SHR

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005634 nucleus	IEA GO_REF:0000044	ACCEPT	Summary: SHR enters the nucleus of the stele and of the adjacent endodermal cell layer, where it functions in transcriptional regulation. Nuclear localization is core to function. Reason: Nuclear localization is well established experimentally and is the compartment where SHR exerts its transcriptional regulatory function. The IEA from the Swiss-Prot subcellular location mapping is corroborated by direct experimental evidence. Supporting Evidence: PMID:11565032 the SHR protein, a putative transcription factor, moves from the stele to a single layer of adjacent cells, where it enters the nucleus.
GO:0005737 cytoplasm	IEA GO_REF:0000044	ACCEPT	Summary: SHR is present in the cytoplasm of stele cells, and a cytoplasmic pool is required for its intercellular movement. Reason: Cytoplasmic localization is experimentally documented and is mechanistically important for SHR trafficking, although the cytoplasm is not where SHR exerts its transcriptional function. Supporting Evidence: PMID:15498493 SHR must be present in the cytoplasm to move, providing evidence that SHR movement is regulated.
GO:0005769 early endosome	IEA GO_REF:0000044	KEEP AS NON CORE	Summary: SHR associates with early endosomes in a SIEL-dependent manner as part of its intercellular trafficking machinery, not as a site of transcriptional function. Reason: Endosomal localization is real and experimentally supported, but it reflects the cell-to-cell movement route of SHR rather than its core nuclear transcriptional function. Supporting Evidence: PMID:25124761 in the cytoplasm of root or leaf cells, SHR localizes to endosomes in a SIEL-dependent manner. Interference of early and late endosomes disrupts intercellular movement of SHR.
GO:0005770 late endosome	IEA GO_REF:0000044	KEEP AS NON CORE	Summary: SHR is found on late endosomes; perturbing late endosomes disrupts SHR intercellular movement. Reason: Part of the endomembrane trafficking route enabling SHR movement, not a core functional compartment. Supporting Evidence: PMID:25124761 Interference of early and late endosomes disrupts intercellular movement of SHR.
GO:0006355 regulation of DNA-templated transcription	IEA GO_REF:0000108	ACCEPT	Summary: SHR is a transcriptional regulator that controls expression of SCR and other downstream genes (MGP, NUC, SCL3) within its expression/movement domain. Reason: This IBA/inference-level BP term captures the core function of SHR at an appropriate level of specificity. SHR regulates transcription, whether acting as a direct cofactor in complexes with IDD TFs. Supporting Evidence: PMID:16640459 this demonstrates that SHR has transcription factor activity and, most important, confirms that at least four of the eight direct targets identified by the meta-analysis are directly bound by SHR in vivo. file:ARATH/SHR/SHR-deep-research-falcon.md of developmental regulators and cell-cycle components in recipient cells, often in partnership with SCR and other factors.
GO:0055037 recycling endosome	IEA GO_REF:0000044	KEEP AS NON CORE	Summary: SHR is detected on recycling endosomes as part of its endomembrane-dependent trafficking. Reason: Trafficking-related localization, not a core functional compartment. Supporting Evidence: PMID:25124761 in the cytoplasm of root or leaf cells, SHR localizes to endosomes in a SIEL-dependent manner.
GO:0005515 protein binding	IPI PMID:17446396 An evolutionarily conserved mechanism delimiting SHR movemen...	MODIFY	Summary: SHR interacts directly with SCARECROW (SCR); SCR sequesters SHR into the nucleus through this protein-protein interaction, delimiting SHR movement. Reason: Bare "protein binding" is uninformative. The SHR-SCR interaction is a defining GRAS-GRAS heterodimerization central to SHR function. Replace with a protein dimerization term capturing the SCR heterodimer. Proposed replacements: protein dimerization activity Supporting Evidence: PMID:17446396 SCARECROW (SCR) blocks SHR movement by sequestering it into the nucleus through protein-protein interaction.
