SHORT VEGETATIVE PHASE (SVP/AGL22; At2g22540) encodes a nuclear MIKC-type MADS-box transcription factor in Arabidopsis thaliana. The protein has a conserved N-terminal MADS DNA-binding domain and a K-box domain typical of plant MADS transcription factors that form homo- and heteromeric regulatory complexes. The best-supported role of SVP is repression of the floral transition and early floral developmental programs through RNA polymerase II-dependent transcriptional regulation. SVP binds CArG-containing cis-regulatory regions at floral regulator genes such as FT and TFS1 and acts with partner MADS proteins, including FLC, FLM, and AP1, and with SEU/LUG corepressor-associated complexes in context-dependent transcriptional repression. Genetic and expression evidence place SVP in ambient-temperature, circadian/light, and vernalization-linked flowering-time networks, but these developmental and environmental phenotypes are downstream consequences of its core nuclear transcription factor activity rather than separate biochemical activities.
Definition: Any process that decreases the rate, frequency, or extent of the transition of a shoot apical meristem from vegetative to reproductive development.
Justification: SVP literature repeatedly describes repression of the floral transition, which is more specific than negative regulation of flower development but is not represented by a specific negative-regulation child term in the local GO cache.
Parent term: negative regulation of flower development
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0009266 response to temperature stimulus | IMP PMID:17322399 Role of SVP in the control of flowering time by ambient temp... | KEEP AS NON CORE | Summary: SVP is experimentally involved in ambient-temperature control of flowering; svp mutants show altered temperature responsiveness and later work places SVP-FLM-beta complex abundance in thermosensory flowering. Reason: The annotation is biologically supported, but it describes the environmental pathway context rather than SVP's core biochemical activity. The core function is nuclear transcriptional repression of floral regulators. |
| GO:0009910 negative regulation of flower development | IMP PMID:10758486 Molecular cloning of SVP: a negative regulator of the floral... | ACCEPT | Summary: The source identifies SVP as a repressor of the floral transition; svp loss-of-function plants flower early. The GO term is broader than the best biological description but captures the negative regulatory direction. Reason: Retain as a supported core biological process annotation, while noting that a more specific term for negative regulation of the vegetative-to-reproductive meristem transition would better capture the evidence. Supporting Evidence: |
| GO:0045892 negative regulation of DNA-templated transcription | IDA PMID:17322399 Role of SVP in the control of flowering time by ambient temp... | MODIFY | Summary: SVP directly represses FT expression through CArG-motif binding, so the negative transcriptional regulation call is correct but should be made RNA polymerase II-specific for a plant protein-coding target gene. Reason: GO:0000122 is the more precise current term for SVP-mediated repression of protein-coding floral regulator transcription. Proposed replacements: negative regulation of transcription by RNA polymerase II Supporting Evidence: |
| GO:0000900 mRNA regulatory element binding translation repressor activity | IDA PMID:17322399 Role of SVP in the control of flowering time by ambient temp... | MODIFY | Summary: The cited SVP paper supports transcriptional repression of FT through DNA binding, not mRNA binding or translational repression. Reason: Replace this misleading molecular function with the RNA polymerase II-specific DNA-binding transcription factor activity supported by SVP's MADS domain and the direct FT regulatory evidence. This is an upstream TAIR/GOA mechanistic-level annotation error: the PMID:17322399 experiment supports CArG-box DNA binding and transcriptional repression, not mRNA regulatory element binding or translational repression. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific |
| GO:0000977 RNA polymerase II transcription regulatory region sequence-specific DNA binding | IEA GO_REF:0000002 | ACCEPT | Summary: SVP has a conserved MADS DNA-binding domain and experimental evidence for CArG-motif binding at floral regulator loci. The electronic InterPro assignment is consistent with this core molecular function. Reason: Retain as a valid cis-regulatory DNA-binding molecular function, while relying on more specific RNA polymerase II transcription factor terms for the synthesized core function. Supporting Evidence: GO_REF:0000002 file:interpro/panther/PTHR48019/PTHR48019-metadata.yaml |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of RNA polymerase II cis-regulatory DNA binding is appropriate for SVP, a MIKC-type MADS transcription