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Volumn 3, Issue , 2007, Pages 1-14

Metabolic modeling of a mutualistic microbial community

Author keywords

Desulfovibrio; Flux balance modeling; Interspecies hydrogen transfer; Methanococcus; Syntrophy

Indexed keywords

HYDROGEN; LACTIC ACID; METHANE;

EID: 33947276100     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb4100131     Document Type: Article
Times cited : (403)

References (54)
  • 4
    • 20444397992 scopus 로고    scopus 로고
    • Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism
    • Borodina I, Krabben P, Nielsen J (2005) Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism. Genome Res 15: 820-829
    • (2005) Genome Res , vol.15 , pp. 820-829
    • Borodina, I.1    Krabben, P.2    Nielsen, J.3
  • 8
    • 0028241256 scopus 로고
    • Energy-spilling reaction of Streptococcus bovis and resistance of its membrane to proton conductance
    • Cook GM, Russell JB (1994) Energy-spilling reaction of Streptococcus bovis and resistance of its membrane to proton conductance. Appl Environ Microbiol 60: 1942-1948
    • (1994) Appl Environ Microbiol , vol.60 , pp. 1942-1948
    • Cook, G.M.1    Russell, J.B.2
  • 9
    • 0037008673 scopus 로고    scopus 로고
    • Transcriptional regulation in constraints-based metabolic models of Escherichia coli
    • Covert M, Palsson B (2002) Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J Biol Chem 277: 28058-28064
    • (2002) J Biol Chem , vol.277 , pp. 28058-28064
    • Covert, M.1    Palsson, B.2
  • 10
    • 11144347500 scopus 로고    scopus 로고
    • The membrane-bound electron transport system of Methanosarcina species
    • Deppenmeier U (2004) The membrane-bound electron transport system of Methanosarcina species. J Bioenerg Biomemb 36: 55-64
    • (2004) J Bioenerg Biomemb , vol.36 , pp. 55-64
    • Deppenmeier, U.1
  • 11
    • 0036001069 scopus 로고    scopus 로고
    • Metabolic modelling of microbes: The flux-balance approach
    • Edwards JS, Covert M, Palsson B (2002) Metabolic modelling of microbes: the flux-balance approach. Environ Microbiol 4: 133-140
    • (2002) Environ Microbiol , vol.4 , pp. 133-140
    • Edwards, J.S.1    Covert, M.2    Palsson, B.3
  • 12
    • 0034625143 scopus 로고    scopus 로고
    • The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
    • Edwards JS, Palsson BO (2000a) The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc Natl Acad Sci USA 97: 5528-5533
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 5528-5533
    • Edwards, J.S.1    Palsson, B.O.2
  • 13
    • 0034519221 scopus 로고    scopus 로고
    • Robustness analysis of the Escherichia coli metabolic network
    • Edwards JS, Palsson BO (2000b) Robustness analysis of the Escherichia coli metabolic network. Biotechnol Prog 16: 927-939
    • (2000) Biotechnol Prog , vol.16 , pp. 927-939
    • Edwards, J.S.1    Palsson, B.O.2
  • 14
    • 0344824417 scopus 로고    scopus 로고
    • Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network
    • Famili I, Forster J, Nielson J, Palsson BO (2003) Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proc Natl Acad Sci USA 100: 13134-13139
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 13134-13139
    • Famili, I.1    Forster, J.2    Nielson, J.3    Palsson, B.O.4
  • 15
    • 33645462347 scopus 로고    scopus 로고
    • Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri
    • Fiest AM, Scholten JCM, Palsson BØ, Brockman FJ, Ideker T (2006) Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol Syst Biol 2: E1-E14
    • (2006) Mol Syst Biol , vol.2
