ICE1 (INDUCER OF CBF EXPRESSION 1; also SCREAM/SCRM, bHLH116) is a constitutively expressed nuclear MYC-type (group IIIb) basic helix-loop-helix transcription factor. In the stomatal lineage it is the obligate heterodimerization partner, redundantly with its paralog SCRM2, of the stage-specific bHLHs SPEECHLESS, MUTE and FAMA, specifying the three successive transitions of lineage entry/asymmetric division, meristemoid-to-guard-mother-cell differentiation and guard cell differentiation; scrm scrm2 loss sequentially phenocopies fama, mute and spch. ICE1 also acts as a scaffold that couples the MAP kinases MPK3/MPK6 to SPEECHLESS: a bipartite MAPK-docking/KRAAM (KiDoK) motif binds MPK3/6, promoting phosphorylation and degradation of SCRM and SPCH, and the dominant scrm-D (R236H) mutation in this motif abolishes MAPK binding and converts the whole epidermis into stomata. In the endosperm ICE1 heterodimerizes with ZHOUPI to control endosperm breakdown and seed dormancy (repressing ABI3), and it modulates ABA responses during germination through interactions with ABI5 and DELLA proteins. ICE1 was originally identified as an activator of CBF3/DREB1A and freezing tolerance; it binds MYC elements in CBF promoters and is regulated by HOS1-mediated ubiquitination and SIZ1-mediated sumoylation, but its requirement for cold-induced CBF expression has been disputed because the original ice1-1 CBF3 phenotype was shown to arise from transgene-induced silencing.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000976 transcription cis-regulatory region binding | IPI PMID:27923776 Establishment of Expression in the SHORTROOT-SCARECROW Trans... | KEEP AS NON CORE | Summary: ICE1 bound a promoter fragment (AT1G50640) in a yeast one-hybrid transcriptional network screen of root ground tissue regulators. Reason: Cis-regulatory DNA binding is consistent with ICE1 being a bHLH transcription factor, but this is a high-throughput yeast one-hybrid interaction outside its principal developmental roles. Supporting Evidence: PMID:27923776 We generated a transcriptional network to explore how transcription factor expression is established in the Arabidopsis thaliana root ground tissue. |
| GO:0000987 cis-regulatory region sequence-specific DNA binding | IDA PMID:31123050 The Transcription Factor INDUCER OF CBF EXPRESSION1 Interact... | ACCEPT | Summary: ICE1 binds the promoters of the ABA-responsive EM1/EM6 genes. Reason: Direct evidence of sequence-specific cis-regulatory DNA binding, consistent with ICE1's bHLH activity. Supporting Evidence: PMID:31123050 ICE1 negatively regulates ABA responses during seed germination and directly suppresses ABA-responsive LATE EMBRYOGENESIS ABUNDANT6 (EM6) and EM1 expression. |
| GO:0001046 core promoter sequence-specific DNA binding | IPI PMID:30570804 ICE1 and ZOU determine the depth of primary seed dormancy in... | MODIFY | Summary: ICE1 binds the ABI3 promoter. Reason: The evidence shows ICE1 binding to regulatory regions of ABI3 but does not establish binding to the core promoter specifically; cis-regulatory region sequence-specific DNA binding is the appropriately supported term. Proposed replacements: cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:30570804 We also demonstrate that ICE1 binds to and inhibits expression of ABA INSENSITIVE 3. |
| GO:0003677 DNA binding | IDA PMID:12672693 ICE1: a regulator of cold-induced transcriptome and freezing... | ACCEPT | Summary: ICE1 binds MYC recognition sequences in the CBF3 promoter. Reason: Direct DNA-binding evidence; correct though general. Supporting Evidence: PMID:12672693 ICE1 binds specifically to the MYC recognition sequences in the CBF3 promoter. |
| GO:0003677 DNA binding | TAS PMID:16214899 The Arabidopsis cold-responsive transcriptome and its regula... | ACCEPT | Summary: ICE1 described as an upstream DNA-binding transcription factor in a cold transcriptome study. Reason: Consistent with direct DNA-binding evidence. Supporting Evidence: PMID:16214899 a mutant defective in an upstream transcription factor required for chilling and freezing tolerance |
| GO:0003700 DNA-binding transcription factor activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of DNA-binding transcription factor activity for ICE1/SCRM2 clade. Reason: Core molecular function; ICE1 is a bHLH transcription factor binding E-box/MYC elements and acting as the common heterodimer partner of SPCH, MUTE and FAMA. Supporting Evidence: PMID:18641265 Because a functional DNA binding domain is required for the ectopic stomatal differentiation by the scrm-D gene product, ICE1 R236H , these nuclear-localized bHLH heterodimers most likely act as DNA binding transcription factors. |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a... | ACCEPT | Summary: Classification as a bHLH transcription factor. Reason: Consistent with experimental data. |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:12679534 The basic helix-loop-helix transcription factor family in pl... | ACCEPT | Summary: Classification as a bHLH transcription factor (bHLH116). Reason: Consistent with experimental data. |
