Rad3 is the fission-yeast ortholog of human ATR (and budding yeast Mec1), a large (2386 aa) PIKK-family (phosphatidylinositol-3-kinase-related) serine/threonine protein kinase (EC 2.7.11.1) that is the apical sensor kinase of the DNA-structure checkpoints, responding to both DNA damage and stalled/incomplete DNA replication. Despite its sequence similarity to lipid kinases, Rad3 is a protein kinase that phosphorylates serine or threonine residues within S/T-Q (SQ/TQ) motifs. It functions as a stable heterodimeric complex with its regulatory subunit Rad26 (ATRIP), which is recruited to RPA-coated single-stranded DNA at stalled forks and resected breaks. Together with the checkpoint clamp (Rad1-Rad9-Hus1, the 9-1-1 clamp) and the Rad17 clamp loader, the Rad3-Rad26 complex transduces the checkpoint signal by phosphorylating and activating the effector kinases Chk1 (DNA damage, G2/M arrest via Cdc25 inhibition) and Cds1 (replication checkpoint, S-M coupling), as well as mediators such as Crb2, Mrc1 and Rad9, and the histone variant H2A (generating gamma-H2A). Rad3 also acts in meiotic checkpoints, in telomere maintenance (phosphorylating Ccq1 to recruit telomerase, and redundantly with Tel1/MRN preventing chromosome circularization), and contributes to telomere protection partly through kinase-independent functions of the Rad3-Rad26 complex. It is a nuclear, chromatin-associated kinase that localizes to sites of DNA damage, stalled replication forks and telomeres.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004674 protein serine/threonine kinase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Core molecular function. Rad3/ATR is a protein serine/threonine kinase that phosphorylates SQ/TQ motifs in checkpoint substrates. Strongly supported by phylogenetic inference and abundant experimental data. Reason: Rad3 is the apical checkpoint Ser/Thr kinase; multiple IDA/IMP annotations and direct substrate phosphorylation studies corroborate this phylogenetic call. Supporting Evidence: PMID:11553781 Rad3, a protein kinase related to human ATM and ATR. These kinases phosphorylate serine or threonine followed by glutamine (SQ/TQ). |
| GO:0000077 DNA damage checkpoint signaling | IBA GO_REF:0000033 | ACCEPT | Summary: Core biological process. Rad3 is the apical sensor kinase required for DNA damage checkpoint signaling, transducing damage signals to Chk1 to delay mitosis. Reason: Phylogenetic inference corroborated by classic genetics (rad3 mutants fail G2 arrest after irradiation) and direct Chk1 phosphorylation. Supporting Evidence: PMID:1594599 the mutant cells are unable to arrest in the G2 phase of the cell cycle after DNA damage by gamma-irradiation |
| GO:0005694 chromosome | IBA GO_REF:0000033 | ACCEPT | Summary: Rad3 acts on chromatin/chromosomes, including at sites of DNA damage, stalled replication forks and telomeres. The generic chromosome term is supported. Reason: Consistent with chromatin and telomere ChIP localization; a more specific chromatin term is also annotated. Supporting Evidence: PMID:17531813 Cdc18 persists in a chromatin-bound complex including the checkpoint kinases Rad3 and Rad26. |
| GO:0004672 protein kinase activity | IEA GO_REF:0000117 | MODIFY | Summary: Correct but general parent term. The specific protein serine/threonine kinase activity term is preferred. Reason: Rad3 is specifically a protein Ser/Thr kinase; the more specific term is supported by experimental data, so this general term should be refined. Proposed replacements: protein serine/threonine kinase activity Supporting Evidence: PMID:8978690 immunoprecipitation of overexpressed Rad3 demonstrates an associated protein kinase activity |
