FKF1 (FLAVIN-BINDING, KELCH REPEAT, F-BOX 1; also ADAGIO 3/ADO3) is a blue-light photoreceptor that serves as the substrate-recognition F-box subunit of an SCF (SKP1-CUL1-F-box) E3 ubiquitin ligase in Arabidopsis. It combines an N-terminal LOV (PAS-type, flavin-binding) photosensory domain that covalently binds an FMN chromophore at Cys-91 in a blue-light-dependent, dark-reversible manner, a central F-box that recruits SKP1/ASK proteins into the SCF complex, and C-terminal Kelch repeats forming a beta-propeller that recognizes substrates. Blue light drives formation of an FKF1-GIGANTEA (GI) complex that targets the CYCLING DOF FACTOR (CDF1/CDF2/CDF3) transcriptional repressors for ubiquitin-dependent degradation, relieving repression of CONSTANS (CO) and FLOWERING LOCUS T (FT). FKF1 also binds and stabilizes CO protein in the long-day afternoon. Because FKF1 mRNA oscillates with a circadian rhythm and peaks in the late afternoon, the coincidence of its expression with daytime light in long days underlies day-length measurement and the promotion of photoperiodic flowering. FKF1 localizes to both the nucleus and the cytoplasm. Additional roles have been reported in negative regulation of cellulose biosynthesis and in blue-light chloroplast photorelocation.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005634 nucleus | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Nuclear localization assigned electronically from the UniProt subcellular location. FKF1 is documented in the nucleus by experimental work, so this location is correct, though it is a localization rather than a core molecular function. Reason: Correct subcellular location supported by UniProt and experimental detection of FKF1 in nuclear fractions, but localization is supporting context rather than a core function. Supporting Evidence: file:ARATH/FKF1/FKF1-notes.md UniProt: "SUBCELLULAR LOCATION: Nucleus. Cytoplasm." PMID:22628657 We found FKF1 in both cytosolic and nuclear fractions |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Cytoplasmic localization assigned electronically from the UniProt subcellular location. FKF1 is found in both nuclear and cytosolic fractions, so this is correct supporting context. Reason: Correct cytoplasmic location supported by UniProt and experimental fractionation; a localization, not a core function. Supporting Evidence: PMID:22628657 We found FKF1 in both cytosolic and nuclear fractions file:ARATH/FKF1/FKF1-notes.md UniProt: "SUBCELLULAR LOCATION: Nucleus. Cytoplasm." |
| GO:0006511 ubiquitin-dependent protein catabolic process | IEA GO_REF:0000117 | ACCEPT | Summary: FKF1 is the F-box substrate adaptor of an SCF E3 ubiquitin ligase that targets CDF transcriptional repressors for proteasomal degradation. This electronic annotation captures a genuinely core aspect of FKF1 function. Reason: FKF1 mediates blue-light-dependent ubiquitin-dependent degradation of CDF1 (and other CDFs), a central, experimentally established function. Supporting Evidence: PMID:16002617 FKF1 physically interacts with CDF1, and CDF1 protein is more stable in fkf1 mutants PMID:22628657 FKF1 simultaneously removes CYCLING DOF FACTOR 1 (CDF1), which represses CO and FLOWERING LOCUS T (FT) transcription file:ARATH/FKF1/FKF1-deep-research-falcon.md FKF1 binds CDF1 through its Kelch repeat domain and is implicated in CDF1 degradation, thereby relieving repression of CO and FT transcription. |
| GO:0007623 circadian rhythm | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: Circadian rhythm involvement assigned electronically; duplicates the experimental IDA annotation (PMID:17872410) and the IMP annotation (PMID:10847687). FKF1 mRNA oscillates and FKF1 modulates the clock. Reason: Correct and experimentally supported, but FKF1's circadian involvement is downstream of its photoreceptor/SCF-adaptor activities rather than a core molecular function; redundant with experimental annotations. Supporting Evidence: PMID:10847687 FKF1 mRNA levels oscillate with a circadian rhythm |
