APETALA1 (AP1/AGL7; At1g69120) encodes a 256 amino acid nuclear MIKC-type MADS-box transcription factor required for Arabidopsis floral meristem identity and normal sepal and petal development. AP1 binds CArG-containing cis-regulatory regions through its MADS domain and uses its K domain and C-terminal region to form homo- and heteromeric MADS transcription factor complexes with partners such as SEP3, AP3/PI, AGL24, SVP, SOC1, and SEU/LUG corepressor-associated proteins. The best-supported core function is context-dependent RNA polymerase II transcriptional regulation during the inflorescence-to-floral meristem transition: AP1 acts with LFY/CAL/FUL-related networks to promote floral fate, supports outer-whorl organ identity, activates floral organ programs in some contexts, and directly represses inflorescence or flowering-time genes such as SVP, AGL24, and SOC1 in emerging floral meristems. AP1 belongs to the broad MADS-box/MEF2 transcription factor family (PANTHER PTHR48019), whose conserved MADS and K domains underlie its DNA-binding and dimerization capabilities.
Definition: The developmental process in which a lateral meristem is committed to floral meristem fate rather than shoot or inflorescence meristem fate.
Justification: AP1 literature repeatedly describes "floral meristem identity" or "assignment of floral fate" as distinct from general meristem structural organization and not identical to determinacy. GO:0010582 (floral meristem determinacy) is the closest existing term in the local ontology cache, but a fate-specification term would better capture AP1/LFY/CAL biology.
Parent term: vegetative to reproductive phase transition of meristem
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0006357 regulation of transcription by RNA polymerase II | IBA GO_REF:0000033 | ACCEPT | Summary: AP1 is a DNA-binding MADS transcription factor that directly regulates RNA polymerase II target genes during floral meristem specification. This specific regulatory term is supported by AP1-GR/ChIP evidence showing direct AP1 binding to and repression of SVP, AGL24, and SOC1, plus higher-order MADS complex data. Reason: This is a core AP1 function. Phylogenetic inference is consistent with the conserved MADS transcription factor role, and Arabidopsis experiments provide direct evidence for AP1-dependent regulation of Pol II-transcribed developmental regulators. Supporting Evidence: PMID:17428825 By post-translational activation of an AP1-GR fusion protein and chromatin immunoprecipitation assays, we further demonstrate the repression of these flowering time genes by induced AP1 activity and in vivo AP1 binding to the cis-regulatory regions of these genes. PMID:22238427 Here, we show using affinity purification and mass spectrometry that five major floral homeotic MADS-domain proteins (AP1, AP3, PI, AG, and SEP3) interact in floral tissues as proposed in the "floral quartet" model. file:ARATH/AP1/AP1-deep-research-falcon.md Falcon synthesis supports AP1 as a MIKC-type MADS transcription factor, floral meristem identity regulator, and context-dependent activator and repressor in AP1-containing MADS complexes. |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: AP1 binds cis-regulatory regions of RNA polymerase II target genes as a MADS-domain transcription factor. ChIP assays show AP1 binding to cis-regulatory regions of SVP, AGL24, and SOC1, and MADS complex studies support CArG-box binding by AP1-containing complexes. Reason: This is the most informative molecular-function term among the existing DNA binding annotations and should be retained as core. Supporting Evidence: PMID:17428825 in vivo AP1 binding to the cis-regulatory regions of these genes. PMID:22238427 may compete for partly overlapping sets of DNA-binding sites. file:ARATH/AP1/AP1-deep-research-falcon.md Falcon synthesis highlights AP1's MADS-domain DNA binding, CArG-box target recognition, and higher-order MADS complex context. |
| GO:0000977 RNA polymerase II transcription regulatory region sequence-specific DNA binding | IEA GO_REF:0000002 | MODIFY | Summary: AP1 does bind RNA polymerase II regulatory regions, but GO:0000978 is the current, more precise term already present in GOA for AP1's cis-regulatory-region sequence-specific DNA binding activity. Reason: The annotation is directionally correct but less precise than the existing AP1 IBA term. Replace with the more specific cis-regulatory region binding term supported by AP1 ChIP evidence. Proposed replacements: RNA polymerase II cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:17428825 in vivo AP1 binding to the cis-regulatory regions of these genes. |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | MODIFY | Summary: AP1 is certainly DNA-binding, but this root-level term is too generic for a well-characterized MADS-box transcription factor with direct cis-regulatory binding evidence. Reason: Replace generic DNA binding with AP1's specific RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Proposed replacements: RNA polymerase II cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:15604664 the MADS domain that mediates DNA binding and dimerization PMID:17428825 in vivo AP1 binding to the cis-regulatory regions of these genes. |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | MODIFY | Summary: AP1 is a DNA-binding transcription factor, but the RNA polymerase II-specific child term captures its known role more accurately. Reason: AP1 regulates Pol II-transcribed developmental genes; GO:0000981 is the more specific molecular-function replacement for this generic transcription factor activity term. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: PMID:17428825 directly repressing a group of flowering time genes, including SHORT VEGETATIVE PHASE (SVP), AGAMOUS-LIKE 24 (AGL24) and SUPPRESSOR OF OVEREXPRESSION OF CO1 (SOC1). PMID:12837945 MADS-box transcription factors are key regulators of several plant development processes. |
| GO:0005634 nucleus | IEA GO_REF:0000002 | ACCEPT | Summary: AP1 functions in the nucleus as a DNA-binding transcription factor and participates in nuclear MADS-domain complexes. Reason: Nuclear localization is consistent with domain-based inference, UniProt, and experimental AP1-containing MADS complex studies. Supporting Evidence: PMID:22238427 MADS-domain protein complexes can coexist within the nucleus |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt records AP1 as nuclear, matching its molecular role and experimental evidence that AP1-containing MADS complexes operate in the nucleus. Reason: This cellular component annotation is accurate and biologically central for AP1's transcriptional regulatory function. Supporting Evidence: file:ARATH/AP1/AP1-uniprot.txt SUBCELLULAR LOCATION: Nucleus. PMID:22238427 MADS-domain protein complexes can coexist within the nucleus |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | MODIFY | Summary: AP1 regulates DNA-templated transcription, but for a eukaryotic DNA-binding transcription factor the RNA polymerase II-specific process is the better term and is already present in AP1 GOA. Reason: The broad term should be replaced by regulation of transcription by RNA polymerase II to reflect AP1's target gene context. Proposed replacements: regulation of transcription by RNA polymerase II Supporting Evidence: PMID:17428825 directly suppressing the expression of flowering time genes, thus preventing the continuation of the shoot developmental program. |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: AP1 can contribute to transcriptional activation of floral organ identity programs, but AP1 is also a direct repressor of flowering-time genes in emerging floral meristems. The positive-regulation term captures one supported mode, not AP1's complete core regulatory function. Reason: Retain as a valid context-specific activity, but do not treat it as AP1's full core function because AP1 has both activating and repressing roles. Supporting Evidence: PMID:11206550 vegetative leaves of triply transgenic plants, 35S::PI;35S::AP3;35S::AP1 or 35S::PI;35S::AP3;35S::SEP3, are transformed into petaloid organs PMID:17428825 it acts partly as a master repressor in floral meristems by directly suppressing the expression of flowering time genes |
| GO:0046983 protein dimerization activity | IEA GO_REF:0000002 | ACCEPT | Summary: Dimerization is a conserved and experimentally supported MADS protein property, and AP1 functions in homo- and heteromeric MADS-domain complexes. Reason: Although broad, this term captures a real molecular capability needed for AP1's MADS complex activity. More specific heterodimerization is proposed for individual generic protein-binding rows where the source supports a particular MADS partner interaction. Supporting Evidence: PMID:15604664 the MADS domain that mediates DNA binding and dimerization, and the K domain that mediates protein protein interaction. PMID:22238427 five major floral homeotic MADS-domain proteins (AP1, AP3, PI, AG, and SEP3) interact in floral tissues as proposed in the "floral quartet" model. |
| GO:0005515 protein binding | IPI PMID:11439126 APETALA1 and SEPALLATA3 interact to promote flower developme... | MODIFY | Summary: The source supports AP1 interaction with SEP3 during flower development, but the generic protein binding term is uninformative for a MADS transcription factor complex interaction. Reason: Replace generic protein binding with protein heterodimerization activity, which better captures the AP1-SEP3 MADS partner interaction. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:11439126 Taken together, these studies suggest that SEP3 interacts with AP1 to promote normal flower development. |
| GO:0005515 protein binding | IPI PMID:15604664 Defining subdomains of the K domain important for protein-pr... | REMOVE | Summary: The cached abstract supports MADS and K-domain roles in dimerization and protein interaction but focuses experimentally on AP3/PI/SEP interactions rather than AP1-specific binding. Reason: This PMID does not provide accessible AP1-specific interaction evidence in the cached text, and generic protein binding should not be retained for AP1 when better AP1-specific interaction evidence exists elsewhere. 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. |
