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HORT640 - Metabolic Plant Physiology
References, anaerobic or anox
Aalen N, Steen IH, Birkeland NK, Lien T. Purification and properties of an extremely thermostable NADP+-specific glutamate dehydrogenase from Archaeoglobus fulgidus. Arch. Microbiol. 168: 536-539 (1997).
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).
Abee T, Palmen R, Hellingwerf KJ, Konings WN. Osmoregulation in Rhodobacter sphaeroides. J. Bacteriol. 172: 149-154 (1990).
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).
Adnan S, Susan L, Weiss D. Isolation and characterization of a heat-induced gene, hcit2, encoding a novel 16.5 kDa protein: expression coincides with heat-induced tolerance to chilling stress. Plant Mol. Biol. 36: 935-939 (1998).
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).
Afreen F, Zobayed SM, Armstrong J, Armstrong W. Pressure gradients along whole culms and leaf sheaths, and other aspects of humidity-induced gas transport in Phragmites australis. J. Exp. Bot. 58: 1651-1662 (2007).
Afshar S, Kim C, Monbouquette HG, Schroder I. Effect of tungstate on nitrate reduction by the hyperthermophilic archaeon Pyrobaculum aerophilum. Appl. Environ. Microbiol. 64: 3004-3008 (1998).
Agarwal S, Grover A. Isolation and transcription profiling of low-O2 stress-associated cDNA clones from the flooding-stress-tolerant FR13A rice genotype. Ann. Bot. (Lond.) 96: 831-844 (2005).
Ahn J, Daidou T, Tsuneda S, Hirata A. Transformation of phosphorus and relevant intracellular compounds by a phosphorus-accumulating enrichment culture in the presence of both the electron acceptor and electron donor. Biotechnol. Bioeng. 79: 83-93 (2002).
Ahrens K, Menzel K, Zeng A, Deckwer W. Kinetic, dynamic, and pathway studies of glycerol metabolism by Klebsiella pneumoniae in anaerobic continuous culture: III. Enzymes and fluxes of glycerol dissimilation and 1,3-propanediol formation. Biotechnol. Bioeng. 59: 544-552 (1998).
Akhmanova A, Voncken FG, Hosea KM, Harhangi H, Keltjens JT, Op Den Camp HJ, Vogels GD, Hackstein JH. A hydrogenosome with pyruvate formate-lyase: anaerobic chytrid fungi use an alternative route for pyruvate catabolism. Mol. Microbiol. 32: 1103-1114 (1999).
Akyol I, Shearman CA. Regulation of flpA, flpB and rcfA Promoters in Lactococcus lactis. Curr. Microbiol. 57: 200-205 (2008).
Albers E, Gustafsson L, Niklasson C, Liden G. Distribution of 14C-labelled carbon from glucose and glutamate during anaerobic growth of Saccharomyces cerevisiae. Microbiology 144: 1683-1690 (1998).
Albrecht G, Mustroph A, Fox TC. Sugar and fructan accumulation during metabolic adjustment between respiration and fermentation under low oxygen conditions in wheat roots. Physiol. Plant. 120: 93-105 (2004).
Alferez F, Zhong GY, Burns JK. A citrus abscission agent induces anoxia- and senescence-related gene expression in Arabidopsis. J. Exp. Bot. 58: 2451-2462 (2007).
Allegre A, Silvestre J, Morard P, Kallerhoff J, Pinelli E. Nitrate reductase regulation in tomato roots by exogenous nitrate: a possible role in tolerance to long-term root anoxia. J. Exp. Bot. 55: 2625-2634 (2004).
Allen D, Westerblad H. Lactic acid - the latest performance-enhancing drug. Science 305: 1112-1113 (2004).
Allen JF. A redox switch hypothesis for the origin of two light reactions in photosynthesis. FEBS Lett. 579: 963-968 (2005).
Altaras NE, Cameron DC. Metabolic engineering of a 1,2-propanediol pathway in Escherichia coli. Appl. Environ. Microbiol. 65: 1180-1185 (1999).
Aluru MR, Zola J, Foudree A, Rodermel SR. Chloroplast photooxidation-induced transcriptome reprogramming in Arabidopsis immutans white leaf sectors. Plant Physiol. 150: 904-923 (2009).
Alvarez R, Liden G. The effect of temperature variation on biomethanation at high altitude. Bioresour. Technol. 99: 7278-7284 (2008).
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).
Andrews DL, Cobb BG, Johnson JR, Drew MC. Hypoxic and anoxic induction of alcohol dehydrogenase in roots and shoots of seedlings of Zea mays. ADH transcripts and enzyme activity. Plant Physiol. 101: 407-414 (1993).
Andrews DL, Drew MC, Johnson JR, Cobb BG. The response of maize seedlings of different ages to hypoxic and anoxic stress. Changes in induction of Adh1 mRNA, ADH activity, and survival of anoxia. Plant Physiol. 105: 53-60 (1994).
Andrews DL, MacAlpine DM, Johnson JR, Kelley PM, Cobb BG, Drew MC. Differential induction of mRNAs for the glycolytic and ethanolic fermentative pathways by hypoxia and anoxia in maize seedlings. Plant Physiol. 106: 1575-1582 (1994).
Anesiadis N, Cluett WR, Mahadevan R. Dynamic metabolic engineering for increasing bioprocess productivity. Metab. Eng. 10: 255-266 (2008).
Antipov AN, Lyalikova NN, Khijniak TV, L'vov NP. Molybdenum-free nitrate reductases from vanadate-reducing bacteria. FEBS Lett. 441: 257-260 (1998).
Antipov AN, Lyalikova NN, Khijniak TV, L'vov NP. Vanadate reduction by molybdenum-free dissimilatory nitrate reductases from vanadate-reducing bacteria. IUBMB Life 50: 39-42 (2000).
Antipov AN, Lyalikova NN, Khiznjak TV, L'vov NP. Some properties of dissimilatory nitrate reductases lacking molybdenum and molybdenum cofactor. Biochemistry (Mosc.) 64: 483-487 (1999).
Antipov AN, Sorokin DY, L'vov NP, Kuenen JG. New enzyme belonging to the family of molybdenum-free nitrate reductases. Biochem. J. 369: 185-189 (2003).
Arai H, Igarashi Y, Kodama T. Structure and ANR-dependent transcription of the nir genes for denitrification from Pseudomonas aeruginosa. Biosci. Biotechnol. Biochem. 58: 1286-1291 (1994).
Aranda-Barradas JS, Delia ML, Riba JP. Kinetic study and modelling of the xylitol production using Candida parapsilosis in oxygen-limited culture conditions. Bioprocess Engineering 22: 219-225 (2000).
Arch JR, Newsholme EA. Activities and some properties of 5'-nucleotidase, adenosine kinase and adenosine deaminase in tissues from vertebrates and invertebrates in relation to the control of the concentration and the physiological role of adenosine. Biochem. J. 174: 965-977 (1978).
Argandona M, Martinez-Checa F, Llamas I, Arco Y, Quesada E, Del Moral A. A membrane-bound nitrate reductase encoded by the narGHJI operon is responsible for anaerobic respiration in Halomonas maura. Extremophiles 10: 411-419 (2006).
Armstrong W, Webb T, Darwent M, Beckett PM. Measuring and interpreting respiratory critical oxygen pressures in roots. Ann. Bot. (Lond.) 103: 281-293 (2009).
Arndt C, Gaill F, Felbeck H. Anaerobic sulfur metabolism in thiotrophic symbioses. J. Exp. Biol. 204: 741-750 (2001).
Aschi-Smiti S, Chaibi W, Brouquisse R, Ricard B, Saglio P. Assessment of enzyme induction and aerenchyma formation as mechanisms for flooding tolerance in Trifolium subterraneum 'Park'. Ann. Bot. (Lond.) 91: 195-204 (2003).
Atteia A, van Lis R, Mendoza-Hernandez G, Henze K, Martin W, Riveros-Rosas H, Gonzalez-Halphen D. Bifunctional aldehyde/alcohol dehydrogenase (ADHE) in chlorophyte algal mitochondria. Plant Mol. Biol. 53: 175-188 (2003).
Aurisano N, Bertani A, Reggiani R. Involvement of calcium and calmodulin in protein and amino acid metabolism in rice roots under anoxia. Plant Cell Physiol. 36: 1525-1529 (1995).
Aurisano N, Bertani A, Reggiani R. Anaerobic accumulation of 4-aminobutyrate in rice seedlings: causes and significance. Phytochemistry 38: 1147-1150 (1995).
Babu BN, Brown OR. Quantitative effects of redox-cycling chemicals on the oxidant-sensitive enzyme dihydroxy-acid dehydratase. Microbios. 82: 157-170 (1995).
Bae HS, Im WT, Suwa Y, Lee JM, Lee ST, Chang YK. Characterization of diverse heterocyclic amine-degrading denitrifying bacteria from various environments. Arch. Microbiol. 191: 329-340 (2009).
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).
Bailey-Serres J, Voesenek LA. Flooding stress: acclimations and genetic diversity. Annu. Rev. Plant Biol. 59: 313-339 (2008).
Baker KP, Boxer DH. Regulation of the chlA locus of Escherichia coli K12: involvement of molybdenum cofactor. Mol. Microbiol. 5: 901-907 (1991).
Bakker BM, Michels PAM, Opperdoes FR, Westerhoff HV. Glycolysis in bloodstream form Trypanosoma brucei can be understood in terms of the kinetics of the glycolytic enzymes. J. Biol. Chem. 272: 3207-3215 (1997).
Baliga NS, Pan M, Goo YA, Yi EC, Goodlett DR, Dimitrov K, Shannon P, Aebersold R, Ng WV, Hood L. Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proc. Natl. Acad. Sci. U.S.A. 99: 14913-14918 (2002).
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).
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).
Banti V, Loreti E, Novi G, Santaniello A, Alpi A, Perata P. Heat acclimation and cross-tolerance against anoxia in Arabidopsis. Plant Cell Environ. 31: 1029-1037 (2008).
Basu S, Azarova NA, Font MD, King SB, Hogg N, Gladwin MT, Shiva S, Kim-Shapiro DB. Nitrite reductase activity of cytochrome c. J. Biol. Chem. 283: 32590-32597 (2008).
Baud S, Vaultier MN, Rochat C. Structure and expression profile of the sucrose synthase multigene family in Arabidopsis. J. Exp. Bot. 55: 397-409 (2004).
Baxter-Burrell A, Chang R, Springer P, Bailey-Serres J. Gene and enhancer trap transposable elements reveal oxygen deprivation-regulated genes and their complex patterns of expression in Arabidopsis. Ann. Bot. (Lond.) 91: 129-141 (2003).
Bedzyk L, Wang T, Ye RW. The periplasmic nitrate reductase in Pseudomonas sp. strain G-179 catalyzes the first step of denitrification. J. Bacteriol. 181: 2802-2806 (1999).
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).
Bender KS, Shang C, Chakraborty R, Belchik SM, Coates JD, Achenbach LA. Identification, characterization, and classification of genes encoding perchlorate reductase. J. Bacteriol. 187: 5090-5096 (2005).
Bengtsson O, Hahn-Hagerdal B, Gorwa-Grauslund MF. Xylose reductase from Pichia stipitis with altered coenzyme preference improves ethanolic xylose fermentation by recombinant Saccharomyces cerevisiae. Biotechnol. Biofuels 2: 9 (2009).
Benjdia A, Subramanian S, Leprince J, Vaudry H, Johnson MK, Berteau O. Anaerobic sulfatase-maturating enzymes - first dual substrate radical S-adenosylmethionine enzymes. J. Biol. Chem. 283: 17815-17826 (2008).
Berg BL, Stewart V. Structural genes for nitrate-inducible formate dehydrogenase in Escherichia coli K-12. Genetics 125: 691-702 (1990).
Bergaust L, Shapleigh J, Frostegard A, Bakken L. Transcription and activities of NO(x) reductases in Agrobacterium tumefaciens: the influence of nitrate, nitrite and oxygen availability. Environ. Microbiol. 10: 3070-3081 (2008).
Berks BC, Richardson DJ, Robinson C, Reilly A, Aplin RT, Ferguson SJ. Purification and characterization of the periplasmic nitrate reductase from Thiosphaera pantotropha. Eur. J. Biochem. 220: 117-124 (1994).
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).
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).
Bertoldi M, Dominici P, Moore PS, Maras B, Voltattorni CB. Reaction of dopa decarboxylase with alpha-methyldopa leads to an oxidative deamination producing 3,4-dihydroxyphenylacetone, an active site directed affinity label. Biochemistry 37: 6552-6561 (1998).
Bertoldi M, Voltattorni CB. Dopa decarboxylase exhibits low pH half-transaminase and high pH oxidative deaminase activities toward serotonin (5-hydroxytryptamine). Protein Sci. 10: 1178-1186 (2001).
Bertrand A, Castonguay Y, Nadeau P, Laberge S, Michaud R, Belanger G, Rochette P. Oxygen deficiency affects carbohydrate reserves in overwintering forage crops. J. Exp. Bot. 54: 1721-1730 (2003).
Beun JJ, Dircks K, Van Loosdrecht MC, Heijnen JJ. Poly-beta-hydroxybutyrate metabolism in dynamically fed mixed microbial cultures. Water Res. 36: 1167-1180 (2002).
Beun JJ, Verhoef EV, Van Loosdrecht MC, Heijnen JJ. Stoichiometry and kinetics of poly-beta-hydroxybutyrate metabolism under denitrifying conditions in activated sludge cultures. Biotechnol. Bioeng. 68: 496-507 (2000).
Bhriain NN, Dorman CJ, Higgins CF. An overlap between osmotic and anaerobic stress responses: a potential role for DNA supercoiling in the coordinate regulation of gene expression. Mol. Microbiol. 3: 933-942 (1989).
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).
Biegert T, Altenschmidt U, Eckerskorn C, Fuchs G. Enzymes of anaerobic metabolism of phenolic compounds. 4-Hydroxybenzoate-CoA ligase from a denitrifying Pseudomonas species. Eur. J. Biochem. 213: 555-561 (1993).
Biemelt S, Keetman U, Albrecht G. Re-aeration following hypoxia or anoxia leads to activation of the antioxidative defense system in roots of wheat seedlings. Plant Physiol. 116: 651-658 (1998).
Biemelt S, Keetman U, Mock H-P, Grimm B. Expression and activity of isoenzymes of superoxide dismutase in wheat roots in response to hypoxia and anoxia. Plant Cell Environ. 23: 135-144 (2000).
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, 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).
Bligny R, Douce R. NMR and plant metabolism. Curr. Opin. Plant Biol. 4: 191-196 (2001).
Blokhina O, Virolainen E, Fagerstedt KV. Antioxidants, oxidative damage and oxygen deprivation stress: a review. Ann. Bot. (Lond.) 91: 179-194 (2003).
Blossfeld S, Gansert D. A novel non-invasive optical method for quantitative visualization of pH dynamics in the rhizosphere of plants. Plant Cell Environ. 30: 176-186 (2007).
Boamfa EI, Ram PC, Jackson MB, Reuss J, Harren FJ. Dynamic aspects of alcoholic fermentation of rice seedlings in response to anaerobiosis and to complete submergence: relationship to submergence tolerance. Ann. Bot. (Lond.) 91: 279-290 (2003).
Bond-Lamberty B, Gower ST, Ahl DE. Improved simulation of poorly drained forests using Biome-BGC. Tree Physiol. 27: 703-715 (2007).
Bonnard N, Tresierra-Ayala A, Bedmar EJ, Delgado MJ. Molybdate-dependent expression of the periplasmic nitrate reductase in Bradyrhizobium japonicum. Biochem. Soc. Trans. 33: 127-129 (2005).
Boon L, Geerts WJ, Jonker A, Lamers WH, Van Noorden CJ. High protein diet induces pericentral glutamate dehydrogenase and ornithine aminotransferase to provide sufficient glutamate for pericentral detoxification of ammonia in rat liver lobules. Histochem. Cell Biol. 111: 445-452 (1999).
Borland A, Elliott S, Patterson S, Taybi T, Cushman J, Pater B, Barnes J. Are the metabolic components of Crassulacean acid metabolism up-regulated in response to an increase in oxidative burden? J. Exp. Bot. 57: 319-328 (2006).
Borland AM, Hartwell J, Jenkins GI, Wilkins MB, Nimmo HG. Metabolite control overrides circadian regulation of phosphoenolpyruvate carboxylase kinase and CO(2) fixation in Crassulacean acid metabolism. Plant Physiol. 121: 889-896 (1999).
Botrel A, Kaiser WM. Nitrate reductase activation state in barley roots in relation to the energy and carbohydrate status. Planta 201: 496-501 (1997).
Boulanger MJ, Murphy ME. Crystal structure of the soluble domain of the major anaerobically induced outer membrane protein (AniA) from pathogenic Neisseria: a new class of copper-containing nitrite reductases. J. Mol. Biol. 315: 1111-1127 (2002).
Boulanger Y, Legault P, Tejedor A, Vinay P, Theriault Y. Biochemical characterization and osmolytes in papillary collecting ducts from pig and dog kidneys. Can. J. Physiol. Pharmacol. 66: 1282-1290 (1988).
