|Table of Contents|

Research progress in biochemical pathways of methanogenesis(PDF)

Chinese Journal of Applied & Environmental Biology[ISSN:1006-687X/CN:51-1482/Q]

Issue:
2015 01
Page:
1-9
Research Field:
Reviews
Publishing date:

Info

Title:
Research progress in biochemical pathways of methanogenesis
Author(s):
FANG Xiaoyu LI Jiabao RUI Junpeng LI Xiangzhen
1Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China2Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China3University of Chinese Academy of Sciences, Beijing 100049, China4Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China5Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
Keywords:
methanogen biochemical pathways CO2-reducing methanogenesis aceticlastic methanogenesis methylotrophic methanogenesis
CLC:
Q939.9
PACS:
DOI:
10.3724/SP.J.1145.2014.08019
DocumentCode:

Abstract:
Microbial methanogenesis accounts for approximately 74% of natural methane emission. The process plays a major role in global warming and is important for bioenergy production. This paper reviews the biochemical pathways of methanogenesis. It is currently recognized that methanogenesis proceeds via three biochemical pathways depending on the carbon sources, including hydrogenotrophic, aceticlastic, and methylotrophic methanogenesis. Multiple enzymes and coenzymes are involved in the process, during which Na+ or proton gradient is created across the cell membrane, contributing to limited ATP synthesis. In the hydrogenotrophic pathway, CO2 is reduced to methane with H2 or formate as an electron donor. In the aceticlastic pathway, acetate is split into methyl and carboxyl group, then the carboxyl group is oxidized to produce H2 which is used as the electron donor to reduce methyl group. In the methylotrophic pathway, methyl group is reduced with external H2 or reducing equivalent from the oxidation of its own methyl group. The ATP gained from per mol substrate for different pathways are as follows: hydrogenotrophic > methylotrophic > aceticlastic pathway. Due to the unculturability of most archaeal methanogens, understandings of the biochemical pathways of methanogenesis and the relationships between methanogens and other microbial communities will have to depend on new technologies including bioinformatics, gene engineering and metabolic modelling.

