KEGG   PATHWAY: ret00720
Entry
ret00720                    Pathway                                
Name
Other carbon fixation pathways - Rhizobium etli CFN 42
Description
Carbon fixation is an important pathway for autotrophs living in various environments. Plants and cyanobacteria fix CO2 as organic compounds using solar energy mainly by the reductive pentose phosphate cycle (also called Calvin cycle, Calvin-Benson cycle, or Calvin-Benson-Bassham cycle) [MD:M00165]. There are, at least, five additional carbon fixation pathways known to exist in autotrophic bacteria and archaea, which differ in reducing compounds, energy source, and oxygen sensitivity of enzymes. (i) The reductive citric acid cycle (Arnon-Buchanan cycle) [MD:M00173] is found in microaerophiles and anaerobes, such as green sulfur bacteria. In one complete turn of this cycle, four molecules of CO2 are fixed by the enzymes that are sensitive to oxygen, resulting in the production of one molecule of oxaloacetate, which is itself an intermediate of the cycle. (ii) The reductive acetyl-CoA pathway (Wood-Ljungdahl pathway) [MD:M00377] is found in strictly anaerobic bacteria and archaea (Proteobacteria, Planctomycetes, Spirochaetes, and Euryarchaeota), some of which are methane-forming. A bifunctional enzyme, carbon monoxide dehydrogenase/acetyl-CoA synthase, catalyzes the reactions from CO2 to CO and from CO2 to a methyl group, and then to generate acetyl-CoA. (iii) The 3-hydroxypropionate bicycle [MD:M00376] is found in some green non-sulphur bacteria of the family Chloroflexaceae. In one complete turn of this bicycle, three molecules of bicarbonate are converted into one molecule of pyruvate. In addition, this bicycle provides the secondary benefit of useful intermediates for biosynthesis: acetyl-CoA, glyoxylate, and succinyl-CoA. (iv) The hydroxypropionate-hydroxybutyrate cycle [MD:M00375] is found in aerobic Crenarchaeota, Acidianus, Metallosphaera, and Sulfolobales. Some of the intermediates and the carboxylation reactions are the same as in the 3-hydroxypropionate bicycle. One complete turn of this cycle generates two molecules of acetyl-CoA, one of which is reutilized in the the cycle and the other is removed for cell material biosynthesis. (v) The dicarboxylate-hydroxybutyrate cycle [MD:M00374] was named after its intermediates: succinate (a kind of dicarboxylate) and hydroxybutyrate. This cycle has been found only in Ignicoccus hospitals, a strictly anaerobic hyperthermophilic archaea. Recent genome study suggests that this cycle may exist in Desulfurococcales (to which Ignicoccus belongs) and Thermoproteales (a taxon close to the origin of archaea). The first half of the cycle, from acetyl-CoA to succinate-CoA, corresponds to the reductive citric acid cycle and the latter half of the cycle, from succinate-CoA to two molecules of acetyl-CoA, corresponds to the hydroxypropionate-hydroxybutyrate cycle.
Class
Metabolism; Energy metabolism
Pathway map
ret00720  Other carbon fixation pathways
ret00720

Other DBs
GO: 0015977
Organism
Rhizobium etli CFN 42 [GN:ret]
Gene
RHE_CH00023  accD; acetyl-CoA carboxylase, carboxil transferase beta subunit protein [KO:K01963] [EC:6.4.1.2 2.1.3.15]
RHE_CH00558  fadA; acyl-CoA thiolase protein [KO:K00626] [EC:2.3.1.9]
RHE_CH00694  folDch; methylenetetrahydrofolate dehydrogenase/cyclohydrolase protein [KO:K01491] [EC:1.5.1.5 3.5.4.9]
RHE_CH01003  ppdK; pyruvate phosphate dikinase protein [KO:K01006] [EC:2.7.9.1]
RHE_CH01622  [KO:K05606] [EC:5.1.99.1]
RHE_CH01869  accCch; acetyl-CoA carboxylase, biotin carboxylase protein [KO:K01961] [EC:6.4.1.2 6.3.4.14]
RHE_CH01870  accBch; acetyl-CoA carboxylase, biotin carboxyl carrier protein [KO:K02160]
RHE_CH02383  fumC; fumarate hydratase class II protein [KO:K01679] [EC:4.2.1.2]
RHE_CH02385  fumB; fumarate hydratase class I protein [KO:K01676] [EC:4.2.1.2]
RHE_CH02871  metF; 5,10-methylenetetrahydrofolate reductase protein [KO:K00297] [EC:1.5.1.54]
RHE_CH03078  fhs; formate-tetrahydrofolate ligase protein [KO:K01938] [EC:6.3.4.3]
RHE_CH03441  ackA; acetate kinase protein [KO:K00925] [EC:2.7.2.1]
RHE_CH03773  [KO:K01895] [EC:6.2.1.1]
RHE_CH03828  accA; acetyl-CoA carboxylase carboxyl transferase, alpha subunit protein [KO:K01962] [EC:6.4.1.2 2.1.3.15]
RHE_CH03889  sucD; succinyl-CoA synthetase alpha subunit protein [KO:K01902] [EC:6.2.1.5]
