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Biological carbon fixation or сarbon assimilation is the process by which inorganic carbon (particularly in the form of
carbon dioxide
Carbon dioxide (chemical formula ) is a chemical compound made up of molecules that each have one carbon atom covalently double bonded to two oxygen atoms. It is found in the gas state at room temperature. In the air, carbon dioxide is transpar ...
) is
converted to
organic compound
In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen or carbon-carbon bonds. Due to carbon's ability to catenate (form chains with other carbon atoms), millions of organic compounds are known. The ...
s by living
organism
In biology, an organism () is any living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy into groups such as multicellular animals, plants, and ...
s. The compounds are then used to store energy and as structure for other
biomolecule
A biomolecule or biological molecule is a loosely used term for molecules present in organisms that are essential to one or more typically biological processes, such as cell division, morphogenesis, or development. Biomolecules include large ...
s. Carbon is primarily fixed through
photosynthesis
Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored i ...
, but some organisms use a process called
chemosynthesis
In biochemistry, chemosynthesis is the biological conversion of one or more carbon-containing molecules (usually carbon dioxide or methane) and nutrients into organic matter using the oxidation of inorganic compounds (e.g., hydrogen gas, hydro ...
in the absence of sunlight.
Organisms that grow by fixing carbon are called
autotroph
An autotroph or primary producer is an organism that produces complex organic compounds (such as carbohydrates, fats, and proteins) using carbon from simple substances such as carbon dioxide,Morris, J. et al. (2019). "Biology: How Life Works", ...
s, which include
photoautotrophs Photoautotrophs are organisms that use light energy and inorganic carbon to produce organic materials. Eukaryotic photoautotrophs absorb energy through the chlorophyll molecules in their chloroplasts while prokaryotic photoautotrophs use chlorophy ...
(which use sunlight), and
lithoautotrophs (which use inorganic oxidation).
Heterotroph
A heterotroph (; ) is an organism that cannot produce its own food, instead taking nutrition from other sources of organic carbon, mainly plant or animal matter. In the food chain, heterotrophs are primary, secondary and tertiary consumers, but ...
s are not themselves capable of carbon fixation but are able to grow by consuming the carbon fixed by autotrophs or other heterotrophs. "Fixed carbon", "reduced carbon", and "organic carbon" may all be used interchangeably to refer to various organic compounds.
[ ]Chemosynthesis
In biochemistry, chemosynthesis is the biological conversion of one or more carbon-containing molecules (usually carbon dioxide or methane) and nutrients into organic matter using the oxidation of inorganic compounds (e.g., hydrogen gas, hydro ...
is carbon fixation driven by chemical energy, rather than from sunlight. Sulfur- and hydrogen-oxidizing bacteria often use the Calvin cycle or the reductive citric acid cycle.
Net vs. gross CO2 fixation
The primary form of inorganic carbon that is fixed is carbon dioxide (CO2). It is estimated that approximately 258 billion tons of carbon dioxide are converted by photosynthesis annually. The majority of the fixation occurs in terrestrial environments, especially the tropics. The gross amount of carbon dioxide fixed is much larger since approximately 40% is consumed by respiration following photosynthesis.
Overview of pathways
Seven autotroph
An autotroph or primary producer is an organism that produces complex organic compounds (such as carbohydrates, fats, and proteins) using carbon from simple substances such as carbon dioxide,Morris, J. et al. (2019). "Biology: How Life Works", ...
ic carbon fixation pathways are known. The Calvin cycle
The Calvin cycle, light-independent reactions, bio synthetic phase, dark reactions, or photosynthetic carbon reduction (PCR) cycle of photosynthesis is a series of chemical reactions that convert carbon dioxide and hydrogen-carrier compounds into ...
fixes carbon in the chloroplast
A chloroplast () is a type of membrane-bound organelle known as a plastid that conducts photosynthesis mostly in plant and algal cells. The photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it in ...
s of plants and algae, and in the cyanobacteria
Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, blu ...