References

1 Ferry JG, House CH. The stepwise evolution of early life driven by energy conservation [J]. Mol Biol Evol, 2006, 23 (6): 1286-1292
2 Battistuzzi FU, Feijao A, Hedges SB. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land [J]. BMC Evol Biol, 2004, 4 (44): 1-14
3 Ferry JG. Fundamentals of methanogenic pathways that are key to the biomethanation of complex biomass [J]. Curr Opin Microbiol, 2011, 22 (3): 351-357
4 Lelieveld J, Crutzen P, Brühl C. Climate effects of atmospheric methane [J].Chemosphere, 1993, 26 (1): 739-768
5 陈槐, 周舜, 吴宁, 王艳芬, 罗鹏, 石福孙. 湿地甲烷的产生、氧化及排放通量研究进展[J]. 应用与环境生物学报, 2006, 12 (5): 726-733 [Chen H, Zhou S, Wu N, Wang YF, Luo P, Shi FS. Advance in studies on production, oxidation and emission flux of methane from wetlands [J].Chin J Appl Environ Biol, 2006, 12 (5): 726-733]
6 Lowe DC. Global change: a green source of surprise [J]. Nature, 2006, 439 (7073): 148-149
7 Whitman WB, Bowen TL, Boone DR. The methanogenic bacteria [M]. Springer, 2006
8 Garcia JL, Patel BKC, Ollivier B. Taxonomic, phylogenetic, and ecological diversity of methanogenic archaea [J]. Anaerobe, 2000, 6 (4): 205-226
9 Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms-proposal for the domain archaea, bacteria, and eucarya [J]. Proc Natl Acad Sci USA, 1990, 87 (12): 4576-4579
10 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 [J]. Int J Syst Evol Micr, 2008, 58: 929-936
11 Paul K, Nonoh JO, Mikulski L, Brune A. “Methanoplasmatales,” thermoplasmatales-related archaea in termite guts and other environments, are the seventh order of methanogens [J]. Appl Environ Microb, 2012, 78 (23): 8245-8253
12 Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools [J]. Nucleic Acids Res, 2013, 41: 590-596
13 Conrad R. Control of microbial methane production in wetland rice fields [J]. Nutr Cycl Agroecosys, 2002, 64 (1-2): 59-69
14 傅霖, 辛明秀. 产甲烷菌的生态多样性及工业应用[J]. 应用与环境生物学报, 2009, 15 (2): 574-578 [Fu L, Xin MX. Ecological diversity and industrial application of methanogens. Chin J Appl Environ Biol, 2009, 15 (2): 574-578]
15 Leadbetter JR, Breznak JA. Physiological ecology of Methano-brevibacter cuticularis sp. nov and Methanobrevibacter curvatus sp. nov., isolated from the hindgut of the termite Reticulitermes flavipes [J]. Appl Environ Microb, 1996, 62 (10): 3620-3631
16 Whitman WB, Ankwanda E, Wolfe RS. Nutrition and carbon metabolism of Methanococcus voltae [J]. J Bacteriol, 1982, 149 (3): 852-863
17 Garcia JL. Taxonomy and ecology of methanogens [J]. FEMS Microbiol Lett, 1990, 87 (3-4): 297-308
18 Ferry JG. Enzymology of one-carbon metabolism in methanogenic pathways [J]. FEMS Microbiol Rev, 1999, 23 (1): 13-38
19 Thauer RK, Kaster AK, Seedorf H, Buckel W, Hedderich R. Methanogenic archaea: ecologically relevant differences in energy conservation [J]. Nat Rev Microbiol, 2008, 6 (8): 579-591
20 Abken H-J, Tietze M, Brodersen J, B?umer S, Beifuss U, Deppenmeier U. Isolation and characterization of methanophenazine and function of phenazines in membrane-bound electron transport of Methanosarcinamazei G?1 [J]. J Bacteriol, 1998, 180 (8): 2027-2032
21 Thauer RK. Biochemistry of methanogenesis: a tribute to Marjory Stephenson [J]. Microbiol-Sgm, 1998, 144: 2377-2406
22 Taylor CD, Wolfe RS. Structure and methylation of coenzyme M (HSCH2CH2SO3) [J]. J Biol Chem, 1974, 249 (15): 4879-4885
23 Hedderich R, Whitman WB. Physiology and biochemistry of the methane-producing archaea [M]. Springer, 2006
24 Cheeseman P, Toms-Wood A, Wolfe R. Isolation and properties of a fluorescent compound, Factor420, from Methanobacterium strain MoH [J]. J Bacteriol, 1972, 112 (1): 527-531
25 Edwards T, McBride B. New method for the isolation and identification of methanogenic bacteria [J]. Appl microbiol, 1975, 29 (4): 540-545
26 Large PJ. Methylotrophy and methanogenesis [M]. Washington: American Society for Microbiology, 1983