Bowlus RD, Somero GN. Solute compatibility with enzyme function and structure: rationales for the selection of osmotic agents and end-products of anaerobic metabolism in marine invertebrates. J. Exp. Zool. 208: 137-151 (1979).
Braker G, Tiedje JM. Nitric oxide reductase (norB) genes from pure cultures and environmental samples. Appl. Environ. Microbiol. 69: 3476-3483 (2003).
Branco-Price C, Kaiser KA, Jang CJ, Larive CK, Bailey-Serres J. Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation in Arabidopsis thaliana. Plant J. 56: 743-755 (2008).
Brioukhanov AL, Netrusov AI. Catalase and superoxide dismutase: distribution, properties, and physiological role in cells of strict anaerobes. Biochemistry (Mosc.) 69: 949-962 (2004).
Bro C, Regenberg B, Forster J, Nielsen J. In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production. Metab. Eng. 8: 102-111 (2006).
Brondino CD, Passeggi MCG, Caldeira J, Almendra MJ, Feio MJ, Moura JJG, Moura I. Incorporation of either molybdenum or tungsten into formate dehydrogenase from Desulfovibrio alaskensis NCIMB 13491; EPR assignment of the proximal iron- sulfur cluster to the pterin cofactor in formate dehydrogenases from sulfate- reducing bacteria. J. Biol. Inorg. Chem. 9: 145-151 (2004).
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).
Brusa T, Borin S, Ferrari F, Sorlini C, Corselli C, Daffonchio D. Aromatic hydrocarbon degradation patterns and catechol 2,3-dioxygenase genes in microbial cultures from deep anoxic hypersaline lakes in the eastern Mediterranean sea. Microbiol. Res. 156: 49-58 (2001).
Buchanan BB, Arnon DI. A reverse KREBS cycle in photosynthesis: consensus at last. Photosynth. Res. 24: 47-53 (1990).
Bueno E, Gomez-Hernandez N, Girard L, Bedmar EJ, Delgado MJ. Function of the Rhizobium etli CFN42 nirK gene in nitrite metabolism. Biochem. Soc. Trans. 33: 162-163 (2005).
Bunik VI, Sievers C. Inactivation of the 2-oxo acid dehydrogenase complexes upon generation of intrinsic radical species. Eur. J. Biochem. 269: 5004-5015 (2002).
Burgard AP, Maranas CD. Optimization-based framework for inferring and testing hypothesized metabolic objective functions. Biotechnol. Bioeng. 82: 670-677 (2003).
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).
Cairns AJ, Gallagher JA. Absence of turnover and futile cycling of sucrose in leaves of Lolium temulentum L.: implications for metabolic compartmentation. Planta 219: 836-846 (2004).
Cali BM, Micca JL, Stewart V. Genetic regulation of nitrate assimilation in Klebsiella pneumoniae M5al. J. Bacteriol. 171: 2666-2672 (1989).
Cameron DC, Chaplen FW. Developments in metabolic engineering. Curr. Opin. Biotechnol. 8: 175-80 (1997).
Campbell SC, Olson GJ, Clark TR, McFeters G. Biogenic production of cyanide and its application to gold recovery. J. Ind. Microbiol. Biotechnol. 26: 134-139 (2001).
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).
Carystinos GD, MacDonald HR, Monroy AF, Dhindsa RS, Poole RJ. Vacuolar H(+)-translocating pyrophosphatase is induced by anoxia or chilling in seedlings of rice. Plant Physiol. 108: 641-649 (1995).
Castello PR, David PS, McClure T, Crook Z, Poyton RO. Mitochondrial cytochrome oxidase produces nitric oxide under hypoxic conditions: implications for oxygen sensing and hypoxic signaling in eukaryotes. Cell. Metab. 3: 277-287 (2006).
Castillo F, Dobao MM, Reyes F, Blasco R, Roldán MD, Gavira M, Caballero FJ, Moreno-Vivián C, Martínez-Luque M. Molecular and regulatory properties of the nitrate reducing systems of Rhodobacter. Curr. Microbiol. 33: 341-346 (1996).
Cava F, Zafra O, Berenguer J. A cytochrome c containing nitrate reductase plays a role in electron transport for denitrification in Thermus thermophilus without involvement of the bc respiratory complex. Mol. Microbiol. 70: 507-518 (2008).
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).
Chang C, Meyerowitz EM. Molecular cloning and DNA sequence of the Arabidopsis thaliana alcohol dehydrogenase gene. Proc. Natl. Acad. Sci. U.S.A. 83: 1408-1412 (1986).
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 WW, Huang L, Shen M, Webster C, Burlingame AL, Roberts JK. Patterns of protein synthesis and tolerance of anoxia in root tips of maize seedlings acclimated to a low-oxygen environment, and identification of proteins by mass spectrometry. Plant Physiol. 122: 295-318 (2000).
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).
Chen HP, He M, Huang QR, Liu D, Huang M. Sasanquasaponin protects rat cardiomyocytes against oxidative stress induced by anoxia-reoxygenation injury. Eur. J. Pharmacol. 575: 21-27 (2007).
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).
Chhina N, Kuestermann E, Halliday J, Simpson LJ, Macdonald IA, Bachelard HS, Morris PG. Measurement of human tricarboxylic acid cycle rates during visual activation by 13C magnetic resonance spectroscopy. J. Neurosci. Res. 66: 737-746 (2001).
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).
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).
Chico E, Olavarria JS, Nunez de Castro I. L-Alanine as an end product of glycolysis in Saccharomyces cerevisiae growing under different hypoxic conditions. Antonie Van Leeuwenhoek 44: 193-201 (1978).
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).
Choi WJ. Glycerol-based biorefinery for fuels and chemicals. Recent Pat. Biotechnol. 2: 173-180 (2008).
Cholewa E, Cholewinski AJ, Shelp BJ, Snedden WA, Bown AW. Cold-shock-stimulated gamma-aminobutyric acid synthesis is mediated by an increase in cytosolic Ca2+, not by an increase in cytosolic H+. Can. J. Bot. 75: 375-382 (1997).
Chung HJ, Ferl RJ. Arabidopsis alcohol dehydrogenase expression in both shoots and roots is conditioned by root growth environment. Plant Physiol. 121: 429-436 (1999).
Churchill TA, Kneteman NM. Investigation of a primary requirement of organ preservation solutions: supplemental buffering agents improve hepatic energy production during cold storage. Transplantation 65: 551-559 (1998).
Clark DP. Chromate reductase activity of Enterobacter aerogenes is induced by nitrite. FEMS Microbiol. Lett. 122: 233-237 (1994).
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).
Clements LD, Streips UN, Miller BS. Differential proteomic analysis of Bacillus subtilis nitrate respiration and fermentation in defined medium. Proteomics 2: 1724-1734 (2002).
Colandene JD, Garrett RH. Functional dissection and site-directed mutagenesis of the structural gene for NAD(P)H-nitrite reductase in Neurospora crassa. J. Biol. Chem. 271: 24096-24104 (1996).
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).
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).
Colmer TD. Long-distance transport of gases in plants: a perspective on internal aeration and radial oxygen loss from roots. Plant Cell Environ. 26: 17-36 (2003).
Combourieu B, Elfoul L, Delort AM, Rabot S. Identification of new derivatives of sinigrin and glucotropaeolin produced by the human digestive microflora using H-1 NMR spectroscopy analysis of in vitro incubations. Drug Metab. Dispos. 29: 1440-1445 (2001).
Conley TR, Peng HP, Shih MC. Mutations affecting induction of glycolytic and fermentative genes during germination and environmental stresses in Arabidopsis. Plant Physiol. 119: 599-608 (1999).
Connelly HM, Pelletier DA, Lu TY, Lankford PK, Hettich RL. Characterization of pII family (GlnK1, GlnK2, and GlnB) protein uridylylation in response to nitrogen availability for Rhodopseudomonas palustris. Anal. Biochem. 357: 93-104 (2006).
Converti A, Arni S, Sato S, De Carvalho JC, Aquarone E. Simplified modeling of fed-batch alcoholic fermentation of sugarcane blackstrap molasses. Biotechnol. Bioeng. 84: 88-95 (2003).
Converti A, Perego P. Use of carbon and energy balances in the study of the anaerobic metabolism of Enterobacter aerogenes at variable starting glucose concentrations. Appl. Microbiol. Biotechnol. 59: 303-309 (2002).
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).
Cotter JL, Chinn MS, Grunden AM. Ethanol and acetate production by Clostridium ljungdahlii and Clostridium autoethanogenum using resting cells. Bioprocess. Biosyst. Eng. 32: 369-380 (2009).
Couldwell DL, Dunford R, Kruger NJ, Lloyd DC, Ratcliffe RG, Smith AM. Response of cytoplasmic pH to anoxia in plant tissues with altered activities of fermentation enzymes: application of methyl phosphonate as an NMR pH probe. Ann. Bot. (Lond.) 103: 249-258 (2009).
Covert MW, Schilling CH, Palsson B. Regulation of gene expression in flux balance models of metabolism. J. Theor. Biol. 213: 73-88 (2001).
Covi JA, Hand SC. V-ATPase expression during development of Artemia franciscana embryos: potential role for proton gradients in anoxia signaling. J. Exp. Biol. 208: 2783-2798 (2005).
Cozen AE, Weirauch MT, Pollard KS, Bernick DL, Stuart JM, Lowe TM. Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. J. Bacteriol. 191: 782-794 (2009).
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).
Crawford LA, Bown AW, Breitkreuz KE, Guinel FC. The synthesis of gamma-aminobutyric acid in response to treatments reducing cytosolic pH. Plant Physiol. 104: 865-871 (1994).
Cruz Ramos H, Hoffmann T, Marino M, Nedjari H, Presecan-Siedel E, Dreesen O, Glaser P, Jahn D. Fermentative metabolism of Bacillus subtilis: physiology and regulation of gene expression. J. Bacteriol. 182: 3072-3080 (2000).
Cruz-Garcia C, Murray AE, Klappenbach JA, Stewart V, Tiedje JM. Respiratory nitrate ammonification by Shewanella oneidensis MR-1. J. Bacteriol. 189: 656-662 (2007).
Cunningham L, Guest JR. Transcription and transcript processing in the sdhCDAB-sucABCD operon of Escherichia coli. Microbiology 144: 2113-2123 (1998).
Curatti L, Hernandez JA, Igarashi RY, Soboh B, Zhao D, Rubio LM. In vitro synthesis of the iron-molybdenum cofactor of nitrogenase from iron, sulfur, molybdenum, and homocitrate using purified proteins. Proc. Natl. Acad. Sci. U.S.A. 104: 17626-17631 (2007).
Curic M, de Richelieu M, Henriksen CM, Jochumsen KV, Villadsen J, Nilsson D. Glucose/citrate cometabolism in Lactococcus lactis subsp. lactis biovar diacetylactis with impaired alpha-acetolactate decarboxylase. Metab. Eng. 1: 291-298 (1999).
Cvitkovitch DG, Gutierrez JA, Bleiweis AS. Role of the citrate pathway in glutamate biosynthesis by Streptococcus mutans. J. Bacteriol. 179: 650-655 (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).
Davey HM, Davey CL, Woodward AM, Edmonds AN, Lee AW, Kell DB. Oscillatory, stochastic and chaotic growth rate fluctuations in permittistatically controlled yeast cultures. Biosystems 39: 43-61 (1996).
Davies SE, Brindle KM. Effects of overexpression of phosphofructokinase on glycolysis in the yeast Saccharomyces cerevisiae. Biochemistry 31: 4729-4735 (1992).
Davis K, Foos T, Wu JY, Schloss JV. Oxygen-induced seizures and inhibition of human glutamate decarboxylase and porcine cysteine sulfinic acid decarboxylase by oxygen and nitric oxide. J. Biomed. Sci. 8: 359-364 (2001).
de Bruxelles GL, Peacock WJ, Dennis ES, Dolferus R. Abscisic acid induces the alcohol dehydrogenase gene in Arabidopsis. Plant Physiol. 111: 381-391 (1996).
de Graaf AA, Striegel K, Wittig RM, Laufer B, Schmitz G, Wiechert W, Sprenger GA, Sahm H. Metabolic state of Zymomonas mobilis in glucose-, fructose-, and xylose-fed continuous cultures as analysed by 13C- and 31P-NMR spectroscopy. Arch. Microbiol. 171: 371-385 (1999).
de la Haba P, Aguera E, Benitez L, Maldonado JM. Modulation of nitrate reductase activity in cucumber (Cucumis sativus) roots. Plant Sci. 161: 231-237 (2001).
De S, Perkins M, Dutta SK. Nitrate reductase gene involvement in hexachlorobiphenyl dechlorination by Phanerochaete chrysosporium. J. Hazard. Mater. 135: 350-354 (2006).
de Souza MP, Yoch DC. Differential metabolism of dimethylsulfoniopropionate and acrylate in saline and brackish intertidal sediments. Microb. Ecol. 31: 319-330 (1996).
Deiglmayr K, Philippot L, Tscherko D, Kandeler E. Microbial succession of nitrate-reducing bacteria in the rhizosphere of Poa alpina across a glacier foreland in the Central Alps. Environ. Microbiol. 8: 1600-1612 (2006).
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).
Delgado MJ, Tresierra-Ayala A, Talbi C, Bedmar EJ. Functional characterization of the Bradyrhizobium japonicum modA and modB genes involved in molybdenum transport. Microbiology 152: 199-207 (2006).
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).
DeMoss JA, Hsu PY. NarK enhances nitrate uptake and nitrite excretion in Escherichia coli. J. Bacteriol. 173: 3303-3310 (1991).
Den Haan R, Rose SH, Lynd LR, van Zyl WH. Hydrolysis and fermentation of amorphous cellulose by recombinant Saccharomyces cerevisiae. Metab. Eng. 9: 87-94 (2007).
Dennis ES, Gerlach WL, Walker JC, Lavin M, Peacock WJ. Anaerobically regulated aldolase gene of maize. A chimaeric origin? J. Mol. Biol. 202: 759-767 (1988).
Dietz KJ, Tavakoli N, Kluge C, Mimura T, Sharma SS, Harris GC, Chardonnens AN, Golldack D. Significance of the V-type ATPase for the adaptation to stressful growth conditions and its regulation on the molecular and biochemical level. J. Exp. Bot. 52: 1969-1980 (2001).
Dijkerman R, Ledeboer J, Verhappen ABM, den Camp HJMO, der Drift CV, Vogels GD. The anaerobic fungus Piromyces sp. strain E2: nitrogen requirement and enzymes involved in primary nitrogen metabolism. Arch. Microbiol. 166: 399-404 (1997).
Dixon MH, Hill SA, Jackson MB, Ratcliffe RG, Sweetlove LJ. Physiological and metabolic adaptations of Potamogeton pectinatus L. tubers support rapid elongation of stem tissue in the absence of oxygen. Plant Cell Physiol. 47: 128-140 (2006).
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).
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).
Dolferus R, Jacobs M, Peacock WJ, Dennis ES. Differential interactions of promoter elements in stress responses of the Arabidopsis Adh gene. Plant Physiol. 105: 1075-1087 (1994).
Dolferus R, Klok EJ, Delessert C, Wilson S, Ismond KP, Good AG, Peacock WJ, Dennis ES. Enhancing the anaerobic response. Ann. Bot. (Lond.) 91: 111-117 (2003).
Dordas C, Hasinoff BB, Rivoal J, Hill RD. Class-1 hemoglobins, nitrate and NO levels in anoxic maize cell-suspension cultures. Planta 219: 66-72 (2004).
Draczynska-Lusiak B, Brown OR. Asparagine synthetase: an oxidant-sensitive enzyme in Escherichia coli. Microbios 77: 141-152 (1994).
Drew MC. Oxygen deficiency and root metabolism: injury and acclimation under hypoxia and anoxia. Annu. Rev. Plant Physiol. Plant Mol. Biol. 48: 223-250 (1997).
Du C, Yan H, Zhang Y, Li Y, Cao Z. Use of oxidoreduction potential as an indicator to regulate 1,3-propanediol fermentation by Klebsiella pneumoniae. Appl. Microbiol. Biotechnol. 69: 554-563 (2006).
Duboc P, von Stockar U, Villadsen J. Simple generic model for dynamic experiments with Saccharomyces cerevisiae in continuous culture: decoupling between anabolism and catabolism. Biotechnol. Bioeng. 60: 180-189 (1998).
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).
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).
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).
Ehlert C, Maurel C, Tardieu F, Simonneau T. Aquaporin-mediated reduction in maize root hydraulic conductivity impacts cell turgor and leaf elongation even without changing transpiration. Plant Physiol. 150: 1093-1104 (2009).
Eigenbrode JL, Freeman KH. Late Archean rise of aerobic microbial ecosystems. Proc. Natl. Acad. Sci. U.S.A. 103: 15759-15764 (2006).
Ellington MJ, Richardson DJ, Ferguson SJ. Rhodobacter capsulatus gains a competitive advantage from respiratory nitrate reduction during light-dark transitions. Microbiology 149: 941-948 (2003).
Ellis MH, Dennis ES, Peacock WJ. Arabidopsis roots and shoots have different mechanisms for hypoxic stress tolerance. Plant Physiol. 119: 57-64 (1999).
