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Carbon fixation pathways in prokaryotes
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.
Metabolism; Energy metabolism
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Pathway map
ec00720  Carbon fixation pathways in prokaryotes

Ortholog table
M00173  Reductive citrate cycle (Arnon-Buchanan cycle) [PATH:ec00720]
M00374  Dicarboxylate-hydroxybutyrate cycle [PATH:ec00720]
M00375  Hydroxypropionate-hydroxybutylate cycle [PATH:ec00720]
M00376  3-Hydroxypropionate bi-cycle [PATH:ec00720]
M00377  Reductive acetyl-CoA pathway (Wood-Ljungdahl pathway) [PATH:ec00720]
M00579  Phosphate acetyltransferase-acetate kinase pathway, acetyl-CoA => acetate [PATH:ec00720]
M00620  Incomplete reductive citrate cycle, acetyl-CoA => oxoglutarate [PATH:ec00720]
Other DBs
GO: 0015977
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
Zarzycki J, Brecht V, Muller M, Fuchs G
Identifying the missing steps of the autotrophic 3-hydroxypropionate CO2 fixation cycle in Chloroflexus aurantiacus.
Proc Natl Acad Sci U S A 106:21317-22 (2009)
Teufel R, Kung JW, Kockelkorn D, Alber BE, Fuchs G
3-hydroxypropionyl-coenzyme A dehydratase and acryloyl-coenzyme A reductase, enzymes of the autotrophic 3-hydroxypropionate/4-hydroxybutyrate cycle in the Sulfolobales.
J Bacteriol 191:4572-81 (2009)
Huber H, Gallenberger M, Jahn U, Eylert E, Berg IA, Kockelkorn D, Eisenreich W, Fuchs G
A dicarboxylate/4-hydroxybutyrate autotrophic carbon assimilation cycle in the hyperthermophilic Archaeum Ignicoccus hospitalis.
Proc Natl Acad Sci U S A 105:7851-6 (2008)
Hugler M, Wirsen CO, Fuchs G, Taylor CD, Sievert SM
Evidence for autotrophic CO2 fixation via the reductive tricarboxylic acid cycle by members of the epsilon subdivision of proteobacteria.
J Bacteriol 187:3020-7 (2005)
Seravalli J, Kumar M, Ragsdale SW
Rapid kinetic studies of acetyl-CoA synthesis: evidence supporting the catalytic intermediacy of a paramagnetic NiFeC species in the autotrophic Wood-Ljungdahl pathway.
Biochemistry 41:1807-19 (2002)
Ljungdahl LG
The autotrophic pathway of acetate synthesis in acetogenic bacteria.
Annu Rev Microbiol 40:415-50 (1986)

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