Missing parent: rescue of stalled ribosome (GO:0072344)

[ValWood]

rescue of stalled ribosome (GO:0072344) Definition
A process of translational elongation that takes place when a ribosome has stalled during translation, and results in freeing the ribosome from the stalled translation complex.

Should be a descendant of GO:1990116 ribosome-associated ubiquitin-dependent protein catabolic process (A.k.a Ribosome-associated Quality Control ) The chemical reactions and pathways resulting in the breakdown of a protein or peptide encoded by an aberrant message and associated with a stalled ribosome. Degradation is initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the ribosome-associated protein. PMID:23358411

I'm not sure these are different things?

[pgaudet]

I dont know

@sylvainpoux has annotated these, maybe he knows

[ValWood]

see also https://github.com/geneontology/go-ontology/issues/18610

Also proteins annotated to rescue of stalling are RQC complex (GO:1990112) Definition Parents A multiprotein complex that forms a stable complex with large ribosomal subunits (60S in eukaryotes and 50S in prokaryotes) containing stalled polypeptides and triggers their degradation (ribosomal quality control). In budding yeast, this complex includes Cdc48p, Rkr1p, Tae2p, Rqc1p, Npl4p and Ufd1p proteins. [PMID:23232563, PMID:23178123]

[ValWood]

AT tailing (GO:0140708) Definition Parents The C-terminal elongation of 60S-anchored stalled nascent polypeptide chains with untemplated alanine and threonine tails (CAT tails). CAT tails participate in the recognition of stalled nascent chains by the ribosome quality control sytem. [PMID:32934225, PMID:25554787]

is a child of both terms

[ValWood]

https://www.bmbreports.org/journal/view.html?uid=1605&vmd=Full&#:~:text=The%20ribosome%2Dassociated%20quality%20control,events%20(5%2D8).

OK got it. These are sub processes to ribosome quality control I will createe a grouping term "ribosome quality control" and make both terms children (clean up definitions etc)

[ValWood]

but GO:0072344 rescue of stalled ribosome Should be a descendant of GO:0032790 ribosome disassembly (not all ribosome dissembly is the rescue of stalled ribosomes)

[ValWood]

useful overview

[ValWood]

Also CAT tailing is a child of "rescue of stalled ribosome" but seems that it should be part_of GO:1990116 ribosome-associated ubiquitin-dependent protein catabolic process

[ValWood]

For now I added

GO:0072344 rescue of stalled ribosome is_a GO:0032790 ribosome disassembly

I think we need a grouping term for the QC but I'll look into that later.

[ValWood]

@pgaudet is it OK to make this term GO:0072344 rescue of stalled ribosome GO:0072344 rescue of stalled cytosolic ribosome and GO:0032790 ribosome disassembly cytosolic ribosome disassembly

this would seem to be correct for everything except UniProtKB:Q14197 | MRPL58 which I could create a new term for

Let me know, (currently these annotation don't slim because they don't fall under mitochondrial gene expression, or cytosolic translation)

[pgaudet]

We dont want to distinguishing factor to be the cellular localization. I dont think this is what you are suggesting but if you think two pathways are needed, they need to be clearly distinguished (although I think you could use "cytoplamic"/"mito chondrial" in the labels if there is no better way to label the terms.

Another question: does this process occur in bacteria? (seems like it could, if it also occurs in mitochondria); in this case the bacterial cytoplasmic is likely closer to the eukaryote mitochondrial pathway?

[ValWood]

I don't think we can add easily distinguishing factors at this juncture because we don't know enough -- particularly about the mitochondria pathway, only that they are different because none of the cytosolic components are present in the mitochondria (and it seems to quite a complex recycling pathway in the cytosol)

Ribsome recycling in mitochondria seems to be a relatively simple process using endogenous translation machinery (and elongation factor) and a tRNA hydrolase https://pubmed.ncbi.nlm.nih.gov/33878294/

In higher eukaryotes it involves multiple genes which are not part of canonical translation machinery (e.g. RQT complex, RQC complex, and a ubiquitin ligase, and involves a sub process "CAT tailing"