CDF1

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0000122 negative regulation of transcription by RNA polymerase II	IEA GO_REF:0000108	ACCEPT	Summary: Inferred from the curated DNA-binding transcription repressor activity (GO:0001227) of CDF1. CDF1 represses CO and FT transcription. Reason: Logically sound inference that matches the experimentally established repressor function of CDF1 on CO and FT promoters. Supporting Evidence: PMID:16002617 Thus, FKF1 controls daily CO expression in part by degrading CDF1, a repressor of CO transcription. PMID:28752516 This TPL interaction confers a repressive function on CDF1, as mutations of the N-terminal TPL binding domain largely impair the ability of CDF1 protein to repress its targets.
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA PMID:22628657 FKF1 conveys timing information for CONSTANS stabilization i...	ACCEPT	Summary: Song et al. used ChIP to show HA-CDF1 enrichment on specific FT promoter regions in the morning. Together with the CO promoter binding in Imaizumi et al. 2005 and the Dof-domain/DNA crystal structure, this supports sequence-specific binding of cis-regulatory regions of target genes. Reason: Direct promoter association with defined FT promoter amplicons; CDF1 is a sequence-specific Dof factor. Core function. Supporting Evidence: PMID:22628657 indicating that CDF1 binds to the FT promoter regions in the morning. PMID:40263610 Here we present the crystal structure of the Dof domain of CYCLING DOF FACTOR 1 (CDF1), a well-characterized Dof protein acting as a transcriptional repressor by binding to the CONSTANS promoter to regulate photoperiodic flowering, in complex with DNA containing two cis elements.
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific	IDA PMID:28752516 CYCLING DOF FACTOR 1 represses transcription through the TOP...	ACCEPT	Summary: Goralogia et al. show that CDF1 is a transcriptional repressor of CO and FT whose activity depends on TPL recruitment through its N-terminal domain. Reason: Direct experimental support for CDF1 being a DNA-binding transcriptional repressor; core molecular function. Supporting Evidence: PMID:28752516 This TPL interaction confers a repressive function on CDF1, as mutations of the N-terminal TPL binding domain largely impair the ability of CDF1 protein to repress its targets.
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific	IMP PMID:28752516 CYCLING DOF FACTOR 1 represses transcription through the TOP...	ACCEPT	Summary: Mutation of the TPL-interaction motif impairs CDF1 repression of its targets, supporting the repressor activity by mutant analysis. Reason: Mutational analysis supports the repressor activity; core molecular function. Supporting Evidence: PMID:28752516 This TPL interaction confers a repressive function on CDF1, as mutations of the N-terminal TPL binding domain largely impair the ability of CDF1 protein to repress its targets.
GO:0003677 DNA binding	IBA GO_REF:0000033	MODIFY	Summary: PAINT IBA for DNA binding in the CDF clade of the Dof family; CDF1 itself is among the experimental sources. Reason: Correct but over-general; CDF1 binds specific Dof cis-elements in the CO and FT promoters, so RNA polymerase II cis-regulatory region sequence-specific DNA binding is the informative term. The self-reference in WITH/FROM reflects experimental grounding on CDF1 itself. Proposed replacements: RNA polymerase II cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:16002617 CDF1 and CO are expressed in the same tissues, and CDF1 binds to the CO promoter.
GO:0003677 DNA binding	IDA PMID:16002617 FKF1 F-box protein mediates cyclic degradation of a represso...	MODIFY	Summary: Imaizumi et al. 2005 show that CDF1 binds the CO promoter. Reason: Direct binding to CO promoter DNA; the generic term should be refined to sequence-specific cis-regulatory region binding (GO:0000978). Proposed replacements: RNA polymerase II cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:16002617 CDF1 and CO are expressed in the same tissues, and CDF1 binds to the CO promoter.
GO:0003677 DNA binding	IEA GO_REF:0000002	MODIFY	Summary: InterPro Dof zinc finger (IPR003851) to DNA binding mapping. Reason: The Dof domain is a sequence-specific DNA-binding zinc finger; CDF1 binding to Dof cis-elements in target promoters is experimentally established, so the specific child term is preferred. Proposed replacements: RNA polymerase II cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:40263610 Here we present the crystal structure of the Dof domain of CYCLING DOF FACTOR 1 (CDF1), a well-characterized Dof protein acting as a transcriptional repressor by binding to the CONSTANS promoter to regulate photoperiodic flowering, in complex with DNA containing two cis elements.