Elssner T, Hennig L, Frauendorf H, Haferburg D, Kleber HP. Isolation, identification, and synthesis of gamma-butyrobetainyl-CoA and crotonobetainyl-CoA, compounds involved in carnitine metabolism of E. coli. Biochemistry 39: 10761-10769 (2000).
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).
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).
Eschbach M, Mobitz H, Rompf A, Jahn D. Members of the genus Arthrobacter grow anaerobically using nitrate ammonification and fermentative processes: anaerobic adaptation of aerobic bacteria abundant in soil. FEMS Microbiol. Lett. 223: 227-230 (2003).
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).
Famili I, Forster J, Nielsen J, Palsson BO. Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proc. Natl. Acad. Sci. U.S.A. 100: 13134-13139 (2003).
Fan F, Gadda G. On the catalytic mechanism of choline oxidase. J. Am. Chem. Soc. 127: 2067-2074 (2005).
Fan F, Germann MW, Gadda G. Mechanistic studies of choline oxidase with betaine aldehyde and its isosteric analogue 3,3-dimethylbutyraldehyde. Biochemistry 45: 1979-1986 (2006).
Fan TWM, Higashi RM, Frenkiel TA, Lane AN. Anaerobic nitrate and ammonium metabolism in flood-tolerant rice coleoptiles. J. Exp. Bot. 48: 1655-1666 (1997).
Fan Z, Yuan L, Chatterjee R. Increased hydrogen production by genetic engineering of Escherichia coli. PLoS One 4: e4432 (2009).
Fast B, Lindgren P, Gotz F. Cloning, sequencing, and characterization of a gene (narT) encoding a transport protein involved in dissimilatory nitrate reduction in Staphylococcus carnosus. Arch. Microbiol. 166: 361-367 (1996).
Fedtke I, Kamps A, Krismer B, Gotz F. The nitrate reductase and nitrite reductase operons and the narT gene of Staphylococcus carnosus are positively controlled by the novel two-component system NreBC. J. Bacteriol. 184: 6624-6634 (2002).
Feinberg LF, Srikanth R, Vachet RW, Holden JF. Constraints on anaerobic respiration in the hyperthermophilic Archaea Pyrobaculum islandicum and Pyrobaculum aerophilum. Appl. Environ. Microbiol. 74: 396-402 (2008).
Feitkenhauer H, Fischer D, Fah D. Microbial desizing using starch as model compound: enzyme properties and desizing efficiency. Biotechnol. Prog. 19: 874-879 (2003).
Felle HH. Apoplastic pH during low-oxygen stress in barley. Ann. Bot. (Lond.) 98: 1085-1093 (2006).
Feng K, Yan F, Hutsch BW, Schubert S. Nitrous oxide emission as affected by liming an acidic mineral soil used for arable agriculture. Nutr. Cycl. Agroecosyst. 67: 283-292 (2003).
Ferry JG. Formate dehydrogenase. FEMS Microbiol. Rev. 7: 377-382 (1990).
Filipe CD, Daigger GT, Grady CP Jr. Stoichiometry and kinetics of acetate uptake under anaerobic conditions by an enriched culture of phosphorus-accumulating organisms at different pHs. Biotechnol. Bioeng. 76: 32-43 (2001).
Filipe CD, Daigger GT, Grady CP Jr. A metabolic model for acetate uptake under anaerobic conditions by glycogen accumulating organisms: Stoichiometry, kinetics, and the effect of pH. Biotechnol. Bioeng. 76: 17-31 (2001).
Forestier M, King P, Zhang L, Posewitz M, Schwarzer S, Happe T, Ghirardi ML, Seibert M. Expression of two [Fe]-hydrogenases in Chlamydomonas reinhardtii under anaerobic conditions. Eur. J. Biochem. 270: 2750-2758 (2003).
Forsthoefel NR, Cushman MA, Cushman JC. Posttranscriptional and posttranslational control of enolase expression in the facultative Crassulacean acid metabolism plant Mesembryanthemum crystallinum L. Plant Physiol. 108: 1185-1195 (1995).
Forti G, Caldiroli G. State transitions in Chlamydomonas reinhardtii. The role of the Mehler reaction in state 2-to-state 1 transition. Plant Physiol. 137: 492-499 (2005).
Forti G, Furia A, Bombelli P, Finazzi G. In vivo changes of the oxidation-reduction state of NADP and of the ATP/ADP cellular ratio linked to the photosynthetic activity in Chlamydomonas reinhardtii. Plant Physiol. 132: 1464-1474 (2003).
Fouchard S, Pruvost J, Degrenne B, Titica M, Legrand J. Kinetic modeling of light limitation and sulfur deprivation effects in the induction of hydrogen production with Chlamydomonas reinhardtii: Part I. Model development and parameter identification. Biotechnol. Bioeng. 102: 232-245 (2009).
Fox TC, Green BJ, Kennedy RA, Rumpho ME. Changes in hexokinase activity in Echinochloa phyllopogon and Echinochloa crus-pavonis in response to abiotic stress. Plant Physiol. 118: 1403-1409 (1998).
Fox TC, Mujer CV, Andrews DL, Williams AS, Cobb BG, Kennedy RA, Rumpho ME. Identification and gene expression of anaerobically induced enolase in Echinochloa phyllopogon and Echinochloa crus-pavonis. Plant Physiol. 109: 433-443 (1995).
Franzen CJ. Metabolic flux analysis of RQ-controlled microaerobic ethanol production by Saccharomyces cerevisiae. Yeast 20: 117-132 (2003).
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).
Frey PA, Hegeman AD, Ruzicka FJ. The radical SAM superfamily. Crit. Rev. Biochem. Mol. Biol. 43: 63-88 (2008).
Fujinaga K, Taniguchi Y, Sun Y, Katayama S, Minami J, Matsushita O, Okabe A. Analysis of genes involved in nitrate reduction in Clostridium perfringens. Microbiology 145: 3377-3387 (1999).
Fukao T, Kennedy RA, Yamasue Y, Rumpho ME. Genetic and biochemical analysis of anaerobically-induced enzymes during seed germination of Echinochloa crus-galli varieties tolerant and intolerant of anoxia. J. Exp. Bot. 54: 1421-1429 (2003).
Furukawa K. 'Super bugs' for bioremediation. Trends Biotechnol. 21: 187-190 (2003).
Fyfe PK, Hughes AV, Heathcote P, Jones MR. Proteins, chlorophylls and lipids: X-ray analysis of a three-way relationship. Trends Plant Sci. 10: 275-282 (2005).
Gadjieva R, Eckert HJ, Renger G. Photoinhibition as a function of the ambient redox potential in Tris-washed PS II membrane fragments. Photosynth. Res. 63: 237-248 (2000).
Garrigues C, Goupil-Feuillerat N, Cocaign-Bousquet M, Renault P, Lindley ND, Loubiere P. Glucose metabolism and regulation of glycolysis in Lactococcus lactis strains with decreased lactate dehydrogenase activity. Metab. Eng. 3: 211-217 (2001).
Garza-Quintero R, Ortega-Lopez J, Stein JH, Venkatachalam MA. Alanine protects rabbit proximal tubules against anoxic injury in vitro. Am. J. Physiol. 258: F1075-F1083 (1990).
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).
Geffers R, Cerff R, Hehl R. Anaerobiosis-specific interaction of tobacco nuclear factors with cis-regulatory sequences in the maize GapC4 promoter. Plant Mol. Biol. 43: 11-21 (2000).
Geigenberger P. Regulation of sucrose to starch conversion in growing potato tubers. J. Exp. Bot. 54: 457-465 (2003).
Geigenberger P. Response of plant metabolism to too little oxygen. Curr. Opin. Plant Biol. 6: 247-256 (2003).
Geigenberger P, Fernie AR, Gibon Y, Christ M, Stitt M. Metabolic activity decreases as an adaptive response to low internal oxygen in growing potato tubers. Biol. Chem. 381: 723-740 (2000).
Germain V, Raymond P, Ricard B. Differential expression of two tomato lactate dehydrogenase genes in response to oxygen deficit. Plant Mol. Biol. 35: 711-721 (1997).
Ghanem M, Gadda G. Effects of reversing the protein positive charge in the proximity of the flavin N(1) locus of choline oxidase. Biochemistry 45: 3437-3447 (2006).
Gharbi I, Ricard B, Rolin D, Maucourt M, Andrieu MH, Bizid E, Smiti S, Brouquisse R. Effect of hexokinase activity on tomato root metabolism during prolonged hypoxia. Plant Cell Environ. 30: 508-517 (2007).
Giardina G, Rinaldo S, Castiglione N, Caruso M, Cutruzzola F. A dramatic conformational rearrangement is necessary for the activation of DNR from Pseudomonas aeruginosa. Crystal structure of wild-type DNR. Proteins 77: 174-180 (2009).
Gilberthorpe NJ, Poole RK. Nitric oxide homeostasis in Salmonella typhimurium: roles of respiratory nitrate reductase and flavohemoglobin. J. Biol. Chem. 283: 11146-11154 (2008).
Givan CV. Evolving concepts in plant glycolysis: two centuries of progress. Biol. Rev. Camb. Phil. Soc. 74: 277-309 (1999).
Gladwin MT, Grubina R, Doyle MP. The new chemical biology of nitrite reactions with hemoglobin: R-state catalysis, oxidative denitrosylation, and nitrite reductase/anhydrase. Acc. Chem. Res. 42: 157-167 (2009).
Gladwin MT, Kim-Shapiro DB. The functional nitrite reductase activity of the heme-globins. Blood 112: 2636-2647 (2008).
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).
Gloser V, Zwieniecki MA, Orians CM, Holbrook NM. Dynamic changes in root hydraulic properties in response to nitrate availability. J. Exp. Bot. 58: 2409-2415 (2007).
Gloux K, Touze T, Pagot Y, Jouan B, Blanco C. Mutations of ousA alter the virulence of Erwinia chrysanthemi. Mol. Plant Microbe Interact. 18: 150-157 (2005).
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).
Goldman BS, Roth JR. Genetic structure and regulation of the cysG gene in Salmonella typhimurium. J. Bacteriol. 175: 1457-1466 (1993).
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).
Gonzalez B, de Graaf A, Renaud M, Sahm H. Dynamic in vivo (31)P nuclear magnetic resonance study of Saccharomyces cerevisiae in glucose-limited chemostat culture during the aerobic-anaerobic shift. Yeast 16: 483-497 (2000).
Gonzalez JM, Masuchi Y, Robb FT, Ammerman JW, Maeder DL, Yanagibayashi M, Tamaoka J, Kato C. Pyrococcus horikoshii sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal vent at the Okinawa Trough. Extremophiles 2: 123-130 (1998).
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, 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).
Good AG, Muench DG. Long-term anaerobic metabolism in root tissue. Metabolic products of pyruvate metabolism. Plant Physiol. 101: 1163-1168 (1993).
Good AG, Paetkau DH. Identification and characterization of a hypoxically induced maize lactate dehydrogenase gene. Plant Mol. Biol. 19: 693-697 (1992).
Gorska A, Zwieniecka A, Michele Holbrook N, Zwieniecki MA. Nitrate induction of root hydraulic conductivity in maize is not correlated with aquaporin expression. Planta 228: 989-998 (2008).
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).
Goupry S, Croguennec T, Gentil E, Robins RJ. Metabolic flux in glucose/citrate co-fermentation by lactic acid bacteria as measured by isotopic ratio analysis. FEMS Microbiol. Lett. 182: 207-211 (2000).
Gout E, Boisson AM, Aubert S, Douce R, Bligny R. Origin of the cytoplasmic pH changes during anaerobic stress in higher plant cells. Carbon-13 and phosphorous-31 nuclear magnetic resonance studies. Plant Physiol. 125: 912-925 (2001).
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).
Grafahrend-Belau E, Schreiber F, Koschutzki D, Junker BH. Flux balance analysis of barley seeds: a computational approach to study systemic properties of central metabolism. Plant Physiol. 149: 585-598 (2009).
Grahame DA. Acetate C-C bond formation and decomposition in the anaerobic world: the structure of a central enzyme and its key active-site metal cluster. Trends Biochem. Sci. 28: 221-224 (2003).
Graus M, Schnitzler JP, Hansel A, Cojocariu C, Rennenberg H, Wisthaler A, Kreuzwieser J. Transient release of oxygenated volatile organic compounds during light-dark transitions in grey poplar leaves. Plant Physiol. 135: 1967-1975 (2004).
Greenway H, Armstrong W, Colmer TD. Conditions leading to high CO2 (>5 kPa) in waterlogged-flooded soils and possible effects on root growth and metabolism. Ann. Bot. (Lond.) 98: 9-32 (2006).
Gregerson R, McLean M, Beld M, Gerats AG, Strommer J. Structure, expression, chromosomal location and product of the gene encoding ADH1 in Petunia. Plant Mol. Biol. 17: 37-48 (1991).
Gregerson RG, Cameron L, McLean M, Dennis P, Strommer J. Structure, expression, chromosomal location and product of the gene encoding Adh2 in Petunia. Genetics 133: 999-1007 (1993).
Griffin BM, Schott J, Schink B. Nitrite, an electron donor for anoxygenic photosynthesis. Science 316: 1870 (2007).
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).
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).
Grossman AR, Croft M, Gladyshev VN, Merchant SS, Posewitz MC, Prochnik S, Spalding MH. Novel metabolism in Chlamydomonas through the lens of genomics. Curr. Opin. Plant Biol. 10: 190-198 (2007).
Grotkjaer T, Christakopoulos P, Nielsen J, Olsson L. Comparative metabolic network analysis of two xylose fermenting recombinant Saccharomyces cerevisiae strains. Metab. Eng. 7: 437-444 (2005).
Gunnarsson N, Bruheim P, Nielsen J. Glucose metabolism in the antibiotic producing actinomycete Nonomuraea sp. ATCC 39727. Biotechnol. Bioeng. 88: 652-663 (2004).
Gupta KJ, Stoimenova M, Kaiser WM. In higher plants, only root mitochondria, but not leaf mitochondria reduce nitrite to NO, in vitro and in situ. J. Exp. Bot. 56: 2601-2609 (2005).
Gutthann F, Egert M, Marques A, Appel J. Inhibition of respiration and nitrate assimilation enhances photohydrogen evolution under low oxygen concentrations in Synechocystis sp. PCC 6803. Biochim. Biophys. Acta 1767: 161-169 (2007).
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).
Hakala M, Rantamaki S, Puputti EM, Tyystjarvi T, Tyystjarvi E. Photoinhibition of manganese enzymes: insights into the mechanism of photosystem II photoinhibition. J. Exp. Bot. 57: 1809-1816 (2006).
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).
Hallam SJ, Putnam N, Preston CM, Detter JC, Rokhsar D, Richardson PM, DeLong EF. Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 305: 1457-1462 (2004).
Hallett DS, Clark P, Macaskie LE. Phosphatase production by a Citrobacter sp. growing in batch cultures retarded by anaerobic or osmotic stress, and the effect of the osmoprotectant glycine betaine. FEMS Microbiol. Lett. 62: 7-10 (1991).
Hannig M, Braker G, Dippner J, Jurgens K. Linking denitrifier community structure and prevalent biogeochemical parameters in the pelagial of the central Baltic Proper (Baltic Sea). FEMS Microbiol. Ecol. 57: 260-271 (2006).
Hansch R, Kurz T, Schulze J, Mendel RR, Cerff R, Hehl R. Anaerobic induction of the maize GapC4 promoter in poplar leaves requires light and high CO2. Planta 218: 79-86 (2003).
Hansch R, Mendel RR, Cerff R, Hehl R. Light-dependent anaerobic induction of the maize glyceraldehyde-3-phosphate dehydrogenase 4 (GapC4) promoter in Arabidopsis thaliana and Nicotiana tabacum. Ann. Bot. (Lond.) 91: 149-154 (2003).
Harada T, Satoh S, Yoshioka T, Ishizawa K. Expression of sucrose synthase genes involved in enhanced elongation of pondweed (Potamogeton distinctus) turions under anoxia. Ann. Bot. (Lond.) 96: 683-692 (2005).
Harada T, Satoh S, Yoshioka T, Ishizawa K. Anoxia-enhanced expression of genes isolated by suppression subtractive hybridization from pondweed (Potamogeton distinctus A. Benn.) turions. Planta 226: 1041-1052 (2007).
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).
Harris DM, Myrick TL, Rundle SJ. The Arabidopsis homolog of yeast TAP42 and mammalian alpha4 binds to the catalytic subunit of protein phosphatase 2A and is induced by chilling. Plant Physiol. 121: 609-618 (1999).
Harris GC, Heber U. Effects of anaerobiosis on chlorophyll fluorescence yield in spinach (Spinacia oleracea) leaf discs. Plant Physiol. 101: 1169-1173 (1993).
Hasona A, Self WT, Shanmugam KT. Transcriptional regulation of the moe (molybdate metabolism) operon of Escherichia coli. Arch. Microbiol. 175: 178-188 (2001).
Heber U, Kobayashi Y, Leegood RC, Walker DA. Low fluorescence yield in anaerobic chloroplasts and stimulation of chlorophyll-a fluorescence by oxygen and inhibitors that block electron flow between photosystems II and photosystems I. Proc. Roy. Soc. Lond. B. Biol. Sci. 225: 41-53 (1985).
