Carbon fixation

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Most phototrophic organisms can fix carbon for growth; they are photoautotrophic. These three phyla of green phototrophic Bacteria each use a different pathway for carbon (CO2) fixation: the Calvin cycle (cyanobacteria), reverse TCA cycle (Chlorobi) and the hydroxypropionate pathway (Chloroflexi). Although each is an entirely independent pathway, they share several fundamental features imposed by chemistry: they are cyclical, and require reductant and energy. Another, noncyclical pathway for carbon fixation is known from nonphototrophic acetogenic Bacteria and some methanogens; the reductive acetyl-CoA pathway.

Calvin cycle

The Calvin cycle is the most familiar and common carbon fixation pathway. The key enzyme in this pathway is ribulose bis-phosphate carboxylase/oxidase (“rubisco”), that carboxylates ribulose 1,5-bis-phosphate to form two molecules of 3-phosphoglycerate; this is the step in which CO2 is incorporated into organic carbon. After phosphorylation, the resulting 1,3-diphosphoglycerate is reduced glyceraldehyde 3-phosphate. The remainder of the steps are sugar rearrangements, using enzymes common in carbohydrate metabolism in most organisms, ending in the phosphorylation of ribulose 5-phosphate to regenerate ribulose 1,5-bis-phosphate. For each three molecules of ribulose 1,5-bis-phosphate that enter the cycle, 3 molecules of CO2 are fixed, generating a net of one molecule of glyceraldehyde 3-phosphate that can be siphoned off for metabolism after regenerating three more molecules of ribulose 1,5-bis-phosphate to close the cycle. This glyceraldehyde 3-phosphate feeds directly into general carbohydrate metabolism.

Calvin cycle

Reverse TCA cycle

Many autotrophic organisms that don’t use the Calvin cycle to fix carbon (e.g. the Chlorobi) use the reverse TCA cycle, also know as the reductive TCA cycle. This is the same pathway as the familiar TCA cycle, but all of the reactions are run in the reverse direction. The TCA cycle usually consumes pyruvate, generating ATP, NADH or NADPH, reduced ferridoxin, and waste CO2. The reverse TCA cycle therefore consumes CO2, ATP, NADH/NADPH and reduced ferridoxin to produce pyruvate. In the Chlorobi, two key steps use the oxidation of ferridoxin rather than NADH to drive the reactions in the reverse direction. The acetyl-CoA generated by this pathway can be used directly, or carboxylated further to produce pyruvate in a reverse of the “transition reaction”.

reverse TCA

Hydroxypropionate pathway

The Chloroflexi and many Crenarchaea use a third carbon fixation method, the hydroxypropionate pathway. Some of the reactions used in this pathway are common to the TCA cycle, but it is a unique pathway. The hydroxypropionate generates glyoxylate, which can feed into central metabolism after amidation to glycine.

hydroxypropionate pathway

Reductive acetyl-CoA pathway

Acetogenic Bacteria, as well as some sulfate reducers and some methanogenic Archaea, fix carbon using molecular hydrogen in the Wood reaction, also known as the reductive acetyl-CoA pathway. Unlike the other pathways for carbon fixation, the reductive acetyl-CoA pathway is not cyclic; it has two branches, one the formation of a methyl-corrinoid and the other the generation of carbon monoxide, that come together to produce acetyl-CoA. Unlike in the other pathways, the carbon from CO2 is carried through the reductive transformations on one-carbon carrier cofactors; tetrahydrofolate (in the case of Bacteria) or tetrahydromethanopterin (in the case of Archaea). This pathway is also unusual in that the electrons for reduction of CO2 come directly from hydrogenase rather than NADH or other reduced cofactors. As in the case of the reductive TCA pathway, acetyl-CoA produced can be further carboxylated (fixing another CO2 molecule) to pyruvate by the reverse of the transition reaction. Although acetogenic Bacteria fix carbon using this pathway, they also generate energy (in the form of ATP) using this same pathway, by cleaving acetate from the acetyl-CoA coupled to phosphorylation of ADP to ATP. This acetate is excreted as a waste product.

Wood reaction

This pathway shares many of the reactions of methanogenesis, in which the methyl group from methanopterin or the corrinoid protein would otherwise be transferred to coenzyme M, reduced one step further, and released as methane.