Methanogens: A window into ancient sulfur metabolism

Trends in Microbiology

Volumn 20, Issue 5, 2012, Pages 251-258

  Liu, Yuchen ^a   Beer, Laura L ^b   Whitman, William B ^b  

^a YALE UNIVERSITY   (United States)

^b UNIVERSITY OF GEORGIA   (United States)

Author keywords

Archaea; Methanogenesis; Methanogens; Sulfur metabolism

Indexed keywords

CYSTEINE; IRON SULFUR PROTEIN; METHIONINE; OXYGEN; SULFATE; SULFUR; TRANSFER RNA;

AMINO ACID SYNTHESIS; ASTRONOMY; HABITAT; METABOLISM; METHANOBACTERIALES; METHANOCOCCALES; METHANOGEN; METHANOGENESIS; METHANOMICROBIALES; METHANOPYRALES; METHANOSARCINALES; NONHUMAN; PRIORITY JOURNAL; REDUCTION; REVIEW;

BIOLOGICAL EVOLUTION; EURYARCHAEOTA; METHANE; SULFUR;

EID: 84862815590     PISSN: 0966842X     EISSN: 18784380     Source Type: Journal    
DOI: 10.1016/j.tim.2012.02.002     Document Type: Review

References (72)

1. 2. Science 2005, 308:1730-1732.
2. Ueno Y., et al. Evidence from fluid inclusions for microbial methanogenesis in the early Archaean era. Nature 2006, 440:516-519.
3. Battistuzzi F.U., et al. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol. Biol. 2004, 4:44.
4. Kasting J.F., Siefert J.L. Life and the evolution of Earth's atmosphere. Science 2002, 296:1066-1068.
5. Catling D.C., et al. Biogenic methane, hydrogen escape, and the irreversible oxidation of early Earth. Science 2001, 293:839-843.
6. Wiechert U.H. Earth's early atmosphere. Science 2002, 298:2341-2342.
7. Liu Y., Whitman W.B. Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Ann. N. Y. Acad. Sci. 2008, 1125:171-189.
8. Whitman W.B., et al. The methanogenic bacteria. The Prokaryotes 2006, 165-207. Springer-Verlag. 3rd edn. M. Dworkin (Ed.).
9. Blank C.E. Phylogenomic dating-the relative antiquity of archaeal metabolic and physiological traits. Astrobiology 2009, 9:193-219.
10. Kasting J.F. Earth's early atmosphere. Science 1993, 259:920-926.
11. Vignais P.M., et al. Classification and phylogeny of hydrogenases. FEMS Microbiol. Rev. 2001, 25:455-501.
12. Thauer R.K., et al. Methanogenic archaea: ecologically relevant differences in energy conservation. Nat. Rev. Microbiol. 2008, 6:579-591.
13. Lin W.C., et al. The anabolic pyruvate oxidoreductase from Methanococcus maripaludis. Arch. Microbiol. 2003, 179:444-456.
14. Porat I., et al. Two biosynthetic pathways for aromatic amino acids in the archaeon Methanococcus maripaludis. J. Bacteriol. 2004, 186:4940-4950.
15. Xing R., Whitman W.B. Purification and characterization of the oxygen-sensitive acetohydroxy acid synthase from the archaebacterium Methanococcus aeolicus. J. Bacteriol. 1994, 176:1207-1213.
16. Xing R., Whitman W.B. Characterization of enzymes of the branched-chain amino acid biosynthetic pathway in Methanococcus spp. J. Bacteriol. 1991, 173:2086-2092.
17. Major T.A., et al. Abundance of 4Fe-4S motifs in the genomes of methanogens and other prokaryotes. FEMS Microbiol. Lett. 2004, 239:117-123.
18. Liu Y., et al. Cysteine is not the sulfur source for iron-sulfur cluster and methionine biosynthesis in the methanogenic archaeon Methanococcus maripaludis. J. Biol. Chem. 2010, 285:31923-31929.
19. Imlay J.A. Iron-sulphur clusters and the problem with oxygen. Mol. Microbiol. 2006, 59:1073-1082.
20. Liochev S.I., Fridovich I. Fumarase C, the stable fumarase of Escherichia coli, is controlled by the soxRS regulon. Proc. Natl. Acad. Sci. U.S.A. 1992, 89:5892-5896.
21. Simpson P.G., Whitman W.B. Anabolic pathways in methanogens. Methanogenesis: Ecology, Physiology, Biochemistry, and Genetics 1993, 445-472. Chapman & Hall. J.G. Ferry (Ed.).
