ARF19 is a class-A auxin response factor that binds AuxRE-containing cis-regulatory DNA and activates target transcription. Together with ARF7 it directly regulates LBD genes during lateral-root formation and contributes to leaf expansion, root responses to ethylene and auxin-induced callus formation. Its B3-containing DNA-binding domain, middle activation region and C-terminal PB1 interaction domain couple DNA recognition to partner-dependent regulation. Canonical Aux/IAA proteins repress its activity, whereas noncanonical Aux/IAA interactions need not confer the same regulatory mechanism. ARF19 partitions between nuclei of meristematic root cells and cytoplasmic condensates in mature root cells; PB1 interactions and the disordered middle region contribute to this partitioning.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000976 transcription cis-regulatory region binding | IBA GO_REF:0000033 | ACCEPT | Summary: ARF19 binds specifically to auxin response elements (AuxREs) containing the TGTCTC motif in promoters of target genes. This is a core molecular function well supported by phylogenetic inference and experimental data from the ARF family [PMID:15659631, PMID:17259263]. Reason: ARF transcription factors bind to cis-regulatory AuxRE sequences. This is the fundamental molecular function of the ARF family and has been directly demonstrated for ARF7/ARF19. IBA annotation is appropriate given the conserved function across the ARF family. Supporting Evidence: PMID:17259263 ARF7 and ARF19 directly regulate the auxin-mediated transcription of LATERAL ORGAN BOUNDARIES-DOMAIN16/ASYMMETRIC LEAVES2-LIKE18 (LBD16/ASL18) and/or LBD29/ASL16 in roots PMID:15659631 The AUXIN RESPONSE FACTOR (ARF) gene family products, together with the AUXIN/INDOLE-3-ACETIC ACID proteins, regulate auxin-mediated transcriptional activation/repression |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: ARF19 is nuclear in root cells where it regulates transcription; localization is cell-type dependent. Reason: Figure 1 of PMID:17259263 visualizes ARF19-GFP in root nuclei, and PMID:31421981 independently confirms nuclear protein in meristem cells while identifying cytoplasmic assemblies in mature root cells. These data support nucleus without implying exclusive nuclear residence. Supporting Evidence: url:https://pmc.ncbi.nlm.nih.gov/articles/PMC1820965/ Nuclear localization of ARF7-GFP and ARF19-GFP fusion proteins. PMID:31421981 ARF7-Venus and ARF19-Venus localized to the nucleus in meristem cells near the root tip |
| GO:0006355 regulation of DNA-templated transcription | IBA GO_REF:0000033 | MODIFY | Summary: ARF19 is a transcription factor that regulates transcription by binding to AuxREs. This is the core function of ARF proteins [PMID:15659631]. Reason: ARF19 directly activates auxin-responsive target transcription; the positive direction is supported by target-promoter assays, not merely by a transcription-factor family name. The parent regulation term is true and is refined to that supported direction. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000774836 · PTN000774836 SUPPORTS TRANSFER The inherited general regulatory function at PANTHER:PTN000774836 is supported for ARF19. Target-specific experiments establish the direction used for refinement; no misplaced ancestral node, loss of function, donor-count weakness or circularity is alleged. Proposed replacements: positive regulation of DNA-templated transcription Supporting Evidence: PMID:15659631 The AUXIN RESPONSE FACTOR (ARF) gene family products, together with the AUXIN/INDOLE-3-ACETIC ACID proteins, regulate auxin-mediated transcriptional activation/repression |
| GO:0009733 response to auxin | IBA GO_REF:0000033 | ACCEPT | Summary: ARF19 mediates cellular responses to auxin by activating transcription of auxin-responsive genes upon release from AUX/IAA repression. This is a core function shared across ARF family members [PMID:15659631, PMID:16461383]. Reason: ARF19 is a key effector of auxin responses. Its transcriptional activity is released when auxin triggers degradation of AUX/IAA repressors. This is a core biological process annotation. Supporting Evidence: PMID:16461383 Both arf19 and arf7 mutants isolated from our forward genetic screens are auxin resistant PMID:15659631 Global gene expression analysis revealed that auxin-induced gene expression is severely impaired in the arf7 single and arf7 arf19 double mutants |
| GO:0010311 lateral root formation | IBA GO_REF:0000033 | ACCEPT | Summary: ARF19 together with ARF7 is essential for lateral root formation in Arabidopsis. The arf7 arf19 double mutant is severely impaired in lateral root formation [PMID:15659631, PMID:17259263]. Reason: Direct activation of LBD16/LBD29 and mutant/induction evidence place this ARF in the execution of lateral-root formation, not simply as a gene whose absence causes nonspecific growth failure. This is a major shared native role of ARF7 and ARF19. Supporting Evidence: PMID:15659631 arf7 arf19 has a strong auxin-related phenotype not observed in the arf7 and arf19 single mutants, including severely impaired lateral root formation PMID:17259263 The arf7 arf19 double knockout mutant is severely impaired in lateral root formation |
| GO:0048366 leaf development | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: ARF7 and ARF19 together promote leaf cell expansion. The arf7 arf19 double mutant shows decreased leaf cell expansion [PMID:15960621]. Reason: While ARF7/ARF19 do contribute to leaf development, this is a secondary pleiotropic effect. The primary core function is in lateral root formation and auxin-mediated transcription. Leaf development is a downstream consequence of their transcriptional activity. Supporting Evidence: PMID:15960621 in combination with mutations in NPH4/ARF7, encoding the most closely related ARF, they cause several phenotypes including a drastic decrease in lateral and adventitious root formation and a decrease in leaf cell expansion |
| GO:1990110 callus formation | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: ARF19 together with ARF7 is required for callus formation during cellular dedifferentiation. They recruit ATXR2 to deposit H3K36me3 at LBD gene promoters [PMID:29184030]. Reason: Retain the callus-regeneration context supported by ARF7/ARF19 recruitment of chromatin regulators to LBD targets. This is a specific regeneration output rather than a universal activity in all tissues; the machine-supplied evidence code is preserved. Supporting Evidence: PMID:29184030 Leaf explants from arf7-1arf19-2 double mutants were defective in callus formation and showed reduced H3K36me3 accumulation at LBD promoters |
