FLOWERING LOCUS K (FLK) is a K-homology-domain RNA-binding protein found in the nucleus and cytoplasm. It promotes floral transition by post-transcriptionally repressing FLOWERING LOCUS C (FLC): FLK recognizes an N6-methyladenosine site in the FLC transcript 3′ untranslated region and affects transcript stability and splicing. FLK also associates with PEP, HUA1 and HEN4 in regulation of AGAMOUS pre-mRNA processing and floral organ identity. Its RNA-processing functions therefore extend beyond FLC, and its FLC RNA recognition is distinct from the FCA-associated COOLAIR pathway.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003676 nucleic acid binding | IEA GO_REF:0000002 | MODIFY | Summary: FLK binds mRNA substrates through its KH-domain RNA-recognition machinery. Reason: The KH-domain prediction is broader than the demonstrated substrate class: FLK recognizes FLC mRNA and participates in AG pre-mRNA processing. Refine nucleic acid binding to the already-present mRNA-binding annotation. The separately proposed m6A reader activity describes modification recognition on an adaptor branch, not an is_a descendant of mRNA binding; neither specificity is inferred merely from KH-domain membership. Proposed replacements: mRNA binding Supporting Evidence: PMID:37050878 FLK as a novel mRNA m6A reader protein that directly binds the m6A site in the 3'-untranslated region of FLC transcripts |
| GO:0003723 RNA binding | IEA GO_REF:0000002 | MODIFY | Summary: FLK binds mRNA substrates through its KH-domain RNA-recognition machinery. Reason: FLC transcript recognition and AG pre-mRNA processing identify messenger RNA substrates, supporting the existing mRNA-binding term rather than unspecified RNA binding. Modification recognition is recorded separately as m6A reader activity because the live ontology places that term on the adaptor branch, not below RNA binding. Proposed replacements: mRNA binding Supporting Evidence: PMID:37050878 FLK as a novel mRNA m6A reader protein that directly binds the m6A site in the 3'-untranslated region of FLC transcripts |
| GO:0003729 mRNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: Conserved mRNA binding is directly corroborated on FLK. Reason: The PAINT inference is corroborated by direct recognition of FLC transcripts and by FLK participation in AG pre-mRNA processing. Retain the true substrate-class assertion. The separately proposed GO:1990247 captures m6A-modification recognition; it is not an is_a/part_of ancestor or descendant of mRNA binding in the inspected live ontology, so neither claim replaces the other. Target evidence reinforces the ancestral inference rather than challenging its node placement. Supporting Evidence: PMID:37050878 FLK as a novel mRNA m6A reader protein that directly binds the m6A site in the 3'-untranslated region of FLC transcripts |
| GO:0005515 protein binding | IPI PMID:22960247 The E3 ubiquitin ligase HOS1 regulates low ambient temperatu... | REMOVE | Summary: The physical interaction is retained as mechanistic evidence, but bare protein binding is uninformative. Reason: The cited study supports FLK association with HOS1 or the HUA1/HEN4 RNA-processing machinery. This does not by itself establish a different specific binding activity. Remove only the generic GO:0005515 assertion under the project policy, without denying the measured interaction. |
| GO:0005515 protein binding | IPI PMID:25658099 K-homology nuclear ribonucleoproteins regulate floral organ ... | REMOVE | Summary: The physical interaction is retained as mechanistic evidence, but bare protein binding is uninformative. Reason: The cited study supports FLK association with HOS1 or the HUA1/HEN4 RNA-processing machinery. This does not by itself establish a different specific binding activity. Remove only the generic GO:0005515 assertion under the project policy, without denying the measured interaction. |
| GO:0005515 protein binding | IPI PMID:25658099 K-homology nuclear ribonucleoproteins regulate floral organ ... | REMOVE | Summary: The physical interaction is retained as mechanistic evidence, but bare protein binding is uninformative. Reason: The cited study supports FLK association with HOS1 or the HUA1/HEN4 RNA-processing machinery. This does not by itself establish a different specific binding activity. Remove only the generic GO:0005515 assertion under the project policy, without denying the measured interaction. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: FLK has an experimentally observed nuclear pool. Reason: Functional GFP-FLK is enriched in nuclei in PMID:15310842. The nuclear annotation is retained independently of the separately observed cytoplasmic pool; this source supports the conserved and electronic rows as well as the experimental assertion. Supporting Evidence: PMID:15310842 The GFP-FLK fusion protein was enriched in the nucleus, although it was also found in the cytosol |
| GO:0005634 nucleus | IDA PMID:15310842 Regulation of flowering time in Arabidopsis by K homology do... | ACCEPT | Summary: FLK has an experimentally observed nuclear pool. Reason: Functional GFP-FLK is enriched in nuclei in PMID:15310842. The nuclear annotation is retained independently of the separately observed cytoplasmic pool; this source supports the conserved and electronic rows as well as the experimental assertion. Supporting Evidence: PMID:15310842 The GFP-FLK fusion protein was enriched in the nucleus, although it was also found in the cytosol |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: FLK has an experimentally observed nuclear pool. Reason: Functional GFP-FLK is enriched in nuclei in PMID:15310842. The nuclear annotation is retained independently of the separately observed cytoplasmic pool; this source supports the conserved and electronic rows as well as the experimental assertion. Supporting Evidence: PMID:15310842 The GFP-FLK fusion protein was enriched in the nucleus, although it was also found in the cytosol |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | ACCEPT | Summary: FLK also has an experimentally observed cytoplasmic pool. Reason: PMID:15310842 explicitly reports GFP-FLK in the cytosol as well as enriched in the nucleus. Retain the broad observed cytoplasmic location; nuclear mRNA regulation does not disprove this second pool or require a newly invented cytoplasmic mechanism. Supporting Evidence: PMID:15310842 The GFP-FLK fusion protein was enriched in the nucleus, although it was also found in the cytosol |
