SWE1

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0000086 G2/M transition of mitotic cell cycle	IDA PMID:8253069 Properties of Saccharomyces cerevisiae wee1 and its differen...	MODIFY	Summary: Booher et al. (1993) cloned SWE1 as the S. cerevisiae wee1 homologue and showed that Swe1 immunoprecipitates tyrosine-phosphorylate and inactivate Clb2-Cdc28 but not Cln2-Cdc28, and that SWE1 overexpression arrests cells in G2 with short spindles. Swe1 is therefore a negative regulator of the G2/M transition, not a positive participant in it. Reason: The direction of Swe1's action is what matters biologically: it inhibits the M-cyclin/CDK complex whose activation constitutes the G2/M transition. GO:0000086 is defined as the transition itself and does not capture that Swe1 opposes it; the child term GO:0010972 (negative regulation of G2/M transition of mitotic cell cycle), already carried by SWE1 via IBA, is the accurate and more informative term for exactly this experiment. The essence of the annotation is sound, so MODIFY rather than REMOVE. Proposed replacements: negative regulation of G2/M transition of mitotic cell cycle Supporting Evidence: PMID:8253069 Swe1 immunoprecipitates were capable of tyrosine phosphorylating and inactivating p34CDC28 complexed with Clb2, a G2-type cyclin, but not p34CDC28 complexed with Cln2, a G1-type cyclin, consistent with the inability of Swe1 overexpression to inhibit the G1/S transition. PMID:8253069 SWE1 overexpression arrests cells in G2 with short spindles whereas deletion of SWE1 did not alter the cell cycle but did eliminate the G2 delay observed in mih1- mutants.
GO:0000086 G2/M transition of mitotic cell cycle	IMP PMID:8253069 Properties of Saccharomyces cerevisiae wee1 and its differen...	MODIFY	Summary: Mutant-phenotype evidence from the same paper: swe1 deletion does not alter the unperturbed cell cycle but eliminates the G2 delay of mih1 mutants, and SWE1 overexpression arrests cells in G2. Both phenotypes show Swe1 acting as a brake on mitotic entry that is opposed by the Mih1 (Cdc25) phosphatase. Reason: As for the IDA row, the more specific negative-regulation term GO:0010972 describes the biology (Swe1 delays G2/M) better than the parent transition term; the phenotypes are epistatic with MIH1 and in the direction of inhibition. Proposed replacements: negative regulation of G2/M transition of mitotic cell cycle Supporting Evidence: PMID:8253069 SWE1 overexpression arrests cells in G2 with short spindles whereas deletion of SWE1 did not alter the cell cycle but did eliminate the G2 delay observed in mih1- mutants.
GO:0000320 re-entry into mitotic cell cycle	IGI PMID:15107621 The yeast kinase Swe1 is required for proper entry into cell...	KEEP AS NON CORE	Summary: Saracino et al. (2004) found that additional deletion of SWE1 in sda1-1, rix1-1 or tif6Δ ribosome-biogenesis mutants markedly delays budding and DNA replication when cells are released from the conditional G1 arrest, and that this delay is independent of Cdc28 Tyr19 phosphorylation. Swe1 thus has a Tyr19-independent role in resuming the cycle after such a G1 arrest. Reason: The genetic interaction is documented by the SGD curator from the primary paper (abstract-only in the cache) and describes a genuine phenotype, but it is peripheral: the mechanism is unknown, it is explicitly independent of Swe1's characterised Cdc28-Tyr19 kinase output, and the 'non-dividing state' is a conditional ts-mutant G1 arrest rather than quiescence, which stretches the term definition. Retain as a non-core annotation; the core function remains G2/M inhibition. Supporting Evidence: PMID:15107621 Our data suggest that Swe1 is required for timely entry into cell cycle after a G1 arrest caused by impairment in pre-60S biogenesis and in protein synthesis. PMID:15107621 However, such a prolonged delay is independent of the Tyr19 phosphorylation in Cdc28.
GO:0000320 re-entry into mitotic cell cycle	IGI PMID:15107621 The yeast kinase Swe1 is required for proper entry into cell...	KEEP AS NON CORE	Summary: Saracino et al. (2004) found that additional deletion of SWE1 in sda1-1, rix1-1 or tif6Δ ribosome-biogenesis mutants markedly delays budding and DNA replication when cells are released from the conditional G1 arrest, and that this delay is independent of Cdc28 Tyr19 phosphorylation. Swe1 thus has a Tyr19-independent role in resuming the cycle after such a G1 arrest. Reason: The genetic interaction is documented by the SGD curator from the primary paper (abstract-only in the cache) and describes a genuine phenotype, but it is peripheral: the mechanism is unknown, it is explicitly independent of Swe1's characterised Cdc28-Tyr19 kinase output, and the 'non-dividing state' is a conditional ts-mutant G1 arrest rather than quiescence, which stretches the term definition. Retain as a non-core annotation; the core function remains G2/M inhibition. Supporting Evidence: PMID:15107621 Our data suggest that Swe1 is required for timely entry into cell cycle after a G1 arrest caused by impairment in pre-60S biogenesis and in protein synthesis. PMID:15107621 However, such a prolonged delay is independent of the Tyr19 phosphorylation in Cdc28.
