ARF7 (AUXIN RESPONSE FACTOR 7; NPH4/MSG1/TIR5; At5g20730) is a class A (activator) AUXIN RESPONSE FACTOR transcription factor. It has an N-terminal B3 DNA-binding domain that binds AuxRE-containing regulatory sequences, a glutamine-rich middle region that activates transcription, and a C-terminal PB1 domain through which it homo-oligomerizes and heterodimerizes with Aux/IAA repressors (e.g. IAA14/SLR, IAA18/CRANE, IAA19/MSG2, IAA17). At low auxin, PB1-bound Aux/IAAs recruit TOPLESS co-repressors and restrain ARF7 target expression; auxin-triggered SCF(TIR1/AFB)-mediated Aux/IAA degradation releases ARF7 to activate early auxin-responsive genes. ARF7 acts largely redundantly with its closest paralog ARF19; together they directly activate LBD16/LBD29 (and LBD18) to initiate lateral roots, and they are required for hypocotyl and root tropic growth, leaf cell expansion, auxin-induced callus formation (recruiting the chromatin modifiers ATXR2 and JMJ30 to LBD promoters) and ethylene responses in roots. ARF7 activity is further tuned by BIN2 phosphorylation and by partitioning into cytoplasmic PB1-dependent condensates in tissues with low auxin responsiveness.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000976 transcription cis-regulatory region binding | IBA GO_REF:0000033 | ACCEPT | Summary: ARF family members bind auxin-response elements (TGTCTC/TGTCGG) in cis-regulatory regions through the B3 DNA-binding domain; phylogenetically inferred for the ARF clade. Reason: Core activity: ARF7 directly binds AuxREs of target genes such as LBD16/LBD29. Supporting Evidence: PMID:10318972 Auxin-response factors (ARFs) bind with specificity to TGTCTC auxin-response elements (AuxREs) 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:24485461 We show that ARF DNA-binding domains also homodimerize to generate cooperative DNA binding |
| GO:0003677 DNA binding | IDA PMID:17259263 ARF7 and ARF19 regulate lateral root formation via direct ac... | MODIFY | Summary: Direct DNA binding by ARF7 to target promoters (LBD16/LBD29) shown experimentally. Reason: ARF7 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:0003677 DNA binding | IEA GO_REF:0000002 | MODIFY | Summary: DNA binding from InterPro B3 domain mappings. Reason: ARF7 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:10318972 Auxin-response factors (ARFs) bind with specificity to TGTCTC auxin-response elements (AuxREs) |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a... | MODIFY | Summary: DNA-binding transcription factor activity from a genome-wide transcription factor catalogue. Reason: ARF7 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:10810148 we report that NPH4 encodes the auxin-regulated transcriptional activator ARF7 PMID:10318972 Four ARFs function as activators and contain glutamine-rich activation domains |
| GO:0005515 protein binding | IPI PMID:14729917 MASSUGU2 encodes Aux/IAA19, an auxin-regulated protein that ... | MODIFY | Summary: ARF7 interaction with the Aux/IAA repressor IAA19. Aux/IAAs bind the ARF7 C-terminal PB1 domain and repress ARF7 until auxin triggers their degradation. Reason: Generic protein binding is uninformative. Aux/IAA proteins act as transcriptional co-repressors of ARF activators (recruiting TOPLESS), so the ARF7 side of this interaction is transcription corepressor binding. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:14729917 MSG2/IAA19 protein binds to the C-terminal domain of NPH4/ARF7 in a Saccharomyces cerevisiae (yeast) two-hybrid assay and to the whole latter protein in vitro by pull-down assay PMID:24706860 In the absence of auxin, ARF transcription factors are repressed by interaction with AUXIN/INDOLE 3-ACETIC ACID (Aux/IAA) proteins |
