granular function terms fro tRNA

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The most granular term for tRNA activity appears to be triplet codon-amino acid adaptor activity; GOid=GO:0030533;

I envisaged that there would be a 'specific' function term for each codon, so these can be differentiated using GO.

Perhaps ATG codon-amino acid adaptor activity synonym tRNA methionine etc.

Is this appropriate? if so can they be added as I have my niece here to annotate them as a work placement project.

Soyy if this is duplicated, I thought I sent it last night, but I can't see it in the tracker?

Val

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/4273":https://sourceforge.net/p/geneontology/ontology-requests/4273

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I guess we would want to call these serine codon-amino acid adaptor activity

and if we wanted the anticodons (I wrote a codon above by mistake)

They could be children of these.

I don't need the specific codons (just the amino acids) and the codons might be difficult because of different translation systems.

If these are authorised can they be added, (I am running out of jobs for my neice to do, and I don't want her twiddling her thumbs)

Original comment by: ValWood

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Although I like adding a bit more granularity to the tRNAs, as long as we keep it to which triplet codon is recongnized, and not necessarily mention the specific amino acid.

We need to be careful linking codon to aminoacid because in certain cases a stop codons (UGA) is "read" by seleno-cys-tRNA (bound to a special elongation factor). This happens only in certain mRNAs and only if the special elongation factor is expressed; otherwise, the UGA will be read as stop. In some protozoa, however, the UGA stop codn is used for cysteine tRNA, and only uses UAA and UAG as stop In some Archaea, UAG is used to put pyrolysine into a polypeptide chain. How the translation machinery knows when it encounters UAG whether to insert a tRNA with pyrrolysine or to stop translation is not yet known.

For example Weber et al Nucl. Acids Res > v.18(17); Sep 11, 1990 The potato mitochondrail tRNA(ileu): This tRNA has a lysidine-like minor nucleotide in the first position of the anticodon (position 34). The corresponding mitochondrial gene has been cloned and sequenced. This gene has a CAT anticodon which corresponds to methionine. The C residue in the anticodon must therefore be post-transcriptionally modified. The mature tRNA has isoleucine-accepting activity but no methionine-accepting activity. This is the first report showing that in plant mitochondria a post-transcriptional modification could change the amino-acid specificity of a tRNA, as compared to that of the corresponding gene.

Another example is found for at least three Gram-positive bacteria which lack the enzyme glutaminyl-tRNA synthetase (GlnRS), which covalently links glutamine to the glutamine tRNA (tRNAGln) (2). Instead the glutamine tRNA is first aminoacylated with glutamic acid using glutamyl-tRNA synthetase (GluRS) to form Glu-tRNAGln. In a second step, the Glu-tRNAGln is converted to Gln-tRNAGln by an amidotransferase nowcalled Glu-AdT. Similiar findings have been found in archaebacteria, cyanobacteria, mitochondria, and chloroplasts. In archebacteria, asn-tRNAasn is formed in a two step process from asp-tRNAasn.

In my own experimence with initiator met tRNAs, changing the anticodn CAT to a stop codon reader (CUA, to read UAG), makes the tRNA a substrate for glutamine tRNA synthetase (because the glnRS determinants are not in the anticodn).

Original comment by: hdrabkin

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further comments transferred from email:

Harold: I would only put the amino acid in the comments for consistancy. Certainly the specific binding to the codon occurs reagadless of the amino acid attached to the tRNA (shown a long time ago by chemically altering the amino acid once it was attached to the tRNA). So something like these in the comments GCX usually codes for alanine. AUG usually codes for methionine UGA usuaally specifies termination of protein synthesis. However, in some organisms UGA is read by selenocyteine tRNA bound to a speciallized elongation factor.

..... etc.

This way, we could also use UGA, UAG, and UAA codon binding activity, even thouugh most of the time there is not a tRNA that uses these (release factors usually recognize these codons at the ribosomal A site, and trigger the release of the nascent polypeptide chain.

hjd

Midori Harris wrote: > So could we add child terms that mention codons, but without > specifying which amino acid is brought in? E.g. > > id: GO:new > name: GCG codon-amino acid adaptor activity > def: A triplet codon-amino acid adaptor activity that recognizes a > GCG codon. [GOC:mah] > > For codons that don't vary between the various different genetic > codes, maybe we could name the amino acid too?

