Rationalise 'respiratory chain complex' terms

[sjm41]

Following the similar efforts to rationalise the alpha-ketoglutarate dehydrogenase complexes and TCA cycle complexes (see #26122 and #26882), I propose we do something similar for respiratory chain complexes. We currently have separate terms for each of these (sub)complexes for eukaryotes (labeled as 'mitochondrial X complex' and sometimes also 'chloroplast X complex') and for bacteria (labeled as 'plasma membrane X complex'). And then we have orthogonal grouping systems based on the complex type or the subcellular location ('X respirasome'). This all results in many interconnected terms and an overly complicated tree. These complexes are homologous across species, so I think we can simplify these terms and make things easier for curators/users.

Currently, we have complexes I, II, III and IV grouped under 'respiratory chain complex' like this:

respiratory chain complex
    |__fumarate reductase complex
    |   |__mitochondrial respiratory chain complex II, succinate dehydrogenase complex (ubiquinone)
    |   |__plasma membrane fumarate reductase complex
    |__mitochondrial respiratory chain complex I, membrane segment
    |__mitochondrial respiratory chain complex I, peripheral segment
    |__NarGHI complex
    |__respiratory chain complex I
    |   |__mitochondrial respiratory chain complex I
    |   |    |__mitochondrial respiratory chain complex I, membrane segment
    |   |    |__mitochondrial respiratory chain complex I, peripheral segment
    |   |__plasma membrane respiratory chain complex I
    |__respiratory chain complex II
    |   |__fumarate reductase complex
    |   |   |__mitochondrial respiratory chain complex II, succinate dehydrogenase complex (ubiquinone)
    |   |   |__plasma membrane fumarate reductase complex
    |   |__plasma membrane respiratory chain complex II
    |   |   |__plasma membrane fumarate reductase complex
    |   |   |__plasma membrane succinate dehydrogenase complex
    |   |       |__plasma membrane succinate dehydrogenase complex (ubiquinone)
    |   |__succinate dehydrogenase complex
    |       |__plasma membrane succinate dehydrogenase complex
    |       |   |__plasma membrane succinate dehydrogenase complex (ubiquinone)
    |       |__succinate dehydrogenase complex (ubiquinone)
    |           |__mitochondrial respiratory chain complex II, succinate dehydrogenase complex (ubiquinone)
    |           |__plasma membrane succinate dehydrogenase complex (ubiquinone)
    |__respiratory chain complex III
    |   |__mitochondrial respiratory chain complex III
    |   |__plasma membrane respiratory chain complex III
    |__respiratory chain complex IV
    |   |__mitochondrial respiratory chain complex IV
    |   |__plasma membrane respiratory chain complex IV
    |__succinate dehydrogenase complex
        |__plasma membrane succinate dehydrogenase complex
            |__plasma membrane succinate dehydrogenase complex (ubiquinone)
        |__succinate dehydrogenase complex (ubiquinone)
            |__mitochondrial respiratory chain complex II, succinate dehydrogenase complex (ubiquinone)
            |__plasma membrane succinate dehydrogenase complex (ubiquinone)

And then we have a (completely separate?) tree for complex V under 'proton-transporting ATP synthase complex':