RHE_CH03890  sucC; succinyl-CoA synthetase beta subunit protein [KO:K01903] [EC:6.2.1.5]
RHE_CH03891  mdh; malate dehydrogenase protein [KO:K00024] [EC:1.1.1.37]
RHE_CH03894  sdhB; succinate dehydrogenase subunit B, iron-sulfur protein [KO:K00240] [EC:1.3.5.1]
RHE_CH03895  sdhA; succinate dehydrogenase, flavoprotein subunit protein [KO:K00239] [EC:1.3.5.1]
RHE_CH03896  sdhD; succinate dehydrogenase subunit D, membrane anchor protein [KO:K00242]
RHE_CH03897  sdhC; succinate dehydrogenase cytochrome B-556 subunit protein [KO:K00241]
RHE_CH03944  acnA; aconitate hydratase (citrate hydro-lyase) protein [KO:K27802]
RHE_CH04002  pyc; pyruvate carboxylase protein [KO:K01958] [EC:6.4.1.1]
RHE_CH04018  phbAch; acetyl-CoA acetyltransferase (beta-ketothiolase) protein [KO:K00626] [EC:2.3.1.9]
RHE_CH04112  acsA2; acetyl-CoA synthetase protein [KO:K01895] [EC:6.2.1.1]
RHE_PB00157  bhbA; methylmalonyl-CoA mutase protein [KO:K01847] [EC:5.4.99.2]
RHE_PC00068  [KO:K00626] [EC:2.3.1.9]
RHE_PC00191  accCc; acetyl-CoA carboxylase, biotin carboxylase protein [KO:K01961] [EC:6.4.1.2 6.3.4.14]
RHE_PC00192  accBc; acetyl-CoA carboxylase, biotin carboxyl carrier protein [KO:K02160]
RHE_PE00416  folDe; methylenetetrahydrofolate dehydrogenase/cyclohydrolase protein [KO:K01491] [EC:1.5.1.5 3.5.4.9]
RHE_PF00014  phbAf; acetyl-CoA acetyltransferase (beta-ketothiolase) protein [KO:K00626] [EC:2.3.1.9]
Compound
C00011  CO2
C00022  Pyruvate
C00024  Acetyl-CoA
C00026  2-Oxoglutarate
C00033  Acetate
C00036  Oxaloacetate
C00042  Succinate
C00048  Glyoxylate
C00058  Formate
C00074  Phosphoenolpyruvate
C00083  Malonyl-CoA
C00091  Succinyl-CoA
C00100  Propanoyl-CoA
C00101  Tetrahydrofolate
C00122  Fumarate
C00143  5,10-Methylenetetrahydrofolate
C00149  (S)-Malate
C00158  Citrate
C00222  3-Oxopropanoate
C00227  Acetyl phosphate
C00232  Succinate semialdehyde
C00234  10-Formyltetrahydrofolate
C00237  CO
C00288  HCO3-
C00311  Isocitrate
C00332  Acetoacetyl-CoA
C00417  cis-Aconitate
C00440  5-Methyltetrahydrofolate
C00445  5,10-Methenyltetrahydrofolate
C00566  (3S)-Citryl-CoA
C00683  (S)-Methylmalonyl-CoA
C00877  Crotonoyl-CoA
C00894  Propenoyl-CoA
C00989  4-Hydroxybutanoic acid
C01011  (3S)-Citramalyl-CoA
C01013  3-Hydroxypropanoate
C01144  (S)-3-Hydroxybutanoyl-CoA
C01213  (R)-Methylmalonyl-CoA
C04348  L-Malyl-CoA
C05668  3-Hydroxypropionyl-CoA
C06027  L-erythro-3-Methylmalyl-CoA
C06028  2-Methylfumaryl-CoA
C11062  4-Hydroxybutyryl-CoA
C18323  3-Methylfumaryl-CoA
Reference
  Authors
Zarzycki J, Brecht V, Muller M, Fuchs G
  Title
Identifying the missing steps of the autotrophic 3-hydroxypropionate CO2 fixation cycle in Chloroflexus aurantiacus.
  Journal
Proc Natl Acad Sci U S A 106:21317-22 (2009)
DOI:10.1073/pnas.0908356106
Reference
  Authors
Teufel R, Kung JW, Kockelkorn D, Alber BE, Fuchs G
  Title
3-hydroxypropionyl-coenzyme A dehydratase and acryloyl-coenzyme A reductase, enzymes of the autotrophic 3-hydroxypropionate/4-hydroxybutyrate cycle in the Sulfolobales.
  Journal
J Bacteriol 191:4572-81 (2009)
DOI:10.1128/JB.00068-09
Reference
  Authors
Huber H, Gallenberger M, Jahn U, Eylert E, Berg IA, Kockelkorn D, Eisenreich W, Fuchs G
  Title
A dicarboxylate/4-hydroxybutyrate autotrophic carbon assimilation cycle in the hyperthermophilic Archaeum Ignicoccus hospitalis.
  Journal
Proc Natl Acad Sci U S A 105:7851-6 (2008)
DOI:10.1073/pnas.0801043105
Reference
  Authors
Hugler M, Wirsen CO, Fuchs G, Taylor CD, Sievert SM
  Title
Evidence for autotrophic CO2 fixation via the reductive tricarboxylic acid cycle by members of the epsilon subdivision of proteobacteria.
  Journal
J Bacteriol 187:3020-7 (2005)
DOI:10.1128/JB.187.9.3020-3027.2005
Reference
  Authors
Seravalli J, Kumar M, Ragsdale SW
  Title
Rapid kinetic studies of acetyl-CoA synthesis: evidence supporting the catalytic intermediacy of a paramagnetic NiFeC species in the autotrophic Wood-Ljungdahl pathway.
  Journal
Biochemistry 41:1807-19 (2002)
DOI:10.1021/bi011687i
Reference
PMID:3096193
  Authors
Ljungdahl LG
  Title
The autotrophic pathway of acetate synthesis in acetogenic bacteria.
  Journal
Annu Rev Microbiol 40:415-50 (1986)
DOI:10.1146/annurev.mi.40.100186.002215
Related
pathway
ret00710  Carbon fixation by Calvin cycle
KO pathway
ko00720   

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