, Kane HJ, Andrews TJ. Mutations of an active site threonyl residue promote beta elimination and other side reactions of the enediol intermediate of the ribulose-bisphosphate carboxylase reaction. J. Biol. Chem. 269: 8091-8098 (1994).

Morell MK, Wilkin JM, Kane HJ, Andrews TJ. Side reactions catalyzed by ribulose-bisphosphate carboxylase in the presence and absence of small subunits. J. Biol. Chem. 272: 5445-5451 (1997).

Moreno R, Zafra O, Cava F, Berenguer J. Development of a gene expression vector for Thermus thermophilus based on the promoter of the respiratory nitrate reductase. Plasmid 49: 2-8 (2003).

Mori H, Shibasaki T, Yano K, Ozaki A. Purification and cloning of a proline 3-hydroxylase, a novel enzyme which hydroxylates free L-proline to cis-3-hydroxy-L-proline. J. Bacteriol. 179: 5677-5683 (1997).

Mori K, Kashiwagi A, Urabe I, Yomo T. Evolution of carrying capacity in evolution experiments focusing on a single locus on the Escherichia coli chromosome. Biosystems 95: 114-119 (2009).

Mori N, Shirota K, Kitamoto Y, Ichikawa Y. Cloning and expression in Escherichia coli of the carnitine dehydrogenase gene from Xanthomonas translucens. Agric. Biol. Chem. 52: 851-852 (1988).

Morishige T, Dubouzet E, Choi KB, Yazaki K, Sato F. Molecular cloning of columbamine O-methyltransferase from cultured Coptis japonica cells. Eur. J. Biochem. 269: 5659-5667 (2002).

Morita Y, Hoshino A, Kikuchi Y, Okuhara H, Ono E, Tanaka Y, Fukui Y, Saito N, Nitasaka E, Noguchi H, Iida S. Japanese morning glory dusky mutants displaying reddish-brown or purplish-gray flowers are deficient in a novel glycosylation enzyme for anthocyanin biosynthesis, UDP-glucose:anthocyanidin 3-O-glucoside-2''-O-glucosyltransferase, due to 4-bp insertions .. Plant J. 42: 353-363 (2005).

Morris SM. Vertebrate agmatinases: What role do they play in agmatine catabolism?. Ann. N.Y. Acad.Sci. 1009: 30-33 (2003).

Moschou PN, Sanmartin M, Andriopoulou AH, Rojo E, Sanchez-Serrano JJ, Roubelakis-Angelakis KA. Bridging the gap between plant and mammalian polyamine catabolism: a novel peroxisomal polyamine oxidase responsible for a full back-conversion pathway In Arabidopsis thaliana. Plant Physiol. 147: 1845-1857 (2008).

Moss J, Stanley SJ, Levine RL. Inactivation of bacterial glutamine synthetase by ADP-ribosylation. J. Biol. Chem. 265: 21056-21060 (1990).

Mostertz J, Hecker M. Patterns of protein carbonylation following oxidative stress in wild-type and sigB Bacillus subtilis cells. Mol. Genet. Genomics 269: 640-648 (2003).

Motohashi R, Yamazaki T, Myouga F, Ito T, Ito K, Satou M, Kobayashi M, Nagata N, Yoshida S, Nagashima A, Tanaka K, Takahashi S, Shinozaki K. Chloroplast ribosome release factor 1 (AtcpRF1) is essential for chloroplast development. Plant Mol. Biol. 64: 481-497 (2007).

Motojima K, Yamato I, Anraku Y. Proline transport carrier-defective mutants of Escherichia coli K-12: properties and mapping. J. Bacteriol. 136: 5-9 (1978).

Motono C, Yamagishi A, Oshima T. Urea-induced unfolding and conformational stability of 3-isopropylmalate dehydrogenase from the thermophile Thermus thermophilus and its mesophilic counterpart from Escherichia coli. Biochemistry 38: 1332-1337 (1999).

Motoyama H, Maki K, Anazawa H, Ishino S, Teshiba S. Cloning and nucleotide sequences of the homoserine dehydrogenase genes (hom) and the threonine synthase genes (thrC) of the gram-negative obligate methylotroph Methylobacillus glycogenes. Appl. Environ. Microbiol. 60: 111-119 (1994).

Motoyama H, Yano H, Terasaki Y, Anazawa H. Overproduction of L-lysine from methanol by Methylobacillus glycogenes derivatives carrying a plasmid with a mutated dapA gene. Appl. Environ. Microbiol. 67: 3064-3070 (2001).

Mouillon JM, Ravanel S, Douce R, Rebeille F. Folate synthesis in higher-plant mitochondria: coupling between the dihydropterin pyrophosphokinase and the dihydropteroate synthase activities. Biochem. J. 363: 313-319 (2002).

Mourad GS, Snook BM, Prabhakar JT, Mansfield TA, Schultes NP. A fluoroorotic acid-resistant mutant of Arabidopsis defective in the uptake of uracil. J. Exp. Bot. 57: 3563-3573 (2006).

Moyano E, Martinez-Garcia JF, Martin C. Apparent redundancy in myb gene function provides gearing for the control of flavonoid biosynthesis in antirrhinum flowers. Plant Cell 8: 1519-1532 (1996).

Moye WS, Amuro N, Rao JK, Zalkin H. Nucleotide sequence of yeast GDH1 encoding nicotinamide adenine dinucleotide phosphate-dependent glutamate dehydrogenase. J. Biol. Chem. 260: 8502-8508 (1985).

Mudd EA, Sullivan S, Gisby MF, Mironov A, Kwon CS, Chung WI, Day A. A 125 kDa RNase E/G-like protein is present in plastids and is essential for chloroplast development and autotrophic growth in Arabidopsis. J. Exp. Bot. 59: 2597-2610 (2008).

Mueller C, Schwender J, Zeidler J, Lichtenthaler HK. Properties and inhibition of the first two enzymes of the non-mevalonate pathway of isoprenoid biosynthesis. Biochem. Soc. Trans. 28: 792-793 (2000).

Mueller LA, Zhang P, Rhee SY. AraCyc: a biochemical pathway database for Arabidopsis. Plant Physiol. 132: 453-460 (2003).

Muffler A, Traulsen DD, Lange R, Hengge-Aronis R. Posttranscriptional osmotic regulation of the sigma(s) subunit of RNA polymerase in Escherichia coli. J. Bacteriol. 178: 1607-1613 (1996).

Mukhopadhyay R, Rosen BP. Arsenate reductases in prokaryotes and eukaryotes. Environ. Health Perspect. 110 Suppl. 5: 745-748 (2002).

Mulholland MR, Ohki K, Capone DG. Nutrient controls on nitrogen uptake and metabolism by natural populations and cultures of Trichodesmium (Cyanobacteria). J. Phycol. 37: 1001-1009 (2001).

Muller GL, Drincovich MF, Andreo CS, Lara MV. Nicotiana tabacum NADP-malic enzyme: cloning, characterization and analysis of biological role. Plant Cell Physiol. 49: 469-480 (2008).

Muller K, Garel JR. Stepwise inactivation of Escherichia coli aspartokinase-homoserine dehydrogenase I. Biochemistry 23: 651-654 (1984).

Muller-Dieckmann HJ, Grantz AA, Kim SH. The structure of the signal receiver domain of the Arabidopsis thaliana ethylene receptor ETR1. Structure Fold. Des. 7: 1547-1556 (1999).

Mundree SG, Whittaker A, Thomson JA, Farrant JM. An aldose reductase homolog from the resurrection plant Xerophyta viscosa Baker. Planta 211: 693-700 (2000).

Mungur R, Glass AD, Goodenow DB, Lightfoot DA. Metabolite fingerprinting in transgenic Nicotiana tabacum altered by the Escherichia coli glutamate dehydrogenase gene. J. Biomed. Biotechnol. 2005: 198-214 (2005).

Munoz FJ, Baroja-Fernandez E, Ovecka M, Li J, Mitsui T, Sesma MT, Montero M, Bahaji A, Ezquer I, Pozueta-Romero J. Plastidial localization of a potato "Nudix" hydrolase of ADPglucose linked to starch biosynthesis. Plant Cell Physiol. 49: 1734-1746 (2008).

Munro PM, Gauthier MJ, Breittmayer VA, Bongiovanni J. Influence of osmoregulation processes on starvation survival of Escherichia coli in seawater. Appl. Environ. Microbiol. 55: 2017-2024 (1989).

Mura U, Stadtman ER. Glutamine synthetase adenylylation in permeabilized cells of Escherichia coli. J. Biol. Chem. 256: 13014-13021 (1981).

Murai MJ, Carneiro FR, Gozzo FC, Ierardi DF, Pertinhez TA, Zanchin NI. Identification and characterization of a proteolysis-resistant fragment containing the PCI domain in the Arabidopsis thaliana INT6/eIF3e translation factor. Cell. Biochem. Biophys. 44: 522-529 (2006).

Murakami K, Hashimoto Y, Murooka Y. Cloning and characterization of the gene encoding glutamate 1-semialdehyde 2,1-aminomutase, which is involved in delta-aminolevulinic acid synthesis in Propionibacterium freudenreichii. Appl. Environ. Microbiol. 59: 347-350 (1993).

Muramoto T, Kohchi T, Yokota A, Hwang I, Goodman HM. The Arabidopsis photomorphogenic mutant hy1 is deficient in phytochrome chromophore biosynthesis as a result of a mutation in a plastid heme oxygenase. Plant Cell 11: 335-348 (1999).

Muramoto T, Tsurui N, Terry MJ, Yokota A, Kohchi T. Expression and biochemical properties of a ferredoxin-dependent heme oxygenase required for phytochrome chromophore synthesis. Plant Physiol. 130: 1958-1966 (2002).

Murata T, Hattori T, Amarume S, Koichi A, Usui T. Kinetic studies on endo-beta-galactosidase by a novel colorimetric assay and synthesis of N-acetyllactosamine-repeating oligosaccharide beta-glycosides using its transglycosylation activity. Eur. J. Biochem. 270: 3709-3719 (2003).

Mure M, Brown DE, Saysell C, Rogers MS, Wilmot CM, Kurtis CR, McPherson MJ, Phillips SE, Knowles PF, Dooley DM. Role of the interactions between the active site base and the substrate Schiff base in amine oxidase catalysis. Evidence from structural and spectroscopic studies of the 2-hydrazinopyridine adduct of Escherichia coli amine oxidase. Biochemistry 44: 1568-1582 (2005).

Murfitt LM, Kolosova N, Mann CJ, Dudareva N. Purification and characterization of S-adenosyl-L-methionine:benzoic acid carboxyl methyltransferase, the enzyme responsible for biosynthesis of the volatile ester methyl benzoate in flowers of Antirrhinum majus. Arch. Biochem. Biophys. 382: 145-151 (2000).

Murillo M, Foglia R, Diller A, Lee S, Leustek T. Serine acetyltransferase from Arabidopsis thaliana can functionally complement the cysteine requirement of a cysE mutant strain of Escherichia coli. Cell Mol. Biol. Res. 41: 425-433 (1995).

Murillo M, Leustek T. ATP-sulfurylase from Arabidopsis thaliana and Escherichia coli are functionally equivalent but structurally and kinetically divergent: nucleotide sequence of two ATP-sulfurylase cDNAs from Arabidopsis thaliana and analysis of a recombinant enzyme. Arch. Biochem. Biophys. 323: 195-204 (1995).

Murphy AM, Otto B, Brearley CA, Carr JP, Hanke DE. A role for inositol hexakisphosphate in the maintenance of basal resistance to plant pathogens. Plant J. 56: 638-652 (2008).

Murray TA, McManus MT. Developmental regulation of 1-aminocyclopropane-1-carboxylate synthase gene expression during leaf ontogeny in white clover. Physiol. Plant. 124: 107-120 (2005).

Murry-Brelier A, Goldberg ME. Mechanism of inactivation of the beta 2 subunit of Escherichia coli tryptophan synthase by monoclonal antibodies. J. Biol. Chem. 265: 7987-7993 (1990).

Murthy SS, Zilinskas BA. Molecular cloning and characterization of a cDNA encoding pea monodehydroascorbate reductase. J. Biol. Chem. 269: 31129-31133 (1994).

Muse WB, Bender RA. The amino-terminal 100 residues of the nitrogen assimilation control protein (NAC) encode all known properties of NAC from Klebsiella aerogenes and Escherichia coli. J. Bacteriol. 181: 934-940 (1999).

Muse WB, Bender RA. The nac (nitrogen assimilation control) gene from Escherichia coli. J. Bacteriol. 180: 1166-1173 (1998).

Musfeldt M, Selig M, Schonheit P. Acetyl coenzyme A synthetase (ADP forming) from the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol. 181: 5885-5888 (1999).

Mutalik VK, Shah P, Venkatesh KV. Allosteric interactions and bifunctionality make the response of glutamine synthetase cascade system of Escherichia coli robust and ultrasensitive. J. Biol. Chem. 278: 26327-26332 (2003).

Mutalik VK, Venkatesh KV. A theoretical steady state analysis indicates that induction of Escherichia coli glnALG operon can display all-or-none behavior. Biosystems 90: 1-19 (2007).

Muzac I, Wang J, Anzellotti D, Zhang H, Ibrahim RK. Functional expression of an Arabidopsis cDNA clone encoding a flavonol 3'-O-methyltransferase and characterization of the gene product. Arch. Biochem. Biophys. 375: 385-388 (2000).

Nadaraia S, Lee YH, Becker DF, Tanner JJ. Crystallization and preliminary crystallographic analysis of the proline dehydrogenase domain of the multifunctional PutA flavoprotein from Escherichia coli. Acta Crystallogr. Sect. D-Biol. Crystallogr. 57: 1925-1927 (2001).

Nafisi M, Goregaoker S, Botanga CJ, Glawischnig E, Olsen CE, Halkier BA, Glazebrook J. Arabidopsis cytochrome P450 monooxygenase 71A13 catalyzes the conversion of indole-3-acetaldoxime in camalexin synthesis. Plant Cell 19: 2039-2052 (2007).

Nagahara N, Yoshii T, Abe Y, Matsumura T. Thioredoxin-dependent enzymatic activation of mercaptopyruvate sulfurtransferase. An intersubunit disulfide bond serves as a redox switch for activation. J. Biol. Chem. 282: 1561-1569 (2007).

Nagai YS, Sakulsingharoj C, Edwards GE, Satoh H, Greene TW, Blakeslee B, Okita TW. Control of starch synthesis in cereals: metabolite analysis of transgenic rice expressing an up-regulated cytoplasmic ADP-glucose pyrophosphorylase in developing seeds. Plant Cell Physiol. 50: 635-643 (2009).

Nagashima S, Inagaki R, Kubo A, Hirotani M, Yoshikawa T. cDNA cloning and expression of isoflavonoid-specific glucosyltransferase from Glycyrrhiza echinata cell-suspension cultures. Planta 218: 456-459 (2004).

Nagasu T, Hall BD. Nucleotide sequence of the GDH gene coding for the NADP-specific glutamate dehydrogenase of Saccharomyces cerevisiae. Gene 37: 247-253 (1985).

Nagata N, Tanaka R, Satoh S, Tanaka A. Identification of a vinyl reductase gene for chlorophyll synthesis in Arabidopsis thaliana and implications for the evolution of Prochlorococcus species. Plant Cell 17: 233-240 (2005).

Nagata S. Growth of Escherichia coli ATCC 9637 through the uptake of compatible solutes at high osmolarity. J. Biosci. Bioeng. 92: 324-329 (2001).

Nagata S, Adachi K, Shirai K, Sano H. 23Na NMR spectroscopy of free Na+ in the halotolerant bacterium Brevibacterium sp. and Escherichia coli. Microbiology 141: 729-736 (1995).

Nagata S, Maekawa Y, Ikeuchi T, Wang YB, Ishida A. Effect of compatible solutes on the respiratory activity and growth of Escherichia coli K-12 under NaCl stress. J. Biosci. Bioeng. 94: 384-389 (2002).

Nagegowda DA, Ramalingam S, Hemmerlin A, Bach TJ, Chye ML. Brassica juncea HMG-CoA synthase: localization of mRNA and protein. Planta 221: 844-856 (2005).

Nair RB, Bastress KL, Ruegger MO, Denault JW, Chapple C. The Arabidopsis thaliana reduced epidermal fluorescence1 gene encodes an aldehyde dehydrogenase involved in ferulic acid and sinapic acid biosynthesis. Plant Cell 16: 544-554 (2004).

Najdi TS, Yang CR, Shapiro BE, Hatfield GW, Mjolsness ED. Application of a generalized MWC model for the mathematical simulation of metabolic pathways regulated by allosteric enzymes. J. Bioinform. Comput. Biol. 4: 335-355 (2006).

Najdi TS, Yang CR, Shapiro BE, Hatfield GW, Mjolsness ED. Application of a generalized MWC model for the mathematical simulation of metabolic pathways regulated by allosteric enzymes. Proc. IEEE Comput. Syst. Bioinform. Conf. 2005: 279-288 (2005).

Nakagiri T, Lee JB, Hayashi T. cDNA cloning, functional expression and characterization of ent-copalyl diphosphate synthase from Scoparia dulcis L.. Plant Sci. 169: 760-767 (2005).

Nakai T, Okada K, Akutsu S, Miyahara I, Kawaguchi S, Kato R, Kuramitsu S, Hirotsu K. Structure of Thermus thermophilus HB8 aspartate aminotransferase and its complex with maleate. Biochemistry 38: 2413-2424 (1999).

Nakajima J, Tanaka Y, Yamazaki M, Saito K. Reaction mechanism from leucoanthocyanidin to anthocyanidin 3-glucoside, a key reaction for coloring in anthocyanin biosynthesis. J. Biol. Chem. 276: 25797-25803 (2001).

Nakajima M, Nishino Y, Tamura M, Mase K, Masai E, Otsuka Y, Nakamura M, Sato K, Fukuda M, Shigehara K, Ohara S, Katayama Y, Kajita S. Microbial conversion of glucose to a novel chemical building block, 2-pyrone-4,6-dicarboxylic acid. Metab. Eng. 11: 213-220 (2009).

Nakaminami K, Karlson DT, Imai R. Functional conservation of cold shock domains in bacteria and higher plants. Proc. Natl. Acad. Sci. U.S.A. 103: 10122-10127 (2006).

Nakamori S, Kobayashi S, Nishimura T, Takagi H. Mechanism of L-methionine overproduction by Escherichia coli: the replacement of Ser-54 by Asn in the MetJ protein causes the derepression of L-methionine biosynthetic enzymes. Appl. Microbiol. Biotechnol. 52: 179-185 (1999).

Nakamori S, Kobayashi SI, Kobayashi C, Takagi H. Overproduction of L-cysteine and L-cystine by Escherichia coli strains with a genetically altered serine acetyltransferase. Appl. Environ. Microbiol. 64: 1607-1611 (1998).

Nakamura H. Specific proline accumulation in an acrA mutant of Escherichia coli K12 grown in salt-hypertonic medium. J. Gen. Microbiol. 113: 425-427 (1979).

Nakamura K, Stadtman ER. Oxidative inactivation of glutamine synthetase subunits. Proc. Natl. Acad. Sci. U.S.A. 81: 2011-2015 (1984).

Nakamura T, Katoh Y, Shimizu Y, Matsuba Y, Unemoto T. Cloning and sequencing of novel genes from Vibrio alginolyticus that support the growth of K+ uptake-deficient mutant of Escherichia coli. Biochim. Biophys. Acta 1277: 201-208 (1996).

Nakamura T, Vrinten P, Hayakawa K, Ikeda J. Characterization of a granule-bound starch synthase isoform found in the pericarp of wheat. Plant Physiol. 118: 451-459 (1998).

Nakanishi T, Turner RJ, Burg MB. Osmoregulation of betaine transport in mammalian renal medullary cells. Am. J. Physiol. 258: F1061-F1067 (1990).

Nakano MM, Dailly YP, Zuber P, Clark DP. Characterization of anaerobic fermentative growth of Bacillus subtilis: identification of fermentation end products and genes required for growth. J. Bacteriol. 179: 6749-6755 (1997).

Nakasone K, Ikegami A, Kawano H, Kato C, Usami R, Horikoshi K. Transcriptional regulation under pressure conditions by RNA polymerase sigma(54) factor with a two-component regulatory system in Shewanella violacea. Extremophiles 6: 89-95 (2002).

Nakatsuka T, Sato K, Takahashi H, Yamamura S, Nishihara M. Cloning and characterization of the UDP-glucose:anthocyanin 5-O-glucosyltransferase gene from blue-flowered gentian. J. Exp. Bot. 59: 1241-1252 (2008).

Nakazono M, Tsuji H, Li Y, Saisho D, Arimura Si, Tsutsumi N, Hirai A. Expression of a gene encoding mitochondrial aldehyde dehydrogenase in rice increases under submerged conditions. Plant Physiol. 124: 587-598 (2000).

Nandi A, Welti R, Shah J. The Arabidopsis thaliana dihydroxyacetone phosphate reductase gene suppressor of fatty acid desaturase deficiency1 is required for glycerolipid metabolism and for the activation of systemic acquired resistance. Plant Cell 16: 465-477 (2004).

Nandineni MR, Laishram RS, Gowrishankar J. Osmosensitivity associated with insertions in argP (iciA) or glnE in glutamate synthase-deficient mutants of Escherichia coli. J. Bacteriol. 186: 6391-6399 (2004).

Napolitani C, Mandrich L, Riccio A, Lamberti A, Manco G, Patriarca EJ. Mutational analysis of GstI protein, a glutamine synthetase translational inhibitor of Rhizobium leguminosarum. FEBS Lett. 558: 45-51 (2004).

Nast G, Muller-Rober B. Molecular characterization of potato fumarate hydratase and functional expression in Escherichia coli. Plant Physiol. 112: 1219-1227 (1996).

Natarajan A, Srienc F. Dynamics of glucose uptake by single Escherichia coli cells. Metab. Eng. 1: 320-333 (1999).

Naughton LM, Blumerman SL, Carlberg M, Boyd EF. Osmoadaptation among Vibrio species and unique genomic features and physiological responses of Vibrio parahaemolyticus. Appl. Environ. Microbiol. 75: 2802-2810 (2009).

Navarro F, Chavez S, Candau P, Florencio FJ. Existence of two ferredoxin-glutamate synthases in the cyanobacterium Synechocystis sp. PCC 6803. Isolation and insertional inactivation of gltB and gltS genes. Plant Mol. Biol. 27: 753-767 (1995).

Navarro F, Florencio FJ. The cyanobacterial thioredoxin gene is required for both photoautotrophic and heterotrophic growth. Plant Physiol. 111: 1067-1075 (1996).

Navarro F, Martin-Figueroa E, Candau P, Florencio FJ. Ferredoxin-dependent iron-sulfur flavoprotein glutamate synthase (GlsF) from the cyanobacterium synechocystis sp. PCC 6803: expression and assembly in Escherichia coli. Arch. Biochem. Biophys. 379: 267-276 (2000).

Navarro F, Martin-Figueroa E, Florencio FJ. Electron transport controls transcription of the thioredoxin gene (trxA) in the cyanobacterium Synechocystis sp. PCC 6803. Plant Mol. Biol. 43: 23-32 (2000).

Navarro-Garcia F, Perez-Diaz RM, Negredo AI, Pla J, Nombela C. Cloning and sequence of a 3.835 kbp DNA fragment containing the HIS4 gene and a fragment of a PEX5-like gene from Candida albicans. Yeast 14: 1147-1157 (1998).

Navon A, Schulze AJ, Guillou Y, Zylinski CA, Baleux F, Expert-Bezancon N, Friguet B, Djavadi-Ohaniance L, Goldberg ME. Importance of residues 2-9 in the immunoreactivity, subunit interactions, and activity of the beta 2 subunit of Escherichia coli tryptophan synthase. J. Biol. Chem. 270: 4255-4261 (1995).

Negre F, Kolosova N, Knoll J, Kish CM, Dudareva N. Novel S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase, an enzyme responsible for biosynthesis of methyl salicylate and methyl benzoate, is not involved in floral scent production in snapdragon flowers. Arch. Biochem. Biophys. 406: 261-270 (2002).

Nelms J, Edwards RM, Warwick J, Fotheringham I. Novel mutations in the pheA gene of Escherichia coli K-12 which result in highly feedback inhibition-resistant variants of chorismate mutase/prephenate dehydratase. Appl. Environ. Microbiol. 58: 2592-2598 (1992).

Nemchenko A, Kunze S, Feussner I, Kolomiets M. Duplicate maize 13-lipoxygenase genes are differentially regulated by circadian rhythm, cold stress, wounding, pathogen infection, and hormonal treatments. J. Exp. Bot. 57: 3767-3779 (2006).

Nemeth A, Svingor A, Pocsik M, Dobo J, Magyar C, Szilagyi A, Gal P, Zavodszky P. Mirror image mutations reveal the significance of an intersubunit ion cluster in the stability of 3-isopropylmalate dehydrogenase. FEBS Lett. 468: 48-52 (2000).

Nemoto T, Cho EM, Okada A, Okada K, Otomo K, Kanno Y, Toyomasu T, Mitsuhashi W, Sassa T, Minami E, Shibuya N, Nishiyama M, Nojiri H, Yamane H. Stemar-13-ene synthase, a diterpene cyclase involved in the biosynthesis of the phytoalexin oryzalexin S in rice. FEBS Lett. 571: 182-186 (2004).

Nerlich A, von Orlow M, Rontein D, Hanson AD, Dormann P. Deficiency in phosphatidylserine decarboxylase activity in the psd1 psd2 psd3 triple mutant of Arabidopsis affects phosphatidylethanolamine accumulation in mitochondria. Plant Physiol. 144: 904-914 (2007).

Nersisian AA, Fedorova IuA, Khurges EM. Cloning of genes for proline biosynthesis in Escherichia coli. Genetika 22: 2713-2720 (1986).

Neubauer P, Lin HY, Mathiszik B. Metabolic load of recombinant protein production: Inhibition of cellular capacities for glucose uptake and respiration after induction of a heterologous gene in Escherichia coli. Biotechnol. Bioeng. 83: 53-64 (2003).

Neuefeind T, Huber R, Dasenbrock H, Prade L, Bieseler B. Crystal structure of herbicide-detoxifying maize glutathione S-transferase-I in complex with lactoylglutathione: evidence for an induced-fit mechanism. J. Mol. Biol. 274: 446-453 (1997).

Neuhierl B, Thanbichler M, Lottspeich F, Bock A. A family of S-methylmethionine-dependent thiol/selenol methyltransferases. Role in selenium tolerance and evolutionary relation. J. Biol. Chem. 274: 5407-5414 (1999).

Neumivakin LV, Solovjev VP, Sokhansanj A, Tilba VA, Moseiko NA, Shachbasian RV, Piruzian ES. Increase in osmotolerance of Rhizobium fredii soybean isolate BD32 by the proB proA operon of Escherichia coli. Biochem. Biophys. Res. Commun. 217: 796-801 (1995).

Neumyvakin LV, Kobets NS, Piruzian ES. Isolation of a spontaneous mutant of Escherichia coli superproducing proline and resistant to elevated concentrations of NaCl. Genetika 26: 1370-1379 (1990).

Neuwald AF, Stauffer GV. DNA sequence and characterization of the Escherichia coli serB gene. Nucleic Acids Res. 13: 7025-7039 (1985).

Neuwald AF, Stauffer GV. An Escherichia coli membrane protein with a unique signal sequence. Gene 82: 219-228 (1989).

Newman BM, Cole JA. Lack of a regulatory function for glutamine synthetase protein in the synthesis of glutamate dehydrogenase and nitrite reductase in Escherichia coli K12. J. Gen. Microbiol. 98: 369-377 (1977).

Newman EB, Budman LI, Chan EC, Greene RC, Lin RT, Woldringh CL, D'Ari R. Lack of S-adenosylmethionine results in a cell division defect in Escherichia coli. J. Bacteriol. 180: 3614-3619 (1998).

Newton SS, Duman JG. An osmotin-like cryoprotective protein from the bittersweet nightshade Solanum dulcamara. Plant Mol. Biol. 44: 581-589 (2000).

Nichols BP, Green JM. Cloning and sequencing of Escherichia coli ubiC and purification of chorismate lyase. J. Bacteriol. 174: 5309-5316 (1992).

Nichols BP, Seibold AM, Doktor SZ. Para-aminobenzoate synthesis from chorismate occurs in two steps. J. Biol. Chem. 264: 8597-8601 (1989).

Niegemann E, Schulz A, Bartsch K. Molecular organization of the Escherichia coli gab cluster: nucleotide sequence of the structural genes gabD and gabP and expression of the GABA permease gene. Arch. Microbiol. 160: 454-460 (1993).

Niehaus A, Gisselmann G, Schwenn JD. Primary structure of the Synechococcus PCC 7942 PAPS reductase gene. Plant Mol. Biol. 20: 1179-1183 (1992).

Nielsen JS, Moller BL. Cloning and expression of cytochrome P450 enzymes catalyzing the conversion of tyrosine to p-hydroxyphenylacetaldoxime in the biosynthesis of cyanogenic glucosides in Triglochin maritima. Plant Physiol. 122: 1311-1322 (2000).

Niersbach M, Kreuzaler F, Geerse RH, Postma PW, Hirsch HJ. Cloning and nucleotide sequence of the Escherichia coli K-12 ppsA gene, encoding PEP synthase. Mol. Gen. Genet. 231: 332-336 (1992).

Nihei C, Fukai Y, Kawai K, Osanai A, Yabu Y, Suzuki T, Ohta N, Minagawa N, Nagai K, Kita K. Purification of active recombinant trypanosome alternative oxidase. FEBS Lett. 538: 35-40 (2003).

Nilavongse A, Brondijk TH, Overton TW, Richardson DJ, Leach ER, Cole JA. The NapF protein of the Escherichia coli periplasmic nitrate reductase system: demonstration of a cytoplasmic location and interaction with the catalytic subunit, NapA. Microbiology 152: 3227-3237 (2006).

Nimmo HG, Borthwick AC, Elmansi EMT, HolmsWH, MacKintosh C, Nimmo GA. Regulation of the enzymes at the branchpoint between the citric acid cycle and the glyoxylate bypass in Escherichia coli. Biochem. Soc. Symp. 54: 93-101 (1987).

Nimmo HG, Douglas F, Kleanthous C, Campbell DG, MacKintosh C. Identification of a cysteine residue at the active site of Escherichia coli isocitrate lyase. Biochem. J. 261: 431-435 (1989).

Ninfa AJ, Bennett RL. Identification of the site of autophosphorylation of the bacterial protein kinase/phosphatase NRII. J. Biol. Chem. 266: 6888-6893 (1991).

Ninfa AJ, Jiang P, Atkinson MR, Peliska JA. Integration of antagonistic signals in the regulation of nitrogen assimilation in Escherichia coli. Curr. Top. Cell Regul. 36: 31-75 (2000).

Ninfa AJ, Magasanik B. Covalent modification of the glnG product, NRI, by the glnL product, NRII, regulates the transcription of the glnALG operon in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 83: 5909-5913 (1986).

Ninfa AJ, Selinsky S, Perry N, Atkins S, Xiu Song Q, Mayo A, Arps D, Woolf P, Atkinson MR. Using two-component systems and other bacterial regulatory factors for the fabrication of synthetic genetic devices. Methods Enzymol. 422: 488-512 (2007).

Ninfa AJ, Ueno-Nishio S, Hunt TP, Robustell B, Magasanik B. Purification of nitrogen regulator II, the product of the glnL (ntrB) gene of Escherichia coli. J. Bacteriol. 168: 1002-1004 (1986).

Ninfa EG, Atkinson MR, Kamberov ES, Ninfa AJ. Mechanism of autophosphorylation of Escherichia coli nitrogen regulator II (NRII or NtrB): trans-phosphorylation between subunits. J. Bacteriol. 175: 7024-7032 (1993).

Ninio S, Elbaz Y, Schuldiner S. The membrane topology of EmrE - a small multidrug transporter from Escherichia coli. FEBS Lett. 562: 193-196 (2004).

Nishimaki T, Yamanaka H, Mizugaki M. Acetyl-CoA-dependent chain elongation of fatty acids in Escherichia coli K-12. J. Biochem. (Tokyo) 99: 365-374 (1986).

Nishio K, Morimoto Y, Ishizuka M, Ogasahara K, Tsukihara T, Yutani K. Conformational changes in the alpha-subunit coupled to binding of the beta 2-subunit of tryptophan synthase from Escherichia coli: crystal structure of the tryptophan synthase alpha-subunit alone. Biochemistry 44: 1184-1192 (2005).

Nishiyama M, Kobashi N, Tanaka K, Takahashi H, Tanokura M. Cloning and characterization in Escherichia coli of the gene encoding the principal sigma factor of an extreme thermophile, Thermus thermophilus. FEMS Microbiol. Lett. 172: 179-186 (1999).

Nishiyama M, Kukimoto M, Beppu T, Horinouchi S. An operon encoding aspartokinase and purine phosphoribosyltransferase in Thermus flavus. Microbiology 141: 1211-1219 (1995).

Niu G, Liu G, Tian Y, Tan H. SanJ, an ATP-dependent picolinate-CoA ligase, catalyzes the conversion of picolinate to picolinate-CoA during nikkomycin biosynthesis in Streptomyces ansochromogenes. Metab. Eng. 8: 183-195 (2006).

Niu Y, Kong J, Fu L, Yang J, Xu Y. Identification of a novel C20-elongase gene from the marine microalgae Pavlova viridis and its expression in Escherichia coli. Mar. Biotechnol. (N.Y.) 11: 17-23 (2009).

Niwa R, Niimi T, Honda N, Yoshiyama M, Itoyama K, Kataoka H, Shinoda T. Juvenile hormone acid O-methyltransferase in Drosophila melanogaster. Insect Biochem. Mol. Biol. 38: 714-720 (2008).

Niyogi KK, Fink GR. Two anthranilate synthase genes in Arabidopsis: defense-related regulation of the tryptophan pathway. Plant Cell 4: 721-733 (1992).

Niyogi KK, Last RL, Fink GR, Keith B. Suppressors of trp1 fluorescence identify a new Arabidopsis gene, TRP4, encoding the anthranilate synthase beta subunit. Plant Cell 5: 1011-1027 (1993).

Noctor G, Arisi AC, Jouanin L, Foyer CH. Manipulation of glutathione and amino acid biosynthesis in the chloroplast. Plant Physiol. 118: 471-482 (1998).

Noctor G, Arisi ACM, Jouanin L, Valadier MH, Roux Y, Foyer CH. Light-dependent modulation of foliar glutathione synthesis and associated amino acid metabolism in poplar overexpressing gamma-glutamylcysteine synthetase. Planta 202: 357-369 (1997).

Nogales J, Guijo MI, Quesada A, Merchan F. Functional analysis and regulation of the malate synthase from Chlamydomonas reinhardtii. Planta 219: 325-331 (2004).

Noh K, Wahl A, Wiechert W. Computational tools for isotopically instationary (13)C labeling experiments under metabolic steady state conditions. Metab. Eng. 8: 554-577 (2006).

Noiriel A, Naponelli V, Gregory JF 3rd, Hanson AD. Pterin and folate salvage. Plants and Escherichia coli lack capacity to reduce oxidized pterins. Plant Physiol. 143: 1101-1109 (2007).

Nojiri M, Shirota F, Hira D, Suzuki S. Expression, purification, crystallization and preliminary X-ray diffraction analysis of the soluble domain of PPA0092, a putative nitrite reductase from Propionibacterium acnes. Acta Crystallogr. Sect. F. Struct. Biol. Cryst. Commun. 65: 123-127 (2009).

Nomura M, Hibino T, Takabe T, Sugiyama T, Yokota A, Miyake H, Takabe T. Transgenically produced glycinebetaine protects ribulose 1,5-bisphosphate carboxylase/oxygenase from inactivation in Synechococcus sp. PCC7942 under salt stress. Plant Cell Physiol. 39: 425-432 (1998).

Nomura M, Ishitani M, Takabe T, Rai AK, Takabe T. Synechococcus sp. PCC7942 transformed with Escherichia coli bet genes produces glycine betaine from choline and acquires resistance to salt stress. Plant Physiol. 107: 703-708 (1995).

Nomura M, Nakajima I, Fujita Y, Kobayashi M, Kimoto H, Suzuki I, Aso H. Lactococcus lactis contains only one glutamate decarboxylase gene. Microbiology 145: 1375-1380 (1999).

Nonogaki H, Gee OH, Bradford KJ. A germination-specific endo-beta-mannanase gene is expressed in the micropylar endosperm cap of tomato seeds. Plant Physiol. 123: 1235-1246 (2000).

Noordewier MO, Warren PV. Gene expression microarrays and the integration of biological knowledge. Trends Biotechnol. 19: 412-415 (2001).

Nordling E, Jornvall H, Persson B. Medium-chain dehydrogenases/reductases (MDR). Family characterizations including genome comparisons and active site modeling. Eur. J. Biochem. 269: 4267-4276 (2002).

Nordmann B, Lebert MR, Alam M, Nitz S, Kollmannsberger H, Oesterhelt D, Hazelbauer GL. Identification of volatile forms of methyl groups released by Halobacterium salinarium. J. Biol. Chem. 269: 16449-16454 (1994).

Noronha SB, Yeh HJ, Spande TF, Shiloach J. Investigation of the TCA cycle and the glyoxylate shunt in Escherichia coli BL21 and JM109 using 13C-NMR/MS. Biotechnol. Bioeng. 68: 316-327 (2000).

Norris SR, Shen X, DellaPenna D. Complementation of the Arabidopsis pds1 mutation with the gene encoding p-hydroxyphenylpyruvate dioxygenase. Plant Physiol. 117: 1317-1323 (1998).

Nosarszewski M, Clements AM, Downie AB, Archbold DD. Sorbitol dehydrogenase expression and activity during apple fruit set and early development. Physiol. Plant. 121: 391-398 (2004).

Nowicki M, Muller F, Frentzen M. Cardiolipin synthase of Arabidopsis thaliana. FEBS Lett. 579: 2161-2165 (2005).

Nozaki T, Arase T, Shigeta Y, Asai T, Leustek T, Takeuchi T. Cloning and bacterial expression of adenosine-5'-triphosphate sulfurylase from the enteric protozoan parasite Entamoeba histolytica. Biochim. Biophys. Acta 1429: 284-291 (1998).

Nunez H, Lefimil C, Min B, Soll D, Orellana O. In vivo formation of glutamyl-tRNA(Gln) in Escherichia coli by heterologous glutamyl-tRNA synthetases. FEBS Lett. 557: 133-135 (2004).

Nyyssola A, Kerovuo J, Kaukinen P, von Weymarn N, Reinikainen T. Extreme halophiles synthesize betaine from glycine by methylation. J. Biol. Chem. 275: 22196-22201 (2000).

Nyyssola A, Reinikainen T, Leisola M. Characterization of glycine sarcosine N-methyltransferase and sarcosine dimethylglycine N-methyltransferase. Appl. Environ. Microbiol. 67: 2044-2050 (2001).

O'Donoghue P, Amaro RE, Luthey-Schulten Z. On the structure of hisH: Protein structure prediction in the context of structural and functional genomics. J. Struct. Biol. 134: 257-268 (2001).

O'Gaora P, Maskel D, Coleman D, Cafferkey M, Dougan G. Cloning and characterisation of the serC and aroA genes of Yersinia enterocolitica, and construction of an aroA mutant. Gene 84: 23-30 (1989).

O'Mahony PJ, Oliver MJ. Characterization of a desiccation-responsive small GTP-binding protein (Rab2) from the desiccation-tolerant grass Sporobolus stapfianus. Plant Mol. Biol. 39: 809-821 (1999).

Ober D, Harms R, Hartmann T. Cloning and expression of homospermidine synthase from Senecio vulgaris: a revision. Phytochemistry 55: 305-309 (2000).

Oda T, Kitamura N, Nakanishi S, Ichiyama A. Cloning and expression in Escherichia coli of cDNA for serine:pyruvate aminotransferase of rat liver. Eur. J. Biochem. 150: 415-421 (1985).

Ogahara T, Ohno M, Takayama M, Igarashi K, Kobayashi H. Accumulation of glutamate by osmotically stressed Escherichia coli is dependent on pH. J. Bacteriol. 177: 5987-5890 (1995).

Ogasahara K, Hiraga K, Ito W, Miles EW, Yutani K. Origin of the mutual activation of the alpha and beta 2 subunits in the alpha 2 beta 2 complex of tryptophan synthase. Effect of alanine or glycine substitutions at proline residues in the alpha subunit. J. Biol. Chem. 267: 5222-5228 (1992).

Ogawa M, Herai Y, Koizumi N, Kusano T, Sano H. 7-Methylxanthine methyltransferase of coffee plants. Gene isolation and enzymatic properties. J. Biol. Chem. 276: 8213-8218 (2001).

Ogawa-Miyata Y, Kojima H, Sano K. Mutation analysis of the feedback inhibition site of aspartokinase III of Escherichia coli K-12 and its use in L-threonine production. Biosci. Biotechnol. Biochem. 65: 1149-1154 (2001).

Oh MK, Liao JC. DNA microarray detection of metabolic responses to protein overproduction in Escherichia coli. Metab. Eng. 2: 201-209 (2000).

Oh MK, Rohlin L, Kao KC, Liao JC. Global expression profiling of acetate-grown Escherichia coli. J. Biol. Chem. 277: 13175-13183 (2002).

Ohno H, Zhu GF, Mohan VP, Chu D, Kohno S, Jacobs WR, Chan J. The effects of reactive nitrogen intermediates on gene expression in Mycobacterium tuberculosis. Cell Microbiol. 5: 637-648 (2003).

Ohsawa M, Mogi T, Yamamoto H, Yamato I, Anraku Y. Proline carrier mutant of Escherichia coli K-12 with altered cation sensitivity of substrate-binding activity: cloning, biochemical characterization, and identification of the mutation. J. Bacteriol. 170: 5185-5191 (1988).

Ohta D, Mori I, Ward E. Inhibitors of imidazoleglycerolphosphate dehydratase as herbicides. Weed Sci. 45: 610-620 (1997).

Ohta T, Tokishita S, Tsunoi R, Ohmae S, Yamagata H. Characterization of Trp(+)reversions in Escherichia coli strain WP2uvrA. Mutagenesis 17: 313-316 (2002).

Oishi H, Ebina M. Isolation of cDNA and enzymatic properties of betaine aldehyde dehydrogenase from Zoysia tenuifolia. J. Plant Physiol. 162: 1077-1086 (2005).

Ojima Y, Komaki M, Nishioka M, Iwatani S, Tsujimoto N, Taya M. Introduction of a stress-responsive gene, yggG, enhances the yield of L-phenylalanine with decreased acetic acid production in a recombinant Escherichia coli. Biotechnol. Lett. 31: 525-530 (2009).

Okada S, Nagabuchi M, Takamura Y, Nakagawa T, Shinmyozu K, Nakayama J, Tanaka K. Reconstitution of Arabidopsis thaliana SUMO pathways in E. coli: functional evaluation of SUMO machinery proteins and mapping of SUMOylation sites by mass spectrometry. Plant Cell Physiol. 50: 1049-1061 (2009).

Okada T, Suzuki H, Wada K, Kumagai H, Fukuyama K. Crystal structure of the gamma-glutamyltranspeptidase precursor protein from Escherichia coli. Structural changes upon autocatalytic processing and implications for the maturation mechanism. J. Biol. Chem. 282: 2433-2439 (2007).

Okamoto-Nakazato A, Takahashi K, Kido N, Owaribe K, Katou K. Molecular cloning of yieldins regulating the yield threshold of cowpea cell walls: cDNA cloning and characterization of recombinant yieldin. Plant Cell Environ. 23: 155-164 (2000).

