Editing Photosynthesis (section)

===Carbon concentrating mechanisms===

====On land====
{{Main|C4 carbon fixation|CAM photosynthesis|Alarm photosynthesis}}
[[File:HatchSlackpathway2.svg|thumb|right|upright=1.4|Overview of [[C4 carbon fixation]]. (This image mistakenly shows [[lactic acid]] instead of [[pyruvate]], and all the [[Chemical species|species]] ending in "-ate" are shown as unionized acids, such as [[malic acid]] and so on).]]
In [[Xerophyte|hot and dry conditions]], plants close their [[stomata]] to prevent water loss. Under these conditions, {{co2}} will decrease and oxygen [[gas]], produced by the [[light reactions]] of photosynthesis, will increase, causing an increase of [[photorespiration]] by the [[oxygenase]] activity of [[Rubisco|ribulose-1,5-bisphosphate carboxylase/oxygenase]] (RuBisCO) and decrease in carbon fixation. Some plants have [[evolution|evolved]] mechanisms to increase the {{co2}} concentration in the leaves under these conditions.<ref name="Williams-2013">{{cite journal |vauthors= Williams BP, Johnston IG, Covshoff S, Hibberd JM |date= September 2013 |title= Phenotypic landscape inference reveals multiple evolutionary paths to C4 photosynthesis |journal= [[eLife]] |volume= 2 |pages= e00961 |doi= 10.7554/eLife.00961 |doi-access= free |pmc= 3786385 |pmid= 24082995 }}</ref>

Plants that use the [[C4 carbon fixation|C<sub>4</sub> carbon fixation]] process chemically fix carbon dioxide in the [[Cell (biology)|cells]] of the [[mesophyll]] by adding it to the three-carbon molecule [[phosphoenolpyruvate]] (PEP), a reaction [[Catalysis|catalyzed]] by an [[enzyme]] called [[Phosphoenolpyruvate carboxylase|PEP carboxylase]], creating the four-carbon organic acid [[oxaloacetic acid]]. Oxaloacetic acid or [[malate]] synthesized by this process is then [[Translocation (botany)|translocated]] to specialized [[bundle sheath]] cells where the enzyme [[RuBisCO]] and other Calvin cycle enzymes are located, and where {{co2}} released by [[decarboxylation]] of the four-carbon acids is then fixed by RuBisCO activity to the three-carbon [[3-phosphoglyceric acid]]s. The physical separation of RuBisCO from the oxygen-generating light reactions reduces photorespiration and increases {{co2}} fixation and, thus, the [[photosynthetic capacity]] of the [[leaf]].<ref>{{cite book |vauthors= Taiz L, Geiger E |year= 2006 |title= Plant Physiology |edition= 4th |publisher= [[Sinauer Associates]] |isbn= 978-0-87893-856-8 |url= https://archive.org/details/plantphysiology0000taiz_y5k4 |url-access= registration }}</ref> [[C4 carbon fixation|{{c4}} plants]] can produce more sugar than [[C3 carbon fixation|{{c3}} plants]] in conditions of high light and [[Thermophile|temperature]]. Many important [[crop plants]] are {{c4}} plants, including [[maize]], [[sorghum]], [[sugarcane]], and [[millet]]. Plants that do not use PEP-carboxylase in carbon fixation are called C<sub>3</sub> plants because the primary [[Carboxylation|carboxylation reaction]], catalyzed by RuBisCO, produces the three-carbon 3-phosphoglyceric acids directly in the [[Calvin-Benson cycle]]. Over 90% of plants use {{c3}} carbon fixation, compared to 3% that use {{c4}} carbon fixation;<ref>{{cite book |vauthors= Monson RK, Sage RF |title= C<sub>4</sub> plant biology |publisher= [[Academic Press]] |location=Boston |year=1999 |pages= 551–580 |chapter= The Taxonomic Distribution of {{chem|C|4}} Photosynthesis |isbn= 978-0-12-614440-6 |chapter-url= https://books.google.com/books?id=H7Wv9ZImW-QC&pg=PA551 |access-date= 2019-04-17 |archive-date= 2023-01-19 |archive-url= https://web.archive.org/web/20230119181847/https://books.google.com/books?id=H7Wv9ZImW-QC&pg=PA551 |url-status= live }}</ref> however, the evolution of {{c4}} in over sixty plant lineages makes it a striking example of [[convergent evolution]].<ref name="Williams-2013"/> [[C2 photosynthesis|C<sub>2</sub> photosynthesis]], which involves carbon-concentration by selective breakdown of photorespiratory glycine, is both an evolutionary precursor to {{c4}} and a useful [[#Carbon concentrating mechanisms|carbon-concentrating mechanism]] in its own right.<ref>{{cite journal |vauthors= Lundgren MR |date= December 2020 |title= C 2 photosynthesis: a promising route towards crop improvement? |journal= New Phytologist |volume= 228 |issue= 6 |pages= 1734–1740 |doi= 10.1111/nph.16494 |doi-access= free |pmid= 32080851 |bibcode= 2020NewPh.228.1734L }}</ref>

[[Xerophytes]], such as [[cacti]] and most [[succulents]], also use PEP carboxylase to capture carbon dioxide in a process called [[CAM photosynthesis|Crassulacean acid metabolism]] (CAM). In contrast to {{c4}} metabolism, which ''spatially'' separates the {{co2}} fixation to PEP from the Calvin cycle, CAM ''temporally'' separates these two processes. CAM plants have a different [[Leaf#Anatomy|leaf anatomy]] from {{c3}} plants, and fix the {{co2}} at night, when their stomata are open. CAM plants store the {{co2}} mostly in the form of [[malic acid]] via carboxylation of [[phosphoenolpyruvate]] to [[oxaloacetate]], which is then reduced to malate. Decarboxylation of malate during the day releases {{co2}} inside the leaves, thus allowing carbon fixation to 3-phosphoglycerate by RuBisCO. CAM is used by 16,000 [[species]] of plants.<ref>{{cite journal |vauthors= Dodd AN, Borland AM, Haslam RP, Griffiths H, Maxwell K |date= April 2002 |title= Crassulacean acid metabolism: plastic, fantastic |journal= [[Journal of Experimental Botany]] |volume= 53 |issue= 369 |pages= 569–580 |doi= 10.1093/jexbot/53.369.569 |doi-access= free |pmid= 11886877 }}</ref>