GO:0003700 DNA-binding transcription factor activity	IBA GO_REF:0000033	MODIFY	Summary: PAINT IBA for DNA-binding transcription factor activity in the CDF clade; CDF1 is the experimental seed. Reason: Correct but over-general; CDF1 is a bona fide Dof transcription factor that represses CO and FT, so the repressor-specific child GO:0001227 is the informative term. Proposed replacements: DNA-binding transcription repressor activity, RNA polymerase II-specific Supporting Evidence: PMID:16002617 Thus, FKF1 controls daily CO expression in part by degrading CDF1, a repressor of CO transcription.
GO:0003700 DNA-binding transcription factor activity	IDA PMID:22628657 FKF1 conveys timing information for CONSTANS stabilization i...	MODIFY	Summary: Song et al. 2012 show CDF1 associates with the FT promoter and represses FT independently of CO. Reason: CDF1 binds the FT promoter and represses FT transcription; the repressor child term GO:0001227 is the informative replacement for the generic parent. Proposed replacements: DNA-binding transcription repressor activity, RNA polymerase II-specific Supporting Evidence: PMID:22628657 indicating that CDF1 binds to the FT promoter regions in the morning. PMID:22628657 These results indicate that CDF1 protein represses FT transcription independently of CO transcription.
GO:0003700 DNA-binding transcription factor activity	IEA GO_REF:0000002	MODIFY	Summary: InterPro Dof family (IPR045174) mapping to DNA-binding transcription factor activity. Reason: Correct family-level inference, but experimental data establish CDF1 as a repressor, so the repressor child term is preferred. Proposed replacements: DNA-binding transcription repressor activity, RNA polymerase II-specific Supporting Evidence: PMID:12475498 Dof proteins are members of a major family of plant transcription factors. The proteins have similar DNA-binding properties because of the highly conserved DNA-binding domain.
GO:0003700 DNA-binding transcription factor activity	ISS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a...	MODIFY	Summary: Genome-wide survey of Arabidopsis transcription factors classifying Dof proteins (including CDF1) as transcription factors. Reason: Correct, consistent with experimental evidence (the source is a family survey rather than a CDF1-specific study); CDF1-specific data establish repressor activity, so the repressor child term is preferred. Proposed replacements: DNA-binding transcription repressor activity, RNA polymerase II-specific Supporting Evidence: PMID:16002617 Thus, FKF1 controls daily CO expression in part by degrading CDF1, a repressor of CO transcription.
GO:0003700 DNA-binding transcription factor activity	ISS PMID:12475498 The Dof family of plant transcription factors.	MODIFY	Summary: Review of the Dof family of plant transcription factors; CDF1 is a Dof family member with the conserved DNA-binding domain. Reason: Correct family-level transfer; direct CDF1 data establish repressor activity, so the repressor child term is preferred. Proposed replacements: DNA-binding transcription repressor activity, RNA polymerase II-specific Supporting Evidence: PMID:12475498 Dof proteins are members of a major family of plant transcription factors. The proteins have similar DNA-binding properties because of the highly conserved DNA-binding domain.
GO:0005515 protein binding	IPI PMID:16002617 FKF1 F-box protein mediates cyclic degradation of a represso...	MODIFY	Summary: CDF1 interacts with FKF1 (At1g68050), the F-box substrate adaptor of an SCF E3 ligase, and is degraded in an FKF1-dependent manner. Reason: Generic protein binding is uninformative. CDF1 is the substrate of the SCF(FKF1) ubiquitin ligase; binding to the E3 is better captured as ubiquitin protein ligase binding. Proposed replacements: ubiquitin protein ligase binding Supporting Evidence: PMID:16002617 FKF1 physically interacts with CDF1, and CDF1 protein is more stable in fkf1 mutants.
GO:0005515 protein binding	IPI PMID:16002617 FKF1 F-box protein mediates cyclic degradation of a represso...	MODIFY	Summary: CDF1 interacts with LKP2 (At2g18915), an FKF1/ZTL-family F-box protein, in the same study. Reason: LKP2 is an F-box ubiquitin ligase substrate adaptor paralog of FKF1; ubiquitin protein ligase binding is more informative than protein binding. Proposed replacements: ubiquitin protein ligase binding Supporting Evidence: PMID:16002617 FKF1 physically interacts with CDF1, and CDF1 protein is more stable in fkf1 mutants.
