Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri

Molecular Systems Biology

Volumn 2, Issue , 2006, Pages

  Feist, Adam M ^a   Scholten, Johannes C M ^b   Palsson, Bernhard Ø ^a   Brockman, Fred J ^b   Ideker, Trey ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

Archaeal metabolism; Metabolic modeling; Methanogenesis; Methanosarcina barkeri; Network reconstruction

Indexed keywords

ECH HYDROGENASE; HYDROGENASE; UNCLASSIFIED DRUG;

ARCHAEBACTERIUM; ARTICLE; BACTERIAL GENETICS; BACTERIAL GENOME; ENERGY CONSERVATION; ENVIRONMENTAL FACTOR; ENZYME ACTIVITY; EUKARYOTE; GENOME ANALYSIS; METHANOGENESIS; METHANOSARCINA BARKERI; NONHUMAN; PHENOTYPE; PREDICTION; PRIORITY JOURNAL; PROKARYOTE; REACTION ANALYSIS; SIMULATION; STOICHIOMETRY; VALIDATION PROCESS;

GENOME, BACTERIAL; METABOLISM; METHANE; METHANOSARCINA BARKERI; MODELS, BIOLOGICAL; NITROGENASE; OXIDOREDUCTASES;

ARCHAEA; EUKARYOTA; METHANOSARCINA BARKERI; PROKARYOTA;

EID: 33645462347     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb4100046     Document Type: Article

References (58)

