WHI5 encodes a 295-residue, largely disordered, non-enzymatic transcriptional corepressor that gates Start, the budding-yeast G1/S commitment point. From mitotic exit through early G1, nuclear Whi5 binds the promoter-bound SBF transcription factor (the Swi4-Swi6 heterodimer) at the promoters of G1/S genes such as CLN1, CLN2 and PCL1 and holds the G1/S transcriptional program off, in part by recruiting the Rpd3(L) histone deacetylase complex (with Stb1) and Hos3. Whi5 has no DNA-binding domain of its own and reaches promoters only through SBF; it associates stably with SBF but not with the Mbp1-containing MBF complex, whose corepressor is the paralogous Nrm1. Whi5 is thus the functional analog, but not a homolog, of the metazoan retinoblastoma protein. In late G1, Cln3-Cdc28 (with Pcl9-Pho85) initiates and Cln1/2-Cdc28 complete a Cks1-assisted multisite phosphorylation of Whi5 that dissociates it from SBF and from the HDACs and drives Msn5-dependent nuclear export; because CLN1/CLN2 are SBF targets this is the positive-feedback loop that makes Start switch-like and, under normal conditions, irreversible. Whi5 is synthesized in S/G2/M at a size-independent rate and is stable, so it is diluted as cells grow in G1; small daughters are born with more Whi5 per volume and delay Start longer, which is why whi5 null cells are among the smallest viable yeast mutants and why Whi5 is a central component of cell-size homeostasis. When CDK activity falls at the end of mitosis, Whi5 is re-imported (Kap60-Kap95, with the Ess1 prolyl isomerase acting on its phospho-Ser-Pro nuclear targeting sequences) to repress the next cycle. Nuclear Whi5 also restrains SBF during meiotic entry and cell-wall stress (with its paralog Whi7/Srl3), and a recent study reports that Whi5 is phosphorylated by Atg1 and promotes nitrogen-starvation-induced autophagy.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000082 G1/S transition of mitotic cell cycle | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the Srl3/Whi5 family signature (IPR039198). Both members of this family in S. cerevisiae (Whi5 and Whi7/Srl3) are SBF-bound repressors whose inactivation is the transcriptional switch at Start, so the family-level mapping is biologically correct and matches the experimentally supported rows below. Reason: The mapping reproduces the experimentally established role of Whi5 in the Start switch (PMID:15210110, PMID:15210111). SGD annotates the entire Start machinery, including the other repressors Stb1, Sic1 and Whi7/Srl3, to GO:0000082 rather than to a "negative regulation" child, so this is the convention for the yeast G1/S transition and the IEA term is at an appropriate level for a family mapping. Supporting Evidence: PMID:15210111 Deletion of WHI5 bypasses the requirement for upstream activators of the G1/S transcription factors SBF/MBF and thereby accelerates the G1/S transition. |
| GO:0000082 G1/S transition of mitotic cell cycle | IGI PMID:15210110 Cln3 activates G1-specific transcription via phosphorylation... | ACCEPT | Summary: Genetic interaction with CLN3 (SGD:S000000038): whi5 deletion bypasses the requirement for Cln3 both for G1/S transcriptional activation and for cell-cycle initiation, placing Whi5 downstream of Cln3-Cdc28 as the SBF-bound repressor whose removal constitutes the Start transcriptional switch (de Bruin et al. 2004, abstract-only cache). Reason: Whi5 is the SBF-bound repressor whose Cln3-dependent phosphorylation and dissociation is the transcriptional activation step named in the GO:0000082 definition. The cln3 bypass by whi5 is the defining epistasis result for this gene. SGD uses GO:0000082 (not a negative regulation child) for all components of the Start switch, including the repressors, so the term choice is consistent with the yeast convention; a negative-regulation term (GO:2000134) is used for metazoan Rb but is carried by a single yeast gene and would not be the comparator-consistent choice here. Supporting Evidence: PMID:15210110 Whi5 inactivation bypasses the requirement for Cln3 both for transcriptional activation and cell cycle initiation. PMID:15210110 Inactivation of Whi5 leads to premature expression of G1-specific genes and budding, whereas overexpression retards those processes. |