| GO:0009637 response to blue light | IEA GO_REF:0000117 | ACCEPT | Summary: Response to blue light assigned electronically; FKF1 is a bona fide blue-light photoreceptor (LOV/FMN at Cys-91) whose function and GI interaction are blue-light dependent. Duplicates the experimental IDA. Reason: FKF1 is a blue-light photoreceptor; blue-light response is a core, experimentally established part of its function. Supporting Evidence: PMID:17872410 FKF1 and GI proteins form a complex in a blue-light-dependent manner file:ARATH/FKF1/FKF1-notes.md FMN binds covalently to cysteine after exposure to blue light and is reversed in the dark |
| GO:0005515 protein binding | IPI PMID:14749489 Expression and interaction analysis of Arabidopsis Skp1-rela... | KEEP AS NON CORE | Summary: Generic protein-binding IPI from a Y2H screen showing FKF1 interacts with SKP1/ASK proteins (and SRK2G). This documents SCF assembly but the term itself is uninformative. Reason: Real interaction evidence (F-box binding SKP1/ASK to form SCF), but bare "protein binding" is not an informative molecular function and is not core per curation guidelines. Supporting Evidence: PMID:14749489 ASK1, ASK2, ASK11 and ASK12 interacted well with COI1, FKF1, UFO-like protein |
| GO:0005515 protein binding | IPI PMID:15310821 Identification of ASK and clock-associated proteins as molec... | KEEP AS NON CORE | Summary: Generic protein-binding IPI; in this LKP2 study FKF1 is shown to interact with family members and ASK/SKP1 proteins. Supports SCF/family interactions but is an uninformative term. Reason: Documents real interactions but "protein binding" is uninformative and not a core molecular function. Supporting Evidence: PMID:15310821 LKP2 interacted not only with itself but also with other members of the family, LKP1 and FKF1 |
| GO:0005515 protein binding | IPI PMID:16002617 FKF1 F-box protein mediates cyclic degradation of a represso... | KEEP AS NON CORE | Summary: Generic protein-binding IPI capturing the functionally central FKF1-CDF interactions (CDF1/CDF2/CDF3). Although the binding itself is core to FKF1 substrate recognition, the GO term "protein binding" is uninformative. Reason: Underlying CDF-binding is core to FKF1 substrate recognition, but the bare "protein binding" term does not convey this; the informative function is captured under core_functions (SCF substrate adaptor). Supporting Evidence: PMID:16002617 FKF1 physically interacts with CDF1 |
| GO:0005515 protein binding | IPI PMID:17704763 ZEITLUPE is a circadian photoreceptor stabilized by GIGANTEA... | KEEP AS NON CORE | Summary: Generic protein-binding IPI recording the FKF1-GIGANTEA (GI) interaction (WITH/FROM Q9SQI2). The FKF1-GI complex is functionally central, but the term is uninformative. Reason: FKF1-GI binding is biologically important but recorded with an uninformative term; the informative function is captured in core_functions. Supporting Evidence: PMID:17704763 the ZTL-GI interaction is strongly and specifically enhanced by blue light, through the amino-terminal flavin-binding LIGHT, OXYGEN OR VOLTAGE (LOV) domain |
| GO:0005515 protein binding | IPI PMID:17872410 FKF1 and GIGANTEA complex formation is required for day-leng... | KEEP AS NON CORE | Summary: Generic protein-binding IPI for FKF1 interactions (GI and SRK2G). The blue-light-dependent FKF1-GI complex is central, but the term is uninformative. Reason: Real, important interaction evidence recorded with an uninformative term; not core as stated. Supporting Evidence: PMID:17872410 FKF1 and GI proteins form a complex in a blue-light-dependent manner |
| GO:0005515 protein binding | IPI PMID:21798944 Evidence for network evolution in an Arabidopsis interactome... | KEEP AS NON CORE | Summary: Generic protein-binding IPI from a large-scale binary interactome map (WITH/FROM SKP1B and SRK2G). Background interaction evidence only. Reason: High-throughput interactome data; uninformative term, not a core function. Supporting Evidence: PMID:21798944 a proteome-wide binary protein-protein interaction map for the interactome network of the plant Arabidopsis thaliana |