. It also fixes carbon in the anoxygenic photosynthesis in one type of Pseudomonadota
Pseudomonadota (synonym Proteobacteria) is a major phylum of Gram-negative bacteria. The renaming of phyla in 2021 remains controversial among microbiologists, many of whom continue to use the earlier names of long standing in the literature. The ...
called purple bacteria
Purple bacteria or purple photosynthetic bacteria are Gram-negative proteobacteria that are phototrophic, capable of producing their own food via photosynthesis. They are pigmented with bacteriochlorophyll ''a'' or ''b'', together with various ...
, and in some non-phototrophic Pseudomonadota.[
]
Of the five other autotrophic pathways, two are known only in bacteria
Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...
(the reductive citric acid cycle and the 3-hydroxypropionate cycle), two only in archaea
Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebac ...
(two variants of the 3-hydroxypropionate cycle), and one in both bacteria and archaea (the reductive acetyl CoA pathway).
List of pathways
Calvin cycle
The Calvin cycle accounts for 90% of biological carbon fixation. Consuming ATP and NADPH, the Calvin cycle in plants accounts for the preponderance of carbon fixation on land. In algae
Algae (; singular alga ) is an informal term for a large and diverse group of photosynthetic eukaryotic organisms. It is a polyphyletic grouping that includes species from multiple distinct clades. Included organisms range from unicellular mic ...
and cyanobacteria, it accounts for the preponderance of carbon fixation in the oceans. The Calvin cycle converts carbon dioxide into sugar, as triose
A triose is a monosaccharide, or simple sugar, containing three carbon atoms. There are only three possible trioses (including dihydroxyacetone): L-glyceraldehyde and D-glyceraldehyde, the two enantiomers of glyceraldehyde, which are aldotrios ...
phosphate (TP), which is glyceraldehyde 3-phosphate
Glyceraldehyde 3-phosphate, also known as triose phosphate or 3-phosphoglyceraldehyde and abbreviated as G3P, GA3P, GADP, GAP, TP, GALP or PGAL, is a metabolite that occurs as an intermediate in several central pathways of all organisms.Nelson, D ...
(GAP) together with dihydroxyacetone phosphate
Dihydroxyacetone phosphate (DHAP, also glycerone phosphate in older texts) is the anion with the formula HOCH2C(O)CH2OPO32-. This anion is involved in many metabolic pathways, including the Calvin cycle in plants and glycolysis.Nelson, D. L.; Co ...
(DHAP):
:3 CO2 + 12 e− + 12 H+ + Pi → TP + 4 H2O
An alternative perspective accounts for NADPH (source of e−) and ATP:
:3 CO2 + 6 NADPH + 6 H+ + 9 ATP + 5 H2O → TP + 6 NADP+ + 9 ADP + 8 Pi
The formula for inorganic phosphate (Pi) is HOPO32− + 2H+. Formulas for triose and TP are C2H3O2-CH2OH and C2H3O2-CH2OPO32− + 2H+
Reverse Krebs cycle
The reverse Krebs cycle
The reverse Krebs cycle (also known as the reverse tricarboxylic acid cycle, the reverse TCA cycle, or the reverse citric acid cycle, or the reductive tricarboxylic acid cycle, or the reductive TCA cycle)
is a sequence of chemical reactions that ...
, also known as reverse TCA cycle (rTCA) or reductive citric acid cycle, is an alternative to the standard Calvin-Benson cycle
The Calvin cycle, light-independent reactions, bio synthetic phase, dark reactions, or photosynthetic carbon reduction (PCR) cycle of photosynthesis is a series of chemical reactions that convert carbon dioxide and hydrogen-carrier compounds into ...
for carbon fixation. It has been found in strict anaerobic or microaerobic bacteria
Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...
(as ''Aquificales
The ''Aquificota'' phylum (biology), phylum is a diverse collection of bacteria that live in harsh environmental settings. The name ''Aquificota'' was given to this phylum based on an early genus identified within this group, ''Aquifex'' (“wate ...
