Methanogenesis Biochemistry

Daniel J Lessner, The University of Arkansas‐Fayetteville, Fayetteville, Arkansas, USA

Published online: December 2009

DOI: 10.1002/9780470015902.a0000573.pub2

Methanogenesis is the biological production of methane mediated by anaerobic microorganisms from the Archaea domain commonly called methanogens. The production of methane is the energy-yielding metabolism of methanogens and is unique to these organisms. Methane is produced by three major pathways: (1) reduction of carbon dioxide, (2) fermentation of acetate and (3) dismutation of methanol or methylamines. All three pathways have in common the demethylation of methyl–coenzyme M to methane and the reduction of the heterodisulfide of coenzyme M and coenzyme B catalysed by methyl–coenzyme M and heterodisulfide reductases. Investigations of the biochemistry of the pathways have revealed novel enzymes with metal and cofactor requirements that have introduced new principles of biochemistry.

Key Concepts

  • Methanogenesis is the final step in the biological decomposition of biomass in the absence of oxygen.
  • Approximately 70% of biologically produced methane originates from conversion of the methyl group of acetate to methane.
  • The pathway of methanogenesis involves enzymes with novel cofactor and metal requirements.
  • Nickel is an essential metal that is found in the active site of carbon monoxide dehydrogenase, hydrogenase, and methyl–coenzyme M reductase, an enzyme which is common to all methanogenic pathways.
  • Methyltransferases involved in the metabolism of methylamines by Methanosarcina species contain pyyrolysine, the 22nd amino acid.
  • Comparative genomics combined with biochemical analyses have revealed variations in the enzymes involved in the energy-conservation steps in methanogens.
  • Energy conservation in methanogens is linked to the generation of a chemical gradient that drives ATP synthesis by an ATP synthase.

