Clb5 is the principal S-phase B-type cyclin (cyclin A/B subfamily) of the budding yeast Saccharomyces cerevisiae and, with its paralog Clb6, the regulatory subunit of the S-phase form of the cyclin-dependent kinase Cdc28 (Cdk1). Clb5 has no catalytic activity of its own: it binds Cdc28, induces the active kinase conformation and, through the conserved hydrophobic patch of its cyclin fold, docks RXL/Cy-motif substrates such as Sic1, Orc6 and Cdc6 onto the kinase. CLB5 is transcribed in late G1 as part of the MBF/SBF-dependent G1/S program together with CLN1, CLN2 and the DNA-replication genes; the newly formed Clb5-Cdc28 complex is held inactive by the stoichiometric inhibitor Sic1 until Cln-Cdc28 triggers Sic1 destruction, after which Clb5-Cdc28 phosphorylates replication-initiation factors (Sld2, Sld3 and the ORC/Cdc6 licensing machinery) to fire replication origins on schedule. clb5 cells initiate S phase but fire only early origins and take more than twice as long to complete replication; clb5 clb6 cells cannot initiate replication on time and rely on the mitotic cyclins Clb1-4 for an inefficient S phase, while ectopic CLB5 can drive proliferation in the absence of Cln cyclins. Once origins have fired, origin-bound Clb5-Cdc28 helps prevent re-licensing. Clb5 acts in the nucleus, concentrating there from before budding through S phase and associating with chromosomal origins until mitosis, and it is degraded by APC/C-Cdc20 at metaphase in a destruction-box-dependent manner. Secondary roles include cooperation with Clb3 and Clb4 during S phase to phosphorylate and inactivate APC/C-Cdh1 (Hct1), which allows accumulation of Cin8, Kip1, Ase1 and Clb2 for spindle pole body separation and spindle assembly, and recruitment with Cdk1 to DNA double-strand breaks where it promotes end resection and checkpoint signalling. In meiosis Clb5 and Clb6 are the only B-type cyclins able to drive premeiotic DNA replication; clb5 clb6 diploids fail to replicate, do not activate the Mec1-dependent replication checkpoint and segregate unreplicated chromosomes. CLB5 is not essential for vegetative growth.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000082 G1/S transition of mitotic cell cycle | IBA GO_REF:0000033 | ACCEPT | Summary: IBA propagation of G1/S transition of the mitotic cell cycle from the deep cyclin node PTN000019791 (cyclin E/A/D, Cln3, Clb5/6, cig2 and mitotic B cyclins). Clb5 is one of the experimental donors of this node (SGD:S000006324 is CLB5 itself), which is expected: CLB5 is transcribed at Start with CLN1/CLN2 and the Clb5-Cdc28 kinase, once Sic1 is destroyed, is what commits the cell to S phase. Reason: Unlike the mitotic cyclin Clb2, for which the same propagation overstates the role, Clb5 is the budding-yeast G1/S (S-phase) B-type cyclin: transcripts appear in late G1, clb5 clb6 cells cannot initiate DNA replication on time, and Clb5-associated kinase rather than Cln kinase is proposed to drive S-phase entry. The node placement is sound for this member and the target itself carries IMP/IGI evidence for the term. Supporting Evidence: PMID:8319908 We describe a new family of B-type cyclin genes, CLB5 and CLB6, whose transcripts appear in late G1 along with those of CLN1, CLN2, and many genes required for DNA replication. PMID:8319908 Thus, the kinase activity associated with Clb5/6 and not with Cln cyclins may be responsible for S-phase entry. PMID:8253070 Loss of function mutants are viable, but clb5- mutants exhibit a delay in S phase whereas clb6- mutants show a delay in late G1 and/or S phase. |
| GO:0000082 G1/S transition of mitotic cell cycle | IGI PMID:8253070 A new pair of B-type cyclins from Saccharomyces cerevisiae t... | ACCEPT | Summary: Genetic-interaction annotation from Kuhne & Linder, who cloned CLB5/CLB6 and showed that both are periodically expressed peaking early in the cycle, that clb5 nulls delay S phase, clb6 nulls delay late G1/S, and that the clb5 clb6 double null is more severe. The recorded WITH entity (SGD:S000006324) resolves to the CLB5 locus itself; the genetic interaction described in the paper is the clb5 clb6 double null. Reason: Founding genetics for Clb5 as an early-cycle B-type cyclin acting at the G1/S boundary; the double-mutant analysis with CLB6 establishes partial redundancy of the two S-phase cyclins. Core function. Supporting Evidence: PMID:8253070 Both genes are periodically expressed, peaking early in the cell cycle. PMID:8253070 Loss of function mutants are viable, but clb5- mutants exhibit a delay in S phase whereas clb6- mutants show a delay in late G1 and/or S phase. PMID:8253070 The clb5 mutant phenotype is somewhat more pronounced in a double null mutant. |
| GO:0000082 G1/S transition of mitotic cell cycle | IMP PMID:8253070 A new pair of B-type cyclins from Saccharomyces cerevisiae t... | ACCEPT | Summary: Mutant-phenotype annotation from the same study: clb5 loss-of-function cells are viable but show a delay in S phase, consistent with CLB5 acting at the G1/S transition. Reason: Direct phenotype of the clb5 null; together with the Schwob & Nasmyth data this defines Clb5 as the principal S-phase cyclin. Core function. Supporting Evidence: PMID:8253070 Loss of function mutants are viable, but clb5- mutants exhibit a delay in S phase whereas clb6- mutants show a delay in late G1 and/or S phase. PMID:8253070 Both cyclins have the potential to interact with the p34CDC28 kinase in vivo. |
