Metabolic versatility in methanogens

Current Opinion in Biotechnology

Volumn 29, Issue 1, 2014, Pages 70-75

  Costa, Kyle C ^a   Leigh, John A ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; GLOBAL WARMING; METHANE; METHANOGENS;

ANAEROBIC METABOLISM; ANAEROBIC METHANE OXIDATIONS; BIOINFORMATIC TOOLS; ELECTRON FLOW; METABOLIC VERSATILITY; METHANOGENESIS; METHANOGENIC ARCHAEA; MODEL SPECIES;

METABOLISM;

METHANE; ACETIC ACID; BACTERIAL DNA; CARBON DIOXIDE; DIMETHYL SULFIDE; HYDROGEN; METHANOL; METHYL GROUP; METHYLAMINE; CARBON;

ANAEROBIC METABOLISM; ARCHAEON; BIOFUEL PRODUCTION; GREENHOUSE EFFECT; METABOLIC ENGINEERING; METHANOCOCCUS; METHANOGEN; METHANOGENESIS; METHANOSARCINA; METHYLOTROPH; NONHUMAN; ORGANISMS BY ELECTRON DONOR; OXIDATION; PRIORITY JOURNAL; REVIEW; BACTERIUM CULTURE; BIOINFORMATICS; DNA TRANSFER; ELECTRON TRANSPORT; ENERGY CONSERVATION; ESCHERICHIA COLI; EXPERIMENTAL MODEL; GENETIC MANIPULATION; HYDROGENOTROPHIC METHANOGENESIS; METHANOCOCCALES; METHANOGENIC ARCHAEON; METHANOSARCINALES; METHYLOTROPHIC METHANOGENESIS; HUMAN; METABOLISM;

CARBON; ELECTRON TRANSPORT; HUMANS; HYDROGEN; METHANE;

EID: 84896473466     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2014.02.012     Document Type: Review

References (46)