| GO:0016567 protein ubiquitination | IEA GO_REF:0000041 | ACCEPT | Summary: Protein ubiquitination assigned electronically via UniPathway. As the F-box substrate adaptor of an SCF E3 ligase that ubiquitinates CDF repressors, FKF1 is genuinely involved in protein ubiquitination. Reason: FKF1 is the substrate-recognition subunit of an SCF E3 ubiquitin ligase that promotes ubiquitination/degradation of CDF transcription factors. Supporting Evidence: PMID:16002617 FKF1 controls daily CO expression in part by degrading CDF1, a repressor of CO transcription file:ARATH/FKF1/FKF1-notes.md PATHWAY: Protein modification; protein ubiquitination. |
| GO:0009902 chloroplast relocation | IMP PMID:36771626 FKF1 Interacts with CHUP1 and Regulates Chloroplast Movement... | KEEP AS NON CORE | Summary: Mutant/overexpression analysis shows FKF1 modulates blue-light chloroplast photorelocation (avoidance response) and interacts with CHUP1. A genuine but secondary, pleiotropic role distinct from FKF1's core flowering photoreceptor/SCF function. Reason: Experimentally supported (IMP) and biologically plausible for a blue-light receptor, but a peripheral function relative to FKF1's well-established core role; mechanism remains unresolved. Supporting Evidence: PMID:36771626 overexpression of FKF1 compromised the avoidance response, while the absence of FKF1 enhanced chloroplast movements under high light |
| GO:0005515 protein binding | IPI PMID:23166809 A comprehensive analysis of interaction and localization of ... | KEEP AS NON CORE | Summary: Generic protein-binding IPI from a comprehensive ASK x F-box interaction study (WITH/FROM ASK loci). Supports SCF assembly but is an uninformative term. Reason: Real SCF-assembly interaction evidence recorded with an uninformative term; not core as stated. Supporting Evidence: PMID:23166809 FBX proteins with a Kelch domain had high specificity to ASK13 |
| GO:2001007 negative regulation of cellulose biosynthetic process | IMP PMID:31221729 The Photoperiodic Flowering Time Regulator FKF1 Negatively R... | KEEP AS NON CORE | Summary: Genetic analysis (suppressor screen, T-DNA mutant, overexpression) shows FKF1 negatively regulates cellulose biosynthesis; fkf1 mutants have increased cellulose and CESA expression. A genuine but secondary, pleiotropic role. Reason: Experimentally supported (IMP) but peripheral to FKF1's core photoperiodic flowering / blue-light photoreceptor function. Supporting Evidence: PMID:31221729 The fkf1 mutants showed significant increases in cellulose content and CESA gene expression compared with that in wild-type Columbia-0 plants, suggesting a negative role of FKF1 in cellulose biosynthesis |
| GO:0005634 nucleus | ISM GO_REF:0000122 | KEEP AS NON CORE | Summary: Nuclear localization predicted by sequence-based subcellular prediction (AtSubP). Consistent with experimental detection of FKF1 in nuclear fractions; supporting context. Reason: Correct location (corroborated experimentally) but a prediction-based localization, not a core function. Supporting Evidence: PMID:22628657 We found FKF1 in both cytosolic and nuclear fractions |
| GO:0010468 regulation of gene expression | IMP PMID:22628657 FKF1 conveys timing information for CONSTANS stabilization i... | KEEP AS NON CORE | Summary: Mutant analysis shows FKF1 controls CO/FT expression by degrading CDF repressors and stabilizing CO. The acts_upstream_of_or_within qualifier correctly frames FKF1 as an indirect (post-translational) regulator of gene expression. Reason: Correct and well supported, but very general; FKF1's effect on gene expression is downstream of its core SCF-adaptor/photoreceptor activities. Supporting Evidence: PMID:22628657 FKF1 also controls FT transcription by stabilizing CO protein and simultaneously degrading FT repressors in the long-day afternoon |
| GO:0006355 regulation of DNA-templated transcription | IDA PMID:17872410 FKF1 and GIGANTEA complex formation is required for day-leng... | KEEP AS NON CORE | Summary: FKF1 regulates CO transcription via blue-light-dependent GI complex formation and CDF1 degradation, and associates with CO chromatin. FKF1 is not itself a transcription factor, so the acts_upstream_of_or_within qualifier is appropriate; the molecular event is ubiquitin-mediated proteolysis acting upstream of transcription. Reason: Defensible with the upstream qualifier and experimentally supported, but FKF1 does not directly regulate transcription; it acts indirectly via SCF degradation of CDF repressors, so this is not a core molecular function. Supporting Evidence: PMID:17872410 The timing of this interaction regulates the timing of daytime CO expression PMID:17872410 GI, FKF1, and CDF1 proteins associate with CO chromatin |