GO:0000320 re-entry into mitotic cell cycle	IGI PMID:15107621 The yeast kinase Swe1 is required for proper entry into cell...	KEEP AS NON CORE	Summary: Saracino et al. (2004) found that additional deletion of SWE1 in sda1-1, rix1-1 or tif6Δ ribosome-biogenesis mutants markedly delays budding and DNA replication when cells are released from the conditional G1 arrest, and that this delay is independent of Cdc28 Tyr19 phosphorylation. Swe1 thus has a Tyr19-independent role in resuming the cycle after such a G1 arrest. Reason: The genetic interaction is documented by the SGD curator from the primary paper (abstract-only in the cache) and describes a genuine phenotype, but it is peripheral: the mechanism is unknown, it is explicitly independent of Swe1's characterised Cdc28-Tyr19 kinase output, and the 'non-dividing state' is a conditional ts-mutant G1 arrest rather than quiescence, which stretches the term definition. Retain as a non-core annotation; the core function remains G2/M inhibition. Supporting Evidence: PMID:15107621 Our data suggest that Swe1 is required for timely entry into cell cycle after a G1 arrest caused by impairment in pre-60S biogenesis and in protein synthesis. PMID:15107621 However, such a prolonged delay is independent of the Tyr19 phosphorylation in Cdc28.
GO:0004672 protein kinase activity	HDA PMID:16319894 Global analysis of protein phosphorylation in yeast.	ACCEPT	Summary: Proteome-chip study in which most yeast kinases, Swe1 among them, were assayed for in vitro phosphorylation of ~4,400 immobilised proteins. Confirms Swe1 is an active protein kinase at the generic level. Reason: Accurate parent-level molecular function, corroborated by the direct demonstration that Swe1 phosphorylates Cdc28 (PMID:8253069). The more specific protein tyrosine kinase activity term is the informative one, but the parent is not wrong and high-throughput evidence at this level is appropriate. Supporting Evidence: PMID:16319894 Here we describe, with the use of proteome chip technology, the in vitro substrates recognized by most yeast protein kinases: we identified over 4,000 phosphorylation events involving 1,325 different proteins.
GO:0004672 protein kinase activity	IEA GO_REF:0000002	ACCEPT	Summary: InterPro mapping from the Ser/Thr kinase active-site signature (IPR008271) to the generic protein kinase term. Swe1 has a canonical kinase domain (residues 444-794) with Lys473 as the ATP-binding lysine and Asp579 as the catalytic base (UniProt features). Reason: Correct grouping term consistent with experimentally demonstrated kinase activity; the specific tyrosine kinase annotations capture the function better.
GO:0004674 protein serine/threonine kinase activity	IEA GO_REF:0000003	KEEP AS NON CORE	Summary: EC-number mapping (UniProt assigns EC 2.7.11.1 to SWE1). Wee1-family kinases are dual-specificity enzymes and UniProt states that Swe1 can act on serines as well as tyrosines, so serine/threonine activity is credible; however the physiologically defining reaction is phosphorylation of Cdc28 Tyr19, a tyrosine. Reason: Not wrong (dual-specificity family; UniProt 'Can act both on serines and on tyrosines'), but no physiological serine/threonine substrate of Swe1 is established and the core catalytic output is tyrosine phosphorylation of Cdc28. Kept as a non-core activity rather than promoted to core; the S. pombe wee1 review treats its Ser/Thr rows the same way relative to the Tyr15 kinase activity. Supporting Evidence: PMID:8253069 Swe1 immunoprecipitates were capable of tyrosine phosphorylating and inactivating p34CDC28 complexed with Clb2, a G2-type cyclin, but not p34CDC28 complexed with Cln2, a G1-type cyclin, consistent with the inability of Swe1 overexpression to inhibit the G1/S transition.
GO:0004713 protein tyrosine kinase activity	IBA GO_REF:0000033	ACCEPT	Summary: PAINT inference from the fungal Wee1/Mik1/Swe1 node PTN000867899, seeded by S. pombe wee1 and mik1 and by SWE1's own IDA (SGD:S000003723 in WITH/FROM). Swe1 phosphorylates Cdc28 on Tyr19; this is the defining activity of the subfamily. Reason: Core molecular function. The IBA is grounded on direct experimental evidence in both budding and fission yeast; SWE1 appearing among the descendant sources is expected and marks that the experimental grounding exists on the target itself. Supporting Evidence: PMID:8253069 Swe1 immunoprecipitates were capable of tyrosine phosphorylating and inactivating p34CDC28 complexed with Clb2, a G2-type cyclin, but not p34CDC28 complexed with Cln2, a G1-type cyclin, consistent with the inability of Swe1 overexpression to inhibit the G1/S transition.
GO:0004713 protein tyrosine kinase activity	IDA PMID:8253069 Properties of Saccharomyces cerevisiae wee1 and its differen...	ACCEPT	Summary: Direct biochemical evidence: immunoprecipitated Swe1 phosphorylates Cdc28 on tyrosine and inactivates it when Cdc28 is bound to the mitotic cyclin Clb2, but not when bound to the G1 cyclin Cln2. Reason: Foundational direct demonstration of the core tyrosine kinase activity and of its cyclin-complex selectivity; later work (PMID:16096060) confirmed that Swe1 forms a stable inhibitory complex with Clb2-Cdk1. Supporting Evidence: PMID:8253069 Swe1 immunoprecipitates were capable of tyrosine phosphorylating and inactivating p34CDC28 complexed with Clb2, a G2-type cyclin, but not p34CDC28 complexed with Cln2, a G1-type cyclin, consistent with the inability of Swe1 overexpression to inhibit the G1/S transition.