factor with direct CArG-site binding evidence at target loci. Reason: The term is specific enough for conserved MADS-box DNA binding and is corroborated by Arabidopsis experimental data. |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | MODIFY | Summary: SVP binds DNA as a MADS-box transcription factor, but generic DNA binding is less informative than cis-regulatory, RNA polymerase II-related DNA binding. Reason: Replace the broad parent term with the more specific cis-regulatory region sequence-specific DNA-binding term supported by SVP biology. Proposed replacements: RNA polymerase II cis-regulatory region sequence-specific DNA binding |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | MODIFY | Summary: SVP is a DNA-binding transcription factor, but GO:0003700 is broader than the RNA polymerase II-specific activity appropriate for a plant MADS-box regulator. Reason: Use the more specific RNA polymerase II-specific DNA-binding transcription factor activity term. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: GO_REF:0000002 file:ARATH/SVP/SVP-uniprot.txt |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:10758486 Molecular cloning of SVP: a negative regulator of the floral... | MODIFY | Summary: The original cloning paper supports SVP as a MADS-box transcription factor, but the annotation should use the more specific RNA polymerase II-specific TF activity term. Reason: The protein acts on nuclear protein-coding gene expression through a MADS DNA-binding domain, making GO:0000981 the better replacement. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: |
| GO:0003700 DNA-binding transcription factor activity | TAS PMID:10758486 Molecular cloning of SVP: a negative regulator of the floral... | MODIFY | Summary: The traceable author statement supports SVP as a MADS-box transcription factor, but the term should be modernized to the RNA polymerase II-specific child term. Reason: GO:0000981 better captures the same SVP molecular function with current GO specificity. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a... | MODIFY | Summary: This genome-wide Arabidopsis transcription factor paper provides broad family context rather than SVP-specific experimentation. SVP's independent local evidence still supports a more specific RNA polymerase II-specific TF activity. Reason: Replace the broad transcription factor term with GO:0000981, supported by SVP domain architecture and direct target-gene repression evidence. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:12837945 Molecular and phylogenetic analyses of the complete MADS-box... | MODIFY | Summary: The Arabidopsis MADS-family analysis supports SVP's transcription factor classification, but the existing term is less specific than the appropriate RNA polymerase II-specific TF activity. Reason: GO:0000981 should replace the broad DNA-binding transcription factor term. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific |
| GO:0005515 protein binding | IPI PMID:11439126 APETALA1 and SEPALLATA3 interact to promote flower developme... | MODIFY | Summary: This yeast two-hybrid screen for AP1/CAL partners recovered five MADS-box proteins; the GOA IPI row records SVP (AGL22) as one of the AP1-interacting MADS proteins. The SVP-specific result is in the full text, which is not cached, but an AP1-SVP heterodimer is independently confirmed by PMID:16679456 in this review. Reason: Deferring to the GOA curator who read the full text, the interaction is plausible and consistent with other SVP-AP1 evidence. Generic protein binding is uninformative; the interaction is a MADS-domain heterodimer, so protein heterodimerization activity is the appropriate replacement. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:11439126 Among the five MADS-box genes identified in this screen, the SEPALLATA3 (SEP3) gene was chosen for further study. |
| GO:0005515 protein binding | IPI PMID:15805477 Comprehensive interaction map of the Arabidopsis MADS Box tr... | MODIFY | Summary: This matrix yeast two-hybrid map of nearly all Arabidopsis MADS-box proteins reports mostly specific heterodimers; the GOA IPI rows record SVP partners from this screen. The SVP partner table is in the full text and supplement, which are not cached. Reason: Deferring to the curator on the specific SVP partners, the interactions in this screen are MADS heterodimers, consistent with SVP's well-supported heterodimerization with AP1, FLC and FLM. Replace generic protein binding with protein heterodimerization activity. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:15805477 revealed a collection of specific heterodimers and a few homodimers |