Herbik A, Giritch A, Horstmann C, Becker R, Balzer HJ, Baumlein H, Stephan UW. Iron and copper nutrition-dependent changes in protein expression in a tomato wild type and the nicotianamine-free mutant chloronerva. Plant Physiol. 111: 533-540 (1996).
Hernandez D, Dias FM, Rowe JJ. Nitrate transport and its regulation by O2 in Pseudomonas aeruginosa. Arch. Biochem. Biophys. 286: 159-163 (1991).
Herschbach C, Mult S, Kreuzwieser J, Kopriva S. Influence of anoxia on whole plant sulphur nutrition of flooding-tolerant poplar (Populus tremula x P. alba). Plant Cell Environ. 28: 167-175 (2005).
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).
Hertweck C, Moore BS. A plant-like biosynthesis of benzoyl-CoA in the marine bacterium 'Streptomyces maritimus'. Tetrahedron 56: 9115-9120 (2000).
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).
Hetzel M, Brock M, Selmer T, Pierik AJ, Golding BT, Buckel W. Acryloyl-CoA reductase from Clostridium propionicum. An enzyme complex of propionyl-CoA dehydrogenase and electron-transferring flavoprotein. Eur. J. Biochem. 270: 902-910 (2003).
Hillmer S, Gilroy S, Jones RL. Visualizing enzyme secretion from individual barley (Hordeum vulgare) aleurone protoplasts. Plant Physiol. 102: 279-286 (1993).
Ho QT, Verboven P, Verlinden BE, Lammertyn J, Vandewalle S, Nicolai BM. A continuum model for metabolic gas exchange in pear fruit. PLoS Comput. Biol. 4: e1000023 (2008).
Hochgrafe F, Wolf C, Fuchs S, Liebeke M, Lalk M, Engelmann S, Hecker M. Nitric oxide stress induces different responses but mediates comparable protein thiol protection in Bacillus subtilis and Staphylococcus aureus. J. Bacteriol. 190: 4997-5008 (2008).
Hoffmann T, Frankenberg N, Marino M, Jahn D. Ammonification in Bacillus subtilis utilizing dissimilatory nitrite reductase is dependent on resDE. J. Bacteriol. 180: 186-189 (1998).
Hoffmann T, Troup B, Szabo A, Hungerer C, Jahn D. The anaerobic life of Bacillus subtilis: cloning of the genes encoding the respiratory nitrate reductase system. FEMS Microbiol. Lett. 131: 219-225 (1995).
Hong SH, Lee SY. Metabolic flux distribution in a metabolically engineered Escherichia coli strain producing succinic acid. J. Microbiol. Biotechnol. 10: 496-501 (2000).
Horner DS, Heil B, Happe T, Embley TM. Iron hydrogenases--ancient enzymes in modern eukaryotes. Trends Biochem. Sci. 27: 148-153 (2002).
Hose E, Clarkson DT, Steudle E, Schreiber L, Hartung W. The exodermis: a variable apoplastic barrier. J. Exp. Bot. 52: 2245-2264 (2001).
Hou J, Vemuri GN, Bao X, Olsson L. Impact of overexpressing NADH kinase on glucose and xylose metabolism in recombinant xylose-utilizing Saccharomyces cerevisiae. Appl. Microbiol. Biotechnol. 82: 909-919 (2009).
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).
Huang JY, Chang T, Chang CY, Chen CJ. Crystal structure of nucleoside diphosphate kinase required for coleoptile elongation in rice (Oryza sativa L.). J. Struct. Biol. 150: 309-318 (2005).
Huang S, Colmer TD, Millar AH. Does anoxia tolerance involve altering the energy currency towards PPi? Trends Plant Sci. 13: 221-227 (2008).
Huang S, Greenway H, Colmer TD. Responses by coleoptiles of intact rice seedlings to anoxia: k(+) net uptake from the external solution and translocation from the caryopses. Ann. Bot. (Lond.) 91: 271-278 (2003).
Huang S, Greenway H, Colmer TD. Anoxia tolerance in rice seedlings: exogenous glucose improves growth of an anoxia-'intolerant', but not of a 'tolerant' genotype. J. Exp. Bot. 54: 2363-2373 (2003).
Huang S, Ishizawa K, Greenway H, Colmer TD. Manipulation of ethanol production in anoxic rice coleoptiles by exogenous glucose determines rates of ion fluxes and provides estimates of energy requirements for cell maintenance during anoxia. J. Exp. Bot. 56: 2453-2463 (2005).
Huertas IE, Colman B, Espie GS. Mitochondrial-driven bicarbonate transport supports photosynthesis in a marine microalga. Plant Physiol. 130: 284-291 (2002).
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).
Huq E, Hodges TK. An anaerobically inducible early (aie) gene family from rice. Plant Mol. Biol. 40: 591-601 (1999).
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).
Huynh le N, Vantoai T, Streeter J, Banowetz G. Regulation of flooding tolerance of SAG12:ipt Arabidopsis plants by cytokinin. J. Exp. Bot. 56: 1397-1407 (2005).
Hwang YS, Thomas BR, Rodriguez RL. Differential expression of rice alpha-amylase genes during seedling development under anoxia. Plant Mol. Biol. 40: 911-920 (1999).
Igamberdiev AU, Hill RD. Plant mitochondrial function during anaerobiosis. Ann. Bot. (Lond.) 103: 259-268 (2009).
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).
Ikeda E, Andou S, Iwama U, Kato C, Horikoshi K, Tamegai H. Physiological roles of two dissimilatory nitrate reductases in the deep-sea denitrifier Pseudomonas sp. strain MT-1. Biosci. Biotechnol. Biochem. 73: 896-900 (2009).
Ikuta S, Matuura K, Imamura S, Misaki H, Horiuti Y. Oxidative pathway of choline to betaine in the soluble fraction prepared from Arthrobacter globiformis. J. Biochem. (Tokyo) 82: 157-163 (1977).
Ioannidi E, Kalamaki MS, Engineer C, Pateraki I, Alexandrou D, Mellidou I, Giovannonni J, Kanellis AK. Expression profiling of ascorbic acid-related genes during tomato fruit development and ripening and in response to stress conditions. J. Exp. Bot. 60: 663-678 (2009).
Ismail AM, Ella ES, Vergara GV, Mackill DJ. Mechanisms associated with tolerance to flooding during germination and early seedling growth in rice (Oryza sativa). Ann. Bot. (Lond.) 103: 197-209 (2009).
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).
Ivanov B, Asada K, Kramer DM, Edwards G. Characterization of photosynthetic electron transport in bundle sheath cells of maize. I. Ascorbate effectively stimulates cyclic electron flow around PSI. Planta 220: 572-581 (2005).
Ivanov B, Edwards G. Influence of ascorbate and the Mehler peroxidase reaction on non-photochemical quenching of chlorophyll fluorescence in maize mesophyll chloroplasts. Planta 210: 765-774 (2000).
Iverson TM, Luna-Chavez C, Cecchini G, Rees DC. Structure of the Escherichia coli fumarate reductase respiratory complex. Science 284: 1961-1966 (1999).
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).
Jansen M, Hansen TA. Tetrahydrofolate serves as a methyl acceptor in the demethylation of dimethylsulfoniopropionate in cell extracts of sulfate-reducing bacteria. Arch. Microbiol. 169: 84-87 (1998).
Jarillo JA, Leyva A, Salinas J, Martinez-Zapater JM. Low temperature induces the accumulation of alcohol dehydrogenase mRNA in Arabidopsis thaliana, a chilling-tolerant plant. Plant Physiol. 101: 833-837 (1993).
Jarrett JT, Wan JT. Thermal inactivation of reduced ferredoxin (flavodoxin): NADP(+) oxidoreductase from Escherichia coli. FEBS Lett. 529: 237-242 (2002).
Jayakumar A, O'Mullan GD, Naqvi SW, Ward BB. Denitrifying bacterial community composition changes associated with stages of denitrification in oxygen minimum zones. Microb. Ecol. 58: 350-362 (2009).
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).
Jetten MS. The microbial nitrogen cycle. Environ. Microbiol. 10: 2903-2909 (2008).
Jin T, Huppe HC, Turpin DH. In vitro reconstitution of electron transport from glucose-6-phosphate and NADPH to nitrite. Plant Physiol. 117: 303-309 (1998).
Jin YS, Jeffries TW. Stoichiometric network constraints on xylose metabolism by recombinant Saccharomyces cerevisiae. Metab. Eng. 6: 229-238 (2004).
Jo JH, Lee DS, Kim J, Park JM. Effect of initial glucose concentrations on carbon material and energy balances in hydrogen-producing Clostridium tyrobutyricum JM1. J. Microbiol. Biotechnol. 19: 291-298 (2009).
Johnson ET, Schmidt-Dannert C. Light-energy conversion in engineered microorganisms. Trends Biotechnol. 26: 682-689 (2008).
Johnson JR, Cobb BG, Drew MC. Hypoxic induction of anoxia tolerance in roots of Adh1 null Zea mays L. Plant Physiol. 105: 61-67 (1994).
Jordan A, Reichard P. Ribonucleotide reductases. Annu. Rev. Biochem. 67: 71-98 (1998).
Jung H, Jung K, Kleber HP. L-Carnitine uptake by Escherichia coli. J. Basic Microbiol. 30: 507-514 (1990).
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).
Ka JO, Urbance J, Ye RW, Ahn TY, Tiedje JM. Diversity of oxygen and N-oxide regulation of nitrite reductases in denitrifying bacteria. FEMS Microbiol. Lett. 156: 55-60 (1997).
Kaenjak A, Graham JE, Wilkinson BJ. Choline transport activity in Staphylococcus aureus induced by osmotic stress and low phosphate concentrations. J. Bacteriol. 175: 2400-2406 (1993).
Kaiser WM, Kandlbinder A, Stoimenova M, Glaab J. Discrepancy between nitrate reduction rates in intact leaves and nitrate reductase activity in leaf extracts: what limits nitrate reduction in situ? Planta 210: 801-807 (2000).
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).
Karl T, Curtis AJ, Rosenstiel TN, Monson RK, Fall R. Transient releases of acetaldehyde from tree leaves - products of a pyruvate overflow mechanism?. Plant Cell Environ. 25: 1121-1131 (2002).
Keppler F, Hamilton JT, Brass M, Rockmann T. Methane emissions from terrestrial plants under aerobic conditions. Nature 439: 187-191 (2006).
Kerfeld CA, Krogmann DW. Photosynthetic cytochromes C in cyanobacteria, algae, and plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 49: 397-425 (1998).
Khan A, Sarkar D. Identification of a respiratory-type nitrate reductase and its role for survival of Mycobacterium smegmatis in Wayne model. Microb. Pathog. 41: 90-95 (2006).
Kiene RP, Visscher PT. Production and fate of methylated sulfur compounds from methionine and dimethylsulfoniopropionate in anoxic salt marsh sediments. Appl. Environ. Microbiol. 53: 2426-2434 (1987).
Kiley PJ, Reznikoff WS. Fnr mutants that activate gene expression in the presence of oxygen. J. Bacteriol. 173: 16-22 (1991).
Kim JI, Varner JD, Ramkrishna D. A hybrid model of anaerobic E. coli GJT001: combination of elementary flux modes and cybernetic variables. Biotechnol. Prog. 24: 993-1006 (2008).
King T, Ferenci T. Divergent roles of RpoS in Escherichia coli under aerobic and anaerobic conditions. FEMS Microbiol. Lett. 244: 323-327 (2005).
Kinnersley AM, Turano FJ. Gamma aminobutyric acid (GABA) and plant responses to stress. Crit. Rev. Plant Sci. 19: 479-509 (2000).
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).
Kleerebezem R, Stams AJ. Kinetics of syntrophic cultures: a theoretical treatise on butyrate fermentation. Biotechnol. Bioeng. 67: 529-543 (2000).
Kleerebezem R, van Loosdrecht MC. Mixed culture biotechnology for bioenergy production. Curr. Opin. Biotechnol. 18: 207-212 (2007).
Klok EJ, Wilson IW, Wilson D, Chapman SC, Ewing RM, Somerville SC, Peacock WJ, Dolferus R, Dennis ES. Expression profile analysis of the low-oxygen response in Arabidopsis root cultures. Plant Cell 14: 2481-2494 (2002).
Klotz MG, Schmid MC, Strous M, Op den Camp HJ, Jetten MS, Hooper AB. Evolution of an octahaem cytochrome c protein family that is key to aerobic and anaerobic ammonia oxidation by bacteria. Environ. Microbiol. 10: 3150-3163 (2008).
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).
Kohler U, Liaud MF, Mendel RR, Cerff R, Hehl R. The maize GapC4 promoter confers anaerobic reporter gene expression and shows homology to the maize anthocyanin regulatory locus C1. Plant Mol. Biol. 29: 1293-1298 (1995).
Kolb RM, Rawyler A, Braendle R. Parameters affecting the early seedling development of four neotropical trees under oxygen deprivation stress. Ann. Bot. (Lond.) 89: 551-558 (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).
Kong QX, Cao LM, Zhang AL, Chen X. Overexpressing GLT1 in gpd1Delta mutant to improve the production of ethanol of Saccharomyces cerevisiae. Appl. Microbiol. Biotechnol. 73: 1382-1386 (2007).
Kong QX, Gu JG, Cao LM, Zhang AL, Chen X, Zhao XM. Improved production of ethanol by deleting FPS1 and over-expressing GLT1 in Saccharomyces cerevisiae. Biotechnol. Lett. 28: 2033-2038 (2006).
Kopp RE, Kirschvink JL, Hilburn IA, Nash CZ. The Paleoproterozoic snowball Earth: a climate disaster triggered by the evolution of oxygenic photosynthesis. Proc. Natl. Acad. Sci. U.S.A. 102: 11131-11136 (2005).
Korzeniewski B. Is it possible to predict any properties of oxidative phosphorylation in a theoretical way? Mol. Cell Biochem. 184: 345-358 (1998).
Kostera J, Youngblut MD, Slosarczyk JM, Pacheco AA. Kinetic and product distribution analysis of NO. reductase activity in Nitrosomonas europaea hydroxylamine oxidoreductase. J. Biol. Inorg. Chem. 13: 1073-1083 (2008).
Koutny M, Kucera I, Tesarik R, Turanek J, Van Spanning RJ. Pseudoazurin mediates periplasmic electron flow in a mutant strain of Paracoccus denitrificans lacking cytochrome c550. FEBS Lett. 448: 157-159 (1999).
Koziol S, Zagulski M, Bilinski T, Bartosz G. Antioxidants protect the yeast Saccharomyces cerevisiae against hypertonic stress. Free Radic. Res. 39: 365-371 (2005).
Krantz M, Nordlander B, Valadi H, Johansson M, Gustafsson L, Hohmann S. Anaerobicity prepares Saccharomyces cerevisiae cells for faster adaptation to osmotic shock. Eukaryot. Cell 3: 1381-1390 (2004).
Kremeckova H, Svrcula B, Mikes V. Purification and some properties of glutamate dehydrogenase and glutamine synthetase from Paracoccus denitrificans. J. Gen. Microbiol. 138: 1587-1591 (1992).
Kreuzwieser J, Furniss S, Rennenberg H. Impact of waterlogging on the N-metabolism of flood tolerant and non-tolerant tree species. Plant Cell Environ. 25: 1039-1049 (2002).
Kreuzwieser J, Schnitzler JP, Steinbrecher R. Biosynthesis of organic compounds emitted by plants. Plant Biol. 1: 149-159 (1999).
Kucera I. Inhibition by phenylglyoxal of nitrate transport in Paracoccus denitrificans: a comparison with the effect of a protonophorous uncoupler. Arch. Biochem. Biophys. 409: 327-334 (2003).
Kujime M, Izumi C, Tomura M, Hada M, Fujii H. Effect of a tridentate ligand on the structure, electronic structure, and reactivity of the copper(I) nitrite complex: role of the conserved three-histidine ligand environment of the type-2 copper site in copper-containing nitrite reductases. J. Am. Chem. Soc. 130: 6088-6098 (2008).
Kulichikhin KY, Greenway H, Byrne L, Colmer TD. Regulation of intracellular pH during anoxia in rice coleoptiles in acidic and near neutral conditions. J. Exp. Bot. 60: 2119-2128 (2009).
Kurakov AV, Nosikov AN, Skrynnikova EV, L'vov NP. Nitrate reductase and nitrous oxide production by Fusarium oxysporum 11dn1 under aerobic and anaerobic conditions. Curr. Microbiol. 41: 114-119 (2000).
Kursteiner O, Dupuis I, Kuhlemeier C. The pyruvate decarboxylase1 gene of Arabidopsis is required during anoxia but not other environmental stresses. Plant Physiol. 132: 968-978 (2003).
Kwast KE, Lai LC, Menda N, James DT 3rd, Aref S, Burke PV. Genomic analyses of anaerobically induced genes in Saccharomyces cerevisiae: functional roles of Rox1 and other factors in mediating the anoxic response. J. Bacteriol. 184: 250-265 (2002).
Kyozuka J, Fujimoto H, Izawa T, Shimamoto K. Anaerobic induction and tissue-specific expression of maize Adh1 promoter in transgenic rice plants and their progeny. Mol. Gen. Genet. 228: 40-48 (1991).
