SEPALLATA4 (SEP4; AGL3; At2g03710; UniProt P29383) is a MIKC-type MADS-box transcription factor of the SEPALLATA subfamily. AGL3/SEP4 binds CArG-box DNA sequences resembling SRF/MCM1 sites. Unlike SEP1-3 it is also expressed in vegetative above-ground organs, as well as in flowers. sep4 single mutants are near wild type, but sep1 sep2 sep3 sep4 quadruple mutants convert all floral organs, sepals included, into leaf-like organs. SEP4 therefore contributes, redundantly with SEP1-3, to the identity of all four floral organ types. SEP4 also acts with AP1, CAL and FUL in floral meristem identity. SEP4 forms heteromeric complexes with other MADS proteins and is one of the host MADS proteins targeted for degradation by the phytoplasma effector SAP54.
| 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:7632923 We show that AGL3 binds to sequences which resemble the target sequences of SRF and MCM1, and have determined the consensus sequence to which AGL3 binds using random oligonucleotides. |
| 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 SEP4. Supporting Evidence: PMID:7632923 We show that AGL3 binds to sequences which resemble the target sequences of SRF and MCM1, and have determined the consensus sequence to which AGL3 binds using random oligonucleotides. |
| GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific | IBA GO_REF:0000033 | ACCEPT | Summary: SEP4 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 SEP4, consistent with its MADS DNA-binding domain and its genetic role, redundant with the other SEP genes, in floral organ identity. Supporting Evidence: PMID:15530395 SEP4 contributes to the development of petals, stamens, and carpels in addition to sepals and that it plays an important role in meristem identity. |
| 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:7632923 We show that AGL3 binds to sequences which resemble the target sequences of SRF and MCM1, and have determined the consensus sequence to which AGL3 binds using random oligonucleotides. |
| GO:0003677 DNA binding | TAS PMID:7632923 The Arabidopsis MADS-box gene AGL3 is widely expressed and e... | 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:7632923 We show that AGL3 binds to sequences which resemble the target sequences of SRF and MCM1, and have determined the consensus sequence to which AGL3 binds using random oligonucleotides. |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | MODIFY | Summary: SEP4 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:7632923 We show that AGL3 binds to sequences which resemble the target sequences of SRF and MCM1, and have determined the consensus sequence to which AGL3 binds using random oligonucleotides. |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a... | MODIFY | Summary: SEP4 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: SEP4 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:0005515 protein binding | IPI PMID:16080001 Mutant analysis, protein-protein interactions and subcellula... | MODIFY | Summary: Interaction of SEP4 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:24714165 Phytoplasma effector SAP54 hijacks plant reproduction by deg... | REMOVE | Summary: SEP4 is bound and destabilized by the phytoplasma effector SAP54; this is a pathogen-host interaction, not a SEP4 function. Reason: The interaction is real but describes effector targeting of host MADS proteins. Generic protein binding to a bacterial effector does not describe a normal molecular function of the gene product. Removal does not mean the interaction is false. This matches the treatment of the same SAP54 rows on SEP3. Supporting Evidence: PMID:24714165 including the well-characterized floral meristem identity and homeotic proteins AP1 [10], and SEP3 paralogues SEP1, SEP2, and SEP4. PMID:24714165 Destabilization of SEP3 (and AP1) by SAP54 is expected to significantly impair the establishment of the MTF protein complexes that are necessary to regulate floral development, especially if accompanied by the destabilization of SEP1, SEP2, and SEP4. |
| GO:0005515 protein binding | IPI PMID:32612234 Extensive signal integration by the phytohormone protein net... | REMOVE | Summary: High-throughput yeast two-hybrid interaction of SEP4 with the GRAS protein SCL23; 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:32612234 We hypothesized that protein-protein interactions have an important |
| GO:0005515 protein binding | IPI PMID:37965720 Protein interaction mapping reveals widespread targeting of ... | REMOVE | Summary: SEP4 is bound and destabilized by the phytoplasma effector SAP54; this is a pathogen-host interaction, not a SEP4 function. Reason: The interaction is real but describes effector targeting of host MADS proteins. Generic protein binding to a bacterial effector does not describe a normal molecular function of the gene product. Removal does not mean the interaction is false. This matches the treatment of the same SAP54 rows on SEP3. Supporting Evidence: PMID:37965720 We found widespread, but specific, interactions between phytoplasma effectors and host transcription factors, especially those related to host developmental processes. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: SEP4 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/SEP4/SEP4-uniprot.txt SUBCELLULAR LOCATION: Nucleus |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: SEP4 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/SEP4/SEP4-uniprot.txt SUBCELLULAR LOCATION: Nucleus |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: SEP4 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/SEP4/SEP4-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:15530395 SEP4 contributes to the development of petals, stamens, and carpels in addition to sepals and that it plays an important role in meristem identity. |
