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Entry Name Methane metabolism
Description Methane is metabolized principally by methanotrophs and methanogens in the global carbon cycle. Methanotrophs consume methane as the only source of carbon, while methanogens produce methane as a metabolic byproduct. Methylotrophs, which are microorganisms that can obtain energy for growth by oxidizing one-carbon compounds, such as methanol and methane, are situated between methanotrophs and methanogens. Methanogens can obtain energy for growth by converting a limited number of substrates to methane under anaerobic conditions. Three types of methanogenic pathways are known: CO2 to methane [MD:
M00567 ], methanol to methane [MD:
M00356 ], and acetate to methane [MD:
M00357 ]. Methanogens use 2-mercaptoethanesulfonate (CoM; coenzyme M) as the terminal methyl carrier in methanogenesis and have four enzymes for CoM biosynthesis [MD:
M00358 ]. Coenzyme B-Coenzyme M heterodisulfide reductase (Hdr), requiring for the final reaction steps of methanogenic pathway, is divided into two types: cytoplasmic HdrABC in most methanogens and membrane-bound HdrED in Methanosarcina species. In methanotrophs and methyltrophs methane is oxidized to form formaldehyde, which is at the diverging point for further oxidation to CO2 for energy source and assimilation for biosynthesis. There are three pathways that convert formaldehyde to C2 or C3 compounds: serine pathway [MD:
M00346 ], ribulose monophosphate pathway [MD:
M00345 ], and xylulose monophosphate pathway [MD:
M00344 ]. The first two pathways are found in prokaryotes and the third is found in yeast. As a special case of methylotrophs, various amines can be used as carbon sources in trimethylamine metabolism [MD:
M00563 ].
Class Metabolism; Energy metabolismBRITE hierarchy
Pathway map Module M00020 Serine biosynthesis, glycerate-3P => serine [PATH:ko00680 ]
M00174 Methane oxidation, methanotroph, methane => formaldehyde [PATH:ko00680 ]
M00344 Formaldehyde assimilation, xylulose monophosphate pathway [PATH:ko00680 ]
M00345 Formaldehyde assimilation, ribulose monophosphate pathway [PATH:ko00680 ]
M00563 Methanogenesis, methylamine/dimethylamine/trimethylamine => methane [PATH:ko00680 ]
M00608 2-Oxocarboxylic acid chain extension, 2-oxoglutarate => 2-oxoadipate => 2-oxopimelate => 2-oxosuberate [PATH:ko00680 ]
Other DBs Orthology K00121 frmA, ADH5, adhC; S-(hydroxymethyl)glutathione dehydrogenase / alcohol dehydrogenase [EC:1.1.1.284 1.1.1.1 ]
K00123 fdoG, fdhF, fdwA; formate dehydrogenase major subunit [EC:1.17.1.9 ]
K00124 fdoH, fdsB; formate dehydrogenase iron-sulfur subunit
K00127 fdoI, fdsG; formate dehydrogenase subunit gamma
K00148 fdhA; glutathione-independent formaldehyde dehydrogenase [EC:1.2.1.46 ]
K00169 porA; pyruvate ferredoxin oxidoreductase alpha subunit [EC:1.2.7.1 ]
K00170 porB; pyruvate ferredoxin oxidoreductase beta subunit [EC:1.2.7.1 ]
K00171 porD; pyruvate ferredoxin oxidoreductase delta subunit [EC:1.2.7.1 ]
K00172 porC, porG; pyruvate ferredoxin oxidoreductase gamma subunit [EC:1.2.7.1 ]