GO:0004713 protein tyrosine kinase activity	IEA GO_REF:0000117	ACCEPT	Summary: ARBA machine-learned rule assigning tyrosine kinase activity; coincides with the experimentally demonstrated Cdc28-Tyr19 kinase activity. Reason: Electronic assignment that duplicates the experimentally supported core activity. Supporting Evidence: PMID:8253069 Swe1 immunoprecipitates were capable of tyrosine phosphorylating and inactivating p34CDC28 complexed with Clb2, a G2-type cyclin, but not p34CDC28 complexed with Cln2, a G1-type cyclin, consistent with the inability of Swe1 overexpression to inhibit the G1/S transition.
GO:0005515 protein binding	IPI PMID:11283351 A comprehensive two-hybrid analysis to explore the yeast pro...	REMOVE	Summary: Genome-wide two-hybrid screen (Ito et al. 2001) recording a Swe1-Hsl7 interaction. Hsl7 is the adaptor that, with Hsl1, recruits Swe1 to the daughter side of the bud neck where it is hyperphosphorylated and degraded (PMID:10805747); the interaction is biologically real but the term records only 'binding'. Reason: Bare GO:0005515 conveys no information about what Swe1 does; per repository policy such rows are resolved to an informative molecular function where the paper supports one and otherwise removed. The Swe1-Hsl7 interaction is not in doubt and is recorded in the notes and references, but it describes regulation OF Swe1 (recruitment, phosphorylation or dephosphorylation of the kinase) rather than an activity Swe1 itself performs, so no more specific MF term is warranted. Removal does not assert that the interaction is false. Supporting Evidence: PMID:11283351 Here we have completed the comprehensive analysis using this system to identify 4,549 two-hybrid interactions among 3,278 proteins.
GO:0005515 protein binding	IPI PMID:11438652 Cdc5 interacts with the Wee1 kinase in budding yeast.	REMOVE	Summary: Bartholomew et al. (2001) isolated Swe1 (residues 173-819) in a two-hybrid screen with the Polo kinase Cdc5 and showed that Cdc5 overproduction modifies Swe1 and titrates Swe1-dependent phenotypes; Cdc5 is now known to hyperphosphorylate Swe1 and target it for degradation. Swe1 is the substrate here, not the actor. Reason: Bare GO:0005515 conveys no information about what Swe1 does; per repository policy such rows are resolved to an informative molecular function where the paper supports one and otherwise removed. The Swe1-Cdc5 interaction is not in doubt and is recorded in the notes and references, but it describes regulation OF Swe1 (recruitment, phosphorylation or dephosphorylation of the kinase) rather than an activity Swe1 itself performs, so no more specific MF term is warranted. Removal does not assert that the interaction is false. Supporting Evidence: PMID:11438652 Our work shows that Cdc5, the Polo kinase in budding yeast, interacts with Swe1.
GO:0005515 protein binding	IPI PMID:11805837 Systematic identification of protein complexes in Saccharomy...	REMOVE	Summary: High-throughput affinity-purification/mass-spectrometry complex map (Ho et al. 2002) recording Hsl7 with Swe1. The pairing is consistent with the well-characterised Hsl1-Hsl7-Swe1 bud-neck module (PMID:10805747). Reason: Bare GO:0005515 conveys no information about what Swe1 does; per repository policy such rows are resolved to an informative molecular function where the paper supports one and otherwise removed. The Swe1-Hsl7 interaction is not in doubt and is recorded in the notes and references, but it describes regulation OF Swe1 (recruitment, phosphorylation or dephosphorylation of the kinase) rather than an activity Swe1 itself performs, so no more specific MF term is warranted. Removal does not assert that the interaction is false.
GO:0005515 protein binding	IPI PMID:18719252 High-quality binary protein interaction map of the yeast int...	REMOVE	Summary: Binary two-hybrid interactome (Yu et al. 2008) recording Swe1-Cdc5, reproducing the interaction first described by Bartholomew et al. (PMID:11438652). Reason: Bare GO:0005515 conveys no information about what Swe1 does; per repository policy such rows are resolved to an informative molecular function where the paper supports one and otherwise removed. The Swe1-Cdc5 interaction is not in doubt and is recorded in the notes and references, but it describes regulation OF Swe1 (recruitment, phosphorylation or dephosphorylation of the kinase) rather than an activity Swe1 itself performs, so no more specific MF term is warranted. Removal does not assert that the interaction is false.