    • Fiest, A.M.1    Scholten, J.C.M.2    Palsson, B.3    Brockman, F.J.4    Ideker, T.5
  • 16
    • 0037313750 scopus 로고    scopus 로고
    • Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network
    • Forster J, Famili I, Fu P, Palsson BO, Nielsen J (2003) Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 13: 244-253
    • (2003) Genome Res , vol.13 , pp. 244-253
    • Forster, J.1    Famili, I.2    Fu, P.3    Palsson, B.O.4    Nielsen, J.5
  • 17
    • 0030060333 scopus 로고    scopus 로고
    • Organic carbon utilization by obligately and facultatively autotrophic Beggiatoa strains in homogeneous and gradient cultures
    • Hagen K, Nelson D (1996) Organic carbon utilization by obligately and facultatively autotrophic Beggiatoa strains in homogeneous and gradient cultures. Appl Environ Microbiol 62: 947-953
    • (1996) Appl Environ Microbiol , vol.62 , pp. 947-953
    • Hagen, K.1    Nelson, D.2
  • 19
    • 2342475768 scopus 로고    scopus 로고
    • Heidelberg JF, Seshadri R, Haveman SA, Hemme CL, Paulsen IT, Kolonay JF, Eisen JA, Ward N, Methe B, Brinkac LM, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Fouts D, Haft DH, Selengut J, Peterson JD, Davidsen TM, Zafar N, Zhou L, Radune D, Dimitrov G, Hance M, Tran K, Khouri H, Gill J, Utterback TR, Feldblyum TV, Wall JD, Voordouw G, Fraser CM (2004) The genome sequence of the anaerobic sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nature Biotech 22: 554-559
    • Heidelberg JF, Seshadri R, Haveman SA, Hemme CL, Paulsen IT, Kolonay JF, Eisen JA, Ward N, Methe B, Brinkac LM, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Fouts D, Haft DH, Selengut J, Peterson JD, Davidsen TM, Zafar N, Zhou L, Radune D, Dimitrov G, Hance M, Tran K, Khouri H, Gill J, Utterback TR, Feldblyum TV, Wall JD, Voordouw G, Fraser CM (2004) The genome sequence of the anaerobic sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nature Biotech 22: 554-559
  • 20
    • 4944254822 scopus 로고    scopus 로고
    • Hendrickson EL, Kaul R, Zhou Y, Bovee D, Chapman P, Chung J, de Macario EC, Dodsworth JA, Gillett W, Graham DE, Hackett M, Haydock AK, Kang A, Land ML, Levy R, Lie TJ, Major TA, Moore BC, Porat I, Palmeiri A, Rouse G, Saenphimmachak C, Sö ll D, Van Dien S, Wang T, Whitmann WB, Xia Q, Zhang Y, Larimer FW, OlsonMV, Leigh JA (2004) Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis. J Bacteriol 186: 6956-6969
    • Hendrickson EL, Kaul R, Zhou Y, Bovee D, Chapman P, Chung J, de Macario EC, Dodsworth JA, Gillett W, Graham DE, Hackett M, Haydock AK, Kang A, Land ML, Levy R, Lie TJ, Major TA, Moore BC, Porat I, Palmeiri A, Rouse G, Saenphimmachak C, Sö ll D, Van Dien S, Wang T, Whitmann WB, Xia Q, Zhang Y, Larimer FW, OlsonMV, Leigh JA (2004) Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis. J Bacteriol 186: 6956-6969
  • 21
    • 0002620715 scopus 로고
    • Characterization of Methanococcus maripaludis sp nov, a new methanogen isolated from salt marsh sediment
    • Jones WJ, Paynter MJB, Gupta R (1983) Characterization of Methanococcus maripaludis sp nov, a new methanogen isolated from salt marsh sediment. Arch Microbiol 135: 91-97
    • (1983) Arch Microbiol , vol.135 , pp. 91-97
    • Jones, W.J.1    Paynter, M.J.B.2    Gupta, R.3
  • 22
    • 0037197159 scopus 로고    scopus 로고
    • Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria
    • Klamt S, Schuster S, Gilles ED (2002) Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria. Biotechnol Bioeng 77: 734-751
    • (2002) Biotechnol Bioeng , vol.77 , pp. 734-751
