SEPALLATA1 (SEP1; AGL2; At5g15800; UniProt P29382) is a MIKC-type MADS-box transcription factor of the E-class (SEPALLATA) subfamily. It has an N-terminal MADS DNA-binding domain, an I region and a K-box coiled-coil region that mediate dimerization and higher-order complex formation. SEP1 is expressed throughout the young floral meristem and in the primordia of all four organ types, and later in ovules and developing seeds. Recombinant SEP1 binds CArG-box DNA as a dimer. With SEP2, SEP3 and SEP4 it is redundantly required for floral organ identity: sep1 sep2 sep3 triple mutants make sepals in every whorl, because the B- and C-class MADS proteins (AP3/PI, AG) need SEP partners to form active tetrameric 'floral quartet' complexes. SEP1 interacts with AG, AP1, ABS/TT16, SHP and other MIKC proteins. SEP dosage is also needed for ovule identity within STK/SHP/AG-containing complexes.
| 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. Supporting Evidence: PMID:8597661 We demonstrate that both proteins are sequence-specific DNA binding proteins |
| 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 SEP1. Supporting Evidence: PMID:8597661 We demonstrate that both proteins are sequence-specific DNA binding proteins |
| GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific | IBA GO_REF:0000033 | ACCEPT | Summary: SEP1 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 SEP1, 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. Proposed replacements: RNA polymerase II cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:8597661 We demonstrate that both proteins are sequence-specific DNA binding proteins |
| GO:0003700 DNA-binding transcription factor activity | IDA PMID:8597661 DNA binding properties of two Arabidopsis MADS domain protei... | MODIFY | Summary: SEP1 is a MADS-domain DNA-binding transcription factor; the general term can be made more specific. Reason: This study directly shows sequence-specific, dimeric DNA binding by AGL2/SEP1. That supports SEP1 as a DNA-binding transcription factor. The RNA-polymerase-II-specific child term is the preferred representation for a plant MADS transcription factor. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: PMID:8597661 We demonstrate that both proteins are sequence-specific DNA binding proteins 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: SEP1 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. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: PMID:8597661 We demonstrate that both proteins are sequence-specific DNA binding proteins |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a... | MODIFY | Summary: SEP1 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: SEP1 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: SEP1 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:15604664 Defining subdomains of the K domain important for protein-pr... | MODIFY | Summary: Interaction of SEP1 with the MADS-domain protein AP1 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:15604664 Here we report on our studies on the interactions of the B class MADS proteins AP3 and PI with the E class MADS proteins SEP1, SEP2, and SEP3. 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:15805477 Comprehensive interaction map of the Arabidopsis MADS Box tr... | MODIFY | Summary: Interaction of SEP1 with the MADS-domain protein AGL16 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:15805477 A matrix-based yeast two-hybrid screen of >100 members of this family revealed a collection of specific heterodimers and a few homodimers. 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:16080001 Mutant analysis, protein-protein interactions and subcellula... | MODIFY | Summary: Interaction of SEP1 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:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | MODIFY | Summary: Interaction of SEP1 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:28650476 We observed highly significant preferential intrafamily interactions among family members known to dimerize including the bHLH, MADS, bZIP, NAC, WRKY, AUX-IAAs, and ARF families. 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:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | MODIFY | Summary: Interaction of SEP1 with the MADS-domain protein AGL24 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:28650476 We observed highly significant preferential intrafamily interactions among family members known to dimerize including the bHLH, MADS, bZIP, NAC, WRKY, AUX-IAAs, and ARF families. 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:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | MODIFY | Summary: Interaction of SEP1 with the MADS-domain protein SHP2/AGL5 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:28650476 We observed highly significant preferential intrafamily interactions among family members known to dimerize including the bHLH, MADS, bZIP, NAC, WRKY, AUX-IAAs, and ARF families. 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:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | MODIFY | Summary: Interaction of SEP1 with the MADS-domain protein AP1 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:28650476 We observed highly significant preferential intrafamily interactions among family members known to dimerize including the bHLH, MADS, bZIP, NAC, WRKY, AUX-IAAs, and ARF families. 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:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | REMOVE | Summary: High-throughput yeast two-hybrid interaction of SEP1 with a Myb/SANT-domain protein (At3g24490); no functional context. Reason: Generic protein binding from a large-scale binary interactome screen with a non-MADS partner. It carries no information about molecular function, and there is no independent evidence that the interaction matters for SEP biology. Removal does not mean the interaction is false. Supporting Evidence: PMID:28650476 We observed highly significant preferential intrafamily interactions among family members known to dimerize including the bHLH, MADS, bZIP, NAC, WRKY, AUX-IAAs, and ARF families. |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | REMOVE | Summary: High-throughput yeast two-hybrid interaction of SEP1 with ARF46 (B3-domain protein); no functional context. Reason: Generic protein binding from a large-scale binary interactome screen with a non-MADS partner. It carries no information about molecular function, and there is no independent evidence that the interaction matters for SEP biology. Removal does not mean the interaction is false. Supporting Evidence: PMID:28650476 We observed highly significant preferential intrafamily interactions among family members known to dimerize including the bHLH, MADS, bZIP, NAC, WRKY, AUX-IAAs, and ARF families. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: SEP1 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/SEP1/SEP1-uniprot.txt SUBCELLULAR LOCATION: Nucleus |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: SEP1 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/SEP1/SEP1-uniprot.txt SUBCELLULAR LOCATION: Nucleus |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: SEP1 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/SEP1/SEP1-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: SEP1 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:0009908 flower development | IDA PMID:7948914 Spatially and temporally regulated expression of the MADS-bo... | MODIFY | Summary: AGL2/SEP1 is expressed throughout the floral meristem and all four organ primordia. The broad flower-development annotation is correct but a more specific process is supported genetically. Reason: The source paper is an expression study, which cannot itself show involvement. The genetic evidence for SEP1 (sep1 sep2 sep3 triple mutant) supports the more specific process specification of floral organ identity. Proposed replacements: specification of floral organ identity Supporting Evidence: PMID:7948914 The AGL2 transcript is very abundant and uniform throughout the floral meristem and in the primordia of all four floral organs: sepals, petals, stamens and carpels. PMID:10821278 Triple mutant Arabidopsis plants lacking the activity of all three SEP genes produce flowers in which all organs develop as sepals. |
| 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 SEP1. Reason: Carpels are converted to sepals (sep1/2/3) or leaf-like organs (sep1/2/3/4) when SEP activity is removed, so SEP1 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: SEP1 acts redundantly with SEP2/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 SEP1. 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 SEP1 rather than SEP3 in vivo, and do any target genes depend specifically on SEP1-containing complexes?
Experiment: Profile native-promoter tagged SEP1 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: SEP1 occupies a subset of SEP3 target sites and forms distinct tetramers.
Type: paralog-specific ChIP-seq and complex proteomics
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