43 tRNA aminoacylation terms are going

Substrate-specific tRNA charging BPs merge into GO:0006418 and GO:0070127

AI Gene Review · projects/AMINO_ACID_ACTIVATION_OBSOLETION · 2026

Bottom line

  • GO is obsoleting 43 BP terms that name the amino acid charged onto tRNA; specificity already lives on the <aa>-tRNA ligase MF terms.
  • 33 reviews here touch the obsoleted terms, 26 inside strictly validated core_functions.
  • 16 reviews argue the opposite of GO: they mark GO:0006418 over-annotated because the specific child "already captures" the process. No review has been edited yet.

Old terms → replacements

Why GO is doing this

  • Each obsoleted BP has an exact 1:1 MF counterpart (GO:0006419 ↔ GO:0004813 alanine-tRNA ligase).
  • Compartment is not an MF distinction either: mitochondrial twins map to the same MF.
  • The mitochondrial block is barely used: 24 experimental annotations across 20 terms, 6 terms with none.
  • Surrounding hierarchy already fixed: #32537 and #32541 merged in August 2026.

The inverted judgment

gtpbp3: a laundering risk

  • GO:0070153 and GO:0070155 each have one annotation in all of GOA: zebrafish gtpbp3, IMP, PMID:30916346.
  • gtpbp3 is a tRNA-modifying GTPase, not a synthetase. Our review marks all six rows MARK_AS_OVER_ANNOTATED.
  • A bulk merge would turn six visible over-annotations into one plausible GO:0070127 row. Withdraw, don't migrate.

Repo impact today

Group Reviews Note
PSEPK synthetases 21 15 mark GO:0006418 over-annotated
PSEPK gatA/gatB/gatC 3 GO:0070681 row UNDECIDED
human AARS1, AARS2 2 AARS2 proposes GO:0070143, itself obsolete
POPTR ALARS, GATC; METTP gatC 3 core_functions on obsoleted ids
DANRE gtpbp3 1 six IMP rows, over-annotated
human AARSD1, DARS2; DROME TyrRS 3 annotation rows only

Counted from genes///*-ai-review.yaml on 2026-09-26. The page's own tables predate the PSEPK batch (#2899).

Status and next steps

  1. Wait for go-ontology#15375 to land; module text notes QuickGO's 2026-09-22 snapshot already obsoletes GO:0006421, GO:0006425, GO:0070681.
  2. Comment on go-annotation#6525: withdraw the gtpbp3 cluster; confirm GO:0070681 is in the batch.
  3. Re-argue the 16 inverted reviews; re-point core_functions in 26.
  4. Refresh modules/bacterial_aminoacyl_trna_charging.yaml.

Read more: projects/AMINO_ACID_ACTIVATION_OBSOLETION.md