| GO:0000082 G1/S transition of mitotic cell cycle | IMP PMID:8319908 CLB5 and CLB6, a new pair of B cyclins involved in DNA repli... | ACCEPT | Summary: Schwob & Nasmyth: CLB5/CLB6 transcripts appear in late G1 with CLN1/CLN2 and replication genes; clb5 deletion greatly extends S phase and the clb5 clb6 double deletion prevents timely initiation of DNA replication; ectopic CLB5 lets cells proliferate without Cln cyclins, so Clb5/6-associated kinase is the activity that drives S-phase entry. Reason: The defining paper for Clb5 as the S-phase-entry cyclin; the G1/S transition is the core process in which the Clb5-Cdc28 kinase acts (it phosphorylates the replication-initiation substrates once Sic1 is removed). Cached record is abstract-only but the abstract itself states the phenotype. Supporting Evidence: PMID:8319908 Deletion of CLB6 has little or no effect, but deletion of CLB5 greatly extends S phase, and deleting both genes prevents the timely initiation of DNA replication. PMID:8319908 Thus, the kinase activity associated with Clb5/6 and not with Cln cyclins may be responsible for S-phase entry. PMID:8319908 Transcription of CLB5 and CLB6 is normally dependent on Cln activity, but ectopic CLB5 expression allows cells to proliferate in the absence of Cln cyclins. |
| GO:0000086 G2/M transition of mitotic cell cycle | IMP PMID:8319908 CLB5 and CLB6, a new pair of B cyclins involved in DNA repli... | KEEP AS NON CORE | Summary: Same paper: besides S phase, Clb5 shares with Clb3 and Clb4 a function in mitotic spindle formation, and the authors describe CLB5 as involved in the initiation of both S phase and mitosis. Later work showed the mechanism: the early Clb3/4/5 kinases inactivate APC-Hct1 during S phase so that Cin8/Kip1/Ase1 and Clb2 accumulate for SPB separation and mitotic entry. Reason: Genuine but redundant contribution: Clb5-Cdc28 does part of the work (Hct1 phosphorylation) and the clb3 clb4 clb5 triple mutant arrests before mitosis without a spindle, yet in wild-type cells the G2/M transition is driven by Clb1/Clb2 and Clb5 is being degraded by APC/C-Cdc20 by metaphase. Retained as a non-core mitotic output of the S-phase kinase. Supporting Evidence: PMID:8319908 Clb5 also has a function, along with Clb3 and Clb4, in the formation of mitotic spindles. PMID:8319908 Our observation that CLB5 is involved in the initiation of both S phase and mitosis suggests that a single primordial B-type cyclin might have been sufficient for regulating the cell cycle of the common ancestor of many, if not all, eukaryotes. PMID:11438663 Here we show that this relationship between anaphase-promoting complex (APC) and Clb proteins is reversed in S phase such that the early Clb kinases (Clb3, Clb4, and Clb5 kinases) inactivate APC Hct1 to allow Clb2 accumulation. |
| GO:0000307 cyclin-dependent protein kinase holoenzyme complex | IBA GO_REF:0000033 | ACCEPT | Summary: IBA part_of the cyclin-dependent protein kinase holoenzyme complex from node PTN000019791; Clb5 itself is a donor. Clb5 is the regulatory subunit of the Clb5-Cdc28 S-phase CDK, co-immunoprecipitating with Cdc28 in mitotic and meiotic extracts. Reason: The cyclin fold is the defining component of a CDK holoenzyme and every functional assay of Clb5 measures the Clb5-Cdc28 complex; sound phylogenetic transfer grounded on the target. Supporting Evidence: PMID:8253070 Both cyclins have the potential to interact with the p34CDC28 kinase in vivo. PMID:9732268 Clb5 is also detected in association with Cdc28 in extracts from meiotic cells |
| GO:0000307 cyclin-dependent protein kinase holoenzyme complex | IPI PMID:8319908 CLB5 and CLB6, a new pair of B cyclins involved in DNA repli... | ACCEPT | Summary: Physical-interaction annotation from Schwob & Nasmyth, whose full text (not cached) reports Clb5-associated Cdc28 kinase activity; the abstract attributes S-phase entry to the kinase activity associated with Clb5/6. Reason: Clb5 forms a holoenzyme with Cdc28 (UniProt IntAct NbExp=6; Cdc28 co-purification in Kuhne & Linder and Stuart & Wittenberg). Complex membership is correct and core. Supporting Evidence: PMID:8319908 Thus, the kinase activity associated with Clb5/6 and not with Cln cyclins may be responsible for S-phase entry. PMID:8253070 Both cyclins have the potential to interact with the p34CDC28 kinase in vivo. |