| GO:0003677 DNA binding | IEA GO_REF:0000120 | MODIFY | Summary: ARF19 contains a B3-type DNA binding domain and binds to AuxRE sequences. This IEA annotation is correct but overly general [PMID:15659631]. Reason: ARF19 recognizes AuxRE sequences in regulatory DNA. Sequence-specific cis-regulatory DNA binding is supported by the target-gene/biochemical evidence and is more precise than unrestricted DNA binding. Proposed replacements: cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:15659631 The AUXIN RESPONSE FACTOR (ARF) gene family products, together with the AUXIN/INDOLE-3-ACETIC ACID proteins, regulate auxin-mediated transcriptional activation/repression |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: ARF19 is nuclear in root cells where it regulates transcription; localization is cell-type dependent. Reason: Figure 1 of PMID:17259263 visualizes ARF19-GFP in root nuclei, and PMID:31421981 independently confirms nuclear protein in meristem cells while identifying cytoplasmic assemblies in mature root cells. These data support nucleus without implying exclusive nuclear residence. Supporting Evidence: url:https://pmc.ncbi.nlm.nih.gov/articles/PMC1820965/ Nuclear localization of ARF7-GFP and ARF19-GFP fusion proteins. PMID:31421981 ARF7-Venus and ARF19-Venus localized to the nucleus in meristem cells near the root tip |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | MODIFY | Summary: IEA annotation based on InterPro mapping. Correct and consistent with ARF19's role as a transcription factor. Reason: ARF19 directly activates auxin-responsive target transcription; the positive direction is supported by target-promoter assays, not merely by a transcription-factor family name. The parent regulation term is true and is refined to that supported direction. Proposed replacements: positive regulation of DNA-templated transcription Supporting Evidence: PMID:15659631 The AUXIN RESPONSE FACTOR (ARF) gene family products, together with the AUXIN/INDOLE-3-ACETIC ACID proteins, regulate auxin-mediated transcriptional activation/repression |
| GO:0009725 response to hormone | IEA GO_REF:0000002 | MODIFY | Summary: This is a parent term of "response to auxin". The annotation is correct but less specific than the available specific term. Reason: ARF19 participates in auxin-responsive transcription and in the experimentally documented interaction between auxin and ethylene growth responses. Both supported hormone-response descendants are retained; this does not make ARF19 an ethylene receptor. Proposed replacements: response to auxin response to ethylene Supporting Evidence: PMID:16461383 Here we show that ARF19 and ARF7 not only participate in auxin signaling, but also play a critical role in ethylene responses in Arabidopsis (Arabidopsis thaliana) roots, indicating that the ARFs serve as a cross talk point between the two hormones |
| GO:0009734 auxin-activated signaling pathway | IEA GO_REF:0000043 | ACCEPT | Summary: GO:0009734 includes the auxin-signaling series that begins with auxin perception and ends with modulation of downstream cellular processes such as transcription. ARF19 is a canonical downstream transcriptional effector in this pathway. Reason: ARF19 does not bind auxin directly, but the GO term explicitly covers the pathway through transcriptional output. Mutant and transcriptomic evidence show that auxin-induced gene expression is impaired when ARF7/ARF19 function is lost, supporting ARF19's participation in auxin-activated signaling and avoiding an overly narrow receptor/proximal-transduction interpretation of this GO term. Supporting Evidence: PMID:15659631 Global gene expression analysis revealed that auxin-induced gene expression is severely impaired in the arf7 single and arf7 arf19 double mutants |
| GO:0005515 protein binding | IPI PMID:15889151 Developmental specificity of auxin response by pairs of ARF ... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA3/SHY2 (UniProtKB:Q38822) from a study of matched ARF-Aux/IAA pairs (stabilized shy2-2 inhibits ARF7/ARF19-dependent gravitropism and auxin-induced root gene expression). Reason: The cited study reports ARF19 binding to IAA3/SHY2; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:15889151 gravitropism and auxin-induced gene expression in the root, which were promoted by functionally redundant NPH4/ARF7 and ARF19 proteins, were inhibited by shy2-2, but not by bdl protein |
| GO:0005515 protein binding | IPI PMID:16236149 Tissue-specific expression of stabilized SOLITARY-ROOT/IAA14... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA14/SLR (UniProtKB:Q38832) from yeast two-hybrid assays accompanying tissue-specific expression of stabilized mIAA14. Reason: The cited study reports ARF19 binding to IAA14/SLR; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:16236149 IAA14 interacted with ARF7 and ARF19 in yeasts |
| GO:0005515 protein binding | IPI PMID:18505759 Domain II mutations in CRANE/IAA18 suppress lateral root for... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA18 (UniProtKB:O24408) from yeast two-hybrid assays in the CRANE/IAA18 study. Reason: The cited study reports ARF19 binding to IAA18; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:18505759 IAA18 interacts with AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 |
