rad3 (S. pombe) review notes

UniProt: Q02099. PomBase SPBC216.05. Protein kinase rad3, EC 2.7.11.1, 2386 aa. Ortholog of human ATR (and budding yeast Mec1/Esr1). PIKK family, ATM/ATR-related subfamily. Partner subunit Rad26 (ATRIP).

Identity / family

• Rad3 is the homologue of S. cerevisiae ESR1 (MEC1/SAD3) and Drosophila mei-41; required for all DNA structure checkpoints; member of the 'lipid kinase' (PIKK) subclass that includes ATM. Immunoprecipitated overexpressed Rad3 has associated protein kinase activity. PMID:8978690
• The human gene ATR (ATM and Rad3-related) was identified as closely related and complements esr1-1. PMID:8978690
• Despite PIKK/PI3-kinase sequence similarity, Rad3 is a protein Ser/Thr kinase, phosphorylating S/T-Q (SQ/TQ) motifs. PMID:11553781 UniProt assigns EC 2.7.11.1 (protein serine/threonine kinase).

Molecular function

• Protein Ser/Thr kinase: phosphorylates Chk1 at Ser-345 (damage checkpoint). PMID:11553781
• Phosphorylates Cds1 at Thr-11 (replication checkpoint). PMID:11313465
• Phosphorylates the mediator Mrc1 (with Tel1). PMID:14585996
• Phosphorylates Rad9 (T412/S423). PMID:15155581
• Phosphorylates Crb2 (Thr-73, Ser-80) to promote Chk1 association; direct Rad3-Crb2 interaction. PMID:14739927
• Histone H2A kinase (gamma-H2A), redundantly with Tel1. PMID:15226425 -> PomBase EXP GO:0140995 histone H2A kinase activity.
• Phosphorylates telomere protein Ccq1 Thr-93 (with Tel1). PMID:22302936
• Phosphorylates Mek1 (S12/S14/T15) during meiosis. PMID:21084840
• Kinase domain alone is necessary but NOT sufficient; needs N-terminal sequences (leucine zipper etc.). PMID:10512862

Biological process — checkpoints

• Apical sensor kinase of DNA damage and DNA replication (DNA synthesis) checkpoints. rad3-136 fails G2 arrest after gamma-irradiation and fails to maintain dependence of mitosis on completion of DNA synthesis; also role in DNA repair. PMID:1594599
• Required for all DNA-integrity checkpoint responses; forms stable Rad3-Rad26 complex; Rad26 phosphorylation is the first biochemical marker of Rad3 function (DNA-damage recognition). PMID:10559981
• Replication checkpoint: Cds1 activation requires Rad3 + Mrc1; two-stage mechanism. PMID:16618806
• Intra-S checkpoint generated when forks encounter damage; depends on six checkpoint-Rad proteins, Cds1, Rad4/Cut5. PMID:12032307
• Mus81/Rhp51/Rqh1 epistatic pathway downstream of Cds1 for S-phase DNA damage checkpoint slowing. PMID:19037101 (rad3 IMP for mitotic intra-S DNA damage checkpoint signaling).
• Hsk1/Cdc45 needed for replication-stress checkpoint via Rad3-Mrc1. PMID:21099360

Meiotic checkpoints

• Meiotic DNA replication checkpoint requires the mitotic checkpoint Rad genes and Cds1. PMID:10521402
• Meiotic recombination checkpoint / bouquet stage: persistent meiotic DSBs activate Rad3 and Chk1, extending bouquet stage. PMID:29123917
• Positive regulation of initiation of premeiotic DNA replication; Rad3/Tel1->Mek1 cascade. PMID:21084840 (IMP).

Telomeres

• Rad3 (with Rad26) is one of two pathways (Rad3/Rad26 and Tel1/Rad32) required to maintain telomeres and prevent chromosome circularization; Rad3 associates with telomeres by ChIP. PMID:12196391
• Telomere maintenance via Ccq1 Thr-93 phosphorylation recruiting telomerase. PMID:22302936
• Kinase-INDEPENDENT role: Rad3-Rad26 complex recruits Tel1 to telomeres independent of Rad3 kinase domain. PMID:20140190 IGI with this (telomere maintenance, with rad26/SPBC6B1.09c? actually WITH PomBase:SPBC6B1.09c).

Localization

• Nucleus (UniProt subcellular location). ATR-ATRIP (Rad3-Rad26) complex; ComplexPortal CPX-26412. PMID:10559981
• Chromatin/nuclear chromosome: Rad3 anchored to chromatin via Cdc18 during stalled replication. PMID:17531813
• Associates with meiotic chromosomes (asynapsed axes) — based on mammalian Atr ortholog work. PMID:8843195 NOTE: this paper is about mammalian Atr/Atm, not directly S. pombe Rad3; the GO:0000228 nuclear chromosome IDA on PomBase to PMID:8843195 is by analogy and weak for the pombe gene.
• ChIP at telomeres -> chromosome, telomeric repeat region. [PMID:12196391, PMID:20140190]
• nucleolus IDA (PMID:18180284) and cytosol HDA (PMID:16823372) require caution. The repaired PMC fetch recovered the complete main article for PMID:18180284; it contains Rad3 checkpoint genetics but no Rad3 localization assay and no mention of the nucleolus, rDNA, ribosome, or GFP. The nucleolus annotation is therefore likely miscited, but remains MARK_AS_OVER_ANNOTATED rather than REMOVE because separately hosted supplements were not verified. The cytosol HDA from the ORFeome screen contrasts with the well-established nuclear/chromatin function but remains UNDECIDED because the cached record does not expose the Rad3-specific image.