| GO:0006357 regulation of transcription by RNA polymerase II | IBA GO_REF:0000033 | ACCEPT | Summary: SEP4 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:15530395 SEP4 contributes to the development of petals, stamens, and carpels in addition to sepals and that it plays an important role in meristem identity. PMID:22238427 According to the current model, SEP proteins are major mediators of higher-order complex formation of MADS-domain proteins. |
| GO:0010076 maintenance of floral meristem identity | IMP PMID:15530395 The SEP4 gene of Arabidopsis thaliana functions in floral or... | ACCEPT | Summary: SEP4 contributes to floral meristem identity together with AP1/CAL/FUL. Reason: Ditta et al. report that SEP4 plays an important role in meristem identity in addition to organ identity; the acts_upstream_of_or_within qualifier matches the genetic evidence. Supporting Evidence: PMID:15530395 SEP4 contributes to the development of petals, stamens, and carpels in addition to sepals and that it plays an important role in meristem identity. |
| 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 SEP4. Reason: Carpels are converted to sepals (sep1/2/3) or leaf-like organs (sep1/2/3/4) when SEP activity is removed, so SEP4 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:15530395 SEP4 contributes to the development of petals, stamens, and carpels in addition to sepals and that it plays an important role in meristem identity. |
| GO:0048440 carpel development | IMP PMID:15530395 The SEP4 gene of Arabidopsis thaliana functions in floral or... | KEEP AS NON CORE | Summary: SEP4 contributes, redundantly with SEP1-3, to carpel development. Reason: Ditta et al. show that SEP4 adds to SEP1/2/3 function in petals, stamens and carpels in higher-order mutants. The acts_upstream_of_or_within qualifier fits redundant genetic evidence. Kept as non-core because organ development is a downstream consequence of the core organ-identity function captured by GO:0010093. Supporting Evidence: PMID:15530395 SEP4 contributes to the development of petals, stamens, and carpels in addition to sepals and that it plays an important role in meristem identity. |
| GO:0048441 petal development | IMP PMID:15530395 The SEP4 gene of Arabidopsis thaliana functions in floral or... | KEEP AS NON CORE | Summary: SEP4 contributes, redundantly with SEP1-3, to petal development. Reason: The sep1 sep2 sep3 sep4 quadruple mutant converts all floral organs into leaf-like organs, and SEP4 adds to petal development in sensitized backgrounds. The acts_upstream_of_or_within qualifier fits this redundant genetic evidence. Kept as non-core because organ development is a downstream consequence of the core organ-identity function captured by GO:0010093. Supporting Evidence: PMID:15530395 SEP4 contributes to the development of petals, stamens, and carpels in addition to sepals and that it plays an important role in meristem identity. |
| GO:0048442 sepal development | IMP PMID:15530395 The SEP4 gene of Arabidopsis thaliana functions in floral or... | KEEP AS NON CORE | Summary: SEP4 contributes, redundantly with SEP1-3, to sepal development. Reason: The sep1 sep2 sep3 sep4 quadruple mutant converts all floral organs into leaf-like organs, and SEP4 adds to sepal development in sensitized backgrounds. The acts_upstream_of_or_within qualifier fits this redundant genetic evidence. Kept as non-core because organ development is a downstream consequence of the core organ-identity function captured by GO:0010093. Supporting Evidence: PMID:15530395 floral organs are converted into leaf-like organs in sep1 sep2 sep3 sep4 quadruple mutants, indicating the involvement of all four SEP genes in the development of sepals. |
| GO:0048443 stamen development | IMP PMID:15530395 The SEP4 gene of Arabidopsis thaliana functions in floral or... | KEEP AS NON CORE | Summary: SEP4 contributes, redundantly with SEP1-3, to stamen development. Reason: The sep1 sep2 sep3 sep4 quadruple mutant converts all floral organs into leaf-like organs, and SEP4 adds to stamen development in sensitized backgrounds. The acts_upstream_of_or_within qualifier fits this redundant genetic evidence. Kept as non-core because organ development is a downstream consequence of the core organ-identity function captured by GO:0010093. Supporting Evidence: PMID:15530395 SEP4 contributes to the development of petals, stamens, and carpels in addition to sepals and that it plays an important role in meristem identity. |
| GO:0010093 specification of floral organ identity | IMP PMID:15530395 The SEP4 gene of Arabidopsis thaliana functions in floral or... | NEW | Summary: SEP4 acts redundantly with SEP1-3 in specifying the identity of all four floral organ types. Reason: GOA carries organ-development terms for SEP4 from this paper, but the quadruple mutant converts floral organs into leaf-like organs. That is an identity-specification phenotype, and the same term is annotated to SEP3 from the triple-mutant paper. SEP proteins do the work as subunits of the organ-identity MADS complexes. Supporting Evidence: PMID:15530395 floral organs are converted into leaf-like organs in sep1 sep2 sep3 sep4 quadruple mutants, indicating the involvement of all four SEP genes in the development of sepals. PMID:15530395 SEP4 contributes to the development of petals, stamens, and carpels in addition to sepals and that it plays an important role in meristem identity. |
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Download this section (compressed HTML)Q: Which floral MADS tetramers incorporate SEP4 rather than SEP3 in vivo, and do any target genes depend specifically on SEP4-containing complexes?
Q: What is the function of SEP4 in vegetative tissues, where it is expressed unlike SEP1-3?
Experiment: Profile native-promoter tagged SEP4 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: SEP4 occupies a subset of SEP3 target sites and forms distinct tetramers.
Type: paralog-specific ChIP-seq and complex proteomics
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