Pop2 (also called Sud1) is one of the two Cdc4/Fbw7-type F-box/WD40-repeat proteins of Schizosaccharomyces pombe, the other being its paralogue Pop1. It is a non-catalytic substrate-recognition subunit of the SCF (Skp1-Cul1-F-box) ubiquitin ligase: an N-terminal region (residues 1-241) mediates heterooligomerisation with Pop1 and homooligomerisation, a central F-box binds the Skp1 orthologue Psh1, and a C-terminal seven-bladed WD40 beta-propeller reads phosphodegrons on substrates. At endogenous levels Pop2 co-purifies with Pop1, the cullin Pcu1/Cul1, Psh1/Skp1 and the RING subunit Pip1/Rbx1 in a ~500 kDa SCF(Pop1-Pop2) complex, and also assembles a Pop1-independent SCF(Pop2) complex that carries ubiquitin ligase activity. Within the heteromer Pop2 is tethered largely through Pop1 and its own F-box is dispensable for Rum1 degradation, whereas the Pop1 F-box is essential. The defining substrates are the replication initiator Cdc18 (Cdc6) and the cyclin-dependent kinase inhibitor Rum1: Pop2 binds Cdc18 only after CDK phosphorylation at consensus sites, the purified Pop1-Pop2 complex binds CDK-phosphorylated Rum1 and polyubiquitylates it with E1, a Cdc34-class E2, ubiquitin and ATP, and cells lacking pop2 stabilise both proteins (Rum1 half-life rises from ~20 to >100 min). By eliminating Cdc18 after origin licensing and Rum1 at the G1/S boundary, Pop2 restricts DNA replication to once per cell cycle; pop2 deletion causes spontaneous re-replication, diploidization and polyploidy, a phenotype milder than that of pop1 deletion, and the two genes do not cross-complement. Pop2 and Pop1 are additionally required for SCF-dependent instability of the S-phase cyclin Cig2 during G2 and M phase. Pop2 lacks the nuclear localisation signal of Pop1 and is found in both the nucleus, where the complete SCF(Pop1-Pop2) complex and its known substrates reside, and the cytoplasm, where a Pop2-only SCF of unknown substrate specificity has been proposed.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005515 protein binding | IPI PMID:10209119 F-box/WD-repeat proteins pop1p and Sud1p/Pop2p form complexe... | MODIFY | Summary: Pop2 (Sud1) binds the replication initiator Cdc18, its defining substrate; in this paper Cdc18 binding to Pop2 was shown to depend on Pop1, and a Pop2-N-terminus/Pop1 fusion rescued the pop1 pop2 double mutant. Reason: Bare protein binding carries no functional information about Pop2; the informative molecular function behind this interaction is Pop2 acting as the F-box substrate receptor that links the Skp1(Psh1)-Cul1(Pcu1)-Rbx1(Pip1) core of SCF to its phosphorylated substrates, i.e. ubiquitin-like ligase-substrate adaptor activity (GO:1990756). Resolved rather than removed because the cited study is a focused characterisation of substrate (Cdc18) capture by the Pop1-Pop2 receptor, and it is the same paper PomBase uses for the IDA adaptor-activity annotation. The cached record is abstract-only, but the abstract itself states the Cdc18-Pop2 interaction and its Pop1 dependence, and phospho-Cdc18 binding by Sud1/Pop2 is independently established (PMID:9653157). Proposed replacements: ubiquitin-like ligase-substrate adaptor activity Supporting Evidence: PMID:10209119 binding of Cdc18p to Pop2p was dependent on Pop1p PMID:10209119 close physical proximity of two distinct F-box/WD-repeat proteins directs proteolysis mediated by the SCFPop ubiquitin ligase complex PMID:9653157 Sud1-Cdc18 binding requires prior phosphorylation of the Cdc18 polypeptide at CDK consensus sites |