| GO:0005515 protein binding | IPI PMID:10688190 A comprehensive analysis of protein-protein interactions in ... | REMOVE | Summary: Generic protein binding from the Uetz et al. genome-wide two-hybrid screen (interactor: Cdc28, the CDK catalytic subunit). The interaction is real and central, but GO:0005515 conveys no molecular function and the Clb5-Cdc28 relationship is already captured by GO:0016538 and GO:0000307. Reason: Per project curation policy, a bare GO:0005515 protein binding annotation carries no functional information and is removed unless the cited paper supports a more informative molecular function. The partner here is Cdc28 (Cdk1) itself, and Clb5's relationship to Cdc28 is already represented informatively by the cyclin-dependent protein serine/threonine kinase regulator activity rows (GO:0016538, IDA/IBA/IEA) and by the CDK holoenzyme complex row (GO:0000307, IPI), so this high-throughput row adds nothing. Removal does not dispute the reported interaction, which is the best-established physical interaction of Clb5 (UniProt IntAct NbExp=6). Supporting Evidence: PMID:10688190 These approaches resulted in the detection of 957 putative interactions involving 1,004 S. cerevisiae proteins. |
| GO:0005515 protein binding | IPI PMID:20489023 A global protein kinase and phosphatase interaction network ... | REMOVE | Summary: Generic protein binding from the Breitkreutz et al. kinase/phosphatase interaction network (mass spectrometry of purified kinase complexes; interactor: Cdc28). Co-purification of the cyclin with its CDK, consistent with the Clb5-Cdc28 holoenzyme; uninformative as a molecular function. Reason: Per project curation policy, a bare GO:0005515 protein binding annotation carries no functional information and is removed unless the cited paper supports a more informative molecular function. The partner here is Cdc28 (Cdk1) itself, and Clb5's relationship to Cdc28 is already represented informatively by the cyclin-dependent protein serine/threonine kinase regulator activity rows (GO:0016538, IDA/IBA/IEA) and by the CDK holoenzyme complex row (GO:0000307, IPI), so this high-throughput row adds nothing. Removal does not dispute the reported interaction, which is the best-established physical interaction of Clb5 (UniProt IntAct NbExp=6). Supporting Evidence: PMID:20489023 We identified a kinase and phosphatase interaction (KPI) network of 1844 interactions in budding yeast by mass spectrometric analysis of protein complexes. |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | REMOVE | Summary: Generic protein binding from the Michaelis et al. proteome-wide affinity-enrichment MS interactome (interactor: Cdc28). Again the cyclin-CDK pair; no molecular function conveyed. Reason: Per project curation policy, a bare GO:0005515 protein binding annotation carries no functional information and is removed unless the cited paper supports a more informative molecular function. The partner here is Cdc28 (Cdk1) itself, and Clb5's relationship to Cdc28 is already represented informatively by the cyclin-dependent protein serine/threonine kinase regulator activity rows (GO:0016538, IDA/IBA/IEA) and by the CDK holoenzyme complex row (GO:0000307, IPI), so this high-throughput row adds nothing. Removal does not dispute the reported interaction, which is the best-established physical interaction of Clb5 (UniProt IntAct NbExp=6). Supporting Evidence: PMID:37968396 The 4,159 pull-downs generated a highly structured network of 3,927 proteins connected by 31,004 interactions |
| GO:0005515 protein binding | IPI PMID:8253070 A new pair of B-type cyclins from Saccharomyces cerevisiae t... | MODIFY | Summary: Protein binding with Cdc28 from Kuhne & Linder, who showed that Clb5 and Clb6 interact with the p34CDC28 kinase in vivo (Cdc28-associated Clb5 in immunoprecipitates). Because the partner is the CDK catalytic subunit and cyclin binding is what generates and regulates the kinase, the informative molecular function supported by this evidence is the cyclin's CDK regulator activity rather than bare protein binding. Reason: The paper's own conclusion is that Clb5 associates with the p34CDC28 kinase in vivo, i.e. it is the regulatory subunit of a Cdc28 holoenzyme; GO:0016538 (cyclin-dependent protein serine/threonine kinase regulator activity) expresses that relationship, whereas GO:0005515 says nothing. The same term is already carried by IDA/IBA/IEA rows, so this refinement is consistent rather than novel. The interaction itself is not disputed. Proposed replacements: cyclin-dependent protein serine/threonine kinase regulator activity Supporting Evidence: PMID:8253070 Both cyclins have the potential to interact with the p34CDC28 kinase in vivo. PMID:8319908 Thus, the kinase activity associated with Clb5/6 and not with Cln cyclins may be responsible for S-phase entry. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: IBA is_active_in nucleus from node PTN000019791 with Clb5 among the donors. Clb5 is concentrated in the nucleus from before budding through S phase, and its substrates (Sld2, Orc6, Cdc6, Sic1, Hct1) and its site of action (replication origins) are nuclear. Reason: Concordant with the IDA row and with the replication-origin function; the nucleus is where Clb5-Cdc28 acts. Supporting Evidence: PMID:10848575 In unbudded cells, small budded cells, and most large budded cells with an undivided nucleus, Clb5p is concentrated in the nucleus. |