'') and anaerobic archea
Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaeb ...
. 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 vent
A hydrothermal vent is a fissure on the seabed from which geothermally heated water discharges. They are commonly found near volcanically active places, areas where tectonic plates are moving apart at mid-ocean ridges, ocean basins, and hotspot ...
s by the Campylobacterota
Campylobacterota are a phylum of bacteria. All species of this phylum are Gram-negative.
The Campylobacterota consist of few known genera, mainly the curved to spirilloid ''Wolinella'' spp., ''Helicobacter'' spp., and ''Campylobacter'' spp. Most ...
. This feature is very important in oceans. Without it, there would be no primary production in aphotic environments, which would lead to habitats without life. So this kind of primary production is called "dark primary production".
The cycle involves the biosynthesis of acetyl-CoA
Acetyl-CoA (acetyl coenzyme A) is a molecule that participates in many biochemical reactions in protein, carbohydrate and lipid metabolism. Its main function is to deliver the acetyl group to the citric acid cycle (Krebs cycle) to be oxidized for ...
from two molecules of CO2. The key steps of the reverse Krebs cycle are:
* Oxaloacetate
Oxaloacetic acid (also known as oxalacetic acid or OAA) is a crystalline organic compound with the chemical formula HO2CC(O)CH2CO2H. Oxaloacetic acid, in the form of its conjugate base oxaloacetate, is a metabolic intermediate in many processes ...
to malate
Malic acid is an organic compound with the molecular formula . It is a dicarboxylic acid that is made by all living organisms, contributes to the sour taste of fruits, and is used as a food additive. Malic acid has two stereoisomeric forms (L ...
, using NADH
Nicotinamide adenine dinucleotide (NAD) is a coenzyme central to metabolism. Found in all living cells, NAD is called a dinucleotide because it consists of two nucleotides joined through their phosphate groups. One nucleotide contains an aden ...
+ H+
Oxaloacetate + NADH/H+ -> Malate + NAD+
* Fumarate
Fumaric acid is an organic compound with the formula HO2CCH=CHCO2H. A white solid, fumaric acid occurs widely in nature. It has a fruit-like taste and has been used as a food additive. Its E number is E297.
The salts and esters are known as f ...
to succinate
Succinic acid () is a dicarboxylic acid with the chemical formula (CH2)2(CO2H)2. The name derives from Latin ''succinum'', meaning amber. In living organisms, succinic acid takes the form of an anion, succinate, which has multiple biological ro ...
, catalyzed by an oxidoreductase, Fumarate reductase Fumarate reductase is the enzyme that converts fumarate to succinate, and is important in microbial metabolism as a part of anaerobic respiration.
Succinate + acceptor fumarate + reduced acceptor
Fumarate reductases can be divided into two classe ...
Fumarate + FADH2 <=> Succinate + FAD
* Succinate to succinyl-CoA
Succinyl-coenzyme A, abbreviated as succinyl-CoA () or SucCoA, is a thioester of succinic acid and coenzyme A.
Sources
It is an important intermediate in the citric acid cycle, where it is synthesized from α-ketoglutarate by α-ketoglutarate d ...
, an ATP dependent step
Succinate + ATP + CoA -> Succinyl-CoA + ADP + Pi
* Succinyl-CoA to alpha-ketoglutarate, using one molecule of CO2
Succinyl-CoA + CO2 + Fd -> alpha-ketoglutarate + Fd
* Alpha-ketoglutarate to isocitrate
Isocitric acid is a structural isomer of citric acid. Since citric acid and isocitric acid are structural isomers, they share similar physical and chemical properties. Due to these similar properties, it is difficult to separate the isomers. Salt ...