27 Liu Y, Whitman WB. Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea [J]. Ann NY Acad Sci, 2008, 1125 (1): 171-189
28 Shima S, Thauer RK. Methyl-coenzyme M reductase and the anaerobic oxidation of methane in methanotrophic archaea [J]. Curr Opin Microbiol, 2005, 8 (6): 643-648
29 Morris R, Schauer-Gimenez A, Bhattad U, Kearney C, Struble CA, Zitomer D, Maki JS. Methyl coenzyme M reductase (mcrA) gene abundance correlates with activity measurements of methanogenic H2/CO2-enriched anaerobic biomass [J]. Microb Biotechnol, 2014, 7 (1): 77-84
30 Springer E, Sachs MS, Woese CR, Boone DR. Partial gene sequences for the A subunit of methyl-coenzyme M reductase (mcrI) as a phylogenetic tool for the family Methanosarcinaceae [J]. Int J Syst Bacteriol, 1995, 45 (3): 554-559
31 Luton PE, Wayne JM, Sharp RJ, Riley PW. The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill [J]. Microbiology, 2002, 148 (11): 3521-3530
32 Friedmann HC, Klein A, Thauer RK. Structure and function of the nickel porphinoid, coenzyme F430, and of its enzyme, methyl coenzyme M reductase [J]. FEMS Microbiol Lett, 1990, 87 (3): 339-348
33 Prakash D, Wu Y, Suh S-J, Duin EC. Elucidating the process of activation of methyl-coenzyme M reductase [J]. J Bacteriol, 2014, 196: 2491-2498
34 Ermler U, Grabarse W, Shima S, Goubeaud M, Thauer RK. Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation [J]. Science, 1997, 278 (5342): 1457-1462
35 Rospert S, Linder D, Ellermann J, Thauer RK. Two genetically distinct methyl-coenzyme M reductases in Methanobacterium thermoautotrophicum strain Marburg and ΔH [J]. Eur J Biochem, 1990, 194 (3): 871-877
36 N?lling J, Pihl TD, Vriesema A, Reeve JN. Organization and growth phase-dependent transcription of methane genes in two regions of the Methanobacterium thermoautotrophicum genome [J]. J Bacteriol, 1995, 177 (9): 2460-2468
37 Pihl TD, Sharma S, Reeve JN. Growth phase-dependent transcription of the genes that encode the two methyl coenzyme M reductase isoenzymes and N5-methyltetrahydromethanopterin:coenzyme M methyltransferase in Methanobacterium thermoautotrophicum delta H [J]. J Bacteriol, 1994, 176 (20): 6384-6391
38 Bobik TA, Olson KD, Noll KM, Wolfe RS. Evidence that the heterodisulfide of coenzyme-M and 7-mercaptoheptanoyl threonine phosphate is a product of the methanylreductase reaction in Methanobacterium [J]. Biochem Biophys Res Commun, 1987, 149 (2): 455-460
39 Heiden S, Hedderich R, Setzke E, Thauer RK. Purification of a two-subunit cytochrome-b-containing heterodisulfide reductase from methanol-grown Methanosarcina barkeri [J]. Eur J Biochem, 1994, 221 (2): 855-861
40 Stojanowic A, Mander GJ, Duin EC, Hedderich R. Physiological role of the F420-non-reducing hydrogenase (Mvh) from Methanothermobacter marburgensis [J]. Arch Microbiol, 2003, 180 (3): 194-203
41 Buckel W, Thauer RK. Energy conservation via electron bifurcating ferredoxin reduction and proton/Na+ translocating ferredoxin oxidation [J]. Biochim Biophys Acta-Bioenerg, 2013, 1827 (2): 94-113
42 Buan NR, Metcalf WW. Methanogenesis by Methanosarcina acetivorans involves two structurally and functionally distinct classes of heterodisulfide reductase [J]. Mol Microbiol, 2010, 75 (4): 843-853
43 Wood GE, Haydock AK, Leigh JA. Function and regulation of the formate dehydrogenase genes of the methanogenic archaeon Methanococcus maripaludis [J]. J Bacteriol, 2003, 185 (8): 2548-2554
44 Rother M, Oelgeschl?ger E, Metcalf WW. Genetic and proteomic analyses of CO utilization by Methanosarcina acetivorans [J]. Arch Microbiol, 2007, 188 (5): 463-472
45 Ferry JG. CO in methanogenesis [J]. Ann Microbiol, 2010, 60 (1): 1-12
46 Deppenmeier U, Müller V, Gottschalk G. Pathways of energy conservation in methanogenic archaea [J]. Arch Microbiol, 1996, 165 (3): 149-163