L'Her E, Sebert P. Glycolysis in the human muscle: a new approach. J. Lab. Clin. Med. 136: 281-286 (2000).
Lai LC, Kosorukoff AL, Burke PV, Kwast KE. Dynamical remodeling of the transcriptome during short-term anaerobiosis in Saccharomyces cerevisiae: differential response and role of Msn2 and/or Msn4 and other factors in galactose and glucose media. Mol. Cell. Biol. 25: 4075-4091 (2005).
Lal SK, Lee C, Sachs MM. Differential regulation of enolase during anaerobiosis in maize. Plant Physiol. 118: 1285-1293 (1998).
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).
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).
Lapujade P, Cocaign-Bousquet M, Loubiere P. Glutamate biosynthesis in Lactococcus lactis subsp. lactis NCDO 2118. Appl. Environ. Microbiol. 64: 2485-2489 (1998).
Larsson C, Pahlman IL, Ansell R, Rigoulet M, Adler L, Gustafsson L. The importance of the glycerol 3-phosphate shuttle during aerobic growth of Saccharomyces cerevisiae. Yeast 14: 347-357 (1998).
Lasanthi-Kudahettige R, Magneschi L, Loreti E, Gonzali S, Licausi F, Novi G, Beretta O, Vitulli F, Alpi A, Perata P. Transcript profiling of the anoxic rice coleoptile. Plant Physiol. 144: 218-231 (2007).
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).
Le Rudulier D, Bernard T, Goas G, Hamelin J. Osmoregulation in Klebsiella pneumoniae: enhancement of anaerobic growth and nitrogen fixation under stress by proline betaine, gamma-butyrobetaine, and other related compounds. Can. J. Microbiol. 30: 299-305 (1984).
Lee DY, Ramos A, Macomber L, Shapleigh JP. Taxis response of various denitrifying bacteria to nitrate and nitrite. Appl. Environ. Microbiol. 68: 2140-2147 (2002).
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 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).
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).
Leonhartsberger S, Korsa I, Bock A. The molecular biology of formate metabolism in enterobacteria. J. Mol. Microbiol. Biotechnol. 4: 269-276 (2002).
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).
Li Y, Ohtsu K, Nemoto K, Tsutsumi N, Hirai A, Nakazono M. The rice pyruvate decarboxylase 3 gene, which lacks introns, is transcribed in mature pollen. J. Exp. Bot. 55: 145-146 (2004).
Libourel IG, van Bodegom PM, Fricker MD, Ratcliffe RG. Nitrite reduces cytoplasmic acidosis under anoxia. Plant Physiol. 142: 1710-1717 (2006).
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).
Liu F, Vantoai T, Moy LP, Bock G, Linford LD, Quackenbush J. Global transcription profiling reveals comprehensive insights into hypoxic response in Arabidopsis. Plant Physiol. 137: 1115-1129 (2005).
Liu HP, Takio S, Satoh T, Yamamoto I. Involvement in denitrification of the napKEFDABC genes encoding the periplasmic nitrate reductase system in the denitrifying phototrophic bacterium Rhodobacter sphaeroides f. sp. denitrificans. Biosci. Biotechnol. Biochem. 63: 530-536 (1999).
Llamas I, Moral AD, Martinez-Checa F, Arco Y, Arias S, Quesada E. Halomonas maura is a physiologically versatile bacterium of both ecological and biotechnological interest. Antonie. Van. Leeuwenhoek. 89: 395-403 (2006).
Llewellyn DJ, Finnegan EJ, Ellis JG, Dennis ES, Peacock WJ. Structure and expression of an alcohol dehydrogenase 1 gene from Pisum sativum (cv. "Greenfeast"). J. Mol. Biol. 195: 115-123 (1987).
Lockwood BC, Coombs GH. Purification and characterization of methionine gamma-lyase from Trichomonas vaginalis. Biochem. J. 279: 675-682 (1991).
Lopez-Millan AF, Morales F, Gogorcena Y, Abadia A, Abadia J. Iron resupply-mediated deactivation of Fe-deficiency stress responses in roots of sugar beet. Aust. J. Plant Physiol. 28: 171-180 (2001).
Lopez-Vazquez CM, Hooijmans CM, Brdjanovic D, Gijzen HJ, van Loosdrecht MC. Temperature effects on glycogen accumulating organisms. Water Res. 43: 2852-2864 (2009).
Loreti E, Poggi A, Novi G, Alpi A, Perata P. A genome-wide analysis of the effects of sucrose on gene expression in Arabidopsis seedlings under anoxia. Plant Physiol. 137: 1130-1138 (2005).
Loreti E, Yamaguchi J, Alpi A, Perata P. Sugar modulation of alpha-amylase genes under anoxia. Ann. Bot. (Lond.) 91: 143-148 (2003).
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).
Luque-Almagro VM, Blasco R, Saez LP, Roldan MD, Moreno-Vivian C, Castillo F, Martinez-Luque M. Interactions between nitrate assimilation and 2,4-dinitrophenol cometabolism in Rhodobacter capsulatus E1F1. Curr. Microbiol. 53: 37-42 (2006).
Lutz PL, Nilsson GE. Contrasting strategies for anoxic brain survival--glycolysis up or down. J. Exp. Biol. 200: 411-419 (1997).
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).
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).
Maczek J, Junne S, Nowak P, Goetz P. Metabolic flux analysis of the sterol pathway in the yeast Saccharomyces cerevisiae. Bioprocess. Biosyst. Eng. 29: 241-252 (2006).
Magneschi L, Perata P. Rice germination and seedling growth in the absence of oxygen. Ann. Bot. (Lond.) 103: 181-196 (2009).
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).
Mancuso S, Boselli M. Characterisation of the oxygen fluxes in the division, elongation and mature zones of Vitis roots: influence of oxygen availability. Planta 214: 767-774 (2002).
Manjunath S, Lee CH, VanWinkle P, Bailey-Serres J. Molecular and biochemical characterization of cytosolic phosphoglucomutase in maize. Expression during development and in response to oxygen deprivation. Plant Physiol. 117: 997-1006 (1998).
Margis R, Margis-Pinheiro M. Phytocalpains: orthologous calcium-dependent cysteine proteinases. Trends Plant Sci. 8: 58-62 (2003).
Martinez-Espinosa RM, Richardson DJ, Butt JN, Bonete MJ. Respiratory nitrate and nitrite pathway in the denitrifier haloarchaeon Haloferax mediterranei. Biochem. Soc. Trans. 34: 115-117 (2006).
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).
Mattana M, Coraggio I, Bertani A, Reggiani R. Expression of the enzymes of nitrate reduction during the anaerobic germination of rice. Plant Physiol. 106: 1605-1608 (1994).
Mattana M, Ida S, Reggiani R. The root form of ferredoxin-NADP(+) oxidoreductase is expressed in rice coleoptiles for the assimilation of nitrate. Planta 202: 397-401 (1997).
Matthews RG, Koutmos M, Datta S. Cobalamin-dependent and cobamide-dependent methyltransferases. Curr. Opin. Struct. Biol. 18: 658-666 (2008).
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).
Mehboob F, Junca H, Schraa G, Stams AJ. Growth of Pseudomonas chloritidismutans AW-1(T) on n-alkanes with chlorate as electron acceptor. Appl. Microbiol. Biotechnol. 83: 739-747 (2009).
Meijer SC, Van Loosdrecht MC, Heijnen JJ. Metabolic modelling of full-scale biological nitrogen and phosphorus removing wwtp's. Water Res. 35: 2711-2723. (2001).
Melchiorsen CR, Jensen NB, Christensen B, Vaever Jokumsen K, Villadsen J. Dynamics of pyruvate metabolism in Lactococcus lactis. Biotechnol. Bioeng. 74: 271-279 (2001).
Melchiorsen CR, Jokumsen KV, Villadsen J, Israelsen H, Arnau J. The level of pyruvate-formate lyase controls the shift from homolactic to mixed-acid product formation in Lactococcus lactis. Appl. Microbiol. Biotechnol. 58: 338-344 (2002).
Mellies J, Jose J, Meyer TF. The Neisseria gonorrhoeae gene aniA encodes an inducible nitrite reductase. Mol. Gen. Genet. 256: 525-532 (1997).
Menzel K, Ahrens K, Zeng A, Deckwer W. Kinetic, dynamic, and pathway studies of glycerol metabolism by Klebsiella pneumoniae in anaerobic continuous culture: IV. Enzymes and fluxes of pyruvate metabolism. Biotechnol. Bioeng. 60: 617-626 (1998).
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).
Messerschmidt A, Niessen H, Abt D, Einsle O, Schink B, Kroneck PM. Crystal structure of pyrogallol-phloroglucinol transhydroxylase, an Mo enzyme capable of intermolecular hydroxyl transfer between phenols. Proc. Natl. Acad. Sci. U.S.A. 101: 11571-11576 (2004).
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).
Mikami B, Ida S. Spinach ferredoxin-nitrite reductase: characterization of catalytic activity and interaction of the enzyme with substrates. J. Biochem. (Tokyo) 105: 47-50 (1989).
Mikosch CA, Denger K, Schafer EM, Cook AM. Anaerobic oxidations of cysteate: degradation via L-cysteate:2-oxoglutarate aminotransferase in Paracoccus pantotrophus. Microbiology 145: 1153-1160 (1999).
Mikula I, Durocher S, Martasek P, Mutus B, Slama-Schwok A. Isoform-specific differences in the nitrite reductase activity of nitric oxide synthases under hypoxia. Biochem. J. 418: 673-682 (2009).
Milton SL, Prentice HM. Beyond anoxia: the physiology of metabolic downregulation and recovery in the anoxia-tolerant turtle. Comp. Biochem. Physiol. A. Mol. Integr. Physiol. 147: 277-290 (2007).
Min H, Guo H, Xiong J. Rhythmic gene expression in a purple photosynthetic bacterium, Rhodobacter sphaeroides. FEBS Lett. 579: 808-812 (2005).
Minchin PE, Thorpe MR, Farrar JF, Koroleva OA. Source-sink coupling in young barley plants and control of phloem loading. J. Exp. Bot. 53: 1671-1676 (2002).
Moen B, Oust A, Langsrud O, Dorrell N, Marsden GL, Hinds J, Kohler A, Wren BW, Rudi K. Explorative multifactor approach for investigating global survival mechanisms of Campylobacter jejuni under environmental conditions. Appl. Environ. Microbiol. 71: 2086-2094 (2005).
Mohanty B, Ong BL. Contrasting effects of submergence in light and dark on pyruvate decarboxylase activity in roots of rice lines differing in submergence tolerance. Ann. Bot. (Lond.) 91: 291-300 (2003).
Molla G, Motteran L, Job V, Pilone MS, Pollegioni L. Kinetic mechanisms of glycine oxidase from Bacillus subtilis. Eur. J. Biochem. 270: 1474-1482 (2003).
Moons A, Valcke R, Van Montagu M. Low-oxygen stress and water deficit induce cytosolic pyruvate orthophosphate dikinase (PPDK) expression in roots of rice, a C3 plant. Plant J. 15: 89-98 (1998).
Morard P, Lacoste L, Silvestre J. Effect of oxygen deficiency on mineral nutrition of excised tomato roots. J. Plant Nutr. 27: 613-626 (2004).
Morard P, Silvestre J, Lacoste L, Caumes E, Lamaze T. Nitrate uptake and nitrite release by tomato roots in response to anoxia. J. Plant Physiol. 161: 855-865 (2004).
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).
Morozkina EV, Kurakov AV. Dissimilatory nitrate reduction in fungi under conditions of hypoxia and anoxia: a review. Prikl. Biokhim. Mikrobiol. 43: 607-613 (2007).
Muench DG, Archibold OW, Good AG. Hypoxic metabolism in wild rice (Zizania-palustris): enzyme-induction and metabolite production. Physiol. Plant. 89: 165-171 (1993).
Mujer CV, Rumpho ME, Lin JJ, Kennedy RA. Constitutive and inducible aerobic and anaerobic stress proteins in the Echinochloa complex and rice. Plant Physiol. 101: 217-226 (1993).
Mulkidjanian AY, Koonin EV, Makarova KS, Mekhedov SL, Sorokin A, Wolf YI, Dufresne A, Partensky F, Burd H, Kaznadzey D, Haselkorn R, Galperin MY. The cyanobacterial genome core and the origin of photosynthesis. Proc. Natl. Acad. Sci. U.S.A. 103: 13126-13131 (2006).
Murai K, Miyake K, Andoh J, Iijima S. Transcriptional regulation of nir and nor operons of Paracoccus denitrificans. J. Biosci. Bioeng. 89: 384-387 (2000).
Muralidharan V, Rinker KD, Hirsh IS, Bouwer EJ, Kelly RM. Hydrogen transfer between methanogens and fermentative heterotrophs in hyperthermophilic cocultures. Biotechnol. Bioeng. 56: 268-278 (1997).
Murugasu-Oei B, Tay A, Dick T. Upregulation of stress response genes and abc transporters in anaerobic stationary-phase Mycobacterium smegmatis. Mol. Gen. Genet. 262: 677-682 (1999).
Mustroph A, Boamfa EI, Laarhoven LJ, Harren FJ, Albrecht G, Grimm B. Organ-specific analysis of the anaerobic primary metabolism in rice and wheat seedlings. I: Dark ethanol production is dominated by the shoots. Planta 225: 103-114 (2006).
Mustroph A, Boamfa EI, Laarhoven LJ, Harren FJ, Pors Y, Grimm B. Organ specific analysis of the anaerobic primary metabolism in rice and wheat seedlings II: Light exposure reduces needs for fermentation and extends survival during anaerobiosis. Planta 225: 139-152 (2006).
Myers RW, Wray JW, Fish S, Abeles RH. Purification and characterization of an enzyme involved in oxidative carbon-carbon bond cleavage reactions in the methionine salvage pathway of Klebsiella pneumoniae. J. Biol. Chem. 268: 24785-24791 (1993).
Nadais MH, Capela MI, Arroja LM, Duarte AC. Biosorption of milk substrates onto anaerobic flocculent and granular sludge. Biotechnol. Prog. 19: 1053-1055 (2003).
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).
Nakano MM, Hoffmann T, Zhu Y, Jahn D. Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE. J. Bacteriol. 180: 5344-5350 (1998).
Nakano MM, Hulett FM. Adaptation of Bacillus subtilis to oxygen limitation. FEMS Microbiol. Lett. 157: 1-7 (1997).
Nakano MM, Zuber P. Anaerobic growth of a "strict aerobe". Annu. Rev. Microbiol. 52: 165-190 (1998).
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).
Nam H, Ryu T, Lee K, Kim S, Lee D. Computational identification of significantly regulated metabolic reactions by integration of data on enzyme activity and gene expression. BMB Rep. 41: 609-614 (2008).
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).
Neves AR, Ramos A, Nunes MC, Kleerebezem M, Hugenholtz J, de Vos WM, Almeida J, Santos H. In vivo nuclear magnetic resonance studies of glycolytic kinetics in Lactococcus lactis. Biotechnol. Bioeng. 64: 200-212 (1999).
Nevoigt E. Progress in metabolic engineering of Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 72: 379-412 (2008).
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).
Nie X, Durnin DC, Igamberdiev AU, Hill RD. Cytosolic calcium is involved in the regulation of barley hemoglobin gene expression. Planta 223: 542-549 (2006).
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).
Nishimura T, Teramoto H, Vertes AA, Inui M, Yukawa H. ArnR, a novel transcriptional regulator, represses expression of the narKGHJI operon in Corynebacterium glutamicum. J. Bacteriol. 190: 3264-3273 (2008).
Nissen TL, Kielland-Brandt MC, Nielsen J, Villadsen J. Optimization of ethanol production in Saccharomyces cerevisiae by metabolic engineering of the ammonium assimilation. Metab. Eng. 2: 69-77 (2000).
Nissen TL, Schulze U, Nielsen J, Villadsen J. Flux distributions in anaerobic, glucose-limited continuous cultures of Saccharomyces cerevisiae. Microbiology 143: 203-218 (1997).
Nordlund S, Kanemoto RH, Murrell SA, Ludden PW. Properties and regulation of glutamine synthetase from Rhodospirillum rubrum. J. Bacteriol. 161: 13-17 (1985).
Oh IJ, Lee HW, Park CH, Lee SY, Lee J. Succinic acid production from continuous fermentation process using Mannheimia succiniciproducens LPK7. J. Microbiol. Biotechnol. 18: 908-912 (2008).
Ohmori S, Nawata Y, Kiyono K, Murata H, Tsuboi S, Ikeda M, Akagi R, Morohashi K, Ono B. Saccharomyces cerevisiae cultured under aerobic and anaerobic conditions: air-level oxygen stress and protection against stress. Biochim. Biophys. Acta 1472: 587-594 (1999).
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).
Ohta M, Miura R, Yamano T, Miyake Y. Spectroscopic studies on the photoreaction of choline oxidase, a flavoprotein, with covalently bound flavin. J. Biochem. (Tokyo) 94: 879-892 (1983).
