SEPALLATA2 (SEP2; AGL4; At3g02310; UniProt P29384) is a MIKC-type MADS-box transcription factor of the E-class (SEPALLATA) subfamily, closely related to SEP1. Its MADS domain binds CArG-box regulatory DNA, and its K-box mediates heterodimerization and higher-order complex formation with other floral MADS proteins, including AG (originally isolated as an AG K-domain interactor) and ABS/TT16. SEP2 is expressed in floral meristems and organ primordia. Its function is masked by redundancy: sep2 single mutants are near wild type, but sep1 sep2 sep3 triple mutants convert petals, stamens and carpels into sepals. SEP2 therefore acts as an E-class partner that lets B- and C-class proteins specify organ identity within floral quartet MADS complexes, and SEP dosage also contributes to ovule identity.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000977 RNA polymerase II transcription regulatory region sequence-specific DNA binding | IEA GO_REF:0000002 | ACCEPT | Summary: Sequence-specific binding to CArG-box regulatory DNA is the defining activity of the MADS domain. Reason: The InterPro MADS-domain mapping is appropriate. SEP-subfamily MADS proteins bind CArG boxes in cis-regulatory regions of floral genes. The more specific cis-regulatory term GO:0000978 (IBA) is also retained. No SEP2-specific DNA-binding assay is available; binding is inferred from the conserved MADS domain and from direct assays of the closest paralog AGL2/SEP1. Supporting Evidence: PMID:8597661 AGL2 binds to DNA in vitro as a dimer and determined the region of AGL2 that is sufficient for DNA binding and dimerization. |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: Binding of RNA polymerase II cis-regulatory CArG-box elements is a conserved MADS-box/MEF2 family activity. Reason: The IBA reflects the ancestral MADS-box/MEF2 DNA-binding function, and the target falls inside the plant MIKC clade that retains it. No evidence suggests loss of DNA binding in SEP2. No SEP2-specific DNA-binding assay is available; the cited support is the direct assay of the closest paralog AGL2/SEP1. Supporting Evidence: PMID:8597661 AGL2 binds to DNA in vitro as a dimer and determined the region of AGL2 that is sufficient for DNA binding and dimerization. |
| GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific | IBA GO_REF:0000033 | ACCEPT | Summary: SEP2 is a MADS-domain transcription factor regulating floral gene expression. Reason: The IBA-propagated RNA-polymerase-II-specific transcription factor activity is the most appropriate MF term for SEP2, consistent with its MADS DNA-binding domain and its genetic role, redundant with the other SEP genes, in floral organ identity. Supporting Evidence: PMID:10821278 SEP1/2/3 are a class of organ-identity genes that is required for development of petals, stamens and carpels. |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | MODIFY | Summary: Generic DNA binding is correct but uninformative for a sequence-specific CArG-box binding protein. Reason: MADS-domain proteins bind CArG-box cis-regulatory sequences specifically. The more specific term RNA polymerase II cis-regulatory region sequence-specific DNA binding should be used. SEP2 binding is inferred from MADS-family membership and the direct assay of the paralog AGL2/SEP1. Proposed replacements: RNA polymerase II cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:8597661 AGL2 binds to DNA in vitro as a dimer and determined the region of AGL2 that is sufficient for DNA binding and dimerization. |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | MODIFY | Summary: SEP2 is a MADS-domain DNA-binding transcription factor; the general term can be made more specific. Reason: The InterPro mapping is correct in essence. The RNA-polymerase-II-specific child term is preferred. DNA binding by SEP2 is inferred from MADS-family membership and the direct assay of the paralog AGL2/SEP1. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: PMID:8597661 AGL2 binds to DNA in vitro as a dimer and determined the region of AGL2 that is sufficient for DNA binding and dimerization. |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a... | MODIFY | Summary: SEP2 is a MADS-domain DNA-binding transcription factor; the general term can be made more specific. Reason: This sequence-similarity (family-level) annotation is correct in essence. The RNA-polymerase-II-specific child term is preferred, in line with the IBA and the treatment of the paralog SEP3. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: PMID:11118137 Arabidopsis dedicates over 5% of its genome to code for more than 1500 transcription factors |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:12837945 Molecular and phylogenetic analyses of the complete MADS-box... | MODIFY | Summary: SEP2 is a MADS-domain DNA-binding transcription factor; the general term can be made more specific. Reason: This sequence-similarity (family-level) annotation is correct in essence. The RNA-polymerase-II-specific child term is preferred, in line with the IBA and the treatment of the paralog SEP3. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: PMID:12837945 MADS-box transcription factors are key regulators of several plant development processes. |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:1672119 AGL1-AGL6, an Arabidopsis gene family with similarity to flo... | MODIFY | Summary: SEP2 is a MADS-domain DNA-binding transcription factor; the general term can be made more specific. Reason: This sequence-similarity (family-level) annotation is correct in essence. The RNA-polymerase-II-specific child term is preferred, in line with the IBA and the treatment of the paralog SEP3. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: PMID:1672119 We have isolated six new genes from A. thaliana, AGL1-AGL6, which also have this conserved sequence motif. |