| GO:0005515 protein binding | IPI PMID:15805477 Comprehensive interaction map of the Arabidopsis MADS Box tr... | MODIFY | Summary: This MADS interactome study supports specific MADS protein dimers, but the generic protein binding term loses the mechanistic meaning. Reason: Replace with protein heterodimerization activity for AP1's MADS partner interactions identified in the comprehensive MADS-box interaction map. 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. |
| GO:0005515 protein binding | IPI PMID:16854969 APETALA1 and SEPALLATA3 interact with SEUSS to mediate trans... | MODIFY | Summary: AP1 interacts with SEU and participates with SEP3/SEU/LUG in transcriptional repression. Generic protein binding should be replaced with a transcription coregulator binding term. Reason: The biological meaning of the AP1-SEU interaction is recruitment of transcriptional coregulatory machinery, not nonspecific protein binding. Proposed replacements: transcription coregulator binding Supporting Evidence: PMID:16854969 APETALA1 (AP1) and SEPALLATA3 (SEP3), both MADS box DNA-binding proteins, interacted with SEU. PMID:16854969 These results suggest that AP1 and SEP3 may serve as the DNA-binding partners of SEU/LUG. |
| GO:0005515 protein binding | IPI PMID:21798944 Evidence for network evolution in an Arabidopsis interactome... | REMOVE | Summary: The annotation comes from a proteome-wide interactome map and only supports a generic binary interaction, not a mechanistically specific or core AP1 molecular function. Reason: Generic protein binding from broad interactome data is not informative for AP1 curation and should not be retained as a GO function. Supporting Evidence: PMID:21798944 We describe a proteome-wide binary protein-protein interaction map for the interactome network of the plant Arabidopsis thaliana containing about 6200 highly reliable interactions between about 2700 proteins. |
| GO:0005515 protein binding | IPI PMID:24714165 Phytoplasma effector SAP54 hijacks plant reproduction by deg... | MARK AS OVER ANNOTATED | Summary: SAP54 binding to AP1 is a pathogen effector-host interaction that can alter floral development, but generic protein binding is not a core AP1 function. Reason: The interaction is biologically real, but retaining AP1 as simply having "protein binding" overstates the value of this host-pathogen interaction for AP1's normal molecular function. It is best handled as non-core pathogen effector context rather than a generic GO function. Supporting Evidence: PMID:24714165 SAP54) that interacts with members of the MADS-domain transcription factor (MTF) family, including key regulators SEPALLATA3 and APETALA1 |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | MARK AS OVER ANNOTATED | Summary: CrY2H-seq detected AP1 interactions in a large transcription factor interactome screen. The data are useful candidate interactions but do not justify retaining generic protein binding as a curated AP1 function. Reason: High-throughput binary interaction data should be interpreted cautiously, and the GO term protein binding is too generic. Specific AP1 MADS heterodimerization and coregulator binding annotations are preferable when supported by focused studies. Supporting Evidence: PMID:28650476 We report a deep coverage Arabidopsis transcription factor interactome composed of 8,577 binary interactions, 7,994 of which are novel. |
| GO:0005515 protein binding | IPI PMID:37965720 Protein interaction mapping reveals widespread targeting of ... | MARK AS OVER ANNOTATED | Summary: This source maps phytoplasma effector interactions with Arabidopsis transcription factors. Such host-pathogen screening context does not define AP1's normal core molecular function. Reason: The interaction may be relevant to phytoplasma pathogenesis, but retaining a generic protein binding annotation for AP1 over-interprets the evidence for normal AP1 function. Supporting Evidence: PMID:37965720 we generated a protein-protein interaction network between a broad set of phytoplasma effectors and a large, unbiased collection of Arabidopsis thaliana transcription factors and transcriptional regulators. |