|__proton-transporting ATP synthase complex
    |__chloroplast proton-transporting ATP synthase complex
    |   |__chloroplast proton-transporting ATP synthase complex, catalytic core CF(1)
    |   |__chloroplast proton-transporting ATP synthase complex, coupling factor CF(o)
    |__mitochondrial proton-transporting ATP synthase complex
    |   |__mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1)
    |   |   |__mitochondrial proton-transporting ATP synthase, catalytic core
    |   |   |__mitochondrial proton-transporting ATP synthase, central stalk
    |   |__mitochondrial proton-transporting ATP synthase complex, coupling factor F(o)
    |       |__mitochondrial proton-transporting ATP synthase, stator stalk
    |__plasma membrane proton-transporting ATP synthase complex
    |   |__plasma membrane proton-transporting ATP synthase complex, catalytic core F(1)
    |   |   |__plasma membrane proton-transporting ATP synthase, catalytic core
    |   |   |__plasma membrane proton-transporting ATP synthase, central stalk
    |   |__plasma membrane proton-transporting ATP synthase complex, coupling factor F(o)
    |       |__plasma membrane proton-transporting ATP synthase, stator stalk
    |__proton-transporting ATP synthase complex, catalytic core F(1)
    |   |__chloroplast proton-transporting ATP synthase complex, catalytic core CF(1)
    |   |__mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1)
    |   |   |__mitochondrial proton-transporting ATP synthase, catalytic core
    |   |   |__mitochondrial proton-transporting ATP synthase, central stalk
    |   |__plasma membrane proton-transporting ATP synthase complex, catalytic core F(1)
    |   |   |__plasma membrane proton-transporting ATP synthase, catalytic core
    |   |   |__plasma membrane proton-transporting ATP synthase, central stalk
    |   |__proton-transporting ATP synthase, catalytic core
    |   |   |__mitochondrial proton-transporting ATP synthase, catalytic core
    |   |   |__plasma membrane proton-transporting ATP synthase, catalytic core
    |   |__proton-transporting ATP synthase, central stalk
    |       |__mitochondrial proton-transporting ATP synthase, central stalk
    |       |__plasma membrane proton-transporting ATP synthase, central stalk
    |__proton-transporting ATP synthase complex, coupling factor F(o)
        |__chloroplast proton-transporting ATP synthase complex, coupling factor CF(o)
        |__mitochondrial proton-transporting ATP synthase complex, coupling factor F(o)
        |   |__mitochondrial proton-transporting ATP synthase, stator stalk
        |__plasma membrane proton-transporting ATP synthase complex, coupling factor F(o)
        |   |__plasma membrane proton-transporting ATP synthase, stator stalk
        |__proton-transporting ATP synthase, stator stalk
            |__mitochondrial proton-transporting ATP synthase, stator stalk
            |__plasma membrane proton-transporting ATP synthase, stator stalk

I suggest we greatly simply all of the above to this:

respiratory chain complex
|__NarGHI complex*
|__fumarate reductase complex*
|__respiratory chain complex I
    |__ mitochondrial respiratory chain complex I, membrane segment
    |__mitochondrial chain complex I, peripheral segment
|__respiratory chain complex II (succinate dehydrogenase)
|__respiratory chain complex III
|__respiratory chain complex IV
|__proton-transporting ATP synthase complex
    |__proton-transporting ATP synthase complex, catalytic core F(1)
    |   |__proton-transporting ATP synthase, catalytic core
    |   |__proton-transporting ATP synthase, central stalk
    |__proton-transporting ATP synthase complex, coupling factor F(o)
        |__proton-transporting ATP synthase, stator stalk

• I believe that 'NarGHI complex' is a valid bacterial respiratory chain complex but doesn't group under the main 'respiratory chain complex I-V' groupings. Similarly, although the bacterial 'fumarate reductase complex' is homologous to the 'respiratory chain complex II (succinate dehydrogenase)', it works in the opposite direction and is not viewed as a subclass of ''respiratory chain complex II'. Would you agree @dsiegele ?

I'm assigning this to you Raymond, since I know you enjoyed working on the related tickets ;-). If the proposals look good to folks, I can provide a more useful list of the individual terms to obsolete and their 'replace by' terms.