Original comment by: mah11

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Original comment by: mah11

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attaching file trna.obo, with new terms plus enough parents to make the file loadable in OBO-Edit

I've only mentioned the standard genetic code in the comments -- the NCBI taxonomy lists 23 codes (!) and I thought it would get out of hand to try to cram all of that info into comments. But we can add anything that would be useful, now or later.

http://130.14.29.110/Taxonomy/Utils/wprintgc.cgi?mode=c

m File Added: trna.obo

Original comment by: mah11

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from Harold: "I just expanded the comments for the stop codons to make it clear that they are not normally read by a tRNA."

added 64 codon-specific terms!

the list (long and boring:) GO:0033401 TTT codon-amino acid adaptor activity GO:0033402 TTC codon-amino acid adaptor activity GO:0033403 TTA codon-amino acid adaptor activity GO:0033404 TTG codon-amino acid adaptor activity GO:0033405 TCT codon-amino acid adaptor activity GO:0033406 TCC codon-amino acid adaptor activity GO:0033407 TCA codon-amino acid adaptor activity GO:0033408 TCG codon-amino acid adaptor activity GO:0033409 TAT codon-amino acid adaptor activity GO:0033410 TAC codon-amino acid adaptor activity GO:0033411 TAA codon-amino acid adaptor activity GO:0033412 TAG codon-amino acid adaptor activity GO:0033413 TGT codon-amino acid adaptor activity GO:0033414 TGC codon-amino acid adaptor activity GO:0033415 TGA codon-amino acid adaptor activity GO:0033416 TGG codon-amino acid adaptor activity GO:0033417 CTT codon-amino acid adaptor activity GO:0033418 CTC codon-amino acid adaptor activity GO:0033419 CTA codon-amino acid adaptor activity GO:0033420 CTG codon-amino acid adaptor activity GO:0033421 CCT codon-amino acid adaptor activity GO:0033422 CCC codon-amino acid adaptor activity GO:0033423 CCA codon-amino acid adaptor activity GO:0033424 CCG codon-amino acid adaptor activity GO:0033425 CAT codon-amino acid adaptor activity GO:0033426 CAC codon-amino acid adaptor activity GO:0033427 CAA codon-amino acid adaptor activity GO:0033428 CAG codon-amino acid adaptor activity GO:0033429 CGT codon-amino acid adaptor activity GO:0033430 CGC codon-amino acid adaptor activity GO:0033431 CGA codon-amino acid adaptor activity GO:0033432 CGG codon-amino acid adaptor activity GO:0033433 ATT codon-amino acid adaptor activity GO:0033434 ATC codon-amino acid adaptor activity GO:0033435 ATA codon-amino acid adaptor activity GO:0033436 ATG codon-amino acid adaptor activity GO:0033437 ACT codon-amino acid adaptor activity GO:0033438 ACC codon-amino acid adaptor activity GO:0033439 ACA codon-amino acid adaptor activity GO:0033440 ACG codon-amino acid adaptor activity GO:0033441 AAT codon-amino acid adaptor activity GO:0033442 AAC codon-amino acid adaptor activity GO:0033443 AAA codon-amino acid adaptor activity GO:0033444 AAG codon-amino acid adaptor activity GO:0033445 AGT codon-amino acid adaptor activity GO:0033446 AGC codon-amino acid adaptor activity GO:0033447 AGA codon-amino acid adaptor activity GO:0033447 AGA codon-amino acid adaptor activity GO:0033448 AGG codon-amino acid adaptor activity GO:0033449 GTT codon-amino acid adaptor activity GO:0033450 GTC codon-amino acid adaptor activity GO:0033451 GTA codon-amino acid adaptor activity GO:0033452 GTG codon-amino acid adaptor activity GO:0033453 GCT codon-amino acid adaptor activity GO:0033454 GCC codon-amino acid adaptor activity GO:0033455 GCA codon-amino acid adaptor activity GO:0033456 GCG codon-amino acid adaptor activity GO:0033457 GAT codon-amino acid adaptor activity GO:0033458 GAC codon-amino acid adaptor activity GO:0033459 GAA codon-amino acid adaptor activity GO:0033460 GAG codon-amino acid adaptor activity GO:0033461 GGT codon-amino acid adaptor activity GO:0033462 GGC codon-amino acid adaptor activity GO:0033463 GGA codon-amino acid adaptor activity GO:0033464 GGG codon-amino acid adaptor activity

m

Original comment by: mah11

[gocentral]

• labels: --> New term request
• milestone: --> 224410
• assigned_to: nobody --> gomidori
• status: open --> closed-accepted

Original comment by: mah11

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Thanks a million, that'll keep her busy on Monday ;)

Original comment by: ValWood

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• milestone: 224410 --> PomBase

Original comment by: mah11