| GO:0005515 protein binding | IPI PMID:14729917 MASSUGU2 encodes Aux/IAA19, an auxin-regulated protein that ... | MODIFY | Summary: ARF7 C-terminal interaction domain binds IAA1 in the yeast two-hybrid assay reported in PMID:14729917, Figure 9B, bar 5; IAA6 and IAA13 are tested alongside it in bars 6–7. Reason: Retain transcription corepressor binding. The full Results explicitly identify IAA1 among the ARF7 CTD interaction partners, so an IAA19-specific quotation is unnecessary for this row. The interaction assay and the independently established Aux/IAA repressor role support the functional partner class; this does not turn the IAA1 assay into the full-length ARF7–IAA19 pull-down or establish native TPL recruitment for every pair. Proposed replacements: transcription corepressor binding Supporting Evidence: file:publications/url_https___pmc.ncbi.nlm.nih.gov_articles_PMC341911_.md heterodimerizations of ARF7 CTD with the other Aux/IAA proteins, IAA1, IAA6 or IAA13, were also detected to a similar extent PMID:24706860 In the absence of auxin, ARF transcription factors are repressed by interaction with AUXIN/INDOLE 3-ACETIC ACID (Aux/IAA) proteins |
| GO:0005515 protein binding | IPI PMID:16236149 Tissue-specific expression of stabilized SOLITARY-ROOT/IAA14... | MODIFY | Summary: ARF7 interaction with the Aux/IAA repressor IAA14. Aux/IAAs bind the ARF7 C-terminal PB1 domain and repress ARF7 until auxin triggers their degradation. Reason: Generic protein binding is uninformative. Aux/IAA proteins act as transcriptional co-repressors of ARF activators (recruiting TOPLESS), so the ARF7 side of this interaction is transcription corepressor binding. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:16236149 IAA14 interacted with ARF7 and ARF19 in yeasts PMID:24706860 In the absence of auxin, ARF transcription factors are repressed by interaction with AUXIN/INDOLE 3-ACETIC ACID (Aux/IAA) proteins |
| GO:0005515 protein binding | IPI PMID:17675404 The Arabidopsis transcription factor MYB77 modulates auxin s... | MODIFY | Summary: ARF7 C-terminal domain interacts with the R2R3-MYB transcription factor MYB77; MYB77 and ARF7 act synergistically in lateral root formation and co-expression enhances auxin-responsive reporter expression. Reason: Replace generic protein binding with DNA-binding transcription factor binding (MYB77 is a DNA-binding transcription factor). Proposed replacements: DNA-binding transcription factor binding Supporting Evidence: PMID:17675404 MYB77 interacts with auxin response factors (ARFs) in vitro through the C terminus (domains III and IV) of ARFs and the activation domain of MYB77 |
| GO:0005515 protein binding | IPI PMID:18505759 Domain II mutations in CRANE/IAA18 suppress lateral root for... | MODIFY | Summary: ARF7 interaction with the Aux/IAA repressor IAA18. Aux/IAAs bind the ARF7 C-terminal PB1 domain and repress ARF7 until auxin triggers their degradation. Reason: Generic protein binding is uninformative. Aux/IAA proteins act as transcriptional co-repressors of ARF activators (recruiting TOPLESS), so the ARF7 side of this interaction is transcription corepressor binding. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:18505759 IAA18 interacts with AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 PMID:24706860 In the absence of auxin, ARF transcription factors are repressed by interaction with AUXIN/INDOLE 3-ACETIC ACID (Aux/IAA) proteins |
| GO:0005515 protein binding | IPI PMID:21734647 The auxin signalling network translates dynamic input into r... | MODIFY | Summary: ARF7 interaction with the Aux/IAA repressor IAA18. Aux/IAAs bind the ARF7 C-terminal PB1 domain and repress ARF7 until auxin triggers their degradation. Reason: Generic protein binding is uninformative. Aux/IAA proteins act as transcriptional co-repressors of ARF activators (recruiting TOPLESS), so the ARF7 side of this interaction is transcription corepressor binding. 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 PMID:24706860 In the absence of auxin, ARF transcription factors are repressed by interaction with AUXIN/INDOLE 3-ACETIC ACID (Aux/IAA) proteins |