[sjm41]

These wikipedia links are useful: https://en.wikipedia.org/wiki/Electron_transport_chain https://en.wikipedia.org/wiki/Oxidative_phosphorylation

[raymond91125]

Noticed an incorrect relationship GO:0098803 respiratory chain complex PART_OF GO:0070469 respirasome PMID:23828195 "Most of Complex II was found in a free, non-associated form in plant as well as mammalian mitochondria, while only a small proportion associated with supercomplex I/III/IV (Eubel et al., 2003; Acín-Pérez et al., 2008; Muster et al., 2010) (Fig. 1A). While Complex V as dimer co-migrates with other supercomplexes but rarely as part of supercomplexes. " It seems that our definition of respirasome is more expansive than that of wikipedia:Supercomplex or the literature, see https://github.com/geneontology/go-ontology/issues/12846.

[raymond91125]

As it stands, all children of GO:0098803 respiratory chain complex are inferred. I added a relationship: proton-transporting ATP synthase complex part_of repirasome. The resulting hierarchy looks like:

@sjm41 Is this good enough, albeit not as succinct as you typed out?

[sjm41]

Hi @raymond91125 Thanks for working on this. My main proposal here is to obsolete all of the mitochondrial/chloroplast/bacterial ('plasma membrane')-specific complexes that are included under the headings shown in your Protege screenshot. I'm not sure if you've done/considered that suggestion?

[raymond91125]

My main proposal here is to obsolete all of the mitochondrial/chloroplast/bacterial ('plasma membrane')-specific complexes that are included under the headings shown in your Protege screenshot. I'm not sure if you've done/considered that suggestion?

I see. So your proposal is to merge taxon-restricted terms up to the taxon-general parents. Many of these terms carry the reference GOC:mtg_sensu. I wonder if we should make sure there is a consensus to undo taxon considerations on these. Thanks.

[sjm41]

Yep. Definitely be good to check consensus on this. There are 2 thumbs-up on my original comment, but we could bring this up at the next editor's meeting to check wider consensus, and then also see if we feel further outreach is required before making a final decision. Thanks.

[pgaudet]

I think we have decided to not create sensu-specific terms unless we describe widely different CC or BPs. In this case the merge seems correct.

Pinging @cmungall and @thomaspd for confirmation.

Thanks, Pascale

[cmungall]

The proposed merge is valid but would lead to incomplete results - for eukaryotes the complex would no longer be found under mitochondrion. For gene searches this may be less important since most genes are likely independently annotated to the mitochondrial membrane, and we could have a rule to check for this, but this is complex. We could also have a taxon GCI for this but this is also complex.

(analogous issues of course for proks)

I appreciate the need to simplify things for curators, but we should just filter out taxonomically irrelevant terms in the curation UI. We need to balance the proposed simplifications for us with effects on our users.

[sjm41]

for eukaryotes the complex would no longer be found under mitochondrion. For gene searches this may be less important since most genes are likely independently annotated to the mitochondrial membrane, and we could have a rule to check for this, but this is complex.

Yep, that's true. I guess we have to decide whether it's more useful to users & curators to simplify the current terms/connections as proposed (~70 terms/branches reduced to ~15), or if it's better to keep the current situation to allow direct, taxon-specific annotations to mitochondrial/chloroplast/bacterial versions of complexes.

I guess that's a general question that is just exemplified by this ticket....

[pgaudet]

Maybe one way to assess this is to see which terms are being used. Out of the current set of 70, only 15 are being used (all evidence codes included):

• (4685) mitochondrial respiratory chain complex I
• (1271) mitochondrial respiratory chain complex III
• (891) mitochondrial respiratory chain complex IV
• (570) respiratory chain complex IV
• (494) mitochondrial respiratory chain complex II, succinate dehydrogenase complex (ubiquinone)
• (154) respiratory chain complex I
• (128) plasma membrane respiratory chain complex I
• (34) succinate dehydrogenase complex
• (33) respiratory chain complex II
• (28) plasma membrane fumarate reductase complex
• (12) respiratory chain complex III
• (9) NarGHI complex
• (9) plasma membrane succinate dehydrogenase complex
• (9) succinate dehydrogenase complex (ubiquinone)
• (1) mitochondrial respiratory chain complex I, peripheral segment

If we do keep the eukaryotes versus prokaryote distinction, we should make the parent 'do not annotate' and have taxon constraints on the children, shouldn't we?

