geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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reductive tricarboxylic acid cycle incorrect parent? #28429

Closed ValWood closed 1 month ago

ValWood commented 1 month ago

reductive tricarboxylic acid cycle A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria.

is the only child of TCA cycle A pathway leading to the fixation of two molecules of CO2 and the production of one molecule of acetyl-CoA; essentially the oxidative TCA cycle running in reverse. Acetyl-CoA is reductively carboxylated to pyruvate, from which all other central metabolites can be formed. Most of the enzymes of reductive and oxidative TCA cycle are shared, with the exception of three key enzymes that allow the cycle to run in reverse: ATP citrate lyase, 2-oxoglutarate:ferredoxin oxidoreductase, and fumarate reductase. 2-oxoglutarate:ferredoxin oxidoreductase catalyzes the carboxylation of succinyl-CoA to 2-oxoglutarate, ATP citrate lyase the ATP-dependent cleavage of citrate to acetyl-CoA and oxaloacetate, and fumarate reductase the reduction of fumarate forming succinate.

presumably it should be a sibling?

ValWood commented 1 month ago

Twi options:

  1. create a grouping term, and make the existing TCA cycle "oxidative TCA cycle" or
  2. Keep the current labels, but make these 2 terms siblings (with exact synonym "oxidative TCA cycle" on TCA cycle)

Notes: PMID:37164017 In anaerobic S. cerevisiae, the TCA cycle bifurcates, with an oxidative branch running from acetyl- CoA to aKG and a reductive branch starting from the carboxyla- tion of pyruvate to oxaloacetate, with subsequent conversion up to succinate.53 In the absence of respiration, bifurcation of the TCA cycle presumably enables cells to support oxaloacetate and aKG synthesis in a redox-neutral manner.

ValWood commented 1 month ago

Plan to remove the relationship between reductive TCA cycle and TCA cycle add exact synonym oxidative TCA cycle to TCA cycle