22. Wächtershäuser G. On the chemistry and evolution of the pioneer organism. Chem. Biodivers. 2007, 4:584-602.
23. Wächtershäuser G. From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya. Philos. Trans. R. Soc. B 2006, 361:1787-1808.
24. Russell M.J., Martin W. The rocky roots of the acetyl-CoA pathway. Trends Biochem. Sci. 2004, 29:358-363.
25. Berg I.A., et al. Autotrophic carbon fixation in archaea. Nat. Rev. Microbiol. 2010, 8:447-460.
26. Fuchs G. Alternative pathways of carbon dioxide fixation: insights into the early evolution of life?. Annu. Rev. Microbiol. 2011, 65:631-658.
27. Martin W.F. Hydrogen, metals, bifurcating electrons, and proton gradients: the early evolution of biological energy conservation. FEBS Lett. 2012, 586:485-493.
28. Farquhar J., et al. Connections between sulfur cycle evolution, sulfur isotopes, sediments, and base metal sulfide deposits. Econ. Geol. 2010, 105:509-533.
29. Lyons T.W., Gill B.C. Ancient sulfur cycling and oxygenation of the early biosphere. Elements 2010, 6:93-99.
30. Johnston D.T. Multiple sulfur isotopes and the evolution of Earth's surface sulfur cycle. Earth Sci. Rev. 2011, 106:161-183.
31. Canfield D.E., et al. The Archean sulfur cycle and the early history of atmospheric oxygen. Science 2000, 288:658-661.
32. Farquhar J., et al. Atmospheric influence of Earth's earliest sulfur cycle. Science 2000, 289:756-758.
33. Halevy I., et al. Explaining the structure of the Archean mass-independent sulfur isotope record. Science 2010, 329:204-207.
34. Habicht K.S., et al. Calibration of sulfate levels in the Archean ocean. Science 2002, 298:2372-2374.
35. Blank C.E. Evolutionary timing of the origins of mesophilic sulphate reduction and oxygenic photosynthesis: a phylogenomic dating approach. Geobiology 2004, 2:1-20.
36. Blank C.E. Not so old Archaea - the antiquity of biogeochemical processes in the archaeal domain of life. Geobiology 2009, 7:495-514.
37. Sekowska A., et al. Sulfur metabolism in Escherichia coli and related bacteria: facts and fiction. J. Mol. Microbiol. Biotechnol. 2000, 2:145-177.
38. Kessler D. Enzymatic activation of sulfur for incorporation into biomolecules in prokaryotes. FEMS Microbiol. Rev. 2006, 30:825-840.
39. Mueller E.G. Trafficking in persulfides: delivering sulfur in biosynthetic pathways. Nat. Chem. Biol. 2006, 2:185-194.
40. Whitman W.B., et al. Nutrition and carbon metabolism of Methanococcus voltae. J. Bacteriol. 1982, 149:852-863.
41. Whitman W.B., et al. Isolation and characterization of 22 mesophilic methanococci. Syst. Appl. Microbiol. 1986, 7:235-240.
42. Stetter K.O., Gaag G. Reduction of molecular sulphur by methanogenic bacteria. Nature 1983, 305:309-311.
43. Philippot P., et al. Early Archaean microorganisms preferred elemental sulfur, not sulfate. Science 2007, 317:1534-1537.
44. Le Faou A., et al. Thiosulfate, polythionates and elemental sulfur assimilation and reduction in the bacterial world. FEMS Microbiol. Lett. 1990, 75:351-382.
45. Belkin S., et al. Biological and abiological sulfur reduction at high temperatures. Appl. Environ. Microbiol. 1985, 49:1057-1061.
46. Kurr M., et al. Methanopyrus kandleri, gen. and sp. nov. represents a novel group of hyperthermophilic methanogens, growing at 110°C. Arch. Microbiol. 1991, 156:239-247.
47. Daniels L., et al. Assimilatory reduction of sulfate and sulfite by methanogenic bacteria. Appl. Environ. Microbiol. 1986, 51:703-709.
