Methanogenesis Biochemistry


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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Further Reading

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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.

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Lessner, Daniel J(Dec 2009) Methanogenesis Biochemistry. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0000573.pub2]