GO:0005515 protein binding	IPI PMID:20489023 A global protein kinase and phosphatase interaction network ...	REMOVE	Summary: Kinase-phosphatase interaction network by AP-MS (Breitkreutz et al. 2010) recording the Kin1 kinase with Swe1. No functional follow-up for this pair is available in the cached abstract. Reason: Bare GO:0005515 conveys no information about what Swe1 does; per repository policy such rows are resolved to an informative molecular function where the paper supports one and otherwise removed. The Swe1-Kin1 interaction is not in doubt and is recorded in the notes and references, but it describes regulation OF Swe1 (recruitment, phosphorylation or dephosphorylation of the kinase) rather than an activity Swe1 itself performs, so no more specific MF term is warranted. Removal does not assert that the interaction is false. 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:20489023 A global protein kinase and phosphatase interaction network ...	REMOVE	Summary: Kinase-phosphatase interaction network by AP-MS recording Hsl7 with Swe1, consistent with the Hsl1-Hsl7-Swe1 module at the bud neck (PMID:10805747). Reason: Bare GO:0005515 conveys no information about what Swe1 does; per repository policy such rows are resolved to an informative molecular function where the paper supports one and otherwise removed. The Swe1-Hsl7 interaction is not in doubt and is recorded in the notes and references, but it describes regulation OF Swe1 (recruitment, phosphorylation or dephosphorylation of the kinase) rather than an activity Swe1 itself performs, so no more specific MF term is warranted. Removal does not assert that the interaction is false. 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:20489023 A global protein kinase and phosphatase interaction network ...	REMOVE	Summary: Kinase-phosphatase interaction network by AP-MS recording the Cdc14 phosphatase with Swe1; the abstract notes that Cdc14 associated with multiple kinases. Plausibly relevant to Swe1 dephosphorylation but not functionally characterised here. Reason: Bare GO:0005515 conveys no information about what Swe1 does; per repository policy such rows are resolved to an informative molecular function where the paper supports one and otherwise removed. The Swe1-Cdc14 interaction is not in doubt and is recorded in the notes and references, but it describes regulation OF Swe1 (recruitment, phosphorylation or dephosphorylation of the kinase) rather than an activity Swe1 itself performs, so no more specific MF term is warranted. Removal does not assert that the interaction is false. 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:0005524 ATP binding	IEA GO_REF:0000002	ACCEPT	Summary: InterPro-derived ATP binding for the protein kinase domain; UniProt annotates the ATP-binding glycine loop (450-458) and Lys473, and the K473 mutant is kinase-dead (UniProt mutagenesis, PMID:10454545). Reason: Standard, functionally validated cofactor binding required for catalysis.
GO:0005634 nucleus	IBA GO_REF:0000033	ACCEPT	Summary: PAINT inference from the WEE1/PKMYT1-family node PTN000113601; SWE1's own IDA (SGD:S000003723) is among the sources. Swe1 accumulates in the nucleus in G1/S, where it inhibits nuclear Clb-Cdc28, and stabilised Swe1 in hsl1/hsl7 mutants accumulates there (PMID:10805747). Reason: Phylogenetic inference concordant with direct localisation data; the nucleus is a principal site of action on Cdc28. Supporting Evidence: PMID:10805747 The stabilized Swe1p in hsl1 and hsl7 mutants accumulated in the nucleus, which presumably facilitates its inhibition of nuclear Clb-Cdc28p complexes.
GO:0005634 nucleus	IDA PMID:10805747 Septin-dependent assembly of a cell cycle-regulatory module ...	ACCEPT	Summary: Longtine et al. (2000) imaged tagged Swe1p and found it in the nucleus of unbudded cells and in the nucleus and/or at the bud neck of budded cells; stabilised Swe1p in hsl1Δ/hsl7Δ cells accumulated in the nucleus. Reason: Direct localisation evidence; the nucleus is where Swe1 meets its substrate Clb-Cdc28. Supporting Evidence: PMID:10805747 In budded wild-type cells, Swe1p was detected only in the nucleus (12% of the cells examined), only at the neck (23% of the cells), or at both locations (39% of the cells) PMID:10805747 The stabilized Swe1p in hsl1 and hsl7 mutants accumulated in the nucleus, which presumably facilitates its inhibition of nuclear Clb-Cdc28p complexes.
GO:0005634 nucleus	IDA PMID:15282802 Localization of proteins that are coordinately expressed wit...	ACCEPT	Summary: Systematic YFP-tagging of 45 proteins whose transcripts peak in G1 (a set that includes SWE1); SGD curated nuclear and bud-neck localisation for Swe1 from this study. The cached abstract does not name Swe1 individually, but the result agrees with the detailed analysis of PMID:10805747. Reason: Curator-read primary data consistent with independent direct evidence for nuclear localisation; abstract-only cache is not grounds to doubt the annotation. Supporting Evidence: PMID:15282802 Forty-five proteins were tagged with the GFP variant YFP.
GO:0005634 nucleus	IEA GO_REF:0000120	ACCEPT	Summary: Electronic mapping from the UniProt subcellular-location 'Nucleus' keyword, which itself rests on PMID:10805747. Reason: Duplicates experimentally supported nuclear localisation.