| GO:0005737 cytoplasm | IDA PMID:15310842 Regulation of flowering time in Arabidopsis by K homology do... | ACCEPT | Summary: FLK also has an experimentally observed cytoplasmic pool. Reason: PMID:15310842 explicitly reports GFP-FLK in the cytosol as well as enriched in the nucleus. Retain the broad observed cytoplasmic location; nuclear mRNA regulation does not disprove this second pool or require a newly invented cytoplasmic mechanism. Supporting Evidence: PMID:15310842 The GFP-FLK fusion protein was enriched in the nucleus, although it was also found in the cytosol |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: FLK also has an experimentally observed cytoplasmic pool. Reason: PMID:15310842 explicitly reports GFP-FLK in the cytosol as well as enriched in the nucleus. Retain the broad observed cytoplasmic location; nuclear mRNA regulation does not disprove this second pool or require a newly invented cytoplasmic mechanism. Supporting Evidence: PMID:15310842 The GFP-FLK fusion protein was enriched in the nucleus, although it was also found in the cytosol |
| GO:0005737 cytoplasm | ISM GO_REF:0000122 | ACCEPT | Summary: FLK also has an experimentally observed cytoplasmic pool. Reason: PMID:15310842 explicitly reports GFP-FLK in the cytosol as well as enriched in the nucleus. Retain the broad observed cytoplasmic location; nuclear mRNA regulation does not disprove this second pool or require a newly invented cytoplasmic mechanism. Supporting Evidence: PMID:15310842 The GFP-FLK fusion protein was enriched in the nucleus, although it was also found in the cytosol |
| GO:0006396 RNA processing | IBA GO_REF:0000033 | MODIFY | Summary: FLK participates in mRNA processing. Reason: The ancestral RNA-processing assertion is supported. Target experiments on AG pre-mRNA processing and FLC transcript splicing justify the narrower mRNA-processing term without inferring a catalytic RNA-splicing enzyme. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN008497035 SUPPORTS TRANSFER The ancestral RNA-processing assignment is true; direct target work identifies mRNA substrates and supports this refinement. Proposed replacements: mRNA processing Supporting Evidence: PMID:25658099 FLK and PEP also play an important role in the maintenance of the C-function during floral organ identity by post-transcriptionally regulating the MADS-box floral homeotic gene AGAMOUS (AG). |
| GO:0009911 positive regulation of flower development | IEA GO_REF:0000117 | ACCEPT | Summary: FLK promotes flowering and supports floral organ development through RNA regulation. Reason: The original floral-promotion claim is supported by delayed flowering of flk mutants and rescue/overexpression in PMID:15310842. Independent PMID:25658099 additionally establishes a role in AG pre-mRNA processing and floral organ identity, so a general flower-development term is informative across these related roles; it is not used as a synonym solely for FLC repression. Supporting Evidence: PMID:25658099 FLK and PEP also play an important role in the maintenance of the C-function during floral organ identity by post-transcriptionally regulating the MADS-box floral homeotic gene AGAMOUS (AG). |
| GO:0009911 positive regulation of flower development | IMP PMID:15310842 Regulation of flowering time in Arabidopsis by K homology do... | ACCEPT | Summary: FLK promotes flowering and supports floral organ development through RNA regulation. Reason: The original floral-promotion claim is supported by delayed flowering of flk mutants and rescue/overexpression in PMID:15310842. Independent PMID:25658099 additionally establishes a role in AG pre-mRNA processing and floral organ identity, so a general flower-development term is informative across these related roles; it is not used as a synonym solely for FLC repression. Supporting Evidence: PMID:25658099 FLK and PEP also play an important role in the maintenance of the C-function during floral organ identity by post-transcriptionally regulating the MADS-box floral homeotic gene AGAMOUS (AG). |
| GO:1990247 N6-methyladenosine-containing RNA reader activity | IDA PMID:37050878 FLK is an mRNA m(6)A reader that regulates floral transition... | NEW | Summary: FLK recognizes an m6A-modified site in FLC mRNA. Reason: The primary abstract explicitly reports direct recognition of the m6A site in the FLC 3′ untranslated region, loss of FLC binding in the vir-1 writer mutant, and failure of the reader-defective FLK construct to rescue late flowering. These target-specific observations support modification-reader activity, not just generic KH-domain RNA binding. Normal PMID refresh and publisher HTML/PDF attempts did not recover the full article, so no uninspected assay details, mutant residues or quantitative specificity are asserted. GO:1990247 is a live adaptor-activity term with no is_a/part_of ancestry relationship to the existing mRNA-binding term; this single proposal adds modification-recognition coverage without proposing a redundant binding ancestor. Supporting Evidence: PMID:37050878 FLK as a novel mRNA m6A reader protein that directly binds the m6A site in the 3'-untranslated region of FLC transcripts |
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