| GO:0005634 nucleus | IDA PMID:10848575 Testing cyclin specificity in the exit from mitosis. | ACCEPT | Summary: Immunofluorescence of Myc-tagged Clb5 (Jacobson et al.): Clb5 is concentrated in the nucleus in unbudded, small-budded and most large-budded cells with an undivided nucleus, and becomes diffuse at nuclear division, coincident with destruction-box-dependent degradation; retention of nuclear Clb5-db at division is lethal, probably through failure to re-license origins. Reason: Direct localization; nuclear accumulation during G1/S is the functionally relevant pool and its mitotic loss is part of the replication-licensing control. Core location. Supporting Evidence: PMID:10848575 In unbudded cells, small budded cells, and most large budded cells with an undivided nucleus, Clb5p is concentrated in the nucleus. PMID:10848575 Destruction box-dependent Clb5p degradation is strongly increased in mitotic cells |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA is_active_in cytoplasm from the deep cyclin node. For Clb5 the only localization data show nuclear concentration during G1/S and a diffuse whole-cell distribution at nuclear division with significant cytoplasmic signal; no cytoplasm-specific Clb5-Cdc28 activity has been demonstrated. Reason: A cytoplasmic pool exists (Clb5 is synthesised in the cytoplasm and is diffuse at mitosis), so the term is not wrong, but the functional site is the nucleus/replication origins; graded non-core rather than challenged, since the node's cytoplasmic activity (e.g. cyclin B at the spindle/cortex) is a real family feature and there is no target-specific evidence against a cytoplasmic pool. Supporting Evidence: PMID:10848575 In large budded cells with an undivided DNA mass near or spanning the bud neck and in large budded cells with two DNA signals, Clb5p is distributed diffusely throughout the cell. PMID:10848575 These differences in stability correlate with loss of detectable nuclear accumulation of Clb5p in dividing cells (although significant cytoplasmic signal remains). |
| GO:0005815 microtubule organizing center | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: IBA is_active_in microtubule organizing center from sub-node PTN007424001, seeded by S. pombe cdc13 and crs1, human cyclin B1/B2, rat cyclin B and S. cerevisiae Clb2, i.e. mitotic B-type cyclins that decorate the centrosome/SPB. Clb5 contributes genetically to SPB separation (via Hct1 inactivation), but the only Clb5 localization data show nuclear/diffuse staining and no SPB enrichment has been reported for Clb5. Reason: SPB/centrosome localization is a property demonstrated for the mitotic cyclins in this clade; the S-phase cyclin Clb5 acts at replication origins and its known contribution to SPB separation is indirect (inactivation of APC-Cdh1 to stabilize Cin8/Kip1/Ase1), which does not require Clb5 at the SPB. With no positive localization evidence on the target, the propagated MTOC term likely overstates where Clb5 is active; it is flagged rather than removed because absence of evidence is not evidence of loss. Propagation Review Root cause: PROPAGATION BAD Failure modes: COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN007424001 SUPPORTS SOURCE BUT NOT TARGET Node seeded by mitotic B-type cyclins (cdc13, cyclin B1/B2, Clb2) with direct SPB/centrosome localization; the S-phase paralog Clb5 has no reported SPB localization and acts at nuclear replication origins. Supporting Evidence: PMID:10848575 In unbudded cells, small budded cells, and most large budded cells with an undivided nucleus, Clb5p is concentrated in the nucleus. PMID:16688214 Our findings are consistent with a regulatory scheme for SPB separation ( Figure 7B ) in which Cdc28-Clb kinase mediates stabilization of microtubule-associated proteins (Cin8, Kip1 and Ase1) by inactivating Cdh1 via phosphorylation. |
| GO:0006279 premeiotic DNA replication | IGI PMID:9732268 CLB5 and CLB6 are required for premeiotic DNA replication an... | ACCEPT | Summary: Stuart & Wittenberg: diploid clb5 clb6 mutants cannot perform premeiotic DNA replication yet enter the meiotic divisions and segregate unreplicated DNA; clb5/clb5 alone delays and leaves incomplete premeiotic S phase; Clb5-associated Cdc28 kinase accumulates during meiosis. The recorded WITH entity resolves to the CLB5 locus itself; the genetic interaction in the paper is with CLB6. Reason: Clb5 (with Clb6) supplies the CDK activity that initiates premeiotic DNA replication; unlike the mitotic cycle, Clb1-4 cannot substitute, so this is a specific, non-redundant Clb5 function and is graded core. Supporting Evidence: PMID:9732268 Diploid clb5/clb5 clb6/clb6 mutants are unable to perform premeiotic DNA replication. PMID:9732268 Analysis of DNA content by flow cytometry demonstrated that CLB5 and CLB6 are required for efficient premeiotic DNA replication PMID:9732268 Clb5 is also detected in association with Cdc28 in extracts from meiotic cells |
