MAGPIE (MGP; INDETERMINATE DOMAIN 3, IDD3) is a nuclear BIRD/IDD-family C2H2 zinc-finger transcription factor of Arabidopsis. MGP is a direct transcriptional target of the SHORT-ROOT (SHR)-SCARECROW (SCR) complex and is expressed in the ground tissue, including the cortex/endodermis initials. Like its paralog JACKDAW, MGP uses zinc fingers ZF1-ZF3 to bind the IDD consensus DNA motif with high affinity and ZF3-ZF4 to dock the GRAS-domain SHR-SCR heterodimer, binding SHR-SCR in a manner mutually exclusive with JKD. Through these interactions MGP forms part of a SHR-dependent feed-forward loop that sets the range of SHR/SCR action; together with other BIRD proteins (JKD, BLJ, NUC) it contributes to the formative asymmetric division of the ground-tissue initials, to cortex identity and to stabilization of tissue boundaries. MGP/IDD3 also binds DELLA and SCL3 coregulators at gibberellin-responsive promoters and acts positively in gibberellin signalling.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000976 transcription cis-regulatory region binding | IPI PMID:22037706 Enhanced Y1H assays for Arabidopsis. | ACCEPT | Summary: Yeast one-hybrid binding of MGP to a target promoter. Root stele promoter screen. Reason: Promoter binding in a Y1H screen is consistent with MGP's demonstrated high-affinity binding to the IDD consensus motif. The molecular function is therefore well grounded, whatever the physiological relevance of this particular stele target. Supporting Evidence: PMID:28211915 Our DNA binding assay using this consensus sequence with ZFs of MGP showed high affinity (KD value of 50 nM) for ZF1-4 (all four ZFs) |
| GO:0000976 transcription cis-regulatory region binding | IPI PMID:27923776 Establishment of Expression in the SHORTROOT-SCARECROW Trans... | ACCEPT | Summary: Yeast one-hybrid binding of MGP to a target promoter. Screen of regulators of the SHR-SCR cascade. Reason: Promoter binding in a Y1H screen is consistent with MGP's demonstrated high-affinity binding to the IDD consensus motif. The screen targeted the SHR-SCR cascade, which is MGP's own regulatory context, so this annotation also fits its core biology. Supporting Evidence: PMID:28211915 Our DNA binding assay using this consensus sequence with ZFs of MGP showed high affinity (KD value of 50 nM) for ZF1-4 (all four ZFs) |
| GO:0000976 transcription cis-regulatory region binding | IPI PMID:30356219 Transcriptional regulation of nitrogen-associated metabolism... | KEEP AS NON CORE | Summary: Yeast one-hybrid binding of MGP to a target promoter. Nitrogen-metabolism network; target relevance to MGP biology unverified. Reason: The molecular function (cis-regulatory region binding) is real for MGP, so the term is not wrong. However, this row is a single high-throughput Y1H hit in a nitrogen-metabolism network with no in planta validation, so it is kept as non-core rather than as evidence for a role in nitrogen metabolism. Supporting Evidence: PMID:28211915 Our DNA binding assay using this consensus sequence with ZFs of MGP showed high affinity (KD value of 50 nM) for ZF1-4 (all four ZFs) |
| GO:0000976 transcription cis-regulatory region binding | IPI PMID:31806676 A PXY-Mediated Transcriptional Network Integrates Signaling ... | KEEP AS NON CORE | Summary: Yeast one-hybrid binding of MGP to a target promoter. Vascular PXY network; target relevance to MGP biology unverified. Reason: The molecular function (cis-regulatory region binding) is real for MGP, so the term is not wrong. However, this row is a high-throughput Y1H hit in the vascular PXY network with no in planta validation, so it is kept as non-core rather than as evidence for a role in vascular development. Supporting Evidence: PMID:28211915 Our DNA binding assay using this consensus sequence with ZFs of MGP showed high affinity (KD value of 50 nM) for ZF1-4 (all four ZFs) |
