Fix branch GO:0016681 oxidoreductase activity, acting on diphenols and related substances as donors, cytochrome as acceptor

[pgaudet]

This branch has 2 descendants:

• GO:0016681 oxidoreductase activity, acting on diphenols and related substances as donors, cytochrome as acceptor -> EC:1.10.2.- -> obsolete, this class has a single descendant, L-ascorbate-cytochrome-b5 reductase activity (EC:1.10.2.1 ), which will get merged into EC 7.2.1.3, see #20602
• • L-ascorbate-cytochrome-b5 reductase activity -> to obsolete, see #20602
• • GO:0008121 ubiquinol-cytochrome-c reductase activity -> change EC to EC:7.1.1.8 (Formerly EC 1.10.2.2. )

Thanks, Pascale

[pgaudet]

Dear all,

The proposal has been made to obsolete

• [x]  GO:0016681 oxidoreductase activity, acting on diphenols and related substances as donors, cytochrome as acceptor -> EC:1.10.2.- : this class has a single descendant, L-ascorbate-cytochrome-b5 reductase activity (EC:1.10.2.1 ), which will get merged into EC 7.2.1.3, see https://github.com/geneontology/go-ontology/issues/20602
• [x] GO:0047063 L-ascorbate-cytochrome-b5 reductase activity -> we will create a new term, since parentage and defintions are very different from the original ones, see https://github.com/geneontology/go-ontology/issues/20602

There are no annotations to these terms, these terms are not present in any subsets. The EC mappings are to ECs that have been transferred.

You can add comments to the ticket: https://github.com/geneontology/go-ontology/issues/20616

Thanks, Pascale

[pgaudet]

• [x] GO:0008121 ubiquinol-cytochrome-c reductase activity : moved under 'electron transfer activity'; change EC
• [x] GO:0004129 cytochrome-c oxidase activity : change EC from EC 1.9.3.1 to EC:7.1.1.9
• [x] GO:0008137 NADH dehydrogenase (ubiquinone) activity (complex I) -> add subclass GO:0009055 ! electron transfer activity

[pgaudet]

• [x] GO:0045153 electron transporter, transferring electrons within CoQH2-cytochrome c reductase complex activity 172 / 2 EXP SGD soluble cytochrome b562, cytochrome b562, cytochrome b566, cytochrome c1 Def Enables the directed movement of electrons from the CoQH2-cytochrome c reductase complex and the cytochrome c oxidase complex => complex III ===> Merge into GO:0008121 ubiquinol-cytochrome-c reductase activity

[pgaudet]

• [x] obsolete GO:0045155 electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity -> not clearly defined, no corresponding EC or Rhea

[pgaudet]

• [x] GO:0045154 electron transporter, transferring electrons within cytochrome c oxidase complex activity synonyms: cytochrome, cytochrome a, cytochrome a3/copper complex = COMPLEX III DEF:Enables the directed movement of electrons within the cytochrome c oxidase complex No EC, no Rhea -> 2 EXP, complex III: c2, cbb => merge into GO:0008121 ubiquinol-cytochrome-c reductase activity

[sjm41]

Hi @pgaudet

"GO:0008121 ubiquinol-cytochrome-c reductase activity" lost it's immediate parent "oxidoreductase activity, acting on diphenols and related substances as donors, cytochrome as acceptor (GO:0016681)" when that term was obsoleted. But the parent of that obsoleted term still exists ("oxidoreductase activity, acting on diphenols and related substances as donors - GO:0016679"). So, I think "GO:0008121 ubiquinol-cytochrome-c reductase activity" should still have GO:0016679 as a parent (rather than only having the "GO:0009055 electron transfer activity" parent)?

That would also make the parentage of "GO:0008121 ubiquinol-cytochrome-c reductase activity" in line with the multiple parentage of the other 2 related terms mentioned above, by having a more specific oxidoreductase parent as well as the 'electron transfer activity' parent:

GO:0008121 ubiquinol-cytochrome-c reductase activity is_a: GO:0009055 ! electron transfer activity

GO:0004129 cytochrome-c oxidase activity is_a: GO:0009055 ! electron transfer activity is_a: GO:0015002 ! heme-copper terminal oxidase activity is_a: GO:0015078 ! proton transmembrane transporter activity is_a: GO:0016676 ! oxidoreductase activity, acting on a heme group of donors, oxygen as acceptor

GO:0008137 NADH dehydrogenase (ubiquinone) activity is_a: GO:0009055 ! electron transfer activity is_a: GO:0050136 ! NADH dehydrogenase (quinone) activity

[raymond91125]

see https://github.com/geneontology/go-ontology/issues/27410 GO:0050136 ! NADH dehydrogenase (quinone) activity is now renamed to "NADH:ubiquinone reductase (non-electrogenic) activity" per EC 1.6.5.9. Thus GO:0008137 NADH dehydrogenase (ubiquinone) activity cannot be a child. Removed that relationship.

[sjm41]

Hi @raymond91125

I think GO:0008137 NADH dehydrogenase (ubiquinone) activity (Catalysis of the reaction: NADH + ubiquinone + 5 H+(in) = NAD+ + ubiquinol + 4 H+(out).) should retain some parentage in the oxidoreductase branch. Do you think adding back either of these parents would be appropriate (I think the first one)?

NAD(P)H dehydrogenase (quinone) activity GO:0003955 Catalysis of the reaction: NAD(P)H + H+ + a quinone = NAD(P)+ + a hydroquinone. (BTW - should change "a hydroquinone" here to "a quinol".)

oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor GO:0016655 Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a quinone or a similar acceptor molecule.

[raymond91125]

GO:0008137 is EC:7.1.1.2. Thus it's parent should've been EC:7.1.1.- GO:0106187 obsolete translocase activity acting on hydrons linked to oxidoreductase reactions. Instead, all terms of EC:7.1.1. have the parent GO:0015453 oxidoreduction-driven active transmembrane transporter activity. GO:0015453 has LD 'primary active transmembrane transporter activity' and ('has part' some 'oxidoreductase activity'). Perhaps the connection to oxidoreductase branch could be fleshed out via the LD some how.

[sjm41]

Thanks @raymond91125. I've made a new issue for this as there's a wider point here: https://github.com/geneontology/go-ontology/issues/27641

[raymond91125]

NAD(P)H dehydrogenase (quinone) activity GO:0003955 Catalysis of the reaction: NAD(P)H + H+ + a quinone = NAD(P)+ + a hydroquinone. (EC:1.6.5.2)

I am uneasy about using an MF with leaf (4-number) EC as a parent to MF terms.

[pgaudet]

In fact since EC is limited to 4 levels, it can happen that in GO some leaf ECs are not leaf GO terms.

It seems like we may need to make more edits here?