CBF1 (also DREB1B; ERF029) is an Arabidopsis thaliana AP2/ERF-family transcription factor of the ERF subfamily and one of three tandemly arrayed cold-induced CBF/DREB1 factors (CBF1/DREB1B, CBF2/DREB1C, CBF3/DREB1A) on chromosome 4. The 213-residue protein contains a single AP2/ERF DNA-binding domain, a nuclear localization signal, and an acidic C-terminal transcriptional activation domain. CBF1 binds in a sequence-specific manner to the C-repeat/dehydration-responsive element (CRT/DRE, core 5'-[AG]CCGAC-3') present in the promoters of cold-regulated (COR) genes and activates their transcription. Through induction of the COR regulon, CBF1 is a central positive regulator of cold acclimation and freezing tolerance: its overexpression induces COR genes and confers freezing tolerance on non-acclimated plants, and loss of CBF1 (together with CBF3) impairs cold acclimation. CBF1 acts in the nucleus, where its activity is modulated by recruitment of the SAGA-like ADA2/GCN5 coactivator complex (which binds the CBF1 DNA-binding domain) and by 14-3-3 (GRF) proteins that destabilize CBF protein during freezing, and CBF1 is subject to 26S proteasome turnover.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003677 DNA binding | IEA GO_REF:0000002 | ACCEPT | Summary: CBF1 is a sequence-specific DNA-binding protein; it binds the C-repeat/DRE element via its AP2/ERF domain. DNA binding is directly demonstrated experimentally. Reason: The InterPro-based IEA to DNA binding is correct and is corroborated by direct experimental evidence (gel-shift). DNA binding is a true parent of the more specific sequence-specific binding; retained. More specific terms are proposed as new terms. Supporting Evidence: PMID:9023378 Binding of CBF1 to the C-repeat/DRE was demonstrated in gel shift assays using recombinant CBF1 protein expressed in Escherichia coli. file:ARATH/CBF1/CBF1-deep-research-falcon.md recombinant CBF1 binds the CRT/DRE sequence by gel-shift assays |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | ACCEPT | Summary: CBF1 is a transcriptional activator that binds the CRT/DRE element and activates transcription of CRT/DRE-driven reporters and COR genes. This is a core molecular function. Reason: Strongly supported by both InterPro/ISS and direct experimental evidence of sequence-specific DNA binding combined with transactivation. Supporting Evidence: PMID:9023378 expression of CBF1 in yeast was found to activate transcription of reporter genes containing the C-repeat/DRE as an upstream activator sequence but not mutant versions of the DNA element. file:ARATH/CBF1/CBF1-deep-research-falcon.md CBF1 encodes an AP2-domain transcriptional activator that binds CRT/DRE motifs and can activate CRT/DRE-containing reporters in heterologous assays (yeast), supporting that it acts as a bona fide transcriptional activator rather than merely binding DNA. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: CBF1 is a transcription factor with a predicted nuclear localization signal that acts on nuclear COR-gene promoters; 14-3-3 proteins interact with CBF in the nucleus. Nuclear localization is consistent with its function. Reason: Nuclear localization is supported by sequence features (NLS, AP2/ERF domain) and by the requirement to act on chromatin/promoters; UniProt curates Nucleus. Supporting Evidence: PMID:9023378 the protein has a molecular mass of 24 kDa, a potential nuclear localization sequence, and a possible acidic activation domain. file:ARATH/CBF1/CBF1-deep-research-falcon.md multiple primary sources identify a **putative nuclear localization sequence** in the protein sequence, consistent with its function as a transcription factor acting on nuclear DNA. |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | ACCEPT | Summary: CBF1 regulates transcription of COR genes by binding their CRT/DRE promoter elements. Specifically it is a positive (activating) regulator. Reason: Correct but general parent term; the more specific positive regulation of transcription is also annotated (IDA) and accepted. Retained as a valid grouping term. Supporting Evidence: PMID:9525853 Increased expression of Arabidopsis CBF1, a transcriptional activator that binds to the CRT/DRE sequence, induced COR gene expression file:ARATH/CBF1/CBF1-deep-research-falcon.md CBF1 encodes an AP2-domain transcriptional activator that binds CRT/DRE motifs and can activate CRT/DRE-containing reporters in heterologous assays (yeast), supporting that it acts as a bona fide transcriptional activator rather than merely binding DNA. |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: Duplicate nuclear localization annotation from a sequence-based prediction (AtSubP). Consistent with CBF1 being a nuclear transcription factor. Reason: Redundant with the UniProt nucleus annotation but not incorrect; duplicate cellular component annotations are acceptable. Supporting Evidence: PMID:9023378 the protein has a molecular mass of 24 kDa, a potential nuclear localization sequence, and a possible acidic activation domain. file:ARATH/CBF1/CBF1-deep-research-falcon.md multiple primary sources identify a **putative nuclear localization sequence** in the protein sequence, consistent with its function as a transcription factor acting on nuclear DNA. |