GO:0005515 protein binding	IPI PMID:16002617 FKF1 F-box protein mediates cyclic degradation of a represso...	MODIFY	Summary: CDF1 interacts with LKP2 (UniProtKB:Q8W420), an FKF1/ZTL-family F-box protein. Reason: Same interaction as the At2g18915 row; ubiquitin protein ligase binding is more informative. Proposed replacements: ubiquitin protein ligase binding Supporting Evidence: PMID:16002617 FKF1 physically interacts with CDF1, and CDF1 protein is more stable in fkf1 mutants.
GO:0005515 protein binding	IPI PMID:16002617 FKF1 F-box protein mediates cyclic degradation of a represso...	MODIFY	Summary: CDF1 interacts with FKF1 (UniProtKB:Q9C9W9); CDF1 is more stable in fkf1 mutants. Reason: CDF1 is the substrate of SCF(FKF1); ubiquitin protein ligase binding is more informative than protein binding. Proposed replacements: ubiquitin protein ligase binding Supporting Evidence: PMID:16002617 FKF1 physically interacts with CDF1, and CDF1 protein is more stable in fkf1 mutants.
GO:0005515 protein binding	IPI PMID:17872410 FKF1 and GIGANTEA complex formation is required for day-leng...	REMOVE	Summary: GI interacts with CDF1 and controls its stability as part of the FKF1-GI complex on the CO promoter. Reason: Removal concerns only the uninformative protein binding term, not the validity of the interaction, which is real and functionally important (GI is required for FKF1-mediated CDF1 turnover). GI is neither a ligase nor a transcription coregulator, so no more informative binding term applies; the GI-CDF1 relationship is captured in the module and core-function narrative. Supporting Evidence: PMID:17872410 FKF1 function is dependent on GI, which interacts with a CO repressor, CYCLING DOF FACTOR 1 (CDF1), and controls CDF1 stability.
GO:0005515 protein binding	IPI PMID:28752516 CYCLING DOF FACTOR 1 represses transcription through the TOP...	MODIFY	Summary: CDF1 binds the TOPLESS (TPL, At1g15750) co-repressor through a conserved N-terminal non-EAR motif, and this interaction is needed for full repression. Reason: TPL is a transcription co-repressor; transcription corepressor binding captures the mechanism of CDF1 repression. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:28752516 Here we demonstrate that Arabidopsis CDF proteins contain non-EAR motif-like conserved domains required for interaction with the TOPLESS (TPL) co-repressor protein. PMID:28752516 CDF1 bound to TPL in BiFC in epidermal cells of Nicotiana benthamiana, but the inclusion of these mutations in the CDF1 N-terminus abolished the interaction with TPL PMID:28752516 This TPL interaction confers a repressive function on CDF1, as mutations of the N-terminal TPL binding domain largely impair the ability of CDF1 protein to repress its targets.
GO:0005634 nucleus	IDA PMID:16002617 FKF1 F-box protein mediates cyclic degradation of a represso...	ACCEPT	Summary: Imaizumi et al. 2005 localized CDF1 in the nucleus (full text not cached; consistent with all other evidence). Reason: Nuclear localization of a DNA-binding repressor; consistent with CDF1-GFP and BiFC data in later studies. Supporting Evidence: PMID:28752516 We confirmed that both CDF1-ΔN and CDF1-mut proteins were localized to the nucleus, similar to non-mutated CDF1
GO:0005634 nucleus	IEA GO_REF:0000044	ACCEPT	Summary: UniProt subcellular location mapping (nucleus). Reason: Consistent with experimental data. Supporting Evidence: PMID:28752516 We confirmed that both CDF1-ΔN and CDF1-mut proteins were localized to the nucleus, similar to non-mutated CDF1
GO:0005634 nucleus	IPI PMID:28752516 CYCLING DOF FACTOR 1 represses transcription through the TOP...	ACCEPT	Summary: BiFC with TPL and CDF1-GFP localization show nuclear CDF1. Reason: Direct localization evidence. Supporting Evidence: PMID:28752516 We confirmed that both CDF1-ΔN and CDF1-mut proteins were localized to the nucleus, similar to non-mutated CDF1
GO:0005634 nucleus	ISM GO_REF:0000122	ACCEPT	Summary: AtSubP sequence-based prediction of nuclear localization. Reason: Consistent with experimental localization. Supporting Evidence: PMID:28752516 We confirmed that both CDF1-ΔN and CDF1-mut proteins were localized to the nucleus, similar to non-mutated CDF1
GO:0006355 regulation of DNA-templated transcription	IEA GO_REF:0000002	ACCEPT	Summary: InterPro-based mapping to regulation of DNA-templated transcription. Reason: Correct but general; the more specific negative regulation of transcription by RNA polymerase II is supported. Supporting Evidence: PMID:16002617 Thus, FKF1 controls daily CO expression in part by degrading CDF1, a repressor of CO transcription.
GO:0006355 regulation of DNA-templated transcription	TAS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a...	ACCEPT	Summary: Traceable author statement from a genome-wide transcription factor survey. Reason: Correct but general (same decision as the IEA row for this term); the experimental negative-regulation annotations are more specific.
