Editing Citric acid cycle (section)

== Variation ==
While the citric acid cycle is in general highly conserved, there is significant variability in the enzymes found in different taxa<ref name="Citric acid cycle variants at MetaCyc">{{Cite web|url=https://www.biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=TCA-VARIANTS|title=MetaCyc TCA cycle|website=www.biocyc.org}}</ref> (note that the diagrams on this page are specific to the mammalian pathway variant).

Some differences exist between eukaryotes and prokaryotes. The conversion of D-''threo''-isocitrate to 2-oxoglutarate is catalyzed in eukaryotes by the NAD<sup>+</sup>-dependent [http://www.enzyme-database.org/query.php?ec=1.1.1.41 EC 1.1.1.41], while prokaryotes employ the NADP<sup>+</sup>-dependent [http://www.enzyme-database.org/query.php?ec=1.1.1.42 EC 1.1.1.42].<ref name="pmid12005040">{{cite journal|vauthors=Sahara T, Takada Y, Takeuchi Y, Yamaoka N, Fukunaga N|s2cid=12950388|title=Cloning, sequencing, and expression of a gene encoding the monomeric isocitrate dehydrogenase of the nitrogen-fixing bacterium, Azotobacter vinelandii|journal=Bioscience, Biotechnology, and Biochemistry|volume=66|issue=3|pages=489–500|date=March 2002|pmid=12005040|doi=10.1271/bbb.66.489|doi-access=free}}</ref> Similarly, the conversion of (''S'')-malate to oxaloacetate is catalyzed in eukaryotes by the NAD<sup>+</sup>-dependent [http://www.enzyme-database.org/query.php?ec=1.1.1.37 EC 1.1.1.37], while most prokaryotes utilize a quinone-dependent enzyme, [http://www.enzyme-database.org/query.php?ec=1.1.5.4 EC 1.1.5.4].<ref name="pmid11092847">{{cite journal|vauthors=van der Rest ME, Frank C, Molenaar D|title=Functions of the membrane-associated and cytoplasmic malate dehydrogenases in the citric acid cycle of Escherichia coli|journal=Journal of Bacteriology|volume=182|issue=24|pages=6892–9|date=December 2000|pmid=11092847|pmc=94812|doi=10.1128/jb.182.24.6892-6899.2000}}</ref>

A step with significant variability is the conversion of succinyl-CoA to succinate. Most organisms utilize [http://www.enzyme-database.org/query.php?ec=6.2.1.5 EC 6.2.1.5], succinate–CoA ligase (ADP-forming) (despite its name, the enzyme operates in the pathway in the direction of ATP formation). In mammals a GTP-forming enzyme, succinate–CoA ligase (GDP-forming) ([http://www.enzyme-database.org/query.php?ec=6.2.1.4 EC 6.2.1.4]) also operates. The level of utilization of each isoform is tissue dependent.<ref name="pmid15234968">{{cite journal|vauthors=Lambeth DO, Tews KN, Adkins S, Frohlich D, Milavetz BI|title=Expression of two succinyl-CoA synthetases with different nucleotide specificities in mammalian tissues|journal=The Journal of Biological Chemistry|volume=279|issue=35|pages=36621–4|date=August 2004|pmid=15234968|doi=10.1074/jbc.M406884200|doi-access=free}}</ref> In some acetate-producing bacteria, such as ''Acetobacter aceti'', an entirely different enzyme catalyzes this conversion&nbsp;– [http://www.enzyme-database.org/query.php?ec=2.8.3.18 EC 2.8.3.18], succinyl-CoA:acetate CoA-transferase. This specialized enzyme links the TCA cycle with acetate metabolism in these organisms.<ref name="pmid18502856">{{cite journal|vauthors=Mullins EA, Francois JA, Kappock TJ|title=A specialized citric acid cycle requiring succinyl-coenzyme A (CoA):acetate CoA-transferase (AarC) confers acetic acid resistance on the acidophile Acetobacter aceti|journal=Journal of Bacteriology|volume=190|issue=14|pages=4933–40|date=July 2008|pmid=18502856|pmc=2447011|doi=10.1128/JB.00405-08}}</ref> Some bacteria, such as ''Helicobacter pylori'', employ yet another enzyme for this conversion&nbsp;– succinyl-CoA:acetoacetate CoA-transferase ([http://www.enzyme-database.org/query.php?ec=2.8.3.5 EC 2.8.3.5]).<ref name="pmid9325289">{{cite journal|vauthors=Corthésy-Theulaz IE, Bergonzelli GE, Henry H, Bachmann D, Schorderet DF, Blum AL, [[L. Nicholas Ornston|Ornston LN]]|title=Cloning and characterization of Helicobacter pylori succinyl CoA:acetoacetate CoA-transferase, a novel prokaryotic member of the CoA-transferase family|journal=The Journal of Biological Chemistry|volume=272|issue=41|pages=25659–67|date=October 1997|pmid=9325289|doi=10.1074/jbc.272.41.25659|doi-access=free}}</ref>