| GO:0005515 protein binding | IPI PMID:16080001 Mutant analysis, protein-protein interactions and subcellula... | MODIFY | Summary: Interaction of SEP2 with the MADS-domain protein ABS/TT16 reflects SEP-mediated heteromeric MADS complex formation. Reason: Generic protein binding is uninformative. The partner is a MIKC-type MADS-domain transcription factor, and SEP proteins act as heterodimerization and tetramerization partners in floral MADS complexes. Protein heterodimerization activity captures the specific function. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:16080001 Yeast-two-hybrid and three-hybrid analyses indicated that ABS can form dimers with SEPALLATA (SEP) floral homeotic proteins PMID:22238427 According to the current model, SEP proteins are major mediators of higher-order complex formation of MADS-domain proteins. |
| GO:0005515 protein binding | IPI PMID:9418042 Specific interactions between the K domains of AG and AGLs, ... | MODIFY | Summary: Interaction of SEP2 with the MADS-domain protein AG reflects SEP-mediated heteromeric MADS complex formation. Reason: Generic protein binding is uninformative. The partner is a MIKC-type MADS-domain transcription factor, and SEP proteins act as heterodimerization and tetramerization partners in floral MADS complexes. Protein heterodimerization activity captures the specific function. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:9418042 These clones each encode one of four highly related MADS domain proteins: AGL2, AGL4, AGL6 and AGL9. PMID:22238427 According to the current model, SEP proteins are major mediators of higher-order complex formation of MADS-domain proteins. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: SEP2 is a MIKC-type MADS-domain transcription factor that acts in the nucleus. Reason: Nuclear localization is expected for a sequence-specific DNA-binding MADS-domain transcription factor; UniProt records a nuclear location and the paralogous SEP and ABS MADS proteins are experimentally nuclear. This location is consistent with the core transcription-factor function. Supporting Evidence: file:ARATH/SEP2/SEP2-uniprot.txt SUBCELLULAR LOCATION: Nucleus |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: SEP2 is a MIKC-type MADS-domain transcription factor that acts in the nucleus. Reason: Nuclear localization is expected for a sequence-specific DNA-binding MADS-domain transcription factor; UniProt records a nuclear location and the paralogous SEP and ABS MADS proteins are experimentally nuclear. This location is consistent with the core transcription-factor function. Supporting Evidence: file:ARATH/SEP2/SEP2-uniprot.txt SUBCELLULAR LOCATION: Nucleus |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: SEP2 is a MIKC-type MADS-domain transcription factor that acts in the nucleus. Reason: Nuclear localization is expected for a sequence-specific DNA-binding MADS-domain transcription factor; UniProt records a nuclear location and the paralogous SEP and ABS MADS proteins are experimentally nuclear. This location is consistent with the core transcription-factor function. Supporting Evidence: file:ARATH/SEP2/SEP2-uniprot.txt SUBCELLULAR LOCATION: Nucleus |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | MODIFY | Summary: Regulation of transcription is correct but the RNA polymerase II-specific term is more precise. Reason: MADS-domain floral regulators control protein-coding target genes; GO:0006357 (also IBA) is the preferred, more specific term. Proposed replacements: regulation of transcription by RNA polymerase II Supporting Evidence: PMID:10821278 SEP1/2/3 are a class of organ-identity genes that is required for development of petals, stamens and carpels. |
| GO:0006357 regulation of transcription by RNA polymerase II | IBA GO_REF:0000033 | ACCEPT | Summary: SEP2 regulates RNA polymerase II-transcribed floral target genes as part of MADS complexes. Reason: The IBA is consistent with the conserved MADS-box/MEF2 transcription factor function and with the SEP-gene genetic requirement for floral organ identity programs. Supporting Evidence: PMID:10821278 SEP1/2/3 are a class of organ-identity genes that is required for development of petals, stamens and carpels. PMID:22238427 According to the current model, SEP proteins are major mediators of higher-order complex formation of MADS-domain proteins. |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IEA GO_REF:0000002 | ACCEPT | Summary: SEP proteins are thought to contribute transcriptional activation capacity to floral MADS complexes. Reason: InterPro-based inference of positive regulation is reasonable for SEP-subfamily proteins, which with A and B proteins are sufficient to activate the petal program ectopically. Direct activation assays for this paralog are limited; the term is retained as consistent with the family role. Supporting Evidence: PMID:11231153 Here we show that the combined action of the SEP genes, together with the A and B genes, is sufficient to convert leaves into petals. |
