WHY3 (WHIRLY3, AT2G02740, UniProt Q66GR6) - manual literature synthesis

No deep-research API was available for this review. This summary was compiled manually from
cached publications in publications/ and PubMed searches ("(WHY3 OR WHIRLY3) AND Arabidopsis",
17 hits, October 2026).

Identity and family

• Arabidopsis thaliana WHIRLY3 (AT2G02740; GeneID 814803), 268 aa, Swiss-Prot reviewed, member of
  the plant-specific Whirly family (PANTHER PTHR31745). Arabidopsis has three Whirlies: WHY1 and
  WHY3 (plastid) and WHY2 (mitochondrion) PMID:21911368.
• Crystal structure of the Whirly domain (residues 78-245, splice variant lacking Ser175) shows
  the canonical Whirly fold and a C4 tetramer generated by crystallographic symmetry
  [PMID:24192350 "WHY1, WHY2 and WHY3 all exhibit the canonical Whirly fold."; "WHY3 crystallized
  in space group P 42 1 2 with one molecule in the asymmetric unit."]. ssDNA-binding residues
  identified in potato WHY2-DNA complexes are conserved in WHY3 PMID:20551348.

Molecular function: single-stranded DNA binding

• EMSA of leaf extracts: knocking out WHY1 (leaving only WHY3) reduces but does not abolish ssDNA
  binding, which disappears only in the double KO [PMID:19666500 "Only one Whirly is detected in
  the single KOs, and no Whirlies are detected in KO1/3 extracts."; "No signal was observed in
  KO1/3, confirming the absence of ptWhirlies in these plants."]. So WHY3 itself binds ssDNA.
• In chloroplast extracts part of the WHY1/3 pool sits in large DNA-containing complexes
  PMID:21911368.
• KBF1 (a factor containing WHY1 and WHY3) binds single- and double-stranded DNA
  [PMID:19669906, abstract only: "KBF1 is a single and double-stranded DNA-binding factor."].
• RNA binding: WHY3 is captured in mRNA-interactome capture of etiolated seedlings [PMID:27729395,
  abstract only] and in leaf ptRIC PMID:32344669. Biological
  role of RNA binding by WHY3 is not established.

Biological process: plastid genome stability / DNA repair

• why1 why3 double KO plants show maternally inherited variegation caused by amplification of
  plastid DNA regions joined at short direct repeats; single KOs show elevated illegitimate
  recombination at lower frequency [PMID:19666500 "This type of recombination occurs frequently in
  plants lacking both Whirlies, to a lesser extent in single KO plants and rarely in WT
  individuals."; "We suggest that AtWhy1 and AtWhy3 function as antirecombination proteins,
  contributing to safeguard plastid genome integrity."].
• After DSB induction by ciprofloxacin, why1 why3 accumulate more microhomology-mediated plastid
  rearrangements; the effect is organelle-specific PMID:20551348. Proposed mechanism: Whirlies bind resected ssDNA and limit
  microhomology-mediated break-induced replication (MMBIR) PMID:21911368.
• WHY1 K91A (24-mer assembly mutant) fails to complement why1 why3 ciprofloxacin sensitivity,
  linking higher-order assembly to the repair function PMID:21911368.
• why1 why3 interact genetically with RECA1 and POLIB; Whirlies repress U-turn-like rearrangements
  PMID:25800675; plastid genome
  instability in why1why3polIb triggers ROS and retrograde signalling PMID:23969600.

Localization

• Chloroplast: transit peptide, in vitro import and GFP fusion [PMID:15967440, abstract only];
  multiple chloroplast proteomes (PMID:18431481, PMID:20061580 stroma, PMID:16326926 pTAC/nucleoid).
• Mitochondrion: in organello import shows WHY3 is also imported into pea mitochondria,
  competed by a mitochondrial precursor PMID:32490348; GFP fusions earlier showed only chloroplast signal.
• Nucleus: UniProt states nucleus by similarity; GFP fusion did not show nuclear signal
  (NOT nucleus, PMID:15967440). ChIP showing WHY1/WHY3 at the AtKP1 upstream element
  PMID:19669906 implies a nuclear pool, at least in overexpressing or SA-treated material.

Nuclear / signalling roles (weak)

• WHY1 and WHY3 identified by MS as components of KBF1, which binds the KPRE element and
  represses AtKP1; SA induces WHY1/WHY3 transcripts [PMID:19669906, abstract only].
• Defense: Whirly defense-gene regulation is established for AtWHY1 and potato StWHY1, not WHY3
  PMID:15708347.
• Phenotypes with less mechanistic support: delayed flowering and reduced seed longevity in why3
  and why1why3 PMID:37351567; MIR840 targets the overlapping PPR/WHY3 3'UTR in senescence
  PMID:34724261. These are not used as annotation evidence here.