| GO:0005515 protein binding | IPI PMID:10209119 F-box/WD-repeat proteins pop1p and Sud1p/Pop2p form complexe... | MODIFY | Summary: Pop2 heterooligomerises with its paralogue Pop1 through its N-terminal domain (residues 1-241); the heteromer is the functional substrate receptor, and a Pop2(1-241)-Pop1 fusion rescues the pop1 pop2 double deletion. Reason: Bare protein binding carries no functional information about Pop2; the informative molecular function behind this interaction is Pop2 acting as the F-box substrate receptor that links the Skp1(Psh1)-Cul1(Pcu1)-Rbx1(Pip1) core of SCF to its phosphorylated substrates, i.e. ubiquitin-like ligase-substrate adaptor activity (GO:1990756). The Pop1-Pop2 interaction is not an incidental contact: the two genes fail to cross-complement, Cdc18 binding to Pop2 requires Pop1, and physically juxtaposing the two N-termini is sufficient to restore proteolysis, so this interaction is the mechanism by which Pop2 is built into the SCF(Pop1-Pop2) substrate receptor. Resolved to the adaptor activity that the heteromer executes; complex membership itself is recorded under GO:0019005/GO:0043224. Proposed replacements: ubiquitin-like ligase-substrate adaptor activity Supporting Evidence: PMID:10209119 Pop1p and Pop2p formed heterooligomeric complexes when overexpressed PMID:10209119 The Pop1p-Pop2p interaction was mediated by the amino-terminal domain of Pop2p which, when fused to full-length Pop1p, rescued the phenotype of a Deltapop1Deltapop2 double mutant. PMID:10209119 the pop1 and pop2 genes fail to complement each other's deletion phenotypes, indicating that they perform non-redundant, but potentially interdependent, functions in proteolysis |
| GO:0005515 protein binding | IPI PMID:12167173 Combinatorial diversity of fission yeast SCF ubiquitin ligas... | MODIFY | Summary: Endogenous Pop2 co-immunoprecipitates with the cullin Pcu1/Cul1 in a ~500 kDa SCF(Pop1-Pop2) complex that also contains Psh1/Skp1 and Pip1/Rbx1 and polyubiquitylates phosphorylated Rum1 in vitro; Pop2 also binds the Pcu1-Psh1-Pip1 core in the absence of Pop1. Reason: Bare protein binding carries no functional information about Pop2; the informative molecular function behind this interaction is Pop2 acting as the F-box substrate receptor that links the Skp1(Psh1)-Cul1(Pcu1)-Rbx1(Pip1) core of SCF to its phosphorylated substrates, i.e. ubiquitin-like ligase-substrate adaptor activity (GO:1990756). Resolved rather than removed because the cited study is the biochemical reconstitution showing that the Pop2-containing cullin complex is an active ubiquitin ligase whose Rum1 activity is lost when Pip1 complexes are prepared from pop2-deleted cells, which is a direct demonstration of Pop2 bridging the SCF core and its substrate. Membership of the cullin complex itself is recorded under GO:0019005 (IPI with cul1) and GO:0043224. Proposed replacements: ubiquitin-like ligase-substrate adaptor activity Supporting Evidence: PMID:12167173 co-elution of Pip1p with Pop1p, Pop2p, Pcu1p, and Psh1p in a high molecular weight complex of approximately 500 kDa PMID:12167173 Rum1p ubiquitylation was not obtained with Pip1p complexes prepared from cell lysate of pop2 deletion strains, proving the F-box protein dependency of this reaction PMID:12167173 both F-box proteins, in the absence of their respective heterooligomerization partner, could individually bind to Pip1p in complexes that also contained Psh1p and Pcu1p |
| GO:0005515 protein binding | IPI PMID:12167173 Combinatorial diversity of fission yeast SCF ubiquitin ligas... | MODIFY | Summary: Pop1 and Pop2 interact through their N-terminal domains independently of both F-boxes (Pop2 residues 1-241 bind Pop1 residues 228-402), and immunopurified Pop1-Pop2 complexes specifically bind CDK-phosphorylated Rum1. Reason: Bare protein binding carries no functional information about Pop2; the informative molecular function behind this interaction is Pop2 acting as the F-box substrate receptor that links the Skp1(Psh1)-Cul1(Pcu1)-Rbx1(Pip1) core of SCF to its phosphorylated substrates, i.e. ubiquitin-like