| GO:0006279 premeiotic DNA replication | IMP PMID:9732268 CLB5 and CLB6 are required for premeiotic DNA replication an... | ACCEPT | Summary: Mutant-phenotype annotation from the same study: clb5/clb5 diploids are severely defective in sporulation and show delayed, incomplete premeiotic DNA replication by flow cytometry. Reason: Direct single-mutant phenotype for the meiotic S-phase function of Clb5-Cdc28; core. Supporting Evidence: PMID:9732268 DNA replication in clb5/clb5 mutants was first detectable at βΌ8 hr and appeared to be incomplete in many cells even after 24 hr PMID:9732268 The B-type cyclins Clb5 and Clb6 are the primary activators of the S phase function of the budding yeast CDK Cdc28. |
| GO:0006355 regulation of DNA-templated transcription | IMP PMID:8319908 CLB5 and CLB6, a new pair of B cyclins involved in DNA repli... | UNDECIDED | Summary: Regulation of DNA-templated transcription, IMP, from Schwob & Nasmyth. The cached record is abstract-only and the abstract mentions transcription only as an input (CLB5/CLB6 transcription depends on Cln activity); the experiment supporting a transcriptional output of Clb5 (probably the behaviour of Start-dependent transcripts in clb5 clb6 cells or upon ectopic CLB5 expression) is in the uncached full text and could not be retrieved. Reason: Clb-Cdc28 kinases are known to switch off SBF/MBF-dependent G1/S transcription, so a transcriptional effect of Clb5-Cdc28 is biologically plausible, but the specific evidence in this paper cannot be verified from the cached abstract and the term is very general. Per project rules the annotation is neither removed nor endorsed; if retained it would be non-core relative to the replication function. Supporting Evidence: PMID:8319908 Transcription of CLB5 and CLB6 is normally dependent on Cln activity, but ectopic CLB5 expression allows cells to proliferate in the absence of Cln cyclins. |
| GO:0006974 DNA damage response | IDA PMID:26801641 Enrichment of Cdk1-cyclins at DNA double-strand breaks stimu... | KEEP AS NON CORE | Summary: Chen et al.: Cdk1 and cyclins are enriched at an HO-induced double-strand break, with Clb5 among the most enriched; clb5 deletion reduces the rate of extensive resection and sensitizes cells to MMS, CPT and phleomycin, and Clb2/Clb5 redundantly support Fun30 phosphorylation and checkpoint (Rad53/Rad9) activation. Reason: Participation is genuine (Clb5 is recruited to the break and directs Cdk1 to resection/checkpoint substrates, with Clb5-specific and Clb2-redundant contributions), but this is a context-dependent output of the S-phase kinase rather than its core function, mirroring the grading of the same row in the CLB2 review. Supporting Evidence: PMID:26801641 Highest enrichment was observed for Cln2, Clb2 and Clb5 PMID:26801641 We found that clb5Ξ cells show a decreased rate of extensive resection PMID:26801641 Clb2 and Clb5 are needed for resistance of cells to DNA damaging agents |
| GO:0007089 traversing start control point of mitotic cell cycle | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: IBA to traversing the Start control point from node PTN000808767, whose experimental donor is the S. pombe G1/S B-type cyclin cig2 (SPAPB2B4.03). GO:0007089 is defined as commitment to S phase via the positive feedback between transcription and G1 CDK activity. In budding yeast that loop is Cln3-Whi5/SBF-Cln1/2; CLB5 is a product of the Start transcriptional program and Clb5-Cdc28 is held inactive by Sic1 until after Start, then executes S-phase entry. Reason: Clb5's role is the G1/S transition (GO:0000082, accepted) downstream of Start commitment, not the transcription/G1-CDK feedback that defines Start; clb5 clb6 cells pass Start (bud, duplicate SPBs) on schedule and only delay replication. Ectopic CLB5 can drive proliferation without Clns, but that is a bypass, not the native role. The propagated term therefore conflates S-phase execution with Start commitment; the CLB2 review makes the same call for the sister propagation. Propagation Review Root cause: PROPAGATION BAD Failure modes: ROLE CONFLATION Sources checked: PANTHER:PTN000808767 SUPPORTS SOURCE BUT NOT TARGET Node seeded only by fission-yeast cig2, the G1/S B-type cyclin of an organism without separate Cln-type Start cyclins; in budding yeast Start commitment is carried by Cln3/Cln1/Cln2 and Clb5 acts after Start on S-phase entry. Supporting Evidence: PMID:8319908 Deletion of CLB6 has little or no effect, but deletion of CLB5 greatly extends S phase, and deleting both genes prevents the timely initiation of DNA replication. PMID:8319908 Transcription of CLB5 and CLB6 is normally dependent on Cln activity, but ectopic CLB5 expression allows cells to proliferate in the absence of Cln cyclins. PMID:7954792 cdc34 mutants cannot enter S phase because they fail to destroy p40SIC1, which is a potent inhibitor of Clb but not Cln forms of the Cdc28 kinase. |