| GO:0003700 DNA-binding transcription factor activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of TF activity for the BIRD/IDD clade. Reason: Consistent with MGP-specific DNA-binding data. Supporting Evidence: PMID:28211915 Our DNA binding assay using this consensus sequence with ZFs of MGP showed high affinity (KD value of 50 nM) for ZF1-4 (all four ZFs) |
| GO:0003700 DNA-binding transcription factor activity | IDA PMID:24821766 DELLA protein functions as a transcriptional activator throu... | ACCEPT | Summary: AtIDD3 binds the SCL3 promoter and transactivates it with DELLA. Reason: Direct evidence for DNA-binding TF activity. Supporting Evidence: PMID:24821766 we identified five members of indeterminate domain (IDD) protein family which bind physically to both DELLA and the promoter sequence of the GA-positive regulator SCARECROW-LIKE 3 (SCL3) PMID:24821766 a luciferase reporter controlled by the SCL3 promoter was additively transactivated by REPRESSOR of ga1-3 (RGA) and IDDs |
| GO:0003700 DNA-binding transcription factor activity | IMP PMID:26494755 Transcriptional control of tissue formation throughout root ... | ACCEPT | Summary: BIRD mutant analyses and network reconstruction including MGP. Reason: IMP is an indirect evidence type for an MF, but the activity itself is well supported by biochemistry. Supporting Evidence: PMID:26494755 Expression of cortex-specific markers required at least JKD, MGP, and NUC PMID:28211915 Our DNA binding assay using this consensus sequence with ZFs of MGP showed high affinity (KD value of 50 nM) for ZF1-4 (all four ZFs) |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a... | ACCEPT | Summary: Sequence-similarity inference. Reason: The function is correct for MGP and is independently established by direct DNA-binding and transactivation data (see the IDA rows). PMID:11118137 is a genome-wide transcription factor catalogue. Only its abstract is cached and it does not mention MGP, so the curator's ISS call is accepted on deference to the uncached full text. Supporting Evidence: PMID:28211915 Our DNA binding assay using this consensus sequence with ZFs of MGP showed high affinity (KD value of 50 nM) for ZF1-4 (all four ZFs) |
| GO:0005515 protein binding | IPI PMID:17785527 Arabidopsis JACKDAW and MAGPIE zinc finger proteins delimit ... | MODIFY | Summary: Y2H interaction of MGP with SCR (AT3G54220). Reason: SCR is a GRAS transcription coregulator docking on the MGP zinc fingers as SHR-SCR. Proposed replacements: transcription coregulator binding Supporting Evidence: PMID:28211915 of the four ZFs of MGP and possibly JKD, ZF1, ZF2 and ZF3 are responsible for DNA binding, while ZF3 and ZF4 are involved in SHR binding PMID:17785527 JACKDAW and MAGPIE regulate tissue boundaries and asymmetric cell division and can control SHORT-ROOT and SCARECROW activity in a transcriptional and protein interaction network |
| GO:0005515 protein binding | IPI PMID:17785527 Arabidopsis JACKDAW and MAGPIE zinc finger proteins delimit ... | MODIFY | Summary: Y2H interaction of MGP with SHR (AT4G37650). Reason: SHR-SCR binds MGP ZF3-ZF4 with high affinity; transcription coregulator binding. Proposed replacements: transcription coregulator binding Supporting Evidence: PMID:28211915 relatively high affinity of the SHR-SCR complex to MGP ZF3-ZF4 (the KD value of 36 nM) and JKD ZF3-ZF4 (124 nM) |
| GO:0005515 protein binding | IPI PMID:17785527 Arabidopsis JACKDAW and MAGPIE zinc finger proteins delimit ... | MODIFY | Summary: Y2H interaction of MGP with JKD (AT5G03150). Reason: JKD is a DNA-binding IDD TF; DNA-binding transcription factor binding. JKD and MGP compete for SHR-SCR, so the significance of a direct MGP-JKD interaction in planta is uncertain; non-core. Proposed replacements: DNA-binding transcription factor binding Supporting Evidence: PMID:17785527 JACKDAW and MAGPIE regulate tissue boundaries and asymmetric cell division and can control SHORT-ROOT and SCARECROW activity in a transcriptional and protein interaction network PMID:28211915 suggesting that the binding of JKD and MGP is exclusive |
