Microbial Inorganic Carbon Fixation

Abstract

Carbon dioxide fixation is the biological process through which carbon dioxide is converted to organic compounds. Organisms that fix carbon dioxide provide the organic carbon necessary to support the existence of all heterotrophic life on our planet. This article provides an introduction to the various mechanisms of carbon dioxide fixation utilised by microorganisms. The Calvin–Benson–Bassham cycle is shared among plants, algae and many photo‐ and chemoautotrophic bacteria, and is probably the most well known carbon dioxide‐fixation pathway. However, a number of other pathways exist that are unique to the microbial world and the diverse chemistry and strategies they utilise are fascinating. Among the six carbon‐fixing pathways known at present, three pathways harbouring novel enzymes have just been established in the past few years. With the number and diversity of microorganisms still expanding, the possibilities are high that further novel pathways will be identified in the near future.

Key Concepts:

  • Carbon dioxide fixation is the biological process through which carbon dioxide is converted to organic compounds.

  • Organisms that fix carbon dioxide provide the organic carbon necessary to support the existence of all heterotrophic life on our planet.

  • In addition to the Calvin–Benson–Bassham cycle, which is also found in plants and microorganisms harbour a number of unique carbon dioxide‐fixing pathways.

Keywords: carbon dioxide fixation; Calvin–Benson–Bassham cycle; reductive tricarboxylic acid cycle; reductive acetyl‐CoA pathway; 3‐hydroxypropionate/malyl‐CoA cycle; 3‐hydroxypropionate/4‐hydroxybutyrate cycle; dicarboxylate/4‐hydroxybutyrate cycle; archaea; rubisco; autotrophy

Figure 1.

Diagram illustrating the reactions of the Calvin–Benson–Bassham cycle. The corresponding enzymes are: 1: ribulose‐1,5‐bisphosphate carboxylase/oxygenase, 2: phosphoglycerate kinase, 3: glyceraldehyde‐3‐phosphate dehydrogenase, 4: triose phosphate isomerase, 5: fructose‐bisphosphate aldolase, 6: fructose‐1,6‐bisphosphatase, 7: sedoheptulose bisphosphatase, 8: transketolase, 9: ribose‐5‐phosphate isomerase, 10: ribulose‐5‐phosphate 3‐epimerase and 11: phosphoribulokinase. The directions of the arrows represent the direction of the pathway, and do not indicate that the enzyme reactions are irreversible.

Figure 2.

Diagram illustrating the reactions of the reductive tricarboxylic acid cycle. The corresponding enzymes are: 1: malate dehydrogenase, 2: fumarate hydratase, 3: fumarate reductase, 4: succinyl‐CoA synthetase (acetyl‐CoA: succinate CoA transferase is used in Desulfobacter hydrogenophilus), 5: oxoglutarate synthase, 6: isocitrate dehydrogenase, 7: aconitate hydratase, 8: ATP‐citrate lyase, 9: pyruvate synthase, 10: pyruvate carboxylase, 11: phosphoenolpyruvate synthase and 12: phosphoenolpyruvate carboxylase. The directions of the arrows represent the direction of the pathway, and do not indicate that the enzyme reactions are irreversible.

Figure 3.

Diagram illustrating the reactions of the reductive acetyl‐CoA pathway. Coloured pathways indicate related enzymes involved in methanogenesis and acetogenesis. The corresponding enzymes are: 1: formate dehydrogenase, 2: formyl‐H4FA‐synthase, 3: methenyl‐H4FA‐cyclohydrolase, 4: methylene‐H4FA‐dehydrogenase, 5: methylene‐H4FA‐reductase, 6: methyltransferase, 7: carbon monooxide dehydrogenase/acetyl‐CoA synthase, 8: phosphotransacetylase, 9: acetate kinase, 10: formylMF dehydrogenase, 11: formylMF:H4MPT formyltransferase, 12: N5, N10‐methenyl‐H4MPT cyclohydrolase, 13: N5, N10‐methylene‐H4MPT dehydrogenase, 14: N5, N10‐methylene‐H4MPT reductase, 15: N5‐methyl‐H4MPT:coenzyme M methyltransferase, 16: methyl‐coenzyme M reductase and 17: heterodisulfide reductase. The directions of the arrows represent the direction of the pathway, and do not indicate that the enzyme reactions are irreversible. Abbreviations are: H4FA, tetrahydrofolate; MF, methanofuran; H4MPT, tetrahydromethanopterin; CoFe/S‐P, corrinoid‐iron sulfur protein.