[cmungall]

Yep, that's true. I guess we have to decide whether it's more useful to users & curators to simplify the current terms/connections as proposed (~70 terms/branches reduced to ~15), or if it's better to keep the current situation to allow direct, taxon-specific annotations to mitochondrial/chloroplast/bacterial versions of complexes

For curator complexity, do we anticipate new annotations to these well-studied complexes

user complexity - I agree, I dislike taxonomic lattices, but overall I suspect most non-bioinformatics users don't care about the graph display and having complete gene sets for terms like MM is more important (it would be good to proactively survey our users about this though).

If we do keep the eukaryotes versus prokaryote distinction, we should make the parent 'do not annotate' and have taxon constraints on the children, shouldn't we?

Yes and yes, this should the standard pattern when we create taxonomically variable subclasses to accommodate different relationships

[pgaudet]

Ontology call:

@cmungall best solution is the simplification, in conjunction with rules that would make sure that the correct cellular anatomical entity is also annotated, in cases where this can be determined (as in this case).

[raymond91125]

@ValWood These terms respiratory chain complex I, mitochondrial respiratory chain complex I have a taxon constraint never_in_taxon 'Schizosaccharomyces pombe' and 'Saccharomyces cerevisiae'. Is that an error?

[raymond91125]

• [ ] rename GO:0042653 mitochondrial respiratory chain complex I, membrane segment to "respiratory chain complex I, membrane segment"
• [ ] rename GO:0042652 mitochondrial respiratory chain complex I, peripheral segment to "respiratory chain complex I, peripheral segment"

[raymond91125]

@sjm41 Should all 3 terms merge: succinate dehydrogenase complex (ubiquinone), succinate dehydrogenase complex, and respiratory chain complex II?

[sjm41]

@sjm41 Should all 3 terms merge: succinate dehydrogenase complex (ubiquinone), succinate dehydrogenase complex, and respiratory chain complex II?

Yes, I believe so.

[sjm41]

Below, I've tried to list the full set of proposed obsoletions/replace_by. We may want to review the definitions of the remaining terms, especially for complex II.

==

OBSOLETE:

• [x] mitochondrial respiratory chain complex I (GO:0005747)
• [x] plasma membrane respiratory chain complex I (GO:0045272)

REPLACED BY: respiratory chain complex I (GO:0045271)

==

OBSOLETE:

• [x] succinate dehydrogenase complex (GO:0045281)
• [x] succinate dehydrogenase complex (ubiquinone) (GO:0045257)
• [x] plasma membrane succinate dehydrogenase complex (GO:0045282)
• [x] plasma membrane succinate dehydrogenase complex (ubiquinone) (GO:0045258)
• [x] plasma membrane respiratory chain complex II (GO:0045274)
• [x] mitochondrial respiratory chain complex II, succinate dehydrogenase complex (ubiquinone) (GO:0005749)

REPLACED BY: respiratory chain complex II (GO:0045273) (and rename to 'respiratory chain complex II (succinate dehydrogenase)'?)

==

OBSOLETE:

• [x] plasma membrane fumarate reductase complex (GO:0045284)

REPLACED BY: fumarate reductase complex (GO:0045283)

==

OBSOLETE:

• [x] mitochondrial respiratory chain complex III (GO:0005750)
• [x] plasma membrane respiratory chain complex III (GO:0045276)

REPLACED BY: respiratory chain complex III (GO:0045275)

==

OBSOLETE:

• [x] mitochondrial respiratory chain complex IV (GO:0005751)
• [x] plasma membrane respiratory chain complex IV (GO:0045278)

REPLACED BY: respiratory chain complex IV (GO:0045277)

==

OBSOLETE:

• [x] chloroplast proton-transporting ATP synthase complex (GO:0045320)
• [x] chloroplast ATP synthase complex (GO:0009544)
• [x] mitochondrial proton-transporting ATP synthase complex (GO:0005753)
• [x] plasma membrane proton-transporting ATP synthase complex (GO:0045260)

REPLACED BY: proton-transporting ATP synthase complex (GO:0045259)

==

OBSOLETE:

• [x] mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) (GO:0000275)
• [x] plasma membrane proton-transporting ATP synthase complex, catalytic core F(1) (GO:0045262)
• [x] chloroplast proton-transporting ATP synthase complex, catalytic core CF(1) (GO:0033174)

REPLACED BY: proton-transporting ATP synthase complex, catalytic core F(1) (GO:0045261)

==

OBSOLETE:

• [x] mitochondrial proton-transporting ATP synthase, catalytic core (GO:0005754)
• [x] plasma membrane proton-transporting ATP synthase, catalytic core (GO:0045268)

REPLACED BY: proton-transporting ATP synthase, catalytic core (GO:0045267)

==

OBSOLETE:

• [x] mitochondrial proton-transporting ATP synthase, central stalk (GO:0005756)
• [x] plasma membrane proton-transporting ATP synthase, central stalk (GO:0045270)

REPLACED BY: proton-transporting ATP synthase, central stalk (GO:0045269)

==

OBSOLETE:

• [x] mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) (GO:0000276)
• [x] plasma membrane proton-transporting ATP synthase complex, coupling factor F(o) (GO:0045264)
• [x] chloroplast proton-transporting ATP synthase complex, coupling factor CF(o) (GO:0033175)

REPLACED BY: proton-transporting ATP synthase complex, coupling factor F(o) (GO:0045263)

==

OBSOLETE:

• [x] mitochondrial proton-transporting ATP synthase, stator stalk (GO:0000274)
• [x] plasma membrane proton-transporting ATP synthase, stator stalk (GO:0045266)

REPLACED BY: proton-transporting ATP synthase, stator stalk (GO:0045265)

==

OBSOLETE:

• [x] respirasome (GO:0070469)
• [x] mitochondrial respirasome (GO:0005746)
• [x] plasma membrane respirasome (GO:0070470)

REPLACED BY: respiratory chain complex (GO:0098803)

==

[ValWood]

Hi Raymond, no that is correct. Weirdly some (but not all) yeast have no complex I - they use a single unrelated NADH dehydrogenase. The taxon restriction is added because we constantly get mapping errors. v

[sjm41]

One more merge (I've added it to the list above):

id: GO:0045320 [0 annotations] name: chloroplast proton-transporting ATP synthase complex namespace: cellular_component def: "A proton-transporting ATP synthase complex found in the chloroplast thylakoid membrane; it catalyzes the phosphorylation of ADP to ATP during photo-phosphorylation." [GOC:mtg_sensu, GOC:pj, ISBN:0716743663] synonym: "chloroplast hydrogen-translocating F-type ATPase complex" EXACT [] synonym: "chloroplast proton-transporting F-type ATPase complex" EXACT [] synonym: "hydrogen-translocating F-type ATPase complex" BROAD [] intersection_of: GO:0045259 ! proton-transporting ATP synthase complex intersection_of: part_of GO:0009507 ! chloroplast relationship: part_of GO:0009535 ! chloroplast thylakoid membrane

id: GO:0009544 [3 annotations] name: chloroplast ATP synthase complex namespace: cellular_component def: "The protein complex that catalyzes the phosphorylation of ADP to ATP in chloroplasts." [ISBN:0198547684] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0009507 ! chloroplast relationship: part_of GO:0009535 ! chloroplast thylakoid membrane relationship: part_of GO:0009579 ! thylakoid relationship: part_of GO:0016020 ! membrane

[doughowe]

ZFIN done..I updated google sheet to reflect this as well.