| GO:0000082 G1/S transition of mitotic cell cycle | IGI PMID:15210110 Cln3 activates G1-specific transcription via phosphorylation... | ACCEPT | Summary: Genetic interaction with MBP1 (SGD:S000002214), the DNA-binding subunit of MBF, from de Bruin et al. 2004 (abstract-only cache). The full text is not cached, so the specific whi5-mbp1 interaction cannot be quoted; the paper's abstract shows that Whi5 is a stable SBF component that is absent from MBF, and the genetic test presumably probes the SBF-versus-MBF branch dependence of the whi5 phenotype. Reason: The biological claim (Whi5 acts in the G1/S transition) is firmly established by the companion rows and the SGD curator read the full text. The abstract-only cache does not let me quote the mbp1-specific experiment, but there is no reason to doubt it and the term is the SGD convention for the Start machinery. Deferred to the SGD curator. Supporting Evidence: PMID:15210110 Whi5 was identified as a stably bound component of SBF but not MBF. |
| GO:0000082 G1/S transition of mitotic cell cycle | IGI PMID:15210111 CDK activity antagonizes Whi5, an inhibitor of G1/S transcri... | ACCEPT | Summary: Genetic interaction with CLN3 from Costanzo et al. 2004 (abstract-only cache): WHI5 deletion bypasses the requirement for the upstream activators of SBF/MBF (Cln3, Bck2) and accelerates the G1/S transition; Whi5 is the elusive yeast G1 target of CDK analogous to Rb. Reason: Same epistasis logic as the de Bruin et al. row: whi5 deletion suppresses cln3 loss, establishing Whi5 as the CDK-antagonized repressor at the heart of the Start switch. Term choice follows the SGD convention for Start components. Supporting Evidence: PMID:15210111 Deletion of WHI5 bypasses the requirement for upstream activators of the G1/S transcription factors SBF/MBF and thereby accelerates the G1/S transition. |
| GO:0000082 G1/S transition of mitotic cell cycle | IGI PMID:19823668 Dual regulation by pairs of cyclin-dependent protein kinases... | ACCEPT | Summary: Genetic interaction with CLN3 from Huang et al. 2009 (full text cached). A cln3 pho85 double mutant has a G1 delay, slow growth and severely reduced SBF reporter expression, and all of these defects are suppressed by whi5 deletion; conversely WHI5 overexpression arrests cln3 cells in G1 as large unbudded cells, showing that Whi5 is a dose-dependent regulator of Start. Reason: Direct genetic demonstration that the Cln3-dependent G1 delay runs through Whi5. The term follows the SGD convention for Start components. Supporting Evidence: PMID:19823668 The G1 delay phenotype associated with a cln3Ξ pho85Ξ strain is dependent on WHI5. PMID:19823668 cln3Ξ mutants arrest in G1 phase as large unbudded cells in response to increased WHI5 dosage, indicating that Whi5 is a dose-dependent regulator of Start. |
| GO:0000082 G1/S transition of mitotic cell cycle | IGI PMID:19823668 Dual regulation by pairs of cyclin-dependent protein kinases... | ACCEPT | Summary: Genetic interaction with PHO85 (SGD:S000005952). Huang et al. 2009 identify Whi5 as the first physiological substrate of the G1-specific Pcl9-Pho85 CDK: WHI5 overexpression is synthetically toxic in pho85 (and pcl9) mutants, Pcl-Pho85 phosphorylates Whi5 in vitro, and Pho85 and Cdc28 act in parallel to antagonize Whi5 at Start. Reason: Establishes a second CDK input (Pcl9-Pho85) that converges on Whi5 to trigger Start, strengthening the picture of Whi5 as the integration point of the G1/S switch. Term follows the SGD convention for Start components. Supporting Evidence: PMID:19823668 we identify Whi5, to our knowledge, as the first demonstrated physiological substrate for the G1-specific Pcl9-Pho85 CDK |
| GO:0000082 G1/S transition of mitotic cell cycle | IMP PMID:15210110 Cln3 activates G1-specific transcription via phosphorylation... | ACCEPT | Summary: Mutant phenotype from de Bruin et al. 2004: whi5 inactivation causes premature expression of G1-specific genes and premature budding, overexpression delays them, and mutation of the CDK phosphorylation sites (at least five phosphorylated in vivo) reduces SBF-dependent transcription and delays cell-cycle initiation. Reason: Loss- and gain-of-function phenotypes both map onto Start timing, and the phospho-site mutant shows that the CDK-regulated state of Whi5 sets the timing of the transition. Core function of the gene. Supporting Evidence: PMID:15210110 Mutation of putative CDK phosphorylation sites, at least five of which are phosphorylated in vivo, strongly reduces SBF-dependent transcription and delays cell cycle initiation. |
| GO:0000082 G1/S transition of mitotic cell cycle | IMP PMID:15210111 CDK activity antagonizes Whi5, an inhibitor of G1/S transcri... | ACCEPT | Summary: Mutant phenotype from Costanzo et al. 2004: WHI5 deletion accelerates the G1/S transition (small-cell phenotype) and bypasses the need for upstream SBF/MBF activators; CDK-dependent phosphorylation dissociates Whi5 from SBF in late G1. Reason: Defining loss-of-function phenotype of the gene; core function. Supporting Evidence: PMID:15210111 Here we show that the cell size regulator Whi5 inhibits G1/S transcription and that this inhibition is relieved by CDK-mediated phosphorylation. |