| GO:0004674 protein serine/threonine kinase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Core molecular function, electronically inferred from EC 2.7.11.1 / InterPro. Fully consistent with experimental evidence. Reason: Redundant with experimentally supported protein Ser/Thr kinase annotations. Supporting Evidence: PMID:11313465 Rad3 and ATM phosphorylate the N-terminal domain of Cds1 at the motif T(11)Q(12) |
| GO:0006338 chromatin remodeling | IEA GO_REF:0000108 | MARK AS OVER ANNOTATED | Summary: This term was inferred electronically (GO_REF:0000108) from Rad3's histone H2A kinase activity (GO:0140995) via a GO inter-ontology logical link. Rad3 genuinely phosphorylates histone H2A (gamma-H2A), so the inference is internally consistent with GO's logical definitions; however, "chromatin remodeling" most naturally denotes ATP-dependent nucleosome repositioning, and gamma-H2A is better understood as a DNA-damage signaling mark than as remodeling. The annotation is thus over-broad rather than strictly wrong. Reason: Automated inter-ontology inference from Rad3's bona fide histone H2A kinase activity. gamma-H2A is a signaling mark; labeling Rad3 a chromatin "remodeler" over-reaches the inference, so the term is flagged as over-annotated rather than removed (the underlying histone-kinase function is real). Supporting Evidence: PMID:15226425 formation of gamma-H2A redundantly requires the ATR/ATM-related kinases Rad3 and Tel1 |
| GO:0016301 kinase activity | IEA GO_REF:0000002 | MODIFY | Summary: Overly general, derived from the PI3/PI4-kinase InterPro signature. As written it also risks implying lipid kinase activity, which is not supported - Rad3 is a protein Ser/Thr kinase. Should be refined to the specific protein kinase term. Reason: The PIKK signature reflects sequence similarity to lipid kinases, but Rad3 has not been shown to phosphorylate lipids; the informative activity is protein Ser/Thr kinase. Proposed replacements: protein serine/threonine kinase activity Supporting Evidence: PMID:10512862 Despite this similarity, none of the PI3-kinase-related (PI3KR) proteins have been shown to phosphorylate lipids. |
| GO:0035556 intracellular signal transduction | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: Generic parent term. Rad3 is a checkpoint signal-transducing kinase, so this is not wrong, but the specific checkpoint signaling terms are far more informative. Reason: Broadly correct but uninformative; the specific DNA damage/replication checkpoint signaling terms capture the function. Supporting Evidence: PMID:10559981 Rad26 shows Rad3-dependent phosphorylation after DNA damage. |
| GO:0106310 protein serine kinase activity | IEA GO_REF:0000116 | ACCEPT | Summary: RHEA-derived MF consistent with Rad3 being a protein Ser/Thr kinase. The combined Ser/Thr term is preferred as primary, but this is accurate. Reason: Accurate sub-aspect of the kinase activity; redundant with GO:0004674. Supporting Evidence: PMID:11553781 Rad3 and ATM phosphorylate serine-345 of fission yeast Chk1. |
| GO:0005515 protein binding | IPI PMID:14739927 Regulation of checkpoint kinases through dynamic interaction... | REMOVE | Summary: Bare "protein binding" is uninformative. This annotation records the Rad3-Crb2 interaction; the functionally meaningful relationships (Rad3-Rad26 complex, Rad3 phosphorylating Crb2/Chk1) are captured by other terms. Reason: Per curation guidelines, avoid uninformative protein binding; the relevant interaction is better represented by the ATR-ATRIP complex and substrate phosphorylation terms. Supporting Evidence: PMID:14739927 we show direct interaction between Rad3 and Crb2, which is inhibitory to Rad3 activity. |
| GO:0005634 nucleus | NAS PMID:10559981 A Rad3-Rad26 complex responds to DNA damage independently of... | ACCEPT | Summary: Nuclear localization, consistent with Rad3 function. Supported, though the specific chromatin/chromosome and ATR-ATRIP complex terms are more informative. Reason: Correct compartment, corroborated by multiple lines of evidence. Supporting Evidence: PMID:10559981 a stable association between Rad3 and Rad26 in soluble protein extracts |
