Biological carbon fixation

Biological carbon fixation, or carbon assimilation, is the process by which living organisms convert inorganic carbon to organic compounds. These organic compounds are then used to store energy and as structures for other biomolecules. Carbon is primarily fixed through photosynthesis, but some organisms use chemosynthesis in the absence of sunlight. Chemosynthesis is carbon fixation driven by chemical energy rather than from sunlight.
The process of biological carbon fixation plays a crucial role in the global carbon cycle, as it serves as the primary mechanism for removing from the atmosphere and incorporating it into living biomass. The primary production of organic compounds allows carbon to enter the biosphere. Carbon is considered essential for life as a base element for building organic compounds. The flow of carbon from the Earth's atmosphere, oceans and lithosphere into lifeforms and then back into the air, water and soil is one of the key biogeochemical cycles. Understanding biological carbon fixation is essential for comprehending , climate regulation, and the sustainability of life on Earth.
Organisms that grow by fixing carbon, such as most plants and algae, are called autotrophs. These include photoautotrophs and lithoautotrophs. Heterotrophs, such as animals and fungi, are not capable of carbon fixation but are able to grow by consuming the carbon fixed by autotrophs or other heterotrophs.
Seven natural autotrophic carbon fixation pathways are currently known:
"Fixed carbon," "reduced carbon," and "organic carbon" may all be used interchangeably to refer to various organic compounds.

Net vs. gross CO₂ fixation

The primary form of fixed inorganic carbon is carbon dioxide. It is estimated that approximately 250 billion tons of carbon dioxide are converted by photosynthesis annually, nearly one half in the oceans and a bit more in terrestrial environments. The majority of the fixation in terrestrial environments occurs in the tropics. The gross amount of carbon dioxide fixed is much larger since approximately 40% is consumed by respiration following photosynthesis. Historically, it is estimated that approximately 2×10¹¹ billion tons of carbon has been fixed since the origin of life.

Overview of the carbon fixation cycles

Seven autotrophic carbon fixation pathways are known: the Calvin Cycle, the Reverse Krebs Cycle, the reductive acetyl-CoA, the 3-HP bicycle, the 3-HP/4-HB cycle, the DC/4-HB cycles, and the reductive glycine pathway.
The organisms the [|Calvin cycle] is found in are plants, algae, cyanobacteria, aerobic proteobacteria, and purple bacteria. The Calvin cycle fixes carbon in the chloroplasts of plants and algae, and in the cyanobacteria. It also fixes carbon in the anoxygenic photosynthesis in one type of Pseudomonadota called purple bacteria, and in some non-phototrophic Pseudomonadota.
Of the other autotrophic pathways, three are known only in bacteria, two only in archaea, and one in both bacteria and archaea. Sulfur- and hydrogen-oxidizing bacteria often use the Calvin cycle or the reductive citric acid cycle.

List of pathways

Calvin cycle

The Calvin cycle accounts for 90% of biological carbon fixation. Consuming adenosine triphosphate and nicotinamide adenine dinucleotide phosphate, the Calvin cycle in plants accounts for the predominance of carbon fixation on land. In algae and cyanobacteria, it accounts for the dominance of carbon fixation in the oceans. The Calvin cycle converts carbon dioxide into sugar, as triose phosphate, which is glyceraldehyde 3-phosphate together with dihydroxyacetone phosphate :
An alternative perspective accounts for NADPH and ATP:
The formula for inorganic phosphate is HOPO₃²⁻ + 2 H⁺.
Formulas for triose and TP are C₂H₃O₂-CH₂OH and C₂H₃O₂-CH₂OPO₃²⁻ + 2 H⁺.

Reverse Krebs cycle

The reverse Krebs cycle, also known as the reverse TCA cycle or reductive citric acid cycle, is an alternative to the standard Calvin-Benson cycle for carbon fixation. It has been found in strict anaerobic or microaerobic bacteria and anaerobic archea. It was discovered by Evans, Buchanan and Arnon in 1966 working with the photosynthetic green sulfur bacterium Chlorobium limicola. In particular, it is one of the most used pathways in hydrothermal vents by the Campylobacterota. This feature allows primary production in the ocean's aphotic environments, or "dark primary production." Without it, there would be no primary production in aphotic environments, which would lead to habitats without life.
The cycle involves the biosynthesis of acetyl-CoA from two molecules of CO₂. The key steps of the reverse Krebs cycle are:

Oxaloacetate to malate, using NADH + H⁺
:
Fumarate to succinate, catalyzed by an oxidoreductase, Fumarate reductase
:
Succinate to succinyl-CoA, an ATP-dependent step
:
Succinyl-CoA to alpha-ketoglutarate, using one molecule of CO₂
:
Alpha-ketoglutarate to isocitrate, using NADPH + H⁺ and another molecule of CO₂
:
Citrate converted into oxaloacetate and acetyl-CoA, this is an ATP dependent step and the key enzyme is the ATP citrate lyase
:

This pathway is cyclic due to the regeneration of the oxaloacetate.
The bacteria Gammaproteobacteria and Riftia pachyptila switch from the Calvin-Benson cycle to the rTCA cycle in response to concentrations of H₂S.