| GO:0005515 protein binding | IPI PMID:17785527 Arabidopsis JACKDAW and MAGPIE zinc finger proteins delimit ... | MODIFY | Summary: Y2H interaction of MGP with JKD (UniProtKB:Q700D2); duplicate row. Reason: As above. Proposed replacements: DNA-binding transcription factor binding Supporting Evidence: PMID:17785527 JACKDAW and MAGPIE regulate tissue boundaries and asymmetric cell division and can control SHORT-ROOT and SCARECROW activity in a transcriptional and protein interaction network |
| GO:0005515 protein binding | IPI PMID:17785527 Arabidopsis JACKDAW and MAGPIE zinc finger proteins delimit ... | MODIFY | Summary: Y2H interaction of MGP with SCR (UniProtKB:Q9M384). Reason: Transcription coregulator binding (SHR-SCR docking). Proposed replacements: transcription coregulator binding Supporting Evidence: PMID:28211915 GST-MGP was pulled down from a mixture of GST-MGP and the complex between SHR and MBP-SCR |
| GO:0005515 protein binding | IPI PMID:24821766 DELLA protein functions as a transcriptional activator throu... | MODIFY | Summary: Interaction of AtIDD3 with SCL3 (Q9LPR8). Reason: SCL3 is a GRAS coregulator that uses IDDs as DNA-binding scaffolds. Proposed replacements: transcription coregulator binding Supporting Evidence: PMID:24821766 These results suggest that the coregulators DELLA and SCL3, using IDDs as transcriptional scaffolds for DNA binding, antagonistically regulate the expression of their downstream targets to control the GA signaling pathway |
| GO:0005515 protein binding | IPI PMID:24821766 DELLA protein functions as a transcriptional activator throu... | MODIFY | Summary: Interaction of AtIDD3 with DELLA RGA (Q9SLH3). Reason: DELLA acts as a coactivator through IDD DNA binding; transcription coregulator binding. Proposed replacements: transcription coregulator binding Supporting Evidence: PMID:24821766 we identified five members of indeterminate domain (IDD) protein family which bind physically to both DELLA and the promoter sequence of the GA-positive regulator SCARECROW-LIKE 3 (SCL3) PMID:24821766 These results suggest that the coregulators DELLA and SCL3, using IDDs as transcriptional scaffolds for DNA binding, antagonistically regulate the expression of their downstream targets to control the GA signaling pathway |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | REMOVE | Summary: CrY2H-seq interaction of MGP with SCL32 (Q9SN22). Reason: High-throughput binary Y2H; SCL32 is a GRAS protein, so this may reflect the general GRAS-IDD docking mode, but no functional study supports a coregulator role for SCL32 with MGP. Bare protein binding carries no functional information; removal does not imply that the interaction is false. Supporting Evidence: PMID:28650476 uncovering a network of 8,577 interactions among 1,453 transcription factors |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic nuclear inference. Reason: Consistent with MGP function as a TF. Supporting Evidence: PMID:25829440 constraining SHORT-ROOT spread through nuclear retention and transcriptional regulation of key downstream SHORT-ROOT targets, including SCARECROW and CYCLIND6 PMID:28211915 of the four ZFs of MGP and possibly JKD, ZF1, ZF2 and ZF3 are responsible for DNA binding, while ZF3 and ZF4 are involved in SHR binding |
| GO:0005634 nucleus | IDA PMID:17785527 Arabidopsis JACKDAW and MAGPIE zinc finger proteins delimit ... | ACCEPT | Summary: Nuclear MGP fusion protein. Reason: Nuclear localization is consistent with MGP's TF function. PMID:17785527 is abstract-only in the cache, and the abstract does not describe localization, so the curator's IDA is accepted on deference to the uncached full text. |
