rqh1 (Q09811, SPAC2G11.12) — curation notes

Rqh1 (aka rad12, hus2, rec9) is the single RecQ-family ATP-dependent 3'-5' DNA helicase of
Schizosaccharomyces pombe, ortholog of S. cerevisiae Sgs1 and human BLM/WRN/RECQL4.

Identity / domain architecture

• 1328 aa. Helicase ATP-binding domain (528-707), Helicase C-terminal (728-876), HRDC (1115-1195),
  DEAH box motif (651-654), Walker A ATP-binding (555-562). RecQ Zn-binding and RQC domains
  (InterPro). [UniProt Q09811]
• EC 5.6.2.4 (DNA helicase coupling ATP hydrolysis to 3'-5' translocation). [UniProt; PMID:12724426]

Helicase activity / biochemistry

• Rqh1 is a 3'-to-5' DNA helicase that exists with Top3 in a high-MW complex
  PMID:12724426
• Helicase activity confirmed biochemically; T543I (rad12 allele) and K547A/R abolish helicase activity
  [UniProt MUTAGEN 543, 547; PMID:12724426]
• Rqh1p displays 3' to 5' DNA helicase activity but helicase activity is only PARTIALLY required for function in recovery from S-phase arrest/DNA damage
  PMID:12478586

Top3 interaction / RecQ-Top3 complex

• top3 deletion is inviable; suppressed by loss of rqh1 helicase activity or recombination functions
  PMID:12724426
• N-terminal region (first 322 aa) of Rqh1 binds Top3; binding correlates with Rqh1 function
  PMID:15702347
• ComplexPortal/PomBase: RecQ family helicase-topoisomerase III complex (GO:0031422)

Subcellular localization

• Nucleus; nuclear chromosome; nucleolus [PMID:12724426; PMID:12023299]
• Site of double-strand break, nucleolus [PMID:12023299 IDA]
• Nuclear replication fork inferred (IC from RecQ-Top3 complex) PMID:12724426

Recombination control / fork processing (core)

• Rqh1 acts after Rad51 (Rhp51) focus formation, downstream of strand invasion
  PMID:12724426
• Negatively regulates recombination; rqh1Δ shows hyper-recombination, HU and UV sensitivity; DNA damage
  sensitivity alleviated by disrupting recombination
  PMID:19037101
  PMID:19037101
• Prevents blocked forks from collapsing; rqh1- → dramatic increase in deletion events + one-sided DSBs at RTS1 RFB
  PMID:15889146
• Rqh1 limits gross chromosomal rearrangements (GCRs) at collapsed forks by preventing inappropriate ectopic recombination during fork recovery
  PMID:23093942
• Rqh1 counteracts D-loop disassembly (template switch) — antagonized by CAF-1
  PMID:25313826
• Rqh1 (with Fbh1, Srs2, Pfh1) strongly suppresses template switching during recombination-restarted replication
  PMID:30667359

DSB repair / resection

• Rqh1 (Sgs1 ortholog) has a minor role in long-range DSB end resection; Exo1 dominant
  PMID:21931565
• HR repair of IR-induced DSBs in G2; Rqh1-Top3 processes recombination intermediates downstream of Rhp51 foci; controlled by Cdc2-cyclin B via Crb2
  PMID:12023299
• fbh1Δ rqh1Δ double mutant is lethal (suppressed by rhp57Δ) — overlapping roles in processing toxic recombination intermediates
  PMID:16135799

S-phase checkpoint

• Mus81, Rhp51, Rqh1 form an epistatic pathway required for the S-phase DNA damage checkpoint (replication slowing)
  PMID:19037101
  Original gene cloning: rqh1+ required for reversible S phase arrest [PMID:9184215 title]

rDNA maintenance / chromosome segregation

• Deletion of Slx1 or Rqh1 provokes rDNA contraction; slx1 rqh1 double is lethal
  PMID:14528010
• rqh1Δ delayed in anaphase, lagging chromosomal DNA esp. at rDNA; relieving rDNA fork arrest (reb1Δ) partially suppresses
  PMID:16303848

UV damage tolerance / excision repair controversy

• Rqh1 is required for UV damage tolerance/survival during S phase (bypass of damage by replication fork), requires recombination + checkpoint genes + Cds1
  PMID:9372918
• CONTROVERSY: rad12-502 was reported to lack SPDE UV-dimer endonuclease (alternative excision repair)
  PMID:7623848
  BUT the gene's identifiers later refuted this: PMID:9372918
  => GO:0070914 UV-damage excision repair (from PMID:7623848) is likely an over-annotation/historic
  misattribution of a distinct excision-repair endonuclease function to Rqh1. Treated as
  MARK_AS_OVER_ANNOTATED (the SPDE activity is not a property of the RecQ helicase; the true
  UV phenotype is recombination/replication-bypass based per PMID:9372918).