| GO:0070310 ATR-ATRIP complex | IPI PMID:10559981 A Rad3-Rad26 complex responds to DNA damage independently of... | ACCEPT | Summary: Core cellular component. Rad3 (ATR) forms a stable complex with Rad26 (ATRIP), the canonical ATR-ATRIP DNA damage-sensing kinase complex. Reason: Directly demonstrated stable Rad3-Rad26 complex; ComplexPortal CPX-26412. Supporting Evidence: PMID:10559981 a stable association between Rad3 and Rad26 in soluble protein extracts |
| GO:2000779 regulation of double-strand break repair | NAS PMID:10559981 A Rad3-Rad26 complex responds to DNA damage independently of... | KEEP AS NON CORE | Summary: Broadly consistent with Rad3's role as a checkpoint kinase that governs the DNA-damage response to double-strand breaks, but this is an NAS, general annotation rather than a core function. Reason: Plausible regulatory role via checkpoint signaling, but not the primary, directly assayed function. Supporting Evidence: PMID:10559981 Rad3-related checkpoint kinases may have a direct role in DNA-damage recognition. |
| GO:0140995 histone H2A kinase activity | EXP PMID:15226425 Histone H2A phosphorylation controls Crb2 recruitment at DNA... | ACCEPT | Summary: Experimentally supported specific molecular function. Rad3, redundantly with Tel1, phosphorylates the C-terminal SQE motif of histone H2A to generate gamma-H2A at sites of DNA damage. Reason: Direct experimental evidence that gamma-H2A formation requires Rad3 and Tel1. Supporting Evidence: PMID:15226425 formation of gamma-H2A redundantly requires the ATR/ATM-related kinases Rad3 and Tel1 |
| GO:0004674 protein serine/threonine kinase activity | IMP PMID:15155581 Chk1 activation requires Rad9 S/TQ-site phosphorylation to p... | ACCEPT | Summary: Core MF. Rad3 phosphorylates the 9-1-1 clamp subunit Rad9 on C-terminal SQ/TQ sites (T412/S423), required for Chk1 checkpoint activation. Reason: Direct evidence of Rad3-dependent Rad9 SQ/TQ phosphorylation. Supporting Evidence: PMID:15155581 C-terminal T412/S423 phosphorylation of Rad9 by Rad3(ATR) occurs in S phase without replication stress. Rad3(ATR) and Tel1(ATM) phosphorylate these same residues |
| GO:0033315 meiotic G2/MI DNA replication checkpoint signaling | IMP PMID:10521402 Meiotic DNA replication checkpoint control in fission yeast. | ACCEPT | Summary: Supported. The meiotic DNA replication checkpoint that blocks meiosis I when replication is incomplete requires the mitotic checkpoint Rad genes (including rad3) and Cds1. Reason: Genetic evidence that the meiotic replication checkpoint requires the Rad genes. Supporting Evidence: PMID:10521402 The mitotic checkpoint Rad genes and the Cds1 protein kinase are required for the DNA replication checkpoint during meiosis |
| GO:0005515 protein binding | IPI PMID:10559981 A Rad3-Rad26 complex responds to DNA damage independently of... | REMOVE | Summary: Bare "protein binding" recording the Rad3-Rad26 interaction. The Rad3-Rad26 relationship is informatively captured by the ATR-ATRIP complex term. Reason: Uninformative per curation guidelines; the Rad26 (ATRIP) interaction is represented by the ATR-ATRIP complex annotation. Supporting Evidence: PMID:10559981 a stable association between Rad3 and Rad26 in soluble protein extracts |
| GO:0070310 ATR-ATRIP complex | IDA PMID:10559981 A Rad3-Rad26 complex responds to DNA damage independently of... | ACCEPT | Summary: Core cellular component (IDA). Directly demonstrated Rad3-Rad26 (ATR-ATRIP) complex. Reason: Direct co-purification of Rad3 with Rad26. Supporting Evidence: PMID:10559981 a stable association between Rad3 and Rad26 in soluble protein extracts |