Some variability also exists at the previous step&nbsp;– the conversion of 2-oxoglutarate to succinyl-CoA. While most organisms utilize the ubiquitous NAD<sup>+</sup>-dependent 2-oxoglutarate dehydrogenase, some bacteria utilize a ferredoxin-dependent 2-oxoglutarate [[synthase]] ([http://www.enzyme-database.org/query.php?ec=1.2.7.3 EC 1.2.7.3]).<ref name="pmid19936047">{{cite journal|vauthors=Baughn AD, Garforth SJ, Vilchèze C, Jacobs WR|title=An anaerobic-type alpha-ketoglutarate ferredoxin oxidoreductase completes the oxidative tricarboxylic acid cycle of Mycobacterium tuberculosis|journal=PLOS Pathogens|volume=5|issue=11|pages=e1000662|date=November 2009|pmid=19936047|pmc=2773412|doi=10.1371/journal.ppat.1000662|doi-access=free}}</ref>
Other organisms, including obligately autotrophic and methanotrophic bacteria and archaea, bypass succinyl-CoA entirely, and convert 2-oxoglutarate to succinate via [[succinate semialdehyde]], using [http://www.enzyme-database.org/query.php?ec=4.1.1.71 EC 4.1.1.71], 2-oxoglutarate decarboxylase, and [http://www.enzyme-database.org/query.php?ec=1.2.1.79 EC 1.2.1.79], succinate-semialdehyde dehydrogenase.<ref name="pmid22174252">{{cite journal|vauthors=Zhang S, Bryant DA|title=The tricarboxylic acid cycle in cyanobacteria|journal=Science|volume=334|issue=6062|pages=1551–3|date=December 2011|pmid=22174252|doi=10.1126/science.1210858|bibcode=2011Sci...334.1551Z|s2cid=206536295}}</ref>