[[Calcium oxalate|Calcium-oxalate]]-accumulating plants, such as ''[[Amaranthus hybridus]]'' and ''[[Colobanthus quitensis]],'' show a variation of photosynthesis where calcium oxalate [[Druse (botany)|crystals]] function as dynamic [[Carbon sink|carbon pools]], supplying carbon dioxide (CO<sub>2</sub>) to photosynthetic cells when stomata are partially or totally closed. This process was named [[alarm photosynthesis]]. Under [[Stress (biology)|stress]] conditions (e.g., [[Water scarcity|water deficit]]), [[oxalate]] released from calcium oxalate crystals is converted to CO<sub>2</sub> by an [[oxalate oxidase]] enzyme, and the produced CO<sub>2</sub> can support the [[Calvin cycle]] reactions. Reactive [[hydrogen peroxide]] (H<sub>2</sub>O<sub>2</sub>), the [[By-product|byproduct]] of oxalate oxidase reaction, can be [[Neutralization (chemistry)|neutralized]] by [[catalase]]. Alarm photosynthesis represents a photosynthetic variant to be added to the well-known C4 and CAM pathways. However, alarm photosynthesis, in contrast to these pathways, operates as a biochemical pump that collects carbon from the organ interior (or from the [[soil]]) and not from the atmosphere.<ref>{{cite journal | vauthors = Tooulakou G, Giannopoulos A, Nikolopoulos D, Bresta P, Dotsika E, Orkoula MG, Kontoyannis CG, Fasseas C, Liakopoulos G, Klapa MI, Karabourniotis G |display-authors= 6 |date= August 2016 |title= Alarm Photosynthesis: Calcium Oxalate Crystals as an Internal CO2 Source in Plants |journal= Plant Physiology |volume= 171 |issue= 4 |pages= 2577–2585 |doi= 10.1104/pp.16.00111 |pmc= 4972262 |pmid= 27261065 }}</ref><ref>{{cite journal |vauthors= Gómez-Espinoza O, González-Ramírez D, Bresta P, Karabourniotis G, Bravo LA | title=Decomposition of Calcium Oxalate Crystals in ''Colobanthus quitensis'' under CO<sub>2</sub> Limiting Conditions |journal= Plants |volume= 9 |issue= 10 |pages= 1307 | date= October 2020 |doi= 10.3390/plants9101307 |doi-access= free |pmc= 7600318 |pmid= 33023238 | bibcode=2020Plnts...9.1307G }}</ref>

====In water====
[[Cyanobacteria]] possess [[carboxysome]]s, which increase the concentration of {{co2}} around RuBisCO to increase the rate of photosynthesis. An enzyme, [[carbonic anhydrase]], located within the carboxysome, releases CO<sub>2</sub> from dissolved [[Hydrocarbonate|hydrocarbonate ions]] (HCO{{su|b=3|p=−}}). Before the CO<sub>2</sub> can diffuse out<!-- of what? -->, RuBisCO concentrated within the carboxysome quickly sponges it up. HCO{{su|b=3|p=−}} ions are made from CO<sub>2</sub> outside the cell by another carbonic anhydrase and are actively pumped into the cell by a membrane protein. They cannot cross the membrane as they are charged, and within the cytosol they turn back into CO<sub>2</sub> very slowly without the help of carbonic anhydrase. This causes the HCO{{su|b=3|p=−}} ions to accumulate within the cell from where they diffuse into the carboxysomes.<ref>{{cite journal |vauthors= Badger MR, Price GD |date= February 2003 |title= CO2 concentrating mechanisms in cyanobacteria: molecular components, their diversity and evolution |journal= [[Journal of Experimental Botany]] |volume= 54 |issue= 383 |pages= 609–622 |doi= 10.1093/jxb/erg076 |doi-access= free |pmid= 12554704 }}</ref> [[Pyrenoid]]s in [[algae]] and [[hornwort]]s also act to concentrate {{co2}} around RuBisCO.<ref>{{Cite journal |vauthors=Badger MR, Andrews JT, Whitney SM, Ludwig M, Yellowlees DC, Leggat W, Price GD |year= 1998 |title= The diversity and coevolution of Rubisco, plastids, pyrenoids, and chloroplast-based CO<sub>2</sub>-concentrating mechanisms in algae |journal= [[Canadian Journal of Botany]] |volume= 76 |issue= 6 |pages= 1052–1071 |doi= 10.1139/b98-074 |bibcode= 1998CaJB...76.1052B }}</ref><ref>{{cite journal | vauthors=((Robison, T. A.)), ((Oh, Z. G.)), ((Lafferty, D.)), ((Xu, X.)), ((Villarreal, J. C. A.)), ((Gunn, L. H.)), ((Li, F.-W.)) | journal=Nature Plants | title=Hornworts reveal a spatial model for pyrenoid-based CO2-concentrating mechanisms in land plants | pages=63–73 | publisher=Nature Publishing Group | date=3 January 2025 | volume=11 | issue=1 | issn=2055-0278 | doi=10.1038/s41477-024-01871-0| pmid=39753956 }}
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