1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402
2. Batagelj V, Mrvar A (1998) Pajek: Program for large network analysis. Connections 21: 47-57
3. Bobik TA, Donnelly MI, Rinehart Jr KL, Wolfe RS (1987) Structure of a methanofuran derivative found in cell extracts of Methanosarcina barkeri. Arch Biochem Biophys 254: 430-436
4. Bock AK, Prieger-Kraft A, Schoenheit P (1994) Pyruvate - a novel substrate for growth and methane formation in Methanosarcina barkeri. Arch Microbiol 161: 33-46
5. Bock AK, Schonheit P (1995) Growth of Methanosarcina barkeri (Fusaro) under nonmethanogenic conditions by the fermentation of pyruvate to acetate: ATP synthesis via the mechanism of substrate level phosphorylation. J Bacteriol 177: 2002-2007
6. Bomar M, Knoll K, Widdel F (1985) Fixation of molecular nitrogen by Methanosarcina barkeri. FEMS Microbiol Ecol 31: 47-55
7. Borodina I, Krabben P, Nielsen J (2005) Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism. Genome Res 15: 820-829
8. Buchenau B, Thauer RK (2004) Tetrahydrofolate-specific enzymes in Methanosarcina barkeri and growth dependence of this methanogenic archaeon on folic acid or p-aminobenzoic acid. Arch Microbiol 182: 313-325
9. Burgard AP, Pharkya P, Maranas CD (2003) Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 84: 647-657
10. Chien YT, Auerbuch V, Brabban AD, Zinder SH (2000) Analysis of genes encoding an alternative nitrogenase in the archaeon Methanosarcina barkeri 227. J Bacteriol 182: 3247-3253
11. Chunhui L, Henry CS, Jankowski MD, Ionita JA, Hatzimanikatis V, Broadbelt LJ (2004) Computational discovery of biochemical routes to specialty chemicals. Chem Eng Sci 59: 5051-5060
12. Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO (2004) Integrating high-throughput and computational data elucidates bacterial networks. Nature 429: 92-96
13. de Poorter LM, Geerts WG, Theuvenet AP, Keltjens JT (2003) Bioenergetics of the formyl-methanofuran dehydrogenase and heterodisulfide reductase reactions in Methanothermobacter thermautotrophicus. Eur J Biochem 270: 66-75
14. de Poorter LM, Geerts WJ, Keltjens JT (2005) Hydrogen concentrations in methane-forming cells probed by the ratios of reduced and oxidized coenzyme F420. Microbiology 151: 1697-1705
15. Deppenmeier U (2004) The membrane-bound electron transport system of Methanosarcina species. J Bioenerg Biomembr 36: 55-64
16. Duarte NC, Herrgard MJ, Palsson BO (2004) Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res 14: 1298-1309
17. Elferink O, H SJW, Visser A, Hulshoff Pol LW, Stams AJM (1994) Sulfate reduction in methanogenic bioreactors. FEMS Microbiol Rev 15: 119-136
18. Famili I, Forster J, Nielsen 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
19. Fischer M, Schott AK, Romisch W, Ramsperger A, Augustin M, Fidler A, Bacher A, Richter G, Huber R, Eisenreich W (2004) Evolution of vitamin B2 biosynthesis. A novel class of riboflavin synthase in archaea. J Mol Biol 343: 267-278
20. Garcia J-L, Patel BKC, Ollivier B (2000) Taxonomic, phylogenetic, and ecological diversity of methanogenic archaea. Anaerobe 6: 205-226
21. Graham DE, White RH (2002) Elucidation of methanogenic coenzyme biosyntheses: from spectroscopy to genomics. Nat Prod Rep 19: 133-147
22. Graham DE, Xu H, White RH (2003) Identification of the 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase required for coenzyme F(420) biosynthesis. Arch Microbiol 180: 455-464
23. Grahame DE, DeMoll E (1996) Partial reactions catalyzed by protein components of the acetyl-CoA decarbonylase synthase enzyme complex from Methanosarcina barkeri. J Biol Chem 271: 8352-8358
24. Guss AM, Mukhopadhyay B, Zhang JK, Metcalf WW (2005) Genetic analysis of mch mutants in two Methanosarcina species demonstrates multiple roles for the methanopterin-dependent C-1 oxidation/reduction pathway and differences in H metabolism between closely related species. Mol Microbiol 55: 1671-1680
25. Hakobyan M, Sargsyan H, Bagramyan K (2005) Proton translocation coupled to formate oxidation in anaerobically grown fermenting Eschenchia coli. Biophys Chem 115: 55-61
26. Hedderich R (2004) Energy-converting [NiFe] hydrogenases from archaea and extremophiles: ancestors of complex I. J Bioenerg Biomembr 36: 65-75
27. Hippe H, Caspari D, Fiebig K, Gottschalk G (1979) Utilization of trimethylamine and other N-methyl compounds for growth and methane formation by Methanosarcina barkeri. Proc Natl Acad Sci USA 76: 494-498
28. Janssen P, Goldovsky L, Kunin V, Darzentas N, Ouzounis CA (2005) Genome coverage, literally speaking. The challenge of annotating 200 genomes with 4 million publications. EMBO Rep 6: 397-399