| GO:0000976 transcription cis-regulatory region binding | IPI PMID:31806676 A PXY-Mediated Transcriptional Network Integrates Signaling ... | MODIFY | Summary: AP1 can bind transcriptional cis-regulatory regions, but this high-throughput vascular-development network does not discuss AP1 in the cached text, and GO:0000978 is the more precise AP1 term. Reason: Replace the broad cis-regulatory binding term with AP1's more specific RNA polymerase II cis-regulatory region sequence-specific DNA binding term, supported by AP1 ChIP evidence. Proposed replacements: RNA polymerase II cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:31806676 Here, we mapped a putative PXY-mediated transcriptional regulatory network comprising 690 transcription factor-promoter interactions in Arabidopsis (Arabidopsis thaliana). PMID:17428825 in vivo AP1 binding to the cis-regulatory regions of these genes. |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: Nuclear localization predicted by AtSubP is consistent with AP1's DNA-binding transcription factor function and experimental MADS-complex studies. Reason: This is a correct cellular component annotation and belongs with the AP1 core transcriptional regulatory model. Supporting Evidence: PMID:22238427 MADS-domain protein complexes can coexist within the nucleus |
| GO:0005515 protein binding | IPI PMID:16080001 Mutant analysis, protein-protein interactions and subcellula... | UNDECIDED | Summary: The GOA row assigns AP1 protein binding from an ABS/TT16 paper, but the cached abstract does not provide AP1-specific interaction text. Reason: Relevant AP1-specific evidence is unavailable in the cached text. Because generic protein binding should not be accepted without accessible support, this row should remain undecided until the full paper or interaction table can be checked. Supporting Evidence: PMID:16080001 Transgenic plants that ectopically express ABS show changes in the growth and identity of floral organs, suggesting that ABS can interact with floral homeotic proteins. |
| GO:0005634 nucleus | IDA PMID:22238427 Characterization of MADS-domain transcription factor complex... | ACCEPT | Summary: AP1-containing MADS complexes operate in the nucleus during flower development. Reason: The paper explicitly discusses AP1-containing MADS complexes coexisting in the nucleus and binding overlapping DNA sites. Supporting Evidence: PMID:22238427 Based on our in vitro EMSA studies, we propose that different heteromeric MADS-domain protein complexes can coexist within the nucleus and may compete for partly overlapping sets of DNA-binding sites. |
| GO:0045893 positive regulation of DNA-templated transcription | IDA PMID:11206550 Complexes of MADS-box proteins are sufficient to convert lea... | ACCEPT | Summary: AP1-containing MADS complexes can activate floral organ identity programs when combined with AP3/PI and SEP3, as shown by conversion of leaves into petaloid organs. Reason: Positive transcriptional regulation is a real AP1 mode in floral organ identity contexts, even though AP1 also represses other targets in emerging floral meristems. Supporting Evidence: PMID:11206550 vegetative leaves of triply transgenic plants, 35S::PI;35S::AP3;35S::AP1 or 35S::PI;35S::AP3;35S::SEP3, are transformed into petaloid organs |
| GO:0010582 floral meristem determinacy | IGI PMID:20626659 Arabidopsis BLADE-ON-PETIOLE1 and 2 promote floral meristem ... | ACCEPT | Summary: AP1 promotes floral fate and determinacy in parallel with LFY and BOP1/2. Loss of BOP1/2 with AP1 strongly converts flowers toward inflorescence-like shoots. Reason: Floral meristem determinacy is one of the most specific existing biological process terms for AP1's developmental role and is supported by genetic interaction evidence. Supporting Evidence: PMID:20626659 in combination with lfy or ap1, synergistic defects in floral meristem fate and determinacy are revealed. PMID:20626659 flowers are converted into highly branched inflorescence-like shoots. |
| GO:0005515 protein binding | IPI PMID:16679456 AGL24, SHORT VEGETATIVE PHASE, and APETALA1 redundantly cont... | MODIFY | Summary: This paper supports AP1-AGL24/AP1-SVP dimerization and interaction with the LUG-SEU corepressor complex, not a generic protein binding function. Reason: Replace generic protein binding with terms that capture the mechanistic interaction types: MADS protein heterodimerization and transcription coregulator binding. Proposed replacements: protein heterodimerization activity transcription coregulator binding Supporting Evidence: PMID:16679456 Protein interaction studies showed that dimers composed of AP1-AGL24 and AP1-SVP interact with the LUG-SEU corepressor complex. |
| GO:0003677 DNA binding | IDA PMID:17428825 Specification of Arabidopsis floral meristem identity by rep... | MODIFY | Summary: AP1 DNA binding is experimentally supported, but this generic term should be replaced by the specific cis-regulatory DNA binding term supported by the same ChIP evidence. Reason: ChIP evidence shows AP1 binding to cis-regulatory regions of target genes, making GO:0000978 more informative than generic DNA binding. Proposed replacements: RNA polymerase II cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:17428825 in vivo AP1 binding to the cis-regulatory regions of these genes. |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:12837945 Molecular and phylogenetic analyses of the complete MADS-box... | MODIFY | Summary: AP1 is a MADS-box DNA-binding transcription factor, but the RNA polymerase II-specific transcription factor activity term is more precise. Reason: This family-level ISS annotation should be narrowed to GO:0000981 for AP1, based on AP1's experimentally supported regulation of Pol II developmental genes. 