| GO:0005515 protein binding | IPI PMID:21734647 The auxin signalling network translates dynamic input into r... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA16 (UniProtKB:O24407) from the systematic shoot-apex Aux/IAA-ARF yeast two-hybrid interactome. Reason: The cited study reports ARF19 binding to IAA16; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:21734647 The auxin signalling network translates dynamic input into r... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA18 (UniProtKB:O24408) from the systematic shoot-apex Aux/IAA-ARF yeast two-hybrid interactome. Reason: The cited study reports ARF19 binding to IAA18; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:21734647 The auxin signalling network translates dynamic input into r... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA19/MSG2 (UniProtKB:O24409) from the systematic shoot-apex Aux/IAA-ARF yeast two-hybrid interactome. Reason: The cited study reports ARF19 binding to IAA19/MSG2; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:21734647 The auxin signalling network translates dynamic input into r... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA4 (UniProtKB:P33077) from the systematic shoot-apex Aux/IAA-ARF yeast two-hybrid interactome. Reason: The cited study reports ARF19 binding to IAA4; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:21734647 The auxin signalling network translates dynamic input into r... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA5 (UniProtKB:P33078) from the systematic shoot-apex Aux/IAA-ARF yeast two-hybrid interactome. Reason: The cited study reports ARF19 binding to IAA5; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:21734647 The auxin signalling network translates dynamic input into r... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA1 (UniProtKB:P49677) from the systematic shoot-apex Aux/IAA-ARF yeast two-hybrid interactome. Reason: The cited study reports ARF19 binding to IAA1; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:21734647 The auxin signalling network translates dynamic input into r... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA2 (UniProtKB:P49678) from the systematic shoot-apex Aux/IAA-ARF yeast two-hybrid interactome. Reason: The cited study reports ARF19 binding to IAA2; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:21734647 The auxin signalling network translates dynamic input into r... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA17/AXR3 (UniProtKB:P93830) from the systematic shoot-apex Aux/IAA-ARF yeast two-hybrid interactome. Reason: The cited study reports ARF19 binding to IAA17/AXR3; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:21734647 The auxin signalling network translates dynamic input into r... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA3/SHY2 (UniProtKB:Q38822) from the systematic shoot-apex Aux/IAA-ARF yeast two-hybrid interactome. Reason: The cited study reports ARF19 binding to IAA3/SHY2; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:21734647 The auxin signalling network translates dynamic input into r... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA7/AXR2 (UniProtKB:Q38825) from the systematic shoot-apex Aux/IAA-ARF yeast two-hybrid interactome. Reason: The cited study reports ARF19 binding to IAA7/AXR2; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:21734647 The auxin signalling network translates dynamic input into r... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA8 (UniProtKB:Q38826) from the systematic shoot-apex Aux/IAA-ARF yeast two-hybrid interactome. Reason: The cited study reports ARF19 binding to IAA8; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:21734647 The auxin signalling network translates dynamic input into r... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA10 (UniProtKB:Q38828) from the systematic shoot-apex Aux/IAA-ARF yeast two-hybrid interactome. Reason: The cited study reports ARF19 binding to IAA10; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:21734647 The auxin signalling network translates dynamic input into r... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA13 (UniProtKB:Q38831) from the systematic shoot-apex Aux/IAA-ARF yeast two-hybrid interactome. Reason: The cited study reports ARF19 binding to IAA13; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:21734647 The auxin signalling network translates dynamic input into r... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA14/SLR (UniProtKB:Q38832) from the systematic shoot-apex Aux/IAA-ARF yeast two-hybrid interactome. Reason: The cited study reports ARF19 binding to IAA14/SLR; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:21734647 The auxin signalling network translates dynamic input into r... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA32 (UniProtKB:Q8RYC6) from the systematic shoot-apex Aux/IAA-ARF yeast two-hybrid interactome. IAA32 is a non-canonical Aux/IAA that lacks the degron domain II but retains the PB1 domain that mediates ARF heterodimerization. Reason: The reported partner belongs to the noncanonical IAA32/IAA34 repressors. PMID:30944466 establishes their transcriptional-repressor role and stabilization through TMK1 signaling, supporting corepressor binding while excluding the assumption that every Aux/IAA pair uses the canonical TIR1-dependent degradation switch. The interaction screen does not establish TMK1 regulation of this particular ARF19 complex. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:21734647 The auxin signalling network translates dynamic input into r... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA29 (UniProtKB:Q93WC4) from the systematic shoot-apex Aux/IAA-ARF yeast two-hybrid interactome. Reason: The cited study reports ARF19 binding to IAA29; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:21734647 The auxin signalling network translates dynamic input into r... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA34 (UniProtKB:Q9C5X0) from the systematic shoot-apex Aux/IAA-ARF yeast two-hybrid interactome. IAA34 is a non-canonical Aux/IAA that lacks the degron domain II but retains the PB1 domain that mediates ARF heterodimerization. Reason: The reported partner belongs to the noncanonical IAA32/IAA34 repressors. PMID:30944466 establishes their transcriptional-repressor role and stabilization through TMK1 signaling, supporting corepressor binding while excluding the assumption that every Aux/IAA pair uses the canonical TIR1-dependent degradation switch. The interaction screen does not establish TMK1 regulation of this particular ARF19 complex. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:21734647 The auxin signalling network translates dynamic input into r... | MODIFY | Summary: ARF19 binds the noncanonical Aux/IAA protein IAA33 in the cited interaction screen; the regulatory sign of this particular ARF19 pair is not established. Reason: The screen establishes an ARF19–IAA33 interaction. IAA33 is a noncanonical transcriptional coregulator: PMID:31617603 demonstrates competition with IAA5 for repressive ARF10/16, not a universal EAR/TPL recruitment mechanism or canonical auxin-induced degradation. Coregulator binding preserves the supported partner role without claiming that IAA33 directly represses ARF19. Proposed replacements: transcription coregulator binding Supporting Evidence: PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators url:https://pmc.ncbi.nlm.nih.gov/articles/PMC6939196/ IAA33, which has no repression activity on ARFs because of the absence of domain I |