Ohta-Fukuyama M, Miyake Y, Emi S, Yamano T. Identification and properties of the prosthetic group of choline oxidase from Alcaligenes sp. J. Biochem. (Tokyo) 88: 197-203 (1980).
Olive MR, Peacock WJ, Dennis ES. The anaerobic responsive element contains two GC-rich sequences essential for binding a nuclear protein and hypoxic activation of the maize Adh1 promoter. Nucleic Acids Res. 19: 7053-7060 (1991).
Olive MR, Walker JC, Singh K, Dennis ES, Peacock WJ. Functional properties of the anaerobic responsive element of the maize Adh1 gene. Plant Mol. Biol. 15: 593-604 (1990).
Oliveira AP, Nielsen J, Forster J. Modeling Lactococcus lactis using a genome-scale flux model. BMC Microbiol. 5: 39 (2005).
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).
Ollivier B, Caumette P, Garcia JL, Mah RA. Anaerobic bacteria from hypersaline environments. Microbiol. Rev. 58: 27-38 (1994).
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).
op den Camp RG, Kuhlemeier C. Aldehyde dehydrogenase in tobacco pollen. Plant Mol. Biol. 35: 355-365 (1997).
Oren A. Formation and breakdown of glycine betaine and trimethylamine in hypersaline environments. Antonie Van Leeuwenhoek 58: 291-298 (1990).
Oren A. Microbial life at high salt concentrations: phylogenetic and metabolic diversity. Saline Systems 4: 2 (2008).
Oren A. Bioenergetic aspects of halophilism. Microbiol. Mol. Biol. Rev. 63: 334 (1999).
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).
Owen CA, Spano T, Hajjar SE, Tunaru V, Harytunyan S, Filali L, Kalaitzis P. Expression of genes for alcohol dehydrogenase and pyruvate decarboxylase in petals of cut carnation flowers in response to hypoxia and anoxia. Physiol. Plant. 122: 412-418 (2004).
Paarup M, Friedrich MW, Tindall BJ, Finster K. Characterization of the psychrotolerant acetogen strain SyrA5 and the emended description of the species Acetobacterium carbinolicum. Antonie Van Leeuwenhoek 89: 55-69 (2006).
Padiglia A, Medda R, Lorrai A, Murgia B, Pedersen JZ, Finazzi Agro A, Floris G. Characterization of Euphorbia characias latex amine oxidase. Plant Physiol. 117: 1363-1371 (1998).
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).
Panagiotou G, Christakopoulos P, Grotkjaer T, Olsson L. Engineering of the redox imbalance of Fusarium oxysporum enables anaerobic growth on xylose. Metab. Eng. 8: 474-482 (2006).
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).
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).
Parolin P. Submerged in darkness: adaptations to prolonged submergence by woody species of the Amazonian floodplains. Ann. Bot. (Lond.) 103: 359-376 (2009).
Pasentsis K, Falara V, Pateraki I, Gerasopoulos D, Kanellis AK. Identification and expression profiling of low oxygen regulated genes from Citrus flavedo tissues using RT-PCR differential display. J. Exp. Bot. 58: 2203-2216 (2007).
Pasternak C, Haberzettl K, Klug G. Thioredoxin is involved in oxygen-regulated formation of the photosynthetic apparatus of Rhodobacter sphaeroides. J. Bacteriol. 181: 100-106 (1999).
Paul AL, Ferl RJ. In vivo footprinting reveals unique cis-elements and different modes of hypoxic induction in maize Adh1 and Adh2. Plant Cell 3: 159-168 (1991).
Pavelic D, Arpagaus S, Rawyler A, Brandle R. Impact of post-anoxia stress on membrane lipids of anoxia-pretreated potato cells. A re-appraisal. Plant Physiol. 124: 1285-1292 (2000).
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).
Pedersen O, Binzer T, Borum J. Sulphide intrusion in eelgrass (Zostera marina L.). Plant Cell Environ. 27: 595-602 (2004).
Pedersen O, Rich SM, Colmer TD. Surviving floods: leaf gas films improve O(2) and CO(2) exchange, root aeration, and growth of completely submerged rice. Plant J. Dec 10 [Epub ahead of print] (2008).
Peschke VM, Sachs MM. Characterization and expression of transcripts induced by oxygen deprivation in maize (Zea mays L.). Plant Physiol. 104: 387-394 (1994).
Peschke VM, Sachs MM. Multiple pyruvate decarboxylase genes in maize are induced by hypoxia. Mol. Gen. Genet. 240: 206-212 (1993).
Peters F, Rother M, Boll M. Selenocysteine-containing proteins in anaerobic benzoate metabolism of Desulfococcus multivorans. J. Bacteriol. 186: 2156-2163 (2004).
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).
Petschacher B, Nidetzky B. Altering the coenzyme preference of xylose reductase to favor utilization of NADH enhances ethanol yield from xylose in a metabolically engineered strain of Saccharomyces cerevisiae. Microb. Cell Fact. 7: 9 (2008).
Pietrangeli P, Nocera S, Mondovi B, Morpurgo L. Is the catalytic mechanism of bacteria, plant, and mammal copper-TPQ amine oxidases identical? Biochim. Biophys. Acta. 1647: 152-156 (2003).
Pind PF, Angelidaki I, Ahring BK. Dynamics of the anaerobic process: Effects of volatile fatty acids. Biotechnol. Bioeng. 82: 791-801 (2003).
Pino C, Olmo-Mira F, Cabello P, Martinez-Luque M, Castillo F, Roldan MD, Moreno-Vivian C. The assimilatory nitrate reduction system of the phototrophic bacterium Rhodobacter capsulatus E1F1. Biochem. Soc. Trans. 34: 127-129 (2006).
Pinto R, Harrison JS, Hsu T, Jacobs WR Jr, Leyh TS. Sulfite reduction in Mycobacteria. J. Bacteriol. 189: 6714-6722 (2007).
Pitson SM, Mendz GL, Srinivasan S, Hazell SL. The tricarboxylic acid cycle of Helicobacter pylori. Eur. J. Biochem. 260: 258-267 (1999).
Pittman MS, Kelly DJ. Electron transport through nitrate and nitrite reductases in Campylobacter jejuni. Biochem. Soc. Trans. 33: 190-192 (2005).
Planchet E, Jagadis Gupta K, Sonoda M, Kaiser WM. Nitric oxide emission from tobacco leaves and cell suspensions: rate limiting factors and evidence for the involvement of mitochondrial electron transport. Plant J. 41: 732-743 (2005).
Planchet E, Kaiser WM. Nitric oxide (NO) detection by DAF fluorescence and chemiluminescence: a comparison using abiotic and biotic NO sources. J. Exp. Bot. 57: 3043-3055 (2006).
Platteeuw C, Hugenholtz J, Starrenburg M, van Alen-Boerrigter I, de Vos WM. Metabolic engineering of Lactococcus lactis: influence of the overproduction of alpha-acetolactate synthase in strains deficient in lactate dehydrogenase as a function of culture conditions. Appl. Environ. Microbiol. 61: 3967-3971 (1995).
Polcyn W. Nitrate-related down-regulation of respiratory nitrate reductase from Bradyrhizobium sp. (Lupinus). Acta Biochim. Pol. 55: 761-766 (2008).
Polcyn W, Lucinski R. Dissimilatory nitrate reductase from Bradyrhizobium sp. (Lupinus): subcellular location, catalytic properties, and characterization of the active enzyme forms. Curr. Microbiol. 52: 231-237 (2006).
Polcyn W, Lucinski R. Aerobic and anaerobic nitrate and nitrite reduction in free-living cells of Bradyrhizobium sp (Lupinus). FEMS Microbiol. Lett. 226: 331-337 (2003).
Polcyn W, Lucinski R. Effect of N oxyanions on anaerobic induction of nitrate reductase in subcellular fractions of Bradyrhizobium sp. (Lupinus). Antonie Van Leeuwenhoek. 95: 159-164 (2009).
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).
Pomar F, Caballero N, Pedreno MA, Barcelo AR. H2O2 generation during the auto-oxidation of coniferyl alcohol drives the oxidase activity of a highly conserved class III peroxidase involved in lignin biosynthesis. FEBS Lett. 529: 198-202 (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).
Posewitz MC, Smolinski SL, Kanakagiri S, Melis A, Seibert M, Ghirardi ML. Hydrogen photoproduction is attenuated by disruption of an isoamylase gene in Chlamydomonas reinhardtii. Plant Cell 16: 2151-2163 (2004).
Potter L, Millington P, Griffiths L, Cole J. Survival of bacteria during oxygen limitation. Int. J. Food Microbiol. 55: 11-18 (2000).
Povolo S, Casella S. A critical role for aniA in energy-carbon flux and symbiotic nitrogen fixation in Sinorhizobium meliloti. Arch. Microbiol. 174: 42-49 (2000).
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).
Pratscher J, Stichternoth C, Fichtl K, Schleifer KH, Braker G. Application of recognition of individual genes-fluorescence in situ hybridization (RING-FISH) to detect nitrite reductase genes (nirK) of denitrifiers in pure cultures and environmental samples. Appl. Environ. Microbiol. 75: 802-810 (2009).
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).
Qiu F, Guo L, Wen TJ, Liu F, Ashlock DA, Schnable PS. DNA sequence-based "Bar Codes" for tracking the origins of expressed sequence tags from a maize cDNA library constructed using multiple mRNA sources. Plant Physiol. 133: 475-481 (2003).
Qiu ZH, Lin QS. Spectra properties of rat liver mitochondrial choline dehydrogenase. Sci. China B. 33: 955-963 (1990).
Rabeh WM, Mather T, Cook PF. A three-dimensional homology model of the O-acetylserine sulfhydrylase-B from Salmonella typhimurium. Protein Pept. Lett. 13: 7-13 (2006).
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 M, Grover A, Peacock WJ, Dennis ES, Ellis MH. Effects of manipulation of pyruvate decarboxylase and alcohol dehydrogenase levels on the submergence tolerance of rice. Aust. J. Plant Physiol. 28: 1231-1241 (2001).
Raman B, Pan C, Hurst GB, Rodriguez M Jr, McKeown CK, Lankford PK, Samatova NF, Mielenz JR. Impact of pretreated switchgrass and biomass carbohydrates on Clostridium thermocellum ATCC 27405 cellulosome composition: a quantitative proteomic analysis. PLoS One. 4: e5271 (2009).
Ramirez S, Moreno R, Zafra O, Castan P, Valles C, Berenguer J. Two nitrate/nitrite transporters are encoded within the mobilizable plasmid for nitrate respiration of Thermus thermophilus HB8. J. Bacteriol. 182: 2179-2183 (2000).
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).
Ranathunge K, Kotula L, Steudle E, Lafitte R. Water permeability and reflection coefficient of the outer part of young rice roots are differently affected by closure of water channels (aquaporins) or blockage of apoplastic pores. J. Exp. Bot. 55: 433-447 (2004).
Rapheal SV, Swaminathan KR, Lalitha K. Metabolic characteristics of an aerobe isolated from a methylotrophic methanogenic enrichment culture. J. Biosci. 28: 235-242 (2003).
Ratcliffe RG. In vivo NMR studies of the metabolic response of plant tissues to anoxia. Ann. Bot. (Lond.) 79: 39-48 (1997).
Rauh D, Graentzdoerffer A, Granderath K, Andreesen JR, Pich A. Tungsten-containing aldehyde oxidoreductase of Eubacterium acidaminophilum: isolation, characterization and molecular analysis. Eur. J. Biochem. 271: 212-219 (2004).
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).
Rawyler A, Arpagaus S, Braendle R. Impact of oxygen stress and energy availability on membrane stability of plant cells. Ann. Bot. (Lond.) 90: 499-507 (2002).
Rawyler A, Pavelic D, Gianinazzi C, Oberson J, Braendle R. Membrane lipid integrity relies on a threshold of ATP production rate in potato cell cultures submitted to anoxia. Plant Physiol. 120: 293-300 (1999).
Rawyler AJ, Braendle RA. N-Acylphosphatidylethanolamine accumulation in potato cells upon energy shortage caused by anoxia or respiratory inhibitors. Plant Physiol. 127: 240-251 (2001).
Raymond J, Segre D. The effect of oxygen on biochemical networks and the evolution of complex life. Science 311: 1764-1767 (2006).
Raynaud S, Perrin R, Cocaign-Bousquet M, Loubiere P. Metabolic and transcriptomic adaptation of Lactococcus lactis subsp. lactis Biovar diacetylactis in response to autoacidification and temperature downshift in skim milk. Appl. Environ. Microbiol. 71: 8016-8023 (2005).
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).
Reents H, Munch R, Dammeyer T, Jahn D, Hartig E. The Fnr regulon of Bacillus subtilis. J. Bacteriol. 188: 1103-1112 (2006).
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).
Reggiani R. A role for ethylene in low-oxygen signaling in rice roots. Amino Acids 30: 299-301 (2006).
Reggiani R, Bertani A. Anaerobic amino acid metabolism. Russ. J. Plant Physiol. 50: 733-736 (2003).
Reggiani R, Nebuloni M, Mattana M, Brambilla I. Anaerobic accumulation of amino acids in rice roots: role of the glutamine synthetase/glutamate synthase cycle. Amino Acids 18: 207-217 (2000).
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).
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 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).
Rhodes D, Nadolska-Orczyk A. Plant stress physiology. ENCYCLOPEDIA OF LIFE SCIENCES Nature Publishing Group www.els.net (2001).
Richardson DJ, Berks BC, Russell DA, Spiro S, Taylor CJ. Functional, biochemical and genetic diversity of prokaryotic nitrate reductases. Cell Mol. Life Sci. 58: 165-178 (2001).
Richardson DJ, Watmough NJ. Inorganic nitrogen metabolism in bacteria. Curr. Opin. Chem. Biol. 3: 207-219 (1999).
Ricoult C, Cliquet JB, Limami AM. Stimulation of alanine amino transferase (AlaAT) gene expression and alanine accumulation in embryo axis of the model legume Medicago truncatula contribute to anoxia stress tolerance. Physiol. Plant. 123: 30-39 (2005).
Ridley H, Watts CA, Richardson DJ, Butler CS. Resolution of distinct membrane-bound enzymes from Enterobacter cloacae SLD1a-1 that are responsible for selective reduction of nitrate and selenate oxyanions. Appl. Environ. Microbiol. 72: 5173-5180 (2006).
Rivoal J, Hanson AD. Metabolic control of anaerobic glycolysis. Overexpression of lactate dehydrogenase in transgenic tomato roots supports the Davies-Roberts hypothesis and points to a critical role for lactate secretion. Plant Physiol. 106: 1179-1185 (1994).
Rivoal J, Hanson AD. Evidence for a large and sustained glycolytic flux to lactate in anoxic roots of some members of the halophytic genus Limonium. Plant Physiol. 101: 553-560 (1993).
Rivoal J, Thind S, Pradet A, Ricard B. Differential induction of pyruvate decarboxylase subunits and transcripts in anoxic rice seedlings. Plant Physiol. 114: 1021-1029 (1997).
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).
Rock JD, Thomson MJ, Read RC, Moir JW. Regulation of denitrification genes in Neisseria meningitidis by nitric oxide and the repressor NsrR. J. Bacteriol. 189: 1138-1144 (2007).
Rockel P, Strube F, Rockel A, Wildt J, Kaiser WM. Regulation of nitric oxide (NO) production by plant nitrate reductase in vivo and in vitro. J. Exp. Bot. 53: 103-110 (2002).
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).
Rodriguez J, Kleerebezem R, Lema JM, van Loosdrecht MC. Modeling product formation in anaerobic mixed culture fermentations. Biotechnol. Bioeng. 93: 592-606 (2006).
Rolletschek H, Borisjuk L, Koschorreck M, Wobus U, Weber H. Legume embryos develop in a hypoxic environment. J. Exp. Bot. 53: 1099-1107 (2002).
Roth JR, Lawrence JG, Rubenfield M, Kieffer-Higgins S, Church GM. Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium. J. Bacteriol. 175: 3303-3316 (1993).
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).
Rozenzvieg D, Elmaci C, Samach A, Lurie S, Porat R. Isolation of four heat shock protein cDNAs from grapefruit peel tissue and characterization of their expression in response to heat and chilling temperature stresses. Physiol. Plant. 121: 421-428 (2004).
Rumer S, Gupta KJ, Kaiser WM. Plant cells oxidize hydroxylamines to NO. J. Exp. Bot. 60: 2065-2072 (2009).
Rungsrisuriyachai K, Gadda G. On the role of histidine 351 in the reaction of alcohol oxidation catalyzed by choline oxidase. Biochemistry 47: 6762-6769 (2008).
Russell DA, Sachs MM. Differential expression and sequence analysis of the maize glyceraldehyde-3-phosphate dehydrogenase gene family. Plant Cell 1: 793-803 (1989).
Saab IN, Sachs MM. A flooding-induced xyloglucan endo-transglycosylase homolog in maize is responsive to ethylene and associated with aerenchyma. Plant Physiol. 112: 385-391 (1996).
Sabehat A, Lurie S, Weiss D. Expression of small heat-shock proteins at low temperatures. A possible role in protecting against chilling injuries. Plant Physiol. 117: 651-658 (1998).