K00189 vorG, porG; 2-oxoisovalerate/pyruvate ferredoxin oxidoreductase gamma subunit [EC:1.2.7.7 1.2.7.1 ]
K00192 cdhA; anaerobic carbon-monoxide dehydrogenase, CODH/ACS complex subunit alpha [EC:1.2.7.4 ]
K00193 cdhC; acetyl-CoA decarbonylase/synthase, CODH/ACS complex subunit beta [EC:2.3.1.169 ]
K00194 cdhD, acsD; acetyl-CoA decarbonylase/synthase, CODH/ACS complex subunit delta [EC:2.1.1.245 ]
K00195 cdhB; anaerobic carbon-monoxide dehydrogenase, CODH/ACS complex subunit epsilon
K00196 cooF; anaerobic carbon-monoxide dehydrogenase iron sulfur subunit
K00197 cdhE, acsC; acetyl-CoA decarbonylase/synthase, CODH/ACS complex subunit gamma [EC:2.1.1.245 ]
K00198 cooS, acsA; anaerobic carbon-monoxide dehydrogenase catalytic subunit [EC:1.2.7.4 ]
K00200 fwdA, fmdA; formylmethanofuran dehydrogenase subunit A [EC:1.2.7.12 ]
K00201 fwdB, fmdB; formylmethanofuran dehydrogenase subunit B [EC:1.2.7.12 ]
K00202 fwdC, fmdC; formylmethanofuran dehydrogenase subunit C [EC:1.2.7.12 ]
K00203 fwdD, fmdD; formylmethanofuran dehydrogenase subunit D [EC:1.2.7.12 ]
K00204 fwdH; 4Fe-4S ferredoxin
K00205 fwdF, fmdF; 4Fe-4S ferredoxin
K00300 mtdA; methylenetetrahydrofolate/methylenetetrahydromethanopterin dehydrogenase (NADP+)
K00319 mtd; methylenetetrahydromethanopterin dehydrogenase [EC:1.5.98.1 ]
K00320 mer; 5,10-methylenetetrahydromethanopterin reductase [EC:1.5.98.2 ]
K00399 mcrA; methyl-coenzyme M reductase alpha subunit [EC:2.8.4.1 ]
K00400 K00400 ; methyl coenzyme M reductase system, component A2
K00401 mcrB; methyl-coenzyme M reductase beta subunit [EC:2.8.4.1 ]
K00402 mcrG; methyl-coenzyme M reductase gamma subunit [EC:2.8.4.1 ]
K00442 frhD; coenzyme F420 hydrogenase subunit delta
K00577 mtrA; tetrahydromethanopterin S-methyltransferase subunit A [EC:7.2.1.4 ]
K00578 mtrB; tetrahydromethanopterin S-methyltransferase subunit B [EC:7.2.1.4 ]
K00579 mtrC; tetrahydromethanopterin S-methyltransferase subunit C [EC:7.2.1.4 ]
K00580 mtrD; tetrahydromethanopterin S-methyltransferase subunit D [EC:7.2.1.4 ]
K00581 mtrE; tetrahydromethanopterin S-methyltransferase subunit E [EC:7.2.1.4 ]
K00582 mtrF; tetrahydromethanopterin S-methyltransferase subunit F [EC:7.2.1.4 ]
K00583 mtrG; tetrahydromethanopterin S-methyltransferase subunit G [EC:7.2.1.4 ]
K00584 mtrH; tetrahydromethanopterin S-methyltransferase subunit H [EC:7.2.1.4 ]
K00672 ftr; formylmethanofuran--tetrahydromethanopterin N-formyltransferase [EC:2.3.1.101 ]
K01499 mch; methenyltetrahydromethanopterin cyclohydrolase [EC:3.5.4.27 ]
K01624 FBA, fbaA; fructose-bisphosphate aldolase, class II [EC:4.1.2.13 ]
K01834 PGAM, gpmA; 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase [EC:5.4.2.11 ]
K03421 mcrC; methyl-coenzyme M reductase subunit C
K03422 mcrD; methyl-coenzyme M reductase subunit D
K03532 torC; trimethylamine-N-oxide reductase (cytochrome c), cytochrome c-type subunit TorC
K03533 torD; TorA specific chaperone
K04480 mtaB; methanol---5-hydroxybenzimidazolylcobamide Co-methyltransferase [EC:2.1.1.90 ]
K07072 mfnF; (4-(4-[2-(gamma-L-glutamylamino)ethyl]phenoxymethyl)furan-2-yl)methanamine synthase [EC:2.5.1.131 ]
K07144 mfnE; 5-(aminomethyl)-3-furanmethanol phosphate kinase [EC:2.7.4.31 ]