| GO:0005634 nucleus | IDA PMID:24821766 DELLA protein functions as a transcriptional activator throu... | ACCEPT | Summary: Nuclear AtIDD3. Reason: Consistent with TF function. Supporting Evidence: PMID:24821766 These results suggest that the coregulators DELLA and SCL3, using IDDs as transcriptional scaffolds for DNA binding, antagonistically regulate the expression of their downstream targets to control the GA signaling pathway |
| GO:0005634 nucleus | IDA PMID:26494755 Transcriptional control of tissue formation throughout root ... | ACCEPT | Summary: Nuclear MGP in ground tissue. Reason: Consistent with TF function. Supporting Evidence: PMID:26494755 JKD and BALD-IBIS regulate SHR movement by promoting its nuclear retention, and cooperatively with MAGPIE (MGP) and NUTCRACKER (NUC) are required for the formative divisions that pattern the ground tissue into cortex and endodermis |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular location mapping. Reason: Corroborated experimentally. Supporting Evidence: PMID:25829440 constraining SHORT-ROOT spread through nuclear retention and transcriptional regulation of key downstream SHORT-ROOT targets, including SCARECROW and CYCLIND6 PMID:28211915 of the four ZFs of MGP and possibly JKD, ZF1, ZF2 and ZF3 are responsible for DNA binding, while ZF3 and ZF4 are involved in SHR binding |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: AtSubP prediction. Reason: Corroborated experimentally. Supporting Evidence: PMID:25829440 constraining SHORT-ROOT spread through nuclear retention and transcriptional regulation of key downstream SHORT-ROOT targets, including SCARECROW and CYCLIND6 PMID:28211915 of the four ZFs of MGP and possibly JKD, ZF1, ZF2 and ZF3 are responsible for DNA binding, while ZF3 and ZF4 are involved in SHR binding |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA electronic inference. Reason: Correct general process for an IDD TF. Supporting Evidence: PMID:24821766 a luciferase reporter controlled by the SCL3 promoter was additively transactivated by REPRESSOR of ga1-3 (RGA) and IDDs |
| GO:0006355 regulation of DNA-templated transcription | TAS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a... | ACCEPT | Summary: Genome-wide TF survey statement. Reason: Correct but general. The source (PMID:11118137) is a genome-wide transcription factor catalogue whose cached abstract does not mention MGP, so the TAS is accepted on deference. MGP-specific support for transcriptional regulation is cited below. Supporting Evidence: PMID:24821766 a luciferase reporter controlled by the SCL3 promoter was additively transactivated by REPRESSOR of ga1-3 (RGA) and IDDs |
| GO:0008356 asymmetric cell division | IMP PMID:26494755 Transcriptional control of tissue formation throughout root ... | ACCEPT | Summary: BIRD combinations including mgp disrupt the formative asymmetric divisions of the ground tissue. Reason: MGP contributes as a DNA-binding partner of SHR-SCR; acts_upstream_of_or_within is appropriate. Core role, partly redundant with other BIRDs. Supporting Evidence: PMID:26494755 JKD and BALD-IBIS regulate SHR movement by promoting its nuclear retention, and cooperatively with MAGPIE (MGP) and NUTCRACKER (NUC) are required for the formative divisions that pattern the ground tissue into cortex and endodermis PMID:17785527 JACKDAW and MAGPIE regulate tissue boundaries and asymmetric cell division and can control SHORT-ROOT and SCARECROW activity in a transcriptional and protein interaction network |
| GO:0009939 positive regulation of gibberellic acid mediated signaling pathway | IMP PMID:24821766 DELLA protein functions as a transcriptional activator throu... | KEEP AS NON CORE | Summary: IDD3-SRDX dominant-repressor plants show a GA-deficient phenotype. Reason: Supported by a dominant-repressor fusion rather than a loss-of-function allele and peripheral to the root patterning role. Supporting Evidence: PMID:24821766 supported the possibility that AtIDD3 is positively involved in GA signaling |