[pgaudet]

Fixed some relations to address issue reported by @alexsign :

GO:0045282 GO:0045258 P but they already is_a in the other direction

also affects: GO:0045281, GO:0045257, GO:0045273, GO:0045274

[raymond91125]

@sjm41 I've completed the list of tasks and simplified the hierarchy. Please let me know if you spot any error. Thanks.

[dsiegele]

I think there are additional GO terms that could be included as children of 'respiratory chain complex.'

• GO:0009319 cytochrome o ubiquinol oxidase complex
• GO:0030964 NADH dehydrogenase complex
• • I will submit a new term request for ndh
• • Complex I should be described as a narrow synonym instead of an exact synonym
• A new GO term is needed for 'cytochrome bd-1 ubiquinol:oxygen oxidoreductase.' (I couldn't find any terms for cytochrome d oxidases.)
• • I will submit a NTR.

Although the respiratory chain in mitochondria is derived from a bacterial ancestor, not all bacteria capable of respiration utilize the 'canonical' respiratory chain of complexes I-IV. The example I am most familiar with is E. coli which uses different respiratory chains to capture energy released by catabolic pathways depending upon the compound serving as the energy source and the available terminal electron acceptor.

When growing in the presence of O2 and utilizing an energy source whose oxidation yields NADH, E. coli will utilize one or more of the following respiratory chains.

NADH to cytochrome bo oxidase electron transfer I NADH -> NDH-1 -> ubiquinone -> cytochrome bo3 ubiquinol:oxygen oxidoreductase (GO:0009319)

NDH-1 is NADH:ubiquinone oxidoreductase I (H+ transporting). NDH-1 is homologous to complex I so I think it would be annotated to GO:0045271.

NADH to cytochrome bo oxidase electron transfer II NADH -> NDH-2 -> ubiquinone -> cytochrome bo3 ubiquinol:oxygen oxidoreductase (GO:0009319)

NDH-2 is NADH:ubiquinone oxidoreductase II (doesn't translocate protons). NDH-2 is a homodimer so I think it would be annotated to GO:0030964.

NADH to cytochrome bd oxidase electron transfer I NADH -> NDH-1 -> ubiquinone -> cytochrome bd-1 ubiquinol:oxygen oxidoreductase

NADH to cytochrome bd oxidase electron transfer II NADH -> NDH-2 -> ubiquinone -> cytochrome bd-1 ubiquinol:oxygen oxidoreductase

I will add information about the anaerobic respiratory chains in another post.

[dsiegele]

Reply to @sjm41 @raymond91125 about fumarate reductase

Yes, E. coli quinol:fumarate oxidoreductase complex aka fumarate reductase primarily functions to reduce fumarate to succinate. It is essential for anaerobic growth on glycerol, lactate, or formate when fumarate serves as the terminal electron acceptor. So GO:0045283 fumarate reductase complex should remain a child of GO:0098803 respiratory chain complex.

FYI: Not relevant to GO but you might like to know that "The functions of QFR and SQR are partially interchangeable - a plasmid containing the frd genes is able to compensate for the growth deficiency of an sdh mutant [Guest81] while anaerobic expression of succinate dehydrogenase supports the growth of an frd mutant [Maklashina98].

[sjm41]

Thanks a lot @raymond91125 ! Looks good to me. As proposed, here's what we have now:

respiratory chain complex
|__NarGHI complex
|__fumarate reductase complex
|__respiratory chain complex I
    |__ mitochondrial respiratory chain complex I, membrane segment
    |__mitochondrial chain complex I, peripheral segment
|__respiratory chain complex II (succinate dehydrogenase)
|__respiratory chain complex III
|__respiratory chain complex IV
|__proton-transporting ATP synthase complex
    |__proton-transporting ATP synthase complex, catalytic core F(1)
    |   |__proton-transporting ATP synthase, catalytic core
    |   |__proton-transporting ATP synthase, central stalk
    |__proton-transporting ATP synthase complex, coupling factor F(o)
        |__proton-transporting ATP synthase, stator stalk

I notice that the two children (subcomplexes) of "respiratory chain complex I" are the only remaining miso-specific terms - "mitochondrial respiratory chain complex I, membrane segment" has been used in 0 annotations, and "mitochondrial chain complex I, peripheral segment" has been used in 1 annotation.