    • Klamt, S.1    Schuster, S.2    Gilles, E.D.3
  • 23
    • 0037316342 scopus 로고    scopus 로고
    • FluxAnalyzer: Exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps
    • Klamt S, Stelling J, Ginkel M, Gilles ED (2003) FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinformatics 19: 261-269
    • (2003) Bioinformatics , vol.19 , pp. 261-269
    • Klamt, S.1    Stelling, J.2    Ginkel, M.3    Gilles, E.D.4
  • 25
    • 0017700302 scopus 로고
    • Obligatory coupling between proton entry and the synthesis of adenosine 5′-triphosphate in Streptococcus lactis
    • Maloney PC (1977) Obligatory coupling between proton entry and the synthesis of adenosine 5′-triphosphate in Streptococcus lactis. J Bacteriol 132: 564-575
    • (1977) J Bacteriol , vol.132 , pp. 564-575
    • Maloney, P.C.1
  • 26
    • 0020618211 scopus 로고
    • + gradient during glycolysis in Streptococcus lactis
    • + gradient during glycolysis in Streptococcus lactis. J Bacteriol 153: 1461-1470
    • (1983) J Bacteriol , vol.153 , pp. 1461-1470
    • Maloney, P.C.1
  • 28
    • 0032552490 scopus 로고    scopus 로고
    • Unified model describing the role of hydrogen in the growth of Desulfovibrio vulgaris under different environmental conditions
    • Noguera DR, Brusseau GA, Rittmann BE, Stahl DA (1998) Unified model describing the role of hydrogen in the growth of Desulfovibrio vulgaris under different environmental conditions. Biotechnol Bioeng 59: 732-746
    • (1998) Biotechnol Bioeng , vol.59 , pp. 732-746
    • Noguera, D.R.1    Brusseau, G.A.2    Rittmann, B.E.3    Stahl, D.A.4
  • 29
    • 0019444405 scopus 로고
    • D-lactate dehydrogenase of Desulfovibrio vulgaris
    • Ogata M, Arihara K, Yagi T (1981) D-lactate dehydrogenase of Desulfovibrio vulgaris. J Biochem 89: 1423-1431
    • (1981) J Biochem , vol.89 , pp. 1423-1431
    • Ogata, M.1    Arihara, K.2    Yagi, T.3
  • 30
    • 0037207875 scopus 로고    scopus 로고
    • Bioenergetic properties of the thermoalkaliphilic Bacillus sp. strain TA2.A1
    • Olsson K, Keis S, Morgan HW, Dimroth P, Cook GM (2003) Bioenergetic properties of the thermoalkaliphilic Bacillus sp. strain TA2.A1. J Bacteriol 185: 461-465
    • (2003) J Bacteriol , vol.185 , pp. 461-465
    • Olsson, K.1    Keis, S.2    Morgan, H.W.3    Dimroth, P.4    Cook, G.M.5
  • 31
    • 0000698012 scopus 로고
    • The phosphate potential, adenylate charge and proton motive force in growing cells of Streptococcus cremoris
    • Otto RB, Klont B, Brink T, Konings WN (1984) The phosphate potential, adenylate charge and proton motive force in growing cells of Streptococcus cremoris. Arch Microbiol 139: 338-343
    • (1984) Arch Microbiol , vol.139 , pp. 338-343
    • Otto, R.B.1    Klont, B.2    Brink, T.3    Konings, W.N.4
  • 32
    • 0031799670 scopus 로고    scopus 로고
    • Mercury methylation by interspecies hydrogen and acetate transfer between sulfidogens and methanogens
    • Pak KR, Bartha R (1998) Mercury methylation by interspecies hydrogen and acetate transfer between sulfidogens and methanogens. Appl Environ Microbiol 64: 1987-1990
    • (1998) Appl Environ Microbiol , vol.64 , pp. 1987-1990
    • Pak, K.R.1    Bartha, R.2
  • 33
    • 0001863553 scopus 로고
    • 2 in cell suspensions of Desulfovibrio vulgaris (Marburg): Indications for the involvement of an energy driven reaction
    • 2 in cell suspensions of Desulfovibrio vulgaris (Marburg): indications for the involvement of an energy driven reaction. Arch Microbiol 150: 26-31
    • (1988) Arch Microbiol , vol.150 , pp. 26-31