| GO:0005515 protein binding | IPI PMID:16679456 AGL24, SHORT VEGETATIVE PHASE, and APETALA1 redundantly cont... | MODIFY | Summary: The paper supports AP1-SVP dimer formation and interaction of the AP1-SVP dimer with the LUG-SEU corepressor complex during AGAMOUS regulation. Reason: Generic protein binding should be replaced with more informative molecular functions: heterodimerization with AP1 and transcription corepressor binding for the LUG-SEU-associated interaction. Proposed replacements: protein heterodimerization activity transcription corepressor binding Supporting Evidence: |
| GO:0005515 protein binding | IPI PMID:19011118 Circadian clock proteins LHY and CCA1 regulate SVP protein a... | MODIFY | Summary: SVP interacts with FLC, and the two MADS proteins act as partially redundant flowering repressors under continuous-light/circadian-clock perturbation conditions. Reason: The useful molecular function captured by this row is MADS protein heterodimerization, not generic protein binding. Proposed replacements: protein heterodimerization activity Supporting Evidence: |
| GO:0005515 protein binding | IPI PMID:21709243 GIGANTEA directly activates Flowering Locus T in Arabidopsis... | REMOVE | Summary: GI can bind SVP in the context of FT activation and FT repressor antagonism, but the annotation is a generic protein-binding row and does not describe SVP's core molecular activity. Reason: Removal reflects the lack of functional information in a bare protein-binding row, not doubt that the GI-SVP interaction occurred. The interaction is biologically relevant, but generic protein binding adds little curatorial value and there is no precise GO molecular function term for this specific GI-SVP regulatory contact in the local ontology cache. Supporting Evidence: |
| GO:0005515 protein binding | IPI PMID:24030492 Regulation of temperature-responsive flowering by MADS-box t... | MODIFY | Summary: FLM-beta interacts with SVP to form a temperature-responsive MADS repressor complex whose abundance is reduced at high temperatures. Reason: This should be represented as protein heterodimerization activity rather than generic protein binding. Proposed replacements: protein heterodimerization activity Supporting Evidence: |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | REMOVE | Summary: CrY2H-seq is a high-throughput transcription factor interaction resource. The full text of the paper is cached locally, but it is a methods paper that nowhere names SVP; the individual interaction pairs behind this GOA/IntAct assertion are in its supplementary network data, which is not cached. Reason: The SVP partner rows live in the study's supplementary interaction network rather than in the article body, so no partner-specific, more informative molecular function can be assigned from this source. Removal reflects the lack of functional information in a bare protein-binding row, not doubt that the interaction occurred; SVP's informative heterodimerization function is captured by the AP1, FLC and FLM rows. Supporting Evidence: |
| GO:0005515 protein binding | IPI PMID:30946745 Floral regulators FLC and SOC1 directly regulate expression ... | MODIFY | Summary: The GOA row links protein binding to TFS1, but the paper supports TFS1 as an SVP/FLC transcriptional target and reports SVP binding to a CArG-containing TFS1 locus region, not a TFS1 protein interaction. Reason: Replace the apparent protein-binding misannotation with the molecular function actually supported by the paper: RNA polymerase II cis-regulatory region sequence-specific DNA binding. Proposed replacements: RNA polymerase II cis-regulatory region sequence-specific DNA binding Supporting Evidence: |
| GO:0043565 sequence-specific DNA binding | IPI PMID:25132385 A MYB-domain protein EFM mediates flowering responses to env... | ACCEPT | Summary: The EFM paper reports that SVP directly promotes EFM expression; the GOA row (IPI, with the EFM locus) records SVP binding to EFM regulatory DNA. The assay details are in the full text, which is not cached. Sequence-specific CArG-box DNA binding by SVP is independently supported by other sources in this review (e.g. TFS1 and FT loci). Reason: Sequence-specific DNA binding is an integral part of SVP's core MADS-domain transcription factor activity, and the abstract states that EFM is a direct SVP target. Deferring to the curator who read the full text, accept this experimental annotation. Supporting Evidence: PMID:25132385 is directly promoted by another major FT repressor, SHORT VEGETATIVE PHASE |
| GO:0046983 protein dimerization activity | IEA GO_REF:0000002 | MODIFY | Summary: Protein dimerization is consistent with SVP's MADS/K-box architecture and with experimental evidence for SVP heteromeric complexes with AP1, FLC, and FLM. Reason: The broad dimerization term is directionally correct, but the local direct interaction evidence supports the more specific heterodimerization term for SVP complexes with MADS partners. Proposed replacements: protein heterodimerization activity |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | MODIFY | Summary: SVP regulates DNA-templated transcription, but this parent process is less specific than RNA polymerase II transcriptional regulation. Reason: Replace with GO:0006357, which better matches SVP's regulation of protein-coding floral regulator genes. Proposed replacements: regulation of transcription by RNA polymerase II Supporting Evidence: GO_REF:0000002 |