Okamura-Ikeda K, Fujiwara K, Motokawa Y. Molecular cloning of a cDNA encoding chicken T-protein of the glycine cleavage system and expression of the functional protein in Escherichia coli. J. Biol. Chem. 267: 18284-18290 (1992).

Okamura-Ikeda K, Ohmura Y, Fujiwara K, Motokawa Y. Cloning and nucleotide sequence of the gcv operon encoding the Escherichia coli glycine-cleavage system. Eur. J. Biochem. 216: 539-548 (1993).

Okazaki K, Sato N, Tsuji N, Tsuzuki M, Nishida I. The significance of C16 fatty acids in the sn-2 positions of glycerolipids in the photosynthetic growth of Synechocystis sp. PCC6803. Plant Physiol. 141: 546-556 (2006).

Okinaka Y, Yang CH, Perna NT, Keen NT. Microarray profiling of Erwinia chrysanthemi 3937 genes that are regulated during plant infection. Mol. Plant Microbe Interact. 15: 619-629 (2002).

Okorokov AL, Bukanov NO, Beskrovnaia OIu, Voroshilova EB, Gusiatiner MM, Gritsenko VG, Iankovskii NK, Debabov VG. Development of the vector-host system in Corynebacterium. Cloning and expression of homoserine dehydrogenase and homoserine kinase genes in Corynebacterium cells. Genetika 26: 648-656 (1990).

Oldiges M, Kunze M, Degenring D, Sprenger GA, Takors R. Stimulation, monitoring, and analysis of pathway dynamics by metabolic profiling in the aromatic amino acid pathway. Biotechnol. Prog. 20: 1623-1633 (2004).

Ollagnier-de Choudens S, Loiseau L, Sanakis Y, Barras F, Fontecave M. Quinolinate synthetase, an iron-sulfur enzyme in NAD biosynthesis. FEBS Lett. 579: 3737-3743 (2005).

Olmo-Mira MF, Gavira M, Richardson DJ, Castillo F, Moreno-Vivian C, Roldan MD. NapF is a cytoplasmic iron-sulfur protein required for Fe-S cluster assembly in the periplasmic nitrate reductase. J. Biol. Chem. 279: 49727-49735 (2004).

Olszewski NE, Martin FB, Ausubel FM. Specialized binary vector for plant transformation: expression of the Arabidopsis thaliana AHAS gene in Nicotiana tabacum. Nucleic Acids Res. 16: 10765-10782 (1988).

Omagari K, Yoshimura H, Takano M, Hao D, Ohmori M, Sarai A, Suyama A. Systematic single base-pair substitution analysis of DNA binding by the cAMP receptor protein in cyanobacterium Synechocystis sp. PCC 6803. FEBS Lett. 563: 55-58 (2004).

Omori K, Imai Y, Suzuki S, Komatsubara S. Nucleotide sequence of the Serratia marcescens threonine operon and analysis of the threonine operon mutations which alter feedback inhibition of both aspartokinase I and homoserine dehydrogenase I. J. Bacteriol. 175: 785-794 (1993).

Onizuka T, Akiyama H, Endo S, Kanai S, Hirano M, Tanaka S, Miyasaka H. CO2 response for expression of ribulose-1,5-bisphosphate carboxylase/oxygenase genes is inhibited by AT-rich decoy in the cyanobacterium. FEBS Lett. 542: 42-46 (2003).

Oriol E, Mendez-Alvarez S, Barbe J, Gibert I. Cloning of the Rhodobacter sphaeroides hisL gene: unifunctionality of the encoded protein and lack of linkage to other his genes. Microbiology 142: 2071-2078 (1996).

Orr J, Keefer LM, Keim P, Nguyen TD, Wellems T, Heinrikson RL, Haselkorn R. Purification, physical characterization, and NH2-terminal sequence of glutamine synthetase from the cyanobacterium Anabaena 7120. J. Biol. Chem. 256: 13091-13098 (1981).

Orser CS, Goodner BW, Johnston M, Gelvin SB, Csonka LN. The Escherichia coli proB gene corrects the proline auxotrophy of Saccharomyces cerevisiae pro1 mutants. Mol. Gen. Genet. 212: 124-128 (1988).

Orsomando G, de la Garza RD, Green BJ, Peng M, Rea PA, Ryan TJ, Gregory JF 3rd, Hanson AD. Plant gamma-glutamyl hydrolases and folate polyglutamates: characterization, compartmentation, and co-occurrence in vacuoles. J. Biol. Chem. 280: 28877-28884 (2005).

Ortega F, Acerenza L, Westerhoff HV, Mas F, Cascante M. Product dependence and bifunctionality compromise the ultrasensitivity of signal transduction cascades. Proc. Natl. Acad. Sci. U.S.A. 99: 1170-1175 (2002).

Osakabe Y, Nanto K, Kitamura H, Kawai S, Kondo Y, Fujii T, Takabe K, Katayama Y, Morohoshi N. Immunocytochemical localization of phenylalanine ammonia-lyase in tissues of Populus kitakamiensis. Planta 200: 13-19 (1996).

Osborne CB, Lowe KE, Shane B. Regulation of folate and one-carbon metabolism in mammalian cells. I. Folate metabolism in Chinese hamster ovary cells expressing Escherichia coli or human folylpoly-gamma-glutamate synthetase activity. J. Biol. Chem. 268: 21657-21664 (1993).

Osorio AV, Camarena L, Salazar G, Noll-Louzada M, Bastarrachea F. Nitrogen regulation in an Escherichia coli strain with a temperature sensitive glutamyl-tRNA synthetase. Mol. Gen. Genet. 239: 400-408 (1993).

Oster U, Tanaka R, Tanaka A, Rudiger W. Cloning and functional expression of the gene encoding the key enzyme for chlorophyll b biosynthesis (CAO) from Arabidopsis thaliana. Plant J. 21: 305-310 (2000).

Osteras M, Boncompagni E, Vincent N, Poggi MC, Le Rudulier D. Presence of a gene encoding choline sulfatase in Sinorhizobium meliloti bet operon: choline-O-sulfate is metabolized into glycine betaine. Proc. Natl. Acad. Sci. U.S.A. 95: 11394-11399 (1998).

Ostergaard L, Lauvergeat V V, Naested H, Mattsson O, Mundy J. Two differentially regulated Arabidopsis genes define a new branch of the DFR superfamily. Plant Sci. 160: 463-472 (2001).

Osuna D, Galvez-Valdivieso G, Piedras P, Pineda M, Aguilar M. Cloning, characterization and mRNA expression analysis of PVAS1, a type I asparagine synthetase gene from Phaseolus vulgaris. Planta 213: 402-410 (2001).

Ott KH, Kwagh JG, Stockton GW, Sidorov V, Kakefuda G. Rational molecular design and genetic engineering of herbicide resistant crops by structure modeling and site-directed mutagenesis of acetohydroxyacid synthase. J. Mol. Biol. 263: 359-368 (1996).

Ott V, Koch J, Spate K, Morbach S, Kamer R. Regulatory properties and interaction of the C- and N-terminal domains of BetP, an osmoregulated betaine transporter from Corynebacterium glutamicum. Biochemistry 47: 12208-12218 (2008).

Ottenhof HH, Ashurst JL, Whitney HM, Saldanha SA, Schmitzberger F, Gweon HS, Blundell TL, Abell C, Smith AG. Organisation of the pantothenate (vitamin B5) biosynthesis pathway in higher plants. Plant J. 37: 61-72 (2004).

Ottow EA, Polle A, Brosche M, Kangasjarvi J, Dibrov P, Zorb C, Teichmann T. Molecular characterization of PeNhaD1: the first member of the NhaD Na(+)/H(+) antiporter family of plant origin. Plant Mol. Biol. 58: 75-88 (2005).

Oudot C, Jaquinod M, Cortay JC, Cozzone AJ, Jault JM. The isocitrate dehydrogenase kinase/phosphatase from Escherichia coli is highly sensitive to in-vitro oxidative conditions role of cysteine67 and cysteine108 in the formation of a disulfide-bonded homodimer. Eur. J. Biochem. 262: 224-249 (1999).

Oue S, Okamoto A, Yano T, Kagamiyama H. Cocrystallization of a mutant aspartate aminotransferase with a C5-dicarboxylic substrate analog: structural comparison with the enzyme-C4-dicarboxylic analog complex. J. Biochem. (Tokyo) 127: 337-343 (2000).

Oultram JD, Loughlin M, Walmsley R, Gunnery SM, Minton NP. The nucleotide sequence of genes involved in the leucine biosynthetic pathway of Clostridium pasteurianum. DNA Seq. 4: 105-111 (1993).

Ouyang J, Viola RE. Use of structural comparisons to select mutagenic targets in aspartate-beta-semialdehyde dehydrogenase. Biochemistry 34: 6394-6399 (1995).

Ouzounis C, Casari G, Sander C, Tamames J, Valencia A. Computational comparisons of model genomes. Trends Biotechnol. 14: 280-285 (1996).

Overton TW, Griffiths L, Patel MD, Hobman JL, Penn CW, Cole JA, Constantinidou C. Microarray analysis of gene regulation by oxygen, nitrate, nitrite, FNR, NarL and NarP during anaerobic growth of Escherichia coli: new insights into microbial physiology. Biochem. Soc. Trans. 34: 104-107 (2006).

Ow DS, Lee DY, Yap MG, Oh SK. Identification of cellular objective for elucidating the physiological state of plasmid-bearing Escherichia coli using genome-scale in silico analysis. Biotechnol. Prog. 25: 61-67 (2009).

Ozcan N, Kramer R, Morbach S. Chill activation of compatible solute transporters in Corynebacterium glutamicum at the level of transport activity. J. Bacteriol. 187: 4752-4759 (2005).

Padgette SR, Re DB, Gasser CS, Eichholtz DA, Frazier RB, Hironaka CM, Levine EB, Shah DM, Fraley RT, Kishore GM. Site-directed mutagenesis of a conserved region of the 5-enolpyruvylshikimate-3-phosphate synthase active site. J. Biol. Chem. 266: 22364-22369 (1991).

Padidam M, Reddy VS, Beachy RN, Fauquet CM. Molecular characterization of a plant mitochondrial chaperone GrpE. Plant Mol. Biol. 39: 871-881 (1999).

Padilla L, Agosin E. Heterologous expression of Escherichia coli ppsA (phosphoenolpyruvate synthetase) and galU (UDP-glucose pyrophosphorylase) genes in Corynebacterium glutamicum, and its impact on trehalose synthesis. Metab. Eng. 7: 260-268 (2005).

Paessens A, Rudiger H. Purification and chemical characterization of the vitamin-B12-dependent 5-methyltetrahydrofolate: homocysteine methyltransferase from Escherichia coli B. Eur. J. Biochem. 112: 47-51 (1980).

Page L, Griffiths L, Cole JA. Different physiological roles of two independent pathways for nitrite reduction to ammonia by enteric bacteria. Arch. Microbiol. 154: 349-354 (1990).

Pahel G, Tyler B. A new glnA-linked regulatory gene for glutamine synthetase in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 76: 4544-4548 (1979).

Pahel G, Zelenetz AD, Tyler BM. gltB gene and regulation of nitrogen metabolism by glutamine synthetase in Escherichia coli. J. Bacteriol. 133: 139-148 (1978).

Pail M, Peterbauer T, Seiboth B, Hametner C, Druzhinina I, Kubicek CP. The metabolic role and evolution of L-arabinitol 4-dehydrogenase of Hypocrea jecorina. Eur. J. Biochem. 271: 1864-1872 (2004).

Pakhomova S, Luka Z, Grohmann S, Wagner C, Newcomer ME. Glycine N-methyltransferases: a comparison of the crystal structures and kinetic properties of recombinant human, mouse and rat enzymes. Proteins 57: 331-337 (2004).

Pal C, Papp B, Lercher MJ. Horizontal gene transfer depends on gene content of the host. Bioinformatics 21 Suppl. 2: ii222-ii223 (2005).

Pal C, Papp B, Lercher MJ. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat. Genet. 37: 1372-1375 (2005).

Palatnik JF, Valle EM, Carrillo N. Oxidative stress causes ferredoxin-NADP+ reductase solubilization from the thylakoid membranes in methyl viologen-treated plants. Plant Physiol. 115: 1721-1727 (1997).

Palmer T, Santini CL, Iobbi-Nivol C, Eaves DJ, Boxer DH, Giordano G. Involvement of the narJ and mob gene products in distinct steps in the biosynthesis of the molybdoenzyme nitrate reductase in Escherichia coli. Mol. Microbiol. 20: 875-884 (1996).

Palmer T, Vasishta A, Whitty PW, Boxer DH. Isolation of protein FA, a product of the mob locus required for molybdenum cofactor biosynthesis in Escherichia coli. Eur. J. Biochem. 222: 687-692 (1994).

Palombella AL, Dutcher SK. Identification of the gene encoding the tryptophan synthase beta-subunit from Chlamydomonas reinhardtii. Plant Physiol. 117: 455-464 (1998).

Pan GL, Verhagen MFJM, Adams MWW. Characterization of pyridine nucleotide coenzymes in the hyperthermophilic archaeon Pyrococcus furiosus. Extremophiles 5: 393-398 (2001).

Pan X, Chen M, Liu Y, Wang Q, Zeng L, Li L, Liao Z. A new isopentenyl diphosphate isomerase gene from Camptotheca acuminata: cloning, characterization and functional expression in Escherichia coli. DNA Seq. 19: 98-105 (2008).

Pan Y, Durfee T, Bockhorst J, Craven M. Connecting quantitative regulatory-network models to the genome. Bioinformatics 23: i367-i376 (2007).

Pan YT, Carroll JD, Asano N, Pastuszak I, Edavana VK, Elbein AD. Trehalose synthase converts glycogen to trehalose. FEBS J. 275: 3408-3420 (2008).

Pan YT, Carroll JD, Elbein AD. Trehalose-phosphate synthase of Mycobacterium tuberculosis. Cloning, expression and properties of the recombinant enzyme. Eur. J. Biochem. 269: 6091-6100 (2002).

Pan YT, Koroth Edavana V, Jourdian WJ, Edmondson R, Carroll JD, Pastuszak I, Elbein AD. Trehalose synthase of Mycobacterium smegmatis: purification, cloning, expression, and properties of the enzyme. Eur. J. Biochem. 271: 4259-4269 (2004).

Panagiotidis CA, Blackburn S, Low KB, Canellakis ES. Biosynthesis of polyamines in ornithine decarboxylase, arginine decarboxylase, and agmatine ureohydrolase deletion mutants of Escherichia coli strain K-12. Proc. Natl. Acad. Sci. U.S.A. 84: 4423-4427 (1987).

Panagiotidis CA, Huang SC, Canellakis ES. Post-translational and transcriptional regulation of polyamine biosynthesis in Escherichia coli. Int. J. Biochem. 26: 991-1001 (1994).

Pandey J, Koyuturk M, Kim Y, Szpankowski W, Subramaniam S, Grama A. Functional annotation of regulatory pathways. Bioinformatics 23: i377-i386 (2007).

Pang SS, Duggleby RG. Expression, purification, characterization, and reconstitution of the large and small subunits of yeast acetohydroxyacid synthase. Biochemistry 38: 5222-5231 (1999).

Pantel I, Lindgren PE, Neubauer H, Gotz F. Identification and characterization of the Staphylococcus carnosus nitrate reductase operon. Mol. Gen. Genet. 259: 105-114 (1998).

Pappan K, Wang X. Plant phospholipase Dalpha is an acidic phospholipase active at near-physiological Ca(2+) concentrations. Arch. Biochem. Biophys. 368: 347-353 (1999).

Paradisi F, Dean JL, Geoghegan KF, Engel PC. Spontaneous chemical reversion of an active site mutation: deamidation of an asparagine residue replacing the catalytic aspartic acid of glutamate dehydrogenase. Biochemistry 44: 3636-3643 (2005).

Parish T, Liu J, Nikaido H, Stoker NG. A Mycobacterium smegmatis mutant with a defective inositol monophosphate phosphatase gene homolog has altered cell envelope permeability. J. Bacteriol. 179: 7827-7833 (1997).

Park H, Kreunen SS, Cuttriss AJ, DellaPenna D, Pogson BJ. Identification of the carotenoid isomerase provides insight into carotenoid biosynthesis, prolamellar body formation, and photomorphogenesis. Plant Cell 14: 321-332 (2002).

Park J, Osei YD, Churchich JE. Isolation and characterization of recombinant mitochondrial 4-aminobutyrate aminotransferase. J. Biol. Chem. 268: 7636-7699 (1993).

Park KS, Jang YS, Lee H, Kim JS. Phenotypic alteration and target gene identification using combinatorial libraries of zinc finger proteins in prokaryotic cells. J. Bacteriol. 187: 5496-5499 (2005).

Park KS, Kahn ML. Distribution of two isoforms of NADP-dependent isocitrate dehydrogenase in soybean (Glycine max). Plant Mol. Biol. 40: 13-21 (1999).

Park OK, Bauerle R. Metal-catalyzed oxidation of phenylalanine-sensitive 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Escherichia coli: inactivation and destabilization by oxidation of active-site cysteines. J. Bacteriol. 181: 1636-1642 (1999).

Park SJ, Kwak KJ, Oh TR, Kim YO, Kang H. Cold shock domain proteins affect seed germination and growth of Arabidopsis thaliana under abiotic stress conditions. Plant Cell Physiol. 50: 869-878 (2009).

Park SJ, McCabe J, Turna J, Gunsalus RP. Regulation of the citrate synthase (gltA) gene of Escherichia coli in response to anaerobiosis and carbon supply: role of the arcA gene product. J. Bacteriol. 176: 5086-5092 (1994).

Park SJ, Tseng CP, Gunsalus RP. Regulation of succinate dehydrogenase (sdhCDAB) operon expression in Escherichia coli in response to carbon supply and anaerobiosis: role of ArcA and Fnr. Mol. Microbiol. 15: 473-482 (1995).

Park SM, Klapa MI, Sinskey AJ, Stephanopoulos G. Metabolite and isotopomer balancing in the analysis of metabolic cycles: II. Applications. Biotechnol. Bioeng. 62: 392-401 (1999).

Park SY, Beel BD, Simon MI, Bilwes AM, Crane BR. In different organisms, the mode of interaction between two signaling proteins is not necessarily conserved. Proc. Natl. Acad. Sci. U.S.A. 101: 11646-11651 (2004).

Parker NB, Yang X, Hanke J, Mason KA, Schowen RL, Borchardt RT, Yin DH. Trypanosoma cruzi: molecular cloning and characterization of the S-adenosylhomocysteine hydrolase. Exp. Parasitol. 105: 149-158 (2003).

Parr IB, Boehlein SK, Dribben AB, Schuster SM, Richards NG. Mapping the aspartic acid binding site of Escherichia coli asparagine synthetase B using substrate analogs. J. Med. Chem. 39: 2367-2378 (1996).

Parsons JF, Jensen PY, Pachikara AS, Howard AJ, Eisenstein E, Ladner JE. Structure of Escherichia coli aminodeoxychorismate synthase: Architectural conservation and diversity in chorismate-utilizing enzymes. Biochemistry 41: 2198-2208 (2002).

Parsot C. Evolution of biosynthetic pathways: a common ancestor for threonine synthase, threonine dehydratase and D-serine dehydratase. EMBO J. 5: 3013-3019 (1986).

Parsot C, Cohen GN. Cloning and nucleotide sequence of the Bacillus subtilis hom gene coding for homoserine dehydrogenase. Structural and evolutionary relationships with Escherichia coli aspartokinases-homoserine dehydrogenases I and II. J. Biol. Chem. 263: 14654-14660 (1988).

Parsot C, Cossart P, Saint-Girons I, Cohen GN. Nucleotide sequence of thrC and of the transcription termination region of the threonine operon in Escherichia coli K12. Nucleic Acids Res. 11: 7331-7345 (1983).

Parsot C, Mazel D. Cloning and nucleotide sequence of the thrB gene from the cyanobacterium Calothrix PCC 7601. Mol. Microbiol. 1: 45-52 (1987).

Parvathi K, Chen F, Guo D, Blount J, Dixon R. Substrate preferences of O-methyltransferases in alfalfa suggest new pathways for 3-O-methylation of monolignols. Plant J. 25: 193-202 (2001).

Patek M, Hochmannova J, Jelinkova M, Nesvera J, Eggeling L. Analysis of the leuB gene from Corynebacterium glutamicum. Appl. Microbiol. Biotechnol. 50: 42-47 (1998).

Patek M, Hochmannova J, Nesvera J. Production of threonine by Brevibacterium flavum containing threonine biosynthesis genes from Escherichia coli. Folia Microbiol. (Praha) 38: 355-359 (1993).

Patel SS, Picha KM. Structure and function of hexameric helicases. Annu. Rev. Biochem. 69: 651-697 (2000).

Patnaik PR. Are microbes intelligent beings?: An assessment of cybernetic modeling. Biotechnol. Adv. 18: 267-288 (2000).

Patte JC, Akrim M, Mejean V. The leader sequence of the Escherichia coli lysC gene is involved in the regulation of LysC synthesis. FEMS Microbiol. Lett. 169: 165-170 (1998).

Patte JC, Clepet C, Bally M, Borne F, Mejean V, Foglino M. ThrH, a homoserine kinase isozyme with in vivo phosphoserine phosphatase activity in Pseudomonas aeruginosa. Microbiology 145: 845-853 (1999).

Patte JC, Morand P, Boy E, Richaud C, Borne F. The relA locus and the regulation of lysine biosynthesis in Escherichia coli. Mol. Gen. Genet. 179: 319-325 (1980).

Patte JC, Richaud C, Boy E, Reinisch F, Richaud F, Cassan M. Regulation of lysine biosynthesis in Escherichia coli K12. Acta Microbiol. Acad. Sci. Hung. 23: 121-128 (1976).

Patterson WR, Poulos TL. Characterization and crystallization of recombinant pea cytosolic ascorbate peroxidase. J. Biol. Chem. 269: 17020-17024 (1994).

Patton DA, Johnson M, Ward ER. Biotin synthase from Arabidopsis thaliana. cDNA isolation and characterization of gene expression. Plant Physiol. 112: 371-378 (1996).

Pau RN, Lawson DM. Transport, homeostasis, regulation, and binding of molybdate and tungstate to proteins. Met. Ions Biol. Syst. 39: 31-74 (2002).

Paul L, Blumenthal RM, Matthews RG. Activation from a distance: roles of Lrp and integration host factor in transcriptional activation of gltBDF. J. Bacteriol. 183: 3910-398 (2001).

Paulsen IT, Chauvaux S, Choi P, Saier MH Jr. Characterization of glucose-specific catabolite repression-resistant mutants of Bacillus subtilis: identification of a novel hexose:H+ symporter. J. Bacteriol. 180: 498-504 (1998).

Pawelec D, Jagusztyn-Krynicka E. Complete nucleotide sequence of the Campylobacter jejuni 72Dz asd gene. Acta Microbiol. Pol. 45: 299-304 (1996).

Pawlowski K, Gough SP, Kannangara CG, Debruijn FJ. Characterization of a 5-aminolevulinic acid synthase mutant of Azorhizobium caulinodans ORS571. Mol. Plant Microbe Interact. 6: 35-44 (1993).

Peakman T, Busby S, Cole J. Transcriptional control of the cysG gene of Escherichia coli K-12 during aerobic and anaerobic growth. Eur. J. Biochem. 191: 325-331 (1990).

Peakman T, Crouzet J, Mayaux JF, Busby S, Mohan S, Harborne N, Wootton J, Nicolson R, Cole J. Nucleotide sequence, organisation and structural analysis of the products of genes in the nirB-cysG region of the Escherichia coli K-12 chromosome. Eur. J. Biochem. 191: 315-323 (1990).

Peariso K, Zhou ZS, Smith AE, Matthews RG, Penner-Hahn JE. Characterization of the zinc sites in cobalamin-independent and cobalamin-dependent methionine synthase using zinc and selenium X-ray absorption spectroscopy. Biochemistry 40: 987-993 (2001).

Pearson JT, Dabrowski MJ, Kung I, Atkins WM. The central loop of Escherichia coli glutamine synthetase is flexible and functionally passive. Arch. Biochem. Biophys. 436: 397-405 (2005).

Pechous SW, Whitaker BD. Cloning and functional expression of an (E, E)-alpha-farnesene synthase cDNA from peel tissue of apple fruit. Planta 219: 84-94 (2004).

Peddie BA, Chambers ST, Lever M. Is the ability of urinary tract pathogens to accumulate glycine betaine a factor in the virulence of pathogenic strains? J. Lab. Clin. Med. 128: 417-422 (1996).

Peddie BA, Lever M, Hayman CM, Randall K, Chambers ST. Relationship between osmoprotection and the structure and intracellular accumulation of betaines by Escherichia coli. FEMS Microbiol. Lett. 120: 125-131 (1994).

Peddie BA, Lever M, Randall K, Chambers ST. Osmoprotective activity, urea protection, and accumulation of hydrophilic betaines in Escherichia coli and Staphylococcus aureus. Antonie Van Leeuwenhoek 75: 183-189 (1999).

Peddie BA, Wong-She J, Randall K, Lever M, Chambers ST. Osmoprotective properties and accumulation of betaine analogues by Staphylococcus aureus. FEMS Microbiol. Lett. 160: 25-30 (1998).

Peddie BA, Wood JE, Lever M, Happer DA, de Zwart F, Chambers ST. Assessment of antimicrobial activity of hydrophilic betaines in osmotically stressed bacteria. Antonie Van Leeuwenhoek 83: 175-181 (2003).

Peleman J, Boerjan W, Engler G, Seurinck J, Botterman J, Alliotte T, Van Montagu M, Inze D. Strong cellular preference in the expression of a housekeeping gene of Arabidopsis thaliana encoding S-adenosylmethionine synthetase. Plant Cell 1: 81-93 (1989).

Peng HL, Wang PY, Wu CM, Hwang DC, Chang HY. Cloning, sequencing and heterologous expression of a Klebsiella pneumoniae gene encoding an FAD-independent acetolactate synthase. Gene 117: 125-130 (1992).

Peng WT, Wang J, Wu T, Huang JQ, Chiao JS, Zhao GP. Bacterial type I glutamine synthetase of the rifamycin SV producing actinomycete, Amycolatopsis mediterranei U32, is the only enzyme responsible for glutamine synthesis under physiological conditions. Acta Biochim. Biophys. Sin. (Shanghai) 38: 821-830 (2006).

Peoples OP, Liebl W, Bodis M, Maeng PJ, Follettie MT, Archer JA, Sinskey AJ. Nucleotide sequence and fine structural analysis of the Corynebacterium glutamicum hom-thrB operon. Mol. Microbiol. 2: 63-72 (1988).

Perez-Arellano I, Rubio V, Cervera J. Dissection of Escherichia coli glutamate 5-kinase: functional impact of the deletion of the PUA domain. FEBS Lett. 579: 6903-6908 (2005).

Periappuram C, Steinhauer L, Barton DL, Taylor DC, Chatson B, Zou J. The plastidic phosphoglucomutase from Arabidopsis. A reversible enzyme reaction with an important role in metabolic control. Plant Physiol. 122: 1193-1200 (2000).

Perl A, Shaul O, Galili G. Regulation of lysine synthesis in transgenic potato plants expressing a bacterial dihydrodipicolinate synthase in their chloroplasts. Plant Mol. Biol. 19: 815-823 (1992).

Perroud B, Le Rudulier D. Glycine betaine transport in Escherichia coli: osmotic modulation. J. Bacteriol. 161: 393-401 (1985).

Persans MW, Yan X, Patnoe JM, Kramer U, Salt DE. Molecular dissection of the role of histidine in nickel hyperaccumulation in Thlaspi goesingense (Halacsy). Plant Physiol. 121: 1117-1126 (1999).

Peter H, Bader A, Burkovski A, Lambert C, Kramer R. Isolation of the putP gene of Corynebacterium glutamicum and characterization of a low-affinity uptake system for compatible solutes. Arch. Microbiol. 168: 143-151 (1997).

Peter H, Burkovski A, Kramer R. Isolation, characterization, and expression of the Corynebacterium glutamicum betP gene, encoding the transport system for the compatible solute glycine betaine. J. Bacteriol. 178: 5229-5234 (1996).

Peters F, Rother M, Boll M. Selenocysteine-containing proteins in anaerobic benzoate metabolism of Desulfococcus multivorans. J. Bacteriol. 186: 2156-2163 (2004).

Peters MH, Beltzer JP, Kohlhaw GB. Expression of the yeast LEU4 gene is subject to four different modes of control. Arch. Biochem. Biophys. 276: 294-298 (1990).

Petersen JL, Lang DW, Small GD. Cloning and characterization of a class II DNA photolyase from Chlamydomonas. Plant Mol. Biol. 40: 1063-1071 (1999).

Petersen S, Mack C, De Graaf AA, Riedel C, Eikmanns BJ, Sahm H. Metabolic consequences of altered phosphoenolpyruvate carboxykinase activity in Corynebacterium glutamicum reveal anaplerotic regulation mechanisms in vivo. Metab. Eng. 3: 344-361 (2001).

Peterson JD, Ingram LO. Anaerobic respiration in engineered Escherichia coli with an internal electron acceptor to produce fuel ethanol. Ann. N. Y. Acad. Sci. 1125: 363-372 (2008).

Pfeiffer M, Bestgen H, Burger A, Klein A. The vhuU gene encoding a small subunit of a selenium-containing [NiFe]-hydrogenase in Methanococcus voltae appears to be essential for the cell. Arch. Microbiol. 170: 418-426 (1998).

Pfleger BF, Pitera DJ, Newman JD, Martin VJ, Keasling JD. Microbial sensors for small molecules: development of a mevalonate biosensor. Metab. Eng. 9: 30-38 (2007).

Pfluger K, Baumann S, Gottschalk G, Lin W, Santos H, Muller V. Lysine-2,3-aminomutase and beta-lysine acetyltransferase genes of methanogenic archaea are salt induced and are essential for the biosynthesis of N-epsilon-acetyl-beta-lysine and growth at high salinity. Appl. Environ. Microbiol. 69: 6047-6055 (2003).

Pflughoeft KJ, Kierek K, Watnick PI. Role of ectoine in Vibrio cholerae osmoadaptation. Appl. Environ. Microbiol. 69: 5919-5927 (2003).

Phalakornkule C, Lee S, Zhu T, Koepsel R, Ataai MM, Grossmann IE, Domach MM. A MILP-based flux alternative generation and NMR experimental design strategy for metabolic engineering. Metab. Eng. 3: 124-137 (2001).

Pharkya P, Maranas CD. An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems. Metab. Eng. 8: 1-13 (2006).

Philippot L, Clays-Josserand A, Lensi R, Trinsoutreau I, Normand P, Potier P. Purification of the dissimilative nitrate reductase of Pseudomonas fluorescens and the cloning and sequencing of its corresponding genes. Biochim. Biophys. Acta 1350: 272-276 (1997).

Phillips AL, Ward DA, Uknes S, Appleford NE, Lange T, Huttly AK, Gaskin P, Graebe JE, Hedden P. Isolation and expression of three gibberellin 20-oxidase cDNA clones from Arabidopsis. Plant Physiol. 108: 1049-1057 (1995).

Phillips MA, Leon P, Boronat A, Rodriguez-Concepcion M. The plastidial MEP pathway: unified nomenclature and resources. Trends Plant Sci. 13: 619-623 (2008).

Phillips RS, Dua RK. Indole protects tryptophan indole-lyase, but not tryptophan synthase, from inactivation by trifluoroalanine. Arch. Biochem. Biophys. 296: 489-496 (1992).

Phue JN, Noronha SB, Hattacharyya R, Wolfe AJ, Shiloach J.. Glucose metabolism at high density growth of E. coli B and E. coli K: differences in metabolic pathways are responsible for efficient glucose utilization in E. coli B as determined by microarrays and Northern blot analyses. Biotechnol. Bioeng. 90: 805-820 (2005).

Phue JN, Shiloach J. Impact of dissolved oxygen concentration on acetate accumulation and physiology of E. coli BL21, evaluating transcription levels of key genes at different dissolved oxygen conditions. Metab. Eng. 7: 353-363 (2005).

Pi J, Chow H, Pittard AJ. Study of second-site suppression in the PheP gene for the phenylalanine transporter of Escherichia coli. J. Bacteriol. 184: 5842-5847 (2002).

Picaud S, Olsson ME, Brodelius PE. Improved conditions for production of recombinant plant sesquiterpene synthases in Escherichia coli. Protein Expr. Purif. 51: 71-79 (2007).

Pieterse CM, van't Klooster J, van den Berg-Velthuis GC, Govers F. NiaA, the structural nitrate reductase gene of Phytophthora infestans: isolation, characterization and expression analysis in Aspergillus nidulans. Curr. Genet. 27: 359-366 (1995).

Pike CS, Grieve J, Badger MR, Price GD. Thermoprotective properties of small heat shock proteins from rice, tomato and Synechocystis sp PCC6803 overexpressed in, and isolated from, Escherichia coli. Aust. J. Plant Physiol. 28: 1219-1229 (2001).

Pilon-Smits EA, Garifullina GF, Abdel-Ghany S, Kato S, Mihara H, Hale KL, Burkhead JL, Esaki N, Kurihara T, Pilon M. Characterization of a NifS-like chloroplast protein from Arabidopsis. Implications for its role in sulfur and selenium metabolism. Plant Physiol. 130: 1309-1318 (2002).

Pinkofsky HB, Ginsburg A, Reardon I, Heinrikson RL. Lysyl residue 47 is near the subunit ATP-binding site of glutamine synthetase from Escherichia coli. J. Biol. Chem. 259: 9616-9622 (1984).

Pinon V, Ravanel S, Douce R, Alban C. Biotin synthesis in plants. The first committed step of the pathway is catalyzed by a cytosolic 7-keto-8-aminopelargonic acid synthase. Plant Physiol. 139: 1666-1676 (2005).

Pioszak AA, Jiang P, Ninfa AJ. The Escherichia coli PII signal transduction protein regulates the activities of the two-component system transmitter protein NRII by direct interaction with the kinase domain of the transmitter module. Biochemistry 39: 13450-13461 (2000).

Pioszak AA, Ninfa AJ. Mechanism of the PII-activated phosphatase activity of Escherichia coli NRII (NtrB): how the different domains of NRII collaborate to act as a phosphatase. Biochemistry 42: 8885-8899 (2003).

Pioszak AA, Ninfa AJ. Genetic and biochemical analysis of phosphatase activity of Escherichia coli NRII (NtrB) and its regulation by the PII signal transduction protein. J. Bacteriol. 185: 1299-1315 (2003).

Pioszak AA, Ninfa AJ. Mutations altering the N-terminal receiver domain of NRI (NtrC) that prevent dephosphorylation by the NRII-PII complex in Escherichia coli. J. Bacteriol. 186: 5730-5740 (2004).

Piotrowski M, Schonfelder S, Weiler EW. The Arabidopsis thaliana isogene NIT4 and its orthologs in tobacco encode beta-cyano-L-alanine hydratase/nitrilase. J. Biol. Chem. 276: 2616-2621 (2001).

Pisabarro A, Malumbres M, Mateos LM, Oguiza JA, Martin JF. A cluster of three genes (dapA, orf2, and dapB) of Brevibacterium lactofermentum encodes dihydrodipicolinate synthase, dihydrodipicolinate reductase, and a third polypeptide of unknown function. J. Bacteriol. 175: 2743-2749 (1993).

Pitera DJ, Paddon CJ, Newman JD, Keasling JD. Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli. Metab. Eng. 9: 193-207 (2007).

Pitt WG, Ross SA. Ultrasound increases the rate of bacterial cell growth. Biotechnol. Prog. 19: 1038-1044 (2003).

Plamann MD, Rapp WD, Stauffer GV. Escherichia coli K12 mutants defective in the glycine cleavage enzyme system. Mol. Gen. Genet. 192: 15-20 (1983).

Plamann MD, Stauffer LT, Urbanowski ML, Stauffer GV. Complete nucleotide sequence of the E. coli glyA gene. Nucleic Acids Res. 11: 2065-2075 (1983).

Platko JV, Willins DA, Calvo JM. The ilvIH operon of Escherichia coli is positively regulated. J. Bacteriol. 172: 4563-4570 (1990).

Pocard JA, Vincent N, Boncompagni E, Smith LT, Poggi MC, Le Rudulier D. Molecular characterization of the bet genes encoding glycine betaine synthesis in Sinorhizobium meliloti 102F34. Microbiology 143: 1369-1379 (1997).

Pohnert G, Zhang S, Husain A, Wilson DB, Ganem B. Regulation of phenylalanine biosynthesis. Studies on the mechanism of phenylalanine binding and feedback inhibition in the Escherichia coli P-protein. Biochemistry 38: 12212-12217 (1999).

Polacco ML, Cronan JE Jr. A mutant of Escherichia coli conditionally defective in the synthesis of holo-[acyl carrier protein]. J. Biol. Chem. 256: 5750-5754 (1981).

Pollock VV, Conover RC, Johnson MK, Barber MJ. Bacterial expression of the molybdenum domain of assimilatory nitrate reductase: production of both the functional molybdenum-containing domain and the nonfunctional tungsten analog. Arch. Biochem. Biophys. 403: 237-248 (2002).

Pommier J, Mandrand MA, Holt SE, Boxer DH, Giordano G. A second phenazine methosulphate-linked formate dehydrogenase isoenzyme in Escherichia coli. Biochim. Biophys. Acta 1107: 305-313 (1992).

Pomposiello PJ, Bennik MH, Demple B. Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate. J. Bacteriol. 183: 3890-3902 (2001).

Ponce E, Martinez A, Bolivar F, Valle F. Stimulation of glucose catabolism through the pentose pathway by the absence of the two pyruvate kinase isoenzymes in Escherichia coli. Biotechnol. Bioeng. 58: 292-295 (1998).

Posfai G, Plunkett G 3rd, Feher T, Frisch D, Keil GM, Umenhoffer K, Kolisnychenko V, Stahl B, Sharma SS, de Arruda M, Burland V, Harcum SW, Blattner FR. Emergent properties of reduced-genome Escherichia coli. Science 312: 1044-1046 (2006).

Powell JT, Morrison JF. Enzyme-enzyme interaction and the biosynthesis of aromatic amino acids in Escherichia coli. Biochim. Biophys. Acta 568: 467-474 (1979).

Powell JT, Morrison JF. The purification and properties of the aspartate aminotransferase and aromatic-amino-acid aminotransferase from Escherichia coli. Eur. J. Biochem. 87: 391-400 (1978).

Powers SG, Riordan JF. Functional arginyl residues as ATP binding sites of glutamine synthetase and carbamyl phosphate synthetase. Proc. Natl. Acad. Sci. U.S.A. 72: 2616-2620 (1975).

Pramanik J, Keasling JD. Stoichiometric model of Escherichia coli metabolism: incorporation of growth-rate dependent biomass composition and mechanistic energy requirements. Biotechnol. Bioeng. 56: 398-421 (1997).

Prasad BC, Kumar V, Gururaj HB, Parimalan R, Giridhar P, Ravishankar GA. Characterization of capsaicin synthase and identification of its gene (csy1) for pungency factor capsaicin in pepper (Capsicum sp.). Proc. Natl. Acad. Sci. U.S.A. 103: 13315-13320 (2006).

Preiss J. ADPglucose pyrophosphorylase: basic science and applications in biotechnology. Biotechnol. Annu. Rev. 2: 259-279 (1996).

Prest AG, Winson MK, Hammond JR, Stewart GS. The construction and application of a lux-based nitrate biosensor. Lett. Appl. Microbiol. 24: 355-360 (1997).

Pribat A, Jeanguenin L, Lara-Nunez A, Ziemak MJ, Hyde JE, de Crecy-Lagard V, Hanson AD. 6-Pyruvoyltetrahydropterin synthase paralogs replace the folate synthesis enzyme dihydroneopterin aldolase in diverse bacteria. J. Bacteriol. 191: 4158-4165 (2009).

Priestman MA, Healy ML, Funke T, Becker A, Schondbrunn E. Molecular basis for the glyphosate-insensitivity of the reaction of 5-enolpyruvylshikimate 3-phosphate synthase with shikimate. FEBS Lett. 579: 5773-5780 (2005).

Prigent-Combaret C, Vidal O, Dorel C, Lejeune P. Abiotic surface sensing and biofilm-dependent regulation of gene expression in Escherichia coli. J. Bacteriol. 181: 5993-6002 (1999).

Prior A, Uhrig JF, Heins L, Wiesmann A, Lillig CH, Stoltze C, Soll J, Schwenn JD. Structural and kinetic properties of adenylyl sulfate reductase from Catharanthus roseus cell cultures. Biochim. Biophys. Acta 1430: 25-38 (1999).

Privalle CT, Beyer WF Jr, Fridovich I. Anaerobic induction of ProMn-superoxide dismutase in Escherichia coli. J. Biol. Chem. 264: 2758-2763 (1989).

Prohl C, Wackwitz B, Vlad D, Unden G. Functional citric acid cycle in an arcA mutant of Escherichia coli during growth with nitrate under anoxic conditions. Arch. Microbiol. 170: 1-7 (1998).

Prudencio M, Eady RR, Sawers G. The blue copper-containing nitrite reductase from Alcaligenes xylosoxidans: cloning of the nirA gene and characterization of the recombinant enzyme. J. Bacteriol. 181: 2323-2329 (1999).

Przybyla-Zawislak B, Dennis RA, Zakharkin SO, McCammon MT. Genes of succinyl-CoA ligase from Saccharomyces cerevisiae. Eur. J. Biochem. 258: 736-743 (1998).

Puan KJ, Wang H, Dairi T, Kuzuyama T, Morita CT. fldA is an essential gene required in the 2-C-methyl-D-erythritol 4-phosphate pathway for isoprenoid biosynthesis. FEBS Lett. 579: 3802-3806 (2005).

Purta E, Kaminska KH, Kasprzak JM, Bujnicki JM, Douthwaite S. YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA. RNA 14: 2234-2244 (2008).

Purvis JE, Yomano LP, Ingram LO. Enhanced trehalose production improves growth of Escherichia coli under osmotic stress. Appl. Environ. Microbiol. 71: 3761-3769 (2005).

Pyne C, Bognar AL. Replacement of the folC gene, encoding folylpolyglutamate synthetase-dihydrofolate synthetase in Escherichia coli, with genes mutagenized in vitro. J. Bacteriol. 174: 1750-1759 (1992).

Qian ZG, Xia XX, Choi JH, Lee SY. Proteome-based identification of fusion partner for high-level extracellular production of recombinant proteins in Escherichia coli. Biotechnol. Bioeng. 101: 587-601 (2008).

Qin C, Wang X. The Arabidopsis phospholipase D family. Characterization of a calcium-independent and phosphatidylcholine-selective PLDzeta1 with distinct regulatory domains. Plant Physiol. 128: 1057-1068 (2002).

Qin J, Rosen BP, Zhang Y, Wang G, Franke S, Rensing C. Arsenic detoxification and evolution of trimethylarsine gas by a microbial arsenite S-adenosylmethionine methyltransferase. Proc. Natl. Acad. Sci. U.S.A. 103: 2075-2080 (2006).

Qin XT, Martin SA. Cloning of the O-acetylhomoserine sulfhydrylase gene from the ruminal bacterium Selenomonas ruminantium HD4. Curr. Microbiol. 48: 305-311 (2004).

Qiu Y, Davidson JN. Substitutions in the aspartate transcarbamoylase domain of hamster CAD disrupt oligomeric structure. Proc. Natl. Acad. Sci. U.S.A. 97: 97-102 (2000).

Quan R, Shang M, Zhang H, Zhao Y, Zhang J. Engineering of enhanced glycine betaine synthesis improves drought tolerance in maize. Plant Biotechnol. J. 2: 477-486 (2004).

