Stilbene cleavage oxygenases

How a carotenoid term spread to every stilbene cleaver in the family

AI Gene Review · projects/STILBENE_CLEAVAGE_OXYGENASES · 2026

Bottom line

  • SCOs split resveratrol-type stilbenes into two aldehydes, but share a fold and PANTHER family (PTHR10543) with carotenoid cleavers.
  • We reviewed 7 members (6 stilbene cleavers from fungi and bacteria, plus the carotenoid cleaver cao-2 as control).
  • GO:0010436 carotenoid dioxygenase activity was REMOVED on all six stilbene cleavers, whether it came by IBA or TreeGrafter IEA; it was accepted on cao-2.

The propagation error

Why this family

  • Paralog positive controls in two fungi: Neurospora cao-2 (carotenoid) vs cao-1 (stilbene); Ustilago Cco1 vs Rco1.
  • The same family term is right for one paralog and wrong for the other; only target-specific experiments separate them.
  • GO was revising this area in July 2026: GO:1905594 resveratrol binding being obsoleted, GO:7770086 resveratrol dioxygenase activity added.

Actions per gene

Carotene catabolism rows

Gene Organism Propagation GO:0016121 carotene catabolic
cao-1 N. crassa IBA MODIFY → GO:0046272 stilbene catabolic
Rco1 U. maydis IBA MODIFY → GO:0046272
NOV1 (Saro_0802) N. aromaticivorans TreeGrafter IEA MODIFY → GO:0046272
NOV2 (Saro_2809) N. aromaticivorans TreeGrafter IEA MODIFY → GO:0046272
LSD-III (lsdB) S. paucimobilis TreeGrafter IEA REMOVE
LSD-I (Q53353) S. paucimobilis TreeGrafter IEA REMOVE

On LSD-I and LSD-III the carotenoid IEA rows sit beside the genes' own IDA lignostilbene-dioxygenase annotations.

A proposed grouping term

From the cao-1 review: a hydroxystilbene / stilbene α,β-dioxygenase activity term as parent of GO:7770086 and GO:0050054, to carry the family-level annotation.

Status and next steps

  • ✅ 7 reviews written (all still status IN_PROGRESS); cao-1 structure analysis explains its substrate panel (two-ring anchor).
  • ⬜ Propose the grouping term to GO; switch structured slots to GO:7770086 once the validation snapshot has it.
  • ⬜ Compare bacterial (NOV1/NOV2/LsdA) and fungal (CAO-1/Rco1) anchor residues.
  • ⬜ Fix at the family node: a stilbene-cleavage subfamily in PTHR10543.

Read more: projects/STILBENE_CLEAVAGE_OXYGENASES.md · genes/NEUCR/cao-1/ · projects/IBA_REVIEW.md