Action plan summary

• Core MF: protein serine/threonine kinase activity (GO:0004674) — ACCEPT (many IDA/IMP). protein serine kinase (GO:0106310 RHEA) ACCEPT/non-core. histone H2A kinase (GO:0140995) ACCEPT (specific substrate MF). protein kinase activity (GO:0004672) — general, KEEP/ACCEPT as parent but prefer 0004674. kinase activity (GO:0016301), and IEA 0004674 InterPro — general/redundant -> KEEP_AS_NON_CORE or ACCEPT generic; mark less informative ones.
• protein binding (GO:0005515) -> bare protein binding, REMOVE/MARK (uninformative; Crb2 interaction better captured elsewhere).
• Core BP: DNA damage checkpoint signaling (GO:0000077) ACCEPT; mitotic G2 DNA damage checkpoint (GO:0007095) ACCEPT; mitotic intra-S DNA damage checkpoint (GO:0031573) ACCEPT; mitotic DNA replication checkpoint (GO:0033314) ACCEPT; mitotic DNA damage checkpoint (GO:0044773) ACCEPT.
• Meiotic: GO:0033315 meiotic G2/MI DNA replication checkpoint ACCEPT(non-core?); GO:0051598 meiotic recombination checkpoint ACCEPT/non-core; GO:1904514 positive reg premeiotic DNA replication initiation KEEP_AS_NON_CORE.
• Telomere maintenance (GO:0000723) ACCEPT/non-core; chromosome, telomeric repeat region (GO:0140445) ACCEPT.
• DNA repair (GO:0006281) KEEP_AS_NON_CORE (indirect, via checkpoint).
• chromatin remodeling (GO:0006338) IEA from H2A kinase logic -> MARK_AS_OVER_ANNOTATED/REMOVE (Rad3 phosphorylates H2A but is not a chromatin remodeler).
• intracellular signal transduction (GO:0035556) ARBA IEA -> KEEP_AS_NON_CORE (generic parent).
• regulation of double-strand break repair (GO:2000779) NAS ComplexPortal -> KEEP_AS_NON_CORE.
• Localization: nucleus ACCEPT; ATR-ATRIP complex (GO:0070310) ACCEPT (core); chromatin (GO:0000785) ACCEPT; chromosome (GO:0005694) IBA ACCEPT; nuclear chromosome (GO:0000228) is retained as non-core because the cited ortholog study is not sufficient to overrule the experimental curator call; nucleolus (GO:0005730) is under focused evidence review; cytosol (GO:0005829) HDA is UNDECIDED because the cached record does not expose the Rad3-specific imaging result.

2026-09-01 re-review journal

• Refreshed Rad3 through just fetch-gene SCHPO rad3 --force. Current GOA contains 54 rows (50 unique review tuples): six newly seeded rows were manually reviewed, while a retired UniProt-subcellular-location IEA and the superseded PMID:1594599 DNA-repair IMP tuple were removed to match the source.
• The newly current PAINT assertions are consistent with the family phylogeny and target-specific evidence: nucleus is ACCEPT; broad mitotic cell cycle, DNA repair, and telomere maintenance are KEEP_AS_NON_CORE. Rad3 appearing in the IBA source set is expected experimental grounding, not circularity. PMID:1594599 PMID:12196391
• The new ARBA chromatin and combined-automated nucleus calls are ACCEPT because independent S. pombe experiments place Rad3 in a chromatin-bound checkpoint complex. PMID:17531813
• Reclassified the high-throughput cytosol annotation from over-annotated to UNDECIDED. The cached PMID:16823372 record does not expose the Rad3-specific imaging result, so the experimental curator call should not be overruled from incomplete evidence.
• Refreshed PMID:1594599, PMID:8978690, PMID:12196391, and PMID:15226425 through just fetch-pmid --force; publisher restrictions still limited the local records to abstracts, so no full-text claims were made from them. Added manual reference reviews that distinguish these abstract-checked papers from the directly checked full-text records.
• Ran the PANTHER project refresh wrapper and synchronized only the four new Rad3 IBA rows/node decisions; unrelated Pom1 and global family-loss drift was excluded from this one-gene PR.
• Launched a focused OpenScientist job for the GO:0005730 nucleolus IDA. It independently found that PMID:18180284 contains only Rad3 checkpoint-genetic/pathway evidence and no Rad3 localization result, while noting that separately hosted supplements still require curator inspection. PMID:18180284
• The first wrapper fetch of PMID:18180284 silently omitted nested PMC sections. Fixed the PMC HTML fallback in separate PR #2870, shepherded it through the full test suite, merged it, rebased this branch, and regenerated the publication through just fetch-pmid 18180284 --force. The repaired cache now includes Methods, Results, and Discussion (238 lines), including the Rad3 mutant experiments.