GO:0005737 cytoplasm	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: Broad cytoplasm term inferred from the family node PTN000113601 (the fungal donor in WITH/FROM is GCN2, SGD:S000002691, an eIF2-alpha kinase in the same PANTHER family). Swe1 does reside outside the nucleus, at the daughter side of the bud neck, so the term is not wrong, but the informative compartments are the nucleus and the cellular bud neck. Reason: Not incorrect (the bud-neck pool is cytoplasmic) but low-information relative to the specific nucleus and bud-neck annotations; graded the same way as the cytoplasm IBA on S. pombe wee1 and human WEE1. Supporting Evidence: PMID:10805747 In budded wild-type cells, Swe1p was detected only in the nucleus (12% of the cells examined), only at the neck (23% of the cells), or at both locations (39% of the cells)
GO:0005935 cellular bud neck	IDA PMID:10805747 Septin-dependent assembly of a cell cycle-regulatory module ...	ACCEPT	Summary: Swe1p localises to the daughter side of the mother-bud neck in a septin-, Hsl1- and Hsl7-dependent hierarchy; there it is hyperphosphorylated and targeted for degradation. This is the site where the morphogenesis checkpoint is read out on Swe1. Reason: Direct, mechanistically detailed localisation. Although the neck is primarily where Swe1 is inactivated rather than where it phosphorylates Cdc28, it is a defining compartment for the protein and part of how it functions as a checkpoint effector. Supporting Evidence: PMID:10805747 In budded wild-type cells, Swe1p was detected only in the nucleus (12% of the cells examined), only at the neck (23% of the cells), or at both locations (39% of the cells) PMID:10805747 the neck localization of Swe1p requires both Hsl1p and Hsl7p, as well as the septins
GO:0005935 cellular bud neck	IDA PMID:15282802 Localization of proteins that are coordinately expressed wit...	ACCEPT	Summary: YFP-tagged Swe1 scored at the bud neck in the Sundin et al. (2004) localisation survey of G1-expressed proteins; consistent with the septin-dependent neck localisation described by Longtine et al. Reason: Curator-read primary imaging in agreement with independent direct evidence (PMID:10805747). Supporting Evidence: PMID:15282802 Forty-five proteins were tagged with the GFP variant YFP.
GO:0005935 cellular bud neck	IEA GO_REF:0000044	ACCEPT	Summary: Electronic mapping from the UniProt subcellular-location 'Bud neck' keyword, which rests on PMID:10805747. Reason: Duplicates experimentally supported bud-neck localisation.
GO:0008361 regulation of cell size	HMP PMID:12089449 Systematic identification of pathways that couple cell growt...	KEEP AS NON CORE	Summary: Genome-wide cell-size screen of the deletion collection (Jorgensen et al. 2002) in which swe1Δ was scored as size-abnormal. Independent focused work (Harvey & Kellogg 2003, PMID:12593792, not cached) showed that swe1Δ cells are smaller and that Swe1 is required for normal cell-size control at mitotic entry, paralleling the classic 'wee' phenotype in S. pombe, although the effect is much weaker in budding yeast where Start is the main size-control point. Reason: A genuine but modest contribution: Swe1 delays mitotic entry while the bud grows, which sets cell size at division. The evidence here is a high-throughput screen whose abstract does not single out SWE1, so it is retained as a non-core annotation rather than elevated to core. Supporting Evidence: PMID:12089449 We determined cell size distributions for the complete set of approximately 6000 Saccharomyces cerevisiae gene deletion strains and identified approximately 500 abnormally small (whi) or large (lge) mutants.
GO:0010697 negative regulation of mitotic spindle pole body separation	IGI PMID:8887667 Spindle pole body separation in Saccharomyces cerevisiae req...	MARK AS OVER ANNOTATED	Summary: Lim et al. (1996) showed that cdc28-E19 (phosphomimetic Tyr19) cells and cells overexpressing SWE1 duplicate but fail to separate spindle pole bodies, and proposed that Tyr19 dephosphorylation promotes SPB separation. The effect of Swe1 is via its inhibitory phosphorylation of Clb-Cdc28, whose activity drives SPB separation. Reason: The observation is real but the term is an over-specific reading of it: the SPB-separation block is one downstream consequence of Cdc28 Tyr19 phosphorylation (already captured by GO:0010972), was seen only under SWE1 overexpression, and Swe1 does not regulate SPB separation in the unperturbed cycle (swe1Δ has no cell-cycle phenotype, PMID:8253069). Annotating every CDK-dependent event that Swe1 can block as a separate 'negative regulation of X' would multiply terms without adding biology. Supporting Evidence: PMID:8887667 We also find that the overexpression of SWE1, the budding-yeast homolog of wee1, also leads to a failure to segregate SPBs. PMID:8887667 On the basis of these results, we propose that one of the roles of Tyr-19 dephosphorylation is to promote SPB separation.
GO:0010697 negative regulation of mitotic spindle pole body separation	IMP PMID:8887667 Spindle pole body separation in Saccharomyces cerevisiae req...	MARK AS OVER ANNOTATED	Summary: Lim et al. (1996) showed that cdc28-E19 (phosphomimetic Tyr19) cells and cells overexpressing SWE1 duplicate but fail to separate spindle pole bodies, and proposed that Tyr19 dephosphorylation promotes SPB separation. The effect of Swe1 is via its inhibitory phosphorylation of Clb-Cdc28, whose activity drives SPB separation. Reason: The observation is real but the term is an over-specific reading of it: the SPB-separation block is one downstream consequence of Cdc28 Tyr19 phosphorylation (already captured by GO:0010972), was seen only under SWE1 overexpression, and Swe1 does not regulate SPB separation in the unperturbed cycle (swe1Δ has no cell-cycle phenotype, PMID:8253069). Annotating every CDK-dependent event that Swe1 can block as a separate 'negative regulation of X' would multiply terms without adding biology. Supporting Evidence: PMID:8887667 We also find that the overexpression of SWE1, the budding-yeast homolog of wee1, also leads to a failure to segregate SPBs. PMID:8887667 On the basis of these results, we propose that one of the roles of Tyr-19 dephosphorylation is to promote SPB separation.