Queau M, Renault J, Uriac P, Corbel JC, Travert MF, Bernard T, Donnio PY. Antibacterial effect of two glycine betaine analogues against Escherichia coli. Pathol. Biol. 51: 516-519 (2003).

Quentin Y, Fichant G, Denizot F. Inventory, assembly and analysis of Bacillus subtilis ABC transport systems. J. Mol. Biol. 287: 467-484 (1999).

Quick M, Jung H. Aspartate 55 in the Na+/proline permease of Escherichia coli is essential for Na+-coupled proline uptake. Biochemistry 36: 4631-4636 (1997).

Quick M, Tebbe S, Jung H. Ser57 in the Na+/proline permease of Escherichia coli is critical for high-affinity proline uptake. Eur. J. Biochem. 239: 732-736 (1996).

Quinlivan EP, Roje S, Basset G, Shachar-Hill Y, Gregory JF 3rd, Hanson AD. The folate precursor p-aminobenzoate is reversibly converted to its glucose ester in the plant cytosol. J. Biol. Chem. 278: 20731-20737 (2003).

Quinn GB, Trimboli AJ, Prosser IM, Barber MJ. Spectroscopic and kinetic properties of a recombinant form of the flavin domain of spinach NADH: nitrate reductase. Arch. Biochem. Biophys. 327: 151-160 (1996).

Raab T, Lopez-Raez JA, Klein D, Caballero JL, Moyano E, Schwab W, Munoz-Blanco J. FaQR, required for the biosynthesis of the strawberry flavor compound 4-hydroxy-2,5-dimethyl-3(2H)-furanone, encodes an enone oxidoreductase. Plant Cell 18: 1023-1037 (2006).

Racchi ML, Forlani G, Stefanini F, Camussi A. Inheritance of glyphosate tolerance among maize somaclones. Maydica 42: 275-280 (1997).

Racher KI, Voegele RT, Marshall EV, Culham DE, Wood JM, Jung H, Bacon M, Cairns MT, Ferguson SM, Liang WJ, Henderson PJF, White G, Hallett FR. Purification and reconstitution of an osmosensor: transporter ProP of Escherichia coli senses and responds to osmotic shifts. Biochemistry 38: 1676-1684 (1999).

Raczynska-Pawelec A, Pawelec D, Rozynek E, Jagusztyn-Krynicka EK. Characterization of Campylobacter jejuni asd gene cloned in Escherichia coli. Acta Microbiol. Pol. 44: 227-241 (1995).

Radchuk V, Borisjuk L, Radchuk R, Steinbiss HH, Rolletschek H, Broeders S, Wobus U. Jekyll encodes a novel protein involved in the sexual reproduction of barley. Plant Cell 18: 1652-1666 (2006).

Radwanski ER, Zhao J, Last RL. Arabidopsis thaliana tryptophan synthase alpha: gene cloning, expression, and subunit interaction. Mol. Gen. Genet. 248: 657-667 (1995).

Raetz CR, Reynolds CM, Trent MS, Bishop RE. Lipid A modification systems in gram-negative bacteria. Annu. Rev. Biochem. 76: 295-329 (2007).

Rafalski JA, Falco SC. Structure of the yeast HOM3 gene which encodes aspartokinase. J. Biol. Chem. 263: 2146-2151 (1988).

Rager MN, Binet MR, Bouvet OM. 31P and 13C nuclear magnetic resonance studies of metabolic pathways in Pasteurella multocida characterization of a new mannitol-producing metabolic pathway. Eur. J. Biochem. 263: 695-701 (1999).

Raghunathan A, Price ND, Galperin MY, Makarova KS, Purvine S, Picone AF, Cherny T, Xie T, Reilly TJ, Munson R Jr, Tyler RE, Akerley BJ, Smith AL, Palsson BO, Kolker E. In silico metabolic model and protein expression of Haemophilus influenzae strain Rd KW20 in rich medium. OMICS 8: 25-41 (2004).

Rahman A, Wong Ks, Jane Jl, Myers AM, James MG. Characterization of SU1 isoamylase, a determinant of storage starch structure in maize. Plant Physiol. 117: 425-435 (1998).

Rahman M, Hasan MR, Shimizu K. Growth phase-dependent changes in the expression of global regulatory genes and associated metabolic pathways in Escherichia coli. Biotechnol. Lett. 30: 853-860 (2008).

Rahman M, Shimizu K. Altered acetate metabolism and biomass production in several Escherichia coli mutants lacking rpoS-dependent metabolic pathway genes. Mol. Biosyst. 4: 160-169 (2008).

Rahman RN, Fujiwara S, Takagi M, Imanaka T. Sequence analysis of glutamate dehydrogenase (GDH) from the hyperthermophilic archaeon Pyrococcus sp. KOD1 and comparison of the enzymatic characteristics of native and recombinant GDHs. Mol. Gen. Genet. 257: 338-347 (1998).

Rai R, Rieder G. Salt stress sensitivity of nitrogen fixation in enterobacter Agglomerans strains. J. Gen. Appl. Microbiol. 44: 365-370 (1998).

Rais B, Chassagnole C, Letellier T, Fell DA, Mazat JP. Threonine synthesis from aspartate in Escherichia coli cell-free extracts: pathway dynamics. Biochem. J. 356: 425-432 (2001).

Rajagopalan AV, Devi MT, Raghavendra AS. Molecular biology of C4 phosphoenolpyruvate carboxylase: structure, regulation and genetic engineering. Photosynth. Res. 39: 115-135 (1994).

Ramaswamy KS, Endley S, Golden JW. Nitrate reductase activity and heterocyst suppression on nitrate in Anabaena sp. strain PCC 7120 require moeA. J. Bacteriol. 178: 3893-3898 (1996).

Ramilo CA, Evans JN. Overexpression, purification, and characterization of tyrosine-sensitive 3-deoxy-D-arabino-heptulosonic acid 7-phosphate synthase from Escherichia coli. Protein Expr. Purif. 9: 253-261 (1997).

Ramirez RM, Prince WS, Bremer E, Villarejo M. In vitro reconstitution of osmoregulated expression of proU of Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 86: 1153-1157 (1989).

Ramirez-Arcos S, Fernandez-Herrero LA, Berenguer J. A thermophilic nitrate reductase is responsible for the strain specific anaerobic growth of Thermus thermophilus HB8. Biochim. Biophys. Acta 1396: 215-227 (1998).

Ramjee MK, Genschel U, Abell C, Smith AG. Escherichia coli L-aspartate-alpha-decarboxylase: preprotein processing and observation of reaction intermediates by electrospray mass spectrometry. Biochem. J. 323: 661-669 (1997).

Rana NK, Mohanpuria P, Yadav SK. Cloning and characterization of a cytosolic glutamine synthetase from Camellia sinensis (L.) O. Kuntze that is upregulated by ABA, SA, and H2O2. Mol. Biotechnol. 39: 49-56 (2008).

Randall K, Lever M, Peddie BA, Chambers ST. Competitive accumulation of betaines by Escherichia coli K-12 and derivative strains lacking betaine porters. Biochim. Biophys. Acta 1245: 116-120 (1995).

Randall K, Lever M, Peddie BA, Chambers ST. Natural and synthetic betaines counter the effects of high NaCl and urea concentrations. Biochim. Biophys. Acta 1291: 189-194 (1996).

Rangarajan ES, Proteau A, Wagner J, Hung MN, Matte A, Cygler M. Structural snapshots of Escherichia coli histidinol phosphate phosphatase along the reaction pathway. J. Biol. Chem. 281: 37930-37941 (2006).

Ranocha P, Bourgis F, Ziemak MJ, Rhodes D, Gage DA, Hanson AD. Characterization and functional expression of cDNAs encoding methionine-sensitive and -insensitive homocysteine S-methyltransferases from Arabidopsis. J. Biol. Chem. 275: 15962-15968 (2000).

Rao NA, Talwar R, Savithri HS. Molecular organization, catalytic mechanism and function of serine hydroxymethyltransferase--a potential target for cancer chemotherapy. Int. J. Biochem. Cell Biol. 32: 405-416 (2000).

Rao NN, Kornberg A. Inorganic polyphosphate regulates responses of Escherichia coli to nutritional stringencies, environmental stresses and survival in the stationary phase. Prog. Mol. Subcell. Biol. 23: 183-195 (1999).

Raschle T, Amrhein N, Fitzpatrick TB. On the two components of pyridoxal 5'-phosphate synthase from Bacillus subtilis. J. Biol. Chem. 280: 32291-32300 (2005).

Rastogi R, Dulson J, Rothstein SJ. Cloning of tomato (Lycopersicon esculentum Mill.) arginine decarboxylase gene and its expression during fruit ripening. Plant Physiol. 103: 829-834 (1993).

Rathinasabapathi B, Sigua C, Ho J, Gage DA. Osmoprotectant beta-alanine betaine synthesis in the Plumbaginaceae: S-adenosyl-L-methionine dependent N-methylation of beta-alanine to its betaine is via N-methyl and N,N-dimethyl beta-alanines. Physiol. Plant. 109: 225-231 (2000).

Rathinasabapathi B, Wu S, Sundaram S, Rivoal J, Srivastava M, Ma LQ. Arsenic resistance in Pteris vittata L.: identification of a cytosolic triosephosphate isomerase based on cDNA expression cloning in Escherichia coli. Plant Mol. Biol. 62: 845-857 (2006).

Raushel FM, Thoden JB, Holden HM. The amidotransferase family of enzymes: molecular machines for the production and delivery of ammonia. Biochemistry 38: 7891-7899 (1999).

Raushel FM, Thoden JB, Reinhart GD, Holden HM. Carbamoyl phosphate synthetase: a crooked path from substrates to products. Curr. Opin. Chem. Biol. 2: 624-632 (1998).

Raux E, Lanois A, Levillayer F, Warren MJ, Brody E, Rambach A, Thermes C. Salmonella typhimurium cobalamin (vitamin B12) biosynthetic genes: functional studies in S. typhimurium and Escherichia coli. J. Bacteriol. 178: 753-767 (1996).

Raux E, McVeigh T, Peters SE, Leustek T, Warren MJ. The role of Saccharomyces cerevisiae met1p and met8p in sirohaem and cobalamin biosynthesis. Biochem. J. 338: 701-708 (1999).

Ravanel S. Methionine biosynthesis in higher plants: biochemical and molecular characterization of the transsulfuration pathway enzymes. C. R. Acad. Sci. IIII 320: 497-504 (1997).

Ravanel S, Gakiere B, Job D, Douce R. Cystathionine gamma-synthase from Arabidopsis thaliana: purification and biochemical characterization of the recombinant enzyme overexpressed in Escherichia coli. Biochem. J. 331: 639-648 (1998).

Ravanel S, Ruffet ML, Douce R. Cloning of an Arabidopsis thaliana cDNA encoding cystathionine beta-lyase by functional complementation in Escherichia coli. Plant Mol. Biol. 29: 875-882 (1995).

Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL. Hierarchical organization of modularity in metabolic networks. Science 297: 1551-1555 (2002).

Rawlins MR, Leaver CJ, May MJ. Characterisation of an Arabidopsis thaliana cDNA encoding glutathione synthetase. FEBS Lett. 376: 81-86 (1995).

Ray JM, Bauerle R. Purification and properties of tryptophan-sensitive 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Escherichia coli. J. Bacteriol. 173: 1894-1901 (1991).

Raychaudhuri A, Tipton PA. Cloning and expression of the gene for soybean hydroxyisourate hydrolase. Localization and implications for function and mechanism. Plant Physiol. 130: 2061-2068 (2002).

Ream JE, Yuen HK, Frazier RB, Sikorski JA. EPSP synthase: binding studies using isothermal titration microcalorimetry and equilibrium dialysis and their implications for ligand recognition and kinetic mechanism. Biochemistry 31: 5528-5534 (1992).

Reczkowski RS, Markham GD. Structural and functional roles of cysteine 90 and cysteine 240 in S-adenosylmethionine synthetase. J. Biol. Chem. 270: 18484-18490 (1995).

Reddy SG, Sacchettini JC, Blanchard JS. Expression, purification, and characterization of Escherichia coli dihydrodipicolinate reductase. Biochemistry 34: 3492-3501 (1995).

Reddy SG, Scapin G, Blanchard JS. Interaction of pyridine nucleotide substrates with Escherichia coli dihydrodipicolinate reductase: thermodynamic and structural analysis of binary complexes. Biochemistry 35: 13294-13302 (1996).

Redondo-Nevado J, Aguilar M, Caballero JL, Pineda M. Structural and genomic organization, cDNA characterization and expression analysis of the urate oxidase gene from chickpea (Cicer arietinum). Physiol. Plant. 121: 358-368 (2004).

Reed JL, Palsson BO. Thirteen years of building constraint-based in silico models of Escherichia coli. J. Bacteriol. 185: 2692-2699 (2003).

Reed JL, Patel TR, Chen KH, Joyce AR, Applebee MK, Herring CD, Bui OT, Knight EM, Fong SS, Palsson BO. Systems approach to refining genome annotation. Proc. Natl. Acad. Sci. U.S.A. 103: 17480-17484 (2006).

Reents H, Gruner I, Harmening U, Bottger LH, Layer G, Heathcote P, Trautwein AX, Jahn D, Hartig E. Bacillus subtilis Fnr senses oxygen via a [4Fe-4S] cluster coordinated by three cysteine residues without change in the oligomeric state. Mol. Microbiol. 60: 1432-1445 (2006).

Rees WD, Grant SD, Hay SM, Saqib KM. Threonine synthesis from homoserine as a selectable marker in mammalian cells. Biochem. J. 299: 637-644 (1994).

Rees WD, Hay SM. The expression of Escherichia coli threonine synthase and the production of threonine from homoserine in mouse 3T3 cells. Biochem. J. 291: 315-322 (1993).

Rees WD, Hay SM. The biosynthesis of threonine by mammalian cells: expression of a complete bacterial biosynthetic pathway in an animal cell. Biochem. J. 309: 999-1007 (1995).

Rees WD, Hay SM, Flint HJ. Expression of Escherichia coli homoserine kinase in mouse 3T3 cells. Biochem. J. 281: 865-870 (1992).

Reese LM, Cutler KO, Deutch CE. Sensitivity of Escherichia coli to proline analogues during osmotic stress and anaerobiosis. Lett. Appl. Microbiol. 22: 202-205 (1996).

Regan L, Gregory M. Flux analysis of microbial metabolic pathways using a visual programming environment. J. Biotechnol. 42: 151-161 (1995).

Reinert RB, Oberle LM, Wek SA, Bunpo P, Wang XP, Mileva I, Goodwin LO, Aldrich CJ, Durden DL, McNurlan MA, Wek RC, Anthony TG. Role of glutamine depletion in directing tissue-specific nutrient stress responses to L-asparaginase. J. Biol. Chem. 281: 31222-31233 (2006).

Reinhart F, Achebach S, Koch T, Unden G. Reduced apo-fumarate nitrate reductase regulator (apoFNR) as the major form of FNR in aerobically growing Escherichia coli. J. Bacteriol. 190: 879-886 (2008).

Reitzer L. Nitrogen assimilation and global regulation in Escherichia coli. Annu. Rev. Microbiol. 57: 155-176 (2003).

Reshetnikov AS, Mustakhimov II, Khmelenina VN, Trotsenko YA. Cloning, purification, and characterization of diaminobutyrate acetyltransferase from the halotolerant methanotroph Methylomicrobium alcaliphilum 20Z. Biochemistry (Mosc.) 70: 878-883 (2005).

Rex JH, Aronson BD, Somerville RL. The tdh and serA operons of Escherichia coli: mutational analysis of the regulatory elements of leucine-responsive genes. J. Bacteriol. 173: 5944-5953 (1991).

Rexer HU, Schaberle T, Wohlleben W, Engels A. Investigation of the functional properties and regulation of three glutamine synthetase-like genes in Streptomyces coelicolor A3(2). Arch. Microbiol. 186: 447-458 (2006).

Reyes F, Gavira M, Castillo F, Moreno-Vivian C. Periplasmic nitrate-reducing system of the phototrophic bacterium Rhodobacter sphaeroides DSM 158: transcriptional and mutational analysis of the napKEFDABC gene cluster. Biochem. J. 331: 897-904 (1998).

Reyes F, Roldan MD, Klipp W, Castillo F, Moreno-Vivian C. Isolation of periplasmic nitrate reductase genes from Rhodobacter sphaeroides DSM 158: structural and functional differences among prokaryotic nitrate reductases. Mol. Microbiol. 19: 1307-1318 (1996).

Reyes JC, Florencio FJ. A new type of glutamine synthetase in cyanobacteria: the protein encoded by the glnN gene supports nitrogen assimilation in Synechocystis sp. Strain PCC 6803. J. Bacteriol. 176: 1260-1267 (1994).

Reyes JC, Muro-Pastor MI, Florencio FJ. Transcription of glutamine synthetase genes (glnA and glnN) from the cyanobacterium Synechocystis sp. strain PCC 6803 is differently regulated in response to nitrogen availability. J. Bacteriol. 179: 2678-2689 (1997).

Reynaldo LP, Villafranca JJ, Horrocks WD Jr. Investigating the effects of posttranslational adenylylation on the metal binding sites of Escherichia coli glutamine synthetase using lanthanide luminescence spectroscopy. Protein Sci. 5: 2532-2544 (1996).

Rhee SG, Chock PB. Mechanistic studies of glutamine synthetase from Escherichia coli: kinetic evidence for two reaction intermediates in biosynthetic reaction. Proc. Natl. Acad. Sci. U.S.A. 73: 476-480 (1976).

Rhee SG, Chock PB. Purification and characterization of uridylylated and unuridylylated forms of regulatory protein PII involved in the glutamine synthetase regulation in Escherichia coli. Isozymes Curr. Top. Biol. Med. Res. 8: 141-153 (1983).

Rhee SG, Chock PB, Stadtman ER. Mechanistic studies of glutamine synthetase from Escherichia coli. An integrated mechanism for biosynthesis, transferase, ATPase reaction. Biochimie 58: 35-49 (1976).

Rhee SG, Chock PB, Wedler FC, Sugiyama Y. Subunit interaction in unadenylylated glutamine synthetase from Escherichia coli. Evidence from methionine sulfoximine inhibition studies. J. Biol. Chem. 256: 644-648 (1981).

Rhee SG, Park SC, Koo JH. The role of adenylyltransferase and uridylyltransferase in the regulation of glutamine synthetase in Escherichia coli. Curr. Top. Cell Regul. 27: 221-232 (1985).

Rhee SG, Ubom GA, Hunt JB, Chock PB. Fluorometric studies of aza-epsilon-adenylylated glutamine synthetase from Escherichia coli. J. Biol. Chem. 256: 6010-6016 (1981).

Rhee SG, Ubom GA, Hunt JB, Chock PB. Catalytic cycle of the biosynthetic reaction catalyzed by adenylylated glutamine synthetase from Escherichia coli. J. Biol. Chem. 257: 289-297 (1982).

Riba L, Becerril B, Servin-Gonzalez L, Valle F, Bolivar F. Identification of a functional promoter for the Escherichia coli gdhA gene and its regulation. Gene 71: 233-246 (1988).

Ribitsch D, Karl W, Wehrschutz-Sigl E, Tutz S, Remler P, Weber HJ, Gruber K, Stehr R, Bessler C, Hoven N, Sauter K, Maurer KH, Schwab H. Heterologous expression and characterization of choline oxidase from the soil bacterium Arthrobacter nicotianae. Appl. Microbiol. Biotechnol. 81: 875-886 (2009).

Ricci JCD. ADP modulates the dynamic behavior of the glycolytic pathway of Escherichia coli. Biochem. Biophys. Res. Comm. 271: 244-249 (2000).

Rice DW, Yip KS, Stillman TJ, Britton KL, Fuentes A, Connerton I, Pasquo A, Scandura R, Engel PC. Insights into the molecular basis of thermal stability from the structure determination of Pyrococcus furiosus glutamate dehydrogenase. FEMS Microbiol. Rev. 18: 105-117 (1996).

Rice EW, Johnson CH, Dunnigan ME, Reasoner DJ. Rapid glutamate decarboxylase assay for detection of Escherichia coli. Appl. Environ. Microbiol. 59: 4347-4349 (1993).

Richards NG, Schuster SM. An alternative mechanism for the nitrogen transfer reaction in asparagine synthetase. FEBS Lett. 313: 98-102 (1992).

Richaud F, Phuc NH, Cassan M, Patte JC. Regulation of aspartokinase III synthesis in Escherichia coli: isolation of mutants containing lysC-lac fusions. J. Bacteriol. 143: 513-515 (1980).

Richaud F, Richaud C, Ratet P, Patte JC. Chromosomal location and nucleotide sequence of the Escherichia coli dapA gene. J. Bacteriol. 166: 297-300 (1986).

Richman A, Swanson A, Humphrey T, Chapman R, McGarvey B, Pocs R, Brandle J. Functional genomics uncovers three glucosyltransferases involved in the synthesis of the major sweet glucosides of Stevia rebaudiana. Plant J. 41: 56-67 (2005).

Rieble S, Beale SI. Structure and expression of a cyanobacterial ilvC gene encoding acetohydroxyacid isomeroreductase. J. Bacteriol. 174: 7910-7918 (1992).

Rieder C, Eisenreich W, O'Brien J, Richter G, Gotze E, Boyle P, Blanchard S, Bacher A, Simon H. Rearrangement reactions in the biosynthesis of molybdopterin--an NMR study with multiply 13C/15N labelled precursors. Eur. J. Biochem. 255: 24-36 (1998).

Riekhof WR, Andre C, Benning C. Two enzymes, BtaA and BtaB, are sufficient for betaine lipid biosynthesis in bacteria. Arch. Biochem. Biophys. 441: 96-105 (2005).

Riekhof WR, Sears BB, Benning C. Annotation of genes involved in glycerolipid biosynthesis in Chlamydomonas reinhardtii: discovery of the betaine lipid synthase BTA1Cr. Eukaryot. Cell 4: 242-252 (2005).

Riley M, Serres MH. Interim report on genomics of Escherichia coli. Annu. Rev. Microbiol. 54: 341-411 (2000).

Rimmele M, Boos W. Trehalose-6-phosphate hydrolase of Escherichia coli. J. Bacteriol. 176: 5654-5664 (1994).

Ringenberg M, Lichtensteiger C, Vimr E. Redirection of sialic acid metabolism in genetically engineered Escherichia coli. Glycobiology 11: 533-539 (2001).

Ringer KL, Davis EM, Croteau R. Monoterpene metabolism. Cloning, expression, and characterization of (-)-isopiperitenol/(-)-carveol dehydrogenase of peppermint and spearmint. Plant Physiol. 137: 863-872 (2005).

Rippert P, Matringe M. Molecular and biochemical characterization of an Arabidopsis thaliana arogenate dehydrogenase with two highly similar and active protein domains. Plant Mol. Biol. 48: 361-368 (2002).

Rippert P, Matringe M. Purification and kinetic analysis of the two recombinant arogenate dehydrogenase isoforms of Arabidopsis thaliana. Eur. J. Biochem. 269: 4753-4761 (2002).

Rippmann JF, Michalowski CB, Nelson DE, Bohnert HJ. Induction of a ribosome-inactivating protein upon environmental stress. Plant Mol. Biol. 35: 701-709 (1997).

Rishavy MA, Cleland WW. 13C and 15N kinetic isotope effects on the reaction of aspartate aminotransferase and the tyrosine-225 to phenylalanine mutant. Biochemistry 39: 7546-7551 (2000).

Rishavy MA, Cleland WW, Lusty CJ. 15N isotope effects in glutamine hydrolysis catalyzed by carbamyl phosphate synthetase: evidence for a tetrahedral intermediate in the mechanism. Biochemistry 39: 7309-7315 (2000).

Ritchie SW, Redinbaugh MG, Shiraishi N, Vrba JM, Campbell WH. Identification of a maize root transcript expressed in the primary response to nitrate: characterization of a cDNA with homology to ferredoxin-NADP+ oxidoreductase. Plant Mol. Biol. 26: 679-690 (1994).

Rittmann D, Lindner SN, Wendisch VF. Engineering of a glycerol utilization pathway for amino acid production by Corynebacterium glutamicum. Appl. Environ. Microbiol. 74: 6216-6222 (2008).

Rivera MC, Jain R, Moore JE, Lake JA. Genomic evidence for two functionally distinct gene classes. Proc. Natl. Acad. Sci. U.S.A. 95: 6239-6244 (1998).

Rivett AJ, Levine RL. Metal-catalyzed oxidation of Escherichia coli glutamine synthetase: correlation of structural and functional changes. Arch. Biochem. Biophys. 278: 26-34 (1990).

Robatzek S, Bittel P, Chinchilla D, Kochner P, Felix G, Shiu SH, Boller T. Molecular identification and characterization of the tomato flagellin receptor LeFLS2, an orthologue of Arabidopsis FLS2 exhibiting characteristically different perception specificities. Plant Mol. Biol. 64: 539-547 (2007).

Robert H, Le Marrec C, Blanco C, Jebbar M. Glycine betaine, carnitine, and choline enhance salinity tolerance and prevent the accumulation of sodium to a level inhibiting growth of Tetragenococcus halophila. Appl. Environ. Microbiol. 66: 509-517 (2000).

Roberts EL, Shu N, Howard MJ, Broadhurst RW, Chapman-Smith A, Wallace JC, Morris T, Cronan JE Jr, Perham RN. Solution structures of apo and holo biotinyl domains from acetyl coenzyme A carboxylase of Escherichia coli determined by triple-resonance nuclear magnetic resonance spectroscopy. Biochemistry 38: 5045-5053 (1999).

Roberts MA, Wray JL. Cloning and characterization of an Arabidopsis thaliana cDNA clone encoding an organellar isoform of serine acetyltransferase. Plant Mol. Biol. 30: 1041-1049 (1996).

Robinson P, Neelon K, Schreier HJ, Roberts MF. beta-Glutamate as a substrate for glutamine synthetase. Appl. Environ. Microbiol. 67: 4458-4463 (2001).

Roca I, Ballana E, Panosa A, Torrents E, Gibert I. Fumarate and nitrate reduction (FNR) dependent activation of the Escherichia coli anaerobic ribonucleotide reductase nrdDG promoter. Int. Microbiol. 11: 49-56 (2008).

Rochefort DA, Benson DR. Molecular cloning, sequencing, and expression of the glutamine synthetase II (glnII) gene from the actinomycete root nodule symbiont Frankia sp. strain CpI1. J. Bacteriol. 172: 5335-5342 (1990).

Rock CO, Jackowski S. Regulation of phospholipid synthesis in Escherichia coli. Composition of the acyl-acyl carrier protein pool in vivo. J. Biol. Chem. 257: 10759-10765 (1982).

Rock CO, Park HW, Jackowski S. Role of feedback regulation of pantothenate kinase (CoaA) in control of coenzyme A levels in Escherichia coli. J. Bacteriol. 185: 3410-3415 (2003).

Rodionov DA, Dubchak IL, Arkin AP, Alm EJ, Gelfand MS. Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks. PLoS Comput. Biol. 1: e55 (2005).

Rodríguez-Prados JC, de Atauri P, Maury J, Ortega F, Portais JC, Chassagnole C, Acerenza L, Lindley ND, Cascante M. In silico strategy to rationally engineer metabolite production: a case study for threonine in Escherichia coli. Biotechnol. Bioeng. 103: 609-620 (2009).

Rogers SG, Brand LA, Holder SB, Sharps ES, Brackin MJ. Amplification of the aroA gene from Escherichia coli results in tolerance to the herbicide glyphosate. Appl. Environ. Microbiol. 46: 37-43 (1983).

Rognes SE, Lea PJ, Miflin BJ. S-Adenosylmethionine - a novel regulator of aspartate kinase. Nature 287: 357-359 (1980).

Rohde B, Hans J, Martens S, Baumert A, Hunziker P, Matern U. Anthranilate N-methyltransferase, a branch-point enzyme of acridone biosynthesis. Plant J. 53: 541-553 (2008).

Rohdich F, Lauw S, Kaiser J, Feicht R, Kohler P, Bacher A, Eisenreich W. Isoprenoid biosynthesis in plants - 2C-methyl-D-erythritol-4-phosphate synthase (IspC protein) of Arabidopsis thaliana. FEBS J. 273: 4446-4458 (2006).

Rohdich F, Wungsintaweekul J, Eisenreich W, Richter G, Schuhr CA, Hecht S, Zenk MH, Bacher A. Biosynthesis of terpenoids: 4-diphosphocytidyl-2C-methyl-D-erythritol synthase of Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A. 97: 6451-6456 (2000).

Rohdich F, Wungsintaweekul J, Luttgen H, Fischer M, Eisenreich W, Schuhr CA, Fellermeier M, Schramek N, Zenk MH, Bacher A. Biosynthesis of terpenoids: 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase from tomato. Proc. Natl. Acad. Sci. U.S.A. 97: 8251-8256 (2000).

Rohwer JM, Postma PW, Kholodenko BN, Westerhoff HV. Implications of macromolecular crowding for signal transduction and metabolite channeling. Proc. Natl. Acad. Sci. U.S.A. 95: 10547-10552 (1998).

Roisch U, Lingens F. The mechanism of action of the herbicide N-(phosphonomethyl)glycine: its effect on the growth and the enzymes of aromatic amino acid biosynthesis in Escherichia coli. Hoppe Seylers Z. Physiol. Chem. 361: 1049-1058 (1980).

Rojsajjakul T, Wintrode P, Vadrevu R, Robert Matthews C, Smith DL. Multi-state unfolding of the alpha subunit of tryptophan synthase, a TIM barrel protein: insights into the secondary structure of the stable equilibrium intermediates by hydrogen exchange mass spectrometry. J. Mol. Biol. 341: 241-253 (2004).

Rokenes TP, Lamark T, Strom AR. DNA-binding properties of the BetI repressor protein of Escherichia coli: the inducer choline stimulates BetI-DNA complex formation. J. Bacteriol. 178: 1663-1670 (1996).

Rokov J, Soll D, Weygand-Durasevic I. Maize mitochondrial seryl-tRNA synthetase recognizes Escherichia coli tRNA(Ser) in vivo and in vitro. Plant Mol. Biol. 38: 497-502 (1998).

Romeo Y, Bouvier J, Gutierrez C. Osmotic regulation of transcription in Lactococcus lactis: ionic strength-dependent binding of the BusR repressor to the busA promoter. FEBS Lett. 581: 3387-3390 (2007).

Romero M, Guzman-Leon S, Aranda C, Gonzalez-Halphen D, Valenzuela L, Gonzalez A. Pathways for glutamate biosynthesis in the yeast Kluyveromyces lactis. Microbiology 146: 239-245 (2000).

Rondard P, Bedouelle H. Mutational scanning of a hairpin loop in the tryptophan synthase beta-subunit implicated in allostery and substrate channeling. Biol. Chem. 381: 1185-1193 (2000).

Rontein D, Nishida I, Tashiro G, Yoshioka K, Wu WI, Voelker DR, Basset G, Hanson AD. Plants synthesize ethanolamine by direct decarboxylation of serine using a pyridoxal phosphate enzyme. J. Biol. Chem. 276: 35523-35529 (2001).

Rosales-Mendoza S, Alpuche-Solís A, Soria-Guerra R, Moreno-Fierros L, Martínez-Gonzalez L, Herrera-Diaz A, Korban SS. Expression of an Escherichia coli antigenic fusion protein comprising the heat labile toxin B subunit and the heat stable toxin and its assembly as a functional oligomer in transplastomic tobacco plants. Plant J. 57: 45-54 (2009).

Rosales-Mendoza S, Soria-Guerra RE, Lopez-Revilla R, Moreno-Fierros L, Alpuche-Solís AG. Ingestion of transgenic carrots expressing the Escherichia coli heat-labile enterotoxin B subunit protects mice against cholera toxin challenge. Plant Cell Rep. 27: 79-84 (2008).

Rosas S, Soria R, Correa N, Abdala G. Jasmonic acid stimulates the expression of nod genes in Rhizobium. Plant Mol. Biol. 38: 1161-1168 (1998).

Roseboom W, Blokesch M, Bock A, Albracht SP. The biosynthetic routes for carbon monoxide and cyanide in the Ni-Fe active site of hydrogenases are different. FEBS Lett. 579: 469-472 (2005).

Roseman JE, Levine RL. Purification of a protease from Escherichia coli with specificity for oxidized glutamine synthetase. J. Biol. Chem. 262: 2101-2110 (1987).

Rosen BP. Biochemistry of arsenic detoxification. FEBS Lett. 529: 86-92 (2002).

Rosen R, Becher D, Buttner K, Biran D, Hecker M, Ron EZ. Probing the active site of homoserine trans-succinylase. FEBS Lett. 577: 386-392 (2004).

Rosler J, Krekel F, Amrhein N, Schmid J. Maize phenylalanine ammonia-lyase has tyrosine ammonia-lyase activity. Plant Physiol. 113: 175-179 (1997).

Rossbach S, Hennecke H. Identification of glyA as a symbiotically essential gene in Bradyrhizobium japonicum. Mol. Microbiol. 5: 39-47 (1991).

Rosselli LK, Oliveira CL, Azzoni AR, Tada SF, Catani CF, Saraiva AM, Soares JS, Medrano FJ, Torriani IL, Souza AP. A new member of the aldo-keto reductase family from the plant pathogen Xylella fastidiosa. Arch. Biochem. Biophys. 453: 143-150 (2006).

Rossi F, Gatto V, Marzotto M, Torriani S. A genetic insight into peptide and amino-acid utilization by Propionibacterium freudenreichii LMG 16415. Curr. Microbiol. 52: 464-468 (2006).

Rossi JJ, Vender J, Berg CM, Coleman WH. Partial purification and some properties of delta1-pyrroline-5-carboxylate reductase from Escherichia coli. J. Bacteriol. 129: 108-114 (1977).

Roth WG, Leckie MP, Dietzler DN. Restoration of colony-forming activity in osmotically stressed Escherichia coli by betaine. Appl. Environ. Microbiol. 54: 3142-3146 (1988).

Rothery RA, Blasco F, Magalon A, Weiner JH. The diheme cytochrome b subunit (Narl) of Escherichia coli nitrate reductase A (NarGHI): structure, function, and interaction with quinols. J. Mol. Microbiol. Biotechnol. 3: 273-283 (2001).

Rothery RA, Blasco F, Weiner JH. Electron transfer from heme bL to the [3Fe-4S] cluster of Escherichia coli nitrate reductase A (NarGHI). Biochemistry 40: 5260-5268 (2001).

Rothery RA, Magalon A, Giordano G, Guigliarelli B, Blasco F, Weiner JH. The molybdenum cofactor of Escherichia coli nitrate reductase A (NarGHI). Effect of a mobAB mutation and interactions with [Fe-S] clusters. J. Biol. Chem. 273: 7462-7469 (1998).

Rothman N, Rothstein D, Foor F, Magasanik B. Role of glnA-linked genes in regulation of glutamine synthetase and histidase formation in Klebsiella aerogenes. J. Bacteriol. 150: 221-230 (1982).

Rott R, Liveanu V, Drager RG, Higgs D, Stern DB, Schuster G. Altering the 3 UTR endonucleolytic cleavage site of a Chlamydomonas chloroplast mRNA affects 3-end maturation in vitro but not in vivo. Plant Mol. Biol. 40: 679-686 (1999).

Rouhier N, Gelhaye E, Sautiere PE, Brun A, Laurent P, Tagu D, Gerard J, de Fay E, Meyer Y, Jacquot JP. Isolation and characterization of a new peroxiredoxin from poplar sieve tubes that uses either glutaredoxin or thioredoxin as a proton donor. Plant Physiol. 127: 1299-1309 (2001).

Roumy V, Fabre N, Portet B, Bourdy G, Acebey L, Vigor C, Valentin A, Moulis C. Four anti-protozoal and anti-bacterial compounds from Tapirira guianensis. Phytochemistry 70: 305-311 (2009).

Rowbury RJ, Humphrey TJ, Goodson M. Properties of an L-glutamate-induced acid tolerance response which involves the functioning of extracellular induction components. J. Appl. Microbiol. 86: 325-330 (1999).

Rowe JJ, Ubbink-Kok T, Molenaar D, Konings WN, Driessen AJ. NarK is a nitrite-extrusion system involved in anaerobic nitrate respiration by Escherichia coli. Mol. Microbiol. 12: 579-586 (1994).

Rozwadowski KL, Khachatourians GG, Selvaraj G. Choline oxidase, a catabolic enzyme in Arthrobacter pascens, facilitates adaptation to osmotic stress in Escherichia coli. J. Bacteriol. 173: 472-478 (1991).

Rubenhagen R, Morbach S, Kramer R. The osmoreactive betaine carrier BetP from Corynebacterium glutamicum is a sensor for cytoplasmic K(+). EMBO J. 20: 5412-5420 (2001).

Rubenhagen R, Ronsch H, Jung H, Kramer R, Morbach S. Osmosensor and osmoregulator properties of the betaine carrier betP from Corynebacterium glutamicum in proteoliposomes. J. Biol. Chem. 275: 735-741 (2000).

Rubio LM, Flores E, Herrero A. The narA locus of Synechococcus sp. strain PCC 7942 consists of a cluster of molybdopterin biosynthesis genes. J. Bacteriol. 180: 1200-1206 (1998).

Rubio LM, Flores E, Herrero A. Molybdopterin guanine dinucleotide cofactor in Synechococcus sp. nitrate reductase: identification of mobA and isolation of a putative moeB gene. FEBS Lett. 462: 358-362 (1999).

Rubio LM, Flores E, Herrero A. Purification, cofactor analysis, and site-directed mutagenesis of Synechococcus ferredoxin-nitrate reductase. Photosynth. Res. 72: 13-26 (2002).

Rubio LM, Herrero A, Flores E. A cyanobacterial narB gene encodes a ferredoxin-dependent nitrate reductase. Plant Mol. Biol. 30: 845-850 (1996).

Rubio V, Llorente P, Britton HG. Mechanism of carbamoyl phosphate synthetase from Escherichia coli--binding of the ATP molecules used in the reaction and sequestration by the enzyme of the ATP molecule that yields carbamoyl phosphate. Eur. J. Biochem. 255: 262-270 (1998).

Rudd KE. EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res. 28: 60-64 (2000).

Rudnick P, Kunz C, Gunatilaka MK, Hines ER, Kennedy C. Role of GlnK in NifL-mediated regulation of NifA activity in Azotobacter vinelandii. J. Bacteriol. 184: 812-820 (2002).

Ruffert S, Berrier C, Kramer R, Ghazi A. Identification of mechanosensitive ion channels in the cytoplasmic membrane of Corynebacterium glutamicum. J. Bacteriol. 181: 1673-1676 (1999).

Ruffert S, Lambert C, Peter H, Wendisch VF, Kramer R. Efflux of compatible solutes in Corynebacterium glutamicum mediated by osmoregulated channel activity. Eur. J. Biochem. 247: 572-580 (1997).

Ruffet ML, Lebrun M, Droux M, Douce R. Subcellular distribution of serine acetyltransferase from Pisum sativum and characterization of an Arabidopsis thaliana putative cytosolic isoform. Eur. J. Biochem. 227: 500-509 (1995).

Ruppert M, Woll J, Giritch A, Genady E, Ma X, Stockigt J. Functional expression of an ajmaline pathway-specific esterase from Rauvolfia in a novel plant-virus expression system. Planta 222: 888-898 (2005).

Rushlow KE, Deutch AH, Smith CJ. Identification of a mutation that relieves gamma-glutamyl kinase from allosteric feedback inhibition by proline. Gene 39: 109-112 (1985).

Russel M, Model P, Holmgren A. Thioredoxin or glutaredoxin in Escherichia coli is essential for sulfate reduction but not for deoxyribonucleotide synthesis. J. Bacteriol. 172: 1923-1929 (1990).

Russell R, Scopes RK. Use of hydrophobic chromatography for purification of the membrane-located choline dehydrogenase from a Pseudomonas strain. Bioseparation 4: 279-284 (1994).

Rutschmann F, Stalder U, Piotrowski M, Oecking C, Schaller A. LeCPK1, a calcium-dependent protein kinase from tomato. Plasma membrane targeting and biochemical characterization. Plant Physiol. 129: 156-168 (2002).

Saab-Rincon G, Juarez VR, Osuna J, Sanchez F, Soberon X. Different strategies to recover the activity of monomeric triosephosphate isomerase by directed evolution. Protein Eng. 14: 149-155 (2001).

Sabaty M, Avazeri C, Pignol D, Vermeglio A. Characterization of the reduction of selenate and tellurite by nitrate reductases. Appl. Environ. Microbiol. 67: 5122-5126 (2001).

Sadanandom A, Poghosyan Z, Fairbairn DJ, Murphy DJ. Differential regulation of plastidial and cytosolic isoforms of peptide methionine sulfoxide reductase in Arabidopsis. Plant Physiol. 123: 255-264 (2000).

Saez-Vasquez J, Raynal M, Delseny M. A rapeseed cold-inducible transcript encodes a phosphoenolpyruvate carboxykinase. Plant Physiol. 109: 611-618 (1995).

Safo MK, Musayev FN, di Salvo ML, Hunt S, Claude JB, Schirch V. Crystal structure of pyridoxal kinase from the Escherichia coli pdxK gene: implications for the classification of pyridoxal kinases. J. Bacteriol. 188: 4542-4552 (2006).

Sage AE, Vasil AI, Vasil ML. Molecular characterization of mutants affected in the osmoprotectant-dependent induction of phospholipase C in Pseudomonas aeruginosa PAO1. Mol. Microbiol. 23: 43-56 (1997).

Sage AE, Vasil ML. Osmoprotectant-dependent expression of plcH, encoding the hemolytic phospholipase C, is subject to novel catabolite repression control in Pseudomonas aeruginosa PAO1. J. Bacteriol. 179: 4874-4881 (1997).

Sagher D, Brunell D, Brot N, Vallee BL, Weissbach H. Selenocompounds can serve as oxido-reductants with the methionine sulfoxide reductase enzymes. J. Biol. Chem. 281: 31184-31187 (2006).

Saha S, Enugutti B, Rajakumari S, Rajasekharan R. Cytosolic triacylglycerol biosynthetic pathway in oilseeds. Molecular cloning and expression of peanut cytosolic diacylglycerol acyltransferase. Plant Physiol. 141: 1533-1543 (2006).

Sahr T, Ravanel S, Basset G, Nichols BP, Hanson AD, Rebeille F. Folate synthesis in plants: purification, kinetic properties, and inhibition of aminodeoxychorismate synthase. Biochem. J. 396: 157-162 (2006).

Saida F, Uzan M, Lallemand JY, Bontems F. New system for positive selection of recombinant plasmids and dual expression in yeast and bacteria based on the restriction ribonuclease RegB. Biotechnol. Prog. 19: 727-733 (2003).

Saier MH Jr. Multiple mechanisms controlling carbon metabolism in bacteria. Biotechnol. Bioeng. 58: 170-174 (1998).

Saimi Y, Martinac B, Gustin MC, Culbertson MR, Adler J, Kung C. Ion channels of Paramecium, yeast and Escherichia coli. Trends Biochem. Sci. 13: 304-309 (1988).

Saint-Girons I, Parsot C, Zakin MM, Barzu O, Cohen GN. Methionine biosynthesis in Enterobacteriaceae: biochemical, regulatory, and evolutionary aspects. CRC Crit. Rev. Biochem. 23: S1-S42 (1988).

Saito K, Miura N, Yamazaki M, Hirano H, Murakoshi I. Molecular cloning and bacterial expression of cDNA encoding a plant cysteine synthase. Proc. Natl. Acad. Sci. U.S.A. 89: 8078-8082 (1992).