Core function synthesis

• MF: ATP-dependent 3'-5' DNA helicase activity (EC 5.6.2.4); ATP binding; ATP hydrolysis; DNA binding.
• CC: nucleus / nuclear chromosome / nucleolus; RecQ-Top3(-Rmi1) complex; site of DSB; nuclear replication fork.
• BP: suppression of inappropriate/hyper-recombination; processing of stalled/collapsed replication forks
  and recovery from replication stress; dissolution of recombination intermediates (double HJ / D-loops)
  with Top3; DSB repair via HR (resection minor role; intermediate processing major role); S-phase DNA
  damage checkpoint (replication slowing); rDNA maintenance & chromosome segregation.

Re-review journal — 2026-09-01

• Refreshed UniProt and GOA through just fetch-gene SCHPO rqh1 --force; the current
  50-row GOA added three IBA tuples: GO:0043138, GO:0000724 and GO:0009378.
• Accepted the 3'-5' helicase and HR-repair IBAs because Rqh1's own experimental
  annotations ground both ancestral nodes [PMID:12478586 "the Rqh1p protein displays
  3' to 5' DNA helicase activity"; PMID:12724426 "Rqh1 functions after Rad51 focus
  formation during DNA repair"]. Its appearance among PAINT descendants is expected
  target grounding, not circularity.
• Retained four-way junction helicase activity as a non-core conserved RecQ-family
  substrate specialization. PAINT places it on PTN000344873 with same-subfamily BLM and sibling
  WRN/plant RecQ evidence, and Rqh1 independently disassembles branched D-loops
  PMID:25313826. Direct purified-Rqh1 activity on a four-way substrate remains an explicit
  experimental question, not an asserted direct assay.
• Refreshed the PANTHER IBA project through just refresh-panther-iba-project, then
  isolated the Rqh1 changes from unrelated live PAINT drift. The committed project
  data now reproduce 160 IBAs, 90 with subfamily-mappable UniProt seeds, and 36
  cross-subfamily flags.
• Launched the focused OpenScientist hypothesis through the project wrapper. The
  run completed successfully and found the four-way-junction claim partially/weakly
  supported by orthology rather than a direct Rqh1 assay
  [file:SCHPO/rqh1/rqh1-hypotheses/free-text-schizosaccharomyces-pombe-rqh1-directly-unwinds-four-way-holliday-junction-dna-substra/openscientist.md
  "Targeted literature searches did not identify any primary paper demonstrating
  in-vitro four-way-junction unwinding or branch migration by purified Rqh1"]. This
  supports retaining GO:0009378 as IBA while explicitly avoiding any experimental
  evidence upgrade; the existing reconstitution experiment remains the decisive gap.
• The full text also reports an informative assay limitation and negative observation:
  the RTS1-repeat Holliday junctions cannot branch migrate in vitro and therefore
  cannot be dissolved, and HJ-like intermediates did not accumulate in rqh1-d
  relative to wild type PMID:25313826. This is not a refutation of four-way-junction unwinding because
  the assay design precludes the relevant branch-migration/dissolution reaction;
  it reinforces the need for a direct purified-Rqh1 substrate assay.
• Removed generic helicase/pathway quotes from cellular-component annotations after
  checking that they did not demonstrate localization. Refreshing PMID:12023299 and
  PMID:12724426 through just fetch-pmid ... --force recovered their Results sections,
  including direct observations that Rqh1 is nuclear, predominantly nucleolar and
  relocalizes to chromatin foci after irradiation [PMID:12724426 "Rqh1 localized
  to the nucleus throughout the cell cycle"; PMID:12023299 "Rqh1 relocalized from
  a predominantly nucleolar distribution to discrete foci in the chromatin compartment
  1 h postirradiation"]. The localization annotations now cite those assay-relevant
  passages.