Carbon fixation

Cyanobacteria such as these carry out photosynthesis. Their emergence foreshadowed the evolution of many photosynthetic plants, changing the earth's atmosphere.

Carbon fixation or сarbon assimilation refers to the conversion process of inorganic carbon (carbon dioxide) to organic compounds by living organisms. The most prominent example is photosynthesis, although chemosynthesis is another form of carbon fixation that can take place in the absence of sunlight. Organisms that grow by fixing carbon are called autotrophs. Autotrophs include photoautotrophs, which synthesize organic compounds using the energy of sunlight, and lithoautotrophs, which synthesize organic compounds using the energy of inorganic oxidation. Heterotrophs are organisms that grow using the carbon fixed by autotrophs. The organic compounds are used by heterotrophs to produce energy and to build body structures. "Fixed carbon", "reduced carbon", and "organic carbon" are equivalent terms for various organic compounds.^[1]

Net vs gross CO₂ fixation

Graphic showing net annual amounts of CO₂ fixation by land and sea-based organisms.

It is estimated that approximately 258 billion tons of carbon dioxide are converted by photosynthesis annually. The majority of the fixation occurs in marine environments, especially areas of high nutrients. The gross amount of carbon dioxide fixed is much larger since approximately 40% is consumed by respiration following photosynthesis.^[1] Given the scale of this process, it is understandable that RuBisCO is the most abundant protein on earth.

Overview of pathways

Six autotrophic carbon fixation pathways are known as of 2011. The Calvin cycle fixes carbon in the chloroplasts of plants and algae, and in the cyanobacteria. It also fixes carbon in the anoxygenic photosynthetic proteobacteria called purple bacteria, and in some non-phototrophic proteobacteria.^[2]

Oxygenic photosynthesis

In photosynthesis, energy from sunlight drives the carbon fixation pathway. Oxygenic photosynthesis is used by the primary producers—plants, algae, and cyanobacteria. They contain the pigment chlorophyll, and use the Calvin cycle to fix carbon autotrophically. The process works like this:

2H₂O → 4e⁻ + 4H⁺ + O₂

CO₂ + 4e⁻ + 4H⁺ → CH₂O + H₂O

In the first step, water is dissociated into electrons, protons, and free oxygen. This allows the use of water, one of the most abundant substances on Earth, as an electron donor—as a source of reducing power. The release of free oxygen is a side-effect of enormous consequence. The first step uses the energy of sunlight to oxidize water to O₂, and, ultimately, to produce ATP

ADP + P_i ATP + H₂O

and the reductant, NADPH

NADP⁺ + 2e⁻ + 2H⁺ NADPH + H⁺

In the second step, called the Calvin cycle, the actual fixation of carbon dioxide is carried out. This process consumes ATP and NADPH. The Calvin cycle in plants accounts for the preponderance of carbon fixation on land. In algae and cyanobacteria, it accounts for the preponderance of carbon fixation in the oceans. The Calvin cycle converts carbon dioxide into sugar, as triose phosphate (TP), which is glyceraldehyde 3-phosphate (GAP) together with dihydroxyacetone phosphate (DHAP):

3 CO₂ + 12 e⁻ + 12 H⁺ + P_i → 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 P_i

The formula for inorganic phosphate (P_i) is HOPO₃²⁻ + 2H⁺. Formulas for triose and TP are C₂H₃O₂-CH₂OH and C₂H₃O₂-CH₂OPO₃²⁻ + 2H⁺

Evolutionary considerations

Somewhere between 3.5 and 2.3 billion years ago, the ancestors of cyanobacteria evolved oxygenic photosynthesis, enabling the use of the abundant yet relatively oxidized molecule H₂O as an electron donor to the electron tranport chain of light-catalyzed proton-pumping responsible for efficient ATP synthesis.^[3][4] When this evolutionary breakthrough occurred, autotrophy (growth using inorganic carbon as the sole carbon source) is believed to have already been developed. However, the proliferation of cyanobacteria, due to their novel ability to exploit water as a source of electrons, radically altered the global environment by oxygenating the atmosphere and by achieving large fluxes of CO₂ consumption. ^[5]

Carbon concentrating mechanisms

Many photosynthetic organisms have acquired inorganic carbon concentrating mechanisms (CCM), which increase the concentration of carbon dioxide available to the initial carboxylase of the Calvin cycle, the enzyme RuBisCO. The benefits of CCM include increased tolerance to low external concentrations of inorganic carbon, and reduced loses to photorespiration. CCM can make plants more tolerant of heat and water stress.