K07811 torA; trimethylamine-N-oxide reductase (cytochrome c) [EC:1.7.2.3 ]
K07812 torZ; trimethylamine-N-oxide reductase (cytochrome c) [EC:1.7.2.3 ]
K07821 torY; trimethylamine-N-oxide reductase (cytochrome c), cytochrome c-type subunit TorY
K10714 mtdB; methylene-tetrahydromethanopterin dehydrogenase [EC:1.5.1.-]
K10945 pmoB-amoB; methane/ammonia monooxygenase subunit B
K10946 pmoC-amoC; methane/ammonia monooxygenase subunit C
K10978 aksF; methanogen homoisocitrate dehydrogenase [EC:1.1.1.87 1.1.1.-]
K11260 fwdG; 4Fe-4S ferredoxin
K11261 fwdE, fmdE; formylmethanofuran dehydrogenase subunit E [EC:1.2.7.12 ]
K11780 cofG; 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase [EC:4.3.1.32 ]
K11781 cofH; 5-amino-6-(D-ribitylamino)uracil---L-tyrosine 4-hydroxyphenyl transferase [EC:2.5.1.147 ]
K12234 cofE; coenzyme F420-0:L-glutamate ligase / coenzyme F420-1:gamma-L-glutamate ligase [EC:6.3.2.31 6.3.2.34 ]
K13942 hmd; 5,10-methenyltetrahydromethanopterin hydrogenase [EC:1.12.98.2 ]
K14028 mdh1, mxaF; methanol dehydrogenase (cytochrome c) subunit 1 [EC:1.1.2.7 ]
K14029 mdh2, mxaI; methanol dehydrogenase (cytochrome c) subunit 2 [EC:1.1.2.7 ]
K14080 mtaA; [methyl-Co(III) methanol/glycine betaine-specific corrinoid protein]:coenzyme M methyltransferase [EC:2.1.1.246 2.1.1.377 ]
K14081 mtaC; methanol corrinoid protein
K14082 mtbA; [methyl-Co(III) methylamine-specific corrinoid protein]:coenzyme M methyltransferase [EC:2.1.1.247 ]
K14083 mttB; trimethylamine---corrinoid protein Co-methyltransferase [EC:2.1.1.250 ]
K14084 mttC; trimethylamine corrinoid protein
K14126 mvhA, vhuA, vhcA; F420-non-reducing hydrogenase large subunit [EC:1.12.99.- 1.8.98.5 ]
K14128 mvhG, vhuG, vhcG; F420-non-reducing hydrogenase small subunit [EC:1.12.99.- 1.8.98.5 ]
K15633 gpmI; 2,3-bisphosphoglycerate-independent phosphoglycerate mutase [EC:5.4.2.12 ]
K15634 gpmB; 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase [EC:5.4.2.11 ]
K15635 apgM; 2,3-bisphosphoglycerate-independent phosphoglycerate mutase [EC:5.4.2.12 ]
K16160 mmoB; methane monooxygenase regulatory protein B
K16162 mmoD; methane monooxygenase component D
K16176 mtmB; methylamine---corrinoid protein Co-methyltransferase [EC:2.1.1.248 ]
K16177 mtmC; monomethylamine corrinoid protein
K16178 mtbB; dimethylamine---corrinoid protein Co-methyltransferase [EC:2.1.1.249 ]
K16179 mtbC; dimethylamine corrinoid protein
K19793 mfnC; (5-formylfuran-3-yl)methyl phosphate transaminase [EC:2.6.1.108 ]
K21071 pfk, pfp; ATP-dependent phosphofructokinase / diphosphate-dependent phosphofructokinase [EC:2.7.1.11 2.7.1.90 ]
K22081 mgsA; methylamine---glutamate N-methyltransferase subunit A [EC:2.1.1.21 ]
K22082 mgsB; methylamine---glutamate N-methyltransferase subunit B [EC:2.1.1.21 ]
K22083 mgsC; methylamine---glutamate N-methyltransferase subunit C [EC:2.1.1.21 ]
K23995 xoxF; lanthanide-dependent methanol dehydrogenase
K24182 PFK9; 6-phosphofructokinase
K24393 comDE; sulfopyruvate decarboxylase
K24998 fbiB; dehydro coenzyme F420 reductase / coenzyme F420-0:L-glutamate ligase / coenzyme F420-1:gamma-L-glutamate ligase