ligase-substrate adaptor activity (GO:1990756). The paper shows the heteromer, not either protein alone, binds phosphorylated Rum1 and that Pop2 is tethered to the SCF core largely through Pop1 (its own F-box being dispensable for Rum1 degradation), so the Pop1 interaction is the means by which Pop2 contributes to substrate recognition. Resolved to the adaptor activity; complex membership is recorded under GO:0019005/GO:0043224. Proposed replacements: ubiquitin-like ligase-substrate adaptor activity Supporting Evidence: PMID:12167173 the Pop1p-Pop2p interaction occurs independently of the F-boxes of both Pop1p and Pop2p PMID:12167173 Pop1p-Pop2p complexes specifically bound phosphorylated Rum1p PMID:12167173 Only the F-box of Pop1p is required for SCFPop1p-Pop2p function, while Pop2p seems to be attracted into the complex through binding to Pop1p PMID:12167173 Pop2p does not seem, to require its F-box to mediate Rum1p degradation in vivo |
| GO:0005515 protein binding | IPI PMID:12167173 Combinatorial diversity of fission yeast SCF ubiquitin ligas... | MODIFY | Summary: Endogenous Pop2 co-immunoprecipitates with Psh1/Skp1 as part of the five-subunit SCF(Pop1-Pop2) complex, and forms a Pop1-independent SCF(Pop2) complex with Psh1, Pcu1 and Pip1 that carries polyubiquitylation activity in vitro. Reason: Bare protein binding carries no functional information about Pop2; the informative molecular function behind this interaction is Pop2 acting as the F-box substrate receptor that links the Skp1(Psh1)-Cul1(Pcu1)-Rbx1(Pip1) core of SCF to its phosphorylated substrates, i.e. ubiquitin-like ligase-substrate adaptor activity (GO:1990756). The Skp1 contact is the canonical F-box/Skp1 attachment of an F-box adaptor; here it is demonstrated at endogenous expression levels within a complex whose ligase activity was reconstituted, and Pop2 retains Psh1 association even without Pop1. Resolved to the adaptor activity, as for the Skp1-Cdc4 row in the yeast CDC4 review; complex membership is recorded under GO:0019005/GO:0043224. Proposed replacements: ubiquitin-like ligase-substrate adaptor activity Supporting Evidence: PMID:12167173 Pip1p, Pop1p, and Pop2p antisera co-precipitated all five proteins from wild-type cell lysate PMID:12167173 both F-box proteins, in the absence of their respective heterooligomerization partner, could individually bind to Pip1p in complexes that also contained Psh1p and Pcu1p PMID:12167173 Pop1p and Pop2p each associate with polyubiquitylation activity even in the absence of their respective heterooligomerizing F-box proteins |
| GO:0005515 protein binding | IPI PMID:15147268 Molecular interactions of fission yeast Skp1 and its role in... | REMOVE | Summary: Skp1 interaction recorded in a systematic co-immunoprecipitation survey of twelve epitope-tagged fission-yeast F-box proteins against wild-type and temperature-sensitive Skp1. Reason: Survey-type record from a paper whose focus is Skp1 and whose cached entry is abstract-only; the Pop2-Skp1(Psh1) interaction is characterised biochemically in the focused SCF(Pop) papers (PMID:12167173, PMID:9990507) and its meaning, membership of the SCF ubiquitin ligase complex, is captured by the GO:0019005 and GO:0043224 annotations. Bare protein binding carries no functional information about Pop2, so the row is removed as uninformative; removal does not mean the reported interaction is false. Supporting Evidence: PMID:15147268 12 F-box proteins and Pcu1 were epitope-tagged, and co-immunoprecipitation performed PMID:15147268 It forms an adapter bridge between Cullin-1 and the substrate-determining component, the F-box protein |
