INDETERMINATE1 (ID1) is a plant-specific zinc finger transcription factor and the founding member of the INDETERMINATE DOMAIN (IDD) family. Its ID domain, a cluster of C2H2 and C2HC zinc fingers, binds an 11 bp DNA motif (5'-TTTGTCG/CT/CT/aT/aT-3') in a zinc-dependent manner, with zinc fingers Z2 and Z3 required for binding. ID1 is a nuclear protein expressed only in immature, non-photosynthetic leaf tissue, and its level does not vary with light, day length or the circadian clock. It is the central regulator of the autonomous (photoperiod-independent) floral transition in day-neutral temperate maize. Acting non-cell-autonomously from developing leaves, ID1 is required for production of the leaf-derived florigenic signal, including high expression of the florigen gene ZCN8 in mature leaves. The ZCN8 effect is probably indirect. id1 mutants produce more than twice the normal number of leaves, flower very late and form aberrant flowers. Orthologs in rice (OsId1/Ehd2/RID1) and sorghum have a similar role in grass flowering.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003700 DNA-binding transcription factor activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference from the IDD clade (PTN002238909), seeded by Arabidopsis IDD proteins with experimental transcription-factor annotations. ID1 is the founding IDD member and binds a specific DNA motif via its ID domain. Reason: ID1 carries the full ID domain shared by the IDD clade, and maize ID1 itself binds an 11 bp consensus motif through that domain in vitro [PMID:15020707]. The IDD family is a family of transcription factors [PMID:16784536]. The rice ortholog activates transcription in yeast [PMID:18774969]. ID1 sits inside the clade that inherited the function, and nothing suggests loss. This is the core molecular function. Supporting Evidence: PMID:15020707 ID1 binds selectively to an 11 bp consensus motif via the ID domain PMID:16784536 the founding member of a transcription factor gene family that encodes a protein with a distinct arrangement of zinc finger motifs PMID:18774969 OsId1 is able to activate transcription in yeast. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of nuclear localization for the IDD clade; maize ID1 has been immunolocalized to nuclei. Reason: Consistent with direct evidence for maize ID1: anti-ID1 immunolocalization detects the protein in the nuclei of all cell types in immature leaves [PMID:17307745]. A nuclear location is where a DNA-binding transcription factor acts. Supporting Evidence: PMID:17307745 Immunolocalization with anti-ID1 antibody shows that ID1 protein is detected in the nuclei of all cell types in immature leaves. |
| GO:0005634 nucleus | IEA GO_REF:0000107 | ACCEPT | Summary: Ensembl Compara projection of nuclear localization from rice EHD2/OsId1 (B1B534). Reason: Consistent with the IBA row and with direct immunolocalization of maize ID1 to nuclei [PMID:17307745]. Supporting Evidence: PMID:17307745 Immunolocalization with anti-ID1 antibody shows that ID1 protein is detected in the nuclei of all cell types in immature leaves. |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000120 | ACCEPT | Summary: Combined automated annotation (ARBA plus rice ortholog projection) that ID1 regulates transcription. Reason: ID1 is a sequence-specific DNA-binding zinc finger protein [PMID:15020707], and loss of id1 changes the expression of many leaf genes, including the florigen gene ZCN8 [PMID:21730358, PMID:17928372]. A 2026 single-cell chromatin and expression preprint (PMID:42818387) proposes candidate direct targets, noted in the manual synthesis. For maize ID1 the direction of regulation at any direct target has not been established, so this term is as precise as the maize evidence allows. The rice-derived 'positive regulation' row is reviewed separately. Supporting Evidence: PMID:15020707 The presence of zinc finger domains that interact with specific DNA sequences is further evidence that maize ID1, and most likely all ID domain proteins, function as transcriptional regulators. PMID:17928372 This analysis revealed 55 genes with a significant 2-fold difference in expression file:MAIZE/id1/id1-deep-research-manual.md reports scATAC/snRNA-seq of id1 |
| GO:0043565 sequence-specific DNA binding | IEA GO_REF:0000107 | ACCEPT | Summary: Ensembl Compara projection from rice EHD2/OsId1. Maize ID1 itself has been shown to bind an 11 bp consensus DNA motif. Reason: Directly shown for maize ID1 by SAAB selection and EMSA: full-length ID1 and the isolated ID domain bind the motif 5'-TTTGTCG/CT/CT/aT/aT-3', and single-base changes abolish or reduce binding [PMID:15020707]. Binding requires zinc fingers Z2 and Z3. GOA lacks an IDA row from this paper; the claim is recorded here rather than as a duplicate NEW row. Supporting Evidence: PMID:15020707 the ID domain is sufficient for mediating specific DNA binding PMID:15020707 mutating the first two cysteines of zinc fingers Z2 or Z3 (Z2M and Z3M, respectively) abolished the binding activity of the ID domain |
