FY is a nuclear WD-repeat protein of the conserved WDR33/Pfs2 family and a component of the Arabidopsis mRNA cleavage and polyadenylation specificity factor complex. It associates stably with CPSF100 and CPSF160 and supports essential RNA 3-prime end formation. Its C-terminal proline-rich motifs engage the RNA-binding regulator FCA, linking alternative RNA processing to repression of FLC and promotion of flowering. FY also interacts with SDG26, connecting RNA processing with chromatin regulation. Association with DDB1/CUL4-containing immunocomplexes has been detected, but an FY-specific ubiquitination substrate remains unresolved.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005515 protein binding | IPI PMID:17008405 Defective RNA processing enhances RNA silencing and influenc... | REMOVE | Summary: IPI with CPSF100 (ESP5) from affinity purification of tagged CPSF100. Reason: Uninformative 'protein binding'; removal does not dispute the interaction. The association reflects FY membership of the CPSF complex, which is captured by GO:0005847. Supporting Evidence: PMID:17008405 The analysis, done in duplicate for each sample, revealed numerous FLAG-CPSF100-specific peptides corresponding to ESP5/CPSF100, CPSF160, CPSF73, ESP4, and FY. |
| GO:0005515 protein binding | IPI PMID:18223036 Characterization of Arabidopsis and rice DWD proteins and th... | REMOVE | Summary: IPI with DDB1A from a screen of DWD-motif proteins as potential CUL4-DDB1 substrate receptors. Reason: The source supports FY-DDB1 association (DDB1a yeast two-hybrid and DDB1b coimmunoprecipitation). Remove only bare protein binding under policy, not the specific interaction. Supporting Evidence: PMID:18223036 DWD proteins PRL1 (At4g15900), TRIP-1 (At2g46280), and FY (At5g13480) were efficiently retrieved from the DDB1b immunocomplex together with CUL4 |
| GO:0005515 protein binding | IPI PMID:18223036 Characterization of Arabidopsis and rice DWD proteins and th... | REMOVE | Summary: IPI with DDB1B from the same DWD-protein screen. Reason: The source supports FY-DDB1 association (DDB1a yeast two-hybrid and DDB1b coimmunoprecipitation). Remove only bare protein binding under policy, not the specific interaction. Supporting Evidence: PMID:18223036 DWD proteins PRL1 (At4g15900), TRIP-1 (At2g46280), and FY (At5g13480) were efficiently retrieved from the DDB1b immunocomplex together with CUL4 |
| GO:0005515 protein binding | IPI PMID:18479511 Arabidopsis mRNA polyadenylation machinery: comprehensive an... | REMOVE | Summary: IPI with CPSF100 from the compilation of Arabidopsis polyadenylation factor interactions. Reason: Uninformative 'protein binding'; the CPSF100-FY association is captured by the CPSF complex cellular component annotation. Supporting Evidence: PMID:18479511 CPSF100 – FYCo-purification from nuclear extracts with tagged protein[31] |
| GO:0005515 protein binding | IPI PMID:19439664 Altered interactions within FY/AtCPSF complexes required for... | REMOVE | Summary: IPI with CPSF160 (co-purification with FY). Reason: Uninformative 'protein binding'; captured by GO:0005847 (CPSF complex membership). Supporting Evidence: PMID:19439664 AtCPSF100 and AtCPSF160, but not FCA, are stably associated with FY in vivo and form a range of different-sized complexes. |
| GO:0005515 protein binding | IPI PMID:19439664 Altered interactions within FY/AtCPSF complexes required for... | REMOVE | Summary: IPI with CPSF100 (co-purification with FY). Reason: Uninformative 'protein binding'; captured by GO:0005847 (CPSF complex membership). Supporting Evidence: PMID:19439664 AtCPSF100 and AtCPSF160, but not FCA, are stably associated with FY in vivo and form a range of different-sized complexes. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: Nuclear localization from UniProt subcellular location mapping. Reason: FY is a pre-mRNA 3'-end processing factor and is nuclear, colocalizing with FCA in nuclear condensates. Supporting Evidence: PMID:32541063 These include FCA, as well as the RRM-containing protein FPA (8, 17), FY (18, 19), and Cleavage/Polyadenylation Specificity Factor 160 (CPSF160), all of which have been shown to associate with FCA and colocalize with FCA in the nuclear condensates (9). |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: Nuclear localization predicted by AtSubP. Reason: Consistent with its role in nuclear pre-mRNA processing. Supporting Evidence: PMID:32541063 These include FCA, as well as the RRM-containing protein FPA (8, 17), FY (18, 19), and Cleavage/Polyadenylation Specificity Factor 160 (CPSF160), all of which have been shown to associate with FCA and colocalize with FCA in the nuclear condensates (9). |