| GO:0005515 protein binding | IPI PMID:21734647 The auxin signalling network translates dynamic input into r... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA28 (UniProtKB:Q9XFM0) from the systematic shoot-apex Aux/IAA-ARF yeast two-hybrid interactome. Reason: The cited study reports ARF19 binding to IAA28; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA16 (UniProtKB:O24407) from the CrY2H-seq transcription-factor interactome. Reason: The cited study reports ARF19 binding to IAA16; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:28650476 we observed a significant preferential family interaction between eight ARF members and 23 AUX/IAA members PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA19/MSG2 (UniProtKB:O24409) from the CrY2H-seq transcription-factor interactome. Reason: The cited study reports ARF19 binding to IAA19/MSG2; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:28650476 we observed a significant preferential family interaction between eight ARF members and 23 AUX/IAA members PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA4 (UniProtKB:P33077) from the CrY2H-seq transcription-factor interactome. Reason: The cited study reports ARF19 binding to IAA4; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:28650476 we observed a significant preferential family interaction between eight ARF members and 23 AUX/IAA members PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA5 (UniProtKB:P33078) from the CrY2H-seq transcription-factor interactome. Reason: The cited study reports ARF19 binding to IAA5; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:28650476 we observed a significant preferential family interaction between eight ARF members and 23 AUX/IAA members PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA1 (UniProtKB:P49677) from the CrY2H-seq transcription-factor interactome. Reason: The cited study reports ARF19 binding to IAA1; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:28650476 we observed a significant preferential family interaction between eight ARF members and 23 AUX/IAA members PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA2 (UniProtKB:P49678) from the CrY2H-seq transcription-factor interactome. Reason: The cited study reports ARF19 binding to IAA2; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:28650476 we observed a significant preferential family interaction between eight ARF members and 23 AUX/IAA members PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA17/AXR3 (UniProtKB:P93830) from the CrY2H-seq transcription-factor interactome. Reason: The cited study reports ARF19 binding to IAA17/AXR3; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:28650476 we observed a significant preferential family interaction between eight ARF members and 23 AUX/IAA members PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA3/SHY2 (UniProtKB:Q38822) from the CrY2H-seq transcription-factor interactome. Reason: The cited study reports ARF19 binding to IAA3/SHY2; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:28650476 we observed a significant preferential family interaction between eight ARF members and 23 AUX/IAA members PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA7/AXR2 (UniProtKB:Q38825) from the CrY2H-seq transcription-factor interactome. Reason: The cited study reports ARF19 binding to IAA7/AXR2; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:28650476 we observed a significant preferential family interaction between eight ARF members and 23 AUX/IAA members PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA8 (UniProtKB:Q38826) from the CrY2H-seq transcription-factor interactome. Reason: The cited study reports ARF19 binding to IAA8; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:28650476 we observed a significant preferential family interaction between eight ARF members and 23 AUX/IAA members PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA10 (UniProtKB:Q38828) from the CrY2H-seq transcription-factor interactome. Reason: The cited study reports ARF19 binding to IAA10; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:28650476 we observed a significant preferential family interaction between eight ARF members and 23 AUX/IAA members PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA11 (UniProtKB:Q38829) from the CrY2H-seq transcription-factor interactome. Reason: The cited study reports ARF19 binding to IAA11; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:28650476 we observed a significant preferential family interaction between eight ARF members and 23 AUX/IAA members PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA13 (UniProtKB:Q38831) from the CrY2H-seq transcription-factor interactome. Reason: The cited study reports ARF19 binding to IAA13; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:28650476 we observed a significant preferential family interaction between eight ARF members and 23 AUX/IAA members PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA14/SLR (UniProtKB:Q38832) from the CrY2H-seq transcription-factor interactome. Reason: The cited study reports ARF19 binding to IAA14/SLR; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:28650476 we observed a significant preferential family interaction between eight ARF members and 23 AUX/IAA members PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA32 (UniProtKB:Q8RYC6) from the CrY2H-seq transcription-factor interactome. IAA32 is a non-canonical Aux/IAA that lacks the degron domain II but retains the PB1 domain that mediates ARF heterodimerization. Reason: The reported partner belongs to the noncanonical IAA32/IAA34 repressors. PMID:30944466 establishes their transcriptional-repressor role and stabilization through TMK1 signaling, supporting corepressor binding while excluding the assumption that every Aux/IAA pair uses the canonical TIR1-dependent degradation switch. The interaction screen does not establish TMK1 regulation of this particular ARF19 complex. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:28650476 we observed a significant preferential family interaction between eight ARF members and 23 AUX/IAA members PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA29 (UniProtKB:Q93WC4) from the CrY2H-seq transcription-factor interactome. Reason: The cited study reports ARF19 binding to IAA29; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:28650476 we observed a significant preferential family interaction between eight ARF members and 23 AUX/IAA members PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA34 (UniProtKB:Q9C5X0) from the CrY2H-seq transcription-factor interactome. IAA34 is a non-canonical Aux/IAA that lacks the degron domain II but retains the PB1 domain that mediates ARF heterodimerization. Reason: The reported partner belongs to the noncanonical IAA32/IAA34 repressors. PMID:30944466 establishes their transcriptional-repressor role and stabilization through TMK1 signaling, supporting corepressor binding while excluding the assumption that every Aux/IAA pair uses the canonical TIR1-dependent degradation switch. The interaction screen does not establish TMK1 regulation of this particular ARF19 complex. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:28650476 we observed a significant preferential family interaction between eight ARF members and 23 AUX/IAA members PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | MODIFY | Summary: ARF19 binds the noncanonical Aux/IAA protein IAA33 in the cited interaction screen; the regulatory sign of this particular ARF19 pair is not established. Reason: The screen establishes an ARF19–IAA33 interaction. IAA33 is a noncanonical transcriptional coregulator: PMID:31617603 demonstrates competition with IAA5 for repressive ARF10/16, not a universal EAR/TPL recruitment mechanism or canonical auxin-induced degradation. Coregulator binding preserves the supported partner role without claiming that IAA33 directly represses ARF19. Proposed replacements: transcription coregulator binding Supporting Evidence: PMID:28650476 we observed a significant preferential family interaction between eight ARF members and 23 AUX/IAA members PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators url:https://pmc.ncbi.nlm.nih.gov/articles/PMC6939196/ IAA33, which has no repression activity on ARFs because of the absence of domain I |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | REMOVE | Summary: ARF19 interaction with NOT9B (Q9LXU1; CCR4-NOT/Rcd1-like protein) from the CrY2H-seq transcription-factor interactome; a single high-throughput Y2H hit. Reason: Generic protein binding from a single high-throughput screen, with no follow-up and no informative molecular-function term for the ARF19 side. Removal does not imply the interaction is false; it simply carries no functional information as protein binding. Supporting Evidence: PMID:28650476 We applied CrY2H-seq to investigate sparsely annotated Arabidopsis thaliana transcription factors interactions |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA28 (UniProtKB:Q9XFM0) from the CrY2H-seq transcription-factor interactome. Reason: The cited study reports ARF19 binding to IAA28; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:28650476 we observed a significant preferential family interaction between eight ARF members and 23 AUX/IAA members PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA27 (UniProtKB:Q9ZSY8) from the CrY2H-seq transcription-factor interactome. Reason: The cited study reports ARF19 binding to IAA27; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:28650476 we observed a significant preferential family interaction between eight ARF members and 23 AUX/IAA members PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:32612234 Extensive signal integration by the phytohormone protein net... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA16 (UniProtKB:O24407) from the phytohormone signalling protein-interaction network (Y2H). Reason: The cited study reports ARF19 binding to IAA16; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:32612234 we experimentally generated a systems-level map of the Arabidopsis phytohormone signalling network, consisting of more than 2,000 binary protein-protein interactions PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:32612234 Extensive signal integration by the phytohormone protein net... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA18 (UniProtKB:O24408) from the phytohormone signalling protein-interaction network (Y2H). Reason: The cited study reports ARF19 binding to IAA18; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:32612234 we experimentally generated a systems-level map of the Arabidopsis phytohormone signalling network, consisting of more than 2,000 binary protein-protein interactions PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:32612234 Extensive signal integration by the phytohormone protein net... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA17/AXR3 (UniProtKB:P93830) from the phytohormone signalling protein-interaction network (Y2H). Reason: The cited study reports ARF19 binding to IAA17/AXR3; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:32612234 we experimentally generated a systems-level map of the Arabidopsis phytohormone signalling network, consisting of more than 2,000 binary protein-protein interactions PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:32612234 Extensive signal integration by the phytohormone protein net... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA7/AXR2 (UniProtKB:Q38825) from the phytohormone signalling protein-interaction network (Y2H). Reason: The cited study reports ARF19 binding to IAA7/AXR2; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:32612234 we experimentally generated a systems-level map of the Arabidopsis phytohormone signalling network, consisting of more than 2,000 binary protein-protein interactions PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:32612234 Extensive signal integration by the phytohormone protein net... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA10 (UniProtKB:Q38828) from the phytohormone signalling protein-interaction network (Y2H). Reason: The cited study reports ARF19 binding to IAA10; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:32612234 we experimentally generated a systems-level map of the Arabidopsis phytohormone signalling network, consisting of more than 2,000 binary protein-protein interactions PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:36088536 The protein-protein interaction landscape of transcription f... | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA27 (UniProtKB:Q9ZSY8) from the gynoecium transcription-factor interaction map (Y2H). Reason: The cited study reports ARF19 binding to IAA27; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:36088536 We analyzed almost 4500 combinations and detected more than 250 protein-protein interactions PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0005515 protein binding | IPI PMID:9342315 Protein-protein interactions among the Aux/IAA proteins. | MODIFY | Summary: ARF19 interaction with the Aux/IAA protein IAA1 (UniProtKB:P49677) from the yeast two-hybrid screen of Aux/IAA protein interactions (IAA1 bait). Reason: The cited study reports ARF19 binding to IAA1; the independently established Aux/IAA repressor role supports the informative corepressor-binding class. This does not establish that every measured pair recruits TPL with the same affinity, operates in the same cells, or confers identical auxin sensitivity. Partner identity is retained in the original supporting entities. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:9342315 Screening an Arabidopsis lambda-ACT cDNA library using IAA1 as a bait reveals heterotypic interactions of IAA1 with known and newly discovered members of the Arabidopsis Aux/IAA gene family PMID:21734647 In this network, the vast majority of the Aux/IAAs interact with all the ARF activators, suggesting that most Aux/IAAs have the potential to act as repressors of the transcriptional activity of ARF activators |
| GO:0000987 cis-regulatory region sequence-specific DNA binding | IDA PMID:29681137 LBD18 uses a dual mode of a positive feedback loop to regula... | ACCEPT | Summary: This paper demonstrates LBD18 binds to ARF19 promoter to regulate its expression. ARF7/ARF19 directly bind AuxRE in LBD18 promoter. This supports ARF19's sequence-specific DNA binding activity [PMID:29681137]. Reason: Excellent, specific annotation for ARF19's molecular function. The IDA evidence from this paper demonstrates direct DNA binding to cis-regulatory sequences. Supporting Evidence: PMID:29681137 We showed that ARF7 and ARF19 directly bind AuxRE in the LBD18 promoter |
| GO:1990110 callus formation | IMP PMID:29184030 Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD ... | KEEP AS NON CORE | Summary: The arf7-1 arf19-2 double mutant is defective in callus formation. ARF19 with ARF7 recruits ATXR2 to LBD promoters to facilitate cellular dedifferentiation [PMID:29184030]. Reason: Retain the callus-regeneration context supported by ARF7/ARF19 recruitment of chromatin regulators to LBD targets. This is a specific regeneration output rather than a universal activity in all tissues; the machine-supplied evidence code is preserved. Supporting Evidence: PMID:29184030 Leaf explants from arf7-1arf19-2 double mutants were defective in callus formation and showed reduced H3K36me3 accumulation at LBD promoters |
| GO:0005515 protein binding | IPI PMID:29184030 Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD ... | MODIFY | Summary: ARF19 interacts with the histone methyltransferase ATXR2 (AGI_LocusCode:AT3G21820), which it recruits to LBD promoters to deposit H3K36me3 during callus formation. Reason: The IPI evidence for ATXR2 interaction is valid, but protein binding is too general. ATXR2 is a histone methyltransferase, so histone methyltransferase binding is the more specific molecular-function term for this interaction. Proposed replacements: histone methyltransferase binding Supporting Evidence: PMID:29184030 ATXR2 was recruited to LBD promoters by the transcription factors AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 |
| GO:0005515 protein binding | IPI PMID:29184030 Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD ... | MODIFY | Summary: ARF19 interacts with the histone methyltransferase ATXR2 (UniProtKB:Q5PP37), which it recruits to LBD promoters to deposit H3K36me3 during callus formation. Reason: The IPI evidence for ATXR2 interaction is valid, but protein binding is too general. ATXR2 is a histone methyltransferase, so histone methyltransferase binding is the more specific molecular-function term for this interaction. Proposed replacements: histone methyltransferase binding Supporting Evidence: PMID:29184030 ATXR2 was recruited to LBD promoters by the transcription factors AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 |
| GO:0005634 nucleus | IDA PMID:29184030 Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD ... | ACCEPT | Summary: ARF19 is nuclear in root cells where it regulates transcription; localization is cell-type dependent. Reason: Figure 1 of PMID:17259263 visualizes ARF19-GFP in root nuclei, and PMID:31421981 independently confirms nuclear protein in meristem cells while identifying cytoplasmic assemblies in mature root cells. These data support nucleus without implying exclusive nuclear residence. Supporting Evidence: url:https://pmc.ncbi.nlm.nih.gov/articles/PMC1820965/ Nuclear localization of ARF7-GFP and ARF19-GFP fusion proteins. PMID:31421981 ARF7-Venus and ARF19-Venus localized to the nucleus in meristem cells near the root tip |
| GO:0005515 protein binding | IPI PMID:29923261 JMJ30-mediated demethylation of H3K9me3 drives tissue identi... | MODIFY | Summary: ARF19 interacts with the JmjC histone demethylase JMJ30 (UniProtKB:Q8RWR1), which binds LBD16/LBD29 promoters together with ARF7/ARF19 to remove H3K9me3 during callus formation. Reason: The IPI evidence for the ARF19-JMJ30 interaction is valid, but protein binding is too general. GO has no histone demethylase binding term (see suggested_questions), so enzyme binding is the most specific available molecular-function term. Proposed replacements: enzyme binding Supporting Evidence: PMID:29923261 The JMJ30 protein binds to promoters of the LBD16 and LBD29 genes along with AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 and activates LBD expression |