GO:0005515 protein binding	IPI PMID:17785527 Arabidopsis JACKDAW and MAGPIE zinc finger proteins delimit ...	MODIFY	Summary: SHR interacts with the BIRD/IDD zinc-finger transcription factors JACKDAW (JKD, AT1G03840) and MAGPIE (MGP, AT5G03150), which restrict SHR/SCR range of action and provide DNA-binding specificity. Reason: The partners JKD and MGP are DNA-binding zinc-finger transcription factors; SHR acts as a transcriptional cofactor recruited by them. The informative MF is DNA-binding transcription factor binding rather than bare protein binding. Proposed replacements: DNA-binding transcription factor binding Supporting Evidence: PMID:17785527 JACKDAW and MAGPIE genes, which encode members of a plant-specific family of zinc finger proteins, act in a SHR-dependent feed-forward loop to regulate the range of action of SHORT-ROOT and SCARECROW.
GO:0005515 protein binding	IPI PMID:18500650 Large-scale analysis of the GRAS gene family in Arabidopsis ...	MODIFY	Summary: Yeast two-hybrid confirmed the SHR-SCR interaction and identified SCARECROW-LIKE23 (SCL23) as a new SHR-interacting GRAS protein. Reason: The interaction is GRAS-GRAS heterodimerization (SCR, SCL23). Replace bare protein binding with protein dimerization activity. Proposed replacements: protein dimerization activity Supporting Evidence: PMID:18500650 we confirmed the protein-protein interaction between SHORT-ROOT (SHR) and SCARECROW (SCR). Furthermore, we identified a new SHR-interacting protein, SCARECROW-LIKE23 (SCL23). file:ARATH/SHR/SHR-deep-research-falcon.md and contribute redundantly with SCR to endodermal fate specification.
GO:0005515 protein binding	IPI PMID:22921914 A bistable circuit involving SCARECROW-RETINOBLASTOMA integr...	MODIFY	Summary: SHR partners with SCR to transcriptionally control CYCLIND6;1 within a bistable circuit that informs asymmetric stem cell division (IntAct partner = SCR, Q9M384). Reason: The interaction is the SHR-SCR heterodimer. Replace bare protein binding with protein dimerization activity. Proposed replacements: protein dimerization activity Supporting Evidence: PMID:22921914 This cyclin is itself under transcriptional control of SCR and its partner SHORT ROOT (SHR), creating a robust bistable
GO:0060586 multicellular organismal-level iron ion homeostasis	IMP PMID:19726572 Identification of the endodermal vacuole as the iron storage...	KEEP AS NON CORE	Summary: The cited paper identifies the endodermal vacuole as the embryo iron storage compartment but does not experimentally study SHR; any link to SHR is indirect, via SHR's role in specifying the endodermis. Reason: The reference does not report a direct SHR experiment for iron homeostasis; iron storage in the endodermis is a downstream physiological consequence of SHR-dependent endodermis specification rather than a core molecular role of SHR. Retained as a peripheral, indirect process. Supporting Evidence: PMID:19726572 We have thus unambiguously shown that in dry seeds Fe is primarily stored in the endodermis cell layer, within the vacuoles, from which it is remobilized during germination.
GO:0000976 transcription cis-regulatory region binding	IPI PMID:25533953 An Arabidopsis gene regulatory network for secondary cell wa...	KEEP AS NON CORE	Summary: In an enhanced yeast-one-hybrid secondary-cell-wall gene regulatory network, SHR scored as binding the promoter/cis-regulatory regions of several genes (AT2G40890, AT5G15630, AT5G17420). Reason: Y1H detects promoter association in a heterologous yeast system. Given structural evidence that GRAS proteins including SHR have no detectable direct DNA-binding activity and act as cofactors recruited by IDD transcription factors, this association is most plausibly indirect/context-dependent and is not part of SHR's core endodermis-patterning role. Kept as non-core with this caveat. Supporting Evidence: PMID:25533953 Yeast one-hybrid (Y1H) protein-DNA interaction assays PMID:28211915 there is no evidence for direct binding of SHR-SCR or other GRAS proteins to DNA.
GO:0005634 nucleus	EXP PMID:15498493 Mechanisms regulating SHORT-ROOT intercellular movement.	ACCEPT	Summary: SHR localizes to the nucleus; subcellular partitioning between cytoplasm and nucleus is intrinsic to the protein and regulated. Reason: Direct experimental evidence for nuclear localization, the core functional compartment. Supporting Evidence: PMID:15498493 subcellular localization of SHR in the stele is intrinsic to the SHR protein.