47 Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, Sutton GG, Blake JA, FitzGerald LM, Clayton RA, Gocayne JD, Kerlavage AR, Dougherty BA, Tomb JF, Adams MD, Reich CI, Overbeek R, Kirkness EF, Weinstock KG, Merrick JM, Glodek A, Scott JL, Geoghagen NS, Venter JC. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii [J]. Science, 1996, 273 (5278): 1058-1073
48 Enssle M, Zirngibl C, Linder D, Thauer R. Coenzyme F420 dependent N5, N10-methylenetetrahydromethanopterin dehydrogenase in methanol grown Methanosarcina barkeri [J]. Arch Microbiol, 1991, 155 (5): 483-490
49 Ma K, Linder D, Stetter K, Thauer R. Purification and properties of N5, N10-methylenetetrahydromethanopterin reductase (coenzyme F420-dependent) from the extreme thermophile Methanopyrus kandleri [J]. Arch Microbiol, 1991, 155 (6): 593-600
50 MA K, THAUER RK. Purification and properties of N5, N10-methylenetetrahydromethanopterin reductase from Methanobacterium thermoautotrophicum (strain Marburg) [J]. Eur J Biochem, 1990, 191 (1): 187-193
51 Weiss DS, G?rtner P, Thauer RK. The energetics and sodium-ion dependence of N5-methyltetrahydromethanopterin: coenzyme M methyltransferase studied with Cob (I) alamin as methyl acceptor and methylcob (III) alamin as Methyl Donor [J]. Eur J Biochem, 1994, 226 (3): 799-809
52 Gottschalk G, Thauer RK. The Na+ translocating methyltransferase complex from methanogenic archaea [J]. Biochim Biophys Acta-Bioenerg, 2001, 1505 (1): 28-36
53 Gartner P, Ecker A, Fischer R, Linder D, Fuchs G, Thauer RK. Purification and properties of N5-methyltetrahydromethanopterin: coenzyme M methyltransferase from Methanobacterium thermoautotrophicum [J]. Eur J Biochem, 1993, 213 (1): 537-545
54 Hippler B, Thauer RK. The energy conserving methyltetrahydrome-thanopterin: coenzyme M methyltransferase complex from methano-genic archaea: function of the subunit MtrH [J]. FEBS Lett, 1999, 449 (2): 165-168
55 Gottschalk G, Thauer RK. The Na+-translocating methyltransferase complex from methanogenic archaea [J]. Biochim Biophys Acta-Bioenerg, 2001, 1505 (1): 28-36
56 Jetten MS, Stams AJ, Zehnder AJ. Methanogenesis from acetate: a comparison of the acetate metabolism in Methanothrix soehngenii and Methanosarcina spp. [J]. FEMS Microbiol Lett, 1992, 88 (3): 181-197
57 Abbanat DR, Ferry JG. Resolution of component proteins in an enzyme complex from Methanosarcina thermophila catalyzing the synthesis or cleavage of acetyl-CoA [J]. Proc Natl Acad Sci USA, 1991, 88 (8): 3272-3276
58 Grahame DA, DeMoll E. Partial reactions catalyzed by protein components of the acetyl-CoA decarbonylase synthase enzyme complex from Methanosarcina barkeri [J]. J Biol Chem, 1996, 271 (14): 8352-8358
59 Grahame DA, DeMoll E. Substrate and accessory protein requirements and thermodynamics of acetyl-CoA synthesis and cleavage in Methanosarcina barkeri [J]. Biochemistry, 1995, 34 (14): 4617-4624
60 Ferry JG. Methane from acetate [J]. J Bacteriol, 1992, 174 (17): 5489-5495
61 Jetten MSM, Hagen WR, Pierik AJ, Stams AJM, Zehnder AJB. Paramagnetic centers and acetyl-coenzyme A/CO exchange activity of carbon monoxide dehydrogenase from Methanothrix soehngenii [J]. Eur J Biochem, 1991, 195 (2): 385-391
62 Biavati B, Vasta M, Ferry JG. Isolation and characterization of” Methanosphaera cuniculi” sp. nov. [J]. Appl Environ Microb, 1988, 54 (3): 768-771
63 Fricke WF, Seedorf H, Henne A, Kruer M, Liesegang H, Hedderich R, Gottschalk G, Thauer RK. The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis [J]. J Bacteriol, 2006, 188 (2): 642-658
64 Sauer K, Harms U, Thauer RK. Methanol: coenzyme M methyltransferase from Methanosarcina barkeri purification, properties and encoding genes of the corrinoid protein MT1 [J]. Eur J Biochem, 1997, 243 (3): 670-677
65 Burke SA, Krzycki JA. Reconstitution of monomethylamine: coenzyme M methyl transfer with a corrinoid protein and two methyltransferases purified from Methanosarcina barkeri [J]. J Biol Chem, 1997, 272 (26): 16570-16577