Sakai K, Miyasako Y, Nagatomo H, Watanabe H, Wakayama M, Moriguchi M. L-Ornithine decarboxylase from Hafnia alvei has a novel L-ornithine oxidase activity. J. Biochem. (Tokyo) 122: 961-968 (1997).
Salusjarvi L, Kankainen M, Soliymani R, Pitkanen JP, Penttila M, Ruohonen L. Regulation of xylose metabolism in recombinant Saccharomyces cerevisiae. Microb. Cell Fact. 7: 18 (2008).
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).
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 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).
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).
Sato T, Harada T, Ishizawa K. Stimulation of glycolysis in anaerobic elongation of pondweed (Potamogeton distinctus) turions. J. Exp. Bot. 53: 1847-1856 (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).
Savchenko G, Wiese C, Neimanis S, Hedrich R, Heber U. pH regulation in apoplastic and cytoplasmic cell compartments of leaves. Planta 211: 246-255 (2000).
Sawada MT, Ishimoto M. Proton translocation coupled to nitrite reduction in anaerobically grown Escherichia coli. J. Biochem. (Tokyo) 97: 205-211 (1985).
Sawai Y, Yamaguchi Y, Miyama D, Yoshitomi H. Cycling treatment of anaerobic and aerobic incubation increases the content of gamma-aminobutyric acid in tea shoots. Amino Acids 20: 331-334 (2001).
Sawers G. The hydrogenases and formate dehydrogenases of Escherichia coli. Antonie Van Leeuwenhoek 66: 57-88 (1994).
Sawers G, Watson G. A glycyl radical solution: oxygen-dependent interconversion of pyruvate formate-lyase. Mol. Microbiol. 29: 945-54 (1998).
Schafer S, Gotz M, Eisenreich W, Bacher A, Fuchs G. 13C-NMR study of autotrophic CO2 fixation in Thermoproteus neutrophilus. Eur. J. Biochem. 184: 151-156 (1989).
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).
Schluter U, Crawford RM. Long-term anoxia tolerance in leaves of Acorus calamus L. and Iris pseudacorus L. J. Exp. Bot. 52: 2213-2225 (2001).
Schmidt I, van Spanning RJ, Jetten MS. Denitrification and ammonia oxidation by Nitrosomonas europaea wild-type, and NirK- and NorB-deficient mutants. Microbiology 150: 4107-4114 (2004).
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).
Schneider S, Mohamed ME, Fuchs G. Anaerobic metabolism of L-phenylalanine via benzoyl-CoA in the denitrifying bacterium Thauera aromatica. Arch. Microbiol. 168: 310-320 (1997).
Schortemeyer M, Atkin OK, McFarlane N, Evans JR. N-2 fixation by Acacia species increases under elevated atmospheric CO2. Plant Cell Environ. 25: 567-579 (2002).
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).
Schubert HL, Raux E, Wilson KS, Warren MJ. Common chelatase design in the branched tetrapyrrole pathways of heme and anaerobic cobalamin synthesis. Biochemistry 38: 10660-10669 (1999).
Schulze U, Liden G, Villadsen J. Dynamics of ammonia uptake in nitrogen limited anaerobic cultures of Saccharomyces cerevisiae. J. Biotechnol. 46: 33-42 (1996).
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).
Scott AI. Discovering nature's diverse pathways to vitamin B12: a 35-year odyssey. J. Org. Chem. 68: 2529-2539 (2003).
Scott C, Partridge JD, Stephenson JR, Green J. DNA target sequence and FNR-dependent gene expression. FEBS Lett. 541: 97-101 (2003).
Sears HJ, Little PJ, Richardson DJ, Berks BC, Spiro S, Ferguson SJ. Identification of an assimilatory nitrate reductase in mutants of Paracoccus denitrificans GB17 deficient in nitrate respiration. Arch. Microbiol. 167: 61-66 (1997).
Sears HJ, Sawers G, Berks BC, Ferguson SJ, Richardson DJ. Control of periplasmic nitrate reductase gene expression (napEDABC) from Paracoccus pantotrophus in response to oxygen and carbon substrates. Microbiology 146: 2977-2985 (2000).
Sedbrook JC, Kronebusch PJ, Borisy GG, Trewavas AJ, Masson PH. Transgenic AEQUORIN reveals organ-specific cytosolic Ca2+ responses to anoxia and Arabidopsis thaliana seedlings. Plant Physiol. 111: 243-257 (1996).
Sekowska A, Denervaud V, Ashida H, Michoud K, Haas D, Yokota A, Danchin A. Bacterial variations on the methionine salvage pathway. BMC Microbiol. 4: 9 (2004).
Selao TT, Nordlund S, Noren A. Comparative proteomic studies in Rhodospirillum rubrum grown under different nitrogen conditions. J. Proteome Res. 7: 3267-3275 (2008).
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).
Sell S, Hehl R. Functional dissection of a small anaerobically induced bZIP transcription factor from tomato. Eur. J. Biochem. 271: 4534-4544 (2004).
Semin BK, Davletshina LN, Novakova AA, Kiseleva TY, Lanchinskaya VY, Aleksandrov AY, Seifulina N, Ivanov II, Seibert M, Rubin AB. Accumulation of ferrous iron in Chlamydomonas reinhardtii. Influence of CO2 and anaerobic induction of the reversible hydrogenase. Plant Physiol. 131: 1756-1764 (2003).
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).
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).
Shaw AJ, Podkaminer KK, Desai SG, Bardsley JS, Rogers SR, Thorne PG, Hogsett DA, Lynd LR. Metabolic engineering of a thermophilic bacterium to produce ethanol at high yield. Proc. Natl. Acad. Sci. U.S.A. 105: 13769-13774 (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).
Shi NQ, Jeffries TW. Anaerobic growth and improved fermentation of Pichia stipitis bearing a URA1 gene from Saccharomyces cerevisiae. Appl. Microbiol. Biotechnol. 50: 339-345 (1998).
Siddiqui RA, Warnecke-Eberz U, Hengsberger A, Schneider B, Kostka S, Friedrich B. Structure and function of a periplasmic nitrate reductase in Alcaligenes eutrophus H16. J. Bacteriol. 175: 5867-5876 (1993).
Simon J. Enzymology and bioenergetics of respiratory nitrite ammonification. FEMS Microbiol. Rev. 26: 285-309 (2002).
Simon J, Einsle O, Kroneck PM, Zumft WG. The unprecedented nos gene cluster of Wolinella succinogenes encodes a novel respiratory electron transfer pathway to cytochrome c nitrous oxide reductase. FEBS Lett. 569: 7-12 (2004).
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).
Singh P, Kaloudas D, Raines CA. Expression analysis of the Arabidopsis CP12 gene family suggests novel roles for these proteins in roots and floral tissues. J. Exp. Bot. 59: 3975-3985 (2008).
Sipma J, Janssen AJ, Hulshoff Pol LW, Lettinga G. Development of a novel process for the biological conversion of H2S and methanethiol to elemental sulfur. Biotechnol. Bioeng. 82: 1-11 (2003).
Sjogren T, Hajdu J. The structure of an alternative form of Paracoccus pantotrophus cytochrome cd1 nitrite reductase. J. Biol. Chem. 276: 29450-29455 (2001).
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).
Smith EC, Williamson EM, Wareham N, Kaatz GW, Gibbons S. Antibacterials and modulators of bacterial resistance from the immature cones of Chamaecyparis lawsoniana. Phytochemistry 68: 210-217 (2007).
Smith I. Mycobacterium tuberculosis pathogenesis and molecular determinants of virulence. Clin. Microbiol. Rev. 16: 463-498 (2003).
Sohaskey CD. Regulation of nitrate reductase activity in Mycobacterium tuberculosis by oxygen and nitric oxide. Microbiology 151: 3803-3810 (2005).
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).
Sorokin DY, Tourova TP, Galinski EA, Muyzer G, Kuenen JG. Thiohalorhabdus denitrificans gen. nov., sp. nov., an extremely halophilic, sulfur-oxidizing, deep-lineage Gammaproteobacterium from hypersaline habitats. Int. J. Syst. Evol. Microbiol. 58: 2890-2897 (2008).
Sorrell BK. Regulation of root anaerobiosis and carbon translocation by light and root aeration in Isoetes alpinus. Plant Cell Environ. 27: 1102-1111 (2004).
Spicer R, Holbrook NM. Within-stem oxygen concentration and sap flow in four temperate tree species: does long-lived xylem parenchyma experience hypoxia?. Plant Cell Environ. 28: 192-201 (2005).
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).
Sridhar J, Eiteman MA. Metabolic flux analysis of Clostridium thermosuccinogenes: effects of pH and culture redox potential. Appl. Biochem. Biotechnol. 94: 51-69 (2001).
Stadtman TC. Discoveries of vitamin B12 and selenium enzymes. Annu. Rev. Biochem. 71: 1-16 (2002).
Starkenburg SR, Arp DJ, Bottomley PJ. Expression of a putative nitrite reductase and the reversible inhibition of nitrite-dependent respiration by nitric oxide in Nitrobacter winogradskyi Nb-255. Environ. Microbiol. 10: 3036-3042 (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).
Steuber J, Rufibach M, Fritz G, Neese F, Dimroth P. Inactivation of the Na+-translocating NADH:ubiquinone oxidoreductase from Vibrio alginolyticus by reactive oxygen species. Eur. J. Biochem. 269: 1287-1292 (2002).
Steunou AS, Bhaya D, Bateson MM, Melendrez MC, Ward DM, Brecht E, Peters JW, Kuhl M, Grossman AR. In situ analysis of nitrogen fixation and metabolic switching in unicellular thermophilic cyanobacteria inhabiting hot spring microbial mats. Proc. Natl. Acad. Sci. U.S.A. 103: 2398-2403 (2006).
Stewart V. Nitrate- and nitrite-responsive sensors NarX and NarQ of proteobacteria. Biochem. Soc. Trans. 31: 1-10 (2003).
Stewart V. Nitrate regulation of anaerobic respiratory gene expression in Escherichia coli. Mol. Microbiol. 9: 425-434 (1993).
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, 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).
Stohr C, Stremlau S. Formation and possible roles of nitric oxide in plant roots. J. Exp. Bot. 57: 463-470 (2006).
Stoimenova M, Igamberdiev AU, Gupta KJ, Hill RD. Nitrite-driven anaerobic ATP synthesis in barley and rice root mitochondria. Planta 226: 465-474 (2007).
Stolz JF, Basu P. Evolution of nitrate reductase: molecular and structural variations on a common function. Chembiochem. 3: 198-206 (2002).
Stutz HE, Quixley KW, McMaster LD, Reid SJ. Co-regulation of the nitrogen-assimilatory gene cluster in Clostridium saccharobutylicum. Microbiology 153: 3081-3090 (2007).
Subbaiah CC, Bush DS, Sachs MM. Mitochondrial contribution to the anoxic Ca2+ signal in maize suspension-cultured cells. Plant Physiol. 118: 759-771 (1998).
Subbaiah CC, Sachs MM. Molecular and cellular adaptations of maize to flooding stress. Ann. Bot. (Lond.) 91: 119-127 (2003).
Subbaiah CC, Sachs MM. Altered patterns of sucrose synthase phosphorylation and localization precede callose induction and root tip death in anoxic maize seedlings. Plant Physiol. 125: 585-594 (2001).
Subbaiah CC, Zhang J, Sachs MM. Involvement of intracellular calcium in anaerobic gene expression and survival of maize seedlings. Plant Physiol. 105: 369-376 (1994).
Subramanyam R, Jolley C, Brune DC, Fromme P, Webber AN. Characterization of a novel photosystem I-LHCI supercomplex isolated from Chlamydomonas reinhardtii under anaerobic (State II) conditions. FEBS Lett. 580: 233-238 (2006).
Suharti, de Vries S. Membrane-bound denitrification in the Gram-positive bacterium Bacillus azotoformans. Biochem. Soc. Trans. 33: 130-133 (2005).
Sun J, Van Den Heuvel J, Soucaille P, Qu Y, Zeng AP. Comparative genomic analysis of dha regulon and related genes for anaerobic glycerol metabolism in bacteria. Biotechnol. Prog. 19: 263-272 (2003).
Suzuki E, Horikoshi N, Kohzuma T. Cloning, sequencing, and transcriptional studies of the gene encoding copper-containing nitrite reductase from Alcaligenes xylosoxidans NCIMB 11015. Biochem. Biophys. Res. Commun. 255: 427-431 (1999).
Suzuki K, Itai R, Suzuki K, Nakanishi H, Nishizawa NK, Yoshimura E, Mori S. Formate dehydrogenase, an enzyme of anaerobic metabolism, is induced by iron deficiency in barley roots. Plant Physiol. 116: 725-732 (1998).
Suzuki M, Hirai T, Arai H, Ishii M, Igarashi Y. Purification, characterization, and gene cloning of thermophilic cytochrome cd1 nitrite reductase from Hydrogenobacter thermophilus TK-6. J. Biosci. Bioeng. 101: 391-397 (2006).
Sweetlove LJ, Dunford R, Ratcliffe RG, Kruger NJ. Lactate metabolism in potato tubers deficient in lactate dehydrogenase activity. Plant Cell Environ. 23: 873-881 (2000).
Tadege M, Dupuis I, Kuhlemeier C. Ethanolic fermentation: new functions for an old pathway. Trends Plant Sci. 4: 320-325 (1999).
Takahashi N, Yamada T. Pathways for amino acid metabolism by Prevotella intermedia and Prevotella nigrescens. Oral Microbiol. Immunol. 15: 96-102 (2000).
Takaichi S, Maoka T, Yamada M, Matsuura K, Haikawa Y, Hanada S. Absence of carotenes and presence of a tertiary methoxy group in a carotenoid from a thermophilic filamentous photosynthetic bacterium Roseiflexus castenholzii. Plant Cell Physiol. 42: 1355-1362 (2001).
Takasaki K, Shoun H, Nakamura A, Hoshino T, Takaya N. Unusual transcription regulation of the niaD gene under anaerobic conditions supporting fungal ammonia fermentation. Biosci. Biotechnol. Biochem. 68: 978-980 (2004).
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).
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).
Teakle N, Flowers T, Real D, Colmer T. Lotus tenuis tolerates the interactive effects of salinity and waterlogging by 'excluding' Na+ and Cl- from the xylem. J. Exp. Bot. 58: 2169-2180 (2007).
Tesniere C, Pradal M, El-Kereamy A, Torregrosa L, Chatelet P, Roustan JP, Chervin C. Involvement of ethylene signalling in a non-climacteric fruit: new elements regarding the regulation of ADH expression in grapevine. J. Exp. Bot. 55: 2235-2240 (2004).
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).
Thalasso F, van der Burgt J, O'Flaherty V, Colleran E. Large-scale anaerobic degradation of betaine. J. Chem. Technol. Biotechnol. 74: 1176-1182 (1999).
Thanakoses P, Black AS, Holtzapple MT. Fermentation of corn stover to carboxylic acids. Biotechnol. Bioeng. 83: 191-200 (2003).
Thauer RK, Shima S. Methane as fuel for anaerobic microorganisms. Ann. N. Y. Acad. Sci. 1125: 158-170 (2008).
Thimm O, Essigmann B, Kloska S, Altmann T, Buckhout TJ. Response of Arabidopsis to iron deficiency stress as revealed by microarray analysis. Plant Physiol. 127: 1030-1043 (2001).
Third KA, Burnett N, Cord-Ruwisch R. Simultaneous nitrification and denitrification using stored substrate (phb) as the electron donor in an SBR. Biotechnol. Bioeng. 83: 706-720 (2003).
Thomas AL, Guerreiro SM, Sodek L. Aerenchyma formation and recovery from hypoxia of the flooded root system of nodulated soybean. Ann. Bot. (Lond.) 96: 1191-1198 (2005).
Thomas SH, Wagner RD, Arakaki AK, Skolnick J, Kirby JR, Shimkets LJ, Sanford RA, Loffler FE. The mosaic genome of Anaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the delta-proteobacteria. PLoS ONE 3: e2103 (2008).
Tielens AG, Rotte C, van Hellemond JJ, Martin W. Mitochondria as we don't know them. Trends Biochem. Sci. 27: 564-572 (2002).
Tiquia SM, Masson SA, Devol A. Vertical distribution of nitrite reductase genes (nir S) in continental margin sediments of the Gulf of Mexico. FEMS Microbiol. Ecol. 58: 464-475 (2006).
Tischner R, Planchet E, Kaiser WM. Mitochondrial electron transport as a source for nitric oxide in the unicellular green alga Chlorella sorokiniana. FEBS Lett. 576: 151-155 (2004).
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).
Toivari MH, Aristidou A, Ruohonen L, Penttila M. Conversion of xylose to ethanol by recombinant Saccharomyces cerevisiae: importance of xylulokinase (XKS1) and oxygen availability. Metab. Eng. 3: 236-249 (2001).
Torry-Smith M, Sommer P, Ahring BK. Purification of bioethanol effluent in an UASB reactor system with simultaneous biogas formation. Biotechnol. Bioeng. 84: 7-12 (2003).
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).
Treusch AH, Leininger S, Kletzin A, Schuster SC, Klenk HP, Schleper C. Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ. Microbiol. 7: 1985-1995 (2005).