| GO:0005515 protein binding | IPI PMID:17016471 Repression of ergosterol level during oxidative stress by fi... | REMOVE | Summary: Skp1 interaction recorded in the Pof14 paper, in which Pop2 serves as a reference F-box protein for Skp1 binding; the paper's subject is Pof14 and ergosterol repression, not Pop2. Reason: The cached full text of this paper does not mention Pop2 in the retained sections, and its biology (Pof14, Erg9, oxidative stress) is unrelated to Pop2 function; the Pop2-Skp1 contact it records is the generic F-box/Skp1 attachment already established in the focused SCF(Pop) papers and captured by the GO:0019005/GO:0043224 annotations. Bare protein binding carries no functional information about Pop2, so the row is removed as uninformative; the interaction itself is not disputed. Supporting Evidence: PMID:17016471 F-box proteins constitute a large family of proteins PMID:17016471 provide substrate specificity to the SCF (Skp1, Cullin, F-box protein) E3 ubiquitin ligases by interacting with the core component Skp1 through their F-box motif |
| GO:0005515 protein binding | IPI PMID:9653157 sud1(+) targets cyclin-dependent kinase-phosphorylated Cdc18... | MODIFY | Summary: Sud1/Pop2 binds Cdc18 in vivo, and binding requires prior CDK phosphorylation of Cdc18: the founding demonstration of phosphorylation-dependent substrate recognition by this F-box protein. Reason: Bare protein binding carries no functional information about Pop2; the informative molecular function behind this interaction is Pop2 acting as the F-box substrate receptor that links the Skp1(Psh1)-Cul1(Pcu1)-Rbx1(Pip1) core of SCF to its phosphorylated substrates, i.e. ubiquitin-like ligase-substrate adaptor activity (GO:1990756). This paper (full text cached) is the primary evidence that Pop2 is a phosphodegron-reading substrate receptor: Sud1 co-purifies with ubiquitinated proteins, binds Cdc18 only when Cdc18 is phosphorylated at CDK consensus sites, and cells lacking sud1 cannot degrade Cdc18 or Rum1. The interaction with Cdc18 is therefore substrate capture, the defining step of ubiquitin-like ligase-substrate adaptor activity, and is resolved to that term rather than removed. Proposed replacements: ubiquitin-like ligase-substrate adaptor activity Supporting Evidence: PMID:9653157 Sud1 itself is associated with the ubiquitin pathway in fission yeast and binds to Cdc18 in vivo PMID:9653157 Sud1-Cdc18 binding requires prior phosphorylation of the Cdc18 polypeptide at CDK consensus sites PMID:9653157 Sud1 interacts with ubiquitinated proteins in fission yeast and binds the Cdc18 polypeptide in a phosphorylation-dependent manner |
| GO:0005515 protein binding | IPI PMID:9990507 Two F-box/WD-repeat proteins Pop1 and Pop2 form hetero- and ... | REMOVE | Summary: Pop2 associates with cullin-1 (Pcu1), identified in this paper as the cullin scaffold of the fission-yeast SCF(Pop1/Pop2) ligase. Reason: The same paper and the same partner (cul1, PomBase:SPAC17G6.12) underlie the PomBase IPI annotation of Pop2 to the SCF ubiquitin ligase complex (GO:0019005), which is the informative content of this interaction; the protein-binding row duplicates it without adding function. Bare protein binding carries no functional information about Pop2, so the row is removed as uninformative; the cullin-1 association is not disputed and is retained through the complex annotation. Supporting Evidence: PMID:9990507 cullin-1 functions as a component of SCFPop1,2 |