| GO:0000122 negative regulation of transcription by RNA polymerase II | IGI PMID:15210110 Cln3 activates G1-specific transcription via phosphorylation... | ACCEPT | Summary: Genetic interaction with CLN3: whi5 inactivation restores G1-specific (SBF-dependent) transcription in the absence of Cln3, showing that Whi5 is the repressor of Pol II transcription at SBF promoters that Cln3-Cdc28 normally inactivates. Reason: Whi5 is a bona fide repressor of RNA polymerase II transcription at G1/S promoters, acting through SBF and HDAC recruitment (PMID:15210110, PMID:19745812). This is the defining molecular role of the gene. Supporting Evidence: PMID:15210110 Whi5 inactivation bypasses the requirement for Cln3 both for transcriptional activation and cell cycle initiation. PMID:15210110 Like mammalian Rb, Whi5 is a G1-specific transcriptional repressor antagonized by CDK. |
| GO:0000122 negative regulation of transcription by RNA polymerase II | IGI PMID:15210110 Cln3 activates G1-specific transcription via phosphorylation... | ACCEPT | Summary: Genetic interaction with MBP1 from de Bruin et al. 2004 (abstract-only cache). The mbp1-specific experiment cannot be quoted from the cache; the abstract establishes Whi5 as the SBF-bound (not MBF-bound) G1-specific transcriptional repressor. Reason: The repressor role is beyond doubt; the specific genetic test with mbp1 was read by the SGD curator in the full text and is not contradicted by anything in the literature. Deferred to the curator. Supporting Evidence: PMID:15210110 Whi5 associates with G1-specific promoters via SBF during early G1 phase, then dissociates coincident with transcriptional activation. |
| GO:0000122 negative regulation of transcription by RNA polymerase II | IGI PMID:15210111 CDK activity antagonizes Whi5, an inhibitor of G1/S transcri... | ACCEPT | Summary: Genetic interaction with CLN3 from Costanzo et al. 2004: Whi5 inhibits G1/S transcription, WHI5 deletion bypasses the need for Cln3, and CDK phosphorylation relieves the inhibition. Reason: Same conclusion reached independently by the two 2004 Cell papers. Core function. Supporting Evidence: PMID:15210111 Here we show that the cell size regulator Whi5 inhibits G1/S transcription and that this inhibition is relieved by CDK-mediated phosphorylation. |
| GO:0000122 negative regulation of transcription by RNA polymerase II | IMP PMID:15210110 Cln3 activates G1-specific transcription via phosphorylation... | ACCEPT | Summary: whi5 loss causes premature expression of G1-specific genes; overexpression retards it; CDK-site mutants of Whi5 reduce SBF-dependent transcription. Reason: Direct loss/gain-of-function evidence for repression of the SBF-dependent Pol II program. Core function. Supporting Evidence: PMID:15210110 Inactivation of Whi5 leads to premature expression of G1-specific genes and budding, whereas overexpression retards those processes. |
| GO:0000122 negative regulation of transcription by RNA polymerase II | IMP PMID:15210111 CDK activity antagonizes Whi5, an inhibitor of G1/S transcri... | ACCEPT | Summary: Whi5 inhibits G1/S transcription; deletion bypasses upstream activators; Whi5 is recruited to G1/S promoter elements through SBF/MBF in vivo and in vitro and re-enters the nucleus at mitotic exit to repress again. Reason: Core repressor function, independently established. Note that Takahata et al. 2009 observed nearly normal CLN1/CLN2 RNA in an asynchronous whi5 single mutant in their strain background, which reflects redundancy with Stb1 and with Whi5 dilution/timing rather than an absence of repressor activity; the repression phenotype is clear in synchronized cells and in sensitized (cln3, pho85, stb1) backgrounds. Supporting Evidence: PMID:15210111 Elimination of CDK activity at the end of mitosis allows Whi5 to reenter the nucleus to again repress G1/S transcription. PMID:19745812 However, RNA measurements show nearly normal expression of CLN1 and CLN2 in whi5 mutants |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IBA GO_REF:0000033 | MODIFY | Summary: PAINT inference at the Whi5/Whi7 node PTN002000919, seeded by the paralog SRL3/WHI7 (SGD:S000001799). Whi5 has no recognizable DNA-binding domain (UniProt features: two disordered regions and compositionally biased acidic/low-complexity segments only). Its promoter occupancy is entirely mediated by SBF: it "associates with G1-specific promoters via SBF" (de Bruin et al. 2004) and "is