Keywords: anaerobic; archaea; cofactors; nickel; bioenergetics

Figure 1. Reactions and enzymes common to all methanogenic pathways. Step 1, methyltransferase; step 2, methyl–coenzyme M reductase and step 3, heterodisulfide reductase.
Figure 2. Cofactors utilized in methanogenic pathways.
Figure 3. The carbon dioxide-reduction pathway for methanogenesis. Step 1, formylmethanofuran dehydrogenase; step 2, formylmethanofuran:tetrahydromethanopterin formyltransferase; step 3, N5,N10-methenyltetrahydromethanopterin cyclohydrolase; step 4, N5,N10-methylenetetrahydromethanopterin dehydrogenase; step 5, N5,N10-methylenetetrahydromethanopterin reductase; steps 6a,b, N5-methyltetrahydromethanopterin:coenzyme M methyltransferase; step 7, methyl–coenzyme M reductase and step 8, heterodisulfide reductase.
Figure 4. The acetate fermentation pathway for methanogenesis by Methanosarcina species. The dashed box shows differences between freshwater Methanosarcina (a) and the marine species Methanosarcina acetivorans (b) in the proposed electron transport system involved in reduction of heterodisulfide and generation of a proton gradient. Ack, acetate kinase; Pta, phosphotransacetylase; CdhABCDE, carbon monoxide dehydrogenase/acetyl–CoA synthase five-subunit complex; THSPt, tetrahydrosarcinapterin; Fd, ferredoxin; CoM, coenzyme M; CoB, coenzyme B; Cam, carbonic anhydrase; Mtr, methyltransferase; Mcr, methylreductase; Ech, Ech hydrogenase; Vho, Vho hydrogenase; MP, methanophenazine; MA-Rnf, Methanosarcina acetivorans Rnf; HdrDE, heterodisulfide (CoM-S-S-CoB) reductase; Mrp, multiple resistance/pH regulation Na+/H+ antiporter; Atp, H+-translocating ATP synthase. The carbon atoms of acetate are marked with an asterisk and a hash-mark to distinguish between the carboxyl and methyl groups.
Figure 5. Mechanism of the carbon monoxide dehydrogenase/acetyl–CoA synthase. CdhABCDE, subunits of the complex. ‘A’, metal cluster A; ‘B’, metal cluster B; ‘C’, metal cluster C, ‘D’, metal cluster D; ‘E’, metal cluster E and ‘F’, metal cluster F. [Co]-CH3, methyl-factor III; THSPt, tetrahydrosarcinapterin and Fd, ferredoxin in the oxidized and reduced states.
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 References
    Abken HJ, Tietze M, Brodersen J et al. (1998) Isolation and characterization of methanophenazine and function of phenazines in membrane-bound electron transport of Methanosarcina mazei Go1. Journal of Bacteriology 180(8): 2027–2032.
    Acharya P, Warkentin E, Ermler U et al. (2006) The structure of formylmethanofuran: tetrahydromethanopterin formyltransferase in complex with its coenzymes. Journal of Molecular Biology 357(3): 870–879.
    Burke SA and Krzycki JA (1997) Reconstitution of monomethylamine:coenzyme M methyl transfer with a corrinoid protein and two methyltransferases purified from Methanosarcina barkeri. Journal of Biological Chemistry 272(26): 16570–16577.
    Ermler U, Grabarse W, Shima S et al. (1997) Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation. Science 278(5342): 1457–1462.
    Ferguson T, Soares JA, Lienard T et al. (2009) RamA, a protein required for reductive activation of corrinoid-dependent methylamine methyltransferase reactions in methanogenic archaea. Journal of Biological Chemistry 284(4): 2285–2295.
    Fricke WF, Seedorf H, Henne A et al. (2006) The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis. Journal of Bacteriology 188(2): 642–658.
    Gencic S and Grahame DA (2003) Nickel in subunit beta of the acetyl-CoA decarbonylase/synthase multienzyme complex in methanogens. Catalytic properties and evidence for a binuclear Ni-Ni site. Journal of Biological Chemistry 278(8): 6101–6110.
    Gong W, Hao B, Wei Z et al. (2008) Structure of the alpha2epsilon2 Ni-dependent CO dehydrogenase component of the Methanosarcina barkeri acetyl-CoA decarbonylase/synthase complex. Proceedings of the National Academy of Sciences of the USA 105(28): 9558–9563.
    Gorrell A, Lawrence SH, Ferry JG et al. (2005) Structural and kinetic analyses of arginine residues in the active site of the acetate kinase from Methanosarcina thermophila. Journal of Biological Chemistry 280(11): 10731–10742.
    Grabarse W, Vaupel M, Holt JA et al. (1999) The crystal structure of methenyltetrahydromethanopterin cyclohydrolase from the hyperthermophilic archaeon Methanopyrus kandleri. Structure 7(10): 1257–1268.
    Grochowski LL and White RH (2008) Promiscuous anaerobes: new and unconventional metabolism in methanogenic archaea. Annals of the New York Academy of Sciences 1125: 190–214.
    Harms U and Thauer RK (1996) The corrinoid-containing 23-kDa subunit MtrA of the energy-conserving N5-methyltetrahydromethanopterin:coenzyme M methyltransferase complex from Methanobacterium thermoautotrophicum. EPR spectroscopic evidence for a histidine residue as a cobalt ligand of the cobamide. European Journal of Biochemistry 241: 149–154.
