#9915 GO:0006099 tricarboxylic acid cycle - odd parentage?

Reactome
closed-fixed
5
2013-01-22
2012-12-31
No

GO:0006099 tricarboxylic acid cycle is_a GO:0046356 acetyl-CoA catabolic process is_a GO:0009109 coenzyme catabolic process.
That seems wrong for two reasons. First, molecules can enter the TCA cycle and be catabolized at several points in the cycle, e.g., glutamate (amino acid) can be transaminated to alpha-ketogliutarate (2-oxoglutarate), that can enter the TCA cycle directly for breakdown or conversion to a glucose precursor, at least in fasting mammals, but we wouldn't say that 2-oxoglutarate catabolism is_a acetyl-CoA catabolic process. Second, even when carbon atoms do enter the TCA cycle as acetyl-CoA, the role of the CoA moiety is to activate the acetyl moiety so its reaction with oxaloacetate is favorable. The CoA moiety is released in the course of that reaction and re-used to activate additional acetate groups - it is not catabolized itself.

Would it be better for TCA cycle to be a direct is_a child of GO:1901575 organic substance catabolic process? I can't think of any more specific child of organic substance that covers all the molecules that can enter the TCA cycle for interconversion or breakdown AND that excludes all the ones that can't enter.

Discussion

  • David Hill

    David Hill - 2013-01-03
    • assigned_to: nobody --> ukemi
     
  • David Hill

    David Hill - 2013-01-04

    Hi Peter,

    Maybe trying to lump this under a chemical definition is just incorrect. What if I moved it to a child of 'cellular catabolic process'? Another possibility would be 'primary metabolic process'. What do you think. I will rely on your expertise here.

    -D

     
  • Peter D\'Eustachio

    "Primary metabolic process" sounds safer: there are ways of running molecules through a few steps if the TCA cycle to convert them into biosynthetic intermediates. Check with Harold as well.

     
  • David Hill

    David Hill - 2013-01-22

    Hi Peter,

    I checked with Harold. We are going to go with 'primary metabolic process'. Thanks!

    David

     
  • David Hill

    David Hill - 2013-01-22
    • status: open --> closed-fixed
     

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