recruited to G1/S promoter elements via its interaction with SBF/MBF" (Costanzo et al. 2004), and promoter association requires an intact Swi4-Swi6 complex. The sequence specificity at SCB elements is contributed by Swi4, not by Whi5 or Whi7, so the sequence-specific DNA-binding claim is a role conflation: ChIP occupancy of a corepressor has been read as DNA binding. Reason: The essence of the annotation (Whi5 is found at Pol II cis-regulatory regions of G1/S genes) is right, but the molecular function it asserts, sequence-specific DNA binding, is performed by the Swi4 subunit of SBF that recruits Whi5. The activity Whi5 itself contributes at those sites is binding to the DNA-bound transcription factor, which is already captured experimentally by GO:0061629 (IDA, PMID:15210111) and is the proposed replacement. If a DNA-occupancy row is wanted for the family, the non-sequence-specific parent GO:0001012 (RNA polymerase II transcription regulatory region DNA binding), as used for the analogous human RB1 IBA in this repository, would be the defensible alternative. This argues with the node placement (the family lacks a DNA-binding domain; neither paralog binds DNA independently), not with the donor count. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: ROLE CONFLATION Sources checked: PANTHER:PTN002000919 SOURCE WEAK OR INFERRED Whi5/Whi7 ancestral node; the family is defined by the Pfam Whi5 (PF08528) G1/S transcription-factor-binding module and carries no DNA-binding domain. SGD:S000001799 Β· SRL3 SUPPORTS SOURCE BUT NOT TARGET Whi7/Srl3 is the SBF-recruited paralog; the evidence behind its own GO:0000978 row was not inspected here, but like Whi5 it reaches promoters through SBF. Proposed replacements: RNA polymerase II-specific DNA-binding transcription factor binding Supporting Evidence: PMID:15210110 Whi5 associates with G1-specific promoters via SBF during early G1 phase, then dissociates coincident with transcriptional activation. PMID:15210111 Whi5 is recruited to G1/S promoter elements via its interaction with SBF/MBF in vivo and in vitro. PMID:19823668 Whi5 associates indirectly with G1 phase-regulated promoters through interaction with SBF and MBF. file:yeast/WHI5/WHI5-deep-research-falcon.md Whi5 does not catalyze a reaction and is not known to bind DNA sequence-specifically by itself. |
| GO:0003712 transcription coregulator activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference at the Whi5/Whi7 node, with WHI5 itself (SGD:S000005609) as the experimental descendant that seeded the IBD. The target appearing in its own WITH/FROM is expected and marks that the experimental grounding lies on Whi5 (transcription corepressor activity, IDA/IMP/IGI rows below). The IBA adds the phylogenetic statement that coregulator activity is the shared, inherited function of the Whi5/Whi7 family. Reason: Correct at the family level; the more specific corepressor term is already carried by direct experimental evidence, and the general coregulator term is the appropriate node placement for a family that includes Whi7, which is also an SBF-bound repressor. Supporting Evidence: PMID:15210110 Like mammalian Rb, Whi5 is a G1-specific transcriptional repressor antagonized by CDK. |
| GO:0003714 transcription corepressor activity | IDA PMID:15210111 CDK activity antagonizes Whi5, an inhibitor of G1/S transcri... | ACCEPT | Summary: Costanzo et al. 2004 show directly that Whi5 inhibits G1/S transcription, is recruited to G1/S promoters through its interaction with the DNA-binding SBF/MBF factors in vivo and in vitro, and is released by CDK phosphorylation. This is the textbook definition of a corepressor: repression of a specific gene set via binding to a DNA-binding transcription factor at its genomic locus. Reason: Core molecular function of Whi5; independently confirmed by de Bruin et al. 2004 and mechanistically extended by the HDAC-recruitment work (PMID:19745812, PMID:19823668). Supporting Evidence: PMID:15210111 Whi5 is recruited to G1/S promoter elements via its interaction with SBF/MBF in vivo and in vitro. PMID:15210111 In late G1 phase, CDK-dependent phosphorylation dissociates Whi5 from SBF and drives Whi5 out of the nucleus. |