| GO:0010075 regulation of meristem growth | IMP PMID:25829440 Arabidopsis BIRD Zinc Finger Proteins Jointly Stabilize Tiss... | KEEP AS NON CORE | Summary: BIRD mutant combinations affect meristem maintenance. Reason: Downstream phenotype; abstract-only cache. Supporting Evidence: PMID:25829440 BIRD proteins promote formative divisions and tissue specification in the Arabidopsis thaliana root meristem ground tissue by tethering and regulating transcriptional competence of SHORT-ROOT complexes |
| GO:0034504 protein localization to nucleus | IMP PMID:25829440 Arabidopsis BIRD Zinc Finger Proteins Jointly Stabilize Tiss... | KEEP AS NON CORE | Summary: BIRD proteins are required for nuclear retention of SHR. Reason: Shown for BIRDs jointly; JKD and BIB are the main SHR-retaining BIRDs while MGP contributes via SHR-SCR binding. Abstract-only cache; accepted as a contributing, non-core role. Supporting Evidence: PMID:25829440 constraining SHORT-ROOT spread through nuclear retention and transcriptional regulation of key downstream SHORT-ROOT targets, including SCARECROW and CYCLIND6 PMID:26494755 JKD and BALD-IBIS regulate SHR movement by promoting its nuclear retention, and cooperatively with MAGPIE (MGP) and NUTCRACKER (NUC) are required for the formative divisions that pattern the ground tissue into cortex and endodermis |
| GO:0043565 sequence-specific DNA binding | IDA PMID:24821766 DELLA protein functions as a transcriptional activator throu... | ACCEPT | Summary: AtIDD3 binds the SCL3 promoter. Reason: Sequence-specific DNA binding, also shown by fluorescence polarization. Supporting Evidence: PMID:24821766 we identified five members of indeterminate domain (IDD) protein family which bind physically to both DELLA and the promoter sequence of the GA-positive regulator SCARECROW-LIKE 3 (SCL3) PMID:28211915 Our DNA binding assay using this consensus sequence with ZFs of MGP showed high affinity (KD value of 50 nM) for ZF1-4 (all four ZFs) |
| GO:0045893 positive regulation of DNA-templated transcription | IDA PMID:24821766 DELLA protein functions as a transcriptional activator throu... | ACCEPT | Summary: IDDs transactivate the SCL3 promoter with RGA. Reason: Supported. Supporting Evidence: PMID:24821766 a luciferase reporter controlled by the SCL3 promoter was additively transactivated by REPRESSOR of ga1-3 (RGA) and IDDs |
| GO:0048364 root development | IGI PMID:26494755 Transcriptional control of tissue formation throughout root ... | KEEP AS NON CORE | Summary: Higher-order BIRD mutants lose ground tissue identity markers. Reason: Correct but broad; root radial pattern formation is the specific role. Supporting Evidence: PMID:26494755 Expression of cortex-specific markers required at least JKD, MGP, and NUC |
| GO:0090057 root radial pattern formation | IGI PMID:26494755 Transcriptional control of tissue formation throughout root ... | NEW | Summary: MGP, with JKD and NUC, is required for cortex marker expression and ground-tissue patterning. Reason: MGP performs a molecular step of the process as a DNA-binding partner of SHR-SCR; comparator SHR/SCR carry radial patterning terms. Specific term preferred over root development. Supporting Evidence: PMID:26494755 Expression of cortex-specific markers required at least JKD, MGP, and NUC PMID:26494755 JKD and BALD-IBIS regulate SHR movement by promoting its nuclear retention, and cooperatively with MAGPIE (MGP) and NUTCRACKER (NUC) are required for the formative divisions that pattern the ground tissue into cortex and endodermis |
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Download this section (compressed HTML)Q: Which target promoters distinguish MGP-SHR-SCR from JKD-SHR-SCR complexes, given that the two BIRDs bind SHR-SCR mutually exclusively?
Q: Is the GA-signalling role of IDD3 (with DELLA/SCL3) relevant to middle-cortex formation in the root ground tissue?
Experiment: ChIP-seq of MGP in wild type and shr backgrounds to define SHR-dependent versus SHR-independent MGP targets.
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