| GO:0000976 transcription cis-regulatory region binding | IPI PMID:25533953 An Arabidopsis gene regulatory network for secondary cell wa... | ACCEPT | Summary: TAIR/GOA records an IPI annotation for ARF19 cis-regulatory region binding from this enhanced yeast one-hybrid secondary cell-wall network study, with target locus AT2G40890 listed in the GOA WITH/FROM field. Reason: The cached article text describes the yeast one-hybrid promoter-binding screen but does not expose all supplementary interaction rows, so this annotation defers to the curator's reading of the full text for the specific target; it is consistent with independently supported ARF19 cis-regulatory binding activity (direct regulation of LBD promoters). Supporting Evidence: PMID:25533953 Our Y1H approach revealed a highly interconnected regulatory network. On average, each cell wall gene promoter was bound by 5 transcription factors PMID:17259263 ARF7 and ARF19 directly regulate the auxin-mediated transcription of LATERAL ORGAN BOUNDARIES-DOMAIN16/ASYMMETRIC LEAVES2-LIKE18 (LBD16/ASL18) and/or LBD29/ASL16 in roots |
| GO:0000976 transcription cis-regulatory region binding | IPI PMID:27650334 Transcriptional Regulation of Arabidopsis Polycomb Repressiv... | ACCEPT | Summary: TAIR/GOA records an IPI annotation for ARF19 binding to a PRC2 gene promoter from this enhanced yeast one-hybrid study, with target locus AT4G02020 listed in the GOA WITH/FROM field. Reason: The cached article text describes enhanced yeast one-hybrid discovery of upstream regulators of PRC2 genes but does not show every protein-DNA interaction row, so this annotation defers to the curator's reading of the full text for the specific target; it is consistent with ARF19's established cis-regulatory binding function. Supporting Evidence: PMID:27650334 Using enhanced yeast one-hybrid analysis, upstream regulators of the PRC2 member genes are identified PMID:17259263 ARF7 and ARF19 directly regulate the auxin-mediated transcription of LATERAL ORGAN BOUNDARIES-DOMAIN16/ASYMMETRIC LEAVES2-LIKE18 (LBD16/ASL18) and/or LBD29/ASL16 in roots |
| GO:0000976 transcription cis-regulatory region binding | IPI PMID:30356219 Transcriptional regulation of nitrogen-associated metabolism... | ACCEPT | Summary: TAIR/GOA records IPI annotations for ARF19 cis-regulatory binding to nitrogen-associated metabolism/growth genes from this transcriptional regulatory network study, with target loci AT4G04955, AT5G07440, and AT5G26340 listed in the GOA WITH/FROM field. Reason: The cached abstract summarizes the transcriptional regulatory network study but does not expose individual protein-DNA interaction rows, so this annotation defers to the curator's reading of the full text for the specific targets; it is consistent with ARF19's established cis-regulatory binding function. Supporting Evidence: PMID:30356219 Here we present a transcriptional regulatory network and twenty-one transcription factors that regulate the architecture of root and shoot systems in response to changes in nitrogen availability. PMID:17259263 ARF7 and ARF19 directly regulate the auxin-mediated transcription of LATERAL ORGAN BOUNDARIES-DOMAIN16/ASYMMETRIC LEAVES2-LIKE18 (LBD16/ASL18) and/or LBD29/ASL16 in roots |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: ARF19 is nuclear in root cells where it regulates transcription; localization is cell-type dependent. Reason: Figure 1 of PMID:17259263 visualizes ARF19-GFP in root nuclei, and PMID:31421981 independently confirms nuclear protein in meristem cells while identifying cytoplasmic assemblies in mature root cells. These data support nucleus without implying exclusive nuclear residence. Supporting Evidence: url:https://pmc.ncbi.nlm.nih.gov/articles/PMC1820965/ Nuclear localization of ARF7-GFP and ARF19-GFP fusion proteins. PMID:31421981 ARF7-Venus and ARF19-Venus localized to the nucleus in meristem cells near the root tip |
| GO:0043565 sequence-specific DNA binding | IDA PMID:23020607 BAT1, a putative acyltransferase, modulates brassinosteroid ... | ACCEPT | Summary: ARF19 has sequence-specific DNA-binding activity, including binding of AuxRE-containing LBD regulatory DNA. Reason: The original IDA claim is consistent with independently established ARF19 DNA recognition; the abstract-only PMID:23020607 record does not justify inventing an exact assayed promoter. The direct LBD evidence independently supports this activity. Supporting Evidence: PMID:29681137 ARF7 and ARF19 directly bind AuxRE in the LBD18 promoter |
| GO:0010311 lateral root formation | IGI PMID:17259263 ARF7 and ARF19 regulate lateral root formation via direct ac... | ACCEPT | Summary: The arf7 arf19 double mutant is severely impaired in lateral root formation, demonstrating genetic interaction between these functionally redundant transcription factors [PMID:17259263]. Reason: Direct activation of LBD16/LBD29 and mutant/induction evidence place this ARF in the execution of lateral-root formation, not simply as a gene whose absence causes nonspecific growth failure. This is a major shared native role of ARF7 and ARF19. Supporting Evidence: PMID:17259263 The arf7 arf19 double knockout mutant is severely impaired in lateral root formation |
| GO:0048366 leaf development | IGI PMID:15960621 NPH4/ARF7 and ARF19 promote leaf expansion and auxin-induced... | KEEP AS NON CORE | Summary: The arf7 arf19 double mutant shows decreased leaf cell expansion, indicating redundant roles in leaf development [PMID:15960621]. Reason: Valid IGI evidence for ARF19 contribution to leaf development. However, this is a secondary pleiotropic effect compared to the primary lateral root function. Supporting Evidence: PMID:15960621 in combination with mutations in NPH4/ARF7, encoding the most closely related ARF, they cause several phenotypes including a drastic decrease in lateral and adventitious root formation and a decrease in leaf cell expansion |
| GO:0048527 lateral root development | IGI PMID:15960621 NPH4/ARF7 and ARF19 promote leaf expansion and auxin-induced... | MODIFY | Summary: The arf7 arf19 double mutant shows drastic decrease in lateral root formation [PMID:15960621]. Reason: The directly resolved shared ARF7/ARF19 role is activation of the LBD program that initiates lateral-root formation (PMID:17259263). Refine the developmental parent to the already-supported formation term, without denying participation in the broader developmental process. Proposed replacements: lateral root formation Supporting Evidence: PMID:15960621 in combination with mutations in NPH4/ARF7, encoding the most closely related ARF, they cause several phenotypes including a drastic decrease in lateral and adventitious root formation |