Reductive acetyl CoA pathway

The reductive acetyl CoA pathway pathway, also known as the Wood-Ljungdahl pathway uses CO₂ as electron acceptor and carbon source, and H₂ as an electron donor to form acetic acid. This metabolism is widespread within the phylum Bacillota, especially in the Clostridia.
The pathway is also used by methanogens, which are mainly Euryarchaeota, and several anaerobic chemolithoautotrophs, such as sulfate-reducing bacteria and archaea. It is probably performed also by the Brocadiales, an order of Planctomycetota that oxidize ammonia in anaerobic conditions. Hydrogenotrophic methanogenesis, which is only found in certain archaea and accounts for 80% of global methanogenesis, is also based on the reductive acetyl CoA pathway.
The Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase is the oxygen-sensitive enzyme that permits the reduction of CO₂ to CO and the synthesis of acetyl-CoA in several reactions.
One branch of this pathway, the methyl branch, is similar but non-homologous between bacteria and archaea. In this branch happens the reduction of CO₂ to a methyl residue bound to a cofactor. The intermediates are formate for bacteria and formyl-methanofuran for archaea, and also the carriers, tetrahydrofolate and tetrahydropterins respectively in bacteria and archaea, are different, such as the enzymes forming the cofactor-bound methyl group.
Otherwise, the carbonyl branch is homologous between the two domains and consists of the reduction of another molecule of CO₂ to a carbonyl residue bound to an enzyme, catalyzed by the CO dehydrogenase/acetyl-CoA synthase. This key enzyme is also the catalyst for the formation of acetyl-CoA starting from the products of the previous reactions, the methyl and the carbonyl residues.
This carbon fixation pathway requires only one molecule of ATP for the production of one molecule of pyruvate, which makes this process one of the main choice for chemolithoautotrophs limited in energy and living in anaerobic conditions.

3-Hydroxypropionate (3-HP) bicycle

The 3-hydroxypropionate bicycle, also known as 3-HP/malyl-CoA cycle, discovered only in 1989, is utilized by green non-sulfur phototrophs of Chloroflexaceae family, including the maximum exponent of this family Chloroflexus auranticus by which this way was discovered and demonstrated. The 3-hydroxypropionate bicycle is composed of two cycles, and the name of this way comes from the 3-hydroxypropionate, which corresponds to an intermediate characteristic of it.
The first cycle is a way of synthesis of glyoxylate. During this cycle, two equivalents of bicarbonate are fixed by the action of two enzymes: the acetyl-CoA carboxylase catalyzes the carboxylation of the acetyl-CoA to malonyl-CoA and propionyl-CoA carboxylase catalyses the carboxylation of propionyl-CoA to methylamalonyl-CoA. From this point, a series of reactions lead to the formation of glyoxylate, which will thus become part of the second cycle.
In the second cycle, glyoxylate is approximately one equivalent of propionyl-CoA forming methylamalonyl-CoA. This, in turn, is then converted through a series of reactions into citramalyl-CoA. The citramalyl-CoA is split into pyruvate and acetyl-CoA thanks to the enzyme MMC lyase. The pyruvate is released at this point, while the acetyl-CoA is reused and carboxylated again at malonyl-CoA, thus reconstituting the cycle.
A total of 19 reactions are involved in the 3-hydroxypropionate bicycle, and 13 multifunctional enzymes are used. The multi-functionality of these enzymes is an important feature of this pathway which thus allows the fixation of three bicarbonate molecules.
It is a costly pathway: 7 ATP molecules are consumed to synthesise the new pyruvate and 3 ATP for the phosphate triose.
An important characteristic of this cycle is that it allows the co-assimilation of numerous compounds, making it suitable for the mixotrophic organisms.

Cycles related to the 3-hydroxypropionate cycle

A variant of the 3-hydroxypropionate cycle was found to operate in the aerobic extreme thermoacidophile archaeon Metallosphaera sedula. This pathway is called the 3-hydroxypropionate/4-hydroxybutyrate cycle.
Yet another variant of the 3-hydroxypropionate cycle is the dicarboxylate/4-hydroxybutyrate cycle. It was discovered in anaerobic archaea.
It was proposed in 2008 for the hyperthermophile archeon Ignicoccus hospitalis.