KEGG   PATHWAY: rfa00680
Entry
rfa00680                    Pathway                                
Name
Methane metabolism - Rhodococcus fascians D188
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 metabolism
Pathway map
rfa00680  Methane metabolism
rfa00680

Module
rfa_M00020  Serine biosynthesis, glycerate-3P => serine [PATH:rfa00680]
Other DBs
GO: 0015947
Organism
Rhodococcus fascians D188 [GN:rfa]
Gene
A3L23_00417  fdhA; Glutathione-independent formaldehyde dehydrogenase [KO:K00148] [EC:1.2.1.46]
A3L23_00307  Methanol:N,N-dimethyl-4-nitrosoaniline oxidoreductase [KO:K17067] [EC:1.2.98.1 1.1.99.37]
A3L23_01787  fdnI; Formate dehydrogenase, nitrate-inducible, cytochrome b556(Fdn) subunit [KO:K00127]
A3L23_03011  glyA1; Serine hydroxymethyltransferase 1 [KO:K00600] [EC:2.1.2.1]
A3L23_02144  glyA2; Serine hydroxymethyltransferase 2 [KO:K00600] [EC:2.1.2.1]
A3L23_00498  eno; Enolase [KO:K01689] [EC:4.2.1.11]
A3L23_04347  ppc; Phosphoenolpyruvate carboxylase [KO:K01595] [EC:4.1.1.31]
A3L23_00913  fba_1; Fructose-bisphosphate aldolase [KO:K01624] [EC:4.1.2.13]
A3L23_02579  fba_2; Fructose-bisphosphate aldolase [KO:K01624] [EC:4.1.2.13]
A3L23_03017  glpX; Fructose-1,6-bisphosphatase class 2 [KO:K02446] [EC:3.1.3.11]
A3L23_04741  pfkA; ATP-dependent 6-phosphofructokinase [KO:K21071] [EC:2.7.1.11 2.7.1.90]
A3L23_02647  ackA; Acetate kinase [KO:K00925] [EC:2.7.2.1]
A3L23_02646  pta; Phosphate acetyltransferase [KO:K13788] [EC:2.3.1.8]
A3L23_01437  acsA_3; Acetyl-coenzyme A synthetase [KO:K01895] [EC:6.2.1.1]
A3L23_02401  acsA_4; Acetyl-coenzyme A synthetase [KO:K01895] [EC:6.2.1.1]
A3L23_02793  gpmA; 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase [KO:K01834] [EC:5.4.2.11]
A3L23_01027  pspA_4; Phosphoserine phosphatase 1 [KO:K15634] [EC:5.4.2.11]
A3L23_01019  pspA_3; Phosphoserine phosphatase 1 [KO:K15634] [EC:5.4.2.11]
A3L23_04732  serA; D-3-phosphoglycerate dehydrogenase [KO:K00058] [EC:1.1.1.95 1.1.1.399]
A3L23_00703  serC; Phosphoserine aminotransferase [KO:K00831] [EC:2.6.1.52]
A3L23_04773  serB_2; Phosphoserine phosphatase [KO:K01079] [EC:3.1.3.3]
A3L23_04591  comB; putative 2-phosphosulfolactate phosphatase [KO:K05979] [EC:3.1.3.71]
A3L23_03076  fbiC; FO synthase [KO:K11779] [EC:2.5.1.147 4.3.1.32]
A3L23_04716  cofC; 2-phospho-L-lactate guanylyltransferase [KO:K14941] [EC:2.7.7.68 2.7.7.105]
A3L23_00047  cofD; 2-phospho-L-lactate transferase [KO:K11212] [EC:2.7.8.28]
A3L23_00048  fbiB_1; Coenzyme F420:L-glutamate ligase [KO:K24998] [EC:1.3.8.17 6.3.2.31 6.3.2.34]
Compound
C00011  CO2
C00022  Pyruvate
C00024  Acetyl-CoA
C00033  Acetate
C00036  Oxaloacetate
C00037  Glycine
C00048  Glyoxylate
C00058  Formate
C00065  L-Serine
C00067  Formaldehyde
C00074  Phosphoenolpyruvate
C00082  L-Tyrosine
C00085  D-Fructose 6-phosphate
C00101  Tetrahydrofolate
C00111  Glycerone phosphate
C00118  D-Glyceraldehyde 3-phosphate
C00132  Methanol
C00143  5,10-Methylenetetrahydrofolate
C00149  (S)-Malate
C00168  Hydroxypyruvate
C00184  Glycerone
C00197  3-Phospho-D-glycerate
C00199  D-Ribulose 5-phosphate
C00218  Methylamine
C00227  Acetyl phosphate
C00231  D-Xylulose 5-phosphate
C00237  CO
C00258  D-Glycerate
C00322  2-Oxoadipate
C00354  D-Fructose 1,6-bisphosphate
C00483  Tyramine
C00543  Dimethylamine
C00565  Trimethylamine
C00593  Sulfoacetaldehyde
C00631  2-Phospho-D-glycerate
C00862  Methanofuran
C00876  Coenzyme F420
C01001  Formylmethanofuran
C01005  O-Phospho-L-serine