GO:0010972 negative regulation of G2/M transition of mitotic cell cycle	IBA GO_REF:0000033	ACCEPT	Summary: PAINT inference from node PTN008315181 seeded by S. pombe wee1 and mik1, human PKMYT1 and other metazoan Wee1-family kinases. This is Swe1's defining function: inhibitory Tyr19 phosphorylation of Clb-Cdc28 delays mitotic entry, and SWE1 overexpression arrests cells in G2. Reason: Core function, supported by phylogeny and by direct biochemical and genetic evidence in S. cerevisiae (PMID:8253069, PMID:8930890). Supporting Evidence: PMID:8253069 SWE1 overexpression arrests cells in G2 with short spindles whereas deletion of SWE1 did not alter the cell cycle but did eliminate the G2 delay observed in mih1- mutants. PMID:8930890 We show that the ability of this checkpoint to delay nuclear division requires the SWE1 gene, encoding a protein kinase that inhibits the master cell cycle regulatory kinase Cdc28.
GO:0040020 regulation of meiotic nuclear division	IMP PMID:10619027 The pachytene checkpoint in S. cerevisiae depends on Swe1-me...	MODIFY	Summary: Leu & Roeder (1999): the pachytene (meiotic recombination) checkpoint that arrests zip1/dmc1-type mutants in meiotic prophase requires Swe1, which phosphorylates and inactivates Cdc28; swe1Δ lets such mutants sporulate, and Swe1 accumulates and is hyperphosphorylated in checkpoint-arrested cells. Reason: The annotation is correct but too general. The paper defines Swe1 as the downstream effector of the meiotic recombination (pachytene) checkpoint, which is exactly GO:0051598 (already on SWE1 via the 2026 IGI), and its mechanism, inhibiting Cdc28 to block the prophase-I to MI transition, is GO:0110031 (already on SWE1 via IBA). Either child term is more informative than 'regulation of meiotic nuclear division'. Proposed replacements: meiotic recombination checkpoint signaling negative regulation of G2/MI transition of meiotic cell cycle Supporting Evidence: PMID:10619027 In S. cerevisiae, this checkpoint requires Swe1, which phosphorylates and inactivates the cyclin-dependent kinase Cdc28. PMID:10619027 A swe1 deletion allows mutants that normally arrest in meiotic prophase to sporulate at wild-type levels, though sporulation is delayed.
GO:0044879 mitotic morphogenesis checkpoint signaling	IDA PMID:8930890 Cdc28 tyrosine phosphorylation and the morphogenesis checkpo...	ACCEPT	Summary: Sia et al. (1996) established that the morphogenesis checkpoint delay of nuclear division in cells that cannot make a bud requires SWE1, is exquisitely sensitive to SWE1 and MIH1 dosage, and acts through Cdc28 Tyr19 phosphorylation; budded cells do not depend on this pathway. Reason: Core function: Swe1 is the effector kinase of the morphogenesis checkpoint, the process this term names. The term definition (delay of mitotic onset in response to actin/septin/bud defects) matches the experiments precisely. Supporting Evidence: PMID:8930890 We show that the ability of this checkpoint to delay nuclear division requires the SWE1 gene, encoding a protein kinase that inhibits the master cell cycle regulatory kinase Cdc28. PMID:8930890 The timing of nuclear division in cells that cannot make a bud is exquisitely sensitive to the dosage of SWE1 and MIH1 genes, which control phosphorylation of Cdc28 at tyrosine 19. file:yeast/SWE1/SWE1-deep-research-falcon.md SWE1 is required for the normal delay in nuclear division in cells unable to form a bud, whereas budded cells are much less dependent on Cdc28 Tyr19 phosphorylation for ordinary cell-cycle timing.
GO:0044879 mitotic morphogenesis checkpoint signaling	IMP PMID:9744879 A morphogenesis checkpoint monitors the actin cytoskeleton i...	ACCEPT	Summary: McMillan et al. (1998) showed that actin-cytoskeleton mutants (myo2-66, tpm1Δ, sac6Δ, pfy1-111) and latrunculin-A treatment trigger a Swe1p-dependent delay of nuclear division mediated by Cdc28p tyrosine phosphorylation, that swe1Δ cells lose viability under transient actin disruption, and hence that the checkpoint monitors actin organisation. Reason: Core function; full text is cached and directly documents the swe1Δ phenotypes underlying the IMP. Supporting Evidence: PMID:9744879 Thus, myo2-66 and tpm1Δ mutants experienced a cell cycle delay resulting from Cdc28p tyrosine phosphorylation (reversible by Swe1p elimination or Mih1p overexpression). PMID:9744879 This block to nuclear division was Swe1p dependent because swe1Δ cells completed nuclear division by 2 h
GO:0051447 negative regulation of meiotic cell cycle	IEA GO_REF:0000117	ACCEPT	Summary: ARBA rule assigning negative regulation of the meiotic cell cycle. Consistent with Swe1's role as the Cdc28-inhibiting effector of the meiotic recombination checkpoint (PMID:10619027, PMID:41927924). Reason: An accurate, if general, parent of the experimentally and phylogenetically supported meiotic terms (GO:0110031, GO:0051598); electronic annotations at this level are acceptable. Supporting Evidence: PMID:10619027 In S. cerevisiae, this checkpoint requires Swe1, which phosphorylates and inactivates the cyclin-dependent kinase Cdc28.
