Lipoate biosynthetic process: merged into protein lipoylation

GO:0009107 → GO:0009249 protein lipoylation (definition broadened)

AI Gene Review · projects/LIPOATE_BIOSYNTHESIS_OBSOLETION · 2026

Bottom line

  • Lipoate is built on the carrier protein, so "lipoate biosynthesis" and "protein lipoylation" were the same reactions; GO merged GO:0009107 into GO:0009249 on 2026-08-22.
  • The merge touches 12 experimental rows and 11 mappings upstream, and 5 reviews here: all 9 rows are MODIFY → GO:0009249 and 4 core_functions blocks were cleaned (PR #2784).
  • Open: re-point the GO:0016992 part_of edge upstream, re-fetch GOA, and optionally review B. subtilis lipM / lipL / gcvH.

Old term → merged term

Why the terms collapsed

Upstream impact

  • 12 experimental annotations (QuickGO, 2026-08-15): 5 B. subtilis, 2 E. coli, 1 M. tuberculosis, plus human LIPT2, mouse Lias, fly Las, yeast ACP1.
  • 23,924 annotations in total, most electronic via IPR003698 lipoyl synthase (21,946 proteins) and 4 other InterPro families, plus 6 UniRules.
  • All 11 mappings redirect cleanly to GO:0009249; the MFs (e.g. GO:0016992) are mapped separately.
  • 3 of the 12 rows use acts_upstream_of_or_within (E. coli lipA, lipB; mouse Lias) and may move to involved_in.

What changed in this repo

Review Rows on GO:0009107 Action core_functions
POPTR/LIP1 IBA, IEA MODIFY → GO:0009249 GO:0009107 dropped
POPTR/LIP1P-1 IBA, IEA MODIFY → GO:0009249 GO:0009107 dropped
POPTR/LIP1P-2 IBA, IEA MODIFY → GO:0009249 GO:0009107 dropped
BACSU/lipA IEA, IGI (upstream item #2) MODIFY → GO:0009249 GO:0009107 dropped
PSEPK/lipA IEA MODIFY → GO:0009249 none listed

Each core_functions block already listed GO:0009249, so the fix was a deletion. 10 reviews carry GO:0009249 and gain scope from the broader definition.

Status and next steps

  • Done (2026-08-30, PR #2784): 5 reviews migrated; cache/ontologies/go.tsv row refreshed to obsolete.
  • Open: comment upstream that GO:0016992 lipoate synthase activity loses its only BP link (part_of GO:0009107).
  • Open: re-fetch GOA for the 5 genes once GOA reflects the merge.
  • Optional: review B. subtilis lipM, lipL, gcvH (4 of the 12 experimental rows), the clearest case for the merge.

Upstream: go-annotation#6505 · go-ontology#32418
Read more: projects/LIPOATE_BIOSYNTHESIS_OBSOLETION.md · modules/endogenous_protein_lipoylation.yaml