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, Nagarajan T, Verma SC, Rudulier DL. Inhibition of biosynthesis and activity of nitrogenase in Azospirillum brasilense Sp7 under salinity stress. Curr. Microbiol. 44: 363-367 (2002).
Tugtas AE, Pavlostathis SG. Effect of sulfide on nitrate reduction in mixed methanogenic cultures. Biotechnol. Bioeng. 97: 1448-1459 (2007).
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).
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. 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).
Urban P, Chirat I, Lederer F. Rat kidney L-2-hydroxyacid oxidase. Structural and mechanistic comparison with flavocytochrome b2 from baker's yeast. Biochemistry 27: 7365-7371 (1988).
Usov OM, Sun Y, Grigoryants VM, Shapleigh JP, Scholes CP. EPR-ENDOR of the Cu(I)NO complex of nitrite reductase. J. Am. Chem. Soc. 128: 13102-13111 (2006).
Uttaro AD. Biosynthesis of polyunsaturated fatty acids in lower eukaryotes. IUBMB Life 58: 563-571 (2006).
Uzcategui NL, Szallies A, Pavlovic-Djuranovic S, Palmada M, Figarella K, Boehmer C, Lang F, Beitz E, Duszenko M. Cloning, heterologous expression, and characterization of three aquaglyceroporins from Trypanosoma brucei. J. Biol. Chem. 279: 42669-42676 (2004).
Valadi H, Larsson C, Gustafsson L. Improved ethanol production by glycerol-3-phosphate dehydrogenase mutants of Saccharomyces cerevisiae. Appl. Microbiol. Biotechnol. 50: 434-439 (1998).
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 der Maarel MJ, Jansen M, Haanstra R, Meijer WG, Hansen TA. Demethylation of dimethylsulfoniopropionate to 3-S-methylmercaptopropionate by marine sulfate-reducing bacteria. Appl. Environ. Microbiol. 62: 3978-3984 (1996).
Van Der Maas P, Van De Sandt T, Klapwijk B, Lens P. Biological reduction of nitric oxide in aqueous Fe(II)EDTA solutions. Biotechnol. Prog. 19: 1323-1328 (2003).
van der Star WR, van de Graaf MJ, Kartal B, Picioreanu C, Jetten MS, van Loosdrecht MC. Response of anaerobic ammonium-oxidizing bacteria to hydroxylamine. Appl. Environ. Microbiol. 74: 4417-4426 (2008).
Van Dongen JT, Frohlich A, Ramirez-Aguilar SJ, Schauer N, Fernie AR, Erban A, Kopka J, Clark J, Langer A, Geigenberger P. Transcript and metabolite profiling of the adaptive response to mild decreases in oxygen concentration in the roots of Arabidopsis plants. Ann. Bot. (Lond.) 103: 269-280 (2009).
van Rooyen JM, Abratt VR, Sewell BT. Three-dimensional structure of a type III glutamine synthetase by single-particle reconstruction. J. Mol. Biol. 361: 796-810 (2006).
Van Spanning RJ, De Boer AP, Reijnders WN, Spiro S, Westerhoff HV, Stouthamer AH, Van der Oost J. Nitrite and nitric oxide reduction in Paracoccus denitrificans is under the control of NNR, a regulatory protein that belongs to the FNR family of transcriptional activators. FEBS Lett. 360: 151-154 (1995).
van Walsum GP, Lynd LR. Allocation of ATP to synthesis of cells and hydrolytic enzymes in cellulolytic fermentative microorganisms: bioenergetics, kinetics, and bioprocessing. Biotechnol. Bioeng. 58: 316-320 (1998).
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).
Vanlerberghe GC, Horsey AK, Weger HG, Turpin DH. Anaerobic carbon metabolism by the tricarboxylic acid cycle. Evidence for partial oxidative and reductive pathways during dark ammonium assimilation. Plant Physiol. 91: 1551-1557 (1989).
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).
Vartapetian BB, Andreeva IN, Generozova IP, Polyakova LI, Maslova IP, Dolgikh YI, Stepanova AY. Functional electron microscopy in studies of plant response and adaptation to anaerobic stress. Ann. Bot. (Lond.) 91: 155-172 (2003).
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).
Virolainen E, Blokhina O, Fagerstedt K. Ca2+-induced high amplitude swelling and cytochrome c release from wheat (Triticum aestivum L.) mitochondria under anoxic stress. Ann. Bot. (Lond.) 90: 509-516 (2002).
Vogt AM, Nef H, Schaper J, Poolman M, Fell DA, Kubler W, Elsasser A. Metabolic control analysis of anaerobic glycolysis in human hibernating myocardium replaces traditional concepts of flux control. FEBS Lett. 517: 245-250 (2002).
Vogt AM, Poolman M, Ackermann C, Yildiz M, Schoels W, Fell DA, Kubler W. Regulation of glycolytic flux in ischemic preconditioning. A study employing metabolic control analysis. J. Biol. Chem. 277: 24411-24419 (2002).
Vollack KU, Hartig E, Korner H, Zumft WG. Multiple transcription factors of the FNR family in denitrifying Pseudomonas stutzeri: characterization of four fnr-like genes, regulatory responses and cognate metabolic processes. Mol. Microbiol. 31: 1681-1694 (1999).
Vollack KU, Xie J, Hartig E, Romling U, Zumft WG. Localization of denitrification genes on the chromosomal map of Pseudomonas aeruginosa. Microbiology 144: 441-448 (1998).
Vriezen WH, Zhou Z, Van Der Straeten D. Regulation of submergence-induced enhanced shoot elongation in Oryza sativa L. Ann. Bot. (Lond.) 91: 263-270 (2003).
Wadud S, Onodera R, Or-Rashid MM. Studies on the possibility of histidine biosynthesis from histidinol, imidazolepyruvic acid, imidazoleacetic acid, and imidazolelactic acid by mixed ruminal bacteria, protozoa, and their mixture in vitro. Appl. Microbiol. Biotechnol. 55: 219-225 (2001).
Wagner MA, Jorns MS. Monomeric sarcosine oxidase: 2. Kinetic studies with sarcosine, alternate substrates, and a substrate analogue. Biochemistry 39: 8825-8829 (2000).
Wagner UG, Stupperich E, Kratky C. Structure of the molybdate/tungstate binding protein Mop from Sporomusa ovata. Structure Fold. Des. 8: 1127-1136 (2000).
Wahl RC, Warner CK, Finnerty V, Rajagopalan KV. Drosophila melanogaster ma-l mutants are defective in the sulfuration of desulfo Mo hydroxylases. J. Biol. Chem. 257: 3958-3962 (1982).
Wahlbom CF, Eliasson A, Hahn-Hagerdal B. Intracellular fluxes in a recombinant xylose-utilizing Saccharomyces cerevisiae cultivated anaerobically at different dilution rates and feed concentrations. Biotechnol. Bioeng. 72: 289-296 (2001).
Wahlbom CF, Hahn-Hagerdal B. Furfural, 5-hydroxymethyl furfural, and acetoin act as external electron acceptors during anaerobic fermentation of xylose in recombinant Saccharomyces cerevisiae. Biotechnol. Bioeng. 78: 172-178 (2002).
Walker J, Barrett J. Parasite sulphur amino acid metabolism. Int. J. Parasitol. 27: 883-897 (1997).
Walt A, Kahn ML. The fixA and fixB genes are necessary for anaerobic carnitine reduction in Escherichia coli. J. Bacteriol. 184: 4044-4047 (2002).
Wang A, Crowley DE. Global gene expression responses to cadmium toxicity in Escherichia coli. J. Bacteriol. 187: 3259-3266 (2005).
Wang SS, Brandriss MC. Proline utilization in Saccharomyces cerevisiae: sequence, regulation, and mitochondrial localization of the PUT1 gene product. Mol. Cell Biol. 7: 4431-4440 (1987).
Watson NR, Peschke VM, Russell DA, Sachs MM. Analysis of L-alanine:2-oxoglutarate aminotransferase isozymes in maize. Biochem. Genet. 30: 371-383 (1992).
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).
Weiss B. Evidence for mutagenesis by nitric oxide during nitrate metabolism in Escherichia coli. J. Bacteriol. 188: 829-833 (2006).
Wen Z, Morrison M. The NAD(P)H-dependent glutamate dehydrogenase activities of Prevotella ruminicola B(1)4 can be attributed to one enzyme (GdhA), and gdhA expression is regulated in response to the nitrogen source available for growth. Appl. Environ. Microbiol. 62: 3826-3833 (1996).
Werle M, Kreuzer J, Hofele J, Elsasser A, Ackermann C, Katus HA, Vogt AM. Metabolic control analysis of the Warburg-effect in proliferating vascular smooth muscle cells. J. Biomed. Sci. 12: 827-834 (2005).
Wetson AM, Cassaniti C, Flowers TJ. Do conditions during dormancy influence germination of Suaeda maritima? Ann. Bot. (Lond.) 101: 1319-1327 (2008).
Wiengweera A, Greenway H. Performance of seminal and nodal roots of wheat in stagnant solution: K+ and P uptake and effects of increasing O2 partial pressures around the shoot on nodal root elongation. J. Exp. Bot. 55: 2121-2129 (2004).
Wolff RA, Urben GW, O'Herrin SM, Kenealy WR. Dehydrogenases involved in the conversion of succinate to 4-hydroxybutanoate by Clostridium kluyveri. Appl. Environ. Microbiol. 59: 1876-1882 (1993).
Wolterink AF, Jonker AB, Kengen SW, Stams AJ. Pseudomonas chloritidismutans sp. nov., a non-denitrifying, chlorate-reducing bacterium. Int. J. Syst. Evol. Microbiol. 52: 2183-2190 (2002).
Wood HG. Life with CO or CO2 and H2 as a source of carbon and energy. FASEB J. 5: 156-163 (1991).
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 NJ, Alizadeh T, Bennett S, Pearce J, Ferguson SJ, Richardson DJ, Moir JW. Maximal expression of membrane-bound nitrate reductase in Paracoccus is induced by nitrate via a third FNR-like regulator named NarR. J. Bacteriol. 183: 3606-3613 (2001).
Woods DR, Reid SJ. Recent developments on the regulation and structure of glutamine synthetase enzymes from selected bacterial groups. FEMS Microbiol. Rev. 11: 273-283 (1993).
Wu CY, Bird AJ, Winge DR, Eide DJ. Regulation of the yeast TSA1 peroxiredoxin by ZAP1 is an adaptive response to the oxidative stress of zinc deficiency. J. Biol. Chem. 282: 2184-2195 (2007).
Wu G, Shortt BJ, Lawrence EB, Levine EB, Fitzsimmons KC, Shah DM. Disease resistance conferred by expression of a gene encoding H2O2-generating glucose oxidase in transgenic potato plants. Plant Cell 7: 1357-1368 (1995).
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, Knowles R. Cellular regulation of nitrate uptake in denitrifying Flexibacter canadensis. Can. J. Microbiol. 40: 576-582 (1994).
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).
Xia JH, Roberts J. Improved cytoplasmic pH regulation, increased lactate efflux, and reduced cytoplasmic lactate levels are biochemical traits expressed in root tips of whole maize seedlings acclimated to a low-oxygen environment. Plant Physiol. 105: 651-657 (1994).
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).
Xie Y, Luo W, Ren B, Li F. Morphological and physiological responses to sediment type and light availability in roots of the submerged plant Myriophyllum spicatum. Ann. Bot. (Lond.) 100: 1517-1523 (2007).
Xiong J, Bauer CE. Complex evolution of photosynthesis. Annu. Rev. Plant Biol. 53: 503-521 (2002).
Yamamoto I, Saito H, Ishimoto M. Regulation of synthesis and reversible inactivation in vivo of dual coenzyme-specific glutamate dehydrogenase in Bacteroides fragilis. J. Gen. Microbiol. 133: 2773-2780 (1987).
Yamashita A, Nijo N, Pospisil P, Morita N, Takenaka D, Aminaka R, Yamamoto Y, Yamamoto Y. Quality control of photosystem II: reactive oxygen species are responsible for the damage to photosystem II under moderate heat stress. J. Biol. Chem. 283: 28380-28391 (2008).
Yamazaki S, Nomata J, Fujita Y. Differential operation of dual protochlorophyllide reductases for chlorophyll biosynthesis in response to environmental oxygen levels in the cyanobacterium Leptolyngbya boryana. Plant Physiol. 142: 911-922 (2006).
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, 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, San KY, Bennett GN. Redistribution of metabolic fluxes in Escherichia coli with fermentative lactate dehydrogenase overexpression and deletion. Metab. Eng. 1: 141-152 (1999).
Yazdani SS, Gonzalez R. Anaerobic fermentation of glycerol: a path to economic viability for the biofuels industry. Curr. Opin. Biotechnol. 18: 213-219 (2007).
Yee J, Dennis PP. Isolation and characterization of a NADP-dependent glutamate dehydrogenase gene from the primitive eucaryote Giardia lamblia. J. Biol. Chem. 267: 7539-7544 (1992).
Yoshida K, Miyashita NT, Ishii T. Nucleotide polymorphism in the Adh1 locus region of the wild rice Oryza rufipogon. Theor. Appl. Genet. 109: 1406-1416 (2004).
Yoshino M, Murakami K. Role of glutamate dehydrogenase reaction in the control of citrate pool in yeast. Int. J. Biochem. 25: 1723-1727 (1993).
Young JD, Henne KL, Morgan JA, Konopka AE, Ramkrishna D. Integrating cybernetic modeling with pathway analysis provides a dynamic, systems-level description of metabolic control. Biotechnol. Bioeng. 100: 542-559 (2008).
Yun SH, Hwang TS, Park DH. Metabolic characterization of lactic acid bacterium Lactococcus garvieae sk11, capable of reducing ferric iron, nitrate, and fumarate. J. Microbiol. Biotechnol. 17: 218-225 (2007).
Zabalza A, van Dongen JT, Froehlich A, Oliver SN, Faix B, Gupta KJ, Schmalzlin E, Igal M, Orcaray L, Royuela M, Geigenberger P. Regulation of respiration and fermentation to control the plant internal oxygen concentration. Plant Physiol. 149: 1087-1098 (2009).
Zafra O, Ramirez S, Castan P, Moreno R, Cava F, Valles C, Caro E, Berenguer J. A cytochrome c encoded by the nar operon is required for the synthesis of active respiratory nitrate reductase in Thermus thermophilus. FEBS Lett. 523: 99-102 (2002).
Zajicek RS, Ferguson SJ. The enigma of Paracoccus pantotrophus cytochrome cd(1) activation. Biochem. Soc. Trans. 33: 147-148 (2005).
Zavarzina DG, Sokolova TG, Tourova TP, Chernyh NA, Kostrikina NA, Bonch-Osmolovskaya EA. Thermincola ferriacetica sp. nov., a new anaerobic, thermophilic, facultatively chemolithoautotrophic bacterium capable of dissimilatory Fe(III) reduction. Extremophiles 11: 1-7 (2007).
Zeng RJ, Saunders AM, Yuan Z, Blackall LL, Keller J. Identification and comparison of aerobic and denitrifying polyphosphate-accumulating organisms. Biotechnol. Bioeng. 83: 140-148 (2003).
Zeng RJ, Van Loosdrecht MC, Yuan Z, Keller J. Metabolic model for glycogen-accumulating organisms in anaerobic/aerobic activated sludge systems. Biotechnol. Bioeng. 81: 92-105 (2003).
Zeng RJ, Yuan Z, Keller J. Model-based analysis of anaerobic acetate uptake by a mixed culture of polyphosphate-accumulating and glycogen-accumulating organisms. Biotechnol. Bioeng. 83: 293-302 (2003).
Zeng Y, Wu Y, Avigne WT, Koch KE. Rapid repression of maize invertases by low oxygen. Invertase/sucrose synthase balance, sugar signaling potential, and seedling survival. Plant Physiol. 121: 599-608 (1999).
Zennaro E, Ciabatti I, Cutruzzola F, D'Alessandro R, Silvestrini MC. The nitrite reductase gene of Pseudomonas aeruginosa: effect of growth conditions on the expression and construction of a mutant by gene disruption. FEMS Microbiol. Lett. 109: 243-250 (1993).
Zhang C, Chen Y, Randall AA, Gu G. Anaerobic metabolic models for phosphorus- and glycogen-accumulating organisms with mixed acetic and propionic acids as carbon sources. Water Res. 42: 3745-3756 (2008).
Zhang CL. Stable carbon isotopes of lipid biomarkers: analysis of metabolites and metabolic fates of environmental microorganisms. Curr. Opin. Biotechnol. 13: 25-30 (2002).
Zhang L, Happe T, Melis A. Biochemical and morphological characterization of sulfur-deprived and H2-producing Chlamydomonas reinhardtii (green alga). Planta 214: 552-561 (2002).
Zhang Z, Wei L, Zou X, Tao Y, Liu Z, Zheng Y. Submergence-responsive microRNAs are potentially involved in the regulation of morphological and metabolic adaptations in maize root cells. Ann. Bot. (Lond.) 102: 509-519 (2008).
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).
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).
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).
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).
Zumft WG. Nitric oxide reductases of prokaryotes with emphasis on the respiratory, heme-copper oxidase type. J. Inorg. Biochem. 99: 194-215 (2005).
Number of references = 801
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