NTR: nucleus-vacuole junction complex

[liviap]

Hi I have to request a new term: nucleus-vacuole junction complex, which actually will be, biologically speaking, identical to the already existing term GO:0071561 nucleus-vacuole junction, the reason is that I need it under the protein-complex hierarchy, rather than in the organelle one. The fact is that the 'organelle itself is a protein complex, in yeast, as also indicated in the definition. I'm not totally sure about the 'is_a' annotation... in ref it is stated "Thus, Vac8p is posttranslationally anchored in the cytoplasmic face of the vacuole membrane by N-terminal myristate and palmitate residues, and Nvj1p is an integral membrane protein of the NE whose C-terminal domain extends into the cytosol" so I left the complex as a generic membrane protein complex Thanks a lot Livia

Term1:
 Name: nucleus-vacuole junction complex Def: A protein complex that create the contact site between the vacuole membrane and the outer nuclear membrane. In S. cerevisiae these contacts are mediated through direct physical interaction between Vac8p and Nvj1p. References: GOC:lnp PMID: 10888680 Relationships: is_a GO:0098796 membrane protein complex part_of GO:0071561 nucleus-vacuole junction

DB xref: IntAct: EBI-16585571

[mah11]

If this complex is indeed biologically identical to GO:0071561 nucleus-vacuole junction, then the existing term should be adjusted.

If the nucleus-vacuole junction is only a complex, and not an organelle, GO:0071561 should be moved; if it's both, the 'is_a GO:0098796 membrane protein complex' link can be added (there's precedent - a few other terms have is_a paths to both protein-containing complex and organelle).

On the other hand, what you've actually put in the suggested stanza does not say the new term is identical to GO:0071561. It suggests that the new complex is not all of the GO:0071561 junction, and implies that there is at least one other (unspecified) part, analogous to GO:0032865 ERMES complex part_of GO:0044233 ER-mitochondrion membrane contact site.

[bmeldal]

Livia showed this to me and I really cannot tell weather the existing term was meant to cover more than the complex described by Livia.

If the nucleus-vacuole junction is only a complex, and not an organelle, GO:0071561 should be moved; if it's both, the 'is_a GO:0098796 membrane protein complex' link can be added (there's precedent - a few other terms have is_a paths to both protein-containing complex and organelle).

No, if we retain the original term and create a new complex term then the new term should have is_a GO:0098796 membrane protein complex and part_of GO:0071561 nucleus-vacuole junction - at least that's the pattern we have used so far (is_a 'protein complex' and part_of "subcellular location').

[liviap]

Hi @mah11 and @bmeldal , thanks for your kind help, Biologically speaking, In yeast the nucleus-vacuole junction is only a protein complex complex, however, I couldn't find any evidence in mammals for the nucleus-vacuole contact site to be a protein complex or an higher structure, as far as I could see they appear not to be well described (with just few exceptions). At this point I don't know what is the best choice in term of hierarchy and relations.

[ValWood]

I have a couple of open tickets: These "bridging sites" appear to be quite complicted multi-complex affairs:

For example the mitochondrial inner/outer membrane bridging complex is now known to be SAM, MICOS and some other bridging components https://github.com/geneontology/go-ontology/issues/15245

also https://github.com/geneontology/go-ontology/issues/14861 for ER-plasme membrane contact site

It would probably make sense for @krchristie to look at this one since she has the 2 related ones... @ukemi

[krchristie]

@ukemi & @hdrabkin - I agree with @ValWood that it would make sense to transfer this ticket to me since I already have a couple other tickets related to organellar junctions