, using NADPH + H+ and another molecule of CO2
Alpha-ketoglutarate + CO2 + NAD(P)H/H+ -> Isocitrate + NAD(P)+
* Citrate
Citric acid is an organic compound with the chemical formula HOC(CO2H)(CH2CO2H)2. It is a colorless weak organic acid. It occurs naturally in citrus fruits. In biochemistry, it is an intermediate in the citric acid cycle, which occurs in the ...
converted into oxaloacetate and acetyl-CoA
Acetyl-CoA (acetyl coenzyme A) is a molecule that participates in many biochemical reactions in protein, carbohydrate and lipid metabolism. Its main function is to deliver the acetyl group to the citric acid cycle (Krebs cycle) to be oxidized for ...
, this is an ATP dependent step and the key enzyme is the ATP citrate lyase
ATP citrate synthase (also ATP citrate lyase (ACLY)) is an enzyme that in animals represents an important step in fatty acid biosynthesis. By converting citrate to acetyl-CoA, the enzyme links carbohydrate metabolism, which yields citrate as an ...
Citrate + ATP + CoA -> Oxaloacetate + Acetyl-CoA + ADP + Pi
This pathway is cyclic due to the regeneration of the oxaloacetate.
The bacteria Gammaproteobacteria and ''Riftia pachyptila
''Riftia pachyptila'', commonly known as the giant tube worm and less commonly known as the Giant beardworm, is a marine invertebrate in the phylum Annelida (formerly grouped in phylum Pogonophora and Vestimentifera) related to tube worms ...
'' 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 (CoA) 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 wide spread within the phylum Bacillota
The Bacillota (synonym Firmicutes) are a phylum of bacteria, most of which have gram-positive cell wall structure. The renaming of phyla such as Firmicutes in 2021 remains controversial among microbiologists, many of whom continue to use the earl ...
, especially in the Clostridia
The Clostridia are a highly polyphyletic class of Bacillota, including ''Clostridium'' and other similar genera. They are distinguished from the Bacilli by lacking aerobic respiration. They are obligate anaerobes and oxygen is toxic to them. S ...
.
The pathway is also used by methanogen
Methanogens are microorganisms that produce methane as a metabolic byproduct in hypoxic conditions. They are prokaryotic and belong to the domain Archaea. All known methanogens are members of the archaeal phylum Euryarchaeota. Methanogens are com ...
s, which are mainly Euryarchaeota
Euryarchaeota (from Ancient Greek ''εὐρύς'' eurús, "broad, wide") is a phylum of archaea. Euryarchaeota are highly diverse and include methanogens, which produce methane and are often found in intestines, halobacteria, which survive extre ...
, and several anaerobic chemolithoautotrophs, such as sulfate-reducing bacteria and archaea. It is probably performed also by the Brocadiales, an order of Planctomycetota
The Planctomycetota are a phylum of widely distributed bacteria, occurring in both aquatic and terrestrial habitats. They play a considerable role in global carbon and nitrogen cycles, with many species of this phylum capable of anaerobic ammoniu ...
that oxidize ammonia in anaerobic condition. Hydrogenotrophic methanogenesis
Methanogenesis or biomethanation is the formation of methane coupled to energy conservation by microbes known as methanogens. Organisms capable of producing methane for energy conservation have been identified only from the domain Archaea, a group ...
, 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 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-Hydroxipropionate bicycle is composed of two cycles and the name of this way comes from the 3-Hydroxyporopionate which corresponds to an intermediate characteristic of it.
The first cycle is a way of synthesis of glycoxalate. 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 glycoxylate which will thus become part of the second cycle.
In the second cycle, glycoxlate 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. At this point the pyruvate is released, while the Acetyl-CoA is reused and carboxylated again at Malonyl-coa thus reconstituting the cycle.
A total of 19 reactions are involved in 3-hydroxypropionate bicycle and 13 are the multifunctional enzymes used. The multifunctionality of these enzymes is an important feature of this pathway which thus allows the fixation of 3 bicarbonate molecules.