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. PMID:17428825 directly suppressing the expression of flowering time genes |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a... | MODIFY | Summary: Genome-wide TF family analysis supports AP1 as a transcription factor, but the more specific RNA polymerase II-specific transcription factor activity is preferable. Reason: AP1 is a plant DNA-binding transcription factor regulating Pol II target genes; use GO:0000981 rather than generic GO:0003700. 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 PMID:17428825 directly suppressing the expression of flowering time genes |
| GO:0005634 nucleus | IDA PMID:10948247 Prenylation of the floral transcription factor APETALA1 modu... | ACCEPT | Summary: AP1 nuclear localization is consistent with its transcription factor role and is directly supported by later AP1-containing MADS complex evidence. The cached abstract for the original GFP paper does not include explicit localization text. Reason: Accept the nucleus annotation using the original AP1-GFP functional context together with AP1 MADS complex nuclear evidence; note that the original localization details are not present in the cached abstract. Supporting Evidence: PMID:10948247 AP1 fused to green fluorescent protein (GFP) retained transcription factor activity and directed the expected terminal flower phenotype when ectopically expressed in transgenic Arabidopsis. PMID:22238427 MADS-domain protein complexes can coexist within the nucleus |
| GO:0009908 flower development | IMP PMID:11439126 APETALA1 and SEPALLATA3 interact to promote flower developme... | ACCEPT | Summary: AP1 has a direct and central flower-development role, promoting flower meristem identity and later normal sepal and petal development with SEP3. Reason: This biological process annotation is broad but appropriate for AP1 because flower development is not merely a downstream phenotype; AP1 is a floral homeotic/meristem identity regulator. Supporting Evidence: PMID:11439126 In Arabidopsis, the closely related APETALA1 (AP1) and CAULIFLOWER (CAL) MADS-box genes share overlapping roles in promoting flower meristem identity. PMID:11439126 Later in flower development, the AP1 gene is required for normal development of sepals and petals. file:ARATH/AP1/AP1-deep-research-falcon.md Falcon synthesis summarizes AP1 loss-of-function and ectopic-expression evidence for floral meristem identity and sepal/petal developmental roles. |
| GO:0009933 meristem structural organization | IMP PMID:10368173 Interactions among APETALA1, LEAFY, and TERMINAL FLOWER1 spe... | MODIFY | Summary: The source supports AP1's role in assigning floral fate to lateral meristems, but the existing term is broad and structural rather than fate-specific. Reason: Replace with floral meristem determinacy, which better represents the AP1 meristem identity/fate evidence available in the paper and in later AP1 genetic studies. Proposed replacements: floral meristem determinacy Supporting Evidence: PMID:10368173 Assignment of floral fate to lateral meristems is primarily due to the cooperative activity of the flower meristem identity genes LEAFY (LFY), APETALA1 (AP1), and CAULIFLOWER. |
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Download this section (compressed HTML)Q: Should AP1's GO biological process annotations distinguish floral meristem identity specification from floral meristem determinacy, or is GO:0010582 the intended curator term for both concepts?
Suggested experts: Yanofsky MF, Meyerowitz EM, Kaufmann K
Q: Which AP1 protein interactions should be retained as curated GO molecular functions versus left as interaction database records, especially high-throughput CrY2H/phytoplasma-effector interactions?
Suggested experts: Immink RG, Kaufmann K, Angenent GC
Experiment: Perform stage-resolved AP1 ChIP-seq or CUT&RUN with matched nascent RNA-seq in early floral meristems, combined with AP1 partner perturbations such as SEP3, AGL24/SVP, and SEU/LUG, to classify direct AP1-bound targets by regulatory direction and complex context.
Hypothesis: AP1's direct transcriptional targets in early floral meristems can be divided into activation and repression modules based on partner complex composition.
Type: ChIP/CUT&RUN plus transcriptomics
Experiment: Validate selected AP1 partners from CrY2H-seq and phytoplasma-effector screens by reciprocal co-IP or BiFC in floral meristem/inflorescence tissue, then test whether disrupting each interaction changes AP1 target gene expression or flower development.
Hypothesis: AP1 high-throughput interaction candidates are enriched for non-core or context-specific interactions unless validated in floral tissue.
Type: interaction validation and functional genetics
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