| GO:0005515 protein binding | IPI PMID:28344081 Plasma Membrane CRPK1-Mediated Phosphorylation of 14-3-3 Pro... | KEEP AS NON CORE | Summary: CBF1 interacts with 14-3-3 (GRF) proteins in the nucleus; phosphorylated 14-3-3 proteins bind and destabilize CBF proteins to fine-tune cold signaling. The interaction is real but 'protein binding' is uninformative and regulatory rather than a core molecular function. Reason: The 14-3-3 interaction is experimentally supported but the generic 'protein binding' term carries no functional specificity per curation guidelines. This is a regulatory (CBF-destabilizing) interaction, not the gene's core function, so it is retained as non-core rather than treated as a core annotation. Supporting Evidence: PMID:28344081 they interact with and destabilize the key cold-responsive C-repeat-binding factor (CBF) proteins. |
| GO:0005515 protein binding | IPI PMID:16603259 Physical and functional interactions of Arabidopsis ADA2 tra... | KEEP AS NON CORE | Summary: The DNA-binding domain of CBF1 binds directly to the Arabidopsis ADA2 transcriptional coactivator proteins, linking CBF1 to the SAGA-like ADA2/GCN5 complex that stimulates COR gene expression. Real interaction but 'protein binding' is uninformative. Reason: Experimentally supported coactivator interaction, but the generic term provides no functional information. Relevant to how CBF1 activates transcription; retained as non-core supporting context rather than a core molecular-function annotation. Supporting Evidence: PMID:16603259 the DNA-binding domain of CBF1 (and of a related protein, TINY), rather than its transcriptional activation domain, can bind directly to the Arabidopsis ADA2 proteins. file:ARATH/CBF1/CBF1-deep-research-falcon.md Stockinger et al. (2001) report physical interaction (in vitro pull-down) between CBF1 and Arabidopsis homologs of **Ada/SAGA-like complex** components **ADA2a/ADA2b** and **GCN5** (a histone acetyltransferase). |
| GO:0045893 positive regulation of DNA-templated transcription | IDA PMID:9023378 Arabidopsis thaliana CBF1 encodes an AP2 domain-containing t... | ACCEPT | Summary: CBF1 functions as a transcriptional activator, activating transcription from CRT/DRE-containing promoters. This is a core biological-process role. Reason: Directly demonstrated transactivation of CRT/DRE-driven reporters in yeast and induction of COR genes upon overexpression in planta. Supporting Evidence: PMID:9023378 expression of CBF1 in yeast was found to activate transcription of reporter genes containing the C-repeat/DRE as an upstream activator sequence but not mutant versions of the DNA element. PMID:9525853 Increased expression of Arabidopsis CBF1, a transcriptional activator that binds to the CRT/DRE sequence, induced COR gene expression file:ARATH/CBF1/CBF1-deep-research-falcon.md CBF1 encodes an AP2-domain transcriptional activator that binds CRT/DRE motifs and can activate CRT/DRE-containing reporters in heterologous assays (yeast), supporting that it acts as a bona fide transcriptional activator rather than merely binding DNA. |
| GO:0003677 DNA binding | IDA PMID:9023378 Arabidopsis thaliana CBF1 encodes an AP2 domain-containing t... | ACCEPT | Summary: Direct gel-shift evidence that recombinant CBF1 binds the C-repeat/DRE DNA element specifically (not the mutant element). Confirms DNA binding. Reason: Direct experimental evidence (IDA) for sequence-specific DNA binding via the AP2 domain. More specific MF terms proposed as new terms. Supporting Evidence: PMID:9023378 Binding of CBF1 to the C-repeat/DRE was demonstrated in gel shift assays using recombinant CBF1 protein expressed in Escherichia coli. file:ARATH/CBF1/CBF1-deep-research-falcon.md recombinant CBF1 binds the CRT/DRE sequence by gel-shift assays |