GO:0051598 meiotic recombination checkpoint signaling	IGI PMID:41927924 Polo-like kinase Cdc5 orchestrates Cdk1 regulation via Swe1 ...	ACCEPT	Summary: González-Arranz et al. (2026) revisited the zip1Δ meiotic recombination checkpoint with full-text evidence: Swe1-dependent Cdc28-Tyr19 phosphorylation reinforces the prophase-I arrest, Swe1 is required for checkpoint maintenance rather than activation, and Cdc5 later drives Swe1 degradation (independently of CDK, unlike in mitosis) to permit prophase exit. The IGI partner is ZIP1. Reason: Swe1 does the work of this signalling process: it is the kinase that phosphorylates Cdc28 to enforce the checkpoint delay. Direct genetic evidence (zip1Δ swe1Δ) from a full-text paper, corroborating PMID:10619027. A genuine effector role, secondary to the mitotic morphogenesis checkpoint. Supporting Evidence: PMID:41927924 In addition, Mec1 and Mek1 activity reporters indicate that checkpoint signaling is initially triggered in zip1Δ swe1Δ, but it is prematurely downregulated, allowing faster and more efficient meiotic progression compared to zip1Δ. PMID:41927924 We show that Swe1 is required for checkpoint maintenance but not activation.
GO:0090154 positive regulation of sphingolipid biosynthetic process	IGI PMID:26634277 Regulation of Sphingolipid Biosynthesis by the Morphogenesis...	KEEP AS NON CORE	Summary: Chauhan et al. (2016) found that swe1Δ (and cdc28-Y19F) cells are hypersensitive to the SPT inhibitor myriocin because of reduced long-chain-base synthesis, that phytosphingosine or deletion of the SPT repressors ORM1/ORM2 rescues them, and that the effect is independent of the Ypk1 pathway; the authors propose that Swe1 derepresses SPT, presumably by phosphorylating Orm2. This row records the synergistic myriocin sensitivity of ypk1Δ swe1Δ and ypk2Δ swe1Δ double mutants (IGI partners YPK1 and YPK2). Reason: The genetic evidence that Swe1 positively influences sphingolipid synthesis is solid and the SGD curation faithfully records it, but the mechanism is unresolved: no direct Swe1 phosphorylation of Orm2 is shown ('presumably'), and the cdc28-Y19F phenocopy suggests the effect may run through Cdc28 inhibition rather than a separate Swe1 activity. Retained as a non-core annotation; the core function of Swe1 remains CDK inhibition. Supporting Evidence: PMID:26634277 Importantly, the double deletion mutants ypk1 swe1 and ypk2 swe1 were more sensitive to myriocin than the single deletion mutants, indicating synergistic effects
GO:0090154 positive regulation of sphingolipid biosynthetic process	IGI PMID:26634277 Regulation of Sphingolipid Biosynthesis by the Morphogenesis...	KEEP AS NON CORE	Summary: Chauhan et al. (2016) found that swe1Δ (and cdc28-Y19F) cells are hypersensitive to the SPT inhibitor myriocin because of reduced long-chain-base synthesis, that phytosphingosine or deletion of the SPT repressors ORM1/ORM2 rescues them, and that the effect is independent of the Ypk1 pathway; the authors propose that Swe1 derepresses SPT, presumably by phosphorylating Orm2. This row records that orm1Δ orm2Δ suppresses the myriocin sensitivity of swe1Δ (IGI partners ORM1 and ORM2). Reason: The genetic evidence that Swe1 positively influences sphingolipid synthesis is solid and the SGD curation faithfully records it, but the mechanism is unresolved: no direct Swe1 phosphorylation of Orm2 is shown ('presumably'), and the cdc28-Y19F phenocopy suggests the effect may run through Cdc28 inhibition rather than a separate Swe1 activity. Retained as a non-core annotation; the core function of Swe1 remains CDK inhibition. Supporting Evidence: PMID:26634277 additional deletion of the Orm proteins in the swe1 and cdc28Y19F mutant backgrounds restored growth in the presence of myriocin, linking Swe1 kinase function directly to the regulation of SPT activity.