| GO:0003714 transcription corepressor activity | IGI PMID:19745812 The E2F functional analogue SBF recruits the Rpd3(L) HDAC, v... | ACCEPT | Summary: Genetic interaction with STB1 (SGD:S000005253). Takahata et al. 2009 (full text cached) show by ChIP that Rpd3(L) HDAC binding to the CLN1/CLN2 promoters is lost only in the stb1 whi5 double mutant, that FACT binding to SBF promoters is markedly increased in stb1 whi5, and that stb1 or whi5 mutation suppresses the G1 arrest of cdc28-13; Whi5 and Stb1 are the redundant intermediaries by which SBF recruits the HDAC. Reason: Provides the mechanism of corepression (HDAC recruitment) and the redundancy with Stb1 that explains the mild single-mutant expression phenotype. Core function. Supporting Evidence: PMID:19745812 Rpd3(L) is recruited to SBF genes by both Stb1 and Whi5, and Rpd3(L) binding is only lost in the stb1 whi5 double mutant. PMID:19745812 growth is restored by either a stb1 or whi5 mutation |
| GO:0003714 transcription corepressor activity | IMP PMID:19745812 The E2F functional analogue SBF recruits the Rpd3(L) HDAC, v... | ACCEPT | Summary: Mutant-based evidence from the same paper: whi5 mutation suppresses temperature-sensitive FACT (spt16-11) and cdc28-13 alleles, consistent with Whi5 imposing chromatin repression at G1 cyclin promoters that FACT and Cdc28 must overcome, and Whi5 is required (with Stb1) for Rpd3(L) recruitment to CLN promoters. Reason: Directly supports corepressor activity through HDAC recruitment and genetic antagonism with the chromatin-opening machinery. Core function. Supporting Evidence: PMID:19745812 The SBF activator binds to these promoters but is kept inactive by the Whi5 and Stb1 inhibitors. PMID:19745812 Our chromatin immunoprecipitation (ChIP) experiments show that SBF, Whi5 and Stb1 recruit both Cdc28 and the Rpd3(L) histone deacetylase to CLN promoters, extending the analogy with mammalian G1 cyclin promoters in which Rb recruits histone deacetylases. |
| GO:0005634 nucleus | HDA PMID:14562095 Global analysis of protein localization in budding yeast. | ACCEPT | Summary: Genome-wide GFP localization survey (Huh et al. 2003, abstract-only cache) scoring Whi5-GFP in the nucleus (and cytoplasm) of asynchronous cells, consistent with its cell-cycle regulated nucleocytoplasmic shuttling. Reason: Nuclear localization is where Whi5 functions (G1 repression at SBF promoters) and is confirmed by targeted studies (PMID:15210111, PMID:24470217). Supporting Evidence: PMID:14562095 describe the construction and analysis of a collection of yeast strains |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference at the Whi5/Whi7 node, seeded by both Whi7/Srl3 and Whi5 itself. Whi5 is active in the nucleus, where it binds promoter-bound SBF from mitotic exit through late G1. Reason: The nucleus is the compartment in which the corepressor activity is exerted; Whi5 appearing in its own WITH/FROM is expected because its experimental nuclear annotation seeded the IBD. Supporting Evidence: PMID:15210111 Elimination of CDK activity at the end of mitosis allows Whi5 to reenter the nucleus to again repress G1/S transcription. |
| GO:0005634 nucleus | IDA PMID:15210111 CDK activity antagonizes Whi5, an inhibitor of G1/S transcri... | ACCEPT | Summary: Costanzo et al. 2004 show that Whi5 is nuclear in early G1, is driven out of the nucleus by CDK phosphorylation in late G1, and re-enters when CDK activity is eliminated at the end of mitosis. Reason: Cell-cycle-regulated nuclear localization is the site of the core repressor function. Supporting Evidence: PMID:15210111 In late G1 phase, CDK-dependent phosphorylation dissociates Whi5 from SBF and drives Whi5 out of the nucleus. |
| GO:0005634 nucleus | IDA PMID:24470217 The yeast Ess1 prolyl isomerase controls Swi6 and Whi5 nucle... | ACCEPT | Summary: Atencio et al. 2014 (full text cached) show Whi5-GFP is nuclear in wild-type cells and fails to localize to the nucleus in ess1H164R prolyl-isomerase mutants; Ess1 binds the phosphorylated Ser-Pro motifs of the Whi5 NLS/NES peptides in vitro, implicating cis-trans isomerization in Whi5 nuclear entry/retention. Reason: Direct imaging of nuclear Whi5 and identification of a regulator of its import; consistent with the shuttling described by Costanzo et al. 2004 and with Msn5-dependent export (PMID:19520826). Supporting Evidence: PMID:24470217 In ess1H164R mutant cells, the fusion protein failed to localize to the nucleus and cytoplasmic staining was readily apparent PMID:24470217 Ess1 associated with Swi6 and Whi5 in vivo and bound directly to peptides |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location keyword mapping (Nucleus), itself derived from PMID:15210111. Reason: Consistent with all experimental rows; nucleus is the site of action. |