GO:0005634 nucleus	EXP PMID:25124761 The movement of the non-cell-autonomous transcription factor...	ACCEPT	Summary: SHR is found in the nucleus in addition to cytoplasm/endosomes during its trafficking and function. Reason: Direct experimental support for the core nuclear localization. Supporting Evidence: PMID:25124761 The movement of the non-cell-autonomous transcription factor, SHORT-ROOT relies on the endomembrane system.
GO:0005737 cytoplasm	EXP PMID:11565032 Intercellular movement of the putative transcription factor ...	ACCEPT	Summary: SHR is present in the cytoplasm of stele cells prior to and during its intercellular movement. Reason: Direct experimental evidence; cytoplasmic localization is part of the trafficking route. Supporting Evidence: PMID:11565032 SHR protein, a putative transcription factor, moves from the stele to a single layer of adjacent cells, where it enters the nucleus.
GO:0005737 cytoplasm	EXP PMID:15498493 Mechanisms regulating SHORT-ROOT intercellular movement.	ACCEPT	Summary: A cytoplasmic pool of SHR is required for and regulated during its cell-to-cell movement. Reason: Direct experimental evidence for cytoplasmic localization. Supporting Evidence: PMID:15498493 SHR must be present in the cytoplasm to move.
GO:0005737 cytoplasm	EXP PMID:25124761 The movement of the non-cell-autonomous transcription factor...	ACCEPT	Summary: SHR localizes to the cytoplasm, where it associates with endosomes during SIEL-dependent trafficking. Reason: Direct experimental evidence for cytoplasmic localization. Supporting Evidence: PMID:25124761 in the cytoplasm of root or leaf cells, SHR localizes to endosomes in a SIEL-dependent manner.
GO:0005769 early endosome	EXP PMID:25124761 The movement of the non-cell-autonomous transcription factor...	KEEP AS NON CORE	Summary: SHR associates with early endosomes during its endomembrane-dependent intercellular movement. Reason: Trafficking-related localization rather than a core functional compartment. Supporting Evidence: PMID:25124761 in the cytoplasm of root or leaf cells, SHR localizes to endosomes in a SIEL-dependent manner. Interference of early and late endosomes disrupts intercellular movement of SHR.
GO:0005770 late endosome	EXP PMID:25124761 The movement of the non-cell-autonomous transcription factor...	KEEP AS NON CORE	Summary: SHR localizes to late endosomes; disrupting late endosomes impairs SHR movement. Reason: Trafficking-related localization rather than a core functional compartment. Supporting Evidence: PMID:25124761 Interference of early and late endosomes disrupts intercellular movement of SHR.
GO:0055037 recycling endosome	EXP PMID:25124761 The movement of the non-cell-autonomous transcription factor...	KEEP AS NON CORE	Summary: SHR is detected on recycling endosomes within the endomembrane system required for its movement. Reason: Trafficking-related localization rather than a core functional compartment. Supporting Evidence: PMID:25124761 The movement of the non-cell-autonomous transcription factor, SHORT-ROOT relies on the endomembrane system.
GO:0005634 nucleus	ISM GO_REF:0000122	ACCEPT	Summary: Computational (AtSubP) prediction of nuclear localization, consistent with abundant experimental evidence. Reason: Predicted nuclear localization agrees with direct experimental data; nucleus is the core functional compartment. Supporting Evidence: PMID:11565032 moves from the stele to a single layer of adjacent cells, where it enters the nucleus.
GO:0005515 protein binding	IPI PMID:28211915 Structure of the SHR-SCR heterodimer bound to the BIRD/IDD t...	MODIFY	Summary: Crystal structures show SHR forms a head-to-head GRAS-domain heterodimer with SCR (Q9M384) and that the SHR-SCR dimer binds the zinc fingers of the BIRD/IDD transcription factor JKD/IDD10 (Q700D2); SHR-SCR act as transcriptional cofactors recruited by IDD TFs. Reason: Bare protein binding is uninformative for this load-bearing interaction. The interaction with the DNA-binding IDD factor JKD makes DNA-binding transcription factor binding the most informative MF; the SCR partner is captured separately as dimerization. Proposed replacements: DNA-binding transcription factor binding Supporting Evidence: PMID:28211915 These results suggest that SHR-SCR are transcriptional cofactors that regulate target gene transcription via binding of SHR to BIRD transcription factors. PMID:28211915 SHR and SCR... form a head-to-head 1:1 heterodimer