| GO:0010696 positive regulation of mitotic spindle pole body separation | IGI PMID:11438663 Early expressed Clb proteins allow accumulation of mitotic c... | KEEP AS NON CORE | Summary: Yeong et al.: the early Clb kinases (Clb3, Clb4, Clb5) inactivate APC-Hct1 in S phase; clb5 cells under-phosphorylate Hct1 and accumulate less Clb2, and clb3 clb4 clb5 cells arrest with 2N DNA and no spindle because Clb2 is unstable, a defect rescued by HCT1 deletion. IGI partner: CLB3. Reason: Clb5-Cdc28 does part of the work (Hct1 phosphorylation, shown in vitro) that stabilizes the SPB-separation machinery, so positive regulation of SPB separation is a correct, regulatory-level term; it is redundant with Clb3/Clb4 and secondary to the S-phase function, hence non-core. Supporting Evidence: PMID:11438663 Here we show that this relationship between anaphase-promoting complex (APC) and Clb proteins is reversed in S phase such that the early Clb kinases (Clb3, Clb4, and Clb5 kinases) inactivate APC Hct1 to allow Clb2 accumulation. PMID:11438663 clb5 Ξ cells fail to fully convert Hct1 to a single, low-mobility band PMID:11438663 In vitro assays have shown that Hct1 can also be phosphorylated by Clb5 kinase |
| GO:0010696 positive regulation of mitotic spindle pole body separation | IGI PMID:11438663 Early expressed Clb proteins allow accumulation of mitotic c... | KEEP AS NON CORE | Summary: Same evidence with CLB4 as the IGI partner: the clb3 clb4 clb5 triple mutant fails to form a spindle and loses viability, attributed to hyperactive APC-Hct1 and loss of Clb2. Reason: Redundant Clb3/4/5 contribution to SPB separation through APC-Hct1 inactivation; genuine participation but non-core. Supporting Evidence: PMID:11438663 The explanation put forward for the inviability is that, in the absence of Clb3 and Clb4, Clb5 becomes essential for the biogenesis of mitotic spindle ( 13 ); thus, the clb3 Ξ clb4 Ξ clb5 Ξ mutant fails to form a spindle and eventually loses viability. PMID:11438663 Here we show that this relationship between anaphase-promoting complex (APC) and Clb proteins is reversed in S phase such that the early Clb kinases (Clb3, Clb4, and Clb5 kinases) inactivate APC Hct1 to allow Clb2 accumulation. |
| GO:0010696 positive regulation of mitotic spindle pole body separation | IGI PMID:16688214 Cdk1 regulates centrosome separation by restraining proteoly... | KEEP AS NON CORE | Summary: Crasta et al.: Cdk1 activation (Tyr19 dephosphorylation) prevents APC-Cdh1-mediated proteolysis of Cin8, Kip1 and Ase1; clb3 clb4 clb5 cells are almost devoid of Cdc28-Clb activity, and ectopic stabilized Cin8 restores spindle formation in them, so Cdh1 inactivation is the predominant role of Cdc28-Clb kinase in SPB separation. IGI partner: CLB3. Reason: Defines the mechanism by which the early Clb kinases (including Clb5) promote SPB separation: phosphorylation-dependent inactivation of Cdh1 stabilizes the microtubule-associated force generators. Correct regulatory term; non-core for Clb5. Supporting Evidence: PMID:16688214 Since ectopic expression of proteolysis-resistant Cin8, Kip1 or Ase1 is sufficient for SPB separation even in the absence of Cdc28-Clb activity, we suggest that stabilization of these mechanical force-generating proteins is the predominant role of Cdc28-Clb in centrosome separation. PMID:16688214 that Cin8 overexpression leads to spindle formation in clb3 Ξ clb4 Ξ clb5 Ξ cells even though they are almost completely devoid of Cdc28-Clb kinase activity implies that stabilization of microtubule-associated proteins via Cdh1 inactivation may be the predominant role of Cdc28-Clb kinase in SPB separation. |
| GO:0010696 positive regulation of mitotic spindle pole body separation | IGI PMID:16688214 Cdk1 regulates centrosome separation by restraining proteoly... | KEEP AS NON CORE | Summary: Same study with CLB4 as the IGI partner (clb3 clb4 clb5 triple mutant lacking spindles, rescued by proteolysis-resistant Cin8/Kip1/Ase1). Reason: Redundant Clb3/4/5 role in SPB separation via APC-Cdh1 inactivation; non-core. Supporting Evidence: PMID:16688214 that Cin8 overexpression leads to spindle formation in clb3 Ξ clb4 Ξ clb5 Ξ cells even though they are almost completely devoid of Cdc28-Clb kinase activity implies that stabilization of microtubule-associated proteins via Cdh1 inactivation may be the predominant role of Cdc28-Clb kinase in SPB separation. PMID:16688214 Our findings are consistent with a regulatory scheme for SPB separation ( Figure 7B ) in which Cdc28-Clb kinase mediates stabilization of microtubule-associated proteins (Cin8, Kip1 and Ase1) by inactivating Cdh1 via phosphorylation. |
| GO:0010696 positive regulation of mitotic spindle pole body separation | IGI PMID:16688214 Cdk1 regulates centrosome separation by restraining proteoly... | KEEP AS NON CORE | Summary: Same study with ASE1 as the IGI partner: proteolysis-resistant Ase1 (like Cin8 or Kip1) supports SPB separation even without Cdc28-Clb activity, placing the Clb kinases upstream of Ase1 stabilization. Reason: Epistasis places Clb5-containing Cdc28-Clb kinase upstream of the microtubule-bundling proteins whose stabilization drives SPB separation; correct as positive regulation, non-core for Clb5. Supporting Evidence: PMID:16688214 Since ectopic expression of proteolysis-resistant Cin8, Kip1 or Ase1 is sufficient for SPB separation even in the absence of Cdc28-Clb activity, we suggest that stabilization of these mechanical force-generating proteins is the predominant role of Cdc28-Clb in centrosome separation. PMID:16688214 Our findings are consistent with a regulatory scheme for SPB separation ( Figure 7B ) in which Cdc28-Clb kinase mediates stabilization of microtubule-associated proteins (Cin8, Kip1 and Ase1) by inactivating Cdh1 via phosphorylation. |
