For other uses, see Carbon cycle and Carbon sequestration.
Cyanobacteria such as these carry out photosynthesis. Their emergence foreshadowed the evolution of many photosynthetic plants, changing the earth's atmosphere.
Carbon fixation is the conversion 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]
Contents
- 1 Net vs gross CO2 fixation
- 2 Overview of pathways
- 3 Oxygenic photosynthesis
- 3.1 Evolutionary considerations
- 3.2 Carbon concentrating mechanisms
- 3.2.1 CAM plants
- 3.2.2 C4 plants
- 3.2.3 C3 plants
- 4 Other autotrophic pathways
- 4.1 Reductive citric acid cycle
- 4.2 Reductive acetyl CoA pathway
- 4.3 3-Hydroxypropionate and two related cycles
- 5 Chemosynthesis
- 6 Non-autotrophic pathways
- 7 Carbon isotope discrimination
- 8 References
- 9 Further reading
- 9.1 Descent of plants and algae
Net vs gross CO2 fixation
Graphic showing net annual amounts of CO
2 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 in the evenings following each day of 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 + Pi ATP + H2O
and the reductant, NADPH
- NADP+ + 2e- + 2H+ NADPH + H+
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 3.5 and 2.3 billion years ago, cyanobacteria evolved oxygenic photosynthesis.[3][4][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 reaction
- 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 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 operated 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
- ^ a b Geider, R. J., et al., "Primary productivity of planet earth: biological determinants and physical constraints in terrestrial and aquatic habitats", Global Change Biol. 2001, 7, 849-882. doi:10.1046/j.1365-2486.2001.00448.x
- ^ Swan BK, Martinez-Garcia M, Preston CM, Sczyrba A, Woyke T, Lamy D, Reinthaler T, Poulton NJ, Masland ED, Gomez ML, Sieracki ME, DeLong EF, Herndl GJ, Stepanauskas R (2011). "Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean". Science 333 (6047): 1296–300. Bibcode:2011Sci...333.1296S. doi:10.1126/science.1203690. PMID 21885783.
- ^ Brasier M, McLoughlin N, Green O, Wacey D (2006). "A fresh look at the fossil evidence for early Archaean cellular life". Philos. Trans. R. Soc. Lond., B, Biol. Sci. 361 (1470): 887–902. doi:10.1098/rstb.2006.1835. PMC 1578727. PMID 16754605.
- ^ Kopp RE, Kirschvink JL, Hilburn IA, Nash CZ (2005). "The Paleoproterozoic snowball Earth: a climate disaster triggered by the evolution of oxygenic photosynthesis". Proc. Natl. Acad. Sci. U.S.A. 102 (32): 11131–6. Bibcode:2005PNAS..10211131K. doi:10.1073/pnas.0504878102. PMC 1183582. PMID 16061801.
- ^ Tomitani A, Knoll AH, Cavanaugh CM, Ohno T (2006). "The evolutionary diversification of cyanobacteria: molecular-phylogenetic and paleontological perspectives". Proc. Natl. Acad. Sci. U.S.A. 103 (14): 5442–7. Bibcode:2006PNAS..103.5442T. doi:10.1073/pnas.0600999103. PMID 16569695.
- ^ Dodd AN, Borland AM, Haslam RP, Griffiths H, Maxwell K (2002). "Crassulacean acid metabolism: plastic, fantastic". J. Exp. Bot. 53 (369): 569–580. doi:10.1093/jexbot/53.369.569. PMID 11886877.
- ^ a b c O'Leary MH (1988). "Carbon isotopes in photosynthesis". BioScience 38 (5): 328–336. doi:10.2307/1310735. JSTOR 1310735.
- ^ Sage RF, Meirong L, Monson RK (1999). "16. The Taxonomic Distribution of C4 Photosynthesis". In Sage RF, Monson RK. C4 Plant Biology. pp. 551–580. ISBN 0-12-614440-0.
- ^ Evans MC, Buchanan BB, Arnon DI (1966). "A new ferredoxin-dependent carbon reduction cycle in a photosynthetic bacterium". Proc. Natl. Acad. Sci. U.S.A. 55 (4): 928–34. Bibcode:1966PNAS...55..928E. doi:10.1073/pnas.55.4.928. PMC 224252. PMID 5219700.
- ^ Ljungdahl L, Wood HG (1965). "Incorporation of C-14 from carbon dioxide into sugar phosphates, carboxylic acids, and amino acids by Clostridium thermoaceticum". J. Bacteriol. 89: 1055–64. PMC 277595. PMID 14276095.
- ^ Ljungdahl LG (2009). "A life with acetogens, thermophiles, and cellulolytic anaerobes". Annu. Rev. Microbiol. 63: 1–25. doi:10.1146/annurev.micro.091208.073617. PMID 19575555.
- ^ Herter S, Fuchs G, Bacher A, Eisenreich W (2002). "A bicyclic autotrophic CO2 fixation pathway in Chloroflexus aurantiacus". J. Biol. Chem. 277 (23): 20277–83. doi:10.1074/jbc.M201030200. PMID 11929869.
- ^ Zarzycki J, Brecht V, Müller M, Fuchs G (2009). "Identifying the missing steps of the autotrophic 3-hydroxypropionate CO2 fixation cycle in Chloroflexus aurantiacus". Proc. Natl. Acad. Sci. U.S.A. 106 (50): 21317–22. Bibcode:2009PNAS..10621317Z. doi:10.1073/pnas.0908356106. PMID 19955419.