1. Thauer R.K., Kaster A.K., Seedorf H., Buckel W., Hedderich R. Methanogenic archaea: ecologically relevant differences in energy conservation. Nat Rev Microbiol 2008, 6:579-591.
2. Sakai S., Takaki Y., Shimamura S., Sekine M., Tajima T., Kosugi H., Ichikawa N., Tasumi E., Hiraki A.T., Shimizu A., Kato Y., et al. Genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultivated representative of the order Methanocellales. PLoS One 2011, 6:e22898.
3. Sakai S., Imachi H., Hanada S., Ohashi A., Harada H., Kamagata Y. Methanocella paludicola gen. nov., sp. nov., a methane-producing archaeon, the first isolate of the lineage 'Rice Cluster I', and proposal of the new archaeal order Methanocellales ord. nov. Int J Syst Evol Microbiol 2008, 58:929-936.
4. Borrel G., Harris H.M., Tottey W., Mihajlovski A., Parisot N., Peyretaillade E., Peyret P., Gribaldo S., O'Toole P.W., Brugere J.F. Genome sequence of "candidatus Methanomethylophilus alvus" MX1201, a methanogenic archaeon from the human gut belonging to a seventh order of methanogens. J Bacteriol 2012, 194:6944-6945.
5. Borrel G., O'Toole P.W., Harris H.M., Peyret P., Brugere J.F., Gribaldo S. Phylogenomic data support a seventh order of methylotrophic methanogens and provide insights into the evolution of methanogenesis. Genome Biol Evol 2013, 5:1769-1780.
6. Paul K., Nonoh J.O., Mikulski L., Brune A. "Methanoplasmatales," thermoplasmatales-related Archaea in termite guts and other environments, are the seventh order of methanogens. Appl Environ Microbiol 2012, 78:8245-8253.
7. Fournier G.P., Gogarten J.P. Evolution of acetoclastic methanogenesis in Methanosarcina via horizontal gene transfer from cellulolytic clostridia. J Bacteriol 2008, 190:1124-1127.
8. Martin W.F. Hydrogen, metals, bifurcating electrons, and proton gradients: the early evolution of biological energy conservation. FEBS Lett 2012, 586:485-493.
9. Sousa F.L., Thiergart T., Landan G., Nelson-Sathi S., Pereira I.A., Allen J.F., Lane N., Martin W.F. Early bioenergetic evolution. Philos Trans R Soc Lond B Biol Sci 2013, 368:20130088.
10. +-translocating methyltransferase complex from methanogenic archaea. Biochim Biophys Acta 2001, 1505:28-36.
11. Rother M., Metcalf W.W. Anaerobic growth of Methanosarcina acetivorans C2A on carbon monoxide: an unusual way of life for a methanogenic archaeon. Proc Natl Acad Sci U S A 2004, 101:16929-16934.
12. Oelgeschlager E., Rother M. Carbon monoxide-dependent energy metabolism in anaerobic Bacteria and Archaea. Arch Microbiol 2008, 190:257-269.
13. 2 to methane in CO-grown Methanosarcina acetivorans revealed by proteomics. Proc Natl Acad Sci U S A 2006, 103:17921-17926.
14. Costa K.C., Wong P.M., Wang T., Lie T.J., Dodsworth J.A., Swanson I., Burn J.A., Hackett M., Leigh J.A. Protein complexing in a methanogen suggests electron bifurcation and electron delivery from formate to heterodisulfide reductase. Proc Natl Acad Sci U S A 2010, 107:11050-11055.
15. Kaster A.K., Moll J., Parey K., Thauer R.K. Coupling of ferredoxin and heterodisulfide reduction via electron bifurcation in hydrogenotrophic methanogenic Archaea. Proc Natl Acad Sci U S A 2011, 108:2981-2986.
16. 2 storage. Annu Rev Biochem 2010, 79:507-536.
17. Thauer R.K. The Wolfe cycle comes full circle. Proc Natl Acad Sci U S A 2012, 109:15084-15085.
18. Lie T.J., Costa K.C., Lupa B., Korpole S., Whitman W.B., Leigh J.A. Essential anaplerotic role for the energy-converting hydrogenase Eha in hydrogenotrophic methanogenesis. Proc Natl Acad Sci U S A 2012, 109:15473-15478.
19. Buan N.R., Metcalf W.W. Methanogenesis by Methanosarcina acetivorans involves two structurally and functionally distinct classes of heterodisulfide reductase. Mol Microbiol 2010, 75:843-853.
20. Meyerdierks A., Kube M., Kostadinov I., Teeling H., Glockner F.O., Reinhardt R., Amann R. Metagenome and mRNA expression analyses of anaerobic methanotrophic Archaea of the ANME-1 group. Environ Microbiol 2010, 12:422-439.
21. Haroon M.F., Hu S., Shi Y., Imelfort M., Keller J., Hugenholtz P., Yuan Z., Tyson G.W. Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature 2013, 500:567-570.