| GO:0000977 RNA polymerase II transcription regulatory region sequence-specific DNA binding | IDA PMID:9023378 Arabidopsis thaliana CBF1 encodes an AP2 domain-containing t... | NEW | Summary: CBF1 binds in a sequence-specific manner to the C-repeat/DRE cis-element in the promoters (Pol II regulatory regions) of COR genes. Gel-shift assays with recombinant CBF1 demonstrate direct binding to the C-repeat/DRE, and CBF1 specifically activates transcription from reporters carrying this element but not mutant versions, establishing sequence specificity. This is a more informative molecular-function term than the bare 'DNA binding' (GO:0003677). Reason: Added as a NEW annotation to capture the specific molecular function: sequence-specific binding to a Pol II promoter regulatory element. Directly supported by gel-shift (EMSA) evidence and by the demonstrated specificity of CRT/DRE-driven transactivation versus mutant elements. This term already exists in GO and was previously (incorrectly) listed under proposed_new_terms; it is moved here with IDA evidence. Supporting Evidence: PMID:9023378 Binding of CBF1 to the C-repeat/DRE was demonstrated in gel shift assays using recombinant CBF1 protein expressed in Escherichia coli. PMID:9023378 expression of CBF1 in yeast was found to activate transcription of reporter genes containing the C-repeat/DRE as an upstream activator sequence but not mutant versions of the DNA element. |
| GO:0009631 cold acclimation | IMP PMID:18093929 Arabidopsis CBF1 and CBF3 have a different function than CBF... | ACCEPT | Summary: Loss-of-function (RNAi/antisense) analysis shows CBF1, together with CBF3, is a positive regulator of cold acclimation, activating a subset of the CBF regulon. CBF1/CBF3 RNAi lines are defective in cold acclimation. Reason: Strong genetic loss-of-function evidence that CBF1 is required for the full development of cold acclimation. This is a core biological role. Supporting Evidence: PMID:18093929 CBF1 and CBF3 RNAi lines are defective in cold acclimation but are not affected in their constitutive freezing tolerance. file:ARATH/CBF1/CBF1-deep-research-falcon.md antisense downregulation of **CBF1 and CBF3** reduces cold-induced freezing tolerance by about **60%** |
| GO:0009409 response to cold | IEP PMID:16258011 The cold-induced early activation of phospholipase C and D p... | ACCEPT | Summary: CBF1 acts in the cold-response transcriptional network; this paper relates phospholipase C/D signaling pathways to the CBF pathway during the cold response. CBF1 is part of the response to cold. Reason: Consistent with CBF1's well-established role in cold response. The cited expression study connects cold-signaling pathways to the CBF pathway, supporting involvement in response to cold. Supporting Evidence: PMID:16258011 The connection of these pathways with the CBF pathway, currently the most understood genetic system playing a role in cold acclimation, is discussed. file:ARATH/CBF1/CBF1-deep-research-falcon.md CBF-family transcripts rise rapidly following cold shift (minutes), and COR gene expression follows within hours |
| GO:0009631 cold acclimation | IEP PMID:9735350 An Arabidopsis gene family encoding DRE/CRT binding proteins... | ACCEPT | Summary: CBF1/DREB1B is one of three DRE/CRT-binding factors induced mainly by cold stress and involved in low-temperature-responsive gene expression, consistent with a role in cold acclimation. Reason: Expression (induction) evidence places CBF1 in the cold-acclimation transcriptional program; consistent with the genetic IMP evidence. Supporting Evidence: PMID:9735350 the 3 DREB1 genes are induced mainly by cold stress but not by osmotic stress in leaves, roots, and stems. file:ARATH/CBF1/CBF1-deep-research-falcon.md CBF1 is a core regulator of **cold acclimation**. |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a... | ACCEPT | Summary: Sequence/genome-wide TF analysis classifies CBF1 among Arabidopsis transcription factors with a conserved DNA-binding domain. Consistent with its experimentally demonstrated DNA-binding transcription factor activity. Reason: ISS based on conserved AP2/ERF DNA-binding domain; corroborated by direct experimental evidence. Duplicate of the IEA annotation but acceptable. Supporting Evidence: PMID:11118137 Arabidopsis dedicates over 5% of its genome to code for more than 1500 transcription factors file:ARATH/CBF1/CBF1-deep-research-falcon.md CBF1 encodes an AP2-domain transcriptional activator that binds CRT/DRE motifs and can activate CRT/DRE-containing reporters in heterologous assays (yeast), supporting that it acts as a bona fide transcriptional activator rather than merely binding DNA. |
| GO:0009409 response to cold | IMP PMID:9023378 Arabidopsis thaliana CBF1 encodes an AP2 domain-containing t... | ACCEPT | Summary: CBF1 binds the CRT/DRE element that stimulates transcription in response to low temperature, implicating it in the response to cold. Core biological role of CBF1. Reason: CBF1 is the C-repeat/DRE binding factor mediating cold-induced transcription; its role in the cold response is well established. Supporting Evidence: PMID:9023378 a cis-acting DNA regulatory element in plants, the C-repeat/dehydration responsive element (DRE), that stimulates transcription in response to low temperature and water deficit. file:ARATH/CBF1/CBF1-deep-research-falcon.md CBF-family transcripts rise rapidly following cold shift (minutes), and COR gene expression follows within hours |