- ^ Berg IA, Kockelkorn D, Buckel W, Fuchs G (2007). "A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea". Science 318 (5857): 1782–6. Bibcode:2007Sci...318.1782B. doi:10.1126/science.1149976. PMID 18079405.
- ^ Huber H, Gallenberger M, Jahn U, Eylert E, Berg IA, Kockelkorn D, Eisenreich W, Fuchs G (2008). "A dicarboxylate/4-hydroxybutyrate autotrophic carbon assimilation cycle in the hyperthermophilic Archaeum Ignicoccus hospitalis". Proc. Natl. Acad. Sci. U.S.A. 105 (22): 7851–6. Bibcode:2008PNAS..105.7851H. doi:10.1073/pnas.0801043105. PMID 18511565.
- ^ Encyclopedia of Microbiology. Academic Press. 2009. pp. 83–84. ISBN 9780123739445.
- ^ Nicole Kresge, Robert D. Simoni, Robert L. Hill (2005). "The Discovery of Heterotrophic Carbon Dioxide Fixation by Harland G. Wood". The Journal of Biological Chemistry.
Further reading
- Berg IA (2011). "Ecological aspects of the distribution of different autotrophic CO2 fixation pathways". Appl. Environ. Microbiol. 77 (6): 1925–36. doi:10.1128/AEM.02473-10. PMC 3067309. PMID 21216907.
Descent of plants and algae
- Keeling PJ (2004). "Diversity and evolutionary history of plastids and their hosts". Am. J. Bot. 91 (10): 1481–93. doi:10.3732/ajb.91.10.1481. PMID 21652304.
- Keeling PJ (2009). "Chromalveolates and the evolution of plastids by secondary endosymbiosis". J. Eukaryot. Microbiol. 56 (1): 1–8. doi:10.1111/j.1550-7408.2008.00371.x. PMID 19335769. Retrieved 10 April 2012.
- Keeling PJ (2010). "The endosymbiotic origin, diversification and fate of plastids". Philos. Trans. R. Soc. Lond., B, Biol. Sci. 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 (2012). "Evolution. Contemplating the first Plantae". Science 335 (6070): 809–10. Bibcode:2012Sci...335..809S. doi:10.1126/science.1218515. PMID 22344435.
- Price DC, Chan CX, Yoon HS, Yang EC, Qiu H, Weber AP, Schwacke R, Gross J, Blouin NA, Lane C, Reyes-Prieto A, Durnford DG, Neilson JA, Lang BF, Burger G, Steiner JM, Löffelhardt W, Meuser JE, Posewitz MC, Ball S, Arias MC, Henrissat B, Coutinho PM, Rensing SA, Symeonidi A, Doddapaneni H, Green BR, Rajah VD, Boore J, Bhattacharya D. (2012). "Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants". Science 335 (6070): 843–7. Bibcode:2012Sci...335..843P. doi:10.1126/science.1213561. PMID 22344442. Retrieved 10 April 2012.
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Metabolism (Catabolism, Anabolism)
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| General |
- Metabolic pathway
- Metabolic network
- Primary nutritional groups
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Energy
metabolism |
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Aerobic respiration
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- Glycolysis → Pyruvate Decarboxylation → Citric acid cycle → Oxidative phosphorylation (Electron Transport Chain + ATP synthase)
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Anaerobic respiration
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- Electron acceptors are other than oxygen
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Fermentation
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- Glycolysis →
- Substrate-level phosphorylation
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Specific
paths |
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Protein metabolism
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- Protein synthesis
- Catabolism
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Carbohydrate metabolism
(Carbohydrate catabolism
and anabolism) |
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Human
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- Glycolysis ⇄ Gluconeogenesis
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- Glycogenolysis ⇄ Glycogenesis
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- Pentose phosphate pathway
- Fructolysis
- Galactolysis
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Nonhuman
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- Photosynthesis
- Anoxygenic photosynthesis
- Chemosynthesis
- Carbon fixation
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- Xylose metabolism
- Radiotrophism
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Lipid metabolism
(Lipolysis, Lipogenesis)
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Fatty acid metabolism
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- Fatty acid degradation (Beta oxidation)
- Fatty acid synthesis
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Other
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- Steroid metabolism
- Sphingolipid metabolism
- Eicosanoid metabolism
- Ketosis
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Amino acid
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- Amino acid synthesis
- Urea cycle
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Nucleotide
metabolism
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- Purine metabolism
- Nucleotide salvage
- Pyrimidine metabolism
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Other
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- Metal metabolism
- Ethanol metabolism
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mt, k, c/g/r/p/y/i, f/h/s/l/o/e, a/u, n, m
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k, cgrp/y/i, f/h/s/l/o/e, au, n, m, epon
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m (A16/C10), i (k, c/g/r/p/y/i, f/h/s/o/e, a/u, n, m)
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- Biochemical families: carbohydrates
- alcohols
- glycoproteins
- glycosides
- lipids
- eicosanoids
- fatty acids / intermediates
- phospholipids
- sphingolipids
- steroids
- nucleic acids
- constituents / intermediates
- proteins
- Amino acids / intermediates
- tetrapyrroles / intermediates
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