    • Pankhania, I.P.1    Spormann, A.M.2    Hamilton, W.A.3    Thauer, R.K.4
  • 35
    • 0343035686 scopus 로고    scopus 로고
    • Stoichiometric model of Escherichia coli metabolism: Incorporation of growth-rate dependent biomass composition and mechanistic energy requirements
    • Pramanik J, Keasling JD (1997) Stoichiometric model of Escherichia coli metabolism: incorporation of growth-rate dependent biomass composition and mechanistic energy requirements. Biotechnol Bioeng 56: 398-421
    • (1997) Biotechnol Bioeng , vol.56 , pp. 398-421
    • Pramanik, J.1    Keasling, J.D.2
  • 36
    • 0032552815 scopus 로고    scopus 로고
    • Effect of Escherichia coli biomass composition on central metabolic fluxes predicted by a stoichiometric model
    • Pramanik J, Keasling JD (1998) Effect of Escherichia coli biomass composition on central metabolic fluxes predicted by a stoichiometric model. Biotechnol Bioeng 60: 230-238
    • (1998) Biotechnol Bioeng , vol.60 , pp. 230-238
    • Pramanik, J.1    Keasling, J.D.2
  • 37
    • 9544253891 scopus 로고    scopus 로고
    • Genome-scale models of microbial cells: Evaluating the consequences of constraints
    • Price ND, Reed JL, Palsson BO (2004) Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol 2: 886-897
    • (2004) Nat Rev Microbiol , vol.2 , pp. 886-897
    • Price, N.D.1    Reed, J.L.2    Palsson, B.O.3
  • 38
    • 0028926047 scopus 로고
    • Energetics of bacterial growth: Balance of anabolic and catabolic reactions
    • Russell JB, Cook GM (1995) Energetics of bacterial growth: balance of anabolic and catabolic reactions. Microbiol Rev 59: 48-62
    • (1995) Microbiol Rev , vol.59 , pp. 48-62
    • Russell, J.B.1    Cook, G.M.2
  • 39
    • 0026516223 scopus 로고
    • Network analysis of intermediary metabolism using linear optimization: I. Development of mathematical formalism
    • Savinell JM, Palsson BO (1992) Network analysis of intermediary metabolism using linear optimization: I. Development of mathematical formalism. J Theor Biol 154: 421-454
    • (1992) J Theor Biol , vol.154 , pp. 421-454
    • Savinell, J.M.1    Palsson, B.O.2
  • 40
    • 0030871461 scopus 로고    scopus 로고
    • Energetics of syntrophic cooperation in methanogenic degradation
    • Schink B (1997) Energetics of syntrophic cooperation in methanogenic degradation. Microbiol Mol Biol Rev 61: 262-280
    • (1997) Microbiol Mol Biol Rev , vol.61 , pp. 262-280
    • Schink, B.1
  • 41
    • 0036425986 scopus 로고    scopus 로고
    • Synergistic interactions in the microbial world
    • Schink B (2002) Synergistic interactions in the microbial world. Ant van Leeuwen 81: 257-261
    • (2002) Ant van Leeuwen , vol.81 , pp. 257-261
    • Schink, B.1
  • 43
    • 0028787109 scopus 로고
    • Purification and characterization of the formate dehydrogenase from Desulfovibrio vulgaris Hildenborough
    • Sebban C, Blanchard L, Bruschi M, Guerlesquin F (1995) Purification and characterization of the formate dehydrogenase from Desulfovibrio vulgaris Hildenborough. FEMS Microbiol Lett 133: 143-149
    • (1995) FEMS Microbiol Lett , vol.133 , pp. 143-149
    • Sebban, C.1    Blanchard, L.2    Bruschi, M.3    Guerlesquin, F.4
  • 44
    • 0023447129 scopus 로고
    • Pathway of acetate assimilation in autotrophic and heterotrophic Methanococci
    • Shieh JS, Whitman WB (1987) Pathway of acetate assimilation in autotrophic and heterotrophic Methanococci. J Bacteriol 169: 5327-5329
    • (1987) J Bacteriol , vol.169 , pp. 5327-5329
    • Shieh, J.S.1    Whitman, W.B.2
  • 46
    • 0020084735 scopus 로고