| GO:0005515 protein binding | IPI PMID:9990507 Two F-box/WD-repeat proteins Pop1 and Pop2 form hetero- and ... | MODIFY | Summary: Pop2 forms heterodimers with Pop1 (and homodimers with itself) in vivo, generating three SCF species, SCF(Pop1/Pop1), SCF(Pop1/Pop2) and SCF(Pop2/Pop2), that together control Rum1 and Cdc18 levels. Reason: Bare protein binding carries no functional information about Pop2; the informative molecular function behind this interaction is Pop2 acting as the F-box substrate receptor that links the Skp1(Psh1)-Cul1(Pcu1)-Rbx1(Pip1) core of SCF to its phosphorylated substrates, i.e. ubiquitin-like ligase-substrate adaptor activity (GO:1990756). Kominami et al. cloned pop2 and showed that Pop2 shares with Pop1 the degradation of Rum1 and Cdc18 while being functionally non-interchangeable, and that the hetero- and homo-dimers are the substrate-receptor units of SCF. Resolved to the adaptor activity the dimer executes; cullin-complex membership from the same paper is recorded under GO:0019005. Cached record is abstract-only, but the abstract states the dimerisation and its functional consequence explicitly. Proposed replacements: ubiquitin-like ligase-substrate adaptor activity Supporting Evidence: PMID:9990507 Pop1 and Pop2 form hetero-as well as homo-dimers in the cell PMID:9990507 Pop2 plays a role which overlaps with Pop1 in the degradation of Rum1 and Cdc18 PMID:9990507 By forming three distinct complexes, SCFPop1/Pop1, SCFPop1/Pop2 and SCFPop2/Pop2, SCF has evolved a sophisticated mechanism to control the level of Rum1 and Cdc18 |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: Pop2 is nuclear (and also cytoplasmic): endogenously 13Myc-tagged Pop2 is detected in nuclei by immunofluorescence and in nuclear fractions biochemically, and all five SCF(Pop1-Pop2) subunits coexist in the nucleus where the substrates Cdc18 and Rum1 reside. Reason: The UniProt subcellular-location mapping rests on experimental localisation (PMID:12167173: GFP fusions, endogenous Myc-tagged immunofluorescence and nuclear/cytoplasmic fractionation). The nucleus is where the established function is executed (nuclear substrates Cdc18 and Rum1; nuclear SCF), so this is a core location. Supporting Evidence: PMID:12167173 Pop1p is predominantly localized to cell nuclei, whereas Pop2p is expressed in both the cytoplasm and the nucleus PMID:12167173 Pop1p was detected mostly in nuclear fractions, while Pop2p was apparent in both nuclear and cytoplasmic fractions PMID:12167173 all five SCFPop1p-Pop2p subunits appear to coexist in the nucleus, although all but Pop1p are also present in the cytoplasm |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: A substantial fraction of Pop2, unlike the exclusively nuclear Pop1, is cytoplasmic; a Pop1-independent SCF(Pop2) complex with in vitro ubiquitin ligase activity exists, but its cytoplasmic substrates are unknown. Reason: The localisation is experimentally solid (PMID:12167173: immunofluorescence of endogenous Pop2-13Myc and biochemical fractionation both show cytoplasmic Pop2, and Pop2 lacks the N-terminal NLS of Pop1), and it distinguishes Pop2 from the nuclear-restricted Pop1. It is accepted because the same study shows a Pop1-independent SCF(Pop2) complex with ubiquitin ligase activity, which is the basis of the second core function. Caveat: every characterised substrate (Cdc18, Rum1, Cig2) is nuclear, and the substrates of the cytoplasmic pool remain unidentified (see knowledge gap on the SCF(Pop2) core function). Supporting Evidence: PMID:12167173 Pop1p was detected mostly in nuclear fractions, while Pop2p was apparent in both nuclear and cytoplasmic fractions PMID:12167173 the cytoplasmic localization of Pop2p suggests an activity of SCFPop2p directed toward unknown cytoplasmic substrates PMID:12167173 Pop1p, but not Pop2p, has a functional NLS in its N-terminus file:SCHPO/pop2/pop2-deep-research-falcon.md Pop2 is detected in both the nucleus and cytoplasm, although its established Cdc18/Rum1 cell-cycle function is principally nuclear. |