• [x] So I propose those two annotations are merged into their parent 'respiratory chain complex I'.

[sjm41]

Thanks for the feedback @dsiegele !

• So we'll keep 'fumarate reductase complex' (and NarGHI complex') as children of 'respiratory chain complex'

• [x] We need to add 'GO:0009319 cytochrome o ubiquinol oxidase complex' as another child of 'respiratory chain complex'

• We can add another child term if you want to make a NTR for the 'cytochrome bd-1 ubiquinol:oxygen oxidoreductase.' complex you mentioned above.

• I don't think we should add 'GO:0030964 NADH dehydrogenase complex' as a child of 'respiratory chain complex'. That term is already a parent of 'respiratory chain complex I' and appears to be a orthogonal grouping term for NADH complexes involved in either respiration or photosynthesis:

  NADH dehydrogenase complex
  |_respiratory chain complex I
  |_NADH dehydrogenase complex (plastoquinone)

[ValWood]

Hi @sjm41 will you also consider obsoleting/,merging

GO:0010257 | NADH dehydrogenase complex assembly

I think this refers to Complex I assembly. Yeast have PAINT annotations to this term, but we don't have complex I and our dehydrogenase is single subunit

[raymond91125]

• So I propose those two annotations are merged into their parent 'respiratory chain complex I'.

@sjm41 We could also make these two terms generic, since the membrane/peripheral domain structures are conserved, per PMID:19732833, PMID:32058886. respiratory chain complex I, membrane segment respiratory chain complex I, peripheral segment (Those are action items above that I missed.)

[raymond91125]

@ValWood How about adding a 'never in taxon' Schizosaccharomyces pombe and Saccharomyces cerevisiae, on GO:0030964 NADH dehydrogenase complex, which is used in LD of GO:0010257 | NADH dehydrogenase complex assembly.

[raymond91125]

For reference, an illustration-rich article describing mito NADH dehydrogenases https://www.degruyter.com/document/doi/10.1515/hsz-2020-0254/html.

[ValWood]

Hi, @raymond91125, there are NADH dehydrogenases, but are they monomers or complexes? In GO currently GO:0030964 NADH dehydrogenase complex has exact synonym Complex I | exact so are respiratory complex I and NADH dehydrogenase complex separable?

[sjm41]

@sjm41 We could also make these two terms generic, since the membrane/peripheral domain structures are conserved, per PMID:19732833, PMID:32058886. respiratory chain complex I, membrane segment respiratory chain complex I, peripheral segment (Those are action items above that I missed.)

Looking at this now, I'd still recommend merging these two into the parent. As I said, they have only ever been used in a single annotation, and moreover, the guidelines say that subcomplexes are out of scope for GO (https://wiki.geneontology.org/Protein_complexes#Out_of_scope)

[sjm41]

In GO currently GO:0030964 NADH dehydrogenase complex has exact synonym Complex I | exact so are respiratory complex I and NADH dehydrogenase complex separable?

As noted above, GO:0030964 is a grouping term for NADH complexes involved in either respiration or photosynthesis. And as Debbie said, the 'Complex I' synonym on it should be described as a narrow synonym instead of an exact synonym (or better just removed, given that Complex I is a child).

[ValWood]

In that case, if it's a grouping term for complex I the existing taxon restriction can move up from complex I.

[raymond91125]

@sjm41 Is it all done except NTR which best starts a new ticket? Thanks all!

[sjm41]

Closing. Thanks for all your work on this @raymond91125

[raymond91125]

Thanks, @sjm41