Saito K, Takagi Y, Ling HC, Takahashi H, Noji M. Molecular cloning, characterization and expression of cDNA encoding phosphoserine aminotransferase involved in phosphorylated pathway of serine biosynthesis from spinach. Plant Mol. Biol. 33: 359-366 (1997).

Saito K, Yokoyama H, Noji M, Murakoshi I. Molecular cloning and characterization of a plant serine acetyltransferase playing a regulatory role in cysteine biosynthesis from watermelon. J. Biol. Chem. 270: 16321-16326 (1995).

Sakakibara H, Shimizu H, Hase T, Yamazaki Y, Takao T, Shimonishi Y, Sugiyama T. Molecular identification and characterization of cytosolic isoforms of glutamine synthetase in maize roots. J. Biol. Chem. 271: 29561-29568 (1996).

Sakakibara H, Takei K, Sugiyama T. Isolation and characterization of a cDNA that encodes maize uroporphyrinogen III methyltransferase, an enzyme involved in the synthesis of siroheme, which is prosthetic group of nitrite reductase. Plant J. 10: 883-892 (1996).

Sakakibara H, Watanabe M, Hase T, Sugiyama T. Molecular cloning and characterization of complementary DNA encoding for ferredoxin-dependent glutamate synthase in maize leaf. J. Biol. Chem. 266: 2028-2035 (1991).

Sakamoto A, Murata N. Genetic engineering of glycinebetaine synthesis in plants: current status and implications for enhancement of stress tolerance. J. Exp. Bot. 51: 81-88 (2000).

Sakamoto A, Murata N. The use of bacterial choline oxidase, a glycinebetaine-synthesizing enzyme, to create stress-resistant transgenic plants. Plant Physiol. 125: 180-188 (2001).

Sakamoto A, Tsukamoto S, Yamamoto H, Ueda-Hashimoto M, Takahashi M, Suzuki H, Morikawa H. Functional complementation in yeast reveals a protective role of chloroplast 2-Cys peroxiredoxin against reactive nitrogen species. Plant J. 33: 841-851 (2003).

Sakamoto W. Protein degradation machineries in plastids. Annu. Rev. Plant Biol. 57: 599-621 (2006).

Sakamoto Y, Watanabe H, Nagai M, Nakade K, Takahashi M, Sato T. Lentinula edodes tlg1 encodes a thaumatin-like protein that is involved in lentinan degradation and fruiting body senescence. Plant Physiol. 141: 793-801 (2006).

Sakash JB, Chan RS, Tsuruta H, Kantrowitz ER. Three of the six possible intersubunit stabilizing interactions involving Glu-239 are sufficient for restoration of the homotropic and heterotropic properties of Escherichia coli aspartate transcarbamoylase. J. Biol. Chem. 275: 752-758 (2000).

Sakash JB, Tsen A, Kantrowitz ER. The use of nucleotide analogs to evaluate the mechanism of the heterotropic response of Escherichia coli aspartate transcarbamoylase. Protein Sci. 9: 53-63 (2000).

Sakuraba H, Takamatsu Y, Satomura T, Kawakami R, Ohshima T. Purification, characterization, and application of a novel dye- linked L-proline dehydrogenase from a hyperthermophilic archaeon, Thermococcus profundus. Appl. Environ. Microbiol. 67: 1470-1475 (2001).

Salomon M, Lempert U, Rudiger W. Dimerization of the plant photoreceptor phototropin is probably mediated by the LOV1 domain. FEBS Lett. 572: 8-10 (2004).

Salvini M, Boccardi TM, Sani E, Bernardi R, Tozzi S, Pugliesi C, Durante M. Alpha-tryptophan synthase of Isatis tinctoria: gene cloning and expression. Plant Physiol. Biochem. 46: 715-723 (2008).

Salvucci ME, Van De Loo FJ, Stecher D. Two isoforms of Rubisco activase in cotton, the products of separate genes not alternative splicing. Planta 216: 736-744 (2003).

Samal A, Singh S, Giri V, Krishna S, Raghuram N, Jain S. Low degree metabolites explain essential reactions and enhance modularity in biological networks. BMC Bioinformatics 7: 118 (2006).

Sambasivarao D, Turner RJ, Bilous PT, Rothery RA, Shaw G, Weiner JH. Differential effects of a molybdopterin synthase sulfurylase (moeB) mutation on Escherichia coli molybdoenzyme maturation. Biochem. Cell Biol. 80: 435-443 (2002).

Samsonova NN, Smirnov SV, Novikova AE, Ptitsyn LR. Identification of Escherichia coli K12 YdcW protein as a gamma-aminobutyraldehyde dehydrogenase. FEBS Lett. 579: 4107-4112 (2005).

San KY, Bennett GN, Berrios-Rivera SJ, Vadali RV, Yang YT, Horton E, Rudolph FB, Sariyar B, Blackwood K. Metabolic engineering through cofactor manipulation and its effects on metabolic flux redistribution in Escherichia coli. Metab. Eng. 4: 182-192 (2002).

San Miguel M, Marrington R, Rodger PM, Rodger A, Robinson C. An Escherichia coli twin-arginine signal peptide switches between helical and unstructured conformations depending on the hydrophobicity of the environment. Eur. J. Biochem. 270: 3345-3352 (2003).

Sanangelantoni AM, Barbarini D, Di Pasquale G, Cammarano P, Tiboni O. Cloning and nucleotide sequence of an archaebacterial glutamine synthetase gene: phylogenetic implications. Mol. Gen. Genet. 221: 187-194 (1990).

Sanangelantoni AM, Forlani G, Ambroselli F, Cammarano P, Tiboni O. The glnA gene of the extremely thermophilic eubacterium Thermotoga maritima: cloning, primary structure, and expression in Escherichia coli. J. Gen. Microbiol. 138: 383-393 (1992).

Sancar A. DNA excision repair. Annu. Rev. Biochem. 65: 43-81 (1996).

Sanchez AM, Bennett GN, San KY. Novel pathway engineering design of the anaerobic central metabolic pathway in Escherichia coli to increase succinate yield and productivity. Metab. Eng. 7: 229-239 (2005).

Sanchez AM, Bennett GN, San KY. Batch culture characterization and metabolic flux analysis of succinate-producing Escherichia coli strains. Metab. Eng. 8: 209-226 (2006).

Sanchez R, Cejudo FJ. Identification and expression analysis of a gene encoding a bacterial-type phosphoenolpyruvate carboxylase from Arabidopsis and rice. Plant Physiol. 132: 949-957 (2003).

Sanchez R, Flores A, Cejudo FJ. Arabidopsis phosphoenolpyruvate carboxylase genes encode immunologically unrelated polypeptides and are differentially expressed in response to drought and salt stress. Planta 223: 901-909 (2006).

Sanchez-Crispin JA, Dubourdieu M. Reconstitution "in vitro" of a formate or NADH dependent nitrite reductase activity starting from cytochrome c552 and membrane vesicles from Escherichia coli K-12. Acta Cient. Venez. 35: 350-355 (1984).

Sanchez-Pescador R, Sanvicente E, Valle F, Bolivar F. Recombinant plasmids carrying the glutamate dehydrogenase structural gene from Escherichia coli K-12. Gene 17: 1-8 (1982).

Sandu C, Brandsch R. Functional analysis of the Escherichia coli molybdopterin cofactor biosynthesis protein MoeA by site-directed mutagenesis. Biol. Chem. 383: 319-323 (2002).

Sandu C, Brandsch R. Evidence for MoeA-dependent formation of the molybdenum cofactor from molybdate and molybdopterin in Escherichia coli. Arch. Microbiol. 178: 465-470 (2002).

Sangwan I, O'Brian MR. Expression of the soybean (Glycine max) glutamate 1-semialdehyde aminotransferase gene in symbiotic root nodules. Plant Physiol. 102: 829-834 (1993).

Sangwan I, O'Brian MR. Expression of a soybean gene encoding the tetrapyrrole-synthesis enzyme glutamyl-tRNA reductase in symbiotic root nodules. Plant Physiol. 119: 593-598 (1999).

Sanishvili R, Beasley S, Skarina T, Glesne D, Joachimiak A, Edwards A, Savchenko A. The crystal structure of Escherichia coli MoaB suggests a probable role in molybdenum cofactor synthesis. J. Biol. Chem. 279: 42139-42146 (2004).

Santa-Maria GE, Rubio F, Dubcovsky J, Rodriguez-Navarro A. The HAK1 gene of barley is a member of a large gene family and encodes a high-affinity potassium transporter. Plant Cell 9: 2281-2289 (1997).

Santana A, Salido E, Torres A, Shapiro LJ. Primary hyperoxaluria type 1 in the Canary Islands: a conformational disease due to I244T mutation in the P11L-containing alanine:glyoxylate aminotransferase. Proc. Natl. Acad. Sci. U.S.A. 100: 7277-7282 (2003).

Santerre A, Britt AB. Cloning of a 3-methyladenine-DNA glycosylase from Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A. 91: 2240-2244 (1994).

Santillan M, Mackey MC. Dynamic regulation of the tryptophan operon: a modeling study and comparison with experimental data. Proc. Natl. Acad. Sci. U.S.A. 98: 1364-1369 (2001).

Santini CL, Iobbi-Nivol C, Romane C, Boxer DH, Giordano G. Molybdoenzyme biosynthesis in Escherichia coli: in vitro activation of purified nitrate reductase from a chlB mutant. J. Bacteriol. 174: 7934-7940 (1992).

Santos J, Anton EA, Buslje CM, Valdez SN, Villanueva AL, Sica M, Iacono R, Maffia P, Poskus E, Ermacora MR. Replacement of methionine-161 with threonine eliminates a major by-product of human glutamate decarboxylase 65-kDa variant expression in Escherichia coli. Biotechnol. Appl. Biochem. 31: 205-212 (2000).

Sariyar B, Perk S, Akman U, Hortacsu A. Monte Carlo sampling and principal component analysis of flux distributions yield topological and modular information on metabolic networks. J. Theor. Biol. 242: 389-400 (2006).

Sarkar N. Polyadenylation of mRNA in prokaryotes. Annu. Rev. Biochem. 66: 173-197 (1997).

Saroja GN, Gowrishankar J. Roles of SpoT and FNR in NH4+ assimilation and osmoregulation in GOGAT (glutamate synthase)-deficient mutants of Escherichia coli. J. Bacteriol. 178: 4105-4114 (1996).

Sarria R, Lyznik A, Vallejos CE, Mackenzie SA. A cytoplasmic male sterility-associated mitochondrial peptide in common bean is post-translationally regulated. Plant Cell 10: 1217-1228 (1998).

Sasaki K, Ohara K, Yazaki K. Gene expression and characterization of isoprene synthase from Populus alba. FEBS Lett. 579: 2514-2518 (2005).

Sasaki N, Abe Y, Goda Y, Adachi T, Kasahara K, Ozeki Y. Detection of DOPA 4,5-dioxygenase (DOD) activity using recombinant protein prepared from Escherichia coli cells harboring cDNA encoding DOD from Mirabilis jalapa. Plant Cell Physiol. 50: 1012-1016 (2009).

Satischandran C, Taylor JC, Markham GD. Isozymes of S-adenosylmethionine synthetase are encoded by tandemly duplicated genes in Escherichia coli. Mol. Microbiol. 9: 835-846 (1993).

Satoh T, Itoga A, Isogai Y, Kurihara M, Yamada S, Natori M, Suzuki N, Suruga K, Kawachi R, Arahira M, Nishio T, Fukazawa C, Oku T. Increasing the conformational stability by replacement of heme axial ligand in c-type cytochrome. FEBS Lett. 531: 543-547 (2002).

Sauer U, Lasko DR, Fiaux J, Hochuli M, Glaser R, Szyperski T, Wuthrich K, Bailey JE. Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism. J. Bacteriol. 181: 6679-6688 (1999).

Savioz A, Jeenes DJ, Kocher HP, Haas D. Comparison of proC and other housekeeping genes of Pseudomonas aeruginosa with their counterparts in Escherichia coli. Gene 86: 107-111 (1990).

Sawada MT, Ishimoto M. Proton translocation coupled to nitrite reduction in anaerobically grown Escherichia coli. J. Biochem. (Tokyo) 97: 205-211 (1985).

Sawada Y, Katsumata T, Kitamura J, Kawaide H, Nakajima M, Asami T, Nakaminami K, Kurahashi T, Mitsuhashi W, Inoue Y, Toyomasu T. Germination of photoblastic lettuce seeds is regulated via the control of endogenous physiologically active gibberellin content, rather than of gibberellin responsiveness. J. Exp. Bot. 59: 3383-3393 (2008).

Sawers G. The hydrogenases and formate dehydrogenases of Escherichia coli. Antonie Van Leeuwenhoek 66: 57-88 (1994).

Sawers RJ, Linley PJ, Gutierrez-Marcos JF, Delli-Bovi T, Farmer PR, Kohchi T, Terry MJ, Brutnell TP. The Elm1 (ZmHy2) gene of maize encodes a phytochromobilin synthase. Plant Physiol. 136: 2771-2781 (2004).

Scapin G, Blanchard JS, Sacchettini JC. Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase. Biochemistry 34: 3502-3512 (1995).

Scapin G, Reddy SG, Blanchard JS. Three-dimensional structure of meso-diaminopimelic acid dehydrogenase from Corynebacterium glutamicum. Biochemistry 35: 13540-13551 (1996).

Scapin G, Reddy SG, Zheng R, Blanchard JS. Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase in complex with NADH and the inhibitor 2,6-pyridinedicarboxylate. Biochemistry 36: 15081-15088 (1997).

Scarsdale JN, Radaev S, Kazanina G, Schirch V, Wright HT. Crystal structure at 2.4 A resolution of E. coli serine hydroxymethyltransferase in complex with glycine substrate and 5-formyl tetrahydrofolate. J. Mol. Biol. 296: 155-168 (2000).

Scebba F, Bernacchia G, De Bastiani M, Evangelista M, Cantoni RM, Cella R, Locci MT, Pitto L. Arabidopsis MBD proteins show different binding specificities and nuclear localization. Plant Mol. Biol. 53: 715-731 (2003).

Schaferjohann J, Yoo JG, Kusian B, Bowien B. The cbb operons of the facultative chemoautotroph Alcaligenes eutrophus encode phosphoglycolate phosphatase. J. Bacteriol. 175: 7329-7340 (1993).

Schaller F, Biesgen C, Mussig C, Altmann T, Weiler EW. 12-Oxophytodienoate reductase 3 (OPR3) is the isoenzyme involved in jasmonate biosynthesis. Planta 210: 979-984 (2000).

Schaller M, Schaffhauser M, Sans N, Wermuth B. Cloning and expression of succinic semialdehyde reductase from human brain. Identity with aflatoxin B1 aldehyde reductase. Eur. J. Biochem. 265: 1056-1060 (1999).

Schaub J, Reuss M. In vivo dynamics of glycolysis in Escherichia coli shows need for growth-rate dependent metabolome analysis. Biotechnol. Prog. 24: 1402-1407 (2008).

Scheidig A, Frohlich A, Schulze S, Lloyd JR, Kossmann J. Downregulation of a chloroplast-targeted beta-amylase leads to a starch-excess phenotype in leaves. Plant J. 30: 581-591 (2002).

Schendel FJ, Flickinger MC. Cloning and nucleotide sequence of the gene coding for aspartokinase II from a thermophilic methylotrophic Bacillus sp. Appl. Environ. Microbiol. 58: 2806-2814 (1992).

Schiefner A, Breed J, Bosser L, Kneip S, Gade J, Holtmann G, Diederichs K, Welte W, Bremer E. Cation-pi interactions as determinants for binding of the compatible solutes glycine betaine and proline betaine by the periplasmic ligand-binding protein ProX from Escherichia coli. J. Biol. Chem. 279: 5588-5596 (2004).

Schiffmann S, Schwenn JD. APS-sulfotransferase activity is identical to higher plant APS-kinase (EC FEBS Lett. 355: 229-232 (1994).

Schiller D, Kramer R, Morbach S. Cation specificity of osmosensing by the betaine carrier BetP of Corynebacterium glutamicum. FEBS Lett. 563: 108-112 (2004).

Schiller D, Rubenhagen R, Kramer R, Morbach S. The C-terminal domain of the betaine carrier BetP of Corynebacterium glutamicum is directly involved in sensing K+ as an osmotic stimulus. Biochemistry 43: 5583-5591 (2004).

Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson BO. Genome-scale metabolic model of Helicobacter pylori 26695. J. Bacteriol. 184: 4582-4593 (2002).

Schilling CH, Edwards JS, Letscher D, Palsson BO. Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems. Biotechnol. Bioeng. 71: 286-306 (2000).

Schilling CH, Edwards JS, Palsson BO. Toward metabolic phenomics: analysis of genomic data using flux balances. Biotechnol. Prog. 15: 288-295 (1999).

Schirch V, Hopkins S, Villar E, Angelaccio S. Serine hydroxymethyltransferase from Escherichia coli: purification and properties. J. Bacteriol. 163: 1-7 (1985).

Schlag S, Fuchs S, Nerz C, Gaupp R, Engelmann S, Liebeke M, Lalk M, Hecker M, Gotz F. Characterization of the oxygen-responsive NreABC regulon of Staphylococcus aureus. J. Bacteriol. 190: 7847-7858 (2008).

Schlattner U, Wagner E, Greppin H, Bonzon M. Adenylate kinase in tobacco cell cultures. I. Separation and localization of different activities. Plant Physiol. Biochem. 31: 815-825 (1993).

Schlegel A, Danot O, Richet E, Ferenci T, Boos W. The N terminus of the Escherichia coli transcription activator MalT is the domain of interaction with MalY. J. Bacteriol. 184: 3069-3077 (2002).

Schluepmann H, Van Dijken A, Aghdasi M, Wobbes B, Paul M, Smeekens S. Trehalose mediated growth inhibition of Arabidopsis seedlings is due to trehalose-6-phosphate accumulation. Plant Physiol. 135: 879-890 (2004).

Schmid D, Jaussi R, Christen P. Precursor of mitochondrial aspartate aminotransferase synthesized in Escherichia coli is complexed with heat-shock protein DnaK. Eur. J. Biochem. 208: 699-704 (1992).

Schmid JW, Mauch K, Reuss M, Gilles ED, Kremling A. Metabolic design based on a coupled gene expression-metabolic network model of tryptophan production in Escherichia coli. Metab. Eng. 6: 364-377 (2004).

Schmidheini T, Sperisen P, Paravicini G, Hutter R, Braus G. A single point mutation results in a constitutively activated and feedback-resistant chorismate mutase of Saccharomyces cerevisiae. J. Bacteriol. 171: 1245-1253 (1989).

Schmidlin L, Poutaraud A, Claudel P, Mestre P, Prado E, Santos-Rosa M, Wiedemann-Merdinoglu S, Karst F, Merdinoglu D, Hugueney P. A stress-inducible resveratrol O-methyltransferases involved in the biosynthesis of pterostilbene in grapevine. Plant Physiol. 148: 1630-1639 (2008).

Schmidt A, Gershenzon J. Cloning and characterization of isoprenyl diphosphate synthases with farnesyl diphosphate and geranylgeranyl diphosphate synthase activity from Norway spruce (Picea abies) and their relation to induced oleoresin formation. Phytochemistry 68: 2649-2659 (2007).

Schmidt A, Grimm R, Schmidt J, Scheel D, Strack D, Rosahl S. Cloning and expression of a potato cDNA encoding hydroxycinnamoyl-CoA:tyramine N-(hydroxycinnamoyl)transferase. J. Biol. Chem. 274: 4273-4280 (1999).

Schmidt J, Bubunenko M, Subramanian AR. A novel operon organization involving the genes for chorismate synthase (aromatic biosynthesis pathway) and ribosomal GTPase center proteins (L11, L1, L10, L12: rplKAJL) in cyanobacterium Synechocystis PCC 6803. J. Biol. Chem. 268: 27447-27457 (1993).

Schmidt K, Nielsen J, Villadsen J. Quantitative analysis of metabolic fluxes in Escherichia coli, using two-dimensional NMR spectroscopy and complete isotopomer models. J. Biotechnol. 71: 175-189 (1999).

Schmidt S, Pfluger K, Kugl S, Spanheimer R, Muller V. The salt-induced ABC transporter Ota of the methanogenic archaeon Methanosarcina mazei Go1 is a glycine betaine transporter. FEMS Microbiol. Lett. 277: 44-49 (2007).

Schmidt-Dannert C, Umeno D, Arnold FH. Molecular breeding of carotenoid biosynthetic pathways. Nat. Biotechnol. 18: 750-753 (2000).

Schmitz G, Theres K. Structural and functional analysis of the Bz2 locus of Zea mays: characterization of overlapping transcripts. Mol. Gen. Genet. 233: 269-277 (1992).

Schmitz M, Hirsch E, Bongaerts J, Takors R. Pulse experiments as a prerequisite for the quantification of in vivo enzyme kinetics in aromatic amino acid pathway of Escherichia coli. Biotechnol. Prog. 18: 935-941 (2002).

Schmitzberger F, Smith AG, Abell C, Blundell TL. Comparative analysis of the Escherichia coli ketopantoate hydroxymethyltransferase crystal structure confirms that it is a member of the (betaalpha)8 phosphoenolpyruvate/pyruvate superfamily. J. Bacteriol. 185: 4163-4171 (2003).

Schnappauf G, Strater N, Lipscomb WN, Braus GH. A glutamate residue in the catalytic center of the yeast chorismate mutase restricts enzyme activity to acidic conditions. Proc. Natl. Acad. Sci. U.S.A. 94: 8491-8496 (1997).

Schneider B, Knochel T, Darimont B, Hennig M, Dietrich S, Babinger K, Kirschner K, Sterner R. Role of the N-terminal extension of the (betaalpha)8-barrel enzyme indole-3-glycerol phosphate synthase for its fold, stability, and catalytic activity. Biochemistry 44: 16405-16412 (2005).

Schneider BL, Kiupakis AK, Reitzer LJ. Arginine catabolism and the arginine succinyltransferase pathway in Escherichia coli. J. Bacteriol. 180: 4278-4286 (1998).

Schneider BL, Ruback S, Kiupakis AK, Kasbarian H, Pybus C, Reitzer L. The Escherichia coli gabDTPC operon: specific gamma-aminobutyrate catabolism and nonspecific induction. J. Bacteriol. 184: 6976-6986 (2002).

Schneider BL, Shiau SP, Reitzer LJ. Role of multiple environmental stimuli in control of transcription from a nitrogen-regulated promoter in Escherichia coli with weak or no activator-binding sites. J. Bacteriol. 173: 6355-6363 (1991).

Schnell R, Sandalova T, Hellman U, Lindqvist Y, Schneider G. Siroheme- and [Fe4-S4]-dependent NirA from Mycobacterium tuberculosis is a sulfite reductase with a covalent Cys-Tyr bond in the active site. J. Biol. Chem. 280: 27319-27328 (2005).

Schnizer HG, Boehlein SK, Stewart JD, Richards NG, Schuster SM. Formation and isolation of a covalent intermediate during the glutaminase reaction of a class II amidotransferase. Biochemistry 38: 3677-3682 (1999).

Schnorr KM, Nygaard P, Laloue M. Molecular characterization of Arabidopsis thaliana cDNAs encoding three purine biosynthetic enzymes. Plant J. 6: 113-121 (1994).

Schreier HJ, Sonenshein AL. Altered regulation of the glnA gene in glutamine synthetase mutants of Bacillus subtilis. J. Bacteriol. 167: 35-43 (1986).

Schroder G, Unterbusch E, Kaltenbach M, Schmidt J, Strack D, De Luca V, Schroder J. Light-induced cytochrome P450-dependent enzyme in indole alkaloid biosynthesis: tabersonine 16-hydroxylase. FEBS Lett. 458: 97-102 (1999).

Schroder I, Hederstedt L, Kannangara CG, Gough SP. Glutamyl-transfer RNA reductase activity in Bacillus subtilis is dependent on the hemA gene product. Biochem. J. 281: 843-850 (1992).

Schroder I, Thauer RK. Methylcobalamin:homocysteine methyltransferase from Methanobacterium thermoautotrophicum. Identification as the metE gene product. Eur. J. Biochem. 263: 789-796 (1999).

Schroder I, Wolin CD, Cavicchioli R, Gunsalus RP. Phosphorylation and dephosphorylation of the NarQ, NarX, and NarL proteins of the nitrate-dependent two-component regulatory system of Escherichia coli. J. Bacteriol. 176: 4985-4992 (1994).

Schroder R, Wegrzyn TF, Sharma NN, Atkinson RG. LeMAN4 endo-beta-mannanase from ripe tomato fruit can act as a mannan transglycosylase or hydrolase. Planta 224: 1091-1102 (2006).

Schuller DJ, Fetter CH, Banaszak LJ, Grant GA. Enhanced expression of the Escherichia coli serA gene in a plasmid vector. Purification, crystallization, and preliminary X-ray data of D-3 phosphoglycerate dehydrogenase. J. Biol. Chem. 264: 2645-2648 (1989).

Schuller DJ, Grant GA, Banaszak LJ. The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase. Nat. Struct. Biol. 2: 69-76 (1995).

Schulz AA, Collett HJ, Reid SJ. Nitrogen and carbon regulation of glutamine synthetase and glutamate synthase in Corynebacterium glutamicum ATCC 13032. FEMS Microbiol. Lett. 205: 361-367 (2001).

Schurke P, Freeman JC, Dabrowski MJ, Atkins WM. Metal-dependent self-assembly of protein tubes from Escherichia coli glutamine synthetase. Cu(2+) EPR studies of the ligation and stoichiometry of intermolecular metal binding sites. J. Biol. Chem. 274: 27963-27968 (1999).

Schuster S. Studies on the stoichiometric structure of enzymatic reaction systems. Theor. Biosci. 118: 125-139 (1999).

Schutt BS, Abbadi A, Loddenkotter B, Brummel M, Spener F. beta-Ketoacyl-acyl carrier protein synthase IV: a key enzyme for regulation of medium-chain fatty acid synthesis in Cuphea lanceolata seeds. Planta 215: 847-854 (2002).

Schutt BS, Brummel M, Schuch R, Spener F. The role of acyl carrier protein isoforms from Cuphea lanceolata seeds in the de-novo biosynthesis of medium-chain fatty acids. Planta 205: 263-268 (1998).

Schutz A, Golbik R, Tittmann K, Svergun DI, Koch MH, Hubner G, Konig S. Studies on structure-function relationships of indolepyruvate decarboxylase from Enterobacter cloacae, a key enzyme of the indole acetic acid pathway. Eur. J. Biochem. 270: 2322-2331 (2003).

Schuurmans JA, van Dongen JT, Rutjens BP, Boonman A, Pieterse CM, Borstlap AC. Members of the aquaporin family in the developing pea seed coat include representatives of the PIP, TIP, and NIP subfamilies. Plant Mol. Biol. 53: 633-645 (2003).

Schwan WF, Wetzel KJ, Gomez TS, Stiles MA, Beitlich BD, Grunwald S. Low-proline environments impair growth, proline transport and in vivo survival of Staphylococcus aureus strain-specific putP mutants. Microbiology (U.K.) 150: 1055-1061 (2004).

Schwarte S, Bauwe H. Identification of the photorespiratory 2-phosphoglycolate phosphatase, PGLP1, in Arabidopsis. Plant Physiol. 144: 1580-1586 (2007).

Schwartz CJ, Djaman O, Imlay JA, Kiley PJ. The cysteine desulfurase, IscS, has a major role in in vivo Fe-S cluster formation in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 97: 9009-9014 (2000).

Schwartz SH, Qin X, Loewen MC. The biochemical characterization of two carotenoid cleavage enzymes from Arabidopsis indicates that a carotenoid-derived compound inhibits lateral branching. J. Biol. Chem. 279: 46940-46945 (2004).

Schwarz G, Boxer DH, Mendel RR. Molybdenum cofactor biosynthesis. The plant protein Cnx1 binds molybdopterin with high affinity. J. Biol. Chem. 272: 26811-26814 (1997).

Schwender J, Muller C, Zeidler J, Lichtenthaler HK. Cloning and heterologous expression of a cDNA encoding 1-deoxy-D-xylulose-5-phosphate reductoisomerase of Arabidopsis thaliana. FEBS Lett. 455: 140-144 (1999).

Schwenn JD, Krone FA, Husmann K. Yeast PAPS reductase: properties and requirements of the purified enzyme. Arch. Microbiol. 150: 313-319 (1988).

Schwenn JD, Schriek U. PAPS-reductase from Escherichia coli: characterization of the enzyme as probe for thioredoxins. Z. Naturforsch. [C] 42: 93-102 (1987).

Schwoppe C, Winkler HH, Neuhaus HE. Connection of transport and sensing by UhpC, the sensor for external glucose-6-phosphate in Escherichia coli. Eur. J. Biochem. 270: 1450-1457 (2003).

Scippa GS, Griffiths A, Chiatante D, Bray EA. The H1 histone variant of tomato, H1-S, is targeted to the nucleus and accumulates in chromatin in response to water-deficit stress. Planta 211: 173-181 (2000).

Scofield MA, Lewis WS, Schuster SM. Nucleotide sequence of Escherichia coli asnB and deduced amino acid sequence of asparagine synthetase B. J. Biol. Chem. 265: 12895-12902 (1990).

Scott C, Partridge JD, Stephenson JR, Green J. DNA target sequence and FNR-dependent gene expression. FEBS Lett. 541: 97-101 (2003).

Segre D, Vitkup D, Church GM. Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl. Acad. Sci. U.S.A. 99: 15112-15117 (2002).

Seguin J, Muzac I, Ibrahim RK. Purification and immunological characterization of a recombinant trimethylflavonol 3'-O-methyltransferase. Phytochemistry 49: 319-325 (1998).

Seiffert B, Zhou ZW, Wallbraun M, Lohaus G, Mollers C. Expression of a bacterial asparagine synthetase gene in oilseed rape (Brassica napus) and its effect on traits related to nitrogen efficiency. Physiol. Plant. 121: 656-665 (2004).

Sekhar PN, Amrutha RN, Sangam S, Verma DP, Kishor PB. Biochemical characterization, homology modeling and docking studies of ornithine delta-aminotransferase--an important enzyme in proline biosynthesis of plants. J. Mol. Graph Model. 26: 709-719 (2007).

Sekowska A, Kung HF, Danchin A. Sulfur metabolism in Escherichia coli and related bacteria: facts and fiction. J. Mol. Microbiol. Biotechnol. 2: 145-177 (2000).

Self WT, Grunden AM, Hasona A, Shanmugam KT. Transcriptional regulation of molybdoenzyme synthesis in Escherichia coli in response to molybdenum: ModE-molybdate, a repressor of the modABCD (molybdate transport) operon is a secondary transcriptional activator for the hyc and nar operons. Microbiology 145: 41-55 (1999).

Sella C, Weinstock O, Barak Z, Chipman DM. Subunit association in acetohydroxy acid synthase isozyme III. J. Bacteriol. 175: 5339-5343 (1993).

Selvarasu S, Ow DS, Lee SY, Lee MM, Oh SK, Karimi IA, Lee DY. Characterizing Escherichia coli DH5alpha growth and metabolism in a complex medium using genome-scale flux analysis. Biotechnol. Bioeng. 102: 923-934 (2009).

Sender PD, Martin MG, Peiru S, Magni C. Characterization of an oxaloacetate decarboxylase that belongs to the malic enzyme family. FEBS Lett. 570: 217-222 (2004).

Senecoff JF, Meagher RB. Isolating the Arabidopsis thaliana genes for de novo purine synthesis by suppression of Escherichia coli mutants. I. 5'-Phosphoribosyl-5-aminoimidazole synthetase. Plant Physiol. 102: 387-399 (1993).

Senior PJ. Regulation of nitrogen metabolism in Escherichia coli and Klebsiella aerogenes: studies with the continuous-culture technique. J. Bacteriol. 123: 407-418 (1975).

Seo HS, Song JT, Cheong JJ, Lee YH, Lee YW, Hwang I, Lee JS, Choi YD. Jasmonic acid carboxyl methyltransferase: a key enzyme for jasmonate-regulated plant responses. Proc. Natl. Acad. Sci. U.S.A. 98: 4788-4793 (2001).

Serebrijski I, Reyes O, Leblon G. Corrected gene assignments of Escherichia coli pro- mutations. J. Bacteriol. 177: 7261-7264 (1995).

Serina L, Blondin C, Krin E, Sismeiro O, Danchin A, Sakamoto H, Gilles AM, Barzu O. Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP. Biochemistry 34: 5066-5074 (1995).

Serino G, Maliga P. RNA polymerase subunits encoded by the plastid rpo genes are not shared with the nucleus-encoded plastid enzyme. Plant Physiol. 117: 1165-1170 (1998).

Serrano R. Salt tolerance in plants and microorganisms: toxicity targets and defense responses. Int. Rev. Cytol. 165: 1-52 (1996).

Serrano-Vega MJ, Garces R, Martinez-Force E. Cloning, characterization and structural model of a FatA-type thioesterase from sunflower seeds (Helianthus annuus L.). Planta 221: 868-890 (2005).

Seto Y, Hamada S, Matsuura H, Matsushige M, Satou C, Takahashi K, Masuta C, Ito H, Matsui H, Nabeta K. Purification and cDNA cloning of a wound inducible glucosyltransferase active toward 12-hydroxy jasmonic acid. Phytochemistry 70: 370-379 (2009).

Setya A, Murillo M, Leustek T. Sulfate reduction in higher plants: molecular evidence for a novel 5'-adenylylsulfate reductase. Proc. Natl. Acad. Sci. U.S.A. 93: 13383-13388 (1996).

Sevilla A, Schmid JW, Mauch K, Iborra JL, Reuss M, Canovas M. Model of central and trimethylammonium metabolism for optimizing l-carnitine production by E. coli. Metab. Eng. 7: 401-425 (2005).

Shah S, Li J, Moffatt BA, Glick BR. Isolation and characterization of ACC deaminase genes from two different plant growth-promoting rhizobacteria. Can. J. Microbiol. 44: 833-843 (1998).

Shakoury-Elizeh M, Tiedeman J, Rashford J, Ferea T, Demeter J, Garcia E, Rolfes R, Brown PO, Botstein D, Philpott CC. Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae. Mol. Biol. Cell 15: 1233-1243 (2004).

Shalel-Levanon S, San KY, Bennett GN. Effect of oxygen, and ArcA and FNR regulators on the expression of genes related to the electron transfer chain and the TCA cycle in Escherichia coli. Metab. Eng. 7: 364-374 (2005).

Shalit M, Guterman I, Volpin H, Bar E, Tamari T, Menda N, Adam Z, Zamir D, Vainstein A, Weiss D, Pichersky E, Lewinsohn E. Volatile ester formation in roses. Identification of an acetyl-coenzyme A:geraniol/citronellol acetyltransferase in developing rose petals. Plant Physiol. 131: 1868-1876 (2003).

Shaltiel S, Adler SP, Purich D, Caban C, Senior P, Stadtman ER. Omega-aminoalkyl agaroses in the resolution of enzymes involved in regulation of glutamine metabolism. Proc. Natl. Acad. Sci. U.S.A. 72: 3397-3401 (1975).

Shames SL, Ash DE, Wedler FC, Villafranca JJ. Interaction of aspartate and aspartate-derived antimetabolites with the enzymes of the threonine biosynthetic pathway of Escherichia coli. J. Biol. Chem. 259: 15331-15339 (1984).

Shames SL, Wedler FC. Homoserine kinase of Escherichia coli: kinetic mechanism and inhibition by L-aspartate semialdehyde. Arch. Biochem. Biophys. 235: 359-370 (1984).

Shams Yazdani S, Gonzalez R. Engineering Escherichia coli for the efficient conversion of glycerol to ethanol and co-products. Metab. Eng. 10: 340-351 (2008).

Shanklin J, DeWitt ND, Flanagan JM. The stroma of higher plant plastids contain ClpP and ClpC, functional homologs of Escherichia coli ClpP and ClpA: an archetypal two-component ATP-dependent protease. Plant Cell 7: 1713-1722 (1995).

Shao L, Li Y, Pan A, Cheng Z, Chen M. Molecular cloning, sequencing, and expression in Escherichia coli of the chalcone synthase gene. Chin. J. Biotechnol. 11: 131-135 (1995).

Shapiro BM, Stadtman ER. 5'-Adenylyl-O-tyrosine. The novel phosphodiester residue of adenylylated glutamine synthetase from Escherichia coli. J. Biol. Chem. 243: 3769-3771 (1968).

Sharma D, Balamurali MM, Chakraborty K, Kumaran S, Jeganathan S, Rashid U, Ingallinella P, Varadarajan R. Protein minimization of the gp120 binding region of human CD4. Biochemistry 44: 16192-16202 (2005).

Sharma N, Park SW, Vepachedu R, Barbieri L, Ciani M, Stirpe F, Savary BJ, Vivanco JM. Isolation and characterization of an RIP (ribosome-inactivating protein)-like protein from tobacco with dual enzymatic activity. Plant Physiol. 134: 171-181 (2004).

Sharma S, Zhang A, Wang H, Harcum SW, Chong S. Study of protein splicing and intein-mediated peptide bond cleavage under high-cell-density conditions. Biotechnol. Prog. 19: 1085-1090 (2003).

Sharma SS, Blattner FR, Harcum SW. Recombinant protein production in an Escherichia coli reduced genome strain. Metab. Eng. 9: 133-141 (2007).

Sharma V, Noriega CE, Rowe JJ. Involvement of NarK1 and NarK2 proteins in transport of nitrate and nitrite in the denitrifying bacterium Pseudomonas aeruginosa PAO1. Appl. Environ. Microbiol. 72: 695-701 (2006).

Shatters RG, Liu Y, Kahn ML. Isolation and characterization of a novel glutamine synthetase from Rhizobium meliloti. J. Biol. Chem. 268: 469-475 (1993).

Shaver JM, Bittel DC, Sellner JM, Frisch DA, Somers DA, Gengenbach BG. Single-amino acid substitutions eliminate lysine inhibition of maize dihydrodipicolinate synthase. Proc. Natl. Acad. Sci. U.S.A. 93: 1962-1966 (1996).

Shaw D, Odom JD, Dunlap RB. High expression and steady-state kinetic characterization of methionine site-directed mutants of Escherichia coli methionyl- and selenomethionyl-dihydrofolate reductase. Biochim. Biophys. Acta 1429: 401-410 (1999).

Shekhtman A, Ghose R, Goger M, Cowburn D. NMR structure determination and investigation using a reduced proton (REDPRO) labeling strategy for proteins. FEBS Lett. 524: 177-182 (2002).

Shen CR, Liao JC. Metabolic engineering of Escherichia coli for 1-butanol and 1-propanol production via the keto-acid pathways. Metab. Eng. 10: 312-320 (2008).

Shen J, Gunsalus RP. Role of multiple ArcA recognition sites in anaerobic regulation of succinate dehydrogenase (sdhCDAB) gene expression in Escherichia coli. Mol. Microbiol. 26: 223-236 (1997).

Shen WY, Wei YD, Dauk M, Zheng ZF, Zou JT. Identification of a mitochondrial glycerol-3-phosphate dehydrogenase from Arabidopsis thaliana: evidence for a mitochondrial glycerol-3-phosphate shuttle in plants. FEBS Lett. 536: 92-96 (2003).

Shen-Orr SS, Milo R, Mangan S, Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 31: 64-68 (2002).

Shepard EM, Smith J, Elmore BO, Kuchar JA, Sayre LM, Dooley DM. Towards the development of selective amine oxidase inhibitors. Mechanism-based inhibition of six copper containing amine oxidases. Eur. J. Biochem. 269: 3645-3658 (2002).

Shepherd RW, Bass WT, Houtz RL, Wagner GJ. Phylloplanins of tobacco are defensive proteins deployed on aerial surfaces by short glandular trichomes. Plant Cell 17: 1851-1861 (2005).

Sherson S, Gy I, Medd J, Schmidt R, Dean C, Kreis M, Lecharny A, Cobbett C. The arabinose kinase, ARA1, gene of Arabidopsis is a novel member of the galactose kinase gene family. Plant Mol. Biol. 39: 1003-1012 (1999).

Shewmaker CK, Boyer CD, Wiesenborn DP, Thompson DB, Boersig MR, Oakes JV, Stalker DM. Expression of Escherichia coli glycogen synthase in the tubers of transgenic potatoes (Solanum tuberosum) results in a highly branched starch. Plant Physiol. 104: 1159-1166 (1994).

Shi H, Nikawa J, Shimizu K. Effect of modifying metabolic network on poly-3-hydroxybutyrate biosynthesis in recombinant Escherichia coli. J. Biosci. Bioeng. 87: 666-677 (1999).

Shi H, Xiong L, Stevenson B, Lu T, Zhu JK. The Arabidopsis salt overly sensitive 4 mutants uncover a critical role for vitamin B6 in plant salt tolerance. Plant Cell 14: 575-588 (2002).

Shibasaki T, Mori H, Chiba S, Ozaki A. Microbial proline 4-hydroxylase screening and gene cloning. Appl. Environ. Microbiol. 65: 4028-4031 (1999).

Shibasaki T, Mori H, Ozaki A. Enzymatic production of trans-4-hydroxy-L-proline by regio- and stereospecific hydroxylation of L-proline. Biosci. Biotechnol. Biochem. 64: 746-750 (2000).

Shikanai T, Takeda T, Yamauchi H, Sano S, Tomizawa KI, Yokota A, Shigeoka S. Inhibition of ascorbate peroxidase under oxidative stress in tobacco having bacterial catalase in chloroplasts. FEBS Lett. 428: 47-51 (1998).

Shim J, Im SH, Lee J. Tissue-specific expression, heat inducibility, and biological roles of two hsp16 genes in Caenorhabditis elegans. FEBS Lett. 537: 139-145 (2003).

Shimada N, Aoki T, Sato S, Nakamura Y, Tabata S, Ayabe S. A cluster of genes encodes the two types of chalcone isomerase involved in the biosynthesis of general flavonoids and legume-specific 5-deoxy(iso)flavonoids in Lotus japonicus. Plant Physiol. 131: 941-951 (2003).

Shimada N, Sasaki R, Sato S, Kaneko T, Tabata S, Aoki T, Ayabe S. A comprehensive analysis of six dihydroflavonol 4-reductases encoded by a gene cluster of the Lotus japonicus genome. J. Exp. Bot. 56: 2573-2585 (2005).

Shimaoka T, Miyake C, Yokota A. Mechanism of the reaction catalyzed by dehydroascorbate reductase from spinach chloroplasts. Eur. J. Biochem. 270: 921-928 (2003).

Shimizu K. An overview on metabolic systems engineering approach and its future perspectives for efficient microbial fermentation. J. Chin. Inst. Chem. Eng. 31: 429-442 (2000).

Shin D, Park C. N-terminal extension of canine glutamine synthetase created by splicing alters its enzymatic property. J. Biol. Chem. 279: 1184-1190 (2004).

Shin H, Brown RM Jr. GTPase activity and biochemical characterization of a recombinant cotton fiber annexin. Plant Physiol. 119: 925-934 (1999).

Shin S, Castanie-Cornet MP, Foster JW, Crawford JA, Brinkley C, Kaper JB. An activator of glutamate decarboxylase genes regulates the expression of enteropathogenic Escherichia coli virulence genes through control of the plasmid-encoded regulator, per. Mol. Microbiol. 41: 1133-1150 (2001).

Shiraishi N, Croy C, Kaur J, Campbell WH. Engineering of pyridine nucleotide specificity of nitrate reductase: mutagenesis of recombinant cytochrome b reductase fragment of Neurospora crassa NADPH:nitrate reductase. Arch. Biochem. Biophys. 358: 104-115 (1998).

Shitu JO, Woodley JM, Wnek R, Chartrain M, Hewitt CJ. Induction studies with Escherichia coli expressing recombinant interleukin-13 using multi-parameter flow cytometry. Biotechnol. Lett. 31: 577-584 (2009).