| GO:0005737 cytoplasm | HDA PMID:14562095 Global analysis of protein localization in budding yeast. | KEEP AS NON CORE | Summary: Genome-wide GFP survey scoring Whi5-GFP in the cytoplasm as well as the nucleus of asynchronous cells, reflecting the post-Start (S/G2/M) cytoplasmic pool of phosphorylated Whi5. Reason: Cytoplasmic localization is real but represents the CDK-phosphorylated, exported, inactive state of Whi5 (PMID:15210111; export is Msn5-dependent, PMID:19520826); the corepressor function is exerted in the nucleus. Same treatment as the cytoplasm rows in the human RB1 review. Supporting Evidence: PMID:15210111 In late G1 phase, CDK-dependent phosphorylation dissociates Whi5 from SBF and drives Whi5 out of the nucleus. |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: PAINT inference of cytoplasmic localization at the Whi5/Whi7 node, seeded by Whi5's own experimental cytoplasm annotation. Whi5 is cytoplasmic from Start until mitotic exit, after CDK phosphorylation drives Msn5-dependent export, and Whi7 is more evenly partitioned between nucleus and cytoplasm. Reason: The location is correct for the family, but it is where the phosphorylated, SBF-released protein resides between Start and mitotic exit; no repressor activity is exerted there. The 2025 report of an Atg1-Whi5 interaction during nitrogen starvation (PMID:40365021) is the only suggestion of a cytoplasmic activity and is not yet mechanistically resolved. Supporting Evidence: PMID:19520826 Yen1, Psy4, Pds1, and Whi5 were constitutively localized to the nucleus in an msn5 Ξ mutant, but not by treatment with leptomycin B (LMB), a Crm1 inhibitor |
| GO:0005737 cytoplasm | IDA PMID:15210111 CDK activity antagonizes Whi5, an inhibitor of G1/S transcri... | KEEP AS NON CORE | Summary: Costanzo et al. 2004 show that CDK phosphorylation in late G1 drives Whi5 out of the nucleus into the cytoplasm, where it remains until CDK activity falls at mitotic exit. Reason: Real, cell-cycle-regulated localization of the inactive, exported form; not the site of the core function. Supporting Evidence: PMID:15210111 In late G1 phase, CDK-dependent phosphorylation dissociates Whi5 from SBF and drives Whi5 out of the nucleus. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: UniProt subcellular-location keyword mapping (Cytoplasm), derived from the Huh et al. 2003 survey. Reason: Consistent with the experimental rows; cytoplasm is the location of the exported, inactive pool. |
| GO:0006357 regulation of transcription by RNA polymerase II | IBA GO_REF:0000033 | MODIFY | Summary: PAINT inference at the Whi5/Whi7 node, seeded by Whi5's own experimental annotations. Both family members regulate (repress) SBF-dependent Pol II transcription. Reason: The assertion is correct, but both members of the Whi5/Whi7 node are SBF-bound repressors, so the direction-specific child GO:0000122 (already carried on Whi5 by direct experimental evidence) describes the inherited function better than the direction-neutral parent. This is a granularity refinement, not a challenge to the PAINT node placement. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN002000919 SUPPORTS TRANSFER Whi5/Whi7 node; both extant S. cerevisiae members are SBF-bound repressors, so the inherited function is negative regulation rather than direction-neutral regulation. SGD:S000005609 Β· WHI5 SUPPORTS TRANSFER The target's own experimental GO:0000122 rows (PMID:15210110, PMID:15210111) are the descendant evidence that seeded the node; expected, not circular. Proposed replacements: negative regulation of transcription by RNA polymerase II Supporting Evidence: PMID:15210110 Like mammalian Rb, Whi5 is a G1-specific transcriptional repressor antagonized by CDK. |
| GO:0006357 regulation of transcription by RNA polymerase II | IGI PMID:19823668 Dual regulation by pairs of cyclin-dependent protein kinases... | MODIFY | Summary: Genetic interaction with CLN3 from Huang et al. 2009: the severe SBF-dependent reporter defect of cln3 pho85 cells is alleviated by whi5 deletion, and Whi5 mediates repression partly through interaction with the HDACs Hos3 and Rpd3, an association that Cln3-Cdc28 and Pcl9-Pho85 phosphorylation disrupts. Reason: The evidence in this paper is specifically for repression of SBF-dependent Pol II transcription (reporter expression is restored by removing Whi5; HDAC-dependent repression), so the direction-neutral parent term is less specific than the data warrant. The more specific GO:0000122, which Whi5 already carries from the 2004 papers, is the proposed replacement; the underlying assertion is sound. Proposed replacements: negative regulation of transcription by RNA polymerase II Supporting Evidence: PMID:19823668 deletion of RPD3 partially restored growth in the cln3Ξbck2Ξ strain providing further evidence for an HDAC requirement in Whi5-mediated transcriptional repression PMID:19823668 The G1 delay phenotype associated with a cln3Ξ pho85Ξ strain is dependent on WHI5. |