Carbon concentrating mechanisms use the enzyme carbonic anhydrase (CA), which catalyze both the dehydration of bicarbonate to carbon dioxide and the hydration of carbon dioxide to bicarbonate

HCO₃⁻ + H⁺ CO₂ + H₂O

Lipid membranes are much less permeable to bicarbonate than to carbon dioxide. To capture inorganic carbon more effectively, some plants have adapted the anaplerotic reactions

HCO₃⁻ + H⁺ + PEP → OAA + P_i

catalyzed by PEP carboxylase (PEPC), to carboxylate phosphoenolpyruvate (PEP) to oxaloacetate (OAA) which is a C₄ dicarboxylic acid.

CAM plants

CAM plants that use Crassulacean acid metabolism as an adaptation for arid conditions. CO₂ enters through the stomata during the night and is converted into the 4-carbon compound, malic acid, which releases CO₂ for use in the Calvin cycle during the day, when the stomata are closed. The jade plant (Crassula ovata) and cacti are typical of CAM plants. Sixteen thousand species of plants use CAM.^[6] These plants have a carbon isotope signature of -20 to -10 ‰.^[7]

C₄ plants

C₄ plants preface the Calvin cycle with reactions that incorporate CO₂ into one of the 4-carbon compounds, malic acid or aspartic acid. C₄ plants have a distinctive internal leaf anatomy. Tropical grasses, such as sugar cane and maize are C₄ plants, but there are many broadleaf plants that are C₄. Overall, 7600 species of terrestrial plants use C₄ carbon fixation, representing around 3% of all species.^[8] These plants have a carbon isotope signature of -16 to -10 ‰.^[7]

C₃ plants

The large majority of plants are C₃ plants. They are so-called to distinguish them from the CAM and C₄ plants, and because the carboxylation products of the Calvin cycle are 3-carbon compounds. They lack C₄ dicarboxylic acid cycles, and therefore have higher carbon dioxide compensation points than CAM or C₄ plants. C₃ plants have a carbon isotope signature of -24 to -33‰.^[7]

Other autotrophic pathways

Of the five other autotrophic pathways, two are known only in bacteria, two only in archaea, and one in both bacteria and archaea.

Reductive citric acid cycle

The reductive citric acid cycle is the oxidative citric acid cycle run in reverse. It has been found in anaerobic and microaerobic bacteria. It was proposed in 1966 by Evans, Buchanan and Arnon who were working with the anoxygenic photosynthetic green sulfur bacterium that they called Chlorobium thiosulfatophilum. The reductive citric acid cycle is sometimes called the Arnon-Buchanan cycle.^[9]

Reductive acetyl CoA pathway

The reductive acetyl CoA pathway operated in strictly anaerobic bacteria (acetogens) and archaea (methanogens). The pathway was proposed in 1965 by Ljungdahl and Wood. They were working with the gram-positive acetic acid producing bacterium Clostridium thermoaceticum, which is now named Moorella thermoacetica. Hydrogenotrophic methanogenesis, which is only found in certain archaea and accounts fror 80% of global methanogenesis, is also based on the reductive acetyl CoA pathway. The pathway is often referred to as the Wood-Ljungdahl pathway.^[10][11]

3-Hydroxypropionate and two related cycles

The 3-hydroxypropionate cycle is utilized only by green nonsulfur bacteria. It was proposed in 2002 for the anoxygenic photosynthetic Chloroflexus aurantiacus. None of the enzymes that participate in the 3-hydroxypropionate cycle are especially oxygen sensitive.^[12][13]

A variant of the 3-hydroxypropionate pathway was found to operate in aerobic extreme thermoacidophile archaeon Metallosphaera sedula. This pathway, called the 3-hydroxypropionate/4-hydroxybutyrate cycle .^[14] And yet another variant of the 3-hydroxypropionate pathway is the dicarboxylate/4-hydroxybutyrate cycle. It was discovered in anaerobic archaea. It was proposed in 2008 for the hyperthermophile archeon Ignicoccus hospitalis.^[15]

Chemosynthesis

Chemosynthesis is carbon fixation driven by the oxidation of inorganic substances (e.g., hydrogen gas or hydrogen sulfide). Sulfur- and hydrogen-oxidizing bacteria often use the Calvin cycle or the reductive citric acid cycle.^[16]

Non-autotrophic pathways

Although almost all heterotrophs cannot synthesize complete organic molecules from carbon dioxide, some carbon dioxide is incorporated in their metabolism.^[17] Notably pyruvate carboxylase consumes carbon dioxide (as bicarbonate ions) as part of gluconeogenesis, and carbon dioxide is consumed in various anaplerotic reactions.

Carbon isotope discrimination

Some carboxylases, particularly RuBisCO, preferentially bind the lighter carbon stable isotope carbon-12 over the heavier carbon-13. This is known as carbon isotope discrimination and results in carbon-12 to carbon-13 ratios in the plant that are lower than in the free air. Measurement of this ratio is important in the evaluation of water use efficiency in plants, and also in assessing the possible or likely sources of carbon in global carbon cycle studies.

References

Further reading