Shockey JM, Fulda MS, Browse JA. Arabidopsis contains nine long-chain acyl-coenzyme A synthetase genes that participate in fatty acid and glycerolipid metabolism. Plant Physiol. 129: 1710-1722 (2002).

Shorrosh BS, Subramaniam J, Schubert KR, Dixon RA. Expression and localization of plant protein disulfide isomerase. Plant Physiol. 103: 719-726 (1993).

Shortridge VD, Lazdunski A, Vasil ML. Osmoprotectants and phosphate regulate expression of phospholipase C in Pseudomonas aeruginosa. Mol. Microbiol. 6: 863-871 (1992).

Shostak K, Schirch V. Serine hydroxymethyltransferase: mechanism of the racemization and transamination of D- and L-alanine. Biochemistry 27: 8007-8014 (1988).

Shostak K, Schirch V. Serine hydroxymethyltransferase: mechanism of the racemization and transamination of D- and L-alanine. Biochemistry 27: 8007-8014 (1988).

Shrestha R, Kim SC, Dyer JM, Dixon RA, Chapman KD. Plant fatty acid (ethanol) amide hydrolases. Biochim. Biophys. Acta 1761: 324-334 (2006).

Shul'ga AA, Kurbanov FT, Khristoforov RR, Darii EL, Sukhareva BS. Glutamate decarboxylase of Escherichia coli: expression of gadA gene, purification and properties of GAD alpha. Mol. Biol. 33: 491-497 (1999).

Shuler ML. Single-cell models: promise and limitations. J. Biotechnol. 71: 225-228 (1999).

Shumilin IA, Kretsinger RH, Bauerle RH. Crystal structure of phenylalanine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Escherichia coli. Structure Fold. Des. 7: 865-875 (1999).

Sibilli L, Le Bras G, Le Bras G, Cohen GN. Two regions of the bifunctional protein aspartokinase I- homoserine dehydrogenase I are connected by a short hinge. J. Biol. Chem. 256: 10228-10230 (1981).

Siebert M, Severin K, Heide L. Formation of 4-hydroxybenzoate in Escherichia coli: characterization of the ubiC gene and its encoded enzyme chorismate pyruvate-lyase. Microbiology 140: 897-904 (1994).

Siebert M, Sommer S, Li SM, Wang ZX, Severin K, Heide L. Genetic engineering of plant secondary metabolism. Accumulation of 4-hydroxybenzoate glucosides as a result of the expression of the bacterial ubiC gene in tobacco. Plant Physiol. 112: 811-819 (1996).

Siegenthaler RK, Grimshaw JP, Christen P. Immediate response of the DnaK molecular chaperone system to heat shock. FEBS Lett. 562: 105-110 (2004).

Sienko M, Paszewski A. The metG gene of Aspergillus nidulans encoding cystathionine b-lyase: cloning and analysis. Curr. Genet. 35: 638-646 (1999).

Silk GW, Matthews BF. Soybean DapA mutations encoding lysine-insensitive dihydrodipicolinate synthase. Plant Mol. Biol. 33: 931-933 (1997).

Silk GW, Matthews BF, Somers DA, Gengenbach BG. Cloning and expression of the soybean DapA gene encoding dihydrodipicolinate synthase. Plant Mol. Biol. 26: 989-993 (1994).

Silva Z, Alarico S, Nobre A, Horlacher R, Marugg J, Boos W, Mingote AI, da Costa MS. Osmotic adaptation of Thermus thermophilus RQ-1: lesson from a mutant deficient in synthesis of trehalose. J. Bacteriol. 185: 5943-5952 (2003).

Simard D, Hewitt KA, Lunn F, Iyengar A, Bearne SL. Limited proteolysis of Escherichia coli cytidine 5'-triphosphate synthase. Identification of residues required for CTP formation and GTP-dependent activation of glutamine hydrolysis. Eur. J. Biochem. 270: 2195-2206 (2003).

Simeonidis E, Rison SC, Thornton JM, Bogle ID, Papageorgiou LG. Analysis of metabolic networks using a pathway distance metric through linear programming. Metab. Eng. 5: 211-219 (2003).

Simmons AJ, Rawls JM, Piskur J, Davidson JN. A mutation that uncouples allosteric regulation of carbamyl phosphate synthetase in Drosophila. J. Mol. Biol. 287: 277-285 (1999).

Simmons CR, Fridlender M, Navarro PA, Yalpani N. A maize defense-inducible gene is a major facilitator superfamily member related to bacterial multidrug resistance efflux antiporters. Plant Mol. Biol. 52: 433-446 (2003).

Simon J. Enzymology and bioenergetics of respiratory nitrite ammonification. FEMS Microbiol. Rev. 26: 285-309 (2002).

Simon J, Gross R, Einsle O, Kroneck PM, Kroger A, Klimmek O. A NapC/NirT-type cytochrome c (NrfH) is the mediator between the quinone pool and the cytochrome c nitrite reductase of Wolinella succinogenes. Mol. Microbiol. 35: 686-696 (2000).

Simon M, Hong JS. Direct homocysteine biosynthesis from O-succinylhomoserine in Escherichia coli: an alternate pathway that bypasses cystathionine. J. Bacteriol. 153: 558-561 (1983).

Simpson JP, Di Leo R, Dhanoa PK, Allan WL, Makhmoudova A, Clark SM, Hoover GJ, Mullen RT, Shelp BJ. Identification and characterization of a plastid-localized Arabidopsis glyoxylate reductase isoform: comparison with a cytosolic isoform and implications for cellular redox homeostasis and aldehyde detoxification. J. Exp. Bot. 59: 2545-2554 (2008).

Simpson RJ, Davidson BE. Studies on 3-deoxy-D-arabinoheptulosonate-7-phosphate synthetase(phe) from Escherichia coli K12. 2. Kinetic properties. Eur. J. Biochem. 70: 501-507 (1976).

Simpson RJ, Davidson BE. Studies on 3-deoxy-D-arabinoheptulosonate-7-phosphate synthetase(phe) from Escherichia coli K12. 1. Purification and subunit structure. Eur. J. Biochem. 70: 493-500 (1976).

Singh BN, Mudgil Y, Sopory SK, Reddy MK. Molecular characterization of a nuclear topoisomerase II from Nicotiana tabacum that functionally complements a temperature-sensitive topoisomerase II yeast mutant. Plant Mol. Biol. 52: 1063-1076 (2003).

Singh J, Joshi MC, Bhatnagar R. Cloning and expression of mycobacterial glutamine synthetase gene in Escherichia coli. Biochem. Biophys. Res. Commun. 317: 634-638 (2004).

Singh S, Aziz MA, Khandelwal P, Bhat R, Bhatnagar R. The osmoprotectants glycine and its methyl derivatives prevent the thermal inactivation of protective antigen of Bacillus anthracis. Biochem. Biophys. Res. Commun. 316: 559-564 (2004).

Singh U, Panchanadikar V, Sarkar D. Development of a simple assay protocol for high-throughput screening of Mycobacterium tuberculosis glutamine synthetase for the identification of novel inhibitors. J. Biomol. Screen. 10: 725-729 (2005).

Singh VK, Ghosh I. Kinetic modeling of tricarboxylic acid cycle and glyoxylate bypass in Mycobacterium tuberculosis, and its application to assessment of drug targets. Theor. Biol. Med. Model. 3: 27 (2006).

Sissler M, Delorme C, Bond J, Ehrlich SD, Renault P, Francklyn C. An aminoacyl-tRNA synthetase paralog with a catalytic role in histidine biosynthesis. Proc. Natl. Acad. Sci. U.S.A. 96: 8985-8990 (1999).

Siu KK, Lee JE, Smith GD, Horvatin-Mrakovcic C, Howell PL. Structure of Staphylococcus aureus 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase. Acta Crystallogr. Sect. F. Struct. Biol. Cryst. Commun. 64: 343-350 (2008).

Sjogren LL, Stanne TM, Zheng B, Sutinen S, Clarke AK. Structural and functional insights into the chloroplast ATP-dependent Clp protease in Arabidopsis. Plant Cell 18: 2635-2649 (2006).

Skinner MA, Cooper RA. An Escherichia coli mutant defective in the NAD-dependent succinate semialdehyde dehydrogenase. Arch. Microbiol. 132: 270-275 (1982).

Skipsey M, Cummins I, Andrews CJ, Jepson I, Edwards R. Manipulation of plant tolerance to herbicides through co-ordinated metabolic engineering of a detoxifying glutathione transferase and thiol cosubstrate. Plant Biotechnol. J. 3: 409-420 (2005).

Skogman GS, Sjostrom JE. Factors affecting the biosynthesis of L-tryptophan by genetically modified strains of Escherichia coli. J. Gen. Microbiol. 130: 3091-3100 (1984).

Sleator RD, Gahan CG, Abee T, Hill C. Identification and disruption of BetL, a secondary glycine betaine transport system linked to the salt tolerance of Listeria monocytogenes LO28. Appl. Environ. Microbiol. 65: 2078-2083 (1999).

Sleator RD, Gahan CGM, Hill C. Mutations in the listerial proB gene leading to proline overproduction: Effects on salt tolerance and murine infection. Appl. Environ. Microbiol. 67: 4560-4565 (2001).

Small PL, Waterman SR. Acid stress, anaerobiosis and gadCB: lessons from Lactococcus lactis and Escherichia coli. Trends Microbiol. 6: 214-216 (1998).

Smalley DJ, Whiteley M, Conway T. In search of the minimal Escherichia coli genome. Trends Microbiol. 11: 6-8 (2003).

Smart AG, Amaral LA, Ottino JM. Cascading failure and robustness in metabolic networks. Proc. Natl. Acad. Sci. U.S.A. 105: 13223-13228 (2008).

Smigielski AJ, Muir ME, Wallace BJ. Studies on the accumulation of putrescine and spermidine in Escherichia coli. Aust. J. Biol. Sci. 38: 383-392 (1985).

Smirnova G, Oktyabrsky O. Betaine modulates intracellular thiol and potassium levels in Escherichia coli in medium with high osmolarity and alkaline pH. Arch. Microbiol. 163: 76-78 (1995).

Smit MS. Fungal epoxide hydrolases: new landmarks in sequence-activity space. Trends Biotechnol. 22: 123-129 (2004).

Smith CJ, Deutch AH, Rushlow KE. Purification and characteristics of a gamma-glutamyl kinase involved in Escherichia coli proline biosynthesis. J. Bacteriol. 157: 545-551 (1984).

Smith CS, Weljie AM, Moorhead GB. Molecular properties of the putative nitrogen sensor PII from Arabidopsis thaliana. Plant J. 33: 353-360 (2003).

Smith CS, Zaplachinski ST, Muench DG, Moorhead GB. Expression and purification of the chloroplast putative nitrogen sensor, PII, of Arabidopsis thaliana. Protein Expr. Purif. 25: 342-347 (2002).

Smith DK, Kassam T, Singh B, Elliott JF. Escherichia coli has two homologous glutamate decarboxylase genes that map to distinct loci. J. Bacteriol. 174: 5820-5826 (1992).

Smith LT. Characterization of a gamma-glutamyl kinase from Escherichia coli that confers proline overproduction and osmotic tolerance. J. Bacteriol. 164: 1088-1093 (1985).

Smith LT, Pocard JA, Bernard T, Le Rudulier D. Osmotic control of glycine betaine biosynthesis and degradation in Rhizobium meliloti. J. Bacteriol. 170: 3142-3149 (1988).

Smith MA, Kannangara CG, Grimm B, von Wettstein D. Characterization of glutamate-1-semialdehyde aminotransferase of Synechococcus. Steady-state kinetic analysis. Eur. J. Biochem. 202: 749-757 (1991).

Smith PM, Mann AJ, Goggin DE, Atkins CA. AIR synthetase in cowpea nodules: a single gene product targeted to two organelles? Plant Mol. Biol. 36: 811-820 (1998).

Smolke CD, Martin VJ, Keasling JD. Controlling the metabolic flux through the carotenoid pathway using directed mRNA processing and stabilization. Metab. Eng. 3: 313-321 (2001).

Smulski DR, Huang LXL, McCluskey MP, Reeve MJG, Vollmer AC, Van Dyk TK, LaRossa RA. Combined, functional genomic-biochemical approach to intermediary metabolism: Interaction of acivicin, a glutamine amidotransferase inhibitor, with Escherichia coli K-12. J. Bacteriol. 183: 3353-3364 (2001).

Smykal P, Masin J, Hrdy I, Konopasek I, Zarsky V. Chaperone activity of tobacco HSP18, a small heat-shock protein, is inhibited by ATP. Plant J. 23: 703-713 (2000).

Snedden WA, Koutsia N, Baum G, Fromm H. Activation of a recombinant petunia glutamate decarboxylase by calcium/calmodulin or by a monoclonal antibody which recognizes the calmodulin binding domain. J. Biol. Chem. 271: 4148-4153 (1996).

Snustad DP, Hunsperger JP, Chereskin BM, Messing J. Maize glutamine synthetase cDNAs: isolation by direct genetic selection in Escherichia coli. Genetics 120: 1111-1123 (1988).

So AK, Espie GS. Cloning, characterization and expression of carbonic anhydrase from the cyanobacterium Synechocystis PCC6803. Plant Mol. Biol. 37: 205-215 (1998).

Sobajima H, Takeda M, Sugimori M, Kobashi N, Kiribuchi K, Cho EM, Akimoto C, Yamaguchi T, Minami E, Shibuya N, Schaller F, Weiler EW, Yoshihara T, Nishida H, Nojiri H, Omori T, Nishiyama M, Yamane H. Cloning and characterization of a jasmonic acid-responsive gene encoding 12-oxophytodienoic acid reductase in suspension-cultured rice cells. Planta 216: 692-698 (2003).

Sohaskey CD, Wayne LG. Role of narK2X and narGHJI in hypoxic upregulation of nitrate reduction by Mycobacterium tuberculosis. J. Bacteriol. 185: 7247-7256 (2003).

Sohling B, Gottschalk G. Molecular analysis of the anaerobic succinate degradation pathway in Clostridium kluyveri. J. Bacteriol. 178: 871-880 (1996).

Sokolenko A. SppA peptidases: family diversity from heterotrophic bacteria to photoautotrophic eukaryotes. Physiol. Plant. 123: 391-398 (2005).

Sokolenko A, Lerbs-Mache S, Altschmied L, Herrmann RG. Clp protease complexes and their diversity in chloroplasts. Planta 207: 286-295 (1998).

Sommer S, Kohle A, Yazaki K, Shimomura K, Bechthold A, Heide L. Genetic engineering of shikonin biosynthesis hairy root cultures of Lithospermum erythrorhizon transformed with the bacterial ubiC gene. Plant Mol. Biol. 39: 683-693 (1999).

Son HS, Rhee SG. Cascade control of Escherichia coli glutamine synthetase. Purification and properties of PII protein and nucleotide sequence of its structural gene. J. Biol. Chem. 262: 8690-8695 (1987).

Sonderegger M, Schumperli M, Sauer U. Selection of quiescent Escherichia coli with high metabolic activity. Metab. Eng. 7: 4-9 (2005).

Song HS, Brotherton JE, Gonzales RA, Widholm JM. Tissue culture-specific expression of a naturally occurring tobacco feedback-insensitive anthranilate synthase. Plant Physiol. 117: 533-543 (1998).

Song JM, Rabinowitz JC. The N-terminal, dehydrogenase/cyclohydrolase domain of yeast cytoplasmic trifunctional C1-tetrahydrofolate synthase requires the C-terminal, synthetase domain for the catalytic activity in vitro. FEBS Lett. 376: 229-232 (1995).

Song SK, Choi Y, Moon YH, Kim SG, Choi YD, Lee JS. Systemic induction of a Phytolacca insularis antiviral protein gene by mechanical wounding, jasmonic acid, and abscisic acid. Plant Mol. Biol. 43: 439-450 (2000).

Song WJ, Jackowski S. Cloning, sequencing, and expression of the pantothenate kinase (coaA) gene of Escherichia coli. J. Bacteriol. 174: 6411-6417 (1992).

Song WJ, Jackowski S. Kinetics and regulation of pantothenate kinase from Escherichia coli. J. Biol. Chem. 269: 27051-27058 (1994).

Song Y, Peisach D, Pioszak AA, Xu Z, Ninfa AJ. Crystal structure of the C-terminal domain of the two-component system transmitter protein nitrogen regulator II (NRII; NtrB), regulator of nitrogen assimilation in Escherichia coli. Biochemistry 43: 6670-6678 (2004).

Soriano E, Borth N, Katinger H, Mattanovich D. Flow cytometric analysis of metabolic stress effects due to recombinant plasmids and proteins in Escherichia coli production strains. Metab. Eng. 1: 270-274 (1999).

Sorokin A, Zumstein E, Azevedo V, Ehrlich SD, Serror P. The organization of the Bacillus subtilis 168 chromosome region between the spoVA and serA genetic loci, based on sequence data. Mol. Microbiol. 10: 385-395 (1993).

Sost D, Amrhein N. Substitution of Gly-96 to Ala in the 5-enolpyruvylshikimate-3-phosphate synthase of Klebsiella pneumoniae results in a greatly reduced affinity for the herbicide glyphosate. Arch. Biochem. Biophys. 282: 433-436 (1990).

Soto A, Allona I, Collada C, Guevara MA, Casado R, Rodriguez-Cerezo E, Aragoncillo C, Gomez L. Heterologous expression of a plant small heat-shock protein enhances Escherichia coli viability under heat and cold stress. Plant Physiol. 120: 521-528 (1999).

Soudry E, Ulitzur S, Gepstein S. Accumulation and remobilization of amino acids during senescence of detached and attached leaves: in planta analysis of tryptophan levels by recombinant luminescent bacteria. J. Exp. Bot. 56: 695-702 (2005).

Soupene E, He L, Yan D, Kustu S. Ammonia acquisition in enteric bacteria: physiological role of the ammonium/methylammonium transport B (AmtB) protein. Proc. Natl. Acad. Sci. U.S.A. 95: 7030-7034 (1998).

Soupene E, van Heeswijk WC, Plumbridge J, Stewart V, Bertenthal D, Lee H, Prasad G, Paliy O, Charernnoppakul P, Kustu S. Physiological studies of Escherichia coli strain MG1655: growth defects and apparent cross-regulation of gene expression. J. Bacteriol. 185: 5611-5626 (2003).

Soutourina J, Blanquet S, Plateau P. Role of D-cysteine desulfhydrase in the adaptation of Escherichia coli to D-cysteine. J. Biol. Chem. 276: 40864-40872 (2001).

Souzu H. Fluorescence polarization studies on Escherichia coli membrane stability and its relation to the resistance of the cell to freeze-thawing. II. Stabilization of the membranes by polyamines. Biochim. Biophys. Acta 861: 361-367 (1986).

Sparla F, Fermani S, Falini G, Zaffagnini M, Ripamonti A, Sabatino P, Pupillo P, Trost P. Coenzyme site-directed mutants of photosynthetic A4-GAPDH show selectively reduced NADPH-dependent catalysis, similar to regulatory AB-GAPDH inhibited by oxidized thioredoxin. J. Mol. Biol. 340: 1025-1037 (2004).

Sperling D, Kappler U, Wynen A, Dahl C, Truper HG. Dissimilatory ATP sulfurylase from the hyperthermophilic sulfate reducer Archaeoglobus fulgidus belongs to the group of homo-oligomeric ATP sulfurylases. FEMS Microbiol. Lett. 162: 257-264 (1998).

Spiro S, Guest JR. Regulation and over-expression of the fnr gene of Escherichia coli. J. Gen. Microbiol. 133: 3279-3788 (1987).

Spiro S, Guest JR. FNR and its role in oxygen-regulated gene expression in Escherichia coli. FEMS Microbiol. Rev. 6: 399-428 (1990).

Sprenger GA. Genetics of pentose-phosphate pathway enzymes of Escherichia coli K-12. Arch. Microbiol. 164: 324-330 (1995).

Sprenger GA, Schorken U, Wiegert T, Grolle S, de Graaf AA, Taylor SV, Begley TP, Bringer-Meyer S, Sahm H. Identification of a thiamin-dependent synthase in Escherichia coli required for the formation of the 1-deoxy-D-xylulose 5-phosphate precursor to isoprenoids, thiamin, and pyridoxol. Proc. Natl. Acad. Sci. U.S.A. 94: 12857-12862 (1997).

Sprinzak D, Elowitz MB. Reconstruction of genetic circuits. Nature 438: 443-448 (2005).

Srividhya KV, Krishnaswamy S. A simulation model of Escherichia coli osmoregulatory switch using E-CELL system. BMC Microbiol. 4: 44 (2004).

Stabile H, Curti B, Vanoni MA. Functional properties of recombinant Azospirillum brasilense glutamate synthase, a complex iron-sulfur flavoprotein. Eur. J. Biochem. 267: 2720-2730 (2000).

Stadtman ER, Hohman RJ, Davis JN, Wittenberger M, Chock PB, Rhee SG. Subunit interaction of adenylylated glutamine synthetase. Mol. Biol. Biochem. Biophys. 32: 144-156 (1980).

Stalberg K, Ellerstom M, Ezcurra I, Ablov S, Rask L. Disruption of an overlapping E-box/ABRE motif abolished high transcription of the napA storage-protein promoter in transgenic Brassica napus seeds. Planta 199: 515-519 (1996).

Stalker DM, Hiatt WR, Comai L. A single amino acid substitution in the enzyme 5-enolpyruvylshikimate-3-phosphate synthase confers resistance to the herbicide glyphosate. J. Biol. Chem. 260: 4724-4728 (1985).

Stalmach ME, Grothe S, Wood JM. Two proline porters in Escherichia coli K-12. J. Bacteriol. 156: 481-486 (1983).

Stanley BA, Shantz LM, Pegg AE. Expression of mammalian S-adenosylmethionine decarboxylase in Escherichia coli. Determination of sites for putrescine activation of activity and processing. J. Biol. Chem. 269: 7901-7907 (1994).

Stauffer LT, Fogarty SJ, Stauffer GV. Characterization of the Escherichia coli gcv operon. Gene 142: 17-22 (1994).

Stauffer LT, Ghrist A, Stauffer GV. The Escherichia coli gcvT gene encoding the T-protein of the glycine cleavage enzyme system. DNA Seq. 3: 339-346 (1993).

Stebbins JW, Xu W, Kantrowitz ER. Three residues involved in binding and catalysis in the carbamyl phosphate binding site of Escherichia coli aspartate transcarbamylase. Biochemistry 28: 2592-2600 (1989).

Steegborn C, Messerschmidt A, Laber B, Streber W, Huber R, Clausen T. The crystal structure of cystathionine gamma-synthase from Nicotiana tabacum reveals its substrate and reaction specificity. J. Mol. Biol. 290: 983-996 (1999).

Steen EJ, Chan R, Prasad N, Myers S, Petzold CJ, Redding A, Ouellet M, Keasling JD. Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol. Microb. Cell Fact. 7: 36 (2008).

Steenhoudt O, Keijers V, Okon Y, Vanderleyden J. Identification and characterization of a periplasmic nitrate reductase in Azospirillum brasilense Sp245. Arch. Microbiol. 175: 344-352 (2001).

Steglitz-Morsdorf U, Morsdorf G, Kaltwasser H. Cloning, heterologous expression, and sequencing of the Proteus vulgaris glnAntrBC operon and implications of nitrogen control on heterologous urease expression. FEMS Microbiol. Lett. 106: 157-164 (1993).

Steiert JG, Urbanowski ML, Stauffer LT, Plamann MD, Stauffer GV. Nucleotide sequence of the Salmonella typhimurium glyA gene. DNA Seq. 1: 107-113 (1990).

Steil L, Hoffmann T, Budde I, Volker U, Bremer E. Genome-wide transcriptional profiling analysis of adaptation of Bacillus subtilis to high salinity. J. Bacteriol. 185: 6358-6370 (2003).

Stein DC, Silver LE, Clark VL, Young FE. Cloning genes for proline biosynthesis from Neisseria gonorrhoeae: identification by interspecific complementation of Escherichia coli mutants. J. Bacteriol. 158: 696-700 (1984).

Steiner P, Sauer U. Long-term continuous evolution of acetate resistant Acetobacter aceti. Biotechnol. Bioeng. 84: 40-44 (2003).

Stenberg K, Lindqvist Y. High-level expression, purification, and crystallization of recombinant spinach glycolate oxidase in Escherichia coli. Protein Expr. Purif. 8: 295-298 (1996).

Stenzel O, Teuber M, Drager B. Putrescine N-methyltransferase in Solanum tuberosum L., a calystegine-forming plant. Planta 223: 200-212 (2006).

Stephens CM, Bauerle R. Essential cysteines in 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Escherichia coli. Analysis by chemical modification and site-directed mutagenesis of the phenylalanine-sensitive isozyme. J. Biol. Chem. 267: 5762-5767 (1992).

Stephens CM, Bauerle R. Analysis of the metal requirement of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Escherichia coli. J. Biol. Chem. 266: 20810-20817 (1991).

Stevens RG, Creissen GP, Mullineaux PM. Cloning and characterisation of a cytosolic glutathione reductase cDNA from pea (Pisum sativum L.) and its expression in response to stress. Plant Mol. Biol. 35: 641-654 (1997).

Stevenson CE, Sargent F, Buchanan G, Palmer T, Lawson DM. Crystal structure of the molybdenum cofactor biosynthesis protein MobA from Escherichia coli at near-atomic resolution. Structure Fold. Des. 8: 1115-1125 (2000).

Stewart V. Nitrate regulation of anaerobic respiratory gene expression in Escherichia coli. Mol. Microbiol. 9: 425-434 (1993).

Stewart V. Nitrate- and nitrite-responsive sensors NarX and NarQ of proteobacteria. Biochem. Soc. Trans. 31: 1-10 (2003).

Stewart V, Bledsoe PJ. Fnr-, NarP- and NarL-dependent regulation of transcription initiation from the Haemophilus influenzae Rd napF (periplasmic nitrate reductase) promoter in Escherichia coli K-12. J. Bacteriol. 187: 6928-6935 (2005).

Stewart V, Bledsoe PJ, Chen LL, Cai A. Catabolite repression control of napF (periplasmic nitrate reductase) operon expression in Escherichia coli K-12. J. Bacteriol. 191: 996-1005 (2009).

Stewart V, Bledsoe PJ, Williams SB. Dual overlapping promoters control napF (periplasmic nitrate reductase) operon expression in Escherichia coli K-12. J. Bacteriol. 185: 5862-5870 (2003).

Stewart V, Cali BM. Genetic evidence that NarL function is not required for nitrate regulation of nitrate assimilation in Klebsiella pneumoniae M5al. J. Bacteriol. 172: 4482-4488 (1990).

Stewart V, Lu Y, Darwin AJ. Periplasmic nitrate reductase (NapABC enzyme) supports anaerobic respiration by Escherichia coli K-12. J. Bacteriol. 184: 1314-1323 (2002).

Stewart V, Parales J Jr, Merkel SM. Structure of genes narL and narX of the nar (nitrate reductase) locus in Escherichia coli K-12. J. Bacteriol. 171: 2229-2234 (1989).

Stirling DA, Hulton CS, Waddell L, Park SF, Stewart GS, Booth IR, Higgins CF. Molecular characterization of the proU loci of Salmonella typhimurium and Escherichia coli encoding osmoregulated glycine betaine transport systems. Mol. Microbiol. 3: 1025-1038 (1989).

Stoker PW, O'Leary MH, Boehlein SK, Schuster SM, Richards NG. Probing the mechanism of nitrogen transfer in Escherichia coli asparagine synthetase by using heavy atom isotope effects. Biochemistry 35: 3024-3030 (1996).

Stokes BO, Boyer PD. Rapid transfer of oxygens from inorganic phosphate to glutamine catalyzed by Escherichia coli glutamine synthetase. J. Biol. Chem. 251: 5558-5564 (1976).

Stouthamer AH. Metabolic pathways in Paracoccus denitrificans and closely related bacteria in relation to the phylogeny of prokaryotes. Antonie Van Leeuwenhoek 61: 1-33 (1992).

Stover C, Mayhew MP, Holden MJ, Howard A, Gallagher DT. Crystallization and 1.1-A diffraction of chorismate lyase from Escherichia coli. J. Struct. Biol. 129: 96-99 (2000).

Stover P, Schirch V. Serine hydroxymethyltransferase catalyzes the hydrolysis of 5,10-methenyltetrahydrofolate to 5-formyltetrahydrofolate. J. Biol. Chem. 265: 14227-14233 (1990).

Stranden AM, Roos M, Berger-Bachi B. Glutamine synthetase and heteroresistance in methicillin-resistant Staphylococcus aureus. Microb. Drug Resist. 2: 201-207 (1996).

Strater N, Schnappauf G, Braus G, Lipscomb WN. Mechanisms of catalysis and allosteric regulation of yeast chorismate mutase from crystal structures. Structure 5: 1437-1452 (1997).

Straub PF, Reynolds PH, Althomsons S, Mett V, Zhu Y, Shearer G, Kohl DH. Isolation, DNA sequence analysis, and mutagenesis of a proline dehydrogenase gene (putA) from Bradyrhizobium japonicum. Appl. Environ. Microbiol. 62: 221-229 (1996).

Strauss E, Begley TP. Stereochemical studies on phosphopantothenoylcysteine decarboxylase from Escherichia coli. Bioorg. Med. Chem. Lett. 13: 339-342 (2003).

Strauss E, Begley TP. The antibiotic activity of N-pentylpantothenamide results from its conversion to ethyldethia-coenzyme A, a coenzyme A antimetabolite. J. Biol. Chem. 277: 48205-48209 (2002).

Strauss E, Kinsland C, Ge Y, McLafferty FW, Begley TP. Phosphopantothenoylcysteine synthetase from Escherichia coli. Identification and characterization of the last unidentified coenzyme A biosynthetic enzyme in bacteria. J. Biol. Chem. 276: 13513-13516 (2001).

Streaker ED, Beckett D. The biotin regulatory system: kinetic control of a transcriptional switch. Biochemistry 45: 6417-6425 (2006).

Streicher SL, Bender RA, Magasanik B. Genetic control of glutamine synthetase in Klebiella aerogenes. J. Bacteriol. 121: 320-331 (1975).

Strom AR. Osmoregulation in the model organism Escherichia coli: genes governing the synthesis of glycine betaine and trehalose and their use in metabolic engineering of stress tolerance. J. Biosci. 23: 437-445 (1998).

Strom AR, Kaasen I. Trehalose metabolism in Escherichia coli: stress protection and stress regulation of gene expression. Mol. Microbiol. 8: 205-210 (1993).

Struhl K. Negative control at a distance mediates catabolite repression in yeast. Nature 317: 822-824 (1985).

Stulke J, Hillen W. Carbon catabolite repression in bacteria. Curr. Opin. Microbiol. 2: 195-201 (1999).

Stumpe M, Carsjens JG, Gobel C, Feussner I. Divinyl ether synthesis in garlic bulbs. J. Exp. Bot. 59: 907-915 (2008).

Stutz HE, Quixley KW, McMaster LD, Reid SJ. Co-regulation of the nitrogen-assimilatory gene cluster in Clostridium saccharobutylicum. Microbiology 153: 3081-3090 (2007).

Styrvold OB, Falkenberg P, Landfald B, Eshoo MW, Bjornsen T, Strom AR. Selection, mapping, and characterization of osmoregulatory mutants of Escherichia coli blocked in the choline-glycine betaine pathway. J. Bacteriol. 165: 856-863 (1986).

Su Q, Frick G, Armstrong G, Apel K. POR C of Arabidopsis thaliana: a third light- and NADPH-dependent protochlorophyllide oxidoreductase that is differentially regulated by light. Plant Mol. Biol. 47: 805-813 (2001).

Subrahmanyam S, Cronan JE Jr. Overproduction of a functional fatty acid biosynthetic enzyme blocks fatty acid synthesis in Escherichia coli. J. Bacteriol. 180: 4596-4602 (1998).

Subramaniam K, Abbo S, Ueng PP. Isolation of two differentially expressed wheat ACC synthase cDNAs and the characterization of one of their genes with root-predominant expression. Plant Mol. Biol. 31: 1009-1020 (1996).

Sue M, Yamazaki K, Yajima S, Nomura T, Matsukawa T, Iwamura H, Miyamoto T. Molecular and structural characterization of hexameric {beta}-D-glucosidases in wheat and rye. Plant Physiol. 141: 1237-1247 (2006).

Suen KL, Choi JH. Isolation and sequence analysis of a cDNA clone for a carrot calcium-dependent protein kinase: homology to calcium/calmodulin-dependent protein kinases and to calmodulin. Plant Mol. Biol. 17: 581-590 (1991).

Sugahara T, Liu CC, Pai TG, Collodi P, Suiko M, Sakakibara Y, Nishiyama K, Liu MC. Sulfation of hydroxychlorobiphenyls. Molecular cloning, expression, and functional characterization of zebrafish SULT1 sulfotransferases. Eur. J. Biochem. 270: 2404-2411 (2003).

Sugiyama A, Kato H, Nishioka T, Oda J. Overexpression and purification of asparagine synthetase from Escherichia coli. Biosci. Biotechnol. Biochem. 56: 376-379 (1992).

Sullivan ML, Hatfield RD, Thoma SL, Samac DA. Cloning and characterization of red clover polyphenol oxidase cDNAs and expression of active protein in Escherichia coli and transgenic alfalfa. Plant Physiol. 136: 3234-3244 (2004).

Sullivan TD, Kaneko Y. The maize brittle 1 gene encodes amyloplast membrane polypeptides. Planta 196: 477-484 (1995).

Sun J, Ke J, Johnson JL, Nikolau BJ, Wurtele ES. Biochemical and molecular biological characterization of CAC2, the Arabidopsis thaliana gene coding for the biotin carboxylase subunit of the plastidic acetyl-coenzyme A carboxylase. Plant Physiol. 115: 1371-1383 (1997).

Sun J, Kelemen GH, Fernandez-Abalos JM, Bibb MJ. Green fluorescent protein as a reporter for spatial and temporal gene expression in Streptomyces coelicolor A3(2). Microbiology 145: 2221-2227 (1999).

Sun K, Camardella L, Di Prisco G, Herve G. Properties of aspartate transcarbamylase from TAD1, a psychrophilic bacterial strain isolated from Antarctica. FEMS Microbiol. Lett. 164: 375-382 (1998).

Sun L, Ruppert M, Sheludko Y, Warzecha H, Zhao Y, Stockigt J. Purification, cloning, functional expression and characterization of perakine reductase: the first example from the AKR enzyme family, extending the alkaloidal network of the plant Rauvolfia. Plant Mol. Biol. 67: 455-467 (2008).

Sun Y, Macrae TH. Characterization of novel sequence motifs within N- and C-terminal extensions of p26, a small heat shock protein from Artemia franciscana. FEBS J. 272: 5230-5243 (2005).

Sun Y, Thompson M, Lin G, Butler H, Gao Z, Thornburgh S, Yau K, Smith DA, Shukla VK. Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from maize: molecular and biochemical characterization. Plant Physiol. 144: 1278-1291 (2007).

Sundaram AK, Howe DL, Sheflyan GY, Woodard RW. Probing the potential metal binding site in Escherichia coli 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (phenylalanine-sensitive). FEBS Lett. 441: 195-199 (1998).

Sundaram S, Rathinasabapathi B, Ma LQ, Rosen BP. An arsenate-activated glutaredoxin from the arsenic hyperaccumulator fern Pteris vittata L. regulates intracellular arsenite. J. Biol. Chem. 283: 6095-6101 (2008).

Sundaram S, Wu S, Ma LQ, Rathinasabapathi B. Expression of a Pteris vittata glutaredoxin PvGRX5 in transgenic Arabidopsis thaliana increases plant arsenic tolerance and decreases arsenic accumulation in the leaves. Plant Cell Environ. 32: 851-858 (2009).

Surber MW, Maloy S. Regulation of flavin dehydrogenase compartmentalization: requirements for PutA-membrane association in Salmonella typhimurium. Biochim. Biophys. Acta 1421: 5-18 (1999).

Sutherland L, Cairney J, Elmore MJ, Booth IR, Higgins CF. Osmotic regulation of transcription: induction of the proU betaine transport gene is dependent on accumulation of intracellular potassium. J. Bacteriol. 168: 805-814 (1986).

Suthers PF, Burgard AP, Dasika MS, Nowroozi F, Van Dien S, Keasling JD, Maranas CD. Metabolic flux elucidation for large-scale models using (13)C labeled isotopes. Metab. Eng. 9: 387-405 (2007).

Suvorov AN, Flores AE, Ferrieri P. Cloning of the glutamine synthetase gene from group B streptococci. Infect. Immun. 65: 191-196 (1997).

Suzuki H, Achnine L, Xu R, Matsuda SP, Dixon RA. A genomics approach to the early stages of triterpene saponin biosynthesis in Medicago truncatula. Plant J. 32: 1033-1048 (2002).

Suzuki H, Nakayama T, Yonekura-Sakakibara K, Fukui Y, Nakamura N, Yamaguchi MA, Tanaka Y, Kusumi T, Nishino T. cDNA cloning, heterologous expressions, and functional characterization of malonyl-coenzyme A:anthocyanidin 3-O-glucoside-6"-O-malonyltransferase from Dahlia flowers. Plant Physiol. 130: 2142-2151 (2002).

Suzuki H, Ohnishi Y, Furusho Y, Sakuda S, Horinouchi S. Novel benzene ring biosynthesis from C3 and C4 primary metabolites by two enzymes. J. Biol. Chem. 281: 36944-36951 (2006).

Suzuki I, Kanesaki Y, Hayashi H, Hall JJ, Simon WJ, Slabas AR, Murata N. The histidine kinase hik34 is involved in thermotolerance by regulating the expression of heat shock genes in Synechocystis. Plant Physiol. 138: 1409-1421 (2005).

Suzuki K, Suzuki Y, Kitamura S. Cloning and expression of a UDP-glucuronic acid decarboxylase gene in rice. J. Exp. Bot. 54: 1997-1999 (2003).

Suzuki K, Yamashita I, Tanaka N. Tobacco plants were transformed by Agrobacterium rhizogenes infection during their evolution. Plant J. 32: 775-787 (2002).

Svensson AS AS, Rasmusson AG. Light-dependent gene expression for proteins in the respiratory chain of potato leaves. Plant J. 28: 73-82 (2001).

Sweetlove LJ, Burrell MM, ap Rees T. Starch metabolism in tubers of transgenic potato (Solanum tuberosum) with increased ADPglucose pyrophosphorylase. Biochem. J. 320: 493-498 (1996).

Sweetlove LJ, Burrell MM, ap Rees T. Characterization of transgenic potato (Solanum tuberosum) tubers with increased ADPglucose pyrophosphorylase. Biochem. J. 320: 487-492 (1996).

Swift S, Kuhn J, Stewart GS. Selection and analysis of non-interactive mutants in the Escherichia coli tryptophan synthase alpha subunit. Mol. Gen. Genet. 233: 129-135 (1992).

Sycheva EV, Iampol'skaia TA, Preobrazhenskaia ES, Novikova AE, Matrosov NG, Stoinova NV. Overproduction of noncanonical amino acids by Escherichia coli cells. Mikrobiologiia 76: 805-812 (2007).

Symmons MF, Williams MG, Luisi BF, Jones GH, Carpousis AJ. Running rings around RNA: a superfamily of phosphate-dependent RNases. Trends Biochem. Sci. 27: 11-18 (2002).

Szczesiul M, Wampler DE. Regulation of a metabolic system in vitro: synthesis of threonine from aspartic acid. Biochemistry 15: 2236-2244 (1976).

Szederkenyi J, Komor E, Schobert C. Cloning of the cDNA for glutaredoxin, an abundant sieve-tube exudate protein from Ricinus communis L. and characterisation of the glutathione-dependent thiol-reduction system in sieve tubes. Planta 202: 349-356 (1997).

Szegedi SS, Garrow TA. Oligomerization is required for betaine-homocysteine S-methyltransferase function. Arch. Biochem. Biophys. 426: 32-42 (2004).

Szerszen JB, Szczyglowski K, Bandurski RS. iaglu, a gene from Zea mays involved in conjugation of growth hormone indole-3-acetic acid. Science 265: 1699-1701 (1994).

Tabor CW, Tabor H, Tyagi AK, Cohn MS. The biochemistry, genetics, and regulation of polyamine biosynthesis in Saccharomyces cerevisiae. Fed. Proc. 41: 3084-3088 (1982).

Tabor H. Polyamine biosynthesis in Escherichia coli: construction of polyamine-deficient mutants. Med. Biol. 59: 389-393 (1981).

Tada S, Volrath S, Guyer D, Scheidegger A, Ryals J, Ohta D, Ward E. Isolation and characterization of cDNAs encoding imidazoleglycerolphosphate dehydratase from Arabidopsis thaliana. Plant Physiol. 105: 579-583 (1994).

Tagkopoulos I, Liu YC, Tavazoie S. Predictive behavior within microbial genetic networks. Science 320: 1313-1317 (2008).

Tagmount A, Berken A, Terry N. An essential role of S-adenosyl-L-methionine:L-methionine S-methyltransferase in selenium volatilization by plants. Methylation of selenomethionine to selenium-methyl-L-selenium-methionine, the precursor of volatile selenium. Plant Physiol. 130: 847-856 (2002).

Taguchi G, Shitchi Y, Shirasawa S, Yamamoto H, Hayashida N. Molecular cloning, characterization, and downregulation of an acyltransferase that catalyzes the malonylation of flavonoid and naphthol glucosides in tobacco cells. Plant J. 42: 481-491 (2005).

Tai CH, Cook PF. O-acetylserine sulfhydrylase. Advan. Enzymol. Relat. Areas Mol. Biol. 74: 185-239 (2000).

Tai H, Jaworski JG. 3-Ketoacyl-acyl carrier protein synthase III from spinach (Spinacia oleracea) is not similar to other condensing enzymes of fatty acid synthase. Plant Physiol. 103: 1361-1367 (1993).

Taji T, Ohsumi C, Iuchi S, Seki M, Kasuga M, Kobayashi M, Yamaguchi-Shinozaki K, Shinozaki K. Important roles of drought- and cold-inducible genes for galactinol synthase in stress tolerance in Arabidopsis thaliana. Plant J. 29: 417-426 (2002).

Takabatake R, Hata S, Taniguchi M, Kouchi H, Sugiyama T, Izui K. Isolation and characterization of cDNAs encoding mitochondrial phosphate transporters in soybean, maize, rice, and Arabidopis. Plant Mol. Biol. 40: 479-486 (1999).

Takagi H, Yoshioka K, Awano N, Nakamori S, Ono B. Role of Saccharomyces cerevisiae serine O-acetyltransferase in cysteine biosynthesis. FEMS Microbiol. Lett. 218: 291-297 (2003).

Takahara K, Akashi K, Yokota A. Purification and characterization of glutamate N-acetyltransferase involved in citrulline accumulation in wild watermelon. FEBS J. 272: 5353-5364 (2005).

Takahashi T, Mu JH, Gasch A, Chua NH. Identification by PCR of receptor-like protein kinases from Arabidopsis flowers. Plant Mol. Biol. 37: 587-596 (1998).

Takahashi Y, Hasezawa S, Kusaba M, Nagata T. Expression of the auxin-regulated parA gene in transgenic tobacco and nuclear localization of its gene products. Planta 196: 111-117 (1995).

Takakura Y, Ito T, Saito H, Inoue T, Komari T, Kuwata S. Flower-predominant expression of a gene encoding a novel class I chitinase in rice (Oryza sativa L.). Plant Mol. Biol. 42: 883-897 (2000).