22. Shima S., Krueger M., Weinert T., Demmer U., Kahnt J., Thauer R.K., Ermler U. Structure of a methyl-coenzyme M reductase from black sea mats that oxidize methane anaerobically. Nature 2012, 481:98-101.
23. Milucka J., Ferdelman T.G., Polerecky L., Franzke D., Wegener G., Schmid M., Lieberwirth I., Wagner M., Widdel F., Kuypers M.M. Zero-valent sulphur is a key intermediate in marine methane oxidation. Nature 2012, 491:541-546.
24. Sarmiento F., Leigh J.A., Whitman W.B. Genetic systems for hydrogenotrophic methanogens. Methods Enzymol 2011, 494:43-73.
25. Kohler P.R., Metcalf W.W. Genetic manipulation of Methanosarcina spp. Front Microbiol 2012, 3:259.
26. Dodsworth J.A., Li L., Wei S., Hedlund B.P., Leigh J.A., de Figueiredo P. Interdomain conjugal transfer of DNA from Bacteria to Archaea. Appl Environ Microbiol 2010, 76:5644-5647.
27. Sarmiento F., Mrazek J., Whitman W.B. Genome-scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Methanococcus maripaludis. Proc Natl Acad Sci U S A 2013, 110:4726-4731.
28. Gonnerman M.C., Benedict M.N., Feist A.M., Metcalf W.W., Price N.D. Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746. Biotechnol J 2013, 8:1070-1079.
29. Benedict M.N., Gonnerman M.C., Metcalf W.W., Price N.D. Genome-scale metabolic reconstruction and hypothesis testing in the methanogenic archaeon Methanosarcina acetivorans C2A. J Bacteriol 2012, 194:855-865.
30. Stolyar S., Van Dien S., Hillesland K.L., Pinel N., Lie T.J., Leigh J.A., Stahl D.A. Metabolic modeling of a mutualistic microbial community. Mol Syst Biol 2007, 3:92.
31. Bizukojc M., Dietz D., Sun J., Zeng A.P. Metabolic modelling of syntrophic-like growth of a 1,3-propanediol producer, Clostridium butyricum, and a methanogenic archeon, Methanosarcina mazei, under anaerobic conditions. Bioprocess Biosyst Eng 2010, 33:507-523.
32. Yoon S.H., Reiss D.J., Bare J.C., Tenenbaum D., Pan M., Slagel J., Moritz R.L., Lim S., Hackett M., Menon A.L., et al. Parallel evolution of transcriptome architecture during genome reorganization. Genome Res 2011, 21:1892-1904.
33. Yoon S.H., Turkarslan S., Reiss D.J., Pan M., Burn J.A., Costa K.C., Lie T.J., Slagel J., Moritz R.L., Hackett M., et al. A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen. Genome Res 2013, 23:1839-1851.
34. 2-independent growth of the hydrogenotrophic methanogen Methanococcus maripaludis. MBio 2013, 4.
35. 2 production by the mesophilic methanogen Methanococcus maripaludis. Appl Environ Microbiol 2008, 74:6584-6590.
36. 2 or formate to heterodisulfide reductase in Methanococcus maripaludis. J Bacteriol 2013, 195:5160-5165.
37. Park M.O., Mizutani T., Jones P.R. Glyceraldehyde-3-phosphate ferredoxin oxidoreductase from Methanococcus maripaludis. J Bacteriol 2007, 189:7281-7289.
38. Cheng S., Xing D., Call D.F., Logan B.E. Direct biological conversion of electrical current into methane by electromethanogenesis. Environ Sci Technol 2009, 43:3953-3958.
39. Watkins A.J., Roussel E.G., Parkes R.J., Sass H. Glycine betaine as a direct substrate for methanogens (Methanococcoides spp.). Appl Environ Microbiol 2014, 80:289-293.
40. Watkins A.J., Roussel E.G., Webster G., Parkes R.J., Sass H. Choline and N,N-dimethylethanolamine as direct substrates for methanogens. Appl Environ Microbiol 2012, 78:8298-8303.
41. Bock A.K., Schönheit P. 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 1995, 177:2002-2007.
42. Lessner D.J., Lhu L., Wahal C.S., Ferry J.G. An engineered methanogenic pathway derived from the domains Bacteria and Archaea. MBio 2010, 1:e00243-e310.
43. Zinder S.H. Physiological ecology of methanogens. Methanogenesis: Ecology, Physiology, Biochemistry & Genetics 1993, 128-206. Chapman & Hall, New York. J.G. Ferry (Ed.).
44. McInerney M.J., Beaty P.S. Anaerobic community structure from a nonequilibrium thermodynamic perspective. Can J Microbiol 1988, 34:487-493.
45. Jahreis K., Pimentel-Schmitt E.F., Bruckner R., Titgemeyer F. Ins and outs of glucose transport systems in eubacteria. FEMS Microbiol Rev 2008, 32:891-907.
46. Galagan J.E., Nusbaum C., Roy A., Endrizzi M.G., Macdonald P., FitzHugh W., Calvo S., Engels R., Smirnov S., Atnoor D., et al. The genome of Methanosarcina acetivorans reveals extensive metabolic and physiological diversity. Genome Res 2002, 12:532-542.