GO:0005515 protein binding	IPI PMID:28746306 In vivo FRET-FLIM reveals cell-type-specific protein interac...	MODIFY	Summary: In vivo FRET-FLIM shows SHR forms cell-type-specific complexes with SCR and JKD in Arabidopsis roots, including higher-order complexes whose conformation tunes target-gene regulation. Reason: The interactions are with SCR (GRAS) and JKD (a DNA-binding IDD TF). Replace bare protein binding with DNA-binding transcription factor binding, capturing the functionally important IDD interaction. Proposed replacements: DNA-binding transcription factor binding Supporting Evidence: PMID:28746306 three fully functional fluorescently tagged cell fate regulators establish cell-type-specific interactions at endogenous expression levels and can form higher order complexes. file:ARATH/SHR/SHR-deep-research-falcon.md report that SHR and its network TFs (SCR, SCL23, JKD) are expressed in distinct but overlapping shoot domains, can physically interact
GO:0005634 nucleus	IDA PMID:24517883 SCARECROW, SCR-LIKE 23 and SHORT-ROOT control bundle sheath ...	ACCEPT	Summary: SHR moves into bundle-sheath cells of leaves and localizes to the nucleus, where it directly regulates SCR and SCL23 expression. Reason: Direct experimental evidence (IDA) for nuclear localization, the core functional compartment, in a leaf context. Supporting Evidence: PMID:24517883 the SHR protein moves into the BS cells, where it directly regulates SCR and SCL23 expression.
GO:0048366 leaf development	IMP PMID:24517883 SCARECROW, SCR-LIKE 23 and SHORT-ROOT control bundle sheath ...	KEEP AS NON CORE	Summary: SHR is essential for bundle-sheath cell-fate specification in leaves, moving into BS cells to regulate SCR and SCL23. Reason: A genuine but peripheral developmental role distinct from SHR's core root ground-tissue patterning function. Supported by mutant analysis. Supporting Evidence: PMID:24517883 SHR is also essential for BS cell-fate specification, but it is expressed in the central vascular tissue. However, the SHR protein moves into the BS cells, where it directly regulates SCR and SCL23 expression. file:ARATH/SHR/SHR-deep-research-falcon.md implying intercellular movement from inner to outer layers in developing lateral organ primordia.
GO:0045930 negative regulation of mitotic cell cycle	IMP PMID:20739610 SHORT-ROOT and SCARECROW regulate leaf growth in Arabidopsis...	MODIFY	Summary: In leaves SHR (with SCR) promotes cell proliferation by stimulating S-phase progression (presumably via stimulation of E2F action); shr/scr mutants show reduced division rate. This is a positive, not negative, regulation of the mitotic cell cycle. Reason: The "negative regulation of mitotic cell cycle" term directly contradicts the cited evidence. The paper reports that SHR/SCR stimulate S-phase progression and act as general positive regulators of cell proliferation in leaves; loss of SHR/SCR reduces division. The correct direction is positive regulation. This leaf cell-proliferation role is peripheral to SHR's core root patterning function but should be represented with the correct (positive) term. Proposed replacements: positive regulation of mitotic cell cycle Supporting Evidence: PMID:20739610 SHR and SCR primarily function as general regulators of cell proliferation in leaves... primarily drive S-phase progression, presumably by a stimulation of E2F action.
GO:0048366 leaf development	IMP PMID:20739610 SHORT-ROOT and SCARECROW regulate leaf growth in Arabidopsis...	KEEP AS NON CORE	Summary: SHR and SCR are required for normal leaf growth, acting directly in the shoot to control proliferative cell division. Reason: Genuine but peripheral developmental role relative to the core root ground-tissue patterning function. Supporting Evidence: PMID:20739610 this is a direct consequence of the lack of SHR and SCR function in the shoot rather than an indirect consequence of compromised root growth.