| GO:0006357 regulation of transcription by RNA polymerase II | IBA GO_REF:0000033 | ACCEPT | Summary: SVP regulates RNA polymerase II-transcribed floral regulator genes as a MADS-box transcription factor; phylogenetic inference is consistent with Arabidopsis experimental data. Reason: This is an appropriate core biological process for SVP's transcriptional regulatory activity. |
| GO:0017148 negative regulation of translation | IEA GO_REF:0000108 | REMOVE | Summary: This annotation is an electronic inference from the misleading GO:0000900 translation-repressor activity row. The SVP sources support transcriptional repression, not translational regulation. Reason: No local evidence supports SVP regulating translation; the annotation should be removed rather than propagated from an incorrect logical inference. Because this row derives from the incorrect GO:0000900 translation-repressor annotation, both rows should be flagged upstream to TAIR/GOA as transcription/translation mechanism conflation. Supporting Evidence: GO_REF:0000108 |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IEA GO_REF:0000002 | MODIFY | Summary: Domain-based InterPro evidence does not justify positive regulatory direction for SVP. The dominant curated Arabidopsis evidence supports SVP as a transcriptional repressor of flowering regulators. Reason: Replace the unsupported positive-regulation call with negative regulation of transcription by RNA polymerase II. Proposed replacements: negative regulation of transcription by RNA polymerase II |
| GO:0005634 nucleus | IEA GO_REF:0000002 | ACCEPT | Summary: Nuclear localization is consistent with SVP's MADS-box DNA-binding transcription factor function and UniProt's nuclear location record. Reason: Retain; this is the expected cellular location for SVP's core transcriptional regulatory function. Supporting Evidence: GO_REF:0000002 file:ARATH/SVP/SVP-uniprot.txt |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping places SVP in the nucleus. Reason: Retain as a correct cellular component annotation for a DNA-binding transcription factor. Supporting Evidence: GO_REF:0000044 file:ARATH/SVP/SVP-uniprot.txt |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: AtSubP prediction of nuclear localization agrees with SVP domain biology and UniProt's nuclear location statement. Reason: Retain; computational localization is consistent with independent annotation and SVP's transcription factor function. Supporting Evidence: GO_REF:0000122 file:ARATH/SVP/SVP-uniprot.txt |
| GO:0005634 nucleus | IDA PMID:17322399 Role of SVP in the control of flowering time by ambient temp... | ACCEPT | Summary: The seeded IDA row uses the ambient-temperature paper. The cached abstract does not expose localization details, but the nucleus annotation is independently supported by UniProt and is coherent with SVP's direct promoter-binding function. Reason: Retain the correct cellular component annotation while noting that the specific PMID:17322399 localization evidence could not be checked from the cached abstract alone. |
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Download this section (compressed HTML)Q: Flag to TAIR/GOA: should the historical SVP GO:0000900 and GO:0017148 translation-related annotations be removed globally or mapped to RNA polymerase II-specific transcription factor terms in the upstream annotation source?
Suggested experts: Ahn JH, Lee JH
Q: Should SVP protein-interaction annotations distinguish MADS heterodimerization from corepressor binding, and should high-throughput interaction-only rows be kept out of GO when they do not add functional specificity?
Suggested experts: Kater MM, Angenent GC, Coupland G
Experiment: Express tagged SVP isoforms at comparable levels in svp mutant backgrounds, then compare flowering time rescue, nuclear localization, partner binding by reciprocal co-IP, and target occupancy at FT and TFS1 by ChIP-qPCR or CUT&RUN.
Hypothesis: SVP splice isoforms differ in their ability to dimerize and repress flowering-time targets because isoform 2 lacks most of the K-box and C-terminal region.
Type: isoform-rescue, interaction assay, and chromatin occupancy
Experiment: Perform stage- and temperature-resolved SVP CUT&RUN with matched RNA-seq in wild type and flc, flm, ap1, and seu/lug-perturbed backgrounds to separate direct SVP targets by partner dependency and regulatory direction.
Hypothesis: SVP-containing complexes use different partner combinations to repress distinct target loci in temperature, vernalization, and floral meristem contexts.
Type: chromatin profiling plus transcriptomics
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