Carbon fixation

Carbon fixation or сarbon assimilation is

the process by which inorganic carbon
(particularly in the form of carbon
dioxide) is converted to organic
compounds by living organisms. The
compounds are then used to store
energy and as structure for other
biomolecules. The most prominent
example of carbon fixation is
photosynthesis; another form known as
chemosynthesis can take place in the
absence of sunlight.
Cyanobacteria such as these carry out
photosynthesis. Their emergence foreshadowed the
evolution of many photosynthetic plants, which
oxygenated Earth's atmosphere.

Organisms that grow by fixing carbon are

called autotrophs, which include
photoautotrophs (which use sunlight),
and lithoautotrophs (which use inorganic
oxidation). Heterotrophs 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.[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
terrestrial environments, especially the
tropics. 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
photosynthesis in one type of
proteobacteria called purple bacteria,
and in some non-phototrophic
proteobacteria.[2]

Of the five other autotrophic pathways,

two are known only in bacteria (the
reductive citric acid cycle and the 3-
hydroxypropionate cycle), two only in
archaea (two variants of the 3-
hydroxypropionate cycle), and one in
both bacteria and archaea (the reductive
acetyl CoA pathway).

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 + Pi ⇌ 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+ + 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+
Evolutionary considerations …

Somewhere between 3.8 and 2.3 billion

years ago, the ancestors of
cyanobacteria evolved oxygenic
photosynthesis,[3][4] enabling the use of
the abundant yet relatively oxidized
molecule H2O as an electron donor to the
electron transport chain of light-
catalyzed proton-pumping responsible
for efficient ATP synthesis.[5][6] 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.[7]

CO2 concentrating mechanisms …

Many photosynthetic organisms have not

acquired CO2 concentrating mechanisms
(CCMs), which increase the
concentration of CO2 available to the
initial carboxylase of the Calvin cycle, the
enzyme RuBisCO. The benefits of a CCM
include increased tolerance to low
external concentrations of inorganic
carbon, and reduced losses to
photorespiration. CCMs can make plants
more tolerant of heat and water stress.

CO2 concentrating mechanisms use the

enzyme carbonic anhydrase (CA), which
catalyze both the dehydration of
bicarbonate to CO2 and the hydration of
CO2 to bicarbonate

HCO3− + H+ ⇌ CO2 + H2O

Lipid membranes are much less

permeable to bicarbonate than to CO2.
To capture inorganic carbon more
effectively, some plants have adapted the
anaplerotic reactions

HCO3− + H+ + PEP → OAA + Pi

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 dung jade plant
(Crassula ovata) and cacti are typical of
CAM plants. Sixteen thousand species of
plants use CAM.[8] These plants have a
carbon isotope signature of −20 to −10
‰.[9]

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.[10] These plants have a
carbon isotope signature of −16 to −10
‰.[9]

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
CO2 compensation points than CAM or
C4 plants. C3 plants have a carbon
isotope signature of −24 to −33‰.[9]

Bacteria and cyanobacteria …

Almost all cyanobacteria and some
bacteria utilize carboxysomes to
concentrate carbon dioxide.
Carboxysomes are protein shells filled
with the enzyme RuBisCO and a carbonic
anhydrase. The carbonic anhydrase
produces CO2 from the bicarbonate that
diffuses into the carboxysome. The
surrounding shell provides a barrier to
carbon dioxide loss, helping to increase
its concentration around RuBisCO.

Other autotrophic pathways

Reverse Krebs cycle …

The reverse Krebs cycle, also known as
reverse TCA cycle (rTCA) 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 (as
Aquificales)[11] and anaerobic archea. It
was discovered by Evans, Buchanan and
Arnon in 1966 working with the
photosynthetic green sulfur bacterium
Chlorobium limicola.[12] The cycle
involves the biosynthesis of acetyl-CoA
from two molecules of CO2.[13] 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.[14]

The reverse Krebs cycle is used by

microorganisms in anaerobic
environments. In particular, it is one of
the most used pathways in hydrothermal
vents by the Epsilonproteobacteria.[15]
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".[16]

One other important aspect is the

symbiosis between
Gammaproteobacteria and Riftia
pachyptila. These bacteria can switch
from the Calvin-Benson cycle to the rTCA
cycle and vice versa in response to
different concentrations of H2S in the
environment.[17]

Reductive acetyl CoA pathway …

The reductive acetyl CoA pathway (CoA)
pathway, also known as the Wood-
Ljungdahl pathway, was discovered by
Harland G. Wood and Lars G. Ljungdahl
in 1965, thanks to their studies on
Clostridium thermoaceticum, a Gram
positive bacterium now named Moorella
thermoacetica.[18] It is an acetogen, an
anaerobic bacteria that uses CO2 as
electron acceptor and carbon source,
and H2 as an electron donor to form
acetic acid.[19][20][21][22] This metabolism
is wide spread within the phylum
Firmicutes, especially in the Clostridia.[19]