Takamura Y, Nomura G. Changes in the intracellular concentration of acetyl-CoA and malonyl-CoA in relation to the carbon and energy metabolism of Escherichia coli K12. J. Gen. Microbiol. 134: 2249-2253 (1988).

Takeda Si, Matsushika A, Mizuno T. Repression of the gene encoding succinate dehydrogenase in response to glucose is mediated by the EIICB(Glc) protein in Escherichia coli. J. Biochem. (Tokyo) 126: 354-360 (1999).

Takezawa D. A rapid induction by elicitors of the mRNA encoding CCD-1, a 14kDa Ca2+ -binding protein in wheat cultured cells. Plant Mol. Biol. 42: 807-817 (2000).

Takezawa D, Ramachandiran S, Paranjape V, Poovaiah BW. Dual regulation of a chimeric plant serine/threonine kinase by calcium and calcium/calmodulin. J. Biol. Chem. 271: 8126-8132 (1996).

Takubo K, Morikawa T, Nonaka Y, Mizutani M, Takenaka S, Takabe K, Takahashi MA, Ohta D. Identification and molecular characterization of mitochondrial ferredoxins and ferredoxin reductase from Arabidopsis. Plant Mol. Biol. 52: 817-830 (2003).

Talibart R, Jebbar M, Gouesbet G, Himdi-Kabbab S, Wroblewski H, Blanco C, Bernard T. Osmoadaptation in rhizobia: ectoine-induced salt tolerance. J. Bacteriol. 176: 5210-5217 (1994).

Talibart R, Le Henaff M, Bernard T, Wroblewski H. Identification of bacterial periplasmic glycine betaine-binding protein after electrophoresis and affinity labeling. J. Biochem. Biophys. Methods 21: 155-164 (1990).

Tamakoshi M, Yamagishi A, Oshima T. The organization of the leuC, leuD and leuB genes of the extreme thermophile Thermus thermophilus. Gene 222: 125-132 (1998).

Tamakoshi M, Yaoi T, Oshima T, Yamagishi A. An efficient gene replacement and deletion system for an extreme thermophile, Thermus thermophilus. FEMS Microbiol. Lett. 173: 431-437 (1999).

Tamas MJ, Luyten K, Sutherland FCW, Hernandez A, Albertyn J, Valadi H, Li H, Prior BA, Killan SG, Ramos J, Gustafsson L, Thevelein JM, Hohmann S. Fps1p controls the accumulation and release of the compatible solute glycerol in yeast osmoregulation. Mol. Microbiol. 31: 1087-1104 (1999).

Tamayo MC, Rufat M, Bravo JM, San Segundo B. Accumulation of a maize proteinase inhibitor in response to wounding and insect feeding, and characterization of its activity toward digestive proteinases of Spodoptera littoralis larvae. Planta 211: 62-71 (2000).

Tambasco-Studart M, Titiz O, Raschle T, Forster G, Amrhein N, Fitzpatrick TB. Vitamin B6 biosynthesis in higher plants. Proc. Natl. Acad. Sci. U.S.A. 102: 13687-13692 (2005).

Tameling WI, Elzinga SD, Darmin PS, Vossen JH, Takken FL, Haring MA, Cornelissen BJ. The tomato R gene products I-2 and MI-1 are functional ATP binding proteins with ATPase activity. Plant Cell 14: 2929-2939 (2002).

Tanaka K, Ueguchi C, Mizuno T. Importance of stereospecific positioning of the upstream cis-acting DNA element containing a curved DNA structure for the functioning of the Escherichia coli proV promoter. Biosci. Biotechnol. Biochem. 58: 1097-1101 (1994).

Tanapongpipat S, Reid E, Cole JA, Crooke H. Transcriptional control and essential roles of the Escherichia coli ccm gene products in formate-dependent nitrite reduction and cytochrome c synthesis. Biochem. J. 334: 355-365 (1998).

Tang G, Zhu-Shimoni JX, Amir R, Zchori IB, Galili G. Cloning and expression of an Arabidopsis thaliana cDNA encoding a monofunctional aspartate kinase homologous to the lysine-sensitive enzyme of Escherichia coli. Plant Mol. Biol. 34: 287-293 (1997).

Tang X, Ezaki S, Fujiwara S, Takagi M, Atomi H, Imanaka T. The tryptophan biosynthesis gene cluster trpCDEGFBA from Pyrococcus kodakaraensis KOD1 is regulated at the transcriptional level and expressed as a single mRNA. Mol. Gen. Genet. 262: 815-821 (1999).

Tang XF, Ezaki S, Atomi H, Imanaka T. Anthranilate synthase without an LLES motif from a hyperthermophilic archaeon is inhibited by tryptophan. Biochem. Biophys. Res. Commun. 281: 858-865 (2001).

Tang XF, Ezaki S, Atomi H, Imanaka T. Biochemical analysis of a thermostable tryptophan synthase from a hyperthermophilic archaeon. Eur. J. Biochem. 267: 6369-6377 (2000).

Tanigawa R, Shirokane M, Maeda Si S, Omata T, Tanaka K, Takahashi H. Transcriptional activation of NtcA-dependent promoters of Synechococcus sp. PCC 7942 by 2-oxoglutarate in vitro. Proc. Natl. Acad. Sci. U.S.A. 99: 4251-4255 (2002).

Tanner W, Caspari T. Membrane transport carriers. Annu. Rev. Plant Physiol. Plant Mol. Biol. 47: 595-626 (1996).

Tao L, Jackson RE, Cheng Q. Directed evolution of copy number of a broad host range plasmid for metabolic engineering. Metab. Eng. 7: 10-17 (2005).

Taoka A, Yoshimatsu K, Kanemori M, Fukumori Y. Nitrate reductase from the magnetotactic bacterium Magnetospirillum magnetotacticum MS-1: purification and sequence analyses. Can. J. Microbiol. 49: 197-206 (2003).

Tarrago T, Martinez I, Torrent M, Codina A, Giralt E, Puigdomenech P, Ludevid D. The fuc1 gene product (20 kDa FUC1) of Pisum sativum has no alpha-L-fucosidase activity. Plant Mol. Biol. 51: 877-884 (2003).

Tartakovsky B, Sheintuch M, Hilmer J-M, Scheper T. Modelling of E. coli fermentations: comparison of multicompartment and variable structure models. Bioprocess Engineering 16: 323-329 (1997).

Tarun AS, Lee JS, Theologis A. Random mutagenesis of 1-aminocyclopropane-1-carboxylate synthase: a key enzyme in ethylene biosynthesis. Proc. Natl. Acad. Sci. U.S.A. 95: 9796-9801 (1998).

Tarun AS, Theologis A. Complementation analysis of mutants of 1-aminocyclopropane- 1-carboxylate synthase reveals the enzyme is a dimer with shared active sites. J. Biol. Chem. 273: 12509-12514 (1998).

Tatarko M, Romeo T. Disruption of a global regulatory gene to enhance central carbon flux into phenylalanine biosynthesis in Escherichia coli. Curr. Microbiol. 43: 26-32 (2001).

Tatur J, Hagen WR. The dinuclear iron-oxo ferroxidase center of Pyrococcus furiosus ferritin is a stable prosthetic group with unexpectedly high reduction potentials. FEBS Lett. 579: 4729-4732 (2005).

Tauler A, Rosenberg AH, Colosia A, Studier FW, Pilkis SJ. Expression of the bisphosphatase domain of rat liver 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 85: 6642-6646 (1988).

Tavladoraki P, Rossi MN, Saccuti G, Perez-Amador MA, Polticelli F, Angelini R, Federico R. Heterologous expression and biochemical characterization of a polyamine oxidase from Arabidopsis thaliana involved in polyamine back-conversion. Plant Physiol. 141: 1519-1532 (2006).

Taylor AB, Stoj CS, Ziegler L, Kosman DJ, Hart PJ. The copper-iron connection in biology: structure of the metallo-oxidase Fet3p. Proc. Natl. Acad. Sci. U.S.A. 102: 15459-15464 (2005).

Taylor CJ, Bain LA, Richardson DJ, Spiro S, Russell DA. Construction of a whole-cell gene reporter for the fluorescent bioassay of nitrate. Anal. Biochem. 328: 60-66 (2004).

Taylor JL, Zaharia LI, Chen H, Anderson E, Abrams SR. Biotransformation of adenine and cytokinins by the rhizobacterium Serratia proteamaculans. Phytochemistry 67: 1887-1894 (2006).

Taylor MA, Ross HA, McRae D, Wright F, Viola R, Davies HV. Copy-DNA cloning and characterisation of a potato alpha-glucosidase: expression in Escherichia coli and effects of down-regulation in transgenic potato. Planta 213: 258-264 (2001).

Tei H, Murata K, Kimura A. Molecular cloning of the cys genes (cysC, cysD, cysH, cysI, cysJ, and cysG) responsible for cysteine biosynthesis in Escherichia coli K-12. Biotechnol. Appl. Biochem. 12: 212-216 (1990).

Teller JH, Powers SG, Snell EE. Ketopantoate hydroxymethyltransferase. I. Purification and role in pantothenate biosynthesis. J. Biol. Chem. 251: 3780-3785 (1976).

Temple CA, Rajagopalan KV. Mechanism of assembly of the bis(molybdopterin guanine dinucleotide)molybdenum cofactor in Rhodobacter sphaeroides dimethyl sulfoxide reductase. J. Biol. Chem. 275: 40202-40210 (2000).

Teplyakov A, Lim K, Zhu PP, Kapadia G, Chen CC, Schwartz J, Howard A, Reddy PT, Peterkofsky A, Herzberg O. Structure of phosphorylated enzyme I, the phosphoenolpyruvate:sugar phosphotransferase system sugar translocation signal protein. Proc. Natl. Acad. Sci. U.S.A. 103: 16218-16223 (2006).

Teponno RB, Tapondjou AL, Gatsing D, Djoukeng JD, Abou-Mansour E, Tabacchi R, Tane P, Stoekli-Evans H, Lontsi D. Bafoudiosbulbins A, and B, two anti-salmonellal clerodane diterpenoids from Dioscorea bulbifera L. var sativa. Phytochemistry 67: 1957-1963 (2006).

Terp N, Gobel C, Brandt A, Feussner I. Lipoxygenases during Brassica napus seed germination. Phytochemistry 67: 2030-2040 (2006).

Teusink B, Baganz F, Westerhoff HV, Oliver SG. Metabolic control analysis as a tool in the elucidation of the function of novel genes Yeast Gene Anal. 26: 297-336 (1998).

Teusink B, Wiersma A, Molenaar D, Francke C, de Vos WM, Siezen RJ, Smid EJ. Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model. J. Biol. Chem. 281: 40041-40048 (2006).

Tewari YB, Jensen PY, Kishore N, Mayhew MP, Parsons JF, Eisenstein E, Goldberg RN. Thermodynamics of reactions catalyzed by PABA synthase. Biophys. Chem. 96: 33-51 (2002).

Textor S, Wendisch VF, de Graaf AA, Muller U, Linder MI, Linder D, Buckel W. Propionate oxidation in Escherichia coli: evidence for operation of a methylcitrate cycle in bacteria. Arch. Microbiol. 168: 428-436 (1997).

Thanbichler M, Neuhierl B, Bock A. S-methylmethionine metabolism in Escherichia coli. J. Bacteriol. 181: 662-665 (1999).

Thelen JJ, Mekhedov S, Ohlrogge JB. Brassicaceae express multiple isoforms of biotin carboxyl carrier protein in a tissue-specific manner. Plant Physiol. 125: 2016-2028 (2001).

Thieffry D, Huerta AM, Perez-Rueda E, Collado-Vides J. From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. Bioessays 20: 433-440 (1998).

Thierbach G, Kalinowski J, Bachmann B, Puhler A. Cloning of a DNA fragment from Corynebacterium glutamicum conferring aminoethyl cysteine resistance and feedback resistance to aspartokinase. Appl. Microbiol. Biotechnol. 32: 443-448 (1990).

Thilmony R, Underwood W, He SY. Genome-wide transcriptional analysis of the Arabidopsis thaliana interaction with the plant pathogen Pseudomonas syringae pv. tomato DC3000 and the human pathogen Escherichia coli O157:H7. Plant J. 46: 34-53 (2006).

Thoden JB, Raushel FM, Benning MM, Rayment I, Holden HM. The structure of carbamoyl phosphate synthetase determined to 2.1 A resolution. Acta Crystallogr. D. Biol. Crystallogr. 55: 8-24 (1999).

Thoden JB, Raushel FM, Wesenberg G, Holden HM. The binding of inosine monophosphate to Escherichia coli carbamoyl phosphate synthetase. J. Biol. Chem. 274: 22502-22507 (1999).

Thoden JB, Wesenberg G, Raushel FM, Holden HM. Carbamoyl phosphate synthetase: closure of the B-domain as a result of nucleotide binding. Biochemistry 38: 2347-2357 (1999).

Tholema N, Vor der Bruggen M, Maser P, Nakamura T, Schroeder JI, Kobayashi H, Uozumi N, Bakker EP. All four putative selectivity filter glycine residues in KtrB are essential for high affinity and selective K+ uptake by the KtrAB system from Vibrio alginolyticus. J. Biol. Chem. 280: 41146-41154 (2005).

Tholl D, Chen F, Petri J, Gershenzon J, Pichersky E. Two sesquiterpene synthases are responsible for the complex mixture of sesquiterpenes emitted from Arabidopsis flowers. Plant J. 42: 757-771 (2005).

Tholl D, Kish CM, Orlova I, Sherman D, Gershenzon J, Pichersky E, Dudareva N. Formation of monoterpenes in Antirrhinum majus and Clarkia breweri flowers involves heterodimeric geranyl diphosphate synthases. Plant Cell 16: 977-992 (2004).

Thoma R, Obmolova G, Lang DA, Schwander M, Jeno P, Sterner R, Wilmanns M. Efficient expression, purification and crystallisation of two hyperthermostable enzymes of histidine biosynthesis. FEBS Lett. 454: 1-6 (1999).

Thomas A, Hinsen K, Field MJ, Perahia D. Tertiary and quaternary conformational changes in aspartate transcarbamylase: a normal mode study. Proteins 34: 96-112 (1999).

Thomas D, Barbey R, Surdin-Kerjan Y. Evolutionary relationships between yeast and bacterial homoserine dehydrogenases. FEBS Lett. 323: 289-293 (1993).

Thomas D, Barbey R, Surdin-Kerjan Y. Gene-enzyme relationship in the sulfate assimilation pathway of Saccharomyces cerevisiae. Study of the 3'-phosphoadenylylsulfate reductase structural gene. J. Biol. Chem. 265: 15518-15524 (1990).

Thomas D, Becker A, Surdin-Kerjan Y. Reverse methionine biosynthesis from S-adenosylmethionine in eukaryotic cells. J. Biol. Chem. 275: 40718-40724 (2000).

Thomas D, Surdin-Kerjan Y. SAM1, the structural gene for one of the S-adenosylmethionine synthetases in Saccharomyces cerevisiae. Sequence and expression. J. Biol. Chem. 262: 16704-16709 (1987).

Thomas D, Surdin-Kerjan Y. Metabolism of sulfur amino acids in Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 61: 503-532 (1997).

Thomas G, Potter L, Cole JA. The periplasmic nitrate reductase from Escherichia coli: a heterodimeric molybdoprotein with a double-arginine signal sequence and an unusual leader peptide cleavage site. FEMS Microbiol. Lett. 174: 167-171 (1999).

Thompson D, Lazennec C, Plateau P, Simonson T. Probing electrostatic interactions and ligand binding in aspartyl-tRNA synthetase through site-directed mutagenesis and computer simulations. Proteins 71: 1450-1460 (2008).

Thulasiram HV, Poulter CD. Farnesyl diphosphate synthase: the art of compromise between substrate selectivity and stereoselectivity. J. Am. Chem. Soc. 128: 15819-15823 (2006).

Tian ZX, Li QS, Buck M, Kolb A, Wang YP. The CRP-cAMP complex and downregulation of the glnAp2 promoter provides a novel regulatory linkage between carbon metabolism and nitrogen assimilation in Escherichia coli. Mol. Microbiol. 41: 911-924 (2001).

Tibbot BK, Henson CA, Skadsen RW. Expression of enzymatically active, recombinant barley alpha-glucosidase in yeast and immunological detection of alpha-glucosidase from seed tissue. Plant Mol. Biol. 38: 379-391 (1998).

Tishkov VI, Galkin AG, Fedorchuk VV, Savitsky PA, Rojkova AM, Gieren H, Kula MR. Pilot scale production and isolation of recombinant NAD+- and NADP+-specific formate dehydrogenases. Biotechnol. Bioeng. 64: 187-193 (1999).

Tiss A, Barre O, Michaud-Soret I, Forest E. Characterization of the DNA-binding site in the ferric uptake regulator protein from Escherichia coli by UV crosslinking and mass spectrometry. FEBS Lett. 579: 5454-5460 (2005).

Tissier AF, Lopez MF, Signer ER. Purification and characterization of a DNA strand transferase from broccoli. Plant Physiol. 108: 379-386 (1995).

Tissot G, Pepin R, Job D, Douce R, Alban C. Purification and properties of the chloroplastic form of biotin holocarboxylase synthetase from Arabidopsis thaliana overexpressed in Escherichia coli. Eur. J. Biochem. 258: 586-596 (1998).

Tkachenko AG, Chudinov AA, Churilova NS. The role of intracellular pool of polyamines in the regulation of metabolism in Escherichia coli during aerobic-anaerobic transitions. Mikrobiologiia 58: 709-715 (1989).

Tobey KL, Grant GA. The nucleotide sequence of the serA gene of Escherichia coli and the amino acid sequence of the encoded protein, D-3-phosphoglycerate dehydrogenase. J. Biol. Chem. 261: 12179-12183 (1986).

Toda K, Takano H, Nozaki J, Kuroiwa T. The second serine acetyltransferase, bacterial-type O-acetylserine (thiol) lyase and eukaryotic-type O-acetylserine (thiol) lyase from the primitive red alga Cyanidioschyzon merolae. J. Plant Res. 114: 291-300 (2001).

Todd CD, Gifford DJ. The role of the megagametophyte in maintaining loblolly pine (Pinus taeda L.) seedling arginase gene expression in vitro. Planta 215: 110-118 (2002).

Todd JD, Rogers R, Li YG, Wexler M, Bond PL, Sun L, Curson AR, Malin G, Steinke M, Johnston AW. Structural and regulatory genes required to make the gas dimethyl sulfide in bacteria. Science 315: 666-669 (2007).

Todhunter JA, Purich DL. Use of the sodium borohydride reduction technique to identify a gamma-glutamyl phosphate intermediary in the Escherichia coli glutamine synthetase reaction. J. Biol. Chem. 250: 3505-3509 (1975).

Toh H, Kawamura T, Izui K. Molecular evolution of phosphoenolpyruvate carboxylase. Plant Cell Environ. 17: 31-43 (1994).

Toledano MB, Kumar C, Le Moan N, Spector D, Tacnet F. The system biology of thiol redox system in Escherichia coli and yeast: differential functions in oxidative stress, iron metabolism and DNA synthesis. FEBS Lett. 581: 3598-3607 (2007).

Tomita M. Whole-cell simulation: a grand challenge of the 21st century. Trends Biotechnol. 19: 205-210 (2001).

Toms AV, Kinsland C, McCloskey DE, Pegg AE, Ealick SE. Evolutionary links as revealed by the structure of Thermotoga maritima S-adenosylmethionine decarboxylase. J. Biol. Chem. 279: 33837-33846 (2004).

Tong CG, Reichler S, Blumenthal S, Balk J, Hsieh HL, Roux SJ. Light regulation of the abundance of mRNA encoding a nucleolin-like protein localized in the nucleoli of pea nuclei. Plant Physiol. 114: 643-652 (1997).

Tonsor SJ, Alonso-Blanco C, Koornneef M. Gene function beyond the single trait: natural variation, gene effects, and evolutionary ecology in Arabidopsis thaliana. Plant Cell Environ. 28: 2-20 (2005).

Tormay P, Wilting R, Lottspeich F, Mehta PK, Christen P, Bock A. Bacterial selenocysteine synthase--structural and functional properties. Eur. J. Biochem. 254: 655-661 (1998).

Tovkach A, Zeevi V, Tzfira T. A toolbox and procedural notes for characterizing novel zinc finger nucleases for genome editing in plant cells. Plant J. 57: 747-757 (2009).

Toyomasu T, Kawaide H, Mitsuhashi W, Inoue Y, Kamiya Y. Phytochrome regulates gibberellin biosynthesis during germination of photoblastic lettuce seeds. Plant Physiol. 118: 1517-1523 (1998).

Tozaki H, Kobe T, Aihara K, Iwasaki H. An attempt to reveal a role of a transcription/translation feedback loop in the cyanobacterial KaiC protein-based circadian system by using a semi-synthetic method. Int. J. Bioinform. Res. Appl. 4: 435-444 (2008).

Tramonti A, De Biase D, Giartosio A, Bossa F, John RA. The roles of His-167 and His-275 in the reaction catalyzed by glutamate decarboxylase from Escherichia coli. J. Biol. Chem. 273: 1939-1945 (1998).

Tramonti A, De Canio M, Delany I, Scarlato V, De Biase D. Mechanisms of transcription activation exerted by GadX and GadW at the gadA and gadBC gene promoters of the glutamate-based acid resistance system in Escherichia coli. J. Bacteriol. 188: 8118-8127 (2006).

Tramonti A, John RA, Bossa F, De Biase D. Contribution of Lys276 to the conformational flexibility of the active site of glutamate decarboxylase from Escherichia coli. Eur. J. Biochem. 269: 4913-4920 (2002).

Tran LM, Brynildsen MP, Kao KC, Suen JK, Liao JC. gNCA: a framework for determining transcription factor activity based on transcriptome: identifiability and numerical implementation. Metab. Eng. 7: 128-141 (2005).

Tran QH, Arras T, Becker S, Holighaus G, Ohlberger G, Unden G. Role of glutathione in the formation of the active form of the oxygen sensor FNR ([4Fe-4S].FNR) and in the control of FNR function. Eur. J. Biochem. 267: 4817-4824 (2000).

Tregoning JS, Nixon P, Kuroda H, Svab Z, Clare S, Bowe F, Fairweather N, Ytterberg J, van Wijk KJ, Dougan G, Maliga P. Expression of tetanus toxin fragment C in tobacco chloroplasts. Nucleic Acids Res. 31: 1174-1179 (2003).

Treiber N, Schulz GE. Structure of 2,6-dihydroxypyridine 3-hydroxylase from a nicotine-degrading pathway. J. Mol. Biol. 379: 94-104 (2008).

Tribe DE, Pittard J. Hyperproduction of tryptophan by Escherichia coli: genetic manipulation of the pathways leading to tryptophan formation. Appl. Environ. Microbiol. 38: 181-190 (1979).

Trinh CT, Unrean P, Srienc F. A minimal Escherichia coli cell for most efficient ethanol production from hexoses and pentoses. Appl. Environ. Microbiol. 74: 3634-3643 (2008).

Tripathi AK, Mishra BM. Isolation and cloning of a Azospirillum lipoferum locus that complements Escherichia coli proU mutant. FEMS Microbiol. Lett. 162: 241-247 (1998).

Trotel-Aziz P, Niogret MF, Larher F. Proline level is partly under the control of abscisic acid in canola leaf discs during recovery from hyper-osmotic stress. Physiol. Plant. 110: 376-383 (2000).

Trummler K, Wajant H. Molecular cloning of acetone cyanohydrin lyase from flax (Linum usitatissimum). Definition of a novel class of hydroxynitrile lyases. J. Biol. Chem. 272: 4770-4774 (1997).

Tsai CJ, Ma BY, Kumar S, Wolfson H, Nussinov R. Protein folding: Binding of conformationally fluctuating building blocks via population selection. Crit. Rev. Biochem. Mol. Biol. 36: 399-433 (2001).

Tsang ML. Assimilatory sulfate reduction in Escherichia coli: identification of the alternate cofactor for adenosine 3'-phosphate 5'-phosphosulfate reductase as glutaredoxin. J. Bacteriol. 146: 1059-1066 (1981).

Tsang ML, Schiff JA. Assimilatory sulfate reduction in an Escherichia coli mutant lacking thioredoxin activity. J. Bacteriol. 134: 131-138 (1978).

Tsang ML, Schiff JA. Sulfate-reducing pathway in Escherichia coli involving bound intermediates. J. Bacteriol. 125: 923-933 (1976).

Tsatskis Y, Khambati J, Dobson M, Bogdanov M, Dowhan W, Wood JM. The osmotic activation of transporter ProP is tuned by both its C-terminal coiled-coil and osmotically induced changes in phospholipid composition. J. Biol. Chem. 280: 41387-41394 (2005).

Tseng HC, Martin CH, Nielsen DR, Prather KL. Metabolic engineering of Escherichia coli for enhanced production of (R)- and (S)-3-hydroxybutyrate. Appl. Environ. Microbiol. 75: 3137-3145 (2009).

Tseng TS, Salome PA, McClung CR, Olszewski NE. SPINDLY and GIGANTEA interact and act in Arabidopsis thaliana pathways involved in light responses, flowering, and rhythms in cotyledon movements. Plant Cell 16: 1550-1563 (2004).

Tsou AY, Ransom SC, Gerlt JA, Buechter DD, Babbitt PC, Kenyon GL. Mandelate pathway of Pseudomonas putida: sequence relationships involving mandelate racemase, (S)-mandelate dehydrogenase, and benzoylformate decarboxylase and expression of benzoylformate decarboxylase in Escherichia coli. Biochemistry 29: 9856-9862 (1990).

Tsuchisaka A, Theologis A. Heterodimeric interactions among the 1-amino-cyclopropane-1-carboxylate synthase polypeptides encoded by the Arabidopsis gene family. Proc. Natl. Acad. Sci. U.S.A. 101: 2275-2280 (2004).

Tu CJ, Park SY, Walling LL. Isolation and characterization of the neutral leucine aminopeptidase (LapN) of tomato. Plant Physiol. 132: 243-255 (2003).

Tugarinov V, Hwang PM, Kay LE. Nuclear magnetic resonance spectroscopy of high-molecular-weight proteins. Annu. Rev. Biochem. 73: 107-146 (2004).

Turano FJ, Fang TK. Characterization of two glutamate decarboxylase cDNA clones from Arabidopsis. Plant Physiol. 117: 1411-1421 (1998).

Turnbull J, Cleland WW, Morrison JF. Chorismate mutase-prephenate dehydrogenase from Escherichia coli. 1. Kinetic characterization of the dehydrogenase reaction by use of alternative substrates. Biochemistry 29: 10245-10254 (1990).

Turner SR, Ireland R, Rawsthorne S. Purification and primary amino acid sequence of the L subunit of glycine decarboxylase. Evidence for a single lipoamide dehydrogenase in plant mitochondria. J. Biol. Chem. 267: 7745-7750 (1992).

Tyson K, Busby S, Cole J. Catabolite regulation of two Escherichia coli operons encoding nitrite reductases: role of the Cra protein. Arch. Microbiol. 168: 240-244 (1997).

Tyson K, Metheringham R, Griffiths L, Cole J. Characterisation of Escherichia coli K-12 mutants defective in formate-dependent nitrite reduction: essential roles for hemN and the menFDBCE operon. Arch. Microbiol. 168: 403-411 (1997).

Tyson KL, Cole JA, Busby SJ. Nitrite and nitrate regulation at the promoters of two Escherichia coli operons encoding nitrite reductase: identification of common target heptamers for both NarP- and NarL-dependent regulation. Mol. Microbiol. 13: 1045-1055 (1994).

Ubom GA, Hunt JB, Timmons RB. Spin-labeled analogues of ATP, ADP and AMP: substitutes for normal nucleotides in biochemical systems. Biochim. Biophys. Acta 997: 1-8 (1989).

Uchida T. A novel high-molecular mass mammalian ethanolamine kinase. Biochim. Biophys. Acta 1349: 13-24 (1997).

Uchimura H, Enjoji H, Seki T, Taguchi A, Takaya N, Shoun H. Nitrate reductase-formate dehydrogenase couple involved in the fungal denitrification by Fusarium oxysporum. J. Biochem. 131: 579-586 (2002).

Uefuji H, Ogita S, Yamaguchi Y, Koizumi N, Sano H. Molecular cloning and functional characterization of three distinct N-methyltransferases involved in the caffeine biosynthetic pathway in coffee plants. Plant Physiol. 132: 372-380 (2003).

Ui S, Mimura A, Okuma M, Kudo T. The production of D-acetoin by a transgenic Escherichia coli. Lett. Appl. Microbiol. 26: 275-278 (1998).

Unden G, Achebach S, Holighaus G, Tran HG, Wackwitz B, Zeuner Y. Control of FNR function of Escherichia coli by O2 and reducing conditions. J. Mol. Microbiol. Biotechnol. 4: 263-268 (2002).

Underwood SA, Buszko ML, Shanmugam KT, Ingram LO. Flux through citrate synthase limits the growth of ethanologenic Escherichia coli KO11 during xylose fermentation. Appl. Environ. Microbiol. 68: 1071-1081 (2002).

Underwood SA, Buszko ML, Shanmugam KT, Ingram LO. Lack of protective osmolytes limits final cell density and volumetric productivity of ethanologenic Escherichia coli KO11 during xylose fermentation. Appl. Environ. Microbiol. 70: 2734-2740 (2004).

Unkles SE, Smith J, Kanan GJ, Millar LJ, Heck IS, Boxer DH, Kinghorn JR. The Aspergillus nidulans cnxABC locus is a single gene encoding two catalytic domains required for synthesis of precursor Z, an intermediate in molybdenum cofactor biosynthesis. J. Biol. Chem. 272: 28381-28390 (1997).

Unterlinner B, Lenz R, Kutchan TM. Molecular cloning and functional expression of codeinone reductase: the penultimate enzyme in morphine biosynthesis in the opium poppy Papaver somniferum. Plant J. 18: 465-475 (1999).

Uozumi N, Kim EJ, Rubio F, Yamaguchi T, Muto S, Tsuboi A, Bakker EP, Nakamura T, Schroeder JI. The Arabidopsis HKT1 gene homolog mediates inward Na(+) currents in Xenopus laevis oocytes and Na(+) uptake in Saccharomyces cerevisiae. Plant Physiol. 122: 1249-1260 (2000).

Uozumi N, Nakamura T, Schroeder JI, Muto S. Determination of transmembrane topology of an inward-rectifying potassium channel from Arabidopsis thaliana based on functional expression in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 95: 9773-9778 (1998).

Urbanowski ML, Plamann MD, Stauffer LT, Stauffer GV. Cloning and characterization of the gene for Salmonella typhimurium serine hydroxymethyltransferase. Gene 27: 47-54 (1984).

Urbanowski ML, Stauffer GV. Role of homocysteine in metR-mediated activation of the metE and metH genes in Salmonella typhimurium and Escherichia coli. J. Bacteriol. 171: 3277-3281 (1989).

Urbanowski ML, Stauffer LT, Plamann LS, Stauffer GV. A new methionine locus, metR, that encodes a trans-acting protein required for activation of metE and metH in Escherichia coli and Salmonella typhimurium. J. Bacteriol. 169: 1391-1397 (1987).

Uriarte M, Marina A, Ramon-Maiques S, Fita I, Rubio V. The carbamoyl-phosphate synthetase of Pyrococcus furiosus is enzymologically and structurally a carbamate kinase. J. Biol. Chem. 274: 16295-16303 (1999).

Urrestarazu A, Vissers S, Iraqui I, Grenson M. Phenylalanine- and tyrosine-auxotrophic mutants of Saccharomyces cerevisiae impaired in transamination. Mol. Gen. Genet. 257: 230-237 (1998).

Usha R, Savithri HS, Rao NA. Partial amino acid sequence of sheep liver serine hydroxymethyltransferase and comparison of peptide maps of the enzyme from human, ox livers and Escherichia coli. Indian J. Biochem. Biophys. 29: 183-188 (1992).

Utsumi Y, Nakamura Y. Structural and enzymatic characterization of the isoamylase1 homo-oligomer and the isoamylase1-isoamylase2 hetero-oligomer from rice endosperm. Planta 225: 75-87 (2006).

Uwer U, Willmitzer L, Altmann T. Inactivation of a glycyl-tRNA synthetase leads to an arrest in plant embryo development. Plant Cell 10: 1277-1294 (1998).

Vacca RA, Christen P, Malashkevich VN, Jansonius JN, Sandmeier E. Substitution of apolar residues in the active site of aspartate aminotransferase by histidine. Effects on reaction and substrate specificity. Eur. J. Biochem. 227: 481-487 (1995).

Vadali RV, Bennett GN, San KY. Cofactor engineering of intracellular CoA/acetyl-CoA and its effect on metabolic flux redistribution in Escherichia coli. Metab. Eng. 6: 133-139 (2004).

Vadali RV, Bennett GN, San KY. Applicability of CoA/acetyl-CoA manipulation system to enhance isoamyl acetate production in Escherichia coli. Metab. Eng. 6: 294-299 (2004).

Vadrevu R, Wu Y, Matthews CR. NMR analysis of partially folded states and persistent structure in the alpha subunit of tryptophan synthase: implications for the equilibrium folding mechanism of a 29-kDa TIM barrel protein. J. Mol. Biol. 377: 294-306 (2008).

Vaknin A, Berg HC. Osmotic stress mechanically perturbs chemoreceptors in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 103: 592-596 (2006).

Valentin HE, Lincoln K, Moshiri F, Jensen PK, Qi Q, Venkatesh TV, Karunanandaa B, Baszis SR, Norris SR, Savidge B, Gruys KJ, Last RL. The Arabidopsis vitamin E pathway gene5-1 mutant reveals a critical role for phytol kinase in seed tocopherol biosynthesis. Plant Cell 18: 212-224 (2006).

Valentin HE, Reiser S, Gruys KJ. Poly(3-hydroxybutyrate-co-4-hydroxybutyrate) formation from gamma-aminobutyrate and glutamate. Biotechnol. Bioeng. 67: 291-299 (2000).

Valenzuela-Soto EM, Marquez-Escalante JA, Iturriaga G, Figueroa-Soto CG. Trehalose 6-phosphate synthase from Selaginella lepidophylla: purification and properties. Biochem. Biophys. Res. Commun. 313: 314-319 (2004).

Valerius O, Draht O, Kubler E, Adler K, Hoffmann B, Braus GH. Regulation of hisHF transcription of Aspergillus nidulans by adenine and amino acid limitation. Fungal Genet. Biol. 32: 21-31 (2001).

Valkova C, Georgiev O, Karagyozov L, Milchev G. Silencing of retroviral vector transduced LacZ reporter gene by frameshift mutation. Biotechnol. Bioeng. 84: 1-6 (2003).

Vallari DS, Jackowski S. Biosynthesis and degradation both contribute to the regulation of coenzyme A content in Escherichia coli. J. Bacteriol. 170: 3961-3966 (1988).

Vallari DS, Jackowski S, Rock CO. Regulation of pantothenate kinase by coenzyme A and its thioesters. J. Biol. Chem. 262: 2468-2471 (1987).

Vallari DS, Rock CO. Preparation of high-specific-activity D-[3-3H]pantothenic acid. Anal. Biochem. 154: 671-675 (1986).

Vallari DS, Rock CO. Isolation and characterization of temperature-sensitive pantothenate kinase (coaA) mutants of Escherichia coli. J. Bacteriol. 169: 5795-5800 (1987).

Vallari DS, Rock CO. Pantothenate transport in Escherichia coli. J. Bacteriol. 162: 1156-1161 (1985).

Vallari DS, Rock CO. Isolation and characterization of Escherichia coli pantothenate permease (panF) mutants. J. Bacteriol. 164: 136-142 (1985).

Valle J, Da Re S, Schmid S, Skurnik D, D'Ari R, Ghigo JM. The amino acid valine is secreted in continuous-flow bacterial biofilms. J. Bacteriol. 190: 264-274 (2008).

Valverde F, Losada M, Serrano A. Engineering a central metabolic pathway: glycolysis with no net phosphorylation in an Escherichia coli gap mutant complemented with a plant GapN gene. FEBS Lett. 449: 153-158 (1999).

Van Bergeijk SA, Van der Zee C, Stal LJ. Uptake and excretion of dimethylsulphoniopropionate is driven by salinity changes in the marine benthic diatom Cylindrotheca closterium. Eur. J. Phycol. 38: 341-349 (2003).

van de Walle M, Shiloach J. Proposed mechanism of acetate accumulation in two recombinant Escherichia coli strains during high density fermentation. Biotechnol. Bioeng. 57: 71-78 (1998).

van den Hombergh JP, Moore JD, Charles IG, Hawkins AR. Overproduction in Escherichia coli of the dehydroquinate synthase domain of the Aspergillus nidulans pentafunctional AROM protein. Biochem. J. 284: 861-867 (1992).

Van der Heide T, Poolman B. Glycine betaine transport in Lactococcus lactis is osmotically regulated at the level of expression and translocation activity. J. Bacteriol. 182: 203-206 (2000).

van der Kop DA, Schuyer M, Scheres B, van der Zaal BJ, Hooykaas PJ. Isolation and characterization of an auxin-inducible glutathione S-transferase gene of Arabidopsis thaliana. Plant Mol. Biol. 30: 839-844 (1996).

van der Ploeg JR, Eichhorn E, Leisinger T. Sulfonate-sulfur metabolism and its regulation in Escherichia coli. Arch. Microbiol. 176: 1-8 (2001).

van der Zel A, Lam HM, Winkler ME. Extensive homology between the Escherichia coli K-12 SerC(PdxF) aminotransferase and a protein encoded by a progesterone-induced mRNA in rabbit and human endometria. Nucleic Acids Res. 17: 8379 (1989).

Van Dien SJ, Iwatani S, Usuda Y, Matsui K. Theoretical analysis of amino acid-producing Escherichia coli using a stoichiometric model and multivariate linear regression. J. Biosci. Bioeng. 102: 34-40 (2006).

van Dillewijn P, Wittich RM, Caballero A, Ramos JL. Type II hydride transferases from different microorganisms yield nitrite and diarylamines from polynitroaromatic compounds. Appl. Environ. Microbiol. 74: 6820-6823 (2008).

Van Dommelen A, Keijers V, Somers E, Vanderleyden J. Cloning and characterisation of the Azospirillum brasilense glnD gene and analysis of a glnD mutant. Mol. Genet. Genomics 266: 813-820 (2002).

Van Doorsselaere J, Dumas B, Baucher M, Fritig B, Legrand M, Van Montagu M, Inze D. One-step purification and characterization of a lignin-specific O-methyltransferase from poplar. Gene 133: 213-217 (1993).

Van Dyk TK, Ayers BL, Morgan RW, Larossa RA. Constricted flux through the branched-chain amino acid biosynthetic enzyme acetolactate synthase triggers elevated expression of genes regulated by rpoS and internal acidification. J. Bacteriol. 180: 785-792 (1998).

Van Dyk TK, Wei Y, Hanafey MK, Dolan M, Reeve MJ, Rafalski JA, Rothman-Denes LB, LaRossa RA. A genomic approach to gene fusion technology. Proc. Natl. Acad. Sci. U.S.A. 98: 2555-2560 (2001).

Van Heeke G, Schuster SM. Expression of human asparagine synthetase in Escherichia coli. J. Biol. Chem. 264: 5503-5509 (1989).

Van Heeke G, Schuster SM. Expression of human asparagine synthetase in Saccharomyces cerevisiae. Protein Eng. 3: 739-744 (1990).

van Heeswijk WC, Hoving S, Molenaar D, Stegeman B, Kahn D, Westerhoff HV. An alternative PII protein in the regulation of glutamine synthetase in Escherichia coli. Mol. Microbiol. 21: 133-146 (1996).

van Heeswijk WC, Rabenberg M, Westerhoff HV, Kahn D. The genes of the glutamine synthetase adenylylation cascade are not regulated by nitrogen in Escherichia coli. Mol. Microbiol. 9: 443-457 (1993).

van Heeswijk WC, Stegeman B, Hoving S, Molenaar D, Kahn D, Westerhoff HV. An additional PII in Escherichia coli: a new regulatory protein in the glutamine synthetase cascade. FEMS Microbiol. Lett. 132: 153-157 (1995).

van Heeswijk WC, Wen D, Clancy P, Jaggi R, Ollis DL, Westerhoff HV, Vasudevan SG. The Escherichia coli signal transducers PII (GlnB) and GlnK form heterotrimers in vivo: fine tuning the nitrogen signal cascade. Proc. Natl. Acad. Sci. U.S.A. 97: 3942-3947 (2000).

van Rooijen GJ, Moloney MM. Structural requirements of oleosin domains for subcellular targeting to the oil body. Plant Physiol. 109: 1353-1361 (1995).

Van Spanning RJ, De Boer AP, Reijnders WN, Westerhoff HV, Stouthamer AH, Van Der Oost J. FnrP and NNR of Paracoccus denitrificans are both members of the FNR family of transcriptional activators but have distinct roles in respiratory adaptation in response to oxygen limitation. Mol. Microbiol. 23: 893-907 (1997).

van Wegen RJ, Lee SY, Middelberg AP. Metabolic and kinetic analysis of poly(3-hydroxybutyrate) production by recombinant Escherichia coli. Biotechnol. Bioeng. 74: 70-81 (2001).

van Wonderen JH, Burlat B, Richardson DJ, Cheesman MR, Butt JN. The nitric oxide reductase activity of cytochrome c nitrite reductase from Escherichia coli. J. Biol. Chem. 283: 9587-9594 (2008).

van't Slot KA, Gierlich A, Knogge W. A single binding site mediates resistance- and disease-associated activities of the effector protein NIP1 from the barley pathogen Rhynchosporium secalis. Plant Physiol. 144: 1654-1666 (2007).

Vannelli T, Wei Qi W, Sweigard J, Gatenby AA, Sariaslani FS. Production of p-hydroxycinnamic acid from glucose in Saccharomyces cerevisiae and Escherichia coli by expression of heterologous genes from plants and fungi. Metab. Eng. 9: 142-151 (2007).

Vanoni MA, Fischer F, Ravasio S, Verzotti E, Edmondson DE, Hagen WR, Zanetti G, Curti B. The recombinant alpha subunit of glutamate synthase: spectroscopic and catalytic properties. Biochemistry 37: 1828-1838 (1998).

Vanoni MA, Verzotti E, Zanetti G, Curti B. Properties of the recombinant beta subunit of glutamate synthase. Eur. J. Biochem. 236: 937-946 (1996).

Varma A, Boesch BW, Palsson BO. Biochemical production capabilities of Escherichia coli. Biotechnol. Bioeng. 42: 59-73 (1993).

Varma A, Boesch BW, Palsson BO. Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates. Appl. Environ. Microbiol. 59: 2465-2473 (1993).

Varma A, Palsson BO. Metabolic flux balancing: basic concepts, scientific and practical use. Bio-Technol. 12: 994-998 (1994).

Varma A, Palsson BO. Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl. Environ. Microbiol. 60: 3724-3731 (1994).

Varma GB, Fatope MO, Marwah RG, Deadman ME, Al-Rawahi FK. Production of phenylacetic acid derivatives and 4-epiradicinol in culture by Curvularia lunata. Phytochemistry 67: 1925-1930 (2006).

Varner J, Ramkrishna D. Mathematical models of metabolic pathways. Curr. Opin. Biotechnol. 10: 146-150 (1999).

Varner JD. Large-scale prediction of phenotype: concept. Biotechnol. Bioeng. 69: 664-678 (2000).

Vaupel M, Dietz H, Linder D, Thauer RK. Primary structure of cyclohydrolase (Mch) from Methanobacterium thermoautotrophicum (strain Marburg) and functional expression of the mch gene in Escherichia coli. Eur. J. Biochem. 236: 294-300 (1996).