| GO:0004672 protein kinase activity | IDA PMID:8978690 The Schizosaccharomyces pombe rad3 checkpoint gene. | MODIFY | Summary: Correct but general; immunoprecipitated Rad3 shows associated protein kinase activity. The specific protein Ser/Thr kinase term is preferred. Reason: The activity is a protein Ser/Thr kinase; the more specific term is well supported. Proposed replacements: protein serine/threonine kinase activity Supporting Evidence: PMID:8978690 immunoprecipitation of overexpressed Rad3 demonstrates an associated protein kinase activity |
| GO:0004674 protein serine/threonine kinase activity | IMP PMID:16618806 Two-stage mechanism for activation of the DNA replication ch... | ACCEPT | Summary: Core MF. Rad3 is the upstream kinase that, with the mediator Mrc1, primes the replication checkpoint kinase Cds1 by Rad3-dependent phosphorylation. Reason: Direct evidence of Rad3-dependent phosphorylation priming Cds1 activation. Supporting Evidence: PMID:16618806 Cds1 is then primed for activation by Rad3-dependent phosphorylation. |
| GO:0004674 protein serine/threonine kinase activity | IDA PMID:14585996 Replication checkpoint protein Mrc1 is regulated by Rad3 and... | ACCEPT | Summary: Core MF. Rad3 (with Tel1) phosphorylates the replication-checkpoint mediator Mrc1 at S/TQ motifs to control Cds1 activation. Reason: Direct evidence of Rad3-dependent Mrc1 phosphorylation. Supporting Evidence: PMID:14585996 Rad3 and Tel1 regulate Mrc1 through differential phosphorylation to control Cds1. |
| GO:0051598 meiotic recombination checkpoint signaling | IMP PMID:29123917 The telomere bouquet facilitates meiotic prophase progressio... | ACCEPT | Summary: Supported. Persistent DNA damage from meiotic recombination activates the Rad3-Chk1 checkpoint, extending meiotic prophase (the bouquet stage). Reason: Live-imaging genetics show Rad3 (with Chk1) restrains meiotic prophase exit in response to unrepaired recombination intermediates. Supporting Evidence: PMID:29123917 Persistent DNA damages, induced during meiotic recombination, activate the Rad3 and Chk1 DNA damage checkpoint kinases and extend the bouquet stage beyond the chromosome oscillation period. |
| GO:0000785 chromatin | IDA PMID:17531813 Cdc18 enforces long-term maintenance of the S phase checkpoi... | ACCEPT | Summary: Supported cellular component. The Rad3-Rad26 complex is anchored to chromatin via Cdc18 during stalled replication to maintain the S-phase checkpoint. Reason: Direct evidence of chromatin-bound Rad3-Rad26 complex. Supporting Evidence: PMID:17531813 Cdc18 persists in a chromatin-bound complex including the checkpoint kinases Rad3 and Rad26. |
| GO:0000723 telomere maintenance | IGI PMID:20140190 A kinase-independent role for the Rad3(ATR)-Rad26(ATRIP) com... | KEEP AS NON CORE | Summary: Supported. The Rad3-Rad26 complex contributes to telomere maintenance, including a kinase-independent role in recruiting Tel1 to telomeres. Important for genome stability but not the core checkpoint-kinase function. Reason: Genetic interaction evidence supports a telomere maintenance role; this is a specialized, partly kinase-independent activity rather than the primary function. Supporting Evidence: PMID:20140190 the Rad3(ATR)-Rad26(ATRIP) complex contributes to the recruitment of Tel1(ATM) independently of Rad3(ATR) kinase activity |
| GO:0140445 chromosome, telomeric repeat region | IDA PMID:20140190 A kinase-independent role for the Rad3(ATR)-Rad26(ATRIP) com... | ACCEPT | Summary: Supported. Rad3 (with Rad26) associates with telomeric repeat DNA, where it acts in telomere maintenance. Reason: ChIP evidence of Rad3-Rad26 telomere association. Supporting Evidence: PMID:20140190 both wild-type Rad3ATR and Rad3-kdΞATR proteins associate with telomeric DNA in a Rad26-dependent manner |
