Open ValWood opened 3 years ago
Who can answer this ? Most EXP annotations are from SGD @srengel do you agree to merge those terms?
Actually it might not be so simple. In this historical (open) ticket, https://github.com/geneontology/go-ontology/issues/14384 there is a bit more information. I forgot about this. I think quite a few of the definitions are not quite right. At present they all sound the same.
Also, look at this even older ticket: https://github.com/geneontology/go-ontology/issues/13717
not totally clear what to do here, and reading those 2 older tickets make me even less sure. it's confusing that glycoprotein folding terms are being requested, because those should like instances to me. is glycoprotein folding QC really that different from other protein folding QC?
@srengel you are correct. The ERAD part is the same. However there is a pathway for glycoproteins which proceeds ERAD. glycoproteins see https://ars.els-cdn.com/content/image/1-s2.0-S0014579315006468-gr2_lrg.jpg
Here are some actions we can do immediately.
ERAD pathway (GO:0036503) The protein catabolic pathway which targets endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. It begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein modifications necessary for correct substrate transfer (e.g. ubiquitination), transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome. [PMID:20940304, PMID:21969857]
into ERAD pathway (GO:0036503) these seem to be identical?
into ERAD pathway (GO:0036503) these seem to be identical? (all ERAD is Ubiquitin/proteasome mediated as far as we know?)
Definition | Parents An ERAD pathway whereby endoplasmic reticulum (ER)-resident glycoproteins are targeted for degradation. Includes differential processing of the glycoprotein sugar chains, retrotranslocation to the cytosol and degradation by the ubiquitin-proteasome pathway. A glycoprotein is a compound in which a carbohydrate component is covalently bound to a protein component.
merge into ERAD pathway (GO:0036503)
as a parent of GO:0036503 ERAD pathway GO:0061857 endoplasmic reticulum stress-induced pre-emptive quality control
is_a GO:NEW endoplasmic reticulum quality control Note from the expert: The ERAD pathway (Endoplasmic reticulum glycoprotein associated degradation) is a process that occurs when the previous (QC) mechanism has failed: irreversibly misfolded glycoproteins are retrotranslocated to the cytosol and degraded in proteasomes.
more to follow.....I just need to check the other tickets....
It will and up as quite a 'high level' term.
Finally....
GO:0030968 endoplasmic reticulum unfolded protein response Definition (GO:0030968 GONUTS page) The series of molecular signals generated as a consequence of the presence of unfolded proteins in the endoplasmic reticulum (ER) or other ER-related stress; results in changes in the regulation of transcription and translation. PMID:12042763
and his term in a different part of the ontology GO:0006983 ER overload response The series of molecular signals generated by the accumulation of normal or misfolded proteins in the endoplasmic reticulum and leading to activation of transcription by NF-kappaB. PMID:10390516
seem to be describing the same process.
just ran across this paper that defines a new EGAD pathway (Endosome and Golgi-Associated Degradation) that selectively extracts membrane proteins at Golgi and endosomes for degradation by cytosolic proteasomes. https://pubmed.ncbi.nlm.nih.gov/31368600/
posting here because anyone reading this ticket might also be interested in this EGAD? any problems with me requesting this new term? "EGAD pathway" = "The protein catabolic pathway which selectively extracts ER-resident membrane proteins exported to the Golgi and endosomes for degradation by cytosolic proteasomes. It begins with phosphorylation of the ER-resident membrane protein, which triggers export of the protein from the ER to the Golgi and endosomes, followed by polyubiquitination by the Dsc E3 ubiquitin ligase complex and extraction of the ubiquitinated target, and ends with proteasomal degradation."
These terms seem to be all describing the same process?