    Hedderich R (2004) Energy-converting [NiFe] hydrogenases from archaea and extremophiles: ancestors of complex I. Journal of Bioenergetics and Biomembranes 36(1): 65–75.
    Hedderich R, Hamann N and Bennati M (2005) Heterodisulfide reductase from methanogenic archaea: a new catalytic role for an iron-sulfur cluster. Biological Chemistry 386(10): 961–970.
    Kisker C, Schindelin H, Alber BE et al. (1996) A left-hand beta-helix revealed by the crystal structure of a carbonic anhydrase from the archaeon Methanosarcina thermophila. EMBO Journal 15(10): 2323–2330.
    Klein AR, Hartmann GC and Thauer RK (1995) Hydrogen isotope effects in the reactions catalyzed by H2-forming N5,N10-methylenetetrahydromethanopterin dehydrogenase from methanogenic Archaea. European Journal of Biochemistry 233(1): 372–376.
    Krzycki JA (2005) The direct genetic encoding of pyrrolysine. Current Opinion of Microbiology 8(6): 706–712.
    Lawrence SH, Luther KB and Schindelin H (2006) Structural and functional studies suggest a catalytic mechanism for the phosphotransacetylase from Methanosarcina thermophila. Journal of Bacteriology 188(3): 1143–1154.
    Lessner DJ and Ferry JG (2007) The archaeon Methanosarcina acetivorans contains a protein disulfide reductase with an iron-sulfur cluster. Journal of Bacteriology 189(20): 7475–7484.
    Lessner DJ, Li L, Li Q et al. (2006) An unconventional pathway for reduction of CO2 to methane in CO-grown Methanosarcina acetivorans revealed by proteomics. Proceedings of the National Academy of Sciences of the USA 103(47): 17921–17926.
    Li Q, Li L, Rejtar T et al. (2006) Electron transport in the pathway of acetate conversion to methane in the marine archaeon Methanosarcina acetivorans. Journal of Bacteriology 188(2): 702–710.
    Ragsdale SW (1998) Nickel biochemistry. Current Opinion in Chemical Biology 2: 308–215.
    Rother M and Metcalf WW (2005) Genetic technologies for Archaea. Current Opinion of Microbiology 8(6): 745–751.
    Sauer K, Harms U and Thauer RK (1997) Methanol:coenzyme M methyltransferase from Methanosarcina barkeri. Purification, properties and encoding genes of the corrinoid protein MT1. European Journal of Biochemistry 243(3): 670–677.
    Seedorf H, Dreisbach A, Heddrich R et al. (2004) F420H2 oxidase (FprA) from Methanobrevibacter arboriphilus, a coenzyme F420-dependent enzyme involved in O2 detoxification. Archives of Microbiology 182(2–3): 126–137.
    Shima S, Pilak O, Vogt S et al. (2008) The crystal structure of [Fe]-hydrogenase reveals the geometry of the active site. Science 321(5888): 572–575.
    Smith KS and Ingram-Smith C (2007) Methanosaeta, the forgotten methanogen? Trends in Microbiology 15(4): 150–155.
    Thauer RK, Kaster AK, Seedorf H et al. (2008) Methanogenic archaea: ecologically relevant differences in energy conservation. Nature Reviews. Microbiology 6(8): 579–591.
    Vorholt JA and Thauer RK (1997) The active species of ‘CO2’ utilized by formylmethanofuran dehydrogenase from methanogenic Archaea. European Journal of Biochemistry 248(3): 919–924.
    Zimmerman SA and Ferry JG (2006) Proposal for a hydrogen bond network in the active site of the prototypic gamma-class carbonic anhydrase. Biochemistry 45(16): 5149–5157.
 Further Reading
    Bult CJ, White O, Olsen GJ et al. (1996) Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273: 1058–1073.
    Deppenmeier U (2004) The membrane-bound electron transport system of Methanosarcina species. Journal of Bioenergetics and Biomembranes 36(1): 55–64.
    book Ferry JG (1993) Biochemistry of Methanogenesis. New York: Chapman and Hall.
    Ferry JG (1997) Methane: small molecule, big impact [comment]. Science 278: 1413–1414.
    Ferry JG (1999) Enzymology of one-carbon metabolism in methanogenic pathways. FEMS Microbiology Reviews 23: 13–38.
    Ferry JG and Lessner DJ (2008) Methanogenesis in marine sediments. Annals of the New York Academy of Sciences 1125: 147–157.
    Galagan JE, Nusbaum C, Roy A et al. (2002) The genome of Methanosarcina acetivorans reveals extensive metabolic and physiological diversity. Genome Research 12: 532–524.
    Reeve JN, Nolling J, Morgan RM and Smith DR (1997) Methanogenesis: genes, genomes, and who's on first? Journal of Bacteriology 179: 5975–5986.
    Smith DR, Doucette-Stamm LA, Deloughery C et al. (1997) Complete genome sequence of Methanobacterium thermoautotrophicum delta H: functional analysis and comparative genomics. Journal of Bacteriology 179: 7135–7155.
    Thauer RK (1998) Biochemistry of methanogenesis: a tribute to Marjory Stephenson. Microbiology UK 144: 2377–2406.

Related Sub-Topics:

Enzymes: Structure and Action Mechanism | Bioenergetics | Archaea | Energetics and Catabolism | Microbial Respiration and Fermentation
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Article Title: Methanogenesis Biochemistry
 
How to Cite close
Lessner, Daniel J(Dec 2009) Methanogenesis Biochemistry. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000573.pub2]