GO:0003700 DNA-binding transcription factor activity	TAS PMID:16640459 Whole-genome analysis of the SHORT-ROOT developmental pathwa...	MODIFY	Summary: SHR was inferred to have transcription factor activity from in vivo ChIP promoter occupancy and inducible-activation experiments. However, the SHR-SCR structure shows no direct DNA-binding activity; SHR is a transcriptional cofactor recruited to promoters by DNA-binding IDD transcription factors. Reason: GRAS proteins including SHR have no detectable direct/sequence-specific DNA binding and act via protein complexes with IDD zinc-finger TFs. The ChIP occupancy that supported "transcription factor activity" is consistent with indirect recruitment. The accurate MF is transcription coregulator activity. Proposed replacements: transcription coregulator activity Supporting Evidence: PMID:28211915 there is no evidence for direct binding of SHR-SCR or other GRAS proteins to DNA. We did not find any DNA-binding motifs in our structure of the SHR-SCR complex PMID:28211915 These results suggest that SHR-SCR are transcriptional cofactors that regulate target gene transcription via binding of SHR to BIRD transcription factors.
GO:0032350 regulation of hormone metabolic process	NAS PMID:16640459 Whole-genome analysis of the SHORT-ROOT developmental pathwa...	KEEP AS NON CORE	Summary: The SHR developmental pathway intersects gibberellin, brassinosteroid and auxin pathways via indirect targets (e.g. SNE, BR6ox2), suggesting SHR influences hormone metabolism/signaling indirectly. Reason: NAS-level, indirect downstream effect of the SHR transcriptional network rather than a core molecular role. Retained as peripheral. Supporting Evidence: PMID:16640459 the SHR pathway regulates root development not only through a large transcription regulatory network but also through hormonal pathways and signaling pathways using receptor-like kinases.
GO:0043565 sequence-specific DNA binding	IDA PMID:16640459 Whole-genome analysis of the SHORT-ROOT developmental pathwa...	MARK AS OVER ANNOTATED	Summary: This IDA derives from in vivo ChIP showing SHR occupancy at target promoters (SCR, MGP, NUC, TRI). ChIP detects promoter occupancy but not direct sequence-specific contact; the SHR-SCR structure shows no direct DNA binding. Reason: SHR has no demonstrated direct or sequence-specific DNA-binding activity; structural data establish that DNA contact in SHR-SCR-IDD complexes is provided by the IDD zinc fingers, not SHR. The in vivo promoter occupancy is best explained by indirect recruitment. If retained at all, a coregulator/TF-binding MF is more accurate. Proposed replacements: transcription coregulator activity Supporting Evidence: PMID:28211915 there is no evidence for direct binding of SHR-SCR or other GRAS proteins to DNA. PMID:16640459 Binding of SHR to four of the eight promoter regions was confirmed in vivo using chromatin immunoprecipitation (ChIP)
GO:0043565 sequence-specific DNA binding	IDA PMID:17446396 An evolutionarily conserved mechanism delimiting SHR movemen...	MARK AS OVER ANNOTATED	Summary: SHR occupancy/regulation at the SCR promoter (positive feedback loop) underlies this annotation, but the interaction with DNA is not direct; SHR acts via SCR and IDD partners. Reason: As for the other sequence-specific DNA binding annotation, structural evidence shows SHR does not bind DNA directly. The functional role is transcriptional coregulation through protein complexes. Proposed replacements: transcription coregulator activity Supporting Evidence: PMID:28211915 there is no evidence for direct binding of SHR-SCR or other GRAS proteins to DNA. PMID:17446396 a safeguard mechanism that relies on a SHR/SCR-dependent positive feedback loop for SCR transcription.
GO:0009956 radial pattern formation	IMP PMID:10850497 The SHORT-ROOT gene controls radial patterning of the Arabid...	ACCEPT	Summary: SHR is required for radial patterning of the Arabidopsis root, controlling ground-tissue formation and endodermis specification; shr mutants lose the longitudinal CEI-daughter division and have a single mixed-identity ground tissue layer. Reason: This is a core developmental output of SHR, strongly supported by the foundational mutant and ectopic-expression analyses. Supporting Evidence: PMID:10850497 The SHORT-ROOT (SHR) gene is required for the asymmetric cell division responsible for formation of ground tissue (endodermis and cortex) as well as specification of endodermis in the Arabidopsis root. file:ARATH/SHR/SHR-deep-research-falcon.md Loss-of-function shr mutants show characteristic defects including loss of correct ground tissue layering (single layer instead of cortex+endodermis) and stem-cell niche abnormalities.