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 Planctomycetes
that oxidize ammonia in anaerobic
condition.[13][23][24][25][26][27][28]
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.[29]

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.[13]

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.[29][30]

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.[13]
3-Hydroxypropionate bicycle …

The 3-Hydroxypropionate bicycle, also

known as 3-HP/malyl-CoA cycle, was
discovered by Helge Holo in 1989. It's a
pathway of carbon fixation and 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.[31]

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
glycoxilate. During this cycle two
bicarbonate molecules are fixed thanks
to 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.[32][33]

In the second cycle, glycoxilate is

approximately one molecule 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.[34]

19 are the total reactions 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.[34]
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.[33]

An important characteristic of this cycle

is that it allows the co-assimilation of
numerous compounds making it suitable
for the mixotrophic organisms.[33]

Two other 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.[35]

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.[36]

Chemosynthesis
Chemosynthesis is carbon fixation driven
by energy obtained by oxidating
inorganic substances (e.g., hydrogen gas
or hydrogen sulfide), rather than from
sunlight. Sulfur- and hydrogen-oxidizing
bacteria often use the Calvin cycle or the
reductive citric acid cycle.[37]

Non-autotrophic pathways
Although almost all heterotrophs cannot
synthesize complete organic molecules
from carbon dioxide, some carbon
dioxide is incorporated in their
metabolism.[38] Notably pyruvate
carboxylase consumes carbon dioxide
(as bicarbonate ions) as part of
gluconeogenesis, and carbon dioxide is
consumed in various anaplerotic
reactions. Recently, also 6-
phosphogluconate dehydrogenase was
shown to catalyze the reductive
carboxylation of ribulose 5-phosphate to
6-phosphogluconate in E. coli under
elevated CO2 concentrations.[39]
Considering the CO2 concentration in the
habitat of E. coli (e.g. the mammalian
gut[40]), this reaction might happen also
naturally. In the future, this property could
be exploited for the design of synthetic
carbon fixation routes.

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 higher than in the
free air. Measurement of this ratio is
important in the evaluation of water use
efficiency in plants,[41][42][43] and also in
assessing the possible or likely sources
of carbon in global carbon cycle studies.

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Further reading
Berg IA (March 2011). "Ecological aspects
of the distribution of different autotrophic
CO2 fixation pathways" . Applied and
Environmental Microbiology. 77 (6): 1925–
36. doi:10.1128/AEM.02473-10 .
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Keeling PJ (October 2004). "Diversity and
evolutionary history of plastids and their
hosts" . American Journal of Botany. 91
(10): 1481–93.
doi:10.3732/ajb.91.10.1481 .
PMID 21652304 . S2CID 17522125 .
Keeling PJ (2009). "Chromalveolates and
the evolution of plastids by secondary
endosymbiosis" (PDF). The Journal of
Eukaryotic Microbiology. 56 (1): 1–8.
doi:10.1111/j.1550-7408.2008.00371.x .
PMID 19335769 . S2CID 34259721 .
Archived from the original (PDF) on 9 July
2009.
Keeling PJ (March 2010). "The
endosymbiotic origin, diversification and
fate of plastids" . Philosophical
Transactions of the Royal Society of
London. Series B, Biological Sciences. 365
(1541): 729–48.
doi:10.1098/rstb.2009.0103 .
PMC 2817223 . PMID 20124341 .
Timme RE, Bachvaroff TR, Delwiche CF
(2012). "Broad phylogenomic sampling and
the sister lineage of land plants" . PLOS
ONE. 7 (1): e29696.
Bibcode:2012PLoSO...7E9696T .
doi:10.1371/journal.pone.0029696 .
PMC 3258253 . PMID 22253761 .
Spiegel FW (February 2012). "Evolution.
Contemplating the first Plantae". Science.
335 (6070): 809–10.
Bibcode:2012Sci...335..809S .
doi:10.1126/science.1218515 .
PMID 22344435 . S2CID 36584136 .
Price DC, Chan CX, Yoon HS, Yang EC, Qiu
H, Weber AP, et al. (February 2012).
"Cyanophora paradoxa genome elucidates
origin of photosynthesis in algae and
plants" (PDF). Science. 335 (6070): 843–7.
Bibcode:2012Sci...335..843P .
doi:10.1126/science.1213561 .
PMID 22344442 . S2CID 17190180 .
Archived from the original (PDF) on 14 May
2013.
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