| GO:0005515 protein binding | IPI PMID:21734647 The auxin signalling network translates dynamic input into r... | MODIFY | Summary: ARF7 interaction with the Aux/IAA repressor IAA19. Aux/IAAs bind the ARF7 C-terminal PB1 domain and repress ARF7 until auxin triggers their degradation. Reason: Generic protein binding is uninformative. Aux/IAA proteins act as transcriptional co-repressors of ARF activators (recruiting TOPLESS), so the ARF7 side of this interaction is transcription corepressor binding. 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 PMID:24706860 In the absence of auxin, ARF transcription factors are repressed by interaction with AUXIN/INDOLE 3-ACETIC ACID (Aux/IAA) proteins |
| GO:0005515 protein binding | IPI PMID:21734647 The auxin signalling network translates dynamic input into r... | MODIFY | Summary: ARF7 interaction with the Aux/IAA repressor IAA1. Aux/IAAs bind the ARF7 C-terminal PB1 domain and repress ARF7 until auxin triggers their degradation. Reason: Generic protein binding is uninformative. Aux/IAA proteins act as transcriptional co-repressors of ARF activators (recruiting TOPLESS), so the ARF7 side of this interaction is transcription corepressor binding. 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 PMID:24706860 In the absence of auxin, ARF transcription factors are repressed by interaction with AUXIN/INDOLE 3-ACETIC ACID (Aux/IAA) proteins |
| GO:0005515 protein binding | IPI PMID:21734647 The auxin signalling network translates dynamic input into r... | MODIFY | Summary: ARF7 interaction with the Aux/IAA repressor IAA3. Aux/IAAs bind the ARF7 C-terminal PB1 domain and repress ARF7 until auxin triggers their degradation. Reason: Generic protein binding is uninformative. Aux/IAA proteins act as transcriptional co-repressors of ARF activators (recruiting TOPLESS), so the ARF7 side of this interaction is transcription corepressor binding. 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 PMID:24706860 In the absence of auxin, ARF transcription factors are repressed by interaction with AUXIN/INDOLE 3-ACETIC ACID (Aux/IAA) proteins |
| GO:0005515 protein binding | IPI PMID:21734647 The auxin signalling network translates dynamic input into r... | MODIFY | Summary: ARF7 interaction with the Aux/IAA repressor IAA14. Aux/IAAs bind the ARF7 C-terminal PB1 domain and repress ARF7 until auxin triggers their degradation. Reason: Generic protein binding is uninformative. Aux/IAA proteins act as transcriptional co-repressors of ARF activators (recruiting TOPLESS), so the ARF7 side of this interaction is transcription corepressor binding. 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 PMID:24706860 In the absence of auxin, ARF transcription factors are repressed by interaction with AUXIN/INDOLE 3-ACETIC ACID (Aux/IAA) proteins |
| GO:0005515 protein binding | IPI PMID:24362628 A secreted peptide acts on BIN2-mediated phosphorylation of ... | MODIFY | Summary: ARF7 interaction with the Aux/IAA repressor IAA18. Aux/IAAs bind the ARF7 C-terminal PB1 domain and repress ARF7 until auxin triggers their degradation. Reason: Generic protein binding is uninformative. Aux/IAA proteins act as transcriptional co-repressors of ARF activators (recruiting TOPLESS), so the ARF7 side of this interaction is transcription corepressor binding. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:24362628 BIN2-mediated phosphorylation of ARF7 and ARF19 suppresses their interaction with AUX/IAAs PMID:24706860 In the absence of auxin, ARF transcription factors are repressed by interaction with AUXIN/INDOLE 3-ACETIC ACID (Aux/IAA) proteins |
| GO:0005515 protein binding | IPI PMID:24362628 A secreted peptide acts on