Vauterin M, Frankard V, Jacobs M. Functional rescue of a bacterial dapA auxotroph with a plant cDNA library selects for mutant clones encoding a feedback-insensitive dihydrodipicolinate synthase. Plant J. 21: 239-248 (2000).

Vauterin M, Jacobs M. Isolation of a poplar and an Arabidopsis thaliana dihydrodipicolinate synthase cDNA clone. Plant Mol. Biol. 25: 545-550 (1994).

Vazquez-Flota F, De Carolis E, Alarco AM, De Luca V. Molecular cloning and characterization of desacetoxyvindoline-4-hydroxylase, a 2-oxoglutarate dependent-dioxygenase involved in the biosynthesis of vindoline in Catharanthus roseus (L.) G. Don. Plant Mol. Biol. 34: 935-948 (1997).

Velasco-Garcia R, Mujica-Jimenez C, Mendoza-Hernandez G, Munoz-Clares RA. Rapid purification and properties of betaine aldehyde dehydrogenase from Pseudomonas aeruginosa. J. Bacteriol. 181: 1292-1300 (1999).

Velasco-Garcia R, Villalobos MA, Ramirez-Romero MA, Mujica-Jimenez C, Iturriaga G, Munoz-Clares RA. Betaine aldehyde dehydrogenase from Pseudomonas aeruginosa: cloning, over-expression in Escherichia coli, and regulation by choline and salt. Arch. Microbiol. 185: 14-22 (2006).

Velayos A, Blasco JL, Alvarez MI, Iturriaga EA, Eslava AP. Blue-light regulation of phytoene dehydrogenase (carB) gene expression in Mucor circinelloides. Planta 210: 938-946 (2000).

Velazquez L, Camarena L, Reyes JL, Bastarrachea F. Mutations affecting the Shine-Dalgarno sequences of the untranslated region of the Escherichia coli gltBDF operon. J. Bacteriol. 173: 3261-3264 (1991).

Venkatachalam KV, Akita H, Strott CA. Molecular cloning, expression, and characterization of human bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase and its functional domains. J. Biol. Chem. 273: 19311-19320 (1998).

Venkatesh KV, Bhartiya S, Ruhela A. Multiple feedback loops are key to a robust dynamic performance of tryptophan regulation in Escherichia coli. FEBS Lett. 563: 234-240 (2004).

Venkitasubramanian P, Daniels L, Rosazza JP. Reduction of carboxylic acids by Nocardia aldehyde oxido-reductase requires a phosphopantetheinylated enzyme. J. Biol. Chem. 282: 478-485 (2007).

Verbruggen N, van Montagu M, Messens E. Synthesis of the proline analogue [2,3-3H]azetidine-2-carboxylic acid: Uptake and incorporation in Arabidopsis thaliana and Escherichia coli. FEBS Lett. 308: 261-263 (1992).

Verbruggen N, Villarroel R, Van Montagu M. Osmoregulation of a pyrroline-5-carboxylate reductase gene in Arabidopsis thaliana. Plant Physiol. 103: 771-781 (1993).

Vergnes A, Gouffi-Belhabich K, Blasco F, Giordano G, Magalon A. Involvement of the molybdenum cofactor biosynthetic machinery in the maturation of the Escherichia coli nitrate reductase A. J. Biol. Chem. 279: 41398-41403 (2004).

Vergnes A, Pommier J, Toci R, Blasco F, Giordano G, Magalon A. NarJ chaperone binds on two distinct sites of the aponitrate reductase of Escherichia coli to coordinate molybdenum cofactor insertion and assembly. J. Biol. Chem. 281: 2170-2176 (2006).

Verheul A, Wouters JA, Rombouts FM, Abee T. A possible role of ProP, ProU and CaiT in osmoprotection of Escherichia coli by carnitine. J. Appl. Microbiol. 85: 1036-1046 (1998).

Vermeij P, Kertesz MA. Pathways of assimilative sulfur metabolism in Pseudomonas putida. J. Bacteriol. 181: 5833-5837 (1999).

Vermeulen V, Kunte HJ. Marinococcus halophilus DSM 20408T encodes two transporters for compatible solutes belonging to the betaine-carnitine-choline transporter family: identification and characterization of ectoine transporter EctM and glycine betaine transporter BetM. Extremophiles 8: 175-184 (2004).

Vernon DM, Bohnert HJ. A novel methyl transferase induced by osmotic stress in the facultative halophyte Mesembryanthemum crystallinum. EMBO J. 11: 2077-2085 (1992).

Veron M, Guillou Y, Fazel A, Cohen GN. Reversible dissociation of aspartokinase I/homoserine dehydrogenase I from Escherichia coli K 12. The active species is the tetramer. Eur. J. Biochem. 151: 521-524 (1985).

Verrey F, Jack DL, Paulsen IT, Saier MH, Pfeiffer R. New glycoprotein-associated amino acid transporters. J. Membr. Biol. 172: 181-192 (1999).

Vidmar JJ, Schjoerring JK, Touraine B, Glass AD. Regulation of the hvst1 gene encoding a high-affinity sulfate transporter from Hordeum vulgare. Plant Mol. Biol. 40: 883-892 (1999).

Vieira Dos Santos C, Cuine S, Rouhier N, Rey P. The Arabidopsis plastidic methionine sulfoxide reductase B proteins. Sequence and activity characteristics, comparison of the expression with plastidic methionine sulfoxide reductase A, and induction by photooxidative stress. Plant Physiol. 138: 909-922 (2005).

Viitanen PV, Devine AL, Khan MS, Deuel DL, Van Dyk DE, Daniell H. Metabolic engineering of the chloroplast genome using the Echerichia coli ubiC gene reveals that chorismate is a readily abundant plant precursor for p-hydroxybenzoic acid biosynthesis. Plant Physiol. 136: 4048-4060 (2004).

Vilchez S, Molina L, Ramos C, Ramos JL. Proline catabolism by Pseudomonas putida: cloning, characterization, and expression of the put genes in the presence of root exudates. J. Bacteriol. 182: 91-99 (2000).

Villafranca JJ, Ash DE, Wedler FC. Manganese(II) and substrate interaction with unadenylylated glutamine synthetase (Escherichia coli w). I. Temperature and frequency dependent nuclear magnetic resonance studies. Biochemistry 15: 536-543 (1976).

Vimr ER, Kalivoda KA, Deszo EL, Steenbergen SM. Diversity of microbial sialic acid metabolism. Microbiol. Mol. Biol. Rev. 68: 132-153 (2004).

Vinella D, Gagny B, Joseleau-Petit D, D'Ari R, Cashel M. Mecillinam resistance in Escherichia coli is conferred by loss of a second activity of the AroK protein. J. Bacteriol. 178: 3818-3828 (1996).

Vinod MP, Bellur P, Becker DF. Electrochemical and functional characterization of the proline dehydrogenase domain of the PutA flavoprotein from Escherichia coli. Biochemistry 41: 6525-6532 (2002).

Vinothkumar KR, Raunser S, Jung H, Kuhlbrandt W. Oligomeric structure of the carnitine transporter CaiT from Escherichia coli. J. Biol. Chem. 281: 4795-4801 (2006).

Visser D, Schmid JW, Mauch K, Reuss M, Heijnen JJ. Optimal re-design of primary metabolism in Escherichia coli using linlog kinetics. Metab. Eng. 6: 378-390 (2004).

Visser K, Heimovaara-Dijkstra S, Kijne JW, Wang M. Molecular cloning and characterization of an inorganic pyrophosphatase from barley. Plant Mol. Biol. 37: 131-140 (1998).

Voelker TA, Jones A, Cranmer AM, Davies HM, Knutzon DS. Broad-range and binary-range acyl-acyl-carrier protein thioesterases suggest an alternative mechanism for medium-chain production in seeds. Plant Physiol. 114: 669-677 (1997).

Vogt T, Grimm R, Strack D. Cloning and expression of a cDNA encoding betanidin 5-O-glucosyltransferase, a betanidin- and flavonoid-specific enzyme with high homology to inducible glucosyltransferases from the Solanaceae. Plant J. 19: 509-519 (1999).

Voigt J, Liebich I, Kiess M, Frank R. Subcellular distribution of 14-3-3 proteins in the unicellular green alga Chlamydomonas reinhardtii. Eur. J. Biochem. 268: 6449-6457 (2001).

Vojtechova M, Rodriguez-Sotres R, Munoz-Clares RA. Inactivation of betaine aldehyde dehydrogenase from amaranth leaves by pyridoxal 5 '-phosphate. Plant Sci. 143: 9-17 (1999).

Volz K. A test case for structure-based functional assignment: the 1.2 A crystal structure of the yjgF gene product from Escherichia coli. Protein Sci. 8: 2428-2437 (1999).

von Blohn C, Kempf B, Kappes RM, Bremer E. Osmostress response in Bacillus subtilis: characterization of a proline uptake system (OpuE) regulated by high osmolarity and the alternative transcription factor sigma B. Mol. Microbiol. 25: 175-187 (1997).

von Weymarn N, Nyyssola A, Reinikainen T, Leisola M, Ojamo H. Improved osmotolerance of recombinant Escherichia coli by de novo glycine betaine biosynthesis. Appl. Microbiol. Biotechnol. 55: 214-218 (2001).

Vorwerk S, Biernacki S, Hillebrand H, Janzik I, Muller A, Weiler EW, Piotrowski M. Enzymatic characterization of the recombinant Arabidopsis thaliana nitrilase subfamily encoded by the NIT2/NIT1/NIT3-gene cluster. Planta 212: 508-516 (2001).

Vothknecht UC, Kannangara CG, von Wettstein D. Expression of catalytically active barley glutamyl tRNAGlu reductase in Escherichia coli as a fusion protein with glutathione S-transferase. Proc. Natl. Acad. Sci. U.S.A. 93: 9287-9291 (1996).

Vothknecht UC, Kannangara CG, von Wettstein D. Barley glutamyl tRNAGlu reductase: mutations affecting haem inhibition and enzyme activity. Phytochemistry 47: 513-519 (1998).

Voziyan PA, Fisher MT. Polyols induce ATP-independent folding of GroEL-bound bacterial glutamine synthetase. Arch. Biochem. Biophys. 397: 293-297 (2002).

Vyazmensky M, Sella C, Barak Z, Chipman DM. Isolation and characterization of subunits of acetohydroxy acid synthase isozyme III and reconstitution of the holoenzyme. Biochemistry 35: 10339-10346 (1996).

Wada K, Hasegawa Y, Gong Z, Minami Y, Fukuyama K, Takahashi Y. Crystal structure of Escherichia coli SufA involved in biosynthesis of iron-sulfur clusters: implications for a functional dimer. FEBS Lett. 579: 6543-6548 (2005).

Waditee R, Bhuiyan MN, Hirata E, Hibino T, Tanaka Y, Shikata M, Takabe T. Metabolic engineering for betaine accumulation in microbes and plants. J. Biol. Chem. 282: 34185-34193 (2007).

Wadsworth GJ, Gebhardt JS, Matthews BF. Characterization of a soybean cDNA clone encoding the mitochondrial isozyme of aspartate aminotransferase, AAT4. Plant Mol. Biol. 27: 1085-1095 (1995).

Wagner A, Fell DA. The small world inside large metabolic networks. Proc. Roy. Soc. Lond. B. Biol. Sci. 268: 1803-1810 (2001).

Wagner AF, Demand J, Schilling G, Pils T, Knappe J. A dehydroalanyl residue can capture the 5'-deoxyadenosyl radical generated from S-adenosylmethionine by pyruvate formate-lyase-activating enzyme. Biochem. Biophys. Res. Commun. 254: 306-310 (1999).

Wagner JT, Ludemann H, Farber PM, Lottspeich F, Krauth-Siegel RL. Glutamate dehydrogenase, the marker protein of Plasmodium falciparum--cloning, expression and characterization of the malarial enzyme. Eur. J. Biochem. 258: 813-819 (1998).

Wagner SJ, Thomas SP, Kaufman RI, Nixon BT, Stevens SE Jr. The glnA gene of the cyanobacterium Agmenellum quadruplicatum PR-6 is nonessential for ammonium assimilation. J. Bacteriol. 175: 604-612 (1993).

Wagner T, Shumilin IA, Bauerle R, Kretsinger RH. Structure of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Escherichia coli: comparison of the Mn(2+)*2-phosphoglycolate and the Pb(2+)*2-phosphoenolpyruvate complexes and implications for catalysis. J. Mol. Biol. 301: 389-399 (2000).

Wahls WP, Song JM, Smith GR. Single-stranded DNA binding activity of C1-tetrahydrofolate synthase enzymes. J. Biol. Chem. 268: 23792-23798 (1993).

Wais RJ, Keating DH, Long SR. Structure-function analysis of nod factor-induced root hair calcium spiking in Rhizobium-legume symbiosis. Plant Physiol. 129: 211-224 (2002).

Walbott H, Leulliot N, Grosjean H, Golinelli-Pimpaneau B. The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)-methyltransferase provides insights into its tRNA specificity. Nucleic Acids Res. 36: 4929-4940 (2008).

Wald FA, Kissen R, du Jardin P, Moreno S. Characterization of UDP-glucose:protein transglucosylase genes from potato. Plant Mol. Biol. 52: 705-714 (2003).

Walkenhorst HM, Hemschemeier SK, Eichenlaub R. Molecular analysis of the molybdate uptake operon, modABCD, of Escherichia coli and modR, a regulatory gene. Microbiol. Res. 150: 347-361 (1995).

Walker K, Croteau R. Molecular cloning of a 10-deacetylbaccatin III-10-O-acetyl transferase cDNA from Taxus and functional expression in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 97: 583-587 (2000).

Walker K, Croteau R. Taxol biosynthesis: molecular cloning of a benzoyl-CoA:taxane 2alpha-O-benzoyltransferase cDNA from taxus and functional expression in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 97: 13591-13596 (2000).

Walker K, Long R, Croteau R. The final acylation step in taxol biosynthesis: cloning of the taxoid C13-side-chain N-benzoyltransferase from Taxus. Proc. Natl. Acad. Sci. U.S.A. 99: 9166-9171 (2002).

Wallbrandt P, Tegman V, Jonsson BH, Wieslander A. Identification and analysis of the genes coding for the putative pyruvate dehydrogenase enzyme complex in Acholeplasma laidlawii. J. Bacteriol. 174: 1388-1396 (1992).

Wallon G, Kryger G, Lovett ST, Oshima T, Ringe D, Petsko GA. Crystal structures of Escherichia coli and Salmonella typhimurium 3-isopropylmalate dehydrogenase and comparison with their thermophilic counterpart from Thermus thermophilus. J. Mol. Biol. 266: 1016-1031 (1997).

Wallon G, Yamamoto K, Kirino H, Yamagishi A, Lovett ST, Petsko GA, Oshima T. Purification, catalytic properties and thermostability of 3-isopropylmalate dehydrogenase from Escherichia coli. Biochim. Biophys. Acta 1337: 105-112 (1997).

Walsh TA, Bauer T, Neal R, Merlo AO, Schmitzer PR, Hicks GR, Honma M, Matsumura W, Wolff K, Davies JP. Chemical genetic identification of glutamine phosphoribosylpyrophosphate amidotransferase as the target for a novel bleaching herbicide in Arabidopsis. Plant Physiol. 144: 1292-1304 (2007).

Walt A, Kahn ML. The fixA and fixB genes are necessary for anaerobic carnitine reduction in Escherichia coli. J. Bacteriol. 184: 4044-4047 (2002).

Walter MH, Hans J, Strack D. Two distantly related genes encoding 1-deoxy-d-xylulose 5-phosphate synthases: differential regulation in shoots and apocarotenoid-accumulating mycorrhizal roots. Plant J. 31: 243-254 (2002).

Wang A, Crowley DE. Global gene expression responses to cadmium toxicity in Escherichia coli. J. Bacteriol. 187: 3259-3266 (2005).

Wang AM, Xia Q, Xie WS, Dumonceaux T, Zou JT, Datla R, Selvaraj G. Male gametophyte development in bread wheat (Triticum aestivum L.): molecular, cellular, and biochemical analyses of a sporophytic contribution to pollen wall ontogeny. Plant J. 30: 613-623 (2002).

Wang AQ, Jiao H, Chen XZ, Huang HR. In vivo cloning of proline genes and its expression in Escherichia coli. Chin. J. Biotechnol. 6: 27-34 (1990).

Wang C, Wang X. A novel phospholipase D of Arabidopsis that is activated by oleic acid and associated with the plasma membrane. Plant Physiol. 127: 1102-1112 (2001).

Wang CL, Oliver DJ. Cloning of the cDNA and genomic clones for glutathione synthetase from Arabidopsis thaliana and complementation of a gsh2 mutant in fission yeast. Plant Mol. Biol. 31: 1093-1104 (1996).

Wang Cw, Oh MK, Liao JC. Directed evolution of metabolically engineered Escherichia coli for carotenoid production. Biotechnol. Prog. 16: 922-926 (2000).

Wang F, Blanchard JS, Tang XJ. Hydrogen exchange/electrospray ionization mass spectrometry studies of substrate and inhibitor binding and conformational changes of Escherichia coli dihydrodipicolinate reductase. Biochemistry 36: 3755-3759 (1997).

Wang H, Hao L, Shung CY, Sunter G, Bisaro DM. Adenosine kinase is inactivated by geminivirus AL2 and L2 proteins. Plant Cell 15: 3020-3032 (2003).

Wang H, Liu D, Liu C, Zhang A. The pyridoxal kinase gene TaPdxK from wheat complements vitamin B6 synthesis-defective Escherichia coli. J. Plant Physiol. 161: 1053-1060 (2004).

Wang H, Wang F, Wei D. Impact of oxygen supply on rtPA expression in Escherichia coli BL21 (DE3): ammonia effects. Appl. Microbiol. Biotechnol. 82: 249-259 (2009).

Wang J, Pichersky E. Characterization of S-adenosyl-L-methionine:(iso)eugenol O-methyltransferase involved in floral scent production in Clarkia breweri. Arch. Biochem. Biophys. 349: 153-160 (1998).

Wang LY, Brown L, Elliott M, Elliott T. Regulation of heme biosynthesis in Salmonella typhimurium: activity of glutamyl-tRNA reductase (HemA) is greatly elevated during heme limitation by a mechanism which increases abundance of the protein. J. Bacteriol. 179: 2907-2914 (1997).

Wang MD, Liu L, Wang BM, Berg CM. Cloning and characterization of the Escherichia coli K-12 alanine-valine transaminase (avtA) gene. J. Bacteriol. 169: 4228-4234 (1987).

Wang Q, Calvo JM. Lrp, a global regulatory protein of Escherichia coli, binds co-operatively to multiple sites and activates transcription of ilvIH. J. Mol. Biol. 229: 306-318 (1993).

Wang Q, Chen X, Yang Y, Zhao X. Genome-scale in silico aided metabolic analysis and flux comparisons of Escherichia coli to improve succinate production. Appl. Microbiol. Biotechnol. 73: 887-894 (2006).

Wang W, Poland BW, Honzatko RB, Fromm HJ. Identification of arginine residues in the putative L-aspartate binding site of Escherichia coli adenylosuccinate synthetase. J. Biol. Chem. 270: 13160-13163 (1995).

Wang X, Xu L, Zheng L. Cloning and expression of phosphatidylcholine-hydrolyzing phospholipase D from Ricinus communis L. J. Biol. Chem. 269: 20312-20317 (1994).

Wang XG, Roderick SL. Expression, purification, crystallization and preliminary X-ray data of Escherichia coli galactoside acetyltransferase. Acta Crystallogr. D. Biol. Crystallogr. 55: 1955-1957 (1999).

Wang YM, Meng YL, Ishikawa H, Hibino T, Tanaka Y, Nii N, Takabe T. Photosynthetic adaptation to salt stress in three-color leaves of a C-4 plant Amaranthus tricolor. Plant Cell Physiol. 40: 668-674 (1999).

Wang Z, Xiang L, Shao J, Wegrzyn A, Wegrzyn G. Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism. Microb. Cell Fact. 5: 34 (2006).

Ward DE, Kengen SW, van Der Oost J, de Vos WM. Purification and characterization of the alanine aminotransferase from the hyperthermophilic Archaeon pyrococcus furiosus and its role in alanine production. J. Bacteriol. 182: 2559-2566 (2000).

Warnecke DC, Baltrusch M, Buck F, Wolter FP, Heinz E. UDP-glucose:sterol glucosyltransferase: cloning and functional expression in Escherichia coli. Plant Mol. Biol. 35: 597-603 (1997).

Wasaki J, Yonetani R, Kuroda S, Shinano T, Yazaki J, Fujii F, Shimbo K, Yamamoto K, Sakata K, Sasaki T, Kishimoto N, Kikuchi S, Yamagishi M, Osaki M. Transcriptomic analysis of metabolic changes by phosphorus stress in rice plant roots. Plant Cell Environ. 26: 1515-1523 (2003).

Watanabe K, Suzuki K, Kitamura S. Characterization of a GDP-D-mannose 3'',5''-epimerase from rice. Phytochemistry 67: 338-346 (2006).

Watanabe N, Cherney MM, van Belkum MJ, Marcus SL, Flegel MD, Clay MD, Deyholos MK, Vederas JC, James MN. Crystal structure of LL-diaminopimelate aminotransferase from Arabidopsis thaliana: a recently discovered enzyme in the biosynthesis of L-lysine by plants and Chlamydia. J. Mol. Biol. 371: 685-702 (2007).

Watt G, Leoff C, Harper AD, Bar-Peled M. A bifunctional 3,5-epimerase/4-keto reductase for nucleotide-rhamnose synthesis in Arabidopsis. Plant Physiol. 134: 1337-1346 (2004).

Wattebled F, Ral JP, Dauvillee D, Myers AM, James MG, Schlichting R, Giersch C, Ball SG, D'Hulst C. STA11, a Chlamydomonas reinhardtii locus required for normal starch granule biogenesis, encodes disproportionating enzyme. further evidence for a function of alpha-1,4 glucanotransferases during starch granule biosynthesis in green algae. Plant Physiol. 132: 137-145 (2003).

Watts CA, Ridley H, Condie KL, Leaver JT, Richardson DJ, Butler CS. Selenate reduction by Enterobacter cloacae SLD1a-1 is catalysed by a molybdenum-dependent membrane-bound enzyme that is distinct from the membrane- bound nitrate reductase. FEMS Microbiol. Lett. 228: 273-279 (2003).

Weaver LM, Yu F, Wurtele ES, Nikolau BJ. Characterization of the cDNA and gene coding for the biotin synthase of Arabidopsis thaliana. Plant Physiol. 110: 1021-1028 (1996).

Weber J, Kayser A, Rinas U. Metabolic flux analysis of Escherichia coli in glucose-limited continuous culture. II. Dynamic response to famine and feast, activation of the methylglyoxal pathway and oscillatory behaviour. Microbiology 151: 707-716 (2005).

Weber M, Suter M, Brunold C, Kopriva S. Sulfate assimilation in higher plants characterization of a stable intermediate in the adenosine 5'-phosphosulfate reductase reaction. Eur. J. Biochem. 267: 3647-3653 (2000).

Weber W, Lienhart C, Baba MD, Fussenegger M. A biotin-triggered genetic switch in mammalian cells and mice. Metab. Eng. 11: 117-124 (2009).

Wedler FC, Ley BW. Homoserine dehydrogenase-I (Escherichia coli): action of monovalent ions on catalysis and substrate association-dissociation. Arch. Biochem. Biophys. 301: 416-423 (1993).

Wedler FC, Ley BW. Kinetic and regulatory mechanisms for (Escherichia coli) homoserine dehydrogenase-I. Equilibrium isotope exchange kinetics. J. Biol. Chem. 268: 4880-4888 (1993).

Wedler FC, Ley BW, Shames SL, Rembish SJ, Kushmaul DL. Preferred order random kinetic mechanism for homoserine dehydrogenase of Escherichia coli (Thr-sensitive) aspartokinase/homoserine dehydrogenase-I: equilibrium isotope exchange kinetics. Biochim. Biophys. Acta 1119: 247-249 (1992).

Wedler FC, Shreve DS, Kenney RM, Ashour AE, Carfi J, Rhee SG. Two glutamine synthetases from Bacillus caldolyticus, an extreme thermophile. Isolation, physicochemical and kinetic properties. J. Biol. Chem. 255: 9507-9516 (1980).

Weglenski P, Ninfa AJ, Ueno-Nishio S, Magasanik B. Mutations in the glnG gene of Escherichia coli that result in increased activity of nitrogen regulator I. J. Bacteriol. 171: 4479-4485 (1989).

Wehrmann A, Eggeling L, Sahm H. Analysis of different DNA fragments of Corynebacterium glutamicum complementing dapE of Escherichia coli. Microbiology 140: 3349-3356 (1994).

Wei B, Shin S, LaPorte D, Wolfe AJ, Romeo T. Global regulatory mutations in csrA and rpoS cause severe central carbon stress in Escherichia coli in the presence of acetate. J. Bacteriol. 182: 1632-1640 (2000).

Wei Y, Fu D. Selective metal binding to a membrane embedded aspartate in the Escherichia coli metal transporter YiiP (FieF). J. Biol. Chem. 280: 33716-33724 (2005).

Weimer B, Seefeldt K, Dias B. Sulfur metabolism in bacteria associated with cheese. Antonie Van Leeuwenhoek 76: 247-261 (1999).

Weischet WO, Kirschner K. The binding of indole to the alpha-subunit and beta2-subunit and to the alpha2beta2-complex of tryptophan synthase from Escherichia coli. Identification of a second indole-binding site on the alpha-subunit. Eur. J. Biochem. 64: 313-320 (1976).

Weisemann JM, Matthews BF. Identification and expression of a cDNA from Daucus carota encoding a bifunctional aspartokinase-homoserine dehydrogenase. Plant Mol. Biol. 22: 301-312 (1993).

Weiss B. Evidence for mutagenesis by nitric oxide during nitrate metabolism in Escherichia coli. J. Bacteriol. 188: 829-833 (2006).

Weiss V, Claverie-Martin F, Magasanik B. Phosphorylation of nitrogen regulator I of Escherichia coli induces strong cooperative binding to DNA essential for activation of transcription. Proc. Natl. Acad. Sci. U.S.A. 89: 5088-5092 (1992).

Weissbach H, Brot N. Regulation of methionine synthesis in Escherichia coli. Mol. Microbiol. 5: 1593-1597 (1991).

Welford RW, Kirkpatrick JM, McNeill LA, Puri M, Oldham NJ, Schofield CJ. Incorporation of oxygen into the succinate co-product of iron(II) and 2-oxoglutarate dependent oxygenases from bacteria, plants and humans. FEBS Lett. 579: 5170-5174 (2005).

Wellmann F, Lukacin R, Moriguchi T, Britsch L, Schiltz E, Matern U. Functional expression and mutational analysis of flavonol synthase from Citrus unshiu. Eur. J. Biochem. 269: 4134-4142 (2002).

Welsh DT, Herbert RA. Osmotically induced intracellular trehalose, but not glycine betaine accumulation promotes desiccation tolerance in Escherichia coli. FEMS Microbiol. Lett. 174: 57-63 (1999).

Welsh DT, Reed RH, Herbert RA. The role of trehalose in the osmoadaptation of Escherichia coli NCIB-9484: interaction of trehalose, K+ and glutamate during osmoadaptation in continuous culture. J. Gen. Microbiol. 137: 745-750 (1991).

Wen ZT, Peng LS, Morrison M. The glutamine synthetase of Prevotella bryantii B(1)4 is a family III enzyme (GinN) and glutamine supports growth of mutants lacking glutamate dehydrogenase activity. FEMS Microbiol. Lett. 229: 15-21 (2003).

Wendisch VF, Zimmer DP, Khodursky A, Peter B, Cozzarelli N, Kustu S. Isolation of Escherichia coli mRNA and comparison of expression using mRNA and total RNA on DNA microarrays. Anal. Biochem. 290: 205-213 (2001).

Wengender PA, Miller KJ. Identification of a PutP proline permease gene homolog from Staphylococcus aureus by expression cloning of the high-affinity proline transport system in Escherichia coli. Appl. Environ. Microbiol. 61: 252-259 (1995).

Wernegreen JJ, Moran NA. Vertical transmission of biosynthetic plasmids in aphid endosymbionts (Buchnera). J. Bacteriol. 183: 785-790 (2001).

Wertheimer SJ, Leifer Z. Putrescine and spermidine sensitivity of lysine decarboxylase in Escherichia coli: evidence for a constitutive enzyme and its mode of regulation. Biochem. Biophys. Res. Commun. 114: 882-888 (1983).

Wessel PM, Biou V, Douce R, Dumas R. A loop deletion in the plant acetohydroxy acid isomeroreductase homodimer generates an active monomer with reduced stability and altered magnesium affinity. Biochemistry 37: 12753-12760 (1998).

Wetzel DK, Ehrenshaft M, Denslow SA, Daub ME. Functional complementation between the PDX1 vitamin B6 biosynthetic gene of Cercospora nicotianae and pdxJ of Escherichia coli. FEBS Lett. 564: 143-146 (2004).

Weyand M, Schlichting I, Herde P, Marabotti A, Mozzarelli A. Crystal structure of the beta Ser(178) -> Pro mutant of tryptophan synthase - A "knock-out" allosteric enzyme. J. Biol. Chem. 277: 10653-10660 (2002).

Weyand M, Schlichting I, Marabotti A, Mozzarelli A. Crystal structures of a new class of allosteric effectors complexed to tryptophan synthase. J. Biol. Chem. 277: 10647-10652 (2002).

Whalen WA, Berg CM. Gratuitous repression of avtA in Escherichia coli and Salmonella typhimurium. J. Bacteriol. 158: 571-574 (1984).

Whalen WA, Berg CM. Analysis of an avtA::Mu d1(Ap lac) mutant: metabolic role of transaminase C. J. Bacteriol. 150: 739-746 (1982).

Whalen WA, Wang MD, Berg CM. beta-Chloro-L-alanine inhibition of the Escherichia coli alanine-valine transaminase. J. Bacteriol. 164: 1350-1352 (1985).

Whatmore AM, Chudek JA, Reed RH. The effects of osmotic upshock on the intracellular solute pools of Bacillus subtilis. J. Gen. Microbiol. 136: 2527-2535 (1990).

Whatmore AM, Reed RH. Determination of turgor pressure in Bacillus subtilis: a possible role for K+ in turgor regulation. J. Gen. Microbiol. 136: 2521-2526 (1990).

Whipp MJ, Camakaris H, Pittard AJ. Cloning and analysis of the shiA gene, which encodes the shikimate transport system of Escherichia coli K-12. Gene 209: 185-192 (1998).

Whipp MJ, Pittard AJ. A reassessment of the relationship between aroK- and aroL-encoded shikimate kinase enzymes of Escherichia coli. J. Bacteriol. 177: 1627-1629 (1995).

Whitaker RJ, Berry A, Byng GS, Fiske MJ, Jensen RA. Clues from Xanthomonas campestris about the evolution of aromatic biosynthesis and its regulation. J. Mol. Evol. 21: 139-149 (1984).

White MF, Vasquez J, Yang SF, Kirsch JF. Expression of apple 1-aminocyclopropane-1-carboxylate synthase in Escherichia coli: kinetic characterization of wild-type and active-site mutant forms. Proc. Natl. Acad. Sci. U.S.A. 91: 12428-12432 (1994).

White SW, Zheng J, Zhang YM, Rock. The structural biology of type II fatty acid biosynthesis. Annu. Rev. Biochem. 74: 791-831 (2005).

Whitehead SJ, Rossington KE, Hafiz A, Cotton NP, Jackson JB. Zinc ions selectively inhibit steps associated with binding and release of NADP(H) during turnover of proton-translocating transhydrogenase. FEBS Lett. 579: 2863-2867 (2005).

Whitney SM, Sharwood RE. Construction of a tobacco master line to improve Rubisco engineering in chloroplasts. J. Exp. Bot. 59: 1909-1821 (2008).

Wiback SJ, Mahadevan R, Palsson BO. Using metabolic flux data to further constrain the metabolic solution space and predict internal flux patterns: the Escherichia coli spectrum. Biotechnol. Bioeng. 86: 317-331 (2004).

Widmann M, Christen P. Comparison of folding rates of homologous prokaryotic and eukaryotic proteins. J. Biol. Chem. 275: 18619-18622 (2000).

Wiechert W. Modeling and simulation: tools for metabolic engineering. J. Biotechnol. 94: 37-63 (2002).

Wiese DE 2nd, Ernsting BR, Blumenthal RM, Matthews RG. A nucleoprotein activation complex between the leucine-responsive regulatory protein and DNA upstream of the gltBDF operon in Escherichia coli. J. Mol. Biol. 270: 152-168 (1997).

Wildung MR, Croteau R. A cDNA clone for taxadiene synthase, the diterpene cyclase that catalyzes the committed step of taxol biosynthesis. J. Biol. Chem. 271: 9201-9204 (1996).

Wilhelm T, Behre J, Schuster S. Analysis of structural robustness of metabolic networks. Syst. Biol. (Stevenage) 1: 114-120 (2004).

Wilkie SE, Roper JM, Smith AG, Warren MJ. Isolation, characterisation and expression of a cDNA clone encoding plastid aspartate aminotransferase from Arabidopsis thaliana. Plant Mol. Biol. 27: 1227-1233 (1995).

Willemoes M, Sigurskjold BW. Steady-state kinetics of the glutaminase reaction of CTP synthase from Lactococcus lactis. The role of the allosteric activator GTP incoupling between glutamine hydrolysis and CTP synthesis. Eur. J. Biochem. 269: 4772-4779 (2002).

Williams BA, Sillaots S, Tsang A, Storms R. Isolation by genetic complementation of two differentially expressed genes for beta-isopropylmalate dehydrogenase from Aspergillus niger. Curr. Genet. 30: 305-311 (1996).

Williams J, Phillips AL, Gaskin P, Hedden P. Function and substrate specificity of the gibberellin 3beta-hydroxylase encoded by the Arabidopsis GA4 gene. Plant Physiol. 117: 559-563 (1998).

Williamson CL, Slocum RD. Molecular cloning and characterization of the pyrB1 and pyrB2 genes encoding aspartate transcarbamoylase in pea (Pisum sativum L.). Plant Physiol. 105: 377-384 (1994).

Williamson JM, Brown GM. Purification and properties of L-aspartate-alpha-decarboxylase, an enzyme that catalyzes the formation of beta-alanine in Escherichia coli. J. Biol. Chem. 254: 8074-8082 (1979).

Willows RD, Mayer SM, Foulk MS, DeLong A, Hanson K, Chory J, Beale SI. Phytobilin biosynthesis: the Synechocystis sp. PCC 6803 heme oxygenase-encoding ho1 gene complements a phytochrome-deficient Arabidopsis thalianna hy1 mutant. Plant Mol. Biol. 43: 113-120 (2000).

Wilmanns M, Hyde CC, Davies DR, Kirschner K, Jansonius JN. Structural conservation in parallel beta/alpha-barrel enzymes that catalyze three sequential reactions in the pathway of tryptophan biosynthesis. Biochemistry 30: 9161-9169 (1991).

Wilquet V, Gaspar JA, van de Lande M, Van de Casteele M, Legrain C, Meiering EM, Glansdorff N. Purification and characterization of recombinant Thermotoga maritima dihydrofolate reductase. Eur. J. Biochem. 255: 628-637 (1998).

Wilson CA, Kreychman J, Gerstein M. Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. J. Mol. Biol. 297: 233-249 (2000).

Winefield CS, Reddington BD, Jones WT, Reynolds PH, Farnden KJ. Cloning and characterization of a cDNA encoding aspartate aminotransferase-P1 from Lupinus angustifolius root tips. Plant Physiol. 104: 417-423 (1994).

Winkler HH, Daugherty RM. Proline transport and metabolism in Rickettsia prowazekii. J. Bacteriol. 158: 460-463 (1984).

Winson MK, Goodacre R, Woodward AM, Timmins EM, Jones A, Alsberg BK, Rowland JJ, Kell DB. Diffuse reflectance absorbance spectroscopy taking in chemometrics (DRASTIC). A hyperspectral FT-IR-based approach to rapid screening for metabolite overproduction. Anal. Chim. Acta 348: 273-282 (1997).

Wintrode PL, Rojsajjakul T, Vadrevu R, Matthews CR, Smith DL. An obligatory intermediate controls the folding of the alpha-subunit of tryptophan synthase, a TIM barrel protein. J. Mol. Biol. 347: 911-919 (2005).

Witkowski A, Joshi AK, Lindqvist Y, Smith S. Conversion of a beta-ketoacyl synthase to a malonyl decarboxylase by replacement of the active-site cysteine with glutamine. Biochemistry 38: 11643-1150 (1999).

Witmer MR, Palmieri-Young D, Villafranca JJ. Probing the catalytic roles of n2-site glutamate residues in Escherichia coli glutamine synthetase by mutagenesis. Protein Sci. 3: 1746-1759 (1994).

Witte CP, Isidore E, Tiller SA, Davies HV, Taylor MA. Functional characterisation of urease accessory protein G (ureG) from potato. Plant Mol. Biol. 45: 169-179 (2001).

Witte CP, Rosso MG, Romeis T. Identification of three urease accessory proteins that are required for urease activation in Arabidopsis. Plant Physiol. 139: 1155-1162 (2005).

Witte S, Moco S, Vervoort J, Matern U, Martens S. Recombinant expression and functional characterisation of regiospecific flavonoid glucosyltransferases from Hieracium pilosella L. Planta 229: 1135-1146 (2009).

Wittmann C, Kromer JO, Kiefer P, Binz T, Heinzle E. Impact of the cold shock phenomenon on quantification of intracellular metabolites in bacteria. Anal. Biochem. 327: 135-139 (2004).

Wittstock U, Halkier BA. Cytochrome P450 CYP79A2 from Arabidopsis thaliana L. catalyzes the conversion of L-phenylalanine to phenylacetaldoxime in the biosynthesis of benzylglucosinolate. J. Biol. Chem. 275: 14659-14666 (2000).

Witty M, Jones RM, Robb MS, Jordan PM, Smith AG. Subcellular location of the tetrapyrrole synthesis enzyme porphobilinogen deaminase in higher plants: an immunological investigation. Planta 199: 557-564 (1996).

Wlaschin AP, Trinh CT, Carlson R, Srienc F. The fractional contributions of elementary modes to the metabolism of Escherichia coli and their estimation from reaction entropies. Metab. Eng. 8: 338-352 (2006).

Wolfe-Simon F, Starovoytov V, Reinfelder JR, Schofield O, Falkowski PG. Localization and role of manganese superoxide dismutase in a marine diatom. Plant Physiol. 142: 1701-1709 (2006).

Wolff M, Seemann M, Bui BTS, Frapart Y, Tritsch D, Estrabot AG, Rodriguez-Concepcion M, Boronat A, Marquet A, Rohmer M. Isoprenoid biosynthesis via the methylerythritol phosphate pathway: the (E)-4-hydroxy-3-methylbut-2-enyl diphosphate reductase (LytB/IspH) from Escherichia coli is a [4Fe-4S] protein. FEBS Lett. 541: 115-120 (2003).

Wolter FP, Schmidt R, Heinz E. Chilling sensitivity of Arabidopsis thaliana with genetically engineered membrane lipids. EMBO J. 11: 4685-4692 (1992).

Wolucka BA, Van Montagu M. GDP-mannose 3',5'-epimerase forms GDP-L-gulose, a putative intermediate for the de novo biosynthesis of vitamin C in plants. J. Biol. Chem. 278: 47483-47490 (2003).

Wood JM. Proline porters effect the utilization of proline as nutrient or osmoprotectant for bacteria. J. Membr. Biol. 106: 183-202 (1988).

Wood JM. Osmosensing by bacteria: signals and membrane-based sensors. Microbiol. Mol. Biol. Rev. 63: 230-262 (1999).

Wood JM. Membrane association of proline dehydrogenase in Escherichia coli is redox dependent. Proc. Natl. Acad. Sci. U.S.A. 84: 373-377 (1987).

Wood JM. Genetics of L-proline utilization in Escherichia coli. J. Bacteriol. 146: 895-901 (1981).

Wood JM, Taylor KA, McClellan DJ, Lawrie GG, Krogsrud RL, Beveridge TJ. Isolation and characterization of monoclonal antibodies to proline dehydrogenase from Escherichia coli K-12. Biochem. Cell Biol. 65: 507-513 (1987).

Wood JM, Zadworny D. Characterization of an inducible porter required for L-proline catabolism by Escherichia coli K12. Can. J. Biochem. 57: 1191-1199 (1979).

Wood JM, Zadworny D. Amplification of the put genes and identification of the put gene products in Escherichia coli K12. Can. J. Biochem. 58: 787-796 (1980).

Wood NJ, Alizadeh T, Richardson DJ, Ferguson SJ, Moir JWB. Two domains of a dual-function NarK protein are required for nitrate uptake, the first step of denitrification in Paracoccus pantotrophus. Mol. Microbiol. 44: 157-170 (2002).

Woodcock SC, Raux E, Levillayer F, Thermes C, Rambach A, Warren MJ. Effect of mutations in the transmethylase and dehydrogenase/chelatase domains of sirohaem synthase (CysG) on sirohaem and cobalamin biosynthesis. Biochem. J. 330: 121-129 (1998).

Worley CK, Ling R, Callis J. Engineering in vivo instability of firefly luciferase and Escherichia coli beta-glucuronidase in higher plants using recognition elements from the ubiquitin pathway. Plant Mol. Biol. 37: 337-347 (1998).

Wray JL, Campbell EI, Roberts MA, Gutierrez-Marcos JF. Redefining reductive sulfate assimilation in higher plants: a role for APS reductase, a new member of the thioredoxin superfamily? Chem. Biol. Interact. 109: 153-167 (1998).

Wrenger C, Muller S. Isocitrate dehydrogenase of Plasmodium falciparum. Eur. J. Biochem. 270: 1775-1783 (2003).

Wu B, Georgopoulos C, Ang D. The essential Escherichia coli msgB gene, a multicopy suppressor of a temperature-sensitive allele of the heat shock gene grpE, is identical to dapE. J. Bacteriol. 174: 5258-5264 (1992).

Wu G, Nie L, Zhang W. Integrative analyses of posttranscriptional regulation in the yeast Saccharomyces cerevisiae using transcriptomic and proteomic data. Curr. Microbiol. 57: 18-22 (2008).

Wu J, Masri N, Lee W, Frankel LK, Bricker TM. Random mutagenesis in the large extrinsic loop E and transmembrane alpha-helix VI of the CP 47 protein of Photosystem II. Plant Mol. Biol. 39: 381-386 (1999).

Wu K, Li L, Gage DA, Zeevaart JA. Molecular cloning and photoperiod-regulated expression of gibberellin 20-oxidase from the long-day plant spinach. Plant Physiol. 110: 547-554 (1996).

Wu LF, Mandrand-Berthelot MA, Waugh R, Edmonds CJ, Holt SE, Boxer DH. Nickel deficiency gives rise to the defective hydrogenase phenotype of hydC and fnr mutants in Escherichia coli. Mol. Microbiol. 3: 1709-1718 (1989).

Wu Q, Preisig CL, VanEtten HD. Isolation of the cDNAs encoding (+)6a-hydroxymaackiain 3-O-methyltransferase, the terminal step for the synthesis of the phytoalexin pisatin in Pisum sativum. Plant Mol. Biol. 35: 551-560 (1997).

Wu S, Watanabe N, Mita S, Dohra H, Ueda Y, Shibuya M, Ebizuka Y. The key role of phloroglucinol O-methyltransferase in the biosynthesis of Rosa chinensis volatile 1,3,5-trimethoxybenzene. Plant Physiol. 135: 95-102 (2004).

Wu SP, Liu C, Hwang TS, Chen JT, Tsai H. Improving the catalytic activity of phenylalanine aminotransferase of Escherichia coli by site-specific mutation. Ann. N.Y. Acad. Sci. 864: 561-564 (1998).