    • Oxygen labile L(+) lactate dehydrogenase activity in Desulfovibrio desulfuricans
    • Stams AJM, Hansen TA (1982) Oxygen labile L(+) lactate dehydrogenase activity in Desulfovibrio desulfuricans. FEMS Microbiol Lett 13: 389-394
    • (1982) FEMS Microbiol Lett , vol.13 , pp. 389-394
    • Stams, A.J.M.1    Hansen, T.A.2
  • 47
    • 0037079050 scopus 로고    scopus 로고
    • Metabolic network structure determines key aspects of functionality and regulation
    • Stelling J, Klamt S, Bettenbrock K, Schuster S, Gilles ED (2002) Metabolic network structure determines key aspects of functionality and regulation. Nature 420: 190-193
    • (2002) Nature , vol.420 , pp. 190-193
    • Stelling, J.1    Klamt, S.2    Bettenbrock, K.3    Schuster, S.4    Gilles, E.D.5
  • 48
    • 0028233309 scopus 로고
    • Growth and bioenergetics of alkaliphilic Bacillus firmus OF4 in continuous culture at high pH
    • Sturr MG, Guffanti AA, Krulwich TA (1994) Growth and bioenergetics of alkaliphilic Bacillus firmus OF4 in continuous culture at high pH. J Bacteriol 176: 3111-3116
    • (1994) J Bacteriol , vol.176 , pp. 3111-3116
    • Sturr, M.G.1    Guffanti, A.A.2    Krulwich, T.A.3
  • 49
    • 0021079870 scopus 로고
    • Energetics of growth of a defined mixed culture of Desulfovibrio vulgaris and Methanosarcina barkeri: Interspecies hydrogen transfer in batch and continuous cultures
    • Traore AS, Fardeau ML, Hatchikian CE, Le Gall J, Belaich JP (1983) Energetics of growth of a defined mixed culture of Desulfovibrio vulgaris and Methanosarcina barkeri: interspecies hydrogen transfer in batch and continuous cultures. Appl Environ Microbiol 46: 1152-1156
    • (1983) Appl Environ Microbiol , vol.46 , pp. 1152-1156
    • Traore, A.S.1    Fardeau, M.L.2    Hatchikian, C.E.3    Le Gall, J.4    Belaich, J.P.5
  • 50
    • 0027572102 scopus 로고
    • Metabolic flux distributions in Corynebacterium glutamicum during growth and lysine overproduction
    • Vallino JJ, Stephanopoulos G (1993) Metabolic flux distributions in Corynebacterium glutamicum during growth and lysine overproduction. Biotechnol Bioeng 41: 633-646
    • (1993) Biotechnol Bioeng , vol.41 , pp. 633-646
    • Vallino, J.J.1    Stephanopoulos, G.2
  • 51
    • 0037023907 scopus 로고    scopus 로고
    • Stoichiometric model for evaluating the metabolic capabilities of the facultative methylotroph Methylobacterium extorquens AM1, with application to reconstruction of C-3 and C-4 metabolism
    • Van Dien SJ, Lidstrom ME (2002) Stoichiometric model for evaluating the metabolic capabilities of the facultative methylotroph Methylobacterium extorquens AM1, with application to reconstruction of C-3 and C-4 metabolism. Biotechnol Bioeng 78: 296-312
    • (2002) Biotechnol Bioeng , vol.78 , pp. 296-312
    • Van Dien, S.J.1    Lidstrom, M.E.2
  • 52
    • 0028146781 scopus 로고
    • Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110
    • Varma A, Palsson BO (1994) 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) Appl Environ Microbiol , vol.60 , pp. 3724-3731
    • Varma, A.1    Palsson, B.O.2
  • 54
    • 0037386409 scopus 로고    scopus 로고
    • Function and regulation of the formate dehydrogenase genes of the methanogenic archaeon Methanococcus maripaludis
    • Wood GE, Haydock AK, Leigh JA (2003) Function and regulation of the formate dehydrogenase genes of the methanogenic archaeon Methanococcus maripaludis. J Bacteriol 185: 2548-2554
    • (2003) J Bacteriol , vol.185 , pp. 2548-2554
    • Wood, G.E.1    Haydock, A.K.2    Leigh, J.A.3


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