PANTHER:PTN000207233 yeast have no mitochondrial respiratory chain complex I

[ValWood]

http://amigo.geneontology.org/amigo/gene_product/PomBase:SPBC18E5.10

http://www.pantree.org/node/annotationNode.jsp?id=PTN000207233

so not mitochondrial electron transport, NADH to ubiquinone

or mitochondrial respiratory chain complex I

(I really really thought I got a taxon constraint on this one...)

So, mitochondrial respiratory chain complex I is a huge multifunctional supra-complex...pombe has 2/~44 subunits....

for more detail see https://github.com/geneontology/go-annotation/issues/1207 and linked tickets...

[ValWood]

Also applies to http://amigo.geneontology.org/amigo/gene_product/PomBase:SPAC11E3.12 from http://www.pantree.org/node/annotationNode.jsp?id=PTN000042665

which additioanally has?

respiratory electron transport chain and

plasma membrane respiratory chain complex I (isn't this a bacterial term?)

[ValWood]

note to self, taxon constraints

[ValWood]

plasma membrane respiratory chain complex I has taxon constraints only in bacteria, never in fungi https://www.ebi.ac.uk/QuickGO/term/GO:0045272

requested the other one: https://github.com/geneontology/go-ontology/issues/15521

[pgaudet]

@huaiyumi @thomaspd This could be a test family to check whether touchup works ?

[pgaudet]

@ValWood According to PMID:21115482 the respiratory complex I is present in all species, even in bacteria. So the complex annotation should be OK; or what is the evidence otherwise ?

Thanks, Pascale

[marcfeuermann]

Plasma membrane respiratory chain complex I is indeed a bacterial term. This will be removed from non-bacterial species. I could remove respiratory chain complex I from fungi if you agree.

[ValWood]

I know that pombe and cerevisiae do not have mitochondrial complex I. (they have an alternative NADH dehydrogenase), I'm not sure but I think I discussed this recently with @Antonialock and it was present in some other fungi.

[ValWood]

The evidence that it not present in pombe is well known, but it only has 2/44 subunits out of the in the complex. I suspect that the complex has other activities too.

[Antonialock]

Complex 1 is present in most fungi but not all (eg. absent in saccharomyces cerevisiae and Shizosaccharomyces pombe but present in Yarrowia, Aspergillis and Neurospora). I think all (?) eukaryotes have alternatives to complex 1 (at least 1 or 2 other systems - alternative dehydrogenase and AOX, and there might be an unknown mechanism?)

There was something about if the organism is "roterod sensitive" then it has complex 1.

[pgaudet]

Looking for some references about this: PMC3391107 states that cerevisiae lack complex I. PMID:20025735 has a nice phylogenetic study about this.

@marcfeuermann I think you have removed the annotation ?

[marcfeuermann]

Very interesting paper, thanks Pascale. Figure 2 is really clear. So it seems that yeasts do not have complex I contrary to filamentous fungi. I've removed the propagation of complex I to all fungi, but I could restrict this to yeasts (Saccharomyces/Kluyveromyces clade and pombe clade). Would you agree with that ?

[ValWood]

Sounds good to me. This one will make me very happy, you have no idea how many times I have asked for mappings to this term to be removed for these 2 gene products!

[marcfeuermann]

Okay, Done ! ;-)

[ValWood]

This one should not have come up, already has taxon constraints!

GO:0045271 | respiratory chain complex I | Never in Taxon | 4896 | Schizosaccharomyces pombe |  

GO:0045271 | respiratory chain complex I | Never in Taxon | 4932 | Saccharomyces cerevisiae