Wu WF, Urbanowski ML, Stauffer GV. Role of the MetR regulatory system in vitamin B12-mediated repression of the Salmonella typhimurium metE gene. J. Bacteriol. 174: 4833-4837 (1992).

Wu Y, Matthews CR. Proline replacements and the simplification of the complex, parallel channel folding mechanism for the alpha subunit of Trp synthase, a TIM barrel protein. J. Mol. Biol. 330: 1131-1144 (2003).

Wu Y, Vadrevu R, Yang X, Matthews CR. Specific structure appears at the N terminus in the sub-millisecond folding intermediate of the alpha subunit of tryptophan synthase, a TIM barrel protein. J. Mol. Biol. 351: 445-452 (2005).

Wuebbens MM, Liu MT, Rajagopalan K, Schindelin H. Insights into molybdenum cofactor deficiency provided by the crystal structure of the molybdenum cofactor biosynthesis protein MoaC. Structure Fold. Des. 8: 709-718 (2000).

Wulff-Strobel CR, Wilson DB. Cloning, sequencing, and characterization of a membrane-associated Prevotella ruminicola B(1)4 beta-glucosidase with cellodextrinase and cyanoglycosidase activities. J. Bacteriol. 177: 5884-5890 (1995).

Wunderlich Z, Mirny LA. Using the topology of metabolic networks to predict viability of mutant strains. Biophys. J. 91: 2304-2311 (2006).

Wycliffe P, Sitbon F, Wernersson J, Ezcurra I, Ellerstrom M, Rask L. Continuous expression in tobacco leaves of a Brassica napus PEND homologue blocks differentiation of plastids and development of palisade cells. Plant J. 44: 1-15 (2005).

Wycoff KL, Powell PA, Gonzales RA, Corbin DR, Lamb C, Dixon RA. Stress activation of a bean hydroxyproline-rich glycoprotein promoter is superimposed on a pattern of tissue-specific developmental expression. Plant Physiol. 109: 41-52 (1995).

Xia M, Zhu Y, Cao X, You L, Chen Z. Cloning, sequencing and analysis of a gene encoding Escherichia coli proline dehydrogenase. FEMS Microbiol. Lett. 127: 235-242 (1995).

Xia T, Zhao G, Jensen RA. The pheA/tyrA/aroF region from Erwinia herbicola: an emerging comparative basis for analysis of gene organization and regulation in enteric bacteria. J. Mol. Evol. 36: 107-120 (1993).

Xia ZQ, Costa MA, Pelissier HC, Davin LB, Lewis NG. Secoisolariciresinol dehydrogenase purification, cloning, and functional expression - Implications for human health protection. J. Biol. Chem. 276: 12614-12623 (2001).

Xie DY, Jackson LA, Cooper JD, Ferreira D, Paiva NL. Molecular and biochemical analysis of two cDNA clones encoding dihydroflavonol-4-reductase from Medicago truncatula. Plant Physiol. 134: 979-994 (2004).

Xie G, Bonner CA, Jensen RA. A probable mixed-function supraoperon in Pseudomonas exhibits gene organization features of both intergenomic conservation and gene shuffling. J. Mol. Evol. 49: 108-121 (1999).

Xie G, Brettin TS, Bonner CA, Jensen RA. Mixed-function supraoperons that exhibit overall conservation, albeit shuffled gene organization, across wide intergenomic distances within eubacteria. Microb. Comp. Genomics 4: 5-28 (1999).

Xie L, Lee SA, Hanel BM, Eiteman MA, Altman E. Anaerobic fermentation of Salmonella typhimurium with and without pyruvate carboxylase. Biotechnol. Lett. 23: 111-117 (2001).

Xu B, Jahic M, Enfors SO. Modeling of overflow metabolism in batch and fed-batch cultures of Escherichia coli. Biotechnol. Prog. 15: 81-90 (1999).

Xu C, Jing R, Mao X, Jia X, Chang X. A wheat (Triticum aestivum) protein phosphatase 2A catalytic subunit gene provides enhanced drought tolerance in tobacco. Ann. Bot. (Lond.) 99: 439-450 (2007).

Xu J, Johnson RC. Cyclic AMP receptor protein functions as a repressor of the osmotically inducible promoter proP P1 in Escherichia coli. J. Bacteriol. 179: 2410-2417 (1997).

Xu J, Johnson RC. Fis activates the RpoS-dependent stationary-phase expression of proP in Escherichia coli. J. Bacteriol. 177: 5222-5231 (1995).

Xu X, Dietrich CR, Lessire R, Nikolau BJ, Schnable PS. The endoplasmic reticulum-associated maize GL8 protein is a component of the acyl-coenzyme A elongase ivolved in the production of cuticular waxes. Plant Physiol. 128: 924-934 (2002).

Xu Y, Cheah E, Carr PD, van Heeswijk WC, Westerhoff HV, Vasudevan SG, Ollis DL. GlnK, a PII-homologue: structure reveals ATP binding site and indicates how the T-loops may be involved in molecular recognition. J. Mol. Biol. 282: 149-165 (1998).

Xu Y, Wen D, Brown C, Chen CJ, Carr PD, Ollis DL, Vasudevan SG. Expression, purification and crystallization of the C-terminal domain of Escherichia coli adenylyltransferase. Acta Crystallograph. Sect. F. Struct. Biol. Cryst. Commun. 61: 663-665 (2005).

Xu Y, Zhang R, Joachimiak A, Carr PD, Huber T, Vasudevan SG, Ollis DL. Structure of the N-terminal domain of Escherichia coli glutamine synthetase adenylyltransferase. Structure (Camb.) 12: 861-869 (2004).

Xu YB, Wen DY, Clancy P, Carr PD, Ollis DL, Vasudevan SG. Expression, purification, crystallization, and preliminary X-ray analysis of the N-terminal domain of Escherichia coli adenylyl transferase. Protein Expr. Purif. 34: 142-146 (2004).

Xu ZJ, Nakajima M, Suzuki Y, Yamaguchi I. Cloning and characterization of the abscisic acid-specific glucosyltransferase gene from adzuki bean seedlings. Plant Physiol. 129: 1285-1295 (2002).

Yabe T, Morimoto K, Kikuchi S, Nishio K, Terashima I, Nakai M. The Arabidopsis chloroplastic NifU-like protein CnfU, which can act as an iron-sulfur cluster scaffold protein, is required for biogenesis of ferredoxin and photosystem I. Plant Cell 16: 993-1007 (2004).

Yabuta Y, Maruta T, Yoshimura K, Ishikawa T, Shigeoka S. Two distinct redox signaling pathways for cytosolic APX induction under photooxidative stress. Plant Cell Physiol. 45: 1586-1594 (2004).

Yadegarinia D, Gachkar L, Rezaei MB, Taghizadeh M, Astaneh SA, Rasooli I. Biochemical activities of Iranian Mentha piperita L. and Myrtus communis L. essential oils. Phytochemistry 67: 1249-1255 (2006).

Yaish MW, Doxey AC, McConkey BJ, Moffatt BA, Griffith M. Cold active winter rye glucanases with ice-binding capacity. Plant Physiol. 141: 1459-1472 (2006).

Yamada K, Oura Y, Mori H, Yamaki S. Cloning of NAD-dependent sorbitol dehydrogenase from apple fruit and gene expression. Plant Cell Physiol. 39: 1375-1379 (1998).

Yamada M, Feucht BU, Saier MH Jr. Regulation of gluconeogenesis by the glucitol enzyme III of the phosphotransferase system in Escherichia coli. J. Bacteriol. 169: 5416-5422 (1987).

Yamada M, Saier MH Jr. Physical and genetic characterization of the glucitol operon in Escherichia coli. J. Bacteriol. 169: 2990-2994 (1987).

Yamada M, Saier MH Jr. Glucitol-specific enzymes of the phosphotransferase system in Escherichia coli. Nucleotide sequence of the gut operon. J. Biol. Chem. 262: 5455-5463 (1987).

Yamaguchi K, Prieto S, Beligni MV, Haynes PA, McDonald WH, Yates JR 3rd, Mayfield SP. Proteomic characterization of the small subunit of Chlamydomonas reinhardtii chloroplast ribosome: identification of a novel S1 domain-containing protein and unusually large orthologs of bacterial S2, S3, and S5. Plant Cell 14: 2957-2974 (2002).

Yamaguchi K, Subramanian AR. Proteomic identification of all plastid-specific ribosomal proteins in higher plant chloroplast 30S ribosomal subunit. Eur. J. Biochem. 270: 190-205 (2003).

Yamaguchi S, Sun Tp, Kawaide H, Kamiya Y. The GA2 locus of Arabidopsis thaliana encodes ent-kaurene synthase of gibberellin biosynthesis. Plant Physiol. 116: 1271-1278 (1998).

Yamamoto K, Kataoka E, Miyamoto N, Furukawa K, Ohsuye K, Yabuta M. Genetic engineering of Escherichia coli for production of tetrahydrobiopterin. Metab. Eng. 5: 246-254 (2003).

Yamamoto S, Wakayama M, Tachiki T. Cloning and expression of Pseudomonas taetrolens Y-30 gene encoding glutamine synthetase: an enzyme available for theanine production by coupled fermentation with energy transfer. Biosci. Biotechnol. Biochem. 70: 500-507 (2006).

Yamanaka K, Ogura T, Koonin EV, Niki H, Hiraga S. Multicopy suppressors, mssA and mssB, of an smbA mutation of Escherichia coli. Mol. Gen. Genet. 243: 9-16 (1994).

Yamato I, Anraku Y. Site-specific alteration of cysteine 281, cysteine 344, and cysteine 349 in the proline carrier of Escherichia coli. J. Biol. Chem. 263: 16055-16057 (1988).

Yamazaki Y, Suh DY, Sitthithaworn W, Ishiguro K, Kobayashi Y, Shibuya M, Ebizuka Y, Sankawa U. Diverse chalcone synthase superfamily enzymes from the most primitive vascular plant, Psilotum nudum. Planta 214: 75-84 (2001).

Yanagimachi KS, Stafford DE, Dexter AF, Sinskey AJ, Drew S, Stephanopoulos G. Application of radiolabeled tracers to biocatalytic flux analysis. Eur. J. Biochem. 268: 4950-4960 (2001).

Yanchunas J Jr, Dabrowski MJ, Schurke P, Atkins WM. Supramolecular self-assembly of Escherichia coli glutamine synthetase: characterization of dodecamer stacking and high order association. Biochemistry 33: 14949-14956 (1994).

Yang AH, Yeh KW. Molecular cloning, recombinant gene expression, and antifungal activity of cystatin from taro (Colocasia esculenta cv. Kaosiung no. 1). Planta 221: 493-501 (2005).

Yang C, Hua Q, Shimizu K. Development of a kinetic model for L-lysine biosynthesis in Corynebacterium glutamicum and its application to metabolic control analysis. J. Biosci. Bioeng. 88: 393-403 (1999).

Yang Lh, Ahmed SA, Miles EW. PCR mutagenesis and overexpression of tryptophan synthase from Salmonella typhimurium: on the roles of beta2 subunit Lys-382. Protein Expr. Purif. 8: 126-136 (1996).

Yang LM, Lamppa G. Identification of a chloroplast coenzyme A-binding protein related to the peroxisomal thiolases. Plant Physiol. 112: 1641-1647 (1996).

Yang Q, Lindahl PA, Morgan JJ. Dynamic responses of protein homeostatic regulatory mechanisms to perturbations from steady state. J. Theor. Biol. 222: 407-423 (2003).

Yang Q, Reinhard K, Schiltz E, Matern U. Characterization and heterologous expression of hydroxycinnamoyl/benzoyl-CoA:anthranilate N-hydroxycinnamoyl/benzoyltransferase from elicited cell cultures of carnation, Dianthus caryophyllus L. Plant Mol. Biol. 35: 777-789 (1997).

Yang SH, Berberich T, Miyazaki A, Sano H, Kusano T. Ntdin, a tobacco senescence-associated gene, is involved in molybdenum cofactor biosynthesis. Plant Cell Physiol. 44: 1037-1044 (2003).

Yang TB, Poovaiah BW. Molecular and biochemical evidence for the involvement of calcium/calmodulin in auxin action. J. Biol. Chem. 275: 3137-3143 (2000).

Yang XF, Ji Y, Schneider BL, Reitzer L. Phosphorylation-independent dimer-dimer interactions by the enhancer-binding activator NtrC of Escherichia coli: a third function for the C-terminal domain. J. Biol. Chem. 279: 36708-36714 (2004).

Yang XJ, Ruvinov SB, Miles EW. Overexpression and purification of the separate tryptophan synthase alpha and beta subunits from Salmonella typhimurium. Protein Expr. Purif. 3: 347-354 (1992).

Yang XM, MacKenzie RE. Expression of human NAD-dependent methylenetetrahydrofolate dehydrogenase-methenyltetrahydrofolate cyclohydrolase in Escherichia coli: purification and partial characterization. Protein Expr. Purif. 3: 256-262 (1992).

Yang YL, Liao JC. Determination of functional interactions among signalling pathways in Escherichia coli K-12. Metab. Eng. 7: 280-290 (2005).

Yang YT, Aristidou AA, San KY, Bennett GN. Metabolic flux analysis of Escherichia coli deficient in the acetate production pathway and expressing the Bacillus subtilis acetolactate synthase. Metab. Eng. 1: 26-34 (1999).

Yang YT, Bennett GN, San KY. Effect of inactivation of nuo and ackA-pta on redistribution of metabolic fluxes in Escherichia coli. Biotechnol. Bioeng. 65: 291-297 (1999).

Yang YT, Bennett GN, San KY. Genetic and metabolic engineering. EJB Electronic Journal of Biotechnology 1: 1-8 (1998).

Yang YT, Bennett GN, San KY. The effects of feed and intracellular pyruvate levels on the redistribution of metabolic fluxes in Escherichia coli. Metab. Eng. 3: 115-123 (2001).

Yang YT, Peredelchuk M, Bennett GN, San KY. Effect of variation of Klebsiella pneumoniae acetolactate synthase expression on metabolic flux redistribution in Escherichia coli. Biotechnol. Bioeng. 69: 150-159 (2000).

Yang YT, San KY, Bennett GN. Redistribution of metabolic fluxes in Escherichia coli with fermentative lactate dehydrogenase overexpression and deletion. Metab. Eng. 1: 141-152 (1999).

Yano T, Oue S, Kagamiyama H. Directed evolution of an aspartate aminotransferase with new substrate specificities. Proc. Natl. Acad. Sci. U.S.A. 95: 5511-5515 (1998).

Yao X, Soden C Jr, Summers MF, Beckett D. Comparison of the backbone dynamics of the apo- and holo-carboxy-terminal domain of the biotin carboxyl carrier subunit of Escherichia coli acetyl-CoA carboxylase. Protein Sci. 8: 307-317 (1999).

Yasuno R, Wada H. Biosynthesis of lipoic acid in Arabidopsis: cloning and characterization of the cDNA for lipoic acid synthase. Plant Physiol. 118: 935-943 (1998).

Ye QZ, Liu J, Walsh CT. p-Aminobenzoate synthesis in Escherichia coli: purification and characterization of PabB as aminodeoxychorismate synthase and enzyme X as aminodeoxychorismate lyase. Proc. Natl. Acad. Sci. U.S.A. 87: 9391-9395 (1990).

Yeh CH, Chen YM, Lin CY. Functional regions of rice heat shock protein, Oshsp16.9, required for conferring thermotolerance in Escherichia coli. Plant Physiol. 128: 661-668 (2002).

Yeh S, Moffatt BA, Griffith M, Xiong F, Yang DS, Wiseman SB, Sarhan F, Danyluk J, Xue YQ, Hew CL, Doherty-Kirby A, Lajoie G. Chitinase genes responsive to cold encode antifreeze proteins in winter cereals. Plant Physiol. 124: 1251-1264 (2000).

Yehudai-Resheff S, Portnoy V, Yogev S, Adir N, Schuster G. Domain analysis of the chloroplast polynucleotide phosphorylase reveals discrete functions in RNA degradation, polyadenylation, and sequence homology with exosome proteins. Plant Cell 15: 2003-2019 (2003).

Yevtushenko DP, McLean MD, Peiris S, Van Cauwenberghe OR, Shelp BJ. Calcium/calmodulin activation of two divergent glutamate decarboxylases from tobacco. J. Exp. Bot. 54: 2001-2002 (2003).

Yi J, Li K, Draths KM, Frost JW. Modulation of phosphoenolpyruvate synthase expression increases shikimate pathway product yields in E. coli. Biotechnol. Prog. 18: 1141-1148 (2002).

Yildiz FH, Davies JP, Grossman A. Sulfur availability and the SAC1 gene control adenosine triphosphate sulfurylase gene expression in Chlamydomonas reinhardtii. Plant Physiol. 112: 669-675 (1996).

Yilmaz JL, Bulow L. Enhanced stress tolerance in Escherichia coli and Nicotiana tabacum expressing a betaine aldehyde dehydrogenase/choline dehydrogenase fusion protein. Biotechnol. Prog. 18: 1176-1182 (2002).

Yip KS, Britton KL, Stillman TJ, Lebbink J, de Vos WM, Robb FT, Vetriani C, Maeder D, Rice DW. Insights into the molecular basis of thermal stability from the analysis of ion-pair networks in the glutamate dehydrogenase family. Eur. J. Biochem. 255: 336-346 (1998).

Yokota A, Kawasaki S, Iwano M, Nakamura C, Miyake C, Akashi K. Citrulline and DRIP-1 protein (ArgE homologue) in drought tolerance of wild watermelon. Ann. Bot. (Lond.) 89: 825-832 (2002).

Yomano LP, York SW, Zhou S, Shanmugam KT, Ingram LO. Re-engineering Escherichia coli for ethanol production. Biotechnol. Lett. 30: 2097-2103 (2008).

Yonekura-Sakakibara K, Kojima M, Yamaya T, Sakakibara H. Molecular characterization of cytokinin-responsive histidine kinases in maize. Differential ligand preferences and response to cis-zeatin. Plant Physiol. 134: 1654-1661 (2004).

Yonekura-Sakakibara K, Onda Y, Ashikari T, Tanaka Y, Kusumi T, Hase T. Analysis of reductant supply systems for ferredoxin-dependent sulfite reductase in photosynthetic and nonphotosynthetic organs of maize. Plant Physiol. 122: 887-894 (2000).

Yonekura-Sakakibara K, Tanaka Y, Fukuchi-Mizutani M, Fujiwara H, Fukui Y, Ashikari T, Murakami Y, Yamaguchi M, Kusumi T. Molecular and biochemical characterization of a novel hydroxycinnamoyl-CoA: anthocyanin 3-O-glucoside-6"-O-acyltransferase from Perilla frutescens. Plant Cell Physiol. 41: 495-502 (2000).

Yoon HY, Lee EY, Cho SW. Cassette mutagenesis and photoaffinity labeling of adenine binding domain of ADP regulatory site within human glutamate dehydrogenase. Biochemistry 41: 6817-6823 (2002).

Yoon HY, Lee SH, Cho SW, Lee JE, Yoon CS, Park J, Kim TU, Choi SY. TAT-mediated delivery of human glutamate dehydrogenase into PC12 cells. Neurochem. Int. 41: 37-42 (2002).

Yoon SH, Han MJ, Lee SY, Jeong KJ, Yoo JS. Combined transcriptome and proteome analysis of Escherichia coli during high cell density culture. Biotechnol. Bioeng. 81: 753-767 (2003).

Yoshiba Y, Nanjo T, Miura S, Yamaguchi-Shinozaki K, Shinozaki K. Stress-responsive and developmental regulation of delta1- pyrroline-5-carboxylate synthetase 1 (P5CS1) gene expression in Arabidopsis thaliana. Biochem. Biophys. Res. Commun. 261: 766-772 (1999).

Yoshida K, Fujita Y, Ehrlich SD. Three asparagine synthetase genes of Bacillus subtilis. J. Bacteriol. 181: 6081-6091 (1999).

Yoshida K, Sano H, Miwa Y, Ogasawara N, Fujita Y. Cloning and nucleotide sequencing of a 15 kb region of the Bacillus subtilis genome containing the iol operon. Microbiology 140: 2289-2298 (1994).

Yoshida K, Seki S, Fujimura M, Miwa Y, Fujita Y. Cloning and sequencing of a 36-kb region of the Bacillus subtilis genome between the gnt and iol operons. DNA Res. 2: 61-69 (1995).

Yoshida T, Yamaguchi K, Hagishita T, Mitsunaga T, Miyata A, Tanabe T, Toh H, Ohshiro T, Shimao M, Izumi Y. Cloning and expression of the gene for hydroxypyruvate reductase (D-glycerate dehydrogenase from an obligate methylotroph Hyphomicrobium methylovorum GM2. Eur. J. Biochem. 223: 727-732 (1994).

Yoshihara N, Imayama T, Fukuchi-Mizutani M, Okuhara H, Tanaka Y, Ino I, Yabuya T. cDNA cloning and characterization of UDP-glucose : anthocyanidin 3-O-glucosyltransferase in Iris hollandica. Plant Sci. 169: 496-501 (2005).

Yoshihara R, Imaki T, Hori M, Watanabe C, Yamamoto K, Takimoto K. CPD photolyase gene from Spinacia oleracea: repair of UV-damaged DNA and expression in plant organs. J. Radiat. Res (Tokyo) 46: 157-164 (2005).

Yoshimatsu K, Iwasaki T, Fujiwara T. Sequence and electron paramagnetic resonance analyses of nitrate reductase NarGH from a denitrifying halophilic euryarchaeote Haloarcula marismortui. FEBS Lett. 516: 145-150 (2002).

Yoshimura K, Ishikawa T, Nakamura Y, Tamoi M, Takeda T, Tada T, Nishimura K, Shigeoka S. Comparative study on recombinant chloroplastic and cytosolic ascorbate peroxidase isozymes of spinach. Arch. Biochem. Biophys. 353: 55-63 (1998).

Yoshimura K, Ogawa T, Ueda Y, Shigeoka S. AtNUDX1, an 8-oxo-7,8-dihydro-2'-deoxyguanosine 5'-triphosphate pyrophosphohydrolase, is responsible for eliminating oxidized nucleotides in Arabidopsis. Plant Cell Physiol. 48: 1438-1449 (2007).

Yoshimura K, Yabuta Y, Tamoi M, Ishikawa T, Shigeoka S. Alternatively spliced mRNA variants of chloroplast ascorbate peroxidase isoenzymes in spinach leaves. Biochem. J. 338: 41-48 (1999).

Yoshimura M, Nakano Y, Fukamachi H, Koga T. 3-chloro-DL-alanine resistance by L-methionine-alpha-deamino- gamma-mercaptomethane-lyase activity. FEBS Lett. 523: 119-122 (2002).

You X, Nguyen AW, Jabaiah A, Sheff MA, Thorn KS, Daugherty PS. Intracellular protein interaction mapping with FRET hybrids. Proc. Natl. Acad. Sci. U.S.A. 103: 18458-18463 (2006).

Young PG, Smith CA, Metcalf P, Baker EN. Structures of Mycobacterium tuberculosisfolylpolyglutamate synthase complexed with ADP and AMPPCP. Acta Crystallogr. D. Biol. Crystallogr. 64: 745-753 (2008).

Youngs TL, Tunnicliff G. Substrate analogues and divalent cations as inhibitors of glutamate decarboxylase from Escherichia coli. Biochem. Int. 23: 915-22 (1991).

Yu H, Gerstein M. Genomic analysis of the hierarchical structure of regulatory networks. Proc. Natl. Acad. Sci. U.S.A. 103: 14724-14731 (2006).

Yu J, Yu X, Liu J. A thermostable manganese-containing superoxide dismutase from pathogen Chlamydia pneumoniae. FEBS Lett. 562: 22-26 (2004).

Yu TS, Zeeman SC, Thorneycroft D, Fulton DC, Dunstan H, Lue WL, Hegemann B, Tung SY, Umemoto T, Chapple A, Tsai DL, Wang SM, Smith AM, Chen J, Smith SM. alpha-Amylase is not required for breakdown of transitory starch in Arabidopsis leaves. J. Biol. Chem. 280: 9773-9779 (2005).

Yuan B, Yokochi N, Yoshikane Y, Ohnishi K, Yagi T. Molecular cloning, identification and characterization of 2-methyl-3-hydroxypyridine-5-carboxylic-acid-dioxygenase-coding gene from the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. J. Biosci. Bioeng. 102: 504-510 (2006).

Yuan J, Doucette CD, Fowler WU, Feng XJ, Piazza M, Rabitz HA, Wingreen NS, Rabinowitz JD. Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli. Mol. Syst. Biol. 5: 302 (2009).

Yuan J, Palioura S, Salazar JC, Su D, O'Donoghue P, Hohn MJ, Cardoso AM, Whitman WB, Soll D. RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea. Proc. Natl. Acad. Sci. U.S.A. 103: 18923-18927 (2006).

Yuan LZ, Rouviere PE, Larossa RA, Suh W. Chromosomal promoter replacement of the isoprenoid pathway for enhancing carotenoid production in E. coli. Metab. Eng. 8: 79-90 (2006).

Yuan T, Vogel HJ. Substitution of the methionine residues of calmodulin with the unnatural amino acid analogs ethionine and norleucine: biochemical and spectroscopic studies. Prot. Sci. 8: 113-121 (1999).

Yuasa K, Maeshima M. Purification, properties, and molecular cloning of a novel Ca(2+)-binding protein in radish vacuoles. Plant Physiol. 124: 1069-1078 (2000).

Yumoto N, Kawata Y, Noda S, Tokushige M. Rapid purification and characterization of homoserine dehydrogenase from Saccharomyces cerevisiae. Arch. Biochem. Biophys. 285: 270-275 (1991).

Yun H, Lee JW, Jeong J, Chung J, Park JM, Myoung HN, Lee SY. EcoProDB: the Escherichia coli protein database. Bioinformatics 23: 2501-2503 (2007).

Yun M, Park CG, Kim JY, Rock CO, Jackowski S, Park HW. Structural basis for the feedback regulation of Escherichia coli pantothenate kinase by coenzyme A. J. Biol. Chem. 275: 28093-28099 (2000).

Yutani K, Ogasahara K, Tsujita T, Kanemoto K, Matsumoto M, Tanaka S, Miyashita T, Matsushiro A, Sugino Y, Miles EW. Tryptophan synthase alpha subunit glutamic acid 49 is essential for activity. Studies with 19 mutants at position 49. J. Biol. Chem. 262: 13429-13433 (1987).

Zaboura M, Halpern YS. Regulation of gamma-aminobutyric acid degradation in Escherichia coli by nitrogen metabolism enzymes. J. Bacteriol. 133: 447-451 (1978).

Zahalak M, Pratte B, Werth KJ, Thiel T. Molybdate transport and its effect on nitrogen utilization in the cyanobacterium Anabaena variabilis ATCC 29413. Mol. Microbiol. 51: 539-549 (2004).

Zahiri HS, Yoon SH, Keasling JD, Lee SH, Won Kim S, Yoon SC, Shin YC. Coenzyme Q10 production in recombinant Escherichia coli strains engineered with a heterologous decaprenyl diphosphate synthase gene and foreign mevalonate pathway. Metab. Eng. 8: 406-416 (2006).

Zaigraeva GG, Shakulov RS, Gusiatiner MM, Livshits VA, Zhdanova NI. Functional study of gene relA in the expression of amino acid operons. III. The effect of the allelic state of gene relA on the derepression of the threonine and isoleucine-valine operons of Escherichia coli K-12. Genetika 16: 205-211 (1980).

Zaldivar J, Nielsen J, Olsson L. Fuel ethanol production from lignocellulose: a challenge for metabolic engineering and process integration. Appl. Microbiol. Biotechnol. 56: 17-34 (2001).

Zalkin H, Yanofsky C. Yeast gene TRP5: structure, function, regulation. J. Biol. Chem. 257: 1491-1500 (1982).

Zamboni N, Kummel A, Heinemann M. anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data. BMC Bioinformatics 9: 199 (2008).

Zeth K. Structural analysis of DegS, a stress sensor of the bacterial periplasm. FEBS Lett. 569: 351-358 (2004).

Zettl R, Schell J, Palme K. Photoaffinity labeling of Arabidopsis thaliana plasma membrane vesicles by 5-azido-[7-3H]indole-3-acetic acid: identification of a glutathione S-transferase. Proc. Natl. Acad. Sci. U.S.A. 91: 689-693 (1994).

Zhai S, Sui Z, Yang A, Zhang J. Characterization of a novel phosphoinositide-specific phospholipase C from Zea mays and its expression in Escherichia coli. Biotechnol. Lett. 27: 799-804 (2005).

Zhang CS, Lu Q, Verma DP. Removal of feedback inhibition of delta1-pyrroline-5-carboxylate synthetase, a bifunctional enzyme catalyzing the first two steps of proline biosynthesis in plants. J. Biol. Chem. 270: 20491-20496 (1995).

Zhang H, Ohyama K, Boudet J, Chen Z, Yang J, Zhang M, Muranaka T, Maurel C, Zhu JK, Gong Z. Dolichol biosynthesis and its effects on the unfolded protein response and abiotic stress resistance in Arabidopsis. Plant Cell 20: 1879-1898 (2008).

Zhang K, Qian Q, Huang Z, Wang Y, Li M, Hong L, Zeng D, Gu M, Chu C, Cheng Z. GOLD HULL AND INTERNODE2 encodes a primarily multifunctional cinnamyl-alcohol dehydrogenase in rice. Plant Physiol. 140: 972-983 (2006).

Zhang K, Sawaya MR, Eisenberg DS, Liao JC. Expanding metabolism for biosynthesis of nonnatural alcohols. Proc. Natl. Acad. Sci. U.S.A. 105: 20653-20658 (2008).

Zhang N, Stewart BG, Moore JC, Greasham RL, Robinson DK, Buckland BC, Lee C. Directed evolution of toluene dioxygenase from Pseudomonas putida for improved selectivity toward cis-indandiol during indene bioconversion. Metab. Eng. 2: 339-348 (2000).

Zhang Q, Shirley N, Lahnstein J, Fincher GB. Characterization and expression patterns of UDP-D-glucuronate decarboxylase genes in barley. Plant Physiol. 138: 131-141 (2005).

Zhang WW, Jiang WH, Zhao GP, Yang YL, Chiao JS. Expression in Escherichia coli, purification and kinetic analysis of the aspartokinase and aspartate semialdehyde dehydrogenase from the rifamycin SV-producing Amycolatopsis mediterranei U32. Appl. Microbiol. Biotechnol. 54: 52-58 (2000).

Zhang X, Liu S, Takano T. Two cysteine proteinase inhibitors from Arabidopsis thaliana, AtCYSa and AtCYSb, increasing the salt, drought, oxidation and cold tolerance. Plant Mol. Biol. 68: 131-143 (2008).

Zhang X, Newman E. Deficiency in L-serine deaminase results in abnormal growth and cell division of Escherichia coli K-12. Mol. Microbiol. 69: 870-881 (2008).

Zhang XQ, Lund AA, Sarath G, Cerny RL, Roberts DM, Chollet R. Soybean nodule sucrose synthase (nodulin-100): further analysis of its phosphorylation using recombinant and authentic root-nodule enzymes. Arch. Biochem. Biophys. 371: 70-82 (1999).

Zhang Y, Huang Z, Du C, Li Y, Cao Z. Introduction of an NADH regeneration system into Klebsiella oxytoca leads to an enhanced oxidative and reductive metabolism of glycerol. Metab. Eng. 11: 101-106 (2009).

Zhang Y, Pohlmann EL, Conrad MC, Roberts GP. The poor growth of Rhodospirillum rubrum mutants lacking PII proteins is due to an excess of glutamine synthetase activity. Mol. Microbiol. 61: 497-510 (2006).

Zhang Y, Primavesi LF, Jhurreea D, Andralojc PJ, Mitchell RA, Powers SJ, Schluepmann H, Delatte T, Wingler A, Paul MJ. Inhibition of SNF1-related protein kinase1 activity and regulation of metabolic pathways by trehalose-6-phosphate. Plant Physiol. 149: 1860-1871 (2009).

Zhang YM, Frank MW, Virga KG, Lee RE, Rock CO, Jackowski S. Acyl carrier protein is a cellular target for the antibacterial action of the pantothenamide class of pantothenate antimetabolites. J. Biol. Chem. 279: 50969-50975 (2004).

Zhao C, Johnson BJ, Kositsup B, Beers EP. Exploiting secondary growth in Arabidopsis. Construction of xylem and bark cDNA libraries and cloning of three xylem endopeptidases. Plant Physiol. 123: 1185-1196 (2000).

Zhao G, Winkler ME. 4-Phospho-hydroxy-L-threonine is an obligatory intermediate in pyridoxal 5'-phosphate coenzyme biosynthesis in Escherichia coli K-12. FEMS Microbiol. Lett. 135: 275-280 (1996).

Zhao G, Xia T, Ingram LO, Jensen RA. An allosterically insensitive class of cyclohexadienyl dehydrogenase from Zymomonas mobilis. Eur. J. Biochem. 212: 157-165 (1993).

Zhao GP, Somerville RL. A single amino acid switch within the "hinge" region of the tryptophan synthase beta subunit of Escherichia coli that leads to diminished association with alpha subunit and arrested conversion of ESII to product. J. Biol. Chem. 268: 14921-14931 (1993).

Zhao GP, Somerville RL. Genetic and biochemical characterization of the trpB8 mutation of Escherichia coli tryptophan synthase. An amino acid switch at the sharp turn of the trypsin-sensitive "hinge" region diminishes substrate binding and alters solubility. J. Biol. Chem. 267: 526-541 (1992).

Zhao GP, Somerville RL, Chitnis PR. Synechocystis PCC 6803 contains a single gene for the beta subunit of tryptophan synthase with strong homology to the trpB genes of Arabidopsis and maize (Zea mays L.). Plant Physiol. 104: 461-466 (1994).

Zhao GS, Xia TH, Fischer RS, Jensen RA. Cyclohexadienyl dehydratase from Pseudomonas aeruginosa. Molecular cloning of the gene and characterization of the gene product. J. Biol. Chem. 267: 2487-2493 (1992).

Zhao J, Baba T, Mori H, Shimizu K. Effect of zwf gene knockout on the metabolism of Escherichia coli grown on glucose or acetate. Metab. Eng. 6: 164-174 (2004).

Zhao KJ, Chye ML. Methyl jasmonate induces expression of a novel Brassica juncea chitinase with two chitin-binding domains. Plant Mol. Biol. 40: 1009-1018 (1999).

Zhao L, Allanson NM, Thomson SP, Maclean JK, Barker JJ, Primrose WU, Tyler PD, Lewendon A. Inhibitors of phosphopantetheine adenylyltransferase. Eur. J. Med. Chem. 38: 345-349 (2003).

Zhao N, Guan J, Lin H, Chen F. Molecular cloning and biochemical characterization of indole-3-acetic acid methyltransferase from poplar. Phytochemistry 68: 1537-1544 (2007).

Zhao Q, Kurata H. Maximum entropy decomposition of flux distribution at steady state to elementary modes. J. Biosci. Bioeng. 107: 84-89 (2009).

Zhao Z, Rothery RA, Weiner JH. Transient kinetic studies of heme reduction in Escherichia coli nitrate reductase A (NarGHI) by menaquinol. Biochemistry 42: 5403-5413 (2003).

Zheng D, Schroder G, Schroder J, Hrazdina G. Molecular and biochemical characterization of three aromatic polyketide synthase genes from Rubus idaeus. Plant Mol. Biol. 46: 1-15 (2001).

Zheng L, Kostrewa D, Berneche S, Winkler FK, Li XD. The mechanism of ammonia transport based on the crystal structure of AmtB of Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 101: 17090-17095 (2004).

Zhigang A, Cuijie L, Yuangang Z, Yejie D, Wachter A, Gromes R, Rausch T. Expression of BjMT2, a metallothionein 2 from Brassica juncea, increases copper and cadmium tolerance in Escherichia coli and Arabidopsis thaliana, but inhibits root elongation in Arabidopsis thaliana seedlings. J. Exp. Bot. 57: 3575-3582 (2006).

Zhong S, Khodursky A, Dykhuizen DE, Dean AM. Evolutionary genomics of ecological specialization. Proc. Natl. Acad. Sci. U.S.A. 101: 11719-11724 (2004).

Zhou D, White RH. Early steps of isoprenoid biosynthesis in Escherichia coli. Biochem. J. 273: 627-634 (1991).

Zhou H, Huxtable S, Xin H, Li N. Enhanced high-level expression of soluble 1-aminocyclopropane-1-carboxylase synthase and rapid purification by expanded-bed adsorption. Protein Expr. Purif. 14: 178-184 (1998).

Zhou J, Zhou J, Yang H, Yan C, Huang F. Characterization of a sodium-regulated glutaminase from cyanobacterium Synechocystis sp. PCC 6803. Sci. China C. Life Sci. 51: 1066-1075 (2008).

Zhou L, Lacroute F, Thornburg R. Cloning, expression in Escherichia coli, and characterization of Arabidopsis thaliana UMP/CMP kinase. Plant Physiol. 117: 245-254 (1998).

Zhou M, Xu H, Wei X, Ye Z, Wei L, Gong W, Wang Y, Zhu Z. Identification of a glyphosate-resistant mutant of rice 5-enolpyruvylshikimate 3-phosphate synthase using a directed evolution strategy. Plant Physiol. 140: 184-195 (2006).

Zhou P, Florova G, Reynolds KA. Polyketide synthase acyl carrier protein (ACP) as a substrate and a catalyst for malonyl ACP biosynthesis. Chem. Biol. 6: 577-584 (1999).

Zhou S, Grabar TB, Shanmugam KT, Ingram LO. Betaine tripled the volumetric productivity of D: (-)-lactate by Escherichia coli strain SZ132 in mineral salts edium. Biotechnol. Lett. 28: 671-676 (2006).

Zhou S, Shanmugam KT, Yomano LP, Grabar TB, Ingram LO. Fermentation of 12% (w/v) glucose to 1.2 M: lactate by Escherichia coli strain SZ194 using mineral salts medium. Biotechnol. Lett. 28: 663-670 (2006).

Zhou Y, Zhu W, Bellur PS, Rewinkel D, Becker DF. Direct linking of metabolism and gene expression in the proline utilization A protein from Escherichia coli. Amino Acids 35: 711-718 (2008).

Zhou ZS, Peariso K, Penner-Hahn JE, Matthews RG. Identification of the zinc ligands in cobalamin-independent methionine synthase (MetE) from Escherichia coli. Biochemistry 38: 15915-15926 (1999).

Zhu C, Yamamura S, Koiwa H, Nishihara M, Sandmann G. cDNA cloning and expression of carotenogenic genes during flower development in Gentiana lutea. Plant Mol. Biol. 48: 277-285 (2002).

Zhu D, Cui S, Nagata S. Isolation and characterization of salt-sensitive mutants of the moderately halophilic bacterium Salinivibrio costicola subsp. yaniae. Biosci. Biotechnol. Biochem. 72: 1977-1982 (2008).

Zhu J, Shalel-Levanon S, Bennett G, San KY. Effect of the global redox sensing/regulation networks on Escherichia coli and metabolic flux distribution based on C-13 labeling experiments. Metab. Eng. 8: 619-627 (2006).

Zhu J, Shimizu K. Effect of a single-gene knockout on the metabolic regulation in Escherichia coli for D-lactate production under microaerobic condition. Metab. Eng. 7: 104-115 (2005).

Zhu MM, Skraly FA, Cameron DC. Accumulation of methylglyoxal in anaerobically grown Escherichia coli and its detoxification by expression of the Pseudomonas putida glyoxalase I gene. Metab. Eng. 3: 218-225 (2001).

Zhu XF, Suzuki K, Saito T, Okada K, Tanaka K, Nakagawa T, Matsuda H, Kawamukai M. Geranylgeranyl pyrophosphate synthase encoded by the newly isolated gene GGPS6 from Arabidopsis thaliana is localized in mitochondria. Plant Mol. Biol. 35: 331-341 (1997).

Zhu Y, Eiteman MA, Altman R, Altman E. High glycolytic flux improves pyruvate production by metabolically engineered Escherichia coli. Appl. Environ. Microbiol. 74: 6649-6655 (2008).

Zhu YL, Pilon-Smits EA, Tarun AS, Weber SU, Jouanin L, Terry N. Cadmium tolerance and accumulation in indian mustard is enhanced by overexpressing gamma-glutamylcysteine synthetase. Plant Physiol. 121: 1169-1178 (1999).

Ziegler C, Morbach S, Schiller D, Kramer R, Tziatzios C, Schubert D, Kuhlbrandt W. Projection structure and oligomeric state of the osmoregulated sodium/glycine betaine symporter BetP of Corynebacterium glutamicum. J. Mol. Biol. 337: 1137-1147 (2004).

Zielinski RE. Characterization of three new members of the Arabidopsis thaliana calmodulin gene family: conserved and highly diverged members of the gene family functionally complement a yeast calmodulin null. Planta 214: 446-455 (2002).

Zientz E, Bongaerts J, Unden G. Fumarate regulation of gene expression in Escherichia coli by the DcuSR (dcuSR genes) two-component regulatory system. J. Bacteriol. 180: 5421-5425 (1998).

Zimmer DP, Soupene E, Lee HL, Wendisch VF, Khodursky AB, Peter BJ, Bender RA, Kustu S. Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation. Proc. Natl. Acad. Sci. U.S.A. 97: 14674-14679 (2000).

Zimmer SL, Schein A, Zipor G, Stern DB, Schuster G. Polyadenylation in Arabidopsis and Chlamydomonas organelles: the input of nucleotidyltransferases, poly(A) polymerases and polynucleotide phosphorylase. Plant J. 59: 88-99 (2009).

Zitzewitz JA, Gualfetti PJ, Perkons IA, Wasta SA, Matthews CR. Identifying the structural boundaries of independent folding domains in the alpha subunit of tryptophan synthase, a beta/alpha barrel protein. Protein Sci. 8: 1200-1209 (1999).

Zocher G, Wiesand U, Schulz GE. High resolution structure and catalysis of O-acetylserine sulfhydrylase isozyme B from Escherichia coli. FEBS J. 274: 5382-5389 (2007).

Zoetewey DL, Tripet BP, Kutateladze TG, Overduin MJ, Wood JM, Hodges RS. Solution structure of the C-terminal antiparallel coiled-coil domain from Escherichia coli osmosensor ProP. J. Mol. Biol. 334: 1063-1076 (2003).

Zolkiewski M, Ginsburg A. Thermodynamic effects of active-site ligands on the reversible, partial unfolding of dodecameric glutamine synthetase from Escherichia coli: calorimetric studies. Biochemistry 31: 11991-12000 (1992).

Zolkiewski M, Nosworthy NJ, Ginsburg A. Urea-induced dissociation and unfolding of dodecameric glutamine synthetase from Escherichia coli: calorimetric and spectral studies. Protein Sci. 4: 1544-1552 (1995).

Zou J, Qi Q, Katavic V, Marillia EF, Taylor DC. Effects of antisense repression of an Arabidopsis thaliana pyruvate dehydrogenase kinase cDNA on plant development. Plant Mol. Biol. 41: 837-849 (1999).

Zumft WG. Nitric oxide signaling and NO dependent transcriptional control in bacterial denitrification by members of the FNR-CRP regulator family. J. Mol. Microbiol. Biotechnol. 4: 277-286 (2002).

Number of references = 3707

| PubMed Search | Entrez Protein Search | ISI Web of Knowledge Search | Scirus Search |

David Rhodes
Department of Horticulture & Landscape Architecture
Horticulture Building
625 Agriculture Mall Drive
Purdue University
West Lafayette, IN 47907-2010
Last Update: 10/01/09