| GO:0007623 circadian rhythm | IDA PMID:17872410 FKF1 and GIGANTEA complex formation is required for day-leng... | KEEP AS NON CORE | Summary: FKF1 participates in circadian/diurnal regulation, with blue-light-timed GI complex formation conveying time-of-day information. Supported but downstream of FKF1's photoreceptor/SCF function. Reason: Experimentally supported but a process-level annotation that is not the core molecular function of FKF1. Supporting Evidence: PMID:17872410 FKF1 and GI proteins form a complex in a blue-light-dependent manner |
| GO:0009637 response to blue light | IDA PMID:17872410 FKF1 and GIGANTEA complex formation is required for day-leng... | ACCEPT | Summary: Direct assay support that FKF1 function (GI complex formation) is blue-light dependent, consistent with FKF1 being a blue-light photoreceptor via its LOV/FMN domain (Cys-91 mutagenesis abolishes the response). Reason: Core, directly demonstrated blue-light response of a blue-light photoreceptor. Supporting Evidence: PMID:17872410 FKF1 and GI proteins form a complex in a blue-light-dependent manner file:ARATH/FKF1/FKF1-deep-research-falcon.md FKF1 contains an N-terminal LOV domain that binds flavin chromophore (FMN) and undergoes blue-light-driven photochemistry that changes protein conformation and interaction capacity, enabling light-dependent signaling. |
| GO:0006511 ubiquitin-dependent protein catabolic process | TAS PMID:11019805 Protein degradation in signaling. | ACCEPT | Summary: Traceable author statement (review on protein degradation in plant signaling) supporting FKF1's role in ubiquitin/proteasome-mediated proteolysis. Consistent with the experimentally established SCF(FKF1) degradation of CDF repressors. Reason: Core function: FKF1 mediates ubiquitin-dependent protein catabolism as an SCF substrate adaptor; consistent with later experimental work. Supporting Evidence: PMID:16002617 CDF1 protein is more stable in fkf1 mutants |
| GO:0007623 circadian rhythm | IMP PMID:10847687 FKF1, a clock-controlled gene that regulates the transition ... | KEEP AS NON CORE | Summary: The original FKF1 cloning paper showed fkf1 deletion alters the waveform of clock-controlled gene expression and FKF1 mRNA oscillates, implicating FKF1 in clock modulation. Supported but process-level, not core MF. Reason: Experimentally supported circadian involvement, but downstream of FKF1's core photoreceptor/SCF-adaptor activities. Supporting Evidence: PMID:10847687 deletion of FKF1 alters the waveform of rhythmic expression of two clock-controlled genes, implicating FKF1 in modulating the Arabidopsis circadian clock |
| GO:0009911 positive regulation of flower development | IMP PMID:10847687 FKF1, a clock-controlled gene that regulates the transition ... | ACCEPT | Summary: The fkf1 mutant is late-flowering, establishing FKF1 as a positive regulator of the floral transition. This is the central physiological role of FKF1 in photoperiodic flowering. Reason: Core biological process: FKF1 promotes photoperiodic flowering; loss of FKF1 causes late flowering. Supporting Evidence: PMID:10847687 FKF1, a clock-controlled gene that regulates the transition to flowering in Arabidopsis file:ARATH/FKF1/FKF1-notes.md DISRUPTION PHENOTYPE: Late flowering. |
| GO:0009881 photoreceptor activity | IDA PMID:17872410 FKF1 and GIGANTEA complex formation is required for day-leng... | NEW | Summary: FKF1 is a blue-light photoreceptor whose LOV domain covalently binds an FMN chromophore at Cys-91; light-dependent photochemistry gates the FKF1-GI interaction, with Cys-91 mutagenesis abolishing FMN binding and the response. This molecular function is captured by the UniProt Photoreceptor protein keyword and DR (GO:0009881) but is absent from the curated GOA annotations. Reason: Core blue-light photoreceptor activity is well established experimentally and present in UniProt (keyword/DR) but missing from the GOA molecular function annotations; proposed as a new annotation. Supporting Evidence: PMID:17872410 FKF1 and GI proteins form a complex in a blue-light-dependent manner file:ARATH/FKF1/FKF1-notes.md FMN binds covalently to cysteine after exposure to blue light and is reversed in the dark file:ARATH/FKF1/FKF1-deep-research-falcon.md FKF1 contains an N-terminal LOV domain that binds flavin chromophore (FMN) and undergoes blue-light-driven photochemistry that changes protein conformation and interaction capacity, enabling light-dependent signaling. |