GO:0090154 positive regulation of sphingolipid biosynthetic process	IGI PMID:26634277 Regulation of Sphingolipid Biosynthesis by the Morphogenesis...	KEEP AS NON CORE	Summary: Chauhan et al. (2016) found that swe1Δ (and cdc28-Y19F) cells are hypersensitive to the SPT inhibitor myriocin because of reduced long-chain-base synthesis, that phytosphingosine or deletion of the SPT repressors ORM1/ORM2 rescues them, and that the effect is independent of the Ypk1 pathway; the authors propose that Swe1 derepresses SPT, presumably by phosphorylating Orm2. This row records the interaction with the SPT regulatory subunit gene TSC3 (swe1Δ tsc3Δ double mutant). Reason: The genetic evidence that Swe1 positively influences sphingolipid synthesis is solid and the SGD curation faithfully records it, but the mechanism is unresolved: no direct Swe1 phosphorylation of Orm2 is shown ('presumably'), and the cdc28-Y19F phenocopy suggests the effect may run through Cdc28 inhibition rather than a separate Swe1 activity. Retained as a non-core annotation; the core function of Swe1 remains CDK inhibition. Supporting Evidence: PMID:26634277 Deletion of the Swe1 kinase renders mutant cells sensitive to serine palmitoyltransferase inhibition due to impaired sphingoid long-chain base synthesis.
GO:0090154 positive regulation of sphingolipid biosynthetic process	IMP PMID:26634277 Regulation of Sphingolipid Biosynthesis by the Morphogenesis...	KEEP AS NON CORE	Summary: Chauhan et al. (2016) found that swe1Δ (and cdc28-Y19F) cells are hypersensitive to the SPT inhibitor myriocin because of reduced long-chain-base synthesis, that phytosphingosine or deletion of the SPT repressors ORM1/ORM2 rescues them, and that the effect is independent of the Ypk1 pathway; the authors propose that Swe1 derepresses SPT, presumably by phosphorylating Orm2. Reason: The genetic evidence that Swe1 positively influences sphingolipid synthesis is solid and the SGD curation faithfully records it, but the mechanism is unresolved: no direct Swe1 phosphorylation of Orm2 is shown ('presumably'), and the cdc28-Y19F phenocopy suggests the effect may run through Cdc28 inhibition rather than a separate Swe1 activity. Retained as a non-core annotation; the core function of Swe1 remains CDK inhibition. Supporting Evidence: PMID:26634277 Deletion of the Swe1 kinase renders mutant cells sensitive to serine palmitoyltransferase inhibition due to impaired sphingoid long-chain base synthesis. PMID:26634277 Here we show that the Swe1 checkpoint kinase positively regulates SPT, presumably by phosphorylating Orm2, independently of Ypk1. PMID:26634277 Indeed, PHS supplementation rescued the swe1 and cdc28Y19F growth defect in the presence of myriocin, indicating that the levels of LCBs are growth-limiting in the mutant strains
GO:0106310 protein serine kinase activity	IEA GO_REF:0000116	MODIFY	Summary: Rhea-based mapping of the generic protein-serine phosphorylation reaction. GO:0106310's usage note restricts the term to kinases that specifically phosphorylate serine and directs dual-specificity enzymes to GO:0004674. Swe1 is a Wee1-family dual-specificity kinase whose physiological target residue is Cdc28 Tyr19. Reason: Swe1 is not serine-specific; its defining activity is tyrosine phosphorylation, with serine activity reported only in general terms (UniProt: 'Can act both on serines and on tyrosines'). Per the term's own usage note the appropriate Ser/Thr term is GO:0004674, mirroring the treatment of the same Rhea-derived row on human PKMYT1. Proposed replacements: protein serine/threonine kinase activity Supporting Evidence: PMID:8253069 Swe1 immunoprecipitates were capable of tyrosine phosphorylating and inactivating p34CDC28 complexed with Clb2, a G2-type cyclin, but not p34CDC28 complexed with Cln2, a G1-type cyclin, consistent with the inability of Swe1 overexpression to inhibit the G1/S transition.
GO:0110031 negative regulation of G2/MI transition of meiotic cell cycle	IBA GO_REF:0000033	ACCEPT	Summary: PAINT inference from the same node (PTN008315181) as the mitotic term, seeded by S. pombe wee1 and mik1, which restrain meiotic nuclear divisions via Cdc2 Tyr15 phosphorylation. In S. cerevisiae the equivalent role is documented: Swe1-dependent Cdc28-Tyr19 phosphorylation holds cells in meiotic prophase under the recombination checkpoint (PMID:10619027, PMID:41927924). Reason: Phylogenetic inference corroborated by experimental genetics in the target organism; a genuine meiotic effector role, secondary to the mitotic function. Graded as in the S. pombe wee1 review. Supporting Evidence: PMID:10619027 In S. cerevisiae, this checkpoint requires Swe1, which phosphorylates and inactivates the cyclin-dependent kinase Cdc28. PMID:41927924 We show that Swe1 is required for checkpoint maintenance but not activation.

Gene Description

Existing Annotations Review

Core Functions

Cdc28 (Cdk1) Tyr19-directed protein tyrosine kinase that inhibits mitotic Clb-Cdc28 complexes and delays the G2/M transition; the effector of the morphogenesis checkpoint that couples nuclear division to bud formation and actin/septin organisation.

Meiotic checkpoint effector: Swe1-mediated inhibitory Tyr19 phosphorylation of Cdc28 maintains the pachytene arrest imposed by the meiotic recombination checkpoint, blocking the prophase-I to meiosis-I transition until Cdc5-driven Swe1 degradation releases it.

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