GO:0009658 chloroplast organization	IMP PMID:22383539 Plastids are major regulators of light signaling in Arabidop...	KEEP AS NON CORE	Summary: Ruckle et al. 2012 screened T-DNA alleles of light- and plastid-regulated genes for enhanced deetiolation (end) phenotypes, i.e. accelerated chloroplast biogenesis/greening during deetiolation. The PMC full text (now cached) lists CDF1 among the END genes. Reason: Verified in the full text: a cdf1 T-DNA allele gives an enhanced deetiolation phenotype, supporting acts_upstream_of_or_within chloroplast organization. This is an indirect, light-signalling-related phenotype and not part of CDF1's core role as a photoperiodic repressor of CO and FT. Supporting Evidence: PMID:22383539 Three of these END genes encode transcription factors: SMZ , CDF1 , and RAP2.6 . PMID:22383539 We found that a high proportion of these mutant alleles induce chloroplast biogenesis during deetiolation.
GO:0010228 vegetative to reproductive phase transition of meristem	IMP PMID:28752516 CYCLING DOF FACTOR 1 represses transcription through the TOP...	ACCEPT	Summary: cdf1 mutant / CDF1 misexpression alters the timing of flowering; mutations that disrupt TPL interaction impair repression of CO and FT and alter flowering. Reason: CDF1 is a direct transcriptional regulator of the floral activators CO and FT; acts_upstream_of_or_within the floral transition is appropriate. Supporting Evidence: PMID:28752516 This TPL interaction confers a repressive function on CDF1, as mutations of the N-terminal TPL binding domain largely impair the ability of CDF1 protein to repress its targets.
GO:0045892 negative regulation of DNA-templated transcription	IDA PMID:16002617 FKF1 F-box protein mediates cyclic degradation of a represso...	ACCEPT	Summary: CDF1 represses CO transcription; overexpression reduces CO mRNA. Reason: Supported by direct promoter binding and reduced target expression; core process. Supporting Evidence: PMID:16002617 Plants with elevated levels of CDF1 flower late and have reduced expression of CO. PMID:16002617 Thus, FKF1 controls daily CO expression in part by degrading CDF1, a repressor of CO transcription.
GO:0048510 regulation of timing of transition from vegetative to reproductive phase	IMP PMID:16002617 FKF1 F-box protein mediates cyclic degradation of a represso...	ACCEPT	Summary: Plants with elevated CDF1 flower late, placing CDF1 as a regulator of flowering time. Reason: Correct; CDF1 controls the timing of the floral transition in long days. Supporting Evidence: PMID:16002617 Plants with elevated levels of CDF1 flower late and have reduced expression of CO.
GO:0048579 negative regulation of long-day photoperiodism, flowering	IMP PMID:16002617 FKF1 F-box protein mediates cyclic degradation of a represso...	NEW	Summary: CDF1 directly represses the floral activators CO and FT in the morning; its FKF1-GI-dependent removal in long days is the mechanism that converts day length into CO/FT induction. CDF1 does the regulatory work itself (binding the CO and FT promoters and recruiting TPL). Reason: No existing annotation captures CDF1's specific role in photoperiodic flowering; the existing flowering terms are generic timing terms. CDF1 is the effector that directly represses CO and FT, so the regulation term belongs to it (cf. CO carries positive regulation of long-day photoperiodism, flowering). Supporting Evidence: PMID:16002617 Plants with elevated levels of CDF1 flower late and have reduced expression of CO. PMID:16002617 Thus, FKF1 controls daily CO expression in part by degrading CDF1, a repressor of CO transcription. PMID:22628657 These results indicate that CDF1 protein represses FT transcription independently of CO transcription. PMID:19619493 Combining mutations in four of these, including CYCLING DOF FACTOR 2 (CDF2), caused photoperiod-insensitive early flowering by increasing CO mRNA levels.

Gene Description

Existing Annotations Review

Core Functions

Morning-phased nuclear Dof transcriptional repressor that binds Dof sites in the CO and FT promoters and represses their transcription, thereby preventing photoperiodic induction of flowering until it is removed by FKF1-GI-mediated degradation in long-day afternoons.

Recruits the TOPLESS co-repressor to CO and FT promoters through a conserved N-terminal non-EAR motif; this interaction is required for full CDF1 repressive activity.

References

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Notes

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