merge tRNA uridine/uracil methyltransferase terms?

[gocentral]

There is a term for tRNA (uridine) methyltransferase activity GO:16431 and one for tRNA (uracil) methyltransferase activity GO:16300. One is the nucleobase and the other is the nucleoside but since these molecules are incorporated into tRNA, the base and sugar are there all the time so technically both cases would be the nucleoside, no? Would it make sense to pick one name and merge the two terms?

The same situation exists for guanine/guanosine. For the other bases (A and C) the nucleobase name is used.

-Julie

Reported by: juliep

Original Ticket: "geneontology/ontology-requests/4973":https://sourceforge.net/p/geneontology/ontology-requests/4973

[gocentral]

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This seems reasonable; we should use the one with the more detailed definition as the target. Note that this activity is SAM dependent; there is GO:0030698 which is specfic for U54 to ribo T in some organisms, and is not SAM dependent but depends on methylenetetrahydrofolate.

Original comment by: hdrabkin

[gocentral]

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merged tRNA (guanosine) methyltransferase activity GO:0016424 into tRNA (guanine) methyltransferase activity GO:0016423 tRNA (uridine) methyltransferase activity GO:0016431 into tRNA (uracil) methyltransferase activity GO:0016300

Original comment by: mah11

[gocentral]

• milestone: --> TermGenie
• assigned_to: nobody --> gomidori
• status: open --> closed-accepted

Original comment by: mah11

[gocentral]

Logged In: YES user_id=1510062 Originator: YES

Thanks Midori.

As there are child terms of these terms that sound like they might cause TPVs, how are the SAM-dependent and SAM-independent aspects of this function being dealt with?

-Julie

Original comment by: juliep

[gocentral]

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I've re-checked the paths, and there are no TPVs; some of the terms don't have parents mentioning SAM, whereas others have two parents (for example, compare/contrast GO:0009021 & GO:0030696). I did spot one missing relationship, now added.

m

Original comment by: mah11

[gocentral]

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Ah, great! Thanks Midori!

-Julie

Original comment by: juliep

[gocentral]

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In theory, the GO:0030698 could be a child of the uridine methyltransferases in terms of the final product: riboT; Most organisms to riboT 54 by a SAM dependent enzyme, but The methyl moiety of ribothymidine in the tRNA of Streptococcus faecalis, Bacillus subtitis, Bacillus cereus is derived from a l-carbon folate derivative and not S-adenosylmethionine.In n all Eukarya and many Gram-negative Bacteria, the methyl donor for this reaction is S-adenosyl-l-methionine (S-AdoMet), while in several Gram-positive Bacteria, the source of carbon is N(5), N(10)-methylenetetrahydrofolate (CH(2)H(4)folate).

If you mention SAM being the co-factor in the def, then GO:0030698 can't be a child. However, the def could be worded to indicate the differences, and then make a child term that is S-Adenosyl methionine specific

Original comment by: hdrabkin

[gocentral]

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Harold - huh??? The "topmost" U methyltransferase term doesn't mention a cofactor; some of the descendant terms mention cofactors and have additional parents reflecting the cofactor. The whole thing is fine.

Original comment by: mah11

[gocentral]

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What I meant to convey was IF the parent term did mention only the SAM cofactor, then there would be problem.Not that there was one.

This is a very interesting example of two activities that carry out a similar process (nucleobase methylation), yet do so in very mechanistically different ways. One is more related to the biosynthesis of dTMP (thymidylate synthase).

Original comment by: hdrabkin