| GO:0019005 SCF ubiquitin ligase complex | IPI PMID:9990507 Two F-box/WD-repeat proteins Pop1 and Pop2 form hetero- and ... | ACCEPT | Summary: Pop2 is an F-box subunit of the fission-yeast SCF ubiquitin ligase: it associates with cullin-1 (Pcu1), Skp1 (Psh1) and the RING subunit Pip1 in a ~500 kDa complex, in both Pop1-Pop2 heteromeric and Pop2-only assemblies. Reason: Core cellular component. Kominami et al. showed cullin-1 is the scaffold of SCF(Pop1,2), and Seibert et al. confirmed at endogenous expression levels that Pop2 antisera co-precipitate all five subunits (Pop1, Pop2, Pcu1, Psh1, Pip1) and that the complex is an active ubiquitin ligase toward phospho-Rum1. This is the complex in which the adaptor activity is exercised. Supporting Evidence: PMID:9990507 cullin-1 functions as a component of SCFPop1,2 PMID:9990507 By forming three distinct complexes, SCFPop1/Pop1, SCFPop1/Pop2 and SCFPop2/Pop2, SCF has evolved a sophisticated mechanism to control the level of Rum1 and Cdc18 PMID:12167173 Pip1p, Pop1p, and Pop2p antisera co-precipitated all five proteins from wild-type cell lysate PMID:12167173 co-elution of Pip1p with Pop1p, Pop2p, Pcu1p, and Psh1p in a high molecular weight complex of approximately 500 kDa |
| GO:0031146 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process | ISO GO_REF:0000024 | ACCEPT | Summary: Pop2 participates in SCF-dependent proteasomal degradation as the substrate receptor: Cdc18 is degraded by the ubiquitin-proteasome pathway in a sud1/pop2-dependent manner, SCF(Pop1-Pop2) polyubiquitylates phosphorylated Rum1 in vitro in a pop2-dependent reaction, and Rum1 half-life rises from ~20 to >100 min in pop2 mutants. Reason: Core biological process. Transferred from S. cerevisiae Cdc4 (SGD:S000001885), the founding F-box/WD40 substrate receptor, but fully corroborated in fission yeast by direct evidence: Cdc18 turnover is ubiquitin-proteasome dependent and requires sud1/pop2 (PMID:9653157), and in vitro Rum1 polyubiquitylation by immunopurified SCF(Pop1-Pop2) is lost in pop2-deleted lysates (PMID:12167173). Pop2 performs the substrate-recognition step, so the participation test is met. Propagation Review Root cause: NO FAILURE CORE Sources checked: SGD:S000001885 · CDC4 SUPPORTS TRANSFER Cdc4 is the archetypal SCF F-box/WD40 receptor for phospho-Sic1/Cdc6; Pop2 is its fission-yeast counterpart (identified by tblastn with Cdc4) acting on the analogous substrates Rum1 and Cdc18, with direct S. pombe biochemical support. Supporting Evidence: PMID:9653157 In this paper we verified that Cdc18 is degraded by the ubiquitin-proteasome pathway and have identified one of the cellular factors responsible for this process, which is encoded by the fission yeast sud1 + gene. PMID:12167173 A heterooligomeric SCFPop1p-Pop2p complex mediates polyubiquitylation of phosphorylated Rum1p PMID:12167173 Rum1p ubiquitylation was not obtained with Pip1p complexes prepared from cell lysate of pop2 deletion strains, proving the F-box protein dependency of this reaction PMID:12167173 Rum1p half-life was increased from ~20 minutes in wild-type to greater than 100 minutes in pop1 or pop2 mutants |
| GO:0043224 nuclear SCF ubiquitin ligase complex | ISO GO_REF:0000024 | ACCEPT | Summary: Pop2 is a subunit of the nuclear SCF(Pop1-Pop2) complex: all five subunits (Pop1, Pop2, Pcu1, Psh1, Pip1) coexist in the nucleus, where the substrates Cdc18 and Rum1 are located. Reason: Transferred from S. cerevisiae Cdc4, whose SCF is exclusively nuclear, and directly supported in fission yeast: Pop2 is nuclear (and cytoplasmic) by endogenous-tag immunofluorescence and fractionation, and the complete complex is present in the nuclear compartment (PMID:12167173). The nuclear SCF is the compartment in which the characterised Cdc18/Rum1 function is executed. Propagation Review Root cause: NO FAILURE CORE Sources checked: SGD:S000001885 · CDC4 SUPPORTS TRANSFER Cdc4 is an exclusively nuclear SCF F-box subunit; the transfer to Pop2 is corroborated by direct localisation of Pop2 and all SCF(Pop) subunits to the S. pombe nucleus. Supporting Evidence: PMID:12167173 all five SCFPop1p-Pop2p subunits appear to coexist in the nucleus, although all but Pop1p are also present in the cytoplasm PMID:12167173 Pop1p is predominantly localized to cell nuclei, whereas Pop2p is expressed in both the cytoplasm and the nucleus |