| GO:0004674 protein serine/threonine kinase activity | IDA PMID:21084840 The Mek1 phosphorylation cascade plays a role in meiotic rec... | ACCEPT | Summary: Core MF. Rad3 (and/or Tel1) phosphorylates the meiotic kinase Mek1 at S12/S14/T15 in response to programmed meiotic double-strand breaks. Reason: Direct evidence of Rad3-dependent Mek1 phosphorylation. Supporting Evidence: PMID:21084840 Mek1 is phosphorylated at serine-12 (S12), S14 and threonine-15 (T15) by Rad3 (ATR) and/or Tel1 (ATM) kinases that are activated by meiotic programmed double-strand breaks (DSBs) |
| GO:1904514 positive regulation of initiation of premeiotic DNA replication | IMP PMID:21084840 The Mek1 phosphorylation cascade plays a role in meiotic rec... | KEEP AS NON CORE | Summary: The Rad3-Cds1 pathway coordinates the initiation of meiotic recombination and meiotic divisions with premeiotic DNA synthesis, and Mek1-T15 phosphorylation is important for meiotic S phase. This is a peripheral, meiosis-specific role rather than a core function. Reason: Supported as a meiosis-specific regulatory role, but secondary to Rad3's core checkpoint-kinase function. Supporting Evidence: PMID:21084840 Rad3-Cds1 pathway coordinates the initiation of meiotic recombination and meiotic cell divisions with premeiotic DNA synthesis. |
| GO:0000723 telomere maintenance | IMP PMID:12196391 Telomere binding of checkpoint sensor and DNA repair protein... | KEEP AS NON CORE | Summary: Supported. Rad3/Rad26 is one of two redundant pathways (with Tel1/Rad32) required to maintain telomeres and prevent chromosome circularization. Reason: Well-supported telomere maintenance role; a specialized activity rather than the core checkpoint-signaling function. Supporting Evidence: PMID:12196391 Rad3/Rad26 and Tel1/Rad32 represent two pathways required to maintain telomeres and prevent chromosome circularization |
| GO:0140445 chromosome, telomeric repeat region | IDA PMID:12196391 Telomere binding of checkpoint sensor and DNA repair protein... | ACCEPT | Summary: Supported. ChIP shows Rad3 associates with telomeres, where it contributes to telomere maintenance and protection. Reason: Direct ChIP evidence of Rad3 telomere association. Supporting Evidence: PMID:12196391 Chromatin immunoprecipitation analyses found that Rad3, Rad1, Rad9, Hus1, Rad17, Rad32, and Ku70 associate with telomeres. |
| GO:0004674 protein serine/threonine kinase activity | IDA PMID:11553781 Serine-345 is required for Rad3-dependent phosphorylation an... | ACCEPT | Summary: Core MF. Rad3 directly phosphorylates the effector kinase Chk1 at Ser-345, the key event in DNA damage checkpoint signal transduction. Reason: Direct evidence of Rad3-dependent Chk1 Ser-345 phosphorylation. Supporting Evidence: PMID:11553781 Rad3 and ATM phosphorylate serine-345 of fission yeast Chk1. Mutation of serine-345 (chk1-S345A) abrogates Rad3-dependent phosphorylation of Chk1 in vivo. |
| GO:0033314 mitotic DNA replication checkpoint signaling | IMP PMID:11313465 Threonine-11, phosphorylated by Rad3 and atm in vitro, is re... | ACCEPT | Summary: Core biological process. Rad3 is the upstream kinase of the replication checkpoint; it phosphorylates Cds1 (T11) to enforce the S-M checkpoint coupling mitosis to completion of DNA synthesis. Reason: Direct evidence that Rad3-dependent Cds1 activation enforces the S-M checkpoint. Supporting Evidence: PMID:11313465 Rad3-dependent phosphorylation of Cds1 at threonine-11 is required for Cds1 activation and function. |
| GO:0004674 protein serine/threonine kinase activity | IDA PMID:11313465 Threonine-11, phosphorylated by Rad3 and atm in vitro, is re... | ACCEPT | Summary: Core MF. Rad3 phosphorylates Cds1 at Thr-11 (T11Q12 motif) in vitro, required for Cds1 activation. Reason: Direct in vitro evidence of Rad3-dependent Cds1 phosphorylation. Supporting Evidence: PMID:11313465 Rad3 and ATM phosphorylate the N-terminal domain of Cds1 at the motif T(11)Q(12). |
