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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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NTR - children of GO:0004483 mRNA (nucleoside-2'-O-)-methyltransferase activity #27387

Open sjm41 opened 7 months ago

sjm41 commented 7 months ago

I think we need to create two specific children of this term - there are two different methyltransferase activities involved here, one acting on the first nucleoside and one acting on the second nucleoside, which appear to be catalysed by distinct enzymes (in humans CMTR1 and CMTR2).

id: GO:0004483 name: mRNA (nucleoside-2'-O-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + m7G(5')pppR-RNA = S-adenosyl-L-homocysteine + m7G(5')pppRm-RNA. R may be guanosine or adenosine." [EC:2.1.1.57] synonym: "messenger ribonucleate nucleoside 2'-methyltransferase activity" RELATED [EC:2.1.1.57] synonym: "messenger RNA (nucleoside-2'-)-methyltransferase activity" RELATED [EC:2.1.1.57] synonym: "mRNA (adenosine-2'-O-)-methyltransferase activity" RELATED [EC:2.1.1.57] synonym: "S-adenosyl-L-methionine:mRNA (nucleoside-2'-O-)-methyltransferase activity" RELATED [EC:2.1.1.57] xref: EC:2.1.1.57 xref: MetaCyc:2.1.1.57-RXN is_a: GO:0008171 ! O-methyltransferase activity is_a: GO:0008174 ! mRNA methyltransferase activity

EC:2.1.1.57 is: NAME: methyltransferase cap1 ALT_NAMES: cap1-MTase, messenger RNA (nucleoside-2'-)-methyltransferase, mRNA (nucleoside-2'-O)-methyltransferase REACTION: a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-methionine <=> a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-ribonucleoside) in mRNA + H(+) + S-adenosyl-L-homocysteine COMMENTS: This enzyme catalyzes the methylation of the ribose on the first transcribed nucleotide of mRNA or snRNA molecules.

And there is also EC:2.1.1.296: NAME: methyltransferase cap2 ALT_NAMES: cap2-MTase, mRNA (nucleoside-2'-O)-methyltransferase REACTION: a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-ribonucleoside)-(ribonucleotide) in mRNA + S-adenosyl-L-methionine <=> a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-ribonucleoside)-(2'-O-methyl-ribonucleotide) in mRNA + H(+) + S-adenosyl-L-homocysteine COMMENTS: The enzyme, found in higher eukaryotes including insects and vertebrates, and their viruses, methylates the ribose of the nucleoside at the second transcribed position of mRNAs and snRNAs.

So the 2 new terms would be:

name: mRNA (nucleoside-2'-O-)-methyltransferase cap1 activity def: "Catalysis of the reaction: a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-ribonucleoside) in mRNA + H(+) + S-adenosyl-L-homocysteine. This is the methylation of the ribose of the nucleoside at the first transcribed position of mRNA." synonym: cap1-MTase activity [EC:2.1.1.57] EXACT synonym: messenger RNA (nucleoside-2'-)-methyltransferase activity [EC:2.1.1.57] BROAD synonym: mRNA (nucleoside-2'-O)-methyltransferase activity [EC:2.1.1.57] BROAD xref: EC:2.1.1.57 xref: MetaCyc:2.1.1.57-RXN xref: RHEA:67020 is_a: GO:0004483 ! mRNA (nucleoside-2'-O-)-methyltransferase activity

name: mRNA (nucleoside-2'-O-)-methyltransferase cap2 activity def: "Catalysis of the reaction: a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-ribonucleoside)-(ribonucleotide) in mRNA + S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-ribonucleoside)-(2'-O-methyl-ribonucleotide) in mRNA + H(+) + S-adenosyl-L-homocysteine. This is the methylation of the ribose of the nucleoside at the second transcribed position of mRNA." synonym: cap2-MTase activity [EC:2.1.1.296] EXACT synonym: mRNA (nucleoside-2'-O)-methyltransferase activity [EC:2.1.1.296] BROAD xref: EC:2.1.1.296 xref: MetaCyc:RXN-14928 xref: RHEA:67024 is_a: GO:0004483 ! mRNA (nucleoside-2'-O-)-methyltransferase activity

And then also remove the EC dbxef, EC def xref, EC-based synonyms and MetaCyc xref from the parent GO:0004483.

pgaudet commented 7 months ago

Hi @sjm41 A couple of points:

Thanks, Pascale

sjm41 commented 7 months ago

EC specifies that this acts on both mRNA and snRNA, so dont we need to remove the mRNA from the label - we should move it to a NARROW synonym (and add a similar synonym for snRNA)

Yes, I agree. Which also means the parent on the final terms will need to be GO:0008173 RNA methyltransferase activity

I am not sure how best to convey that the sugar is methylated

My suggested defs above include a final sentence that is meant to convey this. Will that suffice?

Can we do without the grouping term, and only keep cap1, cap2 methyltranferase?

Yep, that's fine with me!

Thanks.