| GO:0005515 protein binding | IPI PMID:16702557 The negative regulator of plant cold responses, HOS1, is a R... | REMOVE | Summary: ICE1 interacts with the RING E3 ligase HOS1 (Q84JU6), which ubiquitinates it. Reason: Generic protein binding is uninformative; ICE1 is the substrate of HOS1, and the relevant biology (HOS1-mediated ICE1 degradation) is a property of HOS1. Removal does not imply the interaction is false. Supporting Evidence: PMID:16702557 HOS1 physically interacts with ICE1 and mediates the ubiquitination of ICE1 both in vitro and in vivo. |
| GO:0005515 protein binding | IPI PMID:17015446 A R2R3 type MYB transcription factor is involved in the cold... | REMOVE | Summary: ICE1 interacts with the MYB15 transcription factor. Reason: Generic protein binding without an informative molecular function; the interaction modulates cold-regulated CBF expression, a role that is now disputed for ICE1. Supporting Evidence: PMID:17015446 The MYB15 protein interacts with ICE1 and binds to Myb recognition sequences in the promoters of CBF genes. |
| GO:0005515 protein binding | IPI PMID:18641265 SCREAM/ICE1 and SCREAM2 specify three cell-state transitiona... | MODIFY | Summary: ICE1/SCRM directly interacts with SPEECHLESS (Q700C7). Reason: The interaction is bHLH heterodimerization between ICE1 and the stage-specific stomatal bHLH SPCH, the basis of ICE1's stomatal function; protein heterodimerization activity is the informative term. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:18641265 Here, we identify two paralogous proteins, SCREAM (SCRM) and SCRM2, which directly interact with and specify the sequential actions of SPCH, MUTE, and FAMA. |
| GO:0005515 protein binding | IPI PMID:22960247 The E3 ubiquitin ligase HOS1 regulates low ambient temperatu... | REMOVE | Summary: HOS1-ICE1 interaction recorded from a flowering-time study. Reason: Generic protein binding is uninformative; the interaction is with the E3 ligase that degrades ICE1. |
| GO:0005515 protein binding | IPI PMID:30072714 MYC-type transcription factors, MYC67 and MYC70, interact wi... | REMOVE | Summary: ICE1 interacts with the MYC-type bHLHs MYC67 and MYC70 (yeast two-hybrid). Reason: Generic protein binding; the functional relationship (negative regulation of cold responses) does not define a specific ICE1 molecular function. Supporting Evidence: PMID:30072714 Two MYC-type transcription factors, MYC67 and MYC70, were identified as ICE1-interacting proteins. |
| GO:0005515 protein binding | IPI PMID:30072714 MYC-type transcription factors, MYC67 and MYC70, interact wi... | REMOVE | Summary: ICE1 interacts with the MYC-type bHLHs MYC67 and MYC70 (yeast two-hybrid). Reason: Generic protein binding; the functional relationship (negative regulation of cold responses) does not define a specific ICE1 molecular function. Supporting Evidence: PMID:30072714 Two MYC-type transcription factors, MYC67 and MYC70, were identified as ICE1-interacting proteins. |
| GO:0005515 protein binding | IPI PMID:31123050 The Transcription Factor INDUCER OF CBF EXPRESSION1 Interact... | REMOVE | Summary: ICE1 interacts with ABI5 and DELLA proteins. Reason: Generic protein binding; partners are heterogeneous transcriptional regulators and no specific molecular function of ICE1 is defined by these interactions. Supporting Evidence: PMID:31123050 Here, we found that INDUCER OF CBF EXPRESSION1 (ICE1) physically associates with ABI5. |
| GO:0005515 protein binding | IPI PMID:31123050 The Transcription Factor INDUCER OF CBF EXPRESSION1 Interact... | REMOVE | Summary: ICE1 interacts with ABI5 and DELLA proteins. Reason: Generic protein binding; partners are heterogeneous transcriptional regulators and no specific molecular function of ICE1 is defined by these interactions. Supporting Evidence: PMID:31123050 Here, we found that INDUCER OF CBF EXPRESSION1 (ICE1) physically associates with ABI5. |
| GO:0005515 protein binding | IPI PMID:37025149 Arabidopsis LFR, a SWI/SNF complex component, interacts with... | REMOVE | Summary: ICE1 interacts with the SWI/SNF component LFR (Q9LS90). Reason: Generic protein binding; uninformative. Supporting Evidence: PMID:37025149 LFR was found to interact directly with ICE1 in yeast and plants. |