48. Rajagopal B.S., Daniels L. Investigation of mercaptans, organic sulfides, and inorganic sulfur compounds as sulfur sources for the growth of methanogenic bacteria. Curr. Microbiol. 1986, 14:137-144.
49. Moura J.G., et al. Isolation of P590 from Methanosarcina barkeri: evidence for the presence of sulfite reductase activity. Biochem. Biophys. Res. Commun. 1982, 108:1002-1009.
50. Moura I., et al. Low-spin sulfite reductases: a new homologous group of non-heme iron-siroheme proteins in anaerobic bacteria. Biochem. Biophys. Res. Commun. 1986, 141:1032-1041.
51. 420-dependent enzyme, from the methanarchaeon Methanocaldococcus jannaschii. J. Biol. Chem. 2005, 280:38776-38786.
52. 420-dependent sulfite reductase-enabled sulfite detoxification and use of sulfite as a sole sulfur source by Methanococcus maripaludis. Appl. Environ. Microbiol. 2008, 74:3591-3595.
53. Stathopoulos C., et al. Cysteinyl-tRNA synthetase is not essential for viability of the archaeon Methanococcus maripaludis. Proc. Natl. Acad. Sci. U.S.A. 2001, 98:14292-14297.
54. Sauerwald A., et al. RNA-dependent cysteine biosynthesis in archaea. Science 2005, 307:1969-1972.
55. Cys formation. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:19003-19008.
56. Jordan I.K., et al. A universal trend of amino acid gain and loss in protein evolution. Nature 2005, 433:633-638.
57. Farahi K., et al. Detection of lateral gene transfer events in the prokaryotic tRNA synthetases by the ratios of evolutionary distances method. J. Mol. Evol. 2004, 58:615-631.
58. Helgadóttir S., et al. Biosynthesis of phosphoserine in the Methanococcales. J. Bacteriol. 2007, 189:575-582.
59. Klipcan L., et al. Presence of tRNA-dependent pathways correlates with high cysteine content in methanogenic Archaea. Trends Genet. 2008, 24:59-63.
60. Boyd J.M., et al. Archaeal ApbC/Nbp35 homologs function as iron-sulfur cluster carrier proteins. J. Bacteriol. 2009, 191:1490-1497.
61. Zheng M., et al. DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide. J. Bacteriol. 2001, 183:4562-4570.
62. Takahashi Y., Tokumoto U. A third bacterial system for the assembly of iron-sulfur clusters with homologs in archaea and plastids. J. Biol. Chem. 2002, 277:28380-28383.
63. Johnson D.C., et al. Structure, function, and formation of biological iron-sulfur clusters. Annu. Rev. Biochem. 2005, 74:247-281.
64. Neidhardt F.C., Umbarger H.E. Chemical composition of Escherichia coli. Escherichia coli and Salmonella 1996, 13-16. ASM Press. F.C. Neidhardt (Ed.).
65. Kredich N.M. Biosynthesis of cysteine. Escherichia coli and Salmonella 1996, 514-527. ASM Press. F.C. Neidhardt (Ed.).
66. Sperandio B., et al. Sulfur amino acid metabolism and its control in Lactococcus lactis IL1403. J. Bacteriol. 2005, 187:3762-3778.
67. Vermeij P., Kertesz M.A. Pathways of assimilative sulfur metabolism in Pseudomonas putida. J. Bacteriol. 1999, 181:5833-5837.
68. Thomas D., Surdin-Kerjan Y. Metabolism of sulfur amino acids in Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 1997, 61:503-532.
69. Cys in Methanosarcina mazei. J. Biol. Chem. 2008, 283:22007-22017.
70. Liu Y., et al. The catalytic mechanism of Sep-tRNA:Cys-tRNA synthase: sulfur transfer is mediated by disulfide and persulfide. J. Biol. Chem. 2011, 287:5426-5433.
71. White R.H. The biosynthesis of cysteine and homocysteine in Methanococcus jannaschii. Biochimi. Biophys. Acta 2003, 1624:46-53.
72. Fukunaga R., Yokoyama S. Structural insights into the second step of RNA-dependent cysteine biosynthesis in archaea: crystal structure of Sep-tRNA:Cys-tRNA synthase from Archaeoglobus fulgidus. J. Mol. Biol. 2007, 370:128-141.