| GO:1903467 negative regulation of mitotic DNA replication initiation | IMP PMID:9653157 sud1(+) targets cyclin-dependent kinase-phosphorylated Cdc18... | ACCEPT | Summary: Sud1/Pop2 prevents re-initiation of DNA replication within a single cell cycle by capturing CDK-phosphorylated Cdc18 for ubiquitin-dependent degradation; sud1-deleted cells hyperaccumulate Cdc18 and Rum1 and undergo spontaneous re-replication and diploidization. Reason: Core biological process, and the participation test is met: Pop2 itself performs the phospho-Cdc18 recognition step that commits the licensing factor to destruction, rather than merely being required for the outcome. The paper (full text cached) shows the re-replication and diploidization phenotype of the sud1 deletion, that hyperaccumulated Rum1 contributes to but does not explain the Cdc18 proteolysis defect, and that Sud1 binds Cdc18 only after CDK phosphorylation. The term is specific and correctly signed (negative regulation of initiation). Supporting Evidence: PMID:9653157 is required to prevent spontaneous re-replication in fission yeast PMID:9653157 Cells lacking sud1(+) accumulate high levels of Cdc18 and the CDK inhibitor Rum1, because they cannot degrade these two key cell cycle regulators PMID:9653157 Through genetic analysis we demonstrated that sud1 + stops unwanted diploidization and ensures stable maintenance of normal chromosomal DNA content in fission yeast. PMID:9653157 hyperaccumulation of Rum1 contributes to re-replication in Deltasud1 cells, but is not the cause of the defect in Cdc18 proteolysis file:SCHPO/pop2/pop2-deep-research-falcon.md Pop2-dependent Cdc18 degradation therefore constitutes an anti-rereplication mechanism and explains much of the ploidy phenotype |
| GO:1990756 ubiquitin-like ligase-substrate adaptor activity | IDA PMID:10209119 F-box/WD-repeat proteins pop1p and Sud1p/Pop2p form complexe... | ACCEPT | Summary: Pop2 is an F-box/WD-repeat substrate adaptor of SCF: it binds the substrate Cdc18 (in a Pop1-dependent manner) and, together with Pop1, directs its proteolysis by the SCF(Pop) ubiquitin ligase. Reason: Core molecular function, correctly typed: Pop2 has no catalytic activity and works by bringing phosphorylated substrates (Cdc18, Rum1) into the Cul1-Rbx1 ligase. Wolf et al. show Cdc18 binding to Pop2 and rescue of the double mutant by a Pop2-N-terminus/Pop1 chimera; phosphorylation-dependent Cdc18 capture (PMID:9653157) and Pop2-dependent in vitro Rum1 polyubiquitylation (PMID:12167173) independently establish the same activity. Supporting Evidence: PMID:10209119 binding of Cdc18p to Pop2p was dependent on Pop1p PMID:10209119 close physical proximity of two distinct F-box/WD-repeat proteins directs proteolysis mediated by the SCFPop ubiquitin ligase complex PMID:9653157 Sud1-Cdc18 binding requires prior phosphorylation of the Cdc18 polypeptide at CDK consensus sites PMID:12167173 Rum1p ubiquitylation was not obtained with Pip1p complexes prepared from cell lysate of pop2 deletion strains, proving the F-box protein dependency of this reaction file:SCHPO/pop2/pop2-deep-research-falcon.md substrate-recruiting component of SCF ubiquitin ligases**, not an enzyme with an independently demonstrated catalytic reaction |