C01031  S-Formylglutathione
C01046  N-Methyl-L-glutamate
C01080  Reduced coenzyme F420
C01104  Trimethylamine N-oxide
C01217  5,6,7,8-Tetrahydromethanopterin
C01274  5-Formyl-5,6,7,8-tetrahydromethanopterin
C01438  Methane
C03232  3-Phosphonooxypyruvate
C03576  Coenzyme M
C03920  2-(Methylthio)ethanesulfonate
C04330  5,10-Methenyltetrahydromethanopterin
C04348  L-Malyl-CoA
C04377  5,10-Methylenetetrahydromethanopterin
C04488  5-Methyl-5,6,7,8-tetrahydromethanopterin
C04628  Coenzyme B
C04732  5-Amino-6-(1-D-ribitylamino)uracil
C04832  Coenzyme M 7-mercaptoheptanoylthreonine-phosphate heterodisulfide
C05528  3-Sulfopyruvate
C06019  D-arabino-Hex-3-ulose 6-phosphate
C11536  (2R)-O-Phospho-3-sulfolactate
C11537  (2R)-3-Sulfolactate
C14180  S-(Hydroxymethyl)glutathione
C16583  (R)-(Homo)2-citrate
C16588  2-Oxopimelate
C16589  2-Oxosuberate
C16590  7-Oxoheptanoic acid
C16593  7-Mercaptoheptanoic acid
C16594  7-Mercaptoheptanoylthreonine
C16597  (-)-threo-Iso(homo)2-citrate
C16598  (R)-(Homo)3-citrate
C16600  (-)-threo-Iso(homo)3-citrate
C18799  5-Methyl-H4SPT
C18802  Tetrahydrosarcinapterin
C19151  Coenzyme F420-3
C19152  Coenzyme F420-1
C19153  Coenzyme F420-0
C19154  7,8-Didemethyl-8-hydroxy-5-deazariboflavin
C19155  (2S)-Lactyl-2-diphospho-5'-guanosine
C19156  (2S)-2-Phospholactate
C20581  cis-(Homo)2-aconitate
C20582  cis-(Homo)3-aconitate
C20926  gamma-Glutamyltyramine
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
J Biol Chem 277:13421-9 (2002)
DOI:10.1074/jbc.M201011200
Reference
  Authors
Deppenmeier U
  Title
The membrane-bound electron transport system of Methanosarcina species.
  Journal
J Bioenerg Biomembr 36:55-64 (2004)
DOI:10.1023/B:JOBB.0000019598.64642.97
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
Science 305:1457-62 (2004)
DOI:10.1126/science.1100025
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
Proc Natl Acad Sci U S A 102:10664-9 (2005)
DOI:10.1073/pnas.0502623102
Reference
  Authors
Yurimoto H, Kato N, Sakai Y
  Title
Assimilation, dissimilation, and detoxification of formaldehyde, a central metabolic intermediate of methylotrophic metabolism.
  Journal
Chem Rec 5:367-75 (2005)
DOI:10.1002/tcr.20056
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
J Bacteriol 188:642-58 (2006)
DOI:10.1128/JB.188.2.642-658.2006
Reference
  Authors
Kato N, Yurimoto H, Thauer RK
  Title
The physiological role of the ribulose monophosphate pathway in bacteria and archaea.
  Journal
Biosci Biotechnol Biochem 70:10-21 (2006)
DOI:10.1271/bbb.70.10
Reference
  Authors
Thauer RK, Kaster AK, Seedorf H, Buckel W, Hedderich R
  Title
Methanogenic archaea: ecologically relevant differences in energy conservation.
  Journal
Nat Rev Microbiol 6:579-91 (2008)
DOI:10.1038/nrmicro1931
Reference
  Authors
Liffourrena AS, Salvano MA, Lucchesi GI
  Title
Pseudomonas putida A ATCC 12633 oxidizes trimethylamine aerobically via two different pathways.
  Journal
Arch Microbiol 192:471-6 (2010)
DOI:10.1007/s00203-010-0577-5
Related
pathway
rfa00010  Glycolysis / Gluconeogenesis
rfa00030  Pentose phosphate pathway
rfa00260  Glycine, serine and threonine metabolism
rfa00300  Lysine biosynthesis
rfa00630  Glyoxylate and dicarboxylate metabolism
rfa00720  Other carbon fixation pathways
rfa00740  Riboflavin metabolism
rfa00790  Folate biosynthesis
rfa00910  Nitrogen metabolism
rfa00920  Sulfur metabolism
KO pathway
ko00680   
LinkDB

DBGET integrated database retrieval system