K25123 hydA2; iron hydrogenase HydA2
K25124 hycB; FeS-containing electron transfer protein
K25528 ysaA; phosphoserine phosphatase
K28205 E2.6.1.52; phosphoserine transaminase
Compound C00118 D-Glyceraldehyde 3-phosphate
C00143 5,10-Methylenetetrahydrofolate
C00354 D-Fructose 1,6-bisphosphate
C01217 5,6,7,8-Tetrahydromethanopterin
C01274 5-Formyl-5,6,7,8-tetrahydromethanopterin
C03920 2-(Methylthio)ethanesulfonate
C04330 5,10-Methenyltetrahydromethanopterin
C04377 5,10-Methylenetetrahydromethanopterin
C04488 5-Methyl-5,6,7,8-tetrahydromethanopterin
C04732 5-Amino-6-(1-D-ribitylamino)uracil
C04832 Coenzyme M 7-mercaptoheptanoylthreonine-phosphate heterodisulfide
C06019 D-arabino-Hex-3-ulose 6-phosphate
C11536 (2R)-O-Phospho-3-sulfolactate
C14180 S-(Hydroxymethyl)glutathione
C16593 7-Mercaptoheptanoic acid
C16594 7-Mercaptoheptanoylthreonine
C16597 (-)-threo-Iso(homo)2-citrate
C16600 (-)-threo-Iso(homo)3-citrate
C18802 Tetrahydrosarcinapterin
C19154 7,8-Didemethyl-8-hydroxy-5-deazariboflavin
C19155 (2S)-Lactyl-2-diphospho-5'-guanosine
C20954 (5-Formylfuran-3-yl)methyl phosphate
C21068 [5-(Aminomethyl)furan-3-yl]methyl phosphate
C21069 [5-(Aminomethyl)furan-3-yl]methyl diphosphate
C21070 (4-{4-[2-(gamma-L-Glutamylamino)ethyl]phenoxymethyl}furan-2-yl)methanamine
C21971 5-Amino-5-(4-hydroxybenzyl)-6-(D-ribitylimino)-5,6-dihydrouracil
C22277 Dehydro coenzyme F420-0
C22297 Enolpyruvoyl-2-diphospho-5'-guanosine
Reference Authors Graham DE, Xu H, White RH
Title Identification of coenzyme M biosynthetic phosphosulfolactate synthase: a new family of sulfonate-biosynthesizing enzymes.
Journal Reference Authors Deppenmeier U
Title The membrane-bound electron transport system of Methanosarcina species.
Journal Reference Authors Hallam SJ, Putnam N, Preston CM, Detter JC, Rokhsar D, Richardson PM, DeLong EF
Title Reverse methanogenesis: testing the hypothesis with environmental genomics.
Journal Reference Authors Welander PV, Metcalf WW
Title Loss of the mtr operon in Methanosarcina blocks growth on methanol, but not methanogenesis, and reveals an unknown methanogenic pathway.
Journal Reference Authors Yurimoto H, Kato N, Sakai Y
Title Assimilation, dissimilation, and detoxification of formaldehyde, a central metabolic intermediate of methylotrophic metabolism.
Journal Reference Authors Fricke WF, Seedorf H, Henne A, Kruer M, Liesegang H, Hedderich R, Gottschalk G, Thauer RK.
Title 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 Reference Authors Kato N, Yurimoto H, Thauer RK
Title The physiological role of the ribulose monophosphate pathway in bacteria and archaea.
Journal Reference Authors Thauer RK, Kaster AK, Seedorf H, Buckel W, Hedderich R
Title Methanogenic archaea: ecologically relevant differences in energy conservation.
Journal Reference Authors Liffourrena AS, Salvano MA, Lucchesi GI
Title Pseudomonas putida A ATCC 12633 oxidizes trimethylamine aerobically via two different pathways.
Journal Related ko00010 Glycolysis / Gluconeogenesis
ko00260 Glycine, serine and threonine metabolism
ko00630 Glyoxylate and dicarboxylate metabolism
ko00720 Other carbon fixation pathways