| GO:0005847 mRNA cleavage and polyadenylation specificity factor complex | IBA GO_REF:0000033 | ACCEPT | Summary: CPSF complex membership propagated from Pfs2p/WDR33 orthologs; supported by FY co-purification with CPSF100/CPSF160. Reason: FY is the plant WDR33/Pfs2p ortholog and is stably associated with AtCPSF subunits in vivo. This is a core localization/complex membership. Supporting Evidence: PMID:19439664 AtCPSF100 and AtCPSF160, but not FCA, are stably associated with FY in vivo and form a range of different-sized complexes. PMID:12809608 FY belongs to a highly conserved group of eukaryotic proteins represented in Saccharomyces cerevisiae by the RNA 3' end-processing factor, Pfs2p. |
| GO:0009793 embryo development ending in seed dormancy | IMP PMID:16033802 An allelic series reveals essential roles for FY in plant de... | KEEP AS NON CORE | Summary: Null fy alleles are embryo lethal. Reason: Embryo lethality reflects the essential, general requirement for CPSF-mediated mRNA 3'-end formation rather than a specific role in embryogenesis. Supporting Evidence: PMID:16033802 Characterisation of an allelic series of fy mutations reveals that null alleles are embryo lethal. |
| GO:0009909 regulation of flower development | IMP PMID:1896021 A genetic and physiological analysis of late flowering mutan... | ACCEPT | Summary: fy mutants are late flowering and highly responsive to vernalization (autonomous pathway phenotype). Reason: Classical genetic evidence; FY promotes flowering by limiting FLC expression via the FCA-FY interaction. Supporting Evidence: PMID:1896021 For mutants at the loci fca, fve, fy and fpa, vernalization has a large effect both under LD and short day (SD) conditions PMID:12809608 The FCA/FY interaction is also required for the downregulation of the floral repressor FLC. |
| GO:0031124 mRNA 3'-end processing | IEA GO_REF:0000002 | ACCEPT | Summary: mRNA 3'-end processing inferred from WDR33/Pfs2 family signature. Reason: Core process for FY, consistent with its CPSF membership and experimental role in poly(A) site choice. Supporting Evidence: PMID:12809608 FY regulates RNA 3' end processing in Arabidopsis as evidenced through its role in FCA regulation. |
| GO:0080008 Cul4-RING E3 ubiquitin ligase complex | IPI PMID:18223036 Characterization of Arabidopsis and rice DWD proteins and th... | KEEP AS NON CORE | Summary: FY co-purifies with a DDB1b immunocomplex that also contains CUL4. Reason: Full PMID:18223036 Figure 4A explicitly identifies FY in DDB1b immunoprecipitates with CUL4. This supports a secondary complex association. Direct CUL4-bait coimmunoprecipitation and AKIN10 degradation experiments concern PRL1; they do not establish an FY-specific substrate or ubiquitin-ligase catalytic activity. Supporting Evidence: PMID:18223036 DWD proteins PRL1 (At4g15900), TRIP-1 (At2g46280), and FY (At5g13480) were efficiently retrieved from the DDB1b immunocomplex together with CUL4 |
| GO:0110104 mRNA alternative polyadenylation | IMP PMID:12809608 FY is an RNA 3' end-processing factor that interacts with FC... | NEW | Summary: NEW. FY (with FCA) is required for efficient selection of the promoter-proximal polyadenylation site in FCA pre-mRNA and proximal sites of COOLAIR. Reason: As a CPSF core subunit that is directly engaged by FCA, FY participates in the cleavage/polyadenylation step whose site choice is regulated. Supporting Evidence: PMID:12809608 FCA expression is autoregulated through the use of different polyadenylation sites within the FCA pre-mRNA, and the FCA/FY interaction is required for efficient selection of the promoter-proximal polyadenylation site. PMID:31043738 Similar to fca, fpa and fy mutants, polyadenylation of proximal sites in COOLAIR and UA proximal polyadenylation was defective in sof78 |
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Download this section (compressed HTML)Q: Does plant FY, like human WDR33, directly contact the poly(A) signal RNA, and does FCA binding to the FY C terminus alter this recognition at proximal sites?
Experiment: Cryo-EM or crosslinking mass spectrometry of Arabidopsis CPSF with and without the FCA WW domain bound to FY PPLPP motifs, combined with in vitro cleavage/polyadenylation assays on COOLAIR proximal and distal poly(A) sites.
Hypothesis: FCA binding remodels FY/CPSF to favour cleavage at proximal poly(A) sites.
Type: Structural biology / in vitro 3'-processing reconstitution
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