| GO:0016538 cyclin-dependent protein serine/threonine kinase regulator activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA cyclin-dependent protein serine/threonine kinase regulator activity from node PTN000019791, with Clb5 among the experimental donors. This is the molecular function of every cyclin and is directly grounded on the target (Clb5-associated Cdc28 kinase activity). Reason: Clb5 binds and activates Cdc28 and confers S-phase substrate specificity through its hydrophobic patch (Orc6, Sic1, Sld2 docking). The more specific child GO:0061575 (activator activity) is used in core_functions; the regulator term additionally covers substrate targeting and is retained. Supporting Evidence: PMID:9732268 The B-type cyclins Clb5 and Clb6 are the primary activators of the S phase function of the budding yeast CDK Cdc28. PMID:8319908 Thus, the kinase activity associated with Clb5/6 and not with Cln cyclins may be responsible for S-phase entry. |
| GO:0016538 cyclin-dependent protein serine/threonine kinase regulator activity | IDA PMID:7954792 The B-type cyclin kinase inhibitor p40SIC1 controls the G1 t... | ACCEPT | Summary: Schwob et al. 1994 (Sic1 paper): DNA replication requires Cdc28 activation by B-type cyclins; a sextuple clb1-6 mutant arrests as multibudded G1 cells, and p40Sic1 is a potent inhibitor of Clb- but not Cln-Cdc28 kinase. The Clb5-specific kinase assays are in the uncached full text. Reason: The cached abstract names only Clb-Cdc28 kinase, but the SGD curator read the full text (which assays Clb5-associated Cdc28 kinase and its inhibition by Sic1); the regulator activity is unambiguously correct for Clb5 and is deferred to the curator per project rules. Supporting Evidence: PMID:7954792 We show that DNA replication also requires activation of Cdc28 by B-type (Clb) cyclins. PMID:7954792 cdc34 mutants cannot enter S phase because they fail to destroy p40SIC1, which is a potent inhibitor of Clb but not Cln forms of the Cdc28 kinase. |
| GO:0016538 cyclin-dependent protein serine/threonine kinase regulator activity | IEA GO_REF:0000120 | ACCEPT | Summary: InterPro/ARBA electronic mapping of the cyclin A/B-like domain (IPR046965) to CDK regulator activity. Reason: Correct family-level mapping, fully corroborated by the experimental and IBA rows. |
| GO:0044772 mitotic cell cycle phase transition | IEA GO_REF:0000120 | ACCEPT | Summary: InterPro/ARBA electronic mapping to mitotic cell cycle phase transition; broad ancestor of the experimentally supported G1/S transition. Reason: Correct, if general; the specific transition (G1/S) is captured by the IMP/IGI/IBA rows. |
| GO:0045740 positive regulation of DNA replication | IGI PMID:8319908 CLB5 and CLB6, a new pair of B cyclins involved in DNA repli... | ACCEPT | Summary: Schwob & Nasmyth genetics: clb5 deletion greatly extends S phase and clb5 clb6 prevents timely replication initiation; Clb5 also cooperates with Clb3/Clb4. IGI partner: CLB3 (the triple/quadruple clb combinations in the full text). Reason: Clb5-Cdc28 supplies the S-CDK activity that fires origins (phosphorylating Sld2/Sld3 and other initiation factors), so it positively regulates DNA replication as a core function. A comparator check shows SGD places cyclins and Cdc28 on this regulatory term and on G1/S transition while reserving GO:0006270 DNA replication initiation for ORC/MCM/Sld/DDK components, so the term is not modified. Supporting Evidence: PMID:8319908 Deletion of CLB6 has little or no effect, but deletion of CLB5 greatly extends S phase, and deleting both genes prevents the timely initiation of DNA replication. PMID:8319908 Thus, the kinase activity associated with Clb5/6 and not with Cln cyclins may be responsible for S-phase entry. |
| GO:0045740 positive regulation of DNA replication | IGI PMID:8319908 CLB5 and CLB6, a new pair of B cyclins involved in DNA repli... | ACCEPT | Summary: Same evidence with CLB6 as the IGI partner: deleting both S-phase cyclins prevents the timely initiation of DNA replication, whereas either single deletion is viable. Reason: The clb5 clb6 double mutant is the classic demonstration that the S-phase cyclins drive replication initiation; core function. Supporting Evidence: PMID:8319908 Deletion of CLB6 has little or no effect, but deletion of CLB5 greatly extends S phase, and deleting both genes prevents the timely initiation of DNA replication. PMID:8253070 The clb5 mutant phenotype is somewhat more pronounced in a double null mutant. |
| GO:0045740 positive regulation of DNA replication | IGI PMID:8319908 CLB5 and CLB6, a new pair of B cyclins involved in DNA repli... | ACCEPT | Summary: Same evidence with CLB4 as the IGI partner (redundancy of the B-type cyclins in driving S phase). Reason: Core function; the IGI partner is a redundant B-type cyclin that can drive an (inefficient) S phase in the absence of Clb5/6. Supporting Evidence: PMID:8319908 Deletion of CLB6 has little or no effect, but deletion of CLB5 greatly extends S phase, and deleting both genes prevents the timely initiation of DNA replication. PMID:9734354 Therefore, Clb5p promotes the timely activation of early and late origins, but Clb6p can activate only early origins. |