It is a very expensive way: 7 ATP molecules are used for the synthesis of 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 mixotroph A mixotroph is an organism that can use a mix of different sources of energy and carbon, instead of having a single trophic mode on the continuum from complete autotrophy at one end to heterotrophy at the other. It is estimated that mixotrophs comp ...
ic 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''.[
]
enoyl-CoA carboxylases/reductases
fixation is catalyzed by enoyl-CoA carboxylases/reductases.
Non-autotrophic pathways
Although no heterotrophs use carbon dioxide in biosynthesis, some carbon dioxide is incorporated in their metabolism. Notably pyruvate carboxylase
Pyruvate carboxylase (PC) encoded by the gene PC is an enzyme () of the ligase class that catalyzes (depending on the species) the physiologically irreversible carboxylation of pyruvate to form oxaloacetate (OAA).
Image:Pyruvic-acid-2D-sk ...
consumes carbon dioxide (as bicarbonate ions) as part of gluconeogenesis
Gluconeogenesis (GNG) is a metabolic pathway that results in the generation of glucose from certain non-carbohydrate carbon substrates. It is a ubiquitous process, present in plants, animals, fungi, bacteria, and other microorganisms. In vertebrat ...
, and carbon dioxide is consumed in various anaplerotic reactions
Anaplerotic reactions, a term coined by Hans Kornberg and originating from the Greeἀνά 'up' anπληρόω 'to fill', are chemical reactions that form intermediates of a metabolic pathway. Examples of such are found in the citric acid cycle (TC ...
.
6-phosphogluconate dehydrogenase
6-Phosphogluconate dehydrogenase (6PGD) is an enzyme in the pentose phosphate pathway. It forms ribulose 5-phosphate from 6-phosphogluconate:
:6-phospho-D-gluconate + NAD(P)+ \rightleftharpoons D-Ribulose 5-phosphate + CO2 + NAD(P)H + H+
It i ...
catalyzes the reductive carboxylation
Carboxylation is a chemical reaction in which a carboxylic acid is produced by treating a substrate with carbon dioxide. The opposite reaction is decarboxylation. In chemistry, the term carbonation is sometimes used synonymously with carboxylatio ...
of ribulose 5-phosphate to 6-phosphogluconate in ''E. coli'' under elevated CO2 concentrations.
Carbon isotope discrimination
Some carboxylases, particularly RuBisCO
Ribulose-1,5-bisphosphate carboxylase-oxygenase, commonly known by the abbreviations RuBisCo, rubisco, RuBPCase, or RuBPco, is an enzyme () involved in the first major step of carbon fixation, a process by which atmospheric carbon dioxide is con ...
, preferentially bind the lighter carbon stable isotope carbon-12 over the heavier carbon-13
Carbon-13 (13C) is a natural, stable isotope of carbon with a nucleus containing six protons and seven neutrons. As one of the environmental isotopes, it makes up about 1.1% of all natural carbon on Earth.
Detection by mass spectrometry
A mass ...
. This is known as carbon isotope discrimination and results in carbon-12 to carbon-13 ratios in the plant that are higher than in the free air. Measurement of this ratio is important in the evaluation of water use efficiency
Water-use efficiency (WUE) refers to the ratio of water used in plant metabolism to water lost by the plant through transpiration. Two types of water-use efficiency are referred to most frequently:
* photosynthetic water-use efficiency (also cal ...
in plants, and also in assessing the possible or likely sources of carbon in global carbon cycle studies.
See also
* Nitrogen fixation
Nitrogen fixation is a chemical process by which molecular nitrogen (), with a strong triple covalent bond, in the air is converted into ammonia () or related nitrogenous compounds, typically in soil or aquatic systems but also in industry. Atmo ...
*Oxygen cycle
Oxygen cycle refers to the movement of oxygen through the atmosphere (air), biosphere (plants and animals) and the lithosphere (the Earth’s crust). The oxygen cycle demonstrates how free oxygen is made available in each of these regions, as wel ...
References
Further reading
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{{MetabolismMap
Photosynthesis
Carbon
Metabolic pathways
Atmospheric chemistry
Microbiology