| GO:0005634 nucleus | EXP PMID:18641265 SCREAM/ICE1 and SCREAM2 specify three cell-state transitiona... | ACCEPT | Summary: Nuclear localization of SCRM/ICE1 in stomatal lineage cells. Reason: Correct. Supporting Evidence: PMID:18641265 these nuclear-localized bHLH heterodimers most likely act as DNA binding transcription factors |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of nuclear localization. Reason: Correct. |
| GO:0005634 nucleus | IDA PMID:12672693 ICE1: a regulator of cold-induced transcriptome and freezing... | ACCEPT | Summary: ICE1-GFP is nuclear. Reason: Correct. |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: Combined automated nuclear localization assignment. Reason: Correct. |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: Sequence-model nuclear localization prediction. Reason: Correct. |
| GO:0006355 regulation of DNA-templated transcription | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of regulation of transcription. Reason: Correct; ICE1 both activates and represses targets depending on partner and context. |
| GO:0009409 response to cold | IEP PMID:12672693 ICE1: a regulator of cold-induced transcriptome and freezing... | MARK AS OVER ANNOTATED | Summary: Annotation of response to cold based on the ICE1 cold-signalling study. Reason: The cited abstract states that ICE1 itself is expressed constitutively, so an expression-pattern (IEP) response to cold is not supported for the gene; moreover, ICE1's requirement for cold-induced CBF3 expression has been disputed (the ice1-1 CBF3 phenotype arose from transgene-induced silencing). The dispute is itself contested (PMID:32068336 reports ICE1 ChIP-seq binding at CBF/COR promoters), which is why response to freezing, backed by the independent ICE1(K393R) transgene, is kept as non-core while this IEP-based cold row is marked as over-annotated. Supporting Evidence: PMID:12672693 ICE1 is expressed constitutively, and its overexpression in wild-type plants enhances the expression of the CBF regulon in the cold and improves freezing tolerance of the transgenic plants. PMID:32034036 We showed that DREB1A repression in ice1-1 results from transgene-induced silencing and not genetic regulation by ICE1. |
| GO:0009738 abscisic acid-activated signaling pathway | IMP PMID:31123050 The Transcription Factor INDUCER OF CBF EXPRESSION1 Interact... | KEEP AS NON CORE | Summary: ice1 mutants are ABA hypersensitive during germination; ICE1 antagonizes ABI5 and DELLAs. Reason: A genuine but secondary role of ICE1 in seed germination. Supporting Evidence: PMID:31123050 ICE1 negatively regulates ABA responses during seed germination and directly suppresses ABA-responsive LATE EMBRYOGENESIS ABUNDANT6 (EM6) and EM1 expression. |
| GO:0009960 endosperm development | IGI PMID:30570804 ICE1 and ZOU determine the depth of primary seed dormancy in... | KEEP AS NON CORE | Summary: ICE1 and ZOU act together in endosperm development. Reason: ICE1 partners ZHOUPI in the endosperm; valid but outside its stomatal role. Supporting Evidence: PMID:30570804 Arabidopsis ICE1 and ZOU determine the depth of primary dormancy during maturation independently of their effect on endosperm development. |
| GO:0010115 regulation of abscisic acid biosynthetic process | IMP PMID:30570804 ICE1 and ZOU determine the depth of primary seed dormancy in... | KEEP AS NON CORE | Summary: ice1 seeds have increased ABA levels. Reason: Indirect, seed-specific regulatory output. Supporting Evidence: PMID:30570804 This increased dormancy is associated with increased ABA levels |
| GO:0010162 seed dormancy process | IGI PMID:30570804 ICE1 and ZOU determine the depth of primary seed dormancy in... | KEEP AS NON CORE | Summary: ice1 zou double mutants show additive increases in seed dormancy. Reason: Valid secondary developmental role. Supporting Evidence: PMID:30570804 We show that ice1 or zou increases seed dormancy and the double mutant has an additive phenotype. |
| GO:0010162 seed dormancy process | IMP PMID:30570804 ICE1 and ZOU determine the depth of primary seed dormancy in... | KEEP AS NON CORE | Summary: ice1 increases primary seed dormancy. Reason: Valid secondary developmental role. Supporting Evidence: PMID:30570804 We show that ice1 or zou increases seed dormancy and the double mutant has an additive phenotype. |
| GO:0010440 stomatal lineage progression | IMP PMID:18641265 SCREAM/ICE1 and SCREAM2 specify three cell-state transitiona... | ACCEPT | Summary: scrm scrm2 loss sequentially phenocopies fama, mute and spch; scrm-D converts the epidermis to stomata. Reason: Core biological process; ICE1/SCRM with SCRM2 specifies the successive transitions of the stomatal lineage. Supporting Evidence: PMID:18641265 Conversely, successive loss of SCRM and SCRM2 recapitulated the phenotypes of fama, mute, and spch, indicating that SCRM and SCRM2 together determined successive initiation, proliferation, and terminal differentiation of stomatal cell lineages. |
