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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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mp GO:0000451 rRNA 2'-O-methylation #13176

Closed ValWood closed 7 years ago

ValWood commented 7 years ago

Add parent?

rRNA base methylation Definition The addition of a methyl group to an atom in the nucleoside base portion of a nucleotide residue in an rRNA molecule.

ValWood commented 7 years ago

GO:0000456 Name dimethylation involved in SSU-rRNA maturation

should also have this parent

ValWood commented 7 years ago

and GO:0000452 - snoRNA guided rRNA 2'-O-methylation

mah11 commented 7 years ago

Looks like GO:0000456 is_a GO:0070475 would be correct, but GO:0000451 and GO:0000452 should not have the additional parent. 2'-O-methylation modifies the sugar portion of the nucleotide residue, not the base.

ValWood commented 7 years ago

OK I was reading nucleotide and processing as 'base'. Maybe these could be grouped under an appropriate "rRNA sugar methylation" term. It seems odd to have one grouping and not the other...

ukemi commented 7 years ago

I'm not sure what the new term would add, but will change the relationship as @mah11 suggests above. There is only one kind of sugar in the molecule, but presumably the bases can be distinguished at some point.

ValWood commented 7 years ago

OK

ValWood commented 7 years ago

I'm still a bit confused. So is this modifying the sugar, but only when uridine is the base? http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0008650#term=ancchart

If there is specificity for the sugar based on the base thats why the grouping is useful....i'm trying to figure what we have missing... http://pombase2.aska.gen.nz/term/GO%3A0008173

hdrabkin commented 7 years ago

Looking through the pubs used for IDA annotations sen in quickgo: " named Mrm2, which is required for methylating U(2791) (PMID:11867542

"Reverse transcriptase primer extension indicated that AviRa is an N-methyltransferase that targets G2535 within helix 91 of the rRNA, whereas AviRb modified the 2'-O-ribose position of nucleotide U2479 within helix 89" PMID:12828631) (at least this suggests a specificity for each protein)

FtsJ is active on ribosomes and on the 50 S ribosomal subunit, but is inactive on free rRNA, suggesting that its natural substrate is ribosomes or a pre-ribosomal ribonucleoprotein particle. We identified the methylated nucleotide as 2'-O-methyluridine 2552, PMID:10748051

I have not looked beyond the abstract, however, I don't think it's clear at all how much the secondary and tertiary structures of the RNA or in one case the RNP (ribosome) contribute to the specificity

ValWood commented 7 years ago

OK what I was actually looking for was a term for tRNA 2'-O-methyltransferase so I'll open a ticket for that... We can ignore this for now... (I'll assign it to you Harold;)