Figure 4.

Diagram illustrating the reactions of the 3‐hydroxypropionate/malyl‐CoA cycle. The corresponding enzymes are: 1: acetyl‐CoA carboxylase, 2: malonyl‐CoA reductase, 3: propionyl‐CoA synthase, 4: propionyl‐CoA carboxylase, 5: methylmalonyl‐CoA epimerase, 6: methylmalonyl‐CoA mutase, 7: succinyl‐CoA:(S)‐malate‐CoA transferase, 8: succinate dehydrogenase, 9: fumarate hydratase, 10‐1, 10‐2, 10‐3: (S)‐malyl‐CoA/β‐methylmalyl‐CoA/(S)‐citramalyl‐CoA (MMC) lyase, 11: mesaconyl‐C1‐CoA hydratase (β‐methylmalyl‐CoA dehydratase), 12: mesaconyl‐CoA C1‐C4 CoA transferase and 13: mesaconyl‐C4‐CoA hydratase. The directions of the arrows represent the direction of the pathway, and do not indicate that the enzyme reactions are irreversible.

Figure 5.

Diagram illustrating the reactions of the 3‐hydroxypropionate/4‐hydroxybutyrate cycle. The corresponding enzymes are: 1: acetyl‐CoA carboxylase, 2: malonyl‐CoA reductase, 3: malonate semialdehyde reductase, 4: 3‐hydroxypropionyl‐CoA synthetase, 5: 3‐hydroxypropionyl‐CoA dehydratase, 6: acryloyl‐CoA reductase, 7: propionyl‐CoA carboxylase, 8: methylmalonyl‐CoA epimerase, 9: methylmalonyl‐CoA mutase, 10: succinyl‐CoA reductase, 11: succinate semialdehyde reductase, 12: 4‐hydroxybutyryl‐CoA synthetase, 13: 4‐hydroxybutyryl‐CoA dehydratase, 14: crotonyl‐CoA hydratase, 15: 3‐hydroxybutyryl‐CoA dehydrogenase and 16: acetoacetyl‐CoA β‐ketothiolase. The directions of the arrows represent the direction of the pathway, and do not indicate that the enzyme reactions are irreversible.

Figure 6.

Diagram illustrating the reactions of the dicarboxylate/4‐hydroxybutyrate cycle. The corresponding enzymes are: 1: pyruvate synthase, 2: pyruvate:water dikinase, 3: phosphoenolpyruvate carboxylase, 4: malate dehydrogenase, 5: fumarate hydratase, 6: fumarate reductase, 7: succinate thiokinase, 8: succinyl‐CoA reductase, 9: succinate semialdehyde reductase, 10: 4‐hydroxybutyryl‐CoA synthetase, 11: 4‐hydroxybutyryl‐CoA dehydratase, 12: crotonyl‐CoA hydratase, 13: 3‐hydroxybutyryl‐CoA dehydrogenase and 14: acetoacetyl‐CoA β‐ketothiolase. The directions of the arrows represent the direction of the pathway, and do not indicate that the enzyme reactions are irreversible.

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Further Reading

Berg IA, Kockelkorn D, Ramos‐Vera WH et al. (2010) Autotrophic carbon fixation in biology: pathways, rules, and speculations. In: Aresta M (ed) Carbon Dioxide as Chemical Feedstock, pp. 33–53. Hoboken, NJ: Wiley InterScience.

Fuchs G (2009) Section III: Diversity of metabolic pathways. In: Lengeler JW, Drews G and Schlegel HG (eds) Biology of the Prokaryotes. Hoboken, NJ: Wiley InterScience.

Thauer RK and Shima S (2007) Methyl‐coenzyme M reductase in methanogens and methanotrophs. In: Garrett RA and Klenk H‐P (eds) Archaea: Evolution, Physiology, and Molecular Biology, 1st edn. Hoboken, NJ: Wiley InterScience.

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Sato, Takaaki, and Atomi, Haruyuki(Sep 2010) Microbial Inorganic Carbon Fixation. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0021900]