=== In cancer ===
{{Main|Oncometabolism#Oncometabolites}}
In [[cancer]], there are substantial [[Warburg effect (oncology)|metabolic derangements]] that occur to ensure the proliferation of tumor cells, and consequently metabolites can accumulate which serve to facilitate [[tumorigenesis]], dubbed oncometabolites.<ref>{{cite journal|vauthors=Dang L, Su SM|title=Isocitrate Dehydrogenase Mutation and (R)-2-Hydroxyglutarate: From Basic Discovery to Therapeutics Development|journal=Annual Review of Biochemistry|volume=86|issue=1|pages=305–331|date=June 2017|pmid=28375741|doi=10.1146/annurev-biochem-061516-044732|doi-access=free}}</ref> Among the best characterized oncometabolites is [[2-hydroxyglutarate]] which is produced through a [[heterozygous]] [[gain-of-function mutation]] (specifically a [[Neomorphic mutation|neomorphic]] one) in [[isocitrate dehydrogenase]] (IDH) (which under normal circumstances catalyzes the [[oxidation]] of [[isocitrate]] to [[oxalosuccinate]], which then spontaneously [[Decarboxylation|decarboxylates]] to [[Alpha ketoglutarate|alpha-ketoglutarate]], as discussed above; in this case an additional [[Organic redox reaction|reduction]] step occurs after the formation of alpha-ketoglutarate via [[NADPH]] to yield 2-hydroxyglutarate), and hence IDH is considered an [[oncogene]]. Under physiological conditions, 2-hydroxyglutarate is a minor product of several metabolic pathways as an error but readily converted to alpha-ketoglutarate via hydroxyglutarate dehydrogenase enzymes ([[L2HGDH]] and [[D2HGDH]])<ref>{{cite journal|vauthors=Yong C, Stewart GD, Frezza C|title=Oncometabolites in renal cancer|journal=Nature Reviews. Nephrology|volume=16|issue=3|pages=156–172|date=March 2020|pmid=31636445|pmc=7030949|doi=10.1038/s41581-019-0210-z}}</ref> but does not have a known physiologic role in mammalian cells; of note, in cancer, 2-hydroxyglutarate is likely a terminal metabolite as isotope labelling experiments of colorectal cancer cell lines show that its conversion back to alpha-ketoglutarate is too low to measure.<ref>{{cite journal|vauthors=Gelman SJ, Mahieu NG, Cho K, Llufrio EM, Wencewicz TA, Patti GJ|title=Evidence that 2-hydroxyglutarate is not readily metabolized in colorectal carcinoma cells|journal=Cancer & Metabolism|volume=3|issue=1|pages=13|date=December 2015|pmid=26629338|doi=10.1186/s40170-015-0139-z|pmc=4665876|doi-access=free}}</ref> In cancer, 2-hydroxyglutarate serves as a [[Competitive inhibition|competitive inhibitor]] for a number of enzymes that facilitate reactions via alpha-ketoglutarate in alpha-ketoglutarate-dependent [[dioxygenase]]s. This mutation results in several important changes to the metabolism of the cell. For one thing, because there is an extra NADPH-catalyzed reduction, this can contribute to depletion of cellular stores of NADPH and also reduce levels of alpha-ketoglutarate available to the cell. In particular, the depletion of NADPH is problematic because NADPH is highly compartmentalized and cannot freely diffuse between the organelles in the cell. It is produced largely via the [[pentose phosphate pathway]] in the cytoplasm. The depletion of NADPH results in increased [[oxidative stress]] within the cell as it is a required cofactor in the production of [[Glutathione|GSH]], and this oxidative stress can result in DNA damage. There are also changes on the genetic and epigenetic level through the function of [[Histone code|histone lysine demethylases]] (KDMs) and [[Ten-Eleven Translocation 2|ten-eleven translocation]] (TET) enzymes; ordinarily TETs hydroxylate [[5-Methylcytosine|5-methylcytosines]] to prime them for demethylation. However, in the absence of alpha-ketoglutarate this cannot be done and there is hence hypermethylation of the cell's DNA, serving to promote [[Epithelial–mesenchymal transition|epithelial-mesenchymal transition (EMT)]] and inhibit cellular differentiation. A similar phenomenon is observed for the Jumonji C family of KDMs which require a hydroxylation to perform demethylation at the epsilon-amino methyl group.<ref>{{cite journal|vauthors=Rotili D, Mai A|title=Targeting Histone Demethylases: A New Avenue for the Fight against Cancer|journal=Genes & Cancer|volume=2|issue=6|pages=663–79|date=June 2011|pmid=21941621|pmc=3174264|doi=10.1177/1947601911417976}}</ref> Additionally, the inability of prolyl hydroxylases to catalyze reactions results in stabilization of [[HIF1A|hypoxia-inducible factor alpha]], which is necessary to promote degradation of the latter (as under conditions of low oxygen there will not be adequate substrate for hydroxylation). This results in a [[Pseudohypoxia|pseudohypoxic]] phenotype in the cancer cell that promotes [[angiogenesis]], metabolic reprogramming, [[cell growth]], and [[Cell migration|migration]].{{cn|date=May 2023}}