29. Kauffman KJ, Prakash P, Edwards JS (2003) Advances in flux balance analysis. Curr Opin Biotechnol 14: 491-496
30. Krzycki JA, Lehman LJ, Zeikus JG (1985) Acetate catabolism by Methanosarcina barkeri: evidence for involvement of carbon monoxide dehydrogenase, methyl coenzyme M, and methylreductase. J Bacteriol 163: 1000-1006
31. Ma HW, Zeng AP (2003) The connectivity structure, giant strong component and centrality of metabolic networks. Bioinformatics 19: 1423-1430
32. Meuer J, Kuettner HC, Zhang JK, Hedderich R, Metcalf WW (2002) Genetic analysis of the archaeon Methanosarcina barkeri Fusaro reveals a central role for Ech hydrogenase and ferredoxin in methanogenesis and carbon fixation. Proc Natl Acad Sci USA 99: 5632-5637
33. Muller V (2004) An exceptional variability in the motor of archaeal A1A0 ATPases: from multimeric to monomeric rotors comprising 6-13 ion binding sites. J Bioenerg Biomembr 36: 115-125
34. Neidhardt FC, Ingraham JL, Schaechter M (1990) Physiology of the Bacterial Cell: A Molecular Approach. Sunderland, MA: Sinauer Associates
35. Nichols BP, Seibold AM, Doktor SZ (1989) para-aminobenzoate synthesis from chorismate occurs in two steps. J Biol Chem 264: 8597-8601
36. Nishihara M, Koga Y (1995) Two new phospholipids, hydroxyarchaetidylglycerol and hydroxyarchaetidylethanolamine, from the Archaea Methanosarcina barkeri. Biochim Biophys Acta 1254: 155-160
37. Peregrin-Alvarez JM, Tsoka S, Ouzounis CA (2003) The phylogenetic extent of metabolic enzymes and pathways. Genome Res 13: 422-427
38. Pirt SJ (1965) The maintenance energy of bacteria in growing cultures. Proc R Soc London B Biol Sci 163: 224-231
39. Price ND, Reed JL, Palsson BO (2004) Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol 2: 886-897
40. Raemakers-Franken PC, Brand RJ, Kortstee AJ, Van der Drift C, Vogels GD (1991) Ammonia assimilation and glutamate incorporation in coenzyme F420 derivatives of Methanosarcina barkeri. Antonie Van Leenwenhoek 59: 243-248
41. Reed JL, Famili I, Thiele I, Palsson BO (2006) Towards multidimensional genome annotation. Nat Rev Genet 7: 130-141
42. Reed JL, Vo TD, Schilling CH, Palsson BO (2003) An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 4: R54
43. Rees DC, Howard JB (2000) Nitrogenase: standing at the crossroads. Curr Opin Chem Biol 4: 559-566
44. Russell JB, Cook GM (1995) Energetics of bacterial growth: balance of anabolic and catabolic reactions. Microbiol Rev 59: 48-62
45. Scherer P, Sahm H (1981) Effect of trace elements and vitamins on the growth of Methanosarcina barkeri. Acta Biotechnol 1: 57-65
46. Schink B (1997) Energetics of syntrophic cooperation in methanogenic degradation. Microbiol Mol Biol Rev 61: 262-280
47. Scott JW, Rasche ME (2002) Purification, overproduction, and partial characterization of beta-RFAP synthase, a key enzyme in the methanopterin biosynthesis pathway. J Bacteriol 184: 4442-4448
48. Smith MR, Mah RA (1978) Growth and methanogenesis by Methanosarcina strain 227 on acetate and methanol. Appl Environ Microbiol 36: 870-879
49. Thauer RK, Jungermann K, Decker K (1977) Energy conservation in chemotrophic anaerobic bacteria. Bacteriol Rev 41: 100-180
50. Tsoka S, Simon D, Ouzounis CA (2004) Automated metabolic reconstruction for Methanococcus jannaschii. Archaea 1: 223-229
51. 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
52. Verhees CH, Kengen SW, Tuininga JE, Schut GJ, Adams MW, De Vos WM, Van Der Oost J (2003) The unique features of glycolytic pathways in Archaea. Biochem J 375: 231-246
53. von Felten P, Bachofen R (2000) Continuous monitoring of the cytoplasmic pH in Methanobacterium thermoautotrophicum using the intracellular factor F(420) as indicator. Microbiology 146 (Part 12): 3245-3250
54. Weimer PJ, Zeikus JG (1978) One carbon metabolism in methanogenic bacteria. Cellular characterization and growth of Methanosarcina barkeri. Arch Microbiol 119: 49-57
55. Welander PV, Metcalf WW (2005) Loss of the mtr operon in Methanosarcina blocks growth on methanol, but not methanogenesis, and reveals an unknown methanogenic pathway. Proc Natl Acad Sci USA 102: 10664-10669
56. Wolin EA, Wolin MJ, Wolfe RS (1963) Formation of methane by bacterial extracts. J Biol Chem 238: 2882-2886
57. Yeh I, Hanekamp T, Tsoka S, Karp PD, Altman RB (2004) Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery. Genome Res 14: 917-924
58. Zinder SH (1993) Physiological ecology of methanogens. In Methanogenesis, Ferry JG (ed), pp 128-206. Routledge, New York: Chapman & Hall