WHY3 review notes

2026-10-28 initial review

• fetch-gene resolved Q66GR6 (TAIR AT2G02740, GeneID 814803), 28 GOA rows.
• Literature compiled manually in WHY3-deep-research-manual.md (no deep-research API keys).
• Core view: plastid (and in vitro also mitochondrial) ssDNA-binding Whirly tetramer that,
  redundantly with WHY1, protects plastid DNA against microhomology-mediated illegitimate
  recombination during DSB repair PMID:19666500.
• All in vivo genetic evidence uses the why1 why3 double mutant; single why3 KO has milder
  increase in illegitimate recombination PMID:19666500.
• Decisions:
• DNA binding rows -> MODIFY to single-stranded DNA binding (EMSA of KO1 extracts, which
  contain only WHY3, still bind ssDNA).
• DNA repair rows -> MODIFY to double-strand break repair (ciprofloxacin/bleomycin DSB-inducing
  treatments, MMBIR model) PMID:20551348.
• Defense response (IEA, TAS) -> over-annotated; defense role established for AtWHY1/StWHY1.
• SA-mediated signaling IDA -> over-annotated; abstract supports only SA induction of the
  transcript. Suspected wrong term recorded as source defect (CHECK).
• NOT nucleus -> UNDECIDED; GFP negative but ChIP implies a nuclear pool.
• Mitochondrion: supported by in organello import PMID:32490348; non-core.
• Considered NEW "negative regulation of DNA recombination" (GO:0045910); not added because
  evidence is mutant-phenotype based; raised as a question instead.