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Source ontology files for the Gene Ontology
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GO:2000311 - regulation of AMPA receptor activity #28028

Open CP-SB opened 3 months ago

CP-SB commented 3 months ago

Hi, Hope you can help. Is there an alternative for this? e.g regulation of AMPA receptor availability? Thanks

Relevant publication: PMID: 37228199

pgaudet commented 3 months ago

Hi @CP-SB

Can you clarify your request? Which gene are you annotating from this paper?

Thanks, Pascale

CP-SB commented 2 months ago

Hi Pascale,

Thank you for your quick response. The paper doesn't pinpoint a specific subunit of the 19S regulatory particle's direct involvement in regulation - but that the 19S subcomplex directs AMPAR flow and AMPAR clustering towards synapses. The GO parent term (GO:0099601) for it would be acceptable but cannot be used in direct annotation and none of the others that I can see seem suitable. Thanks. Suchu

pgaudet commented 2 months ago

Thank you for the clarification. It doesn't seem like the 19S regulatory particle directly regulate the receptor activity (otherwise, I would have suggested neurotransmitter receptor regulator activity)

I see in the paper that the proposed mechanism of action is

Because surface AMPARs are endocytosed at sites distant from synapses (39), it thus appears that the free 19S subcomplex stabilizes the (presumably synaptic) clustering of surface AMPARs and yet facilitates their internalization once they diffuse away. Once internalized, the free 19S subcomplex then stabilizes the reserve pool of AMPARs, preventing them from degradation. In addition, we found that free 19S facilitated AMPAR exocytosis, providing an alternative to their degradation fate (fig. S10D). These results demonstrate that proteasome-independent 19S DUB activity regulates AMPARs at multiple trafficking points, and all of these actions work together to maximize receptor availability at synapses

Do any of these terms work:

Thanks, Pascale

CP-SB commented 2 months ago

Hi Pascale,

I think GO:0099602 would be the closest but the paper doesn't provide the 'direct physical' evidence (at IMEX level - i.e there is confocal microscopy data without physical blots) to support this term - and the AMiGO link (which I'm not sure if I understood correctly) also says 'excludes regulates'. Is the confocal data sufficient without physical evidence for GO? or else it might be best if I take out GO:2000311 than to force it. Thanks for your help. Suchu

p.s Unfortunately the other 2 terms don't work.

pgaudet commented 2 months ago

Hi again @CP-SB I discussed this paper with @vanaukenk and it seems like the exact mechanism by which the S19 subcomplex is regulating the AMPA receptor is unknown. The term you proposed to create, "regulation of AMPA receptor availability", seem to be what we call a read-out (see some annotation documentation here: https://wiki.geneontology.org/Tips_to_Produce_High_Quality_Annotations#Capture_the_conclusion,_not_the_assay).

There may be other terms - but it seems like the data doesn't really show that: GO:0099637 neurotransmitter receptor transport GO:0035418 protein localization to synapse

And/or you could use a more general term about "synaptic function".

Thanks, Pascale