| GO:0045893 positive regulation of DNA-templated transcription | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ensembl Compara projection from rice EHD2/OsId1, which activates transcription in yeast and is required for expression of Ehd1, Hd3a and RFT1. Reason: Plausible by orthology: rice OsId1 activates transcription in yeast and is required for Ehd1 expression [PMID:18774969]. For maize ID1, activation has not been tested. The best-studied maize downstream gene, ZCN8, is probably not a direct target because the two genes are expressed in different parts of the leaf [PMID:21730358]. The row is kept as an orthology-supported claim, but it is not used as the core description of ID1 until a direct maize target is shown to be activated. Supporting Evidence: PMID:18774969 OsId1 is able to activate transcription in yeast. PMID:21730358 Therefore, it is unlikely that ZCN8 is a direct target of the ID1 transcriptional regulator in the way that FT is a direct target of CO |
| GO:0048510 regulation of timing of transition from vegetative to reproductive phase | IEA GO_REF:0000107 | ACCEPT | Summary: Ensembl Compara projection from rice. In maize this is the defining role of ID1: id1 mutants are extremely late flowering. Reason: ID1 controls the timing of the floral transition in maize. id1 mutants make more than twice the normal number of leaves before flowering [PMID:21730358], and id1 acts from the leaf to regulate production of a transmissible floral signal [PMID:9604934]. As a transcription factor whose activity sets the timing of the transition, ID1 regulates this process, which is the standard GO treatment of developmental-timing regulators. GO:0048510 has no descendants, so it is as specific as GO allows. Supporting Evidence: PMID:21730358 Mutant id1 plants exhibit an extreme late flowering phenotype in which they produce more than twice as many leaves as normal maize PMID:9604934 id1 acts non-cell-autonomously to regulate the production of a transmissible signal in the leaf |
| GO:0048574 long-day photoperiodism, flowering | IEA GO_REF:0000107 | MARK AS OVER ANNOTATED | Summary: Ensembl Compara projection from rice EHD2/OsId1. Maize ID1 acts in the autonomous, photoperiod-independent flowering pathway. Reason: GO:0048574 is a photoperiodism term (a phase change "as a result of detection of, or exposure to, a period of light or dark of a given length"). Maize ID1 acts in the autonomous pathway: its mRNA and protein levels are unaffected by day/night regime and photoperiod [PMID:17307745]. Even the rice ortholog acts "regardless of photoperiod" and is needed for flowering in both short and long days [PMID:18774969], which shows a general requirement for flowering rather than a day-length response. Whether ID1 contributes to photoperiod responses in tropical maize is unknown [PMID:21730358]. The timing role is already captured by GO:0048510. Supporting Evidence: PMID:17307745 The finding that ID1 expression is developmentally regulated and is unperturbed by external stimuli such as photoperiod supports the supposition that ID1 acts through the autonomous floral inductive pathway in maize. PMID:18774969 RNAi mutants show a delay in flowering under both short-day (SD) and long-day (LD) conditions. |
| GO:0048575 short-day photoperiodism, flowering | IEA GO_REF:0000107 | MARK AS OVER ANNOTATED | Summary: Ensembl Compara projection from rice EHD2/OsId1. Maize ID1 acts in the autonomous, photoperiod-independent flowering pathway. Reason: Same reasoning as the long-day row. ID1 levels are unaffected by photoperiod [PMID:17307745], and the rice ortholog is required for flowering in both short and long days [PMID:18774969], so the requirement is not a day-length response. In photoperiod-sensitive teosinte, short days induce ZCN8 through an unknown intermediate that the authors do not identify as ID1 [PMID:21730358]. Supporting Evidence: PMID:17307745 ID1 gene expression and protein levels are largely unaffected by variations in light and dark PMID:21730358 Whether id1 has a role in mediating the floral transition in teosinte or other tropical maize that requires SD photoperiods to induce flowering is unknown. |
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Download this section (compressed HTML)Q: Which genes are direct in vivo targets of ID1, and does ID1 activate or repress them? Since all IDD proteins bind the same motif in vitro, what gives ID1 its specificity?
Q: Rice EHD2/OsId1 carries LD and SD photoperiodism-of-flowering annotations, although it acts regardless of photoperiod. Should those source annotations be GO:0048510 instead, so that Compara projection does not spread photoperiodism terms?
Experiment: ChIP-seq or CUT&RUN for ID1 in immature maize leaves, combined with RNA-seq of id1 mutants and transient promoter-reporter assays, to identify direct targets and the sign of regulation.
Type: ChIP-seq
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