| GO:0045740 positive regulation of DNA replication | IMP PMID:8319908 CLB5 and CLB6, a new pair of B cyclins involved in DNA repli... | ACCEPT | Summary: Mutant phenotype: clb5 deletion greatly extends S phase; ectopic CLB5 expression allows proliferation without Cln cyclins. Reason: Direct single-mutant evidence that Clb5 promotes DNA replication; core. Supporting Evidence: PMID:8319908 Deletion of CLB6 has little or no effect, but deletion of CLB5 greatly extends S phase, and deleting both genes prevents the timely initiation of DNA replication. PMID:8319908 Transcription of CLB5 and CLB6 is normally dependent on Cln activity, but ectopic CLB5 expression allows cells to proliferate in the absence of Cln cyclins. |
| GO:0045740 positive regulation of DNA replication | IMP PMID:9734354 CLB5-dependent activation of late replication origins in S. ... | ACCEPT | Summary: Donaldson et al.: clb5 cells activate early but not late replication origins, explaining the long clb5 S phase; Clb5 promotes timely activation of both early and late origins whereas Clb6 activates only early origins, and in clb5 clb6 cells Clb1-4 eventually drive an S phase in which both classes fire. Reason: Defines Clb5's specific replication output, the temporal program of origin firing; core function. Supporting Evidence: PMID:9734354 clb5 cells activate early origins but not late origins, explaining the previously described long clb5 S phase. PMID:9734354 Therefore, Clb5p promotes the timely activation of early and late origins, but Clb6p can activate only early origins. |
| GO:1901673 regulation of mitotic spindle assembly | IGI PMID:8319908 CLB5 and CLB6, a new pair of B cyclins involved in DNA repli... | KEEP AS NON CORE | Summary: Schwob & Nasmyth: Clb5 has a function, along with Clb3 and Clb4, in the formation of mitotic spindles (clb3 clb4 clb5 cells fail to form a spindle). IGI partner: CLB3. Reason: Mechanistically this is the same Hct1-inactivation route that underlies the SPB-separation rows; the regulation term is appropriate (GO has no positive-regulation child of mitotic spindle assembly to move to) and the role is redundant and secondary for Clb5. Supporting Evidence: PMID:8319908 Clb5 also has a function, along with Clb3 and Clb4, in the formation of mitotic spindles. PMID:11438663 The explanation put forward for the inviability is that, in the absence of Clb3 and Clb4, Clb5 becomes essential for the biogenesis of mitotic spindle ( 13 ); thus, the clb3 Ξ clb4 Ξ clb5 Ξ mutant fails to form a spindle and eventually loses viability. |
| GO:1901673 regulation of mitotic spindle assembly | IGI PMID:8319908 CLB5 and CLB6, a new pair of B cyclins involved in DNA repli... | KEEP AS NON CORE | Summary: Same evidence with CLB4 as the IGI partner. Reason: Redundant Clb3/4/5 contribution to spindle assembly via APC-Hct1 inactivation; non-core. Supporting Evidence: PMID:8319908 Clb5 also has a function, along with Clb3 and Clb4, in the formation of mitotic spindles. PMID:16688214 that Cin8 overexpression leads to spindle formation in clb3 Ξ clb4 Ξ clb5 Ξ cells even though they are almost completely devoid of Cdc28-Clb kinase activity implies that stabilization of microtubule-associated proteins via Cdh1 inactivation may be the predominant role of Cdc28-Clb kinase in SPB separation. |
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Download this section (compressed HTML)Q: Which replication-initiation substrates (Sld2, Sld3, Orc6, Cdc6, Mcm3) depend specifically on Clb5 hydrophobic-patch docking in vivo, and does the Clb5 versus Clb6 difference in late-origin firing reflect substrate preference or simply the earlier disappearance of Clb6?
Q: Is Clb5 ever enriched at spindle pole bodies, or is its contribution to SPB separation fully explained by nuclear inactivation of APC/C-Cdh1 (relevant to the propagated microtubule organizing center annotation)?
Q: What transcriptional output, if any, underlies the SGD 'regulation of DNA-templated transcription' IMP from Schwob & Nasmyth 1993 (e.g. Clb5-dependent shut-off of SBF/MBF targets), and is it distinct from the effect of Clb2-Cdc28?
Experiment: Combine an auxin-degron CLB5 allele (in clb6 and clb3 clb4 backgrounds) with synchronized phosphoproteomics and origin-firing profiling (BrdU-IP or Okazaki-fragment sequencing) to define the Clb5-specific Cdc28 substrate set and the origins whose timely firing requires Clb5, using hydrophobic-patch (hpm) mutants to separate docking-dependent targets.
Experiment: Image endogenously tagged Clb5 with SPB (Spc42) and origin markers through a synchronous cycle, including in cdh1 and clb3 clb4 backgrounds, to test whether any Clb5 pool localizes to SPBs or whether its spindle-related function is exerted entirely from the nucleoplasm via Cdh1.
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