| GO:0006357 regulation of transcription by RNA polymerase II | IGI PMID:19823668 Dual regulation by pairs of cyclin-dependent protein kinases... | MODIFY | Summary: Genetic interaction with PHO85 from the same paper: WHI5 overexpression is toxic in pho85 mutants, Pcl9-Pho85 phosphorylates Whi5, and PHO85 regulates G1 transcription via WHI5 (the pho85-dependent G1 transcription defect is Whi5-dependent). Reason: As for the CLN3 row: the data show Whi5-mediated repression of SBF-dependent Pol II transcription, antagonized by Pho85, so the direction-specific GO:0000122 is the better term. Assertion sound. Proposed replacements: negative regulation of transcription by RNA polymerase II Supporting Evidence: PMID:19823668 we identify Whi5, to our knowledge, as the first demonstrated physiological substrate for the G1-specific Pcl9-Pho85 CDK |
| GO:0007089 traversing start control point of mitotic cell cycle | IMP PMID:26390151 Dilution of the cell cycle inhibitor Whi5 controls budding-y... | ACCEPT | Summary: Schmoller et al. 2015 (full text cached) use single-cell time-lapse of Whi5-mCitrine and Cln3 reporters to show that Whi5 is a stable protein synthesized in S/G2/M at a size-independent rate, that its concentration at birth decreases monotonically with cell size, and that the rate at which cells pass Start is set by Whi5 concentration rather than by cell size per se (decoupled with an inducible WHI5 allele). Dilution of Whi5 by growth is proposed as the size-sensing mechanism that triggers Start. Reason: Whi5 is the inhibitory node of the Start positive-feedback loop (SBF -> CLN1/2 -> Cln-Cdc28 -| Whi5 -| SBF) and its concentration is the variable that the loop integrates, so it is a bona fide component of the Start commitment process as defined by GO:0007089. Whether Whi5 dilution is the sole size sensor is contested (see suggested_questions), but that debate does not affect Whi5's participation in Start. Supporting Evidence: PMID:26390151 In this model, cell growth dilutes the cell cycle inhibitor Whi5 to drive progression through the cell cycle, whereas Cln3 concentration remains constant. PMID:26390151 Inhibitor-dilution results in size-dependent cell cycle progression because smaller cells are born with higher Whi5 concentrations. |
| GO:0008361 regulation of cell size | HMP PMID:12089449 Systematic identification of pathways that couple cell growt... | ACCEPT | Summary: Genome-wide cell-size screen of the yeast deletion collection (Jorgensen et al. 2002, abstract-only cache) that identified whi5 as one of the five most potent regulators of critical cell size at Start (with sfp1, sch9, cdh1, prs3). whi5 null cells are roughly 30% smaller than wild type while growing at a normal rate. Reason: Cell-size control is the physiological output of Whi5's Start-gating function, and the dilution mechanism (PMID:26390151) makes Whi5 the size-dependent variable itself; this is a core, not incidental, role. Supporting Evidence: PMID:12089449 govern critical cell size at Start, the most potent of which were Sfp1, Sch9, PMID:26390151 we found that the concentration of Whi5 at cell birth monotonically decreases with cell size |
| GO:0010508 positive regulation of autophagy | IMP PMID:40365021 Omic AI reveals new autophagy regulators from the Atg1 inter... | KEEP AS NON CORE | Summary: Han et al. 2025 (full text cached) used an AI-prioritized screen of Atg1 interactors and substrates; whi5 deletion attenuated GFP-Atg8 cleavage and vacuolar GFP accumulation under nitrogen starvation, Whi5 co-immunoprecipitated with Atg1, Atg1 phosphorylated Whi5 in vitro at predicted sites S78/S149, and a Whi5-2A mutant was impaired in supporting Atg1 puncta formation. The authors themselves describe Whi5 as a "potentially" positive autophagy regulator. Reason: A single recent study with a modest effect size, no mechanism linking Whi5 to the autophagy machinery beyond phosphorylation and puncta counts, and no test of whether the effect is transcriptional (Whi5 represses SBF targets and whi5 cells are small and cycle fast, which could alter starvation responses indirectly). The hedged acts_upstream_of_or_within qualifier applied by SGD is appropriate. Retain as a non-core, provisional role rather than a core function. Supporting Evidence: PMID:40365021 Using the GFP-Atg8 immunoblotting assay, we found that the cleavage of GFP-Atg8 was significantly attenuated in yeast cells with deletion of WHI5 compared to WT cells PMID:40365021 Rgd1 and Whi5 were validated to be potentially positive autophagy regulators |
