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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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tail-anchored membrane protein insertion into ER membrane / posttranslational protein targeting to endoplasmic reticulum membrane #21053

Open ValWood opened 3 years ago

ValWood commented 3 years ago

GET complex proteins seem to be annotated to both tail-anchored membrane protein insertion into ER membrane (GO:0071816) A process of protein insertion into the endoplasmic reticulum (ER) membrane in which a tail-anchored (TA) transmembrane protein is incorporated into an endoplasmic reticulum (ER) membrane. TA transmembrane protein, also named type II transmembrane proteins, contain a single C- terminal transmembrane region.

and

posttranslational protein targeting to endoplasmic reticulum membrane The targeting of proteins to a membrane that occurs after their translation. Some secretory proteins exhibit posttranslational transport into the endoplasmic reticulum (ER) lumen: they are synthesized in their entirety on free cytosolic ribosomes and then released into the cytosol, where they are bound by chaperones which keep them in an unfolded state, and subsequently are translocated across the ER membrane.

which seems ok until you read the definition of "posttranslational protein targeting to endoplasmic reticulum membrane". I wonder if the label for posttranslational protein targeting to endoplasmic reticulum membrane can be improved?

Or are both OK? in which case there should be a relationship between them.

ValWood commented 3 years ago

I think we are conflating 2 pathways, both of which have a targeting step and an insertion or translocation step.

i.e GET complex for tail anchored proteins and SRP for luminal proteins (which may also be membrane attached) https://jcs.biologists.org/content/122/20/3605

https://ars.els-cdn.com/content/image/1-s2.0-S0167488913000797-gr1.jpg

pgaudet commented 3 years ago

Is this a question for @bmeldal ?

bmeldal commented 3 years ago

He he, had a request from UniProt to add human GET and while doing that discovered a bunch of oddities with the yeast one. New version out in a few days (release is going through the process right now).

New/updated annotations: GO:0005524 ATP binding GO:0016887 ATPase activity GO:0030176 integral component of endoplasmic reticulum membrane GO:0032977 membrane insertase activity GO:0045048 protein insertion into ER membrane

pgaudet commented 1 year ago

The definition was updated here: https://github.com/geneontology/go-ontology/issues/20244

There is no link to any MF or BP anymore - should there be?

Please reopen if you want to link to a BP

Thanks, Pascale

ValWood commented 1 year ago

Hi Yes, there should be a link.

Also, get 3 has https://www.pombase.org/gene/SPAC1142.06

Screenshot 2022-09-10 at 15 59 29

which implies that

GO:0006620 | post-translational protein targeting to endoplasmic reticulum membrane should be a parent of tail-anchored membrane protein insertion into ER membrane (GO:0071816)

BUT the definition of GO:0006620 is The targeting of proteins to a membrane that occurs after their translation. Some secretory proteins exhibit posttranslational transport into the endoplasmic reticulum (ER) lumen: they are synthesized in their entirety on free cytosolic ribosomes and then released into the cytosol, where they are bound by chaperones which keep them in an unfolded state, and subsequently are translocated across the ER membrane

which is incorrect for the GET complex and is more specific than the term name. The term is a bit confused, is it about transport into the ER or inserting into the membrane (different pathways)

I suggest to obsolete and force reannotation because any existing annotation based on the term name will be incorrect (i.e GET complex annotations).