| GO:0043565 sequence-specific DNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of sequence-specific DNA binding. Reason: ICE1 binds MYC/E-box elements. Supporting Evidence: PMID:12672693 ICE1 binds specifically to the MYC recognition sequences in the CBF3 promoter. |
| GO:0045892 negative regulation of DNA-templated transcription | IMP PMID:30570804 ICE1 and ZOU determine the depth of primary seed dormancy in... | KEEP AS NON CORE | Summary: ICE1 represses ABI3 expression in seeds. Reason: Valid context-specific repression activity in seeds. Supporting Evidence: PMID:30570804 We also demonstrate that ICE1 binds to and inhibits expression of ABA INSENSITIVE 3. |
| GO:0045893 positive regulation of DNA-templated transcription | IDA PMID:12672693 ICE1: a regulator of cold-induced transcriptome and freezing... | ACCEPT | Summary: ICE1 activates transcription from the CBF3 promoter. Reason: ICE1 is a transcriptional activator (MYC-like bHLH activator); the activation activity itself is well supported, although the in vivo requirement for cold-induced CBF3 expression is disputed. Supporting Evidence: PMID:12672693 ICE1 encodes a MYC-like bHLH transcriptional activator. |
| GO:0046983 protein dimerization activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping of the bHLH domain to protein dimerization activity. Reason: ICE1 functions as a heterodimer partner of SPCH, MUTE, FAMA and ZOU. |
| GO:0048317 seed morphogenesis | IGI PMID:30570804 ICE1 and ZOU determine the depth of primary seed dormancy in... | KEEP AS NON CORE | Summary: ice1 zou seeds have aberrant morphology. Reason: Endosperm-related seed phenotype; secondary. Supporting Evidence: PMID:30570804 reverses the dormancy phenotype without affecting the aberrant seed morphology |
| GO:0048317 seed morphogenesis | IMP PMID:30570804 ICE1 and ZOU determine the depth of primary seed dormancy in... | KEEP AS NON CORE | Summary: ice1 seeds have aberrant morphology. Reason: Endosperm-related seed phenotype; secondary. Supporting Evidence: PMID:30570804 reverses the dormancy phenotype without affecting the aberrant seed morphology |
| GO:0050826 response to freezing | IMP PMID:17416732 SIZ1-mediated sumoylation of ICE1 controls CBF3/DREB1A expre... | KEEP AS NON CORE | Summary: Expression of non-sumoylatable ICE1(K393R) represses CBF3 induction and increases freezing sensitivity. Reason: Supported by a dominant-negative-type transgene experiment independent of the ice1-1 line, but ICE1's genetic requirement for cold-induced CBF expression has since been disputed (loss of ICE1 and SCRM2 did not alter DREB1A expression). Retained as non-core pending resolution. Supporting Evidence: PMID:17416732 ICE1(K393R) expression in wild-type plants repressed cold-induced CBF3/DREB1A expression and increased freezing sensitivity. PMID:32034036 Moreover, neither ICE1 overexpression nor double loss-of-function mutation of ICE1 and its homolog SCRM2 altered DREB1A expression. |
| GO:0030674 protein-macromolecule adaptor activity | IDA PMID:31235876 Bipartite anchoring of SCREAM enforces stomatal initiation b... | NEW | Summary: SCRM scaffolds MPK3/MPK6 to SPEECHLESS via its bipartite KiDoK docking motif. Reason: Structural and biochemical evidence shows that SCRM directly binds MPK3/6 and SPCH, bringing the kinases to their substrate; mutation of the motif (scrm-D) abolishes this and causes uncontrolled stomatal differentiation. Supporting Evidence: PMID:31235876 here, we report that the basic helix-loop-helix protein SCREAM functions as a scaffold that recruits MPK3/6 to downregulate SPEECHLESS, a transcription factor that initiates stomatal cell lineages. |
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Download this section (compressed HTML)Q: Does ICE1 contribute to cold-induced CBF/DREB1 expression in vivo, given that the classic ice1-1 CBF3 phenotype was caused by transgene-induced promoter methylation while ChIP-seq still detects ICE1 at CBF promoters?
Q: Do MUTE-SCRM and FAMA-SCRM heterodimers also recruit MPK3/6 through the KiDoK motif, or is MAPK docking used specifically to restrain SPCH?
Experiment: Assess cold-induced DREB1/CBF expression and freezing tolerance in clean ice1 scrm2 loss-of-function lines (no reporter transgenes) and in KiDoK-motif point mutants, with ICE1 ChIP at CBF promoters under cold.
Type: genetics / ChIP-qPCR
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