| GO:0000785 chromatin | IDA PMID:21945095 Mcm10 interacts with Rad4/Cut5(TopBP1) and its association w... | ACCEPT | Summary: Supported. Rad3 acts on chromatin at replication origins, consistent with its replication-checkpoint surveillance function (Mcm10/Rad4-Cut5/TopBP1 context). Reason: Consistent with chromatin localization at origins/forks. Supporting Evidence: PMID:17531813 Cdc18 persists in a chromatin-bound complex including the checkpoint kinases Rad3 and Rad26. |
| GO:0004674 protein serine/threonine kinase activity | IDA PMID:21099360 Hsk1 kinase and Cdc45 regulate replication stress-induced ch... | ACCEPT | Summary: Core MF. Rad3 acts via the Rad3-Mrc1 (Claspin) pathway to activate Cds1 in response to replication stress. Reason: Consistent with Rad3's established replication-checkpoint kinase activity. Supporting Evidence: PMID:16618806 Activation of Cds1 is known to require the upstream kinase Rad3 and the mediator Mrc1 |
| GO:0005730 nucleolus | IDA PMID:18180284 Minichromosome maintenance proteins interact with checkpoint... | MARK AS OVER ANNOTATED | Summary: The cited paper establishes Rad3-dependent replication-checkpoint phenotypes but does not report a Rad3 localization assay or mention the nucleolus in its accessible full main text. Nucleolar localization therefore lacks support from the cited source, whereas Rad3 is independently established on chromatin and at telomeres. Reason: Focused review of the complete PMC main article found Rad3 only in genetic and pathway experiments, with no nucleolus, rDNA, ribosome, GFP, or Rad3 imaging result. This is likely a reference mismatch, but MARK_AS_OVER_ANNOTATED is retained conservatively because separately hosted supplemental material has not been verified and the experimental curator may have had access to additional evidence. Supporting Evidence: PMID:18180284 This is also the case in Ξ rad3 mutants, because the Rad3 kinase is required for Cds1 phosphorylation and activation. file:SCHPO/rad3/rad3-hypotheses/existing-go-0005730-mark-as-over-annotated/openscientist.md The seed action **MARK_AS_OVER_ANNOTATED is supported and, if anything, conservative.** |
| GO:0044773 mitotic DNA damage checkpoint signaling | EXP PMID:15226425 Histone H2A phosphorylation controls Crb2 recruitment at DNA... | ACCEPT | Summary: Core BP. Rad3 (with Tel1) mediates the DNA-damage checkpoint via gamma-H2A formation, Crb2 recruitment and checkpoint maintenance after DNA breaks. Reason: Experimental evidence that Rad3-dependent gamma-H2A maintains checkpoint arrest after damage. Supporting Evidence: PMID:15226425 Mutation of the SQE motif to AQE (H2A-AQE) in the two histone H2A genes caused sensitivity to a wide range of genotoxic agents, increased spontaneous DNA damage, and impaired checkpoint maintenance. |
| GO:0031573 mitotic intra-S DNA damage checkpoint signaling | IMP PMID:19037101 Mus81, Rhp51(Rad51), and Rqh1 form an epistatic pathway requ... | ACCEPT | Summary: Core BP. Rad3 is required for the S-phase DNA damage checkpoint; the Mus81/Rhp51/Rqh1 pathway acts in this Rad3/Cds1-dependent response. Reason: Genetic evidence places rad3 in the S-phase DNA damage checkpoint. Supporting Evidence: PMID:12032307 The slowing of S phase depends strongly on the six checkpoint-Rad proteins, on Cds1, and on Rad4/Cut5 |
| GO:0007095 mitotic G2 DNA damage checkpoint signaling | IMP PMID:1594599 The rad3+ gene of Schizosaccharomyces pombe is involved in m... | ACCEPT | Summary: Core BP. rad3 mutants fail to arrest in G2 after gamma-irradiation, defining Rad3 as essential for the G2 DNA damage checkpoint. Reason: Classic genetic evidence for the G2 DNA damage checkpoint defect. Supporting Evidence: PMID:1594599 the mutant cells are unable to arrest in the G2 phase of the cell cycle after DNA damage by gamma-irradiation |