| GO:0003677 DNA binding | IDA PMID:17259263 ARF7 and ARF19 regulate lateral root formation via direct ac... | MODIFY | Summary: Direct experimental evidence for ARF19 DNA binding from the foundational paper on ARF7/ARF19 function [PMID:17259263]. Reason: ARF19 recognizes AuxRE sequences in regulatory DNA. Sequence-specific cis-regulatory DNA binding is supported by the target-gene/biochemical evidence and is more precise than unrestricted DNA binding. Proposed replacements: cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:17259263 ARF7 and ARF19 directly regulate the auxin-mediated transcription of LATERAL ORGAN BOUNDARIES-DOMAIN16/ASYMMETRIC LEAVES2-LIKE18 (LBD16/ASL18) and/or LBD29/ASL16 in roots |
| GO:0005634 nucleus | IDA PMID:17259263 ARF7 and ARF19 regulate lateral root formation via direct ac... | ACCEPT | Summary: ARF19 is nuclear in root cells where it regulates transcription; localization is cell-type dependent. Reason: Figure 1 of PMID:17259263 visualizes ARF19-GFP in root nuclei, and PMID:31421981 independently confirms nuclear protein in meristem cells while identifying cytoplasmic assemblies in mature root cells. These data support nucleus without implying exclusive nuclear residence. Supporting Evidence: url:https://pmc.ncbi.nlm.nih.gov/articles/PMC1820965/ Nuclear localization of ARF7-GFP and ARF19-GFP fusion proteins. PMID:31421981 ARF7-Venus and ARF19-Venus localized to the nucleus in meristem cells near the root tip |
| GO:0009733 response to auxin | IMP PMID:15659631 Functional genomic analysis of the AUXIN RESPONSE FACTOR gen... | ACCEPT | Summary: arf19 mutant (and especially arf7 arf19 double mutant) shows impaired auxin-induced gene expression, demonstrating ARF19's role in auxin response [PMID:15659631]. Reason: Strong IMP evidence from mutant phenotype analysis. This is a core annotation for ARF19 function. Supporting Evidence: PMID:15659631 Global gene expression analysis revealed that auxin-induced gene expression is severely impaired in the arf7 single and arf7 arf19 double mutants |
| GO:0009733 response to auxin | IMP PMID:17259263 ARF7 and ARF19 regulate lateral root formation via direct ac... | ACCEPT | Summary: arf7 arf19 double mutant shows severely impaired auxin-mediated responses including lateral root formation [PMID:17259263]. Reason: Additional IMP evidence confirming ARF19's essential role in auxin response. Duplicate GO term with different reference is acceptable. Supporting Evidence: PMID:17259263 ARF7 and ARF19 directly regulate the auxin-mediated transcription of LATERAL ORGAN BOUNDARIES-DOMAIN16/ASYMMETRIC LEAVES2-LIKE18 (LBD16/ASL18) and/or LBD29/ASL16 in roots |
| GO:0005634 nucleus | TAS PMID:9342315 Protein-protein interactions among the Aux/IAA proteins. | ACCEPT | Summary: ARF19 is nuclear in root cells where it regulates transcription; localization is cell-type dependent. Reason: Figure 1 of PMID:17259263 visualizes ARF19-GFP in root nuclei, and PMID:31421981 independently confirms nuclear protein in meristem cells while identifying cytoplasmic assemblies in mature root cells. These data support nucleus without implying exclusive nuclear residence. Supporting Evidence: url:https://pmc.ncbi.nlm.nih.gov/articles/PMC1820965/ Nuclear localization of ARF7-GFP and ARF19-GFP fusion proteins. PMID:31421981 ARF7-Venus and ARF19-Venus localized to the nucleus in meristem cells near the root tip |
| GO:0009723 response to ethylene | IMP PMID:16461383 A role for auxin response factor 19 in auxin and ethylene si... | ACCEPT | Summary: arf19 mutant shows ethylene-insensitive roots, demonstrating ARF19's role in ethylene response integration. ARF19 expression is induced by ethylene [PMID:16461383]. Reason: Valid IMP evidence for ARF19 role in ethylene response. This represents hormone crosstalk function and is a legitimate annotation. Supporting Evidence: PMID:16461383 In addition to being auxin resistant, arf19 has also ethylene-insensitive roots and ARF19 expression is induced by ethylene treatment |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a... | MODIFY | Summary: ARF19 is classified as a transcription factor based on sequence similarity to characterized ARF family members [PMID:11118137]. Reason: ARF19 is an experimentally characterized transcriptional activator. Refine the true general DNA-binding transcription-factor activity to its demonstrated activating function; this does not classify every ARF family member as an activator. Proposed replacements: DNA-binding transcription activator activity Supporting Evidence: PMID:15659631 The AUXIN RESPONSE FACTOR (ARF) gene family products, together with the AUXIN/INDOLE-3-ACETIC ACID proteins, regulate auxin-mediated transcriptional activation/repression PMID:15960621 We show that ARF19, the fifth Q-rich ARF, also activates transcription |
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Download this section (compressed HTML)Q: What is the precise mechanism by which ARF19 recruits chromatin modifiers (ATXR2, JMJ30) to target promoters?
Q: Are there ARF19-specific target genes distinct from ARF7, or do they regulate entirely overlapping gene sets?
Q: What post-translational modifications regulate ARF19 activity beyond AUX/IAA binding?
Q: GO has histone methyltransferase binding (GO:1990226) and histone deacetylase binding (GO:0042826) but no histone demethylase binding term; should one be created to capture the ARF7/ARF19-JMJ30 interaction (currently GO:0019899 enzyme binding)?
Experiment: ChIP-seq comparing ARF19 and ARF7 binding sites genome-wide to identify shared vs. unique target genes
Hypothesis: ARF19 and ARF7 have largely overlapping but not identical target gene sets
Experiment: Structure-function analysis of ARF19 domains to determine requirements for chromatin modifier recruitment
Hypothesis: Specific regions of ARF19 beyond the PB1 domain mediate ATXR2/JMJ30 recruitment
Experiment: Time-resolved transcriptomics in arf19 single mutants vs. arf7 arf19 double mutants to dissect redundant vs. unique functions
Hypothesis: Some genes are uniquely regulated by ARF19 while others require both ARF7 and ARF19
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