GO:0003700 DNA-binding transcription factor activity	ISS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a...	MODIFY	Summary: This ISS reflects classification of SHR as a GRAS-family transcription factor in a genome-wide TF survey. SHR is a transcriptional regulator, but experimental/structural work shows it acts as a cofactor without direct DNA binding. Reason: The sequence-similarity-based assignment of direct DNA-binding TF activity is not supported by the structure of SHR; transcription coregulator activity is the accurate MF for this GRAS protein. Proposed replacements: transcription coregulator activity Supporting Evidence: PMID:28211915 These results suggest that SHR-SCR are transcriptional cofactors that regulate target gene transcription via binding of SHR to BIRD transcription factors.
GO:0005634 nucleus	IDA PMID:11565032 Intercellular movement of the putative transcription factor ...	ACCEPT	Summary: Direct observation that SHR enters the nucleus of cells adjacent to the stele. Reason: Direct experimental evidence for nuclear localization, the core functional compartment. Supporting Evidence: PMID:11565032 moves from the stele to a single layer of adjacent cells, where it enters the nucleus. file:ARATH/SHR/SHR-deep-research-falcon.md SHR is synthesized in one tissue domain but acts in neighboring cells after intercellular movement through plasmodesmata, thereby delivering positional information.
GO:0008356 asymmetric cell division	IMP PMID:10850497 The SHORT-ROOT gene controls radial patterning of the Arabid...	ACCEPT	Summary: SHR is required for the asymmetric (formative) division of the cortex/endodermis initial that generates the separate endodermal and cortical layers. Reason: Core developmental function strongly supported by mutant analysis; this asymmetric division is a defining SHR phenotype. Supporting Evidence: PMID:10850497 The SHORT-ROOT (SHR) gene is required for the asymmetric cell division responsible for formation of ground tissue (endodermis and cortex) file:ARATH/SHR/SHR-deep-research-falcon.md trigger the formative (asymmetric) division that generates separate cortex and endodermis lineages.
GO:0003700 DNA-binding transcription factor activity	ISS PMID:10850497 The SHORT-ROOT gene controls radial patterning of the Arabid...	MODIFY	Summary: SHR was originally described as a "putative transcription factor" based on GRAS homology to SCR. Subsequent structural work shows GRAS proteins act as cofactors without direct DNA binding. Reason: The early putative-TF assignment is superseded by structural evidence that SHR is a transcription cofactor recruited by DNA-binding IDD TFs. Transcription coregulator activity is the accurate MF. Proposed replacements: transcription coregulator activity Supporting Evidence: PMID:10850497 SHR encodes a putative transcription factor with homology to SCARECROW (SCR). PMID:28211915 there is no evidence for direct binding of SHR-SCR or other GRAS proteins to DNA.

Gene Description

Proposed New Ontology Terms

regulated intercellular movement of transcription factor via plasmodesmata

Existing Annotations Review

Core Functions

Acts as a transcriptional coregulator/cofactor that, in a GRAS-domain heterodimer with SCARECROW (SCR), is recruited to target promoters by DNA-binding BIRD/IDD zinc-finger transcription factors (e.g. JKD, MGP) to control transcription of SCR and downstream ground-tissue patterning genes.

Heterodimerizes with the GRAS protein SCARECROW through its GRAS-domain alpha-helical cap; this interaction sequesters SHR in the nucleus, restricts its movement to a single endodermal layer, and is required for the SHR/SCR feedback loop and ground-tissue patterning.

Binds the zinc fingers of BIRD/IDD DNA-binding transcription factors (JKD/IDD10, MGP/IDD3), which provide the sequence-specific DNA contact, enabling the SHR-SCR complex to regulate ground-tissue and quiescent-centre patterning genes.

References

Suggested Questions for Experts

Deep Research

Falcon

📚 Additional Documentation

Notes

📄 View Raw YAML