#11253 Fix small molecule metabolism - GOC meeting action

[Jane Lomax]

Following on from this thread:

https://mailman.stanford.edu/pipermail/go-discuss/2014-September/thread.html#6859

at the consortium meeting we agreed as a first pass to obsolete:

ATP catabolism
GTP catabolism
FAD catabolism

(+ others)

Also fix the ATP biosynthesis parentage.

[Valerie Wood]

Will "catabolic process" be redefined as part of this overhaul?

"The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism."

Or does this definition still work? (its a bit ambiguous as it is unclear whether catabolism always need to generate energy, or building blocks, or both?)

Note that there are some things under catabolism which do not fit the current definition, and from the discussion at the meeting it seems that these might be misplaced
GO:0010498 proteasomal protein catabolic process
http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0010498#term=ancchart
and children
should these be described only as "protein degradation" but not "protein catabolism"?

[Pascale Gaudet]

Val is right - the definition of "catabolic process" needs to be made narrower.

Thanks,
Pascale

[Paola Roncaglia]

On a related note, we have a TG request from Stan for 'regulation of ATP metabolic process' and pos and neg children. I went through Pascale's presentation again and I think we decided to leave 'ATP metabolism' as is, but just checking before I approve Stan's terms.

Thanks,
Paola

[Jane Lomax]

Deleted ATPase activity (GO:0016887) from ATP catabolic process (GO:0006200) with part_of

[Jane Lomax]

Sent out obsoletion email 15 Dec.

[Ruth]

Hi

I was looking at an Na+,K+-ATPase paper yesterday and realised that there is the GO term: GO:0015991: ATP hydrolysis coupled proton transport and I wondered if it would be appropriate to have a GO term:

ATP hydrolysis coupled transport as a parent to the existing GO:0015991 term, as well as

ATP hydrolysis coupled ion transport. (see PMID:18075585).

Some of these terms could then be part_of parents to terms such as GO:0005391 sodium:potassium-exchanging ATPase activity etc.

I apologise if I have misinterpreted the concept behind removing the ATP (etc) catabolism term relationship with these enzymes/transporters.

If you do agree with these terms, please would you add the dbxrefs: GOC:BHF, dbxref: GOC:mtg_cardiac_conduct_nov11, to them.

Thanks

Ruth

[Peter D\'Eustachio]

Another somewhat tangential thought. This thread started with Val wondering about the definition of catabolic process:

Will "catabolic process" be redefined as part of this overhaul?

"The chemical reactions and pathways resulting in the breakdown of substances,
including the breakdown of carbon compounds with the liberation of energy for use by
the cell or organism."

Or does this definition still work? (its a bit ambiguous as it is unclear whether
catabolism always need to generate energy, or building blocks, or both?)

It looks like the current definition may be OK - if "including" points to everything that follows, then all of this is an example of one kind of catabolism and doesn't preclude other kinds that, for instance, degrade excess heme or convert excess purines to uric acid, both for excretion as waste.

[Jane Lomax]

Obsoleted:

regulation of ATP catabolic process ; GO:1903289
positive regulation of ATP catabolic process ; GO:1903291
negative regulation of ATP catabolic process ; GO:1903290
regulation of GTP catabolic process ; GO:0033124
negative regulation of GTP catabolic process ; GO:0033125
positive regulation of GTP catabolic process ; GO:0033126
GO:0006200 'ATP catabolic process'
GO:0006184 'GTP catabolic process'
GO:0032362 'FAD catabolic process'