| GO:0046983 protein dimerization activity | IEA GO_REF:0000002 | MODIFY | Summary: Dimerization through the MADS and K domains is real, but SEP proteins chiefly act as heterodimerization partners. Reason: SEP proteins mediate higher-order MADS complex formation through heteromeric interactions with A, B, C and D class MADS proteins. Protein heterodimerization activity is the more informative term, matching the treatment of SEP3. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:22238427 According to the current model, SEP proteins are major mediators of higher-order complex formation of MADS-domain proteins. PMID:15805477 A matrix-based yeast two-hybrid screen of >100 members of this family revealed a collection of specific heterodimers and a few homodimers. |
| GO:0048440 carpel development | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: SEP genes are redundantly required for carpel identity and development, so the ARBA term is biologically correct for SEP2. Reason: Carpels are converted to sepals (sep1/2/3) or leaf-like organs (sep1/2/3/4) when SEP activity is removed, so SEP2 contributes to carpel development. The term is a downstream consequence of the organ-identity function, so it is kept as non-core; the core role is captured by GO:0010093. Supporting Evidence: PMID:10821278 SEP1/2/3 are a class of organ-identity genes that is required for development of petals, stamens and carpels. |
| GO:0048481 plant ovule development | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: SEP proteins participate in ovule-identity MADS complexes with STK/SHP; ovule development is a later, non-core role. Reason: Reduced SEP dosage (SEP1/sep1 sep2 sep3) transforms ovules into carpel- and leaf-like structures, and SEP proteins bridge STK/SHP/AG complexes. This is a real but secondary role relative to floral organ identity, and is shared redundantly among SEP paralogs. Supporting Evidence: PMID:14555696 a reduction in SEP activity leads to the loss of normal ovule development PMID:14555696 Genetic evidence for the role of SEP proteins in the formation of an ovule identity-promoting complex came from analysis of the SEP1/sep1 sep2 sep3 mutant, in which a large number of ovules lose their identity and are transformed into carpel- and leaf-like structures. |
| GO:0048481 plant ovule development | IMP PMID:14555696 MADS-box protein complexes control carpel and ovule developm... | KEEP AS NON CORE | Summary: SEP proteins participate in ovule-identity MADS complexes with STK/SHP; ovule development is a later, non-core role. Reason: Reduced SEP dosage (SEP1/sep1 sep2 sep3) transforms ovules into carpel- and leaf-like structures, and SEP proteins bridge STK/SHP/AG complexes. This is a real but secondary role relative to floral organ identity, and is shared redundantly among SEP paralogs. Supporting Evidence: PMID:14555696 a reduction in SEP activity leads to the loss of normal ovule development PMID:14555696 Genetic evidence for the role of SEP proteins in the formation of an ovule identity-promoting complex came from analysis of the SEP1/sep1 sep2 sep3 mutant, in which a large number of ovules lose their identity and are transformed into carpel- and leaf-like structures. |
| GO:0010093 specification of floral organ identity | IMP PMID:10821278 B and C floral organ identity functions require SEPALLATA MA... | NEW | Summary: SEP2 acts redundantly with SEP1/SEP3 (and SEP4) to specify petal, stamen and carpel identity, as shown by the sep1 sep2 sep3 triple mutant. Reason: The same paper supports an existing IMP GO:0010093 annotation on SEP3. The genotype removes SEP1, SEP2 and SEP3 together, so the evidence applies equally to SEP2. SEP proteins do the work themselves as DNA-binding subunits of the organ-identity MADS tetramers, so this is participation, not only requirement. Supporting Evidence: PMID:10821278 Triple mutant Arabidopsis plants lacking the activity of all three SEP genes produce flowers in which all organs develop as sepals. PMID:10821278 SEP1/2/3 are a class of organ-identity genes that is required for development of petals, stamens and carpels. |
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Download this section (compressed HTML)Q: Which floral MADS tetramers incorporate SEP2 rather than SEP3 in vivo, and do any target genes depend specifically on SEP2-containing complexes?
Experiment: Profile native-promoter tagged SEP2 by ChIP-seq and IP-MS in staged inflorescences, and compare its occupancy and partners with SEP3 to test for sub-functionalization within the redundant SEP subfamily.
Hypothesis: SEP2 occupies a subset of SEP3 target sites and forms distinct tetramers.
Type: paralog-specific ChIP-seq and complex proteomics
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