| GO:0019005 SCF ubiquitin ligase complex | IPI PMID:14749489 Expression and interaction analysis of Arabidopsis Skp1-rela... | NEW | Summary: As an F-box protein that binds SKP1/ASK proteins, FKF1 is a component of an SCF (SKP1-CUL1-F-box) E3 ubiquitin ligase. This cellular component is present in UniProt DR (GO:0019005, IBA:GO_Central) but absent from the curated GOA annotations. Reason: FKF1 assembles into an SCF complex via its F-box and SKP1/ASK binding; this component term is supported by interaction data and UniProt DR but missing from GOA. Supporting Evidence: PMID:14749489 ASK1, ASK2, ASK11 and ASK12 interacted well with COI1, FKF1, UFO-like protein file:ARATH/FKF1/FKF1-notes.md of an SCF (SKP1-CUL1-F-box) E3 ubiquitin ligase file:ARATH/FKF1/FKF1-deep-research-falcon.md FKF1 contains an F-box that interacts with ASK proteins and TAP-MS recovered ASK1, ASK2, and CUL1 with FKF1, strongly indicating FKF1 forms an SCF^FKF1 complex in vivo. |
| GO:1990756 ubiquitin-like ligase-substrate adaptor activity | IPI PMID:16002617 FKF1 F-box protein mediates cyclic degradation of a represso... | NEW | Summary: As the F-box/Kelch substrate-recognition subunit of SCF-FKF1, FKF1 provides ubiquitin-ligase substrate-adaptor activity, recruiting CDF1/CDF2/CDF3 substrates to the SCF core for blue-light- and GIGANTEA-dependent ubiquitination. Proposed by the reviewer; the catalytic ligase activity itself resides in the RBX1/cullin core, so this adaptor term (not GO:0061630) is the correct molecular function for the F-box subunit. Absent from the curated GOA annotations. Reason: FKF1 bridges substrates (CDF1/2/3) to the SCF ligase via its Kelch-repeat beta-propeller and binds SKP1/ASK via its F-box; this substrate-adaptor molecular function is experimentally supported (FKF1-CDF1 interaction and CDF1 stabilization in fkf1 mutants) but is not in GOA. Supporting Evidence: PMID:16002617 FKF1 physically interacts with CDF1, and CDF1 protein is more stable in fkf1 mutants |
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Download this section (compressed HTML)Q: What is the precise biochemical mechanism by which FKF1 stabilizes CONSTANS protein, and is it separable from its SCF-mediated degradation of CDF repressors?
Suggested experts: Plant photoperiodism researchers, Ubiquitin-proteasome biochemists
Q: Are the secondary roles of FKF1 in cellulose biosynthesis and chloroplast photorelocation mediated by SCF-dependent degradation of specific substrates (e.g. CHUP1), or by non-degradative mechanisms?
Suggested experts: Cell wall biologists, Chloroplast movement researchers
Experiment: Test whether CHUP1 is ubiquitinated and degraded in an FKF1/SCF-dependent, blue-light-dependent manner using in vivo ubiquitination assays, cell-free degradation assays with proteasome inhibitors, and F-box-mutant FKF1 (defective in ASK/SKP1 binding) to determine whether SCF complex formation is required for the effect on CHUP1 abundance.
Hypothesis: FKF1 regulates chloroplast photorelocation by promoting ubiquitin-dependent degradation of CHUP1 via its SCF activity.
Experiment: Use separation-of-function FKF1 alleles (e.g. F-box mutants vs LOV/CO-binding mutants) in cdf and CO backgrounds to dissect the relative contribution of each mechanism to FT transcription, combining time-course ChIP, protein stability assays, and flowering-time phenotyping under controlled photoperiods.
Hypothesis: The balance between FKF1-mediated CDF degradation and FKF1-mediated CO stabilization quantitatively determines FT induction across day lengths.
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