| GO:0033309 SBF transcription complex | IDA PMID:15210110 Cln3 activates G1-specific transcription via phosphorylation... | ACCEPT | Summary: de Bruin et al. 2004 purified SBF and MBF and analyzed them by MudPIT; Whi5 was identified as a stably bound component of SBF but not MBF, associating with G1-specific promoters via SBF in early G1 and dissociating upon phosphorylation. The GO definition of the SBF complex explicitly lists Whi5 as an associated protein. Reason: Direct biochemical identification of Whi5 as an SBF-associated subunit in G1; the association is cell-cycle regulated (lost after CDK phosphorylation), which is consistent with part_of a G1-phase form of the complex. Core. Supporting Evidence: PMID:15210110 Whi5 was identified as a stably bound component of SBF but not MBF. PMID:19745812 Whi5 does not bind to MBF, and only Stb1 is required for Rpd3(L) recruitment to MBF genes. |
| GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding | IDA PMID:15210111 CDK activity antagonizes Whi5, an inhibitor of G1/S transcri... | ACCEPT | Summary: Costanzo et al. 2004 show that Whi5 is recruited to G1/S promoter elements via its interaction with SBF/MBF in vivo and in vitro; Swi4 (and Mbp1) are sequence-specific Pol II transcription factors, so this is the molecular interaction through which Whi5's corepressor activity is targeted. Reason: This is the informative molecular-function representation of the Whi5-SBF interaction and the correct replacement for any generic protein-binding or DNA-binding claim. Core. Later work indicates the stable interaction is with SBF (Swi4-Swi6) rather than MBF (PMID:15210110, PMID:19745812). Supporting Evidence: PMID:15210111 Whi5 is recruited to G1/S promoter elements via its interaction with SBF/MBF in vivo and in vitro. |
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Download this section (compressed HTML)Q: The yeast Start machinery, including the repressors Whi5, Stb1, Sic1 and Whi7, is annotated involved_in GO:0000082 (G1/S transition), whereas metazoan Rb carries GO:2000134 (negative regulation of G1/S transition). Is the "component of the switch" convention for yeast repressors intended, and should Whi5 and Rb be aligned in one direction or the other for cross-species comparison?
Suggested experts: Curt Wittenberg, Mike Tyers, Brenda Andrews
Q: Whi5 dilution (Schmoller et al. 2015) competes with Cln3 titration against SBF sites and with distributed-network models (Swi6 phosphorylation, Bck2) as the size sensor. Which variable is rate-limiting for Start in daughter cells under physiological growth conditions, and is Whi5 concentration or Whi5 phospho-state the operative readout?
Suggested experts: Jan M. Skotheim, Kurt M. Schmoller
Q: Whi5 is now reported to promote nitrogen-starvation-induced autophagy as an Atg1 substrate (Han et al. 2025). Is this a direct, non-transcriptional role of cytoplasmic Whi5, or an indirect consequence of altered SBF-dependent transcription and cell size in whi5 cells?
Experiment: Compare GFP-Atg8 processing and Atg1 puncta formation in whi5 cells complemented with (i) wild-type WHI5, (ii) the Atg1-site mutant WHI5-S78A/S149A, (iii) a WHI5 allele lacking the SBF-binding module so that it cannot repress the G1/S regulon, and (iv) a nuclear-restricted WHI5 (12A/NES-mutant) allele, all expressed from the native promoter and matched for cell size by growth in a swi4 or bck2 background. A direct role predicts that (iii) and (iv) behave differently: the SBF-binding-defective allele should rescue autophagy while the nuclear-trapped allele should not.
Hypothesis: The autophagy phenotype of whi5 cells is a direct consequence of Atg1-dependent phosphorylation of cytoplasmic Whi5, separable from its SBF corepressor function.
Type: structure-function complementation with autophagy flux readouts
Experiment: Perform synchronized (elutriated daughter) time courses of CLN2 nascent transcription (4tU-seq) and promoter histone acetylation in wild type, whi5, rpd3 hos3, and whi5 rpd3 hos3 strains, and in a whi5 allele mutated in the Pfam Whi5 (PF08528) SBF-binding motif. Epistasis of whi5 over rpd3 hos3 for early-G1 repression, combined with in vitro transcription with purified SBF and Whi5 on a chromatinized CLN2 template with and without Rpd3(L), would separate HDAC-dependent from HDAC-independent repression.
Hypothesis: Whi5 corepressor activity at CLN1/CLN2 promoters requires Rpd3(L) and Hos3 recruitment, and the residual repression seen in rpd3 hos3 cells is due to direct masking of the Swi6 activation surface.
Type: genetic epistasis with nascent transcription and in vitro transcription
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