66 Ferguson DJ, Krzycki JA, Grahame DA. Specific roles of methylcobamide: coenzyme M methyltransferase isozymes in metabolism of methanol and methylamines in Methanosarcina barkeri [J]. J Biol Chem, 1996, 271 (9): 5189-5194
67 Ferguson D, Krzycki JA. Reconstitution of trimethylamine-dependent coenzyme M methylation with the trimethylamine corrinoid protein and the isozymes of methyltransferase II from Methanosarcina barkeri [J]. J Bacteriol, 1997, 179 (3): 846-852
68 Rosenblatt DS, Fenton WA. Chemistry and biology of B12 [M]. New York: Wiley-intersciences, 1999: 666
69 Tallant TC, Paul L, Krzycki JA. The MtsA subunit of the methylthiol: coenzyme M methyltransferase of Methanosarcina barkeri catalyses both half-reactions of corrinoid-dependent dimethylsulfide: coenzyme M methyl transfer [J]. J Biol Chem, 2001, 276 (6): 4485-4493
70 Hedderich R, Whitman WB. Physiology and biochemistry of the methane-producing archaea [M]. Springer, 2013.
71 Leigh JA, Albers SV, Atomi H, Allers T. Model organisms for genetics in the domain archaea: methanogens, halophiles, Thermococcales and Sulfolobales [J]. FEMS Microbiol Rev, 2011, 35 (4): 577-608
72 Watkins AJ, Roussel EG, Parkes RJ, Sass H. Glycine betaine as a direct substrate for methanogens (Methanococcoides spp.) [J]. Appl Environ Microb, 2014, 80 (1): 289-293
73 Gardner WL, Whitman WB. Expression vectors for Methanococcus maripaludis: Overexpression of acetohydroxyacid synthase and beta-galactosidase [J]. Genetics, 1999, 152 (4): 1439-1447
74 Metcalf WW, Zhang JK, Apolinario E, Sowers KR, Wolfe RS. A genetic system for archaea of the genus Methanosarcina: Liposome-mediated transformation and construction of shuttle vectors [J]. Proc Natl Acad Sci USA, 1997, 94 (6): 2626-2631
75 Moore BC, Leigh JA. Markerless mutagenesis in Methanococcus maripaludis demonstrates roles for alanine dehydrogenase, alanine racemase, and alanine permease [J]. J Bacteriol, 2005, 187 (3): 972-979
76 Pritchett MA, Zhang JK, Metcalf WW. Development of a markerless genetic exchange method for Methanosarcina acetivorans C2A and its use in construction of new genetic tools for methanogenic archaea [J]. Appl Environ Microb, 2004, 70 (3): 1425-1433
77 Guss AM, Rother M, Zhang JK, Kulkkarni G, Metcalf WW. New methods for tightly regulated gene expression and highly efficient chromosomal integration of cloned genes for Methanosarcina species [J]. Archaea, 2008, 2 (3): 193-203
78 Farkas JA, Picking JW, Santangelo TJ. Genetic techniques for the archaea [J]. Annu Rev Genet, 2013,47: 539-561
79 Costa KC, Leigh JA. Metabolic versatility in methanogens [J]. Curr Opin Microbiol, 2014, 29: 70-75
80 Welander PV, Metcalf WW. Mutagenesis of the C1 oxidation pathway in Methanosarcina barkeri: new insights into the Mtr/Mer bypass pathway [J]. J Bacteriol, 2008, 190 (6): 1928-1936.
81 Lessner DJ, Lhu L, Wahal CS, Ferry JG. An engineered methanogenic pathway derived from the domains bacteria and archaea [J]. MBio, 2010, 1 (5): 1-4
82 Rotaru A-E, Shrestha PM, Liu F, Shrestha M, Shrestha D, Embree M, Zengler K, Wardman C, Nevin KP, Lovley DR. A new model for electron flow during anaerobic digestion: direct interspecies electron transfer to Methanosaeta for the reduction of carbon dioxide to methane [J]. Energy Environ Sci, 2014
83 Feist AM, Scholten JC, Palsson BO, Brockman FJ, Ideker T. Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri [J]. Mol Syst Biol, 2006, 2: 1-14
84 Gonnerman MC, Benedict MN, Feist AM, Metcalf WW, Price ND. Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746 [J]. Biotechnol J, 2013, 8 (9): 1070-1079
85 Kumar VS, Ferry JG, Maranas CD. Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans [J]. BMC Syst Biol, 2011, 5 (28): 1-10
86 Oberhardt MA, Palsson B?, Papin JA. Applications of genome-scale metabolic reconstructions [J]. Mol Syst Biol, 2009, 5 (1): 1-15

Memo

Memo:
-
Last Update: 2015-02-15