| GO:0031573 mitotic intra-S DNA damage checkpoint signaling | IMP PMID:1594599 The rad3+ gene of Schizosaccharomyces pombe is involved in m... | ACCEPT | Summary: Core BP. Rad3 is required to maintain the dependence of mitosis on completion of DNA synthesis, i.e. the intra-S/replication-coupled checkpoint. Reason: Genetic evidence of S-phase checkpoint defect in rad3 mutants. Supporting Evidence: PMID:1594599 incapable of maintaining the dependence of mitosis upon the completion of DNA synthesis |
| GO:0004672 protein kinase activity | IMP PMID:22302936 Tel1(ATM) and Rad3(ATR) phosphorylate the telomere protein C... | MODIFY | Summary: Correct but general. Rad3 phosphorylates the telomere protein Ccq1 (Thr-93); the specific protein Ser/Thr kinase term is preferred. Reason: Rad3 is a protein Ser/Thr kinase; the more specific term should be used. Proposed replacements: protein serine/threonine kinase activity Supporting Evidence: PMID:22302936 the telomere protein Ccq1 is phosphorylated at Thr 93 (threonine residue at amino acid 93) by Tel1(ATM) and Rad3(ATR) both in vitro and in vivo |
| GO:0004674 protein serine/threonine kinase activity | IDA PMID:10512862 Requirement of sequences outside the conserved kinase domain... | ACCEPT | Summary: Core MF. Rad3 has protein kinase activity; the conserved kinase domain is necessary (though not sufficient) for catalytic activity and checkpoint function. Reason: Biochemical/genetic evidence on Rad3 catalytic activity and the requirement of the kinase domain. Supporting Evidence: PMID:10512862 these sequences are required for catalytic activity |
| GO:0005829 cytosol | HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ... | UNDECIDED | Summary: A high-throughput ORFeome study reports cytosolic localization, whereas Rad3's experimentally established checkpoint functions occur in nuclear, chromatin-bound complexes. Reason: The cached record does not expose the Rad3-specific imaging result, so the experimental localization cannot be independently assessed. Retain the curator annotation without asserting that the cytosolic pool is erroneous. |
| GO:0031573 mitotic intra-S DNA damage checkpoint signaling | IMP PMID:12032307 A single unbranched S-phase DNA damage and replication fork ... | ACCEPT | Summary: Core BP. The intra-S-phase checkpoint that slows DNA synthesis when forks encounter damage depends on the checkpoint-Rad proteins including Rad3. Reason: Genetic evidence that the intra-S checkpoint requires the checkpoint-Rad proteins. Supporting Evidence: PMID:12032307 The slowing of S phase depends strongly on the six checkpoint-Rad proteins, on Cds1, and on Rad4/Cut5 |
| GO:0000228 nuclear chromosome | IDA PMID:8843195 The Atr and Atm protein kinases associate with different sit... | KEEP AS NON CORE | Summary: Association with (meiotic) nuclear chromosomes is consistent with Rad3 acting on chromatin, but the cited study primarily characterized the mammalian Atr/Atm orthologs on meiotic chromosomes; for S. pombe Rad3 this is supported by analogy and by direct pombe chromatin/telomere ChIP in other studies. Reason: Compartment is plausible and corroborated by pombe chromatin localization, but the specific cited evidence is largely from orthologs; the generic chromatin/chromosome terms already cover the core site. Supporting Evidence: PMID:8843195 Atr is found at sites along unpaired or asynapsed chromosomal axes |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Rad3 is a nuclear checkpoint kinase that acts in chromatin-bound complexes at stalled replication forks, DNA lesions, and telomeres. The IBA is consistent with direct S. pombe chromatin-localization evidence. Reason: The PAINT inference is corroborated by target-specific experimental evidence and by the independently curated nuclear and chromatin annotations. Supporting Evidence: PMID:17531813 Cdc18 persists in a chromatin-bound complex including the checkpoint kinases Rad3 and Rad26. |