| GO:1990756 ubiquitin-like ligase-substrate adaptor activity | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA machine-learning rule assigning ubiquitin-like ligase-substrate adaptor activity, consistent with the F-box/WD40 architecture and with the experimental IDA/IPI annotations. Reason: The electronic inference lands on exactly the experimentally established molecular function (PomBase IDA from PMID:10209119; IPI from PMID:14970237), so it is accepted as a correct and correctly specific prediction. Supporting Evidence: PMID:10209119 binding of Cdc18p to Pop2p was dependent on Pop1p file:SCHPO/pop2/pop2-deep-research-falcon.md substrate-recruiting component of SCF ubiquitin ligases**, not an enzyme with an independently demonstrated catalytic reaction |
| GO:1990756 ubiquitin-like ligase-substrate adaptor activity | IPI PMID:14970237 Requirement of the SCFPop1/Pop2 Ubiquitin Ligase for Degrada... | ACCEPT | Summary: Pop2, together with Pop1, is required for SCF-dependent instability of the S-phase cyclin Cig2 during G2 and M; the cited interaction partner is Cig2, which binds Pop1 through a phosphorylation-dependent 93-residue region of its cyclin box. Reason: The adaptor-activity term is correct for Pop2 and this paper extends its substrate range to Cig2: both F-box proteins are stated to be responsible for Cig2 instability, and Cig2 turnover in G2/M is SCF-dependent. The cached record is abstract-only and the abstract reports Pop1 (not explicitly Pop2) binding Cig2 in vivo; the PomBase curator read the full text and made the IPI with Cig2 for Pop2, and given Pop2 acts within the SCF(Pop1-Pop2) heteromer I defer to the curator rather than second-guess from the abstract. Supporting Evidence: PMID:14970237 Two F-box/WD proteins Pop1 and Pop2, homologues of budding yeast Cdc4 and human Fbw7, are responsible for Cig2 instability PMID:14970237 Cig2 instability during G(2) and M phase is dependent upon the SCF complex PMID:14970237 Pop1 binds Cig2 in vivo |
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Download this section (compressed HTML)Q: Pop1 carries a PomBase IMP annotation to positive regulation of G1/S transition (GO:1900087) that Pop2 lacks, although Rum1 half-life increases more than five-fold in pop2 deletants (PMID:12167173); is the Pop2 omission a deliberate reflection of the milder pop2 phenotype, or a curation gap?
Q: Does Pop2 contact phospho-Cdc18/phospho-Rum1 directly through its WD40 propeller, or is the degron read by Pop1 with Pop2 serving to dimerise and stabilise the receptor? Pop2 alone does not bind Rum1 and Cdc18 binding to Pop2 requires Pop1, but a Pop2 WD40 point mutant has not been tested.
Q: Should the established substrates (Cdc18, Rum1, Cig2) be modelled as has_input on the Pop2 adaptor activity in a GO-CAM rather than as GO:0005515 rows, and should the SCF(Pop1-Pop2) heteromer be represented as a distinct complex from SCF(Pop2)?
Experiment: Compare ubiquitin-remnant (diGly) proteomes of wild-type, pop1-delta, pop2-delta and pop1-delta pop2-delta cells, and cytoplasmic versus nuclear fractions, to identify proteins whose ubiquitylation depends on Pop2 but not Pop1; validate candidates by cycloheximide chase and co-immunoprecipitation with Pop2-13Myc in a pop1-delta background.
Hypothesis: The Pop1-independent SCF(Pop2) complex ubiquitylates a distinct set of cytoplasmic substrates that account for the pop2-specific phenotypes not shared with pop1.
Type: comparative ubiquitinome in F-box deletion strains
Experiment: Introduce arginine-to-alanine substitutions at the conserved phosphate-binding positions of the Pop2 WD40 propeller (by analogy with Cdc4/Fbw7) at the endogenous locus, confirm Pop1 binding and SCF assembly are intact, and measure phospho-Rum1 and phospho-Cdc18 binding and in vitro polyubiquitylation by the mutant heteromer.
Hypothesis: Pop2's WD40 propeller directly reads the CDK phosphodegrons of Cdc18 and Rum1 within the Pop1-Pop2 heteromer.
Type: structure-guided separation-of-function mutagenesis
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