GO:0001734 mRNA (N6-adenosine)-methyltransferase activity

[sjm41]

id: GO:0001734 name: mRNA (N6-adenosine)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + RRACH = S-adenosyl-L-homocysteine + RRm6ACH; R is a purine, and H is C, A, or U." [GOC:hjd] is_a: GO:0008174 ! mRNA methyltransferase activity

This corresponds to EC:2.1.1.348: EC 2.1.1.348 Accepted Name: mRNA m(6)A methyltransferase Reaction catalysed: an adenosine in mRNA + S-adenosyl-L-methionine <=> an N(6)-methyladenosine in mRNA + H(+) + S-adenosyl-L-homocysteine Comment(s): This enzyme, found in eukaryotes, methylates adenines in mRNA with the consensus sequence RRACH.

• [x] add EC:2.1.1.348 xref
• [x] also add RHEA:55584 and MetaCyc:RXN-19346 xrefs
• [x] Change def to match EC/RHEA, and include EC comment in def.
• [x] Change GO name to match EC

[sjm41]

@pgaudet According to the EC comment, this term should have a taxon constraint of 'only in eukaryotes'. Would you be able to take care of that point?

[pgaudet]

Is the mRNA nomenclature different from the tRNA nomenclature?

See tRNA (adenine(9)-N1)-methyltransferase activity and https://enzyme.expasy.org/EC/2.1.1.218

[pgaudet]

TC added.

[sjm41]

Not sure whether there are systematic/accepted differences in nomenclature for mRNA/tRNA methyltransferases.

The "m(6)A" (or m6A) format (EC 2.1.1.348) is definitely common usage in the literature for the mRNA methyltransferases (and there's no synonyms listed on the EC 2.1.1.348 page). Maybe this is because there's not a specific (numbered) adenine residue involved here?

For tRNA methyltransferases, it seems the "tRNA (adenine(9)-N(1))-methyltransferase" (EC:2.1.1.218) type format is preferred as the 'accepted name' within EC. Though I see the synonyms for EC:2.1.1.218 include "tRNA m(1)A(9)-methyltransferase". Same goes for EC:2.1.1.220 tRNA (adenine(58)-N(1))-methyltransferase, which has synonym 'tRNA m(1)A(58) methyltransferase'.

[kaxelsen]

There are two things at play here, numbering of the atoms in the single nucleotides and numbering of the nucleotides in the RNA chain: m(6)A means methylation at position 6 in adenine. This is (of course) the same for all A's whether they are found in RNA or DNA. LIkewise for m(1)A. Regarding the numbering of the different RNA chains there is a crucial difference. For tRNA's there is a unified numbering system, so all tRNA species have the same numbers, e.g. the anticodon loop is always position 32-34. You can see more about this in Sprinzl et al. (1998), https://academic.oup.com/nar/article/26/1/148/2376733 Contrary to this, rRNA, mRNA etc have no unified numbering so position 1026 is human 26S rRNA is not the same in yeast or sometimes not even in mouse. An example is EC 2.1.1.260. The comment states: "It recognizes Ψ914 in 16S rRNA from the archaeon Methanocaldococcus jannaschii, Ψ1191 in yeast 18S rRNA, and Ψ1248 in human 18S rRNA."

So, in Rhea, we try to always have a generic reaction for rRNA substrates so we can use the same reaction for all species, as for example the reaction for EC 2.1.1.260 actually only is valid for the yeast entry.

[sjm41]

Thanks @kaxelsen

@pgaudet - I'm going to close this ticket. I think we can open another ticket if we want to do a more general review of mRNA/rRNA/tRNA methyltransferase nomenclature in the GO.