| GO:0000278 mitotic cell cycle | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Rad3 couples mitotic progression to completion of DNA synthesis and DNA integrity. The broad mitotic-cell-cycle term is correct, but the specific checkpoint-signaling annotations describe its role more informatively. Reason: Retain the phylogenetic inference as a true broad parent while treating DNA damage and replication checkpoint signaling as the core processes. Supporting Evidence: PMID:1594599 the mutant cells are unable to arrest in the G2 phase of the cell cycle after DNA damage by gamma-irradiation and are also incapable of maintaining the dependence of mitosis upon the completion of DNA synthesis |
| GO:0006281 DNA repair | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Classic rad3 mutant phenotypes support a contribution to DNA repair in addition to checkpoint control. This broad IBA agrees with the independent target-specific IMP annotation but is not the most precise core role. Reason: The phylogenetic assertion is experimentally grounded on Rad3 itself; retain it as a broad secondary process rather than reducing Rad3's core checkpoint-kinase function to generic DNA repair. Supporting Evidence: PMID:1594599 The rad3+ gene is also likely to play a role in DNA repair. |
| GO:0000723 telomere maintenance | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Rad3-Rad26 and Tel1-Rad32 provide partly redundant telomere-maintenance pathways, and Rad3 directly associates with telomeres. This is a genuine conserved function, though secondary to checkpoint signaling. Reason: The IBA is corroborated by S. pombe genetic and ChIP evidence and is not weakened by Rad3 appearing among its experimentally grounded descendants. Supporting Evidence: PMID:12196391 Rad3/Rad26 and Tel1/Rad32 represent two pathways required to maintain telomeres and prevent chromosome circularization. |
| GO:0000785 chromatin | IEA GO_REF:0000117 | ACCEPT | Summary: Rad3 is directly detected in chromatin-bound checkpoint complexes during replication stress. The ARBA localization is therefore consistent with target-specific experimental evidence. Reason: Direct chromatin association is reported independently of the electronic inference and is central to Rad3 checkpoint signaling. Supporting Evidence: PMID:17531813 Cdc18 persists in a chromatin-bound complex including the checkpoint kinases Rad3 and Rad26. |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: Nuclear localization is consistent with Rad3's chromatin-bound checkpoint and telomere functions and duplicates other accepted nuclear annotations. Reason: The combined automated call agrees with UniProt localization and direct S. pombe chromatin evidence. Supporting Evidence: PMID:17531813 Cdc18 persists in a chromatin-bound complex including the checkpoint kinases Rad3 and Rad26. |
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Download this section (compressed HTML)Q: Which Rad3 substrate phosphorylations are direct in vivo versus dependent on additional mediators (Crb2, Mrc1, 9-1-1 clamp), and how is substrate selectivity between the Chk1 (damage) and Cds1 (replication) branches achieved?
Q: What is the molecular basis of the kinase-independent functions of the Rad3-Rad26 complex (e.g. Tel1 recruitment to telomeres), and how widespread are such structural roles?
Experiment: Analog-sensitive (as) rad3 kinase allele combined with quantitative phosphoproteomics to define the in vivo Rad3-dependent SQ/TQ phosphoproteome during DNA damage versus replication stress.
Experiment: Separation-of-function rad3 alleles (kinase-dead vs scaffold-defective) to dissect catalytic versus structural contributions of the Rad3-Rad26 complex in checkpoint signaling and telomere maintenance.
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