| GO:0009409 response to cold | TAS PMID:9707537 Two transcription factors, DREB1 and DREB2, with an EREBP/AP... | ACCEPT | Summary: DREB1 (= CBF) factors function in the low-temperature signal transduction pathway, separate from the DREB2 drought pathway. Confirms response-to-cold role. Reason: Authoritative statement that the DREB1/CBF family acts in the low-temperature-responsive pathway. Duplicate response-to-cold annotation, acceptable. Supporting Evidence: PMID:9707537 two independent families of DREB proteins, DREB1 and DREB2, function as trans-acting factors in two separate signal transduction pathways under low-temperature and dehydration conditions, respectively. |
| GO:0009409 response to cold | TAS PMID:9735350 An Arabidopsis gene family encoding DRE/CRT binding proteins... | ACCEPT | Summary: CBF1/DREB1B is induced by cold and involved in low-temperature-responsive gene expression. Response to cold is a core role. Reason: Author statement that DREB1B (= CBF1) is involved in cold-responsive gene expression and induced by cold. Duplicate response-to-cold annotation, acceptable. Supporting Evidence: PMID:9735350 DREB1A and CBF1 were shown to be involved in low-temperature-responsive gene expression. |
| GO:0009414 response to water deprivation | IEP PMID:9023378 Arabidopsis thaliana CBF1 encodes an AP2 domain-containing t... | KEEP AS NON CORE | Summary: The CRT/DRE element bound by CBF1 stimulates transcription in response to both low temperature and water deficit, and CBF1 overexpression confers some drought tolerance via the regulon. However, CBF1/DREB1 transcript itself is induced mainly by cold, not by osmotic stress, so a direct role of CBF1 in the water-deprivation response is peripheral. Reason: CBF1 acts primarily in the cold arm of the DRE response; the DREB1/CBF branch is distinguished from the DREB2 drought branch, and DREB1 genes are induced by cold but not osmotic stress. The water-deprivation link is real (shared cis-element, downstream tolerance) but not a core function of CBF1. Supporting Evidence: PMID:9023378 a cis-acting DNA regulatory element in plants, the C-repeat/dehydration responsive element (DRE), that stimulates transcription in response to low temperature and water deficit. PMID:9735350 the 3 DREB1 genes are induced mainly by cold stress but not by osmotic stress in leaves, roots, and stems. file:ARATH/CBF1/CBF1-deep-research-falcon.md The CRT/DRE element is a shared regulatory node for cold- and dehydration-responsive gene expression, and CBF/DREB-type factors are widely used to connect these stress responses. |
| GO:0009631 cold acclimation | IMP PMID:9525853 Arabidopsis CBF1 overexpression induces COR genes and enhanc... | ACCEPT | Summary: Overexpression of CBF1 induces COR genes and increases freezing tolerance of non-acclimated plants, identifying CBF1 as a regulator of the cold acclimation response. Core biological role. Reason: Gain-of-function evidence directly linking CBF1 to COR-gene induction and freezing tolerance, the molecular basis of cold acclimation. Supporting Evidence: PMID:9525853 Increased expression of Arabidopsis CBF1, a transcriptional activator that binds to the CRT/DRE sequence, induced COR gene expression and increased the freezing tolerance of nonacclimated Arabidopsis plants. file:ARATH/CBF1/CBF1-deep-research-falcon.md CBF1 is a core regulator of **cold acclimation**. |
Loading supporting content…
Download this section (compressed HTML)Q: Has CBF1 nuclear localization been demonstrated directly in planta (e.g., fluorescent fusion), or is it inferred from the NLS and function?
Q: To what extent does CBF1 contribute directly to the water-deprivation/drought response versus acting only through the shared CRT/DRE element, given that CBF1 transcript is induced by cold but not osmotic stress?
Q: What is the genome-wide set of direct CBF1 target promoters (ChIP-seq) and how much does it overlap with CBF3 versus CBF2?
Experiment: Confirm in planta nuclear localization of CBF1 using a fluorescent (GFP/YFP) fusion transformed into Arabidopsis under a native or estradiol-inducible promoter, comparing wild-type CBF1 with an NLS-mutant variant.
Experiment: Map direct CBF1-bound promoters by ChIP-seq from cold-treated Arabidopsis seedlings using a tagged CBF1 line, and compare the binding-site set with parallel ChIP-seq for CBF2 and CBF3 to define CBF1-specific versus shared targets.
Experiment: Dissect CBF1 versus CBF3 contribution to drought response by RNA-seq of cbf1 single, cbf3 single, and cbf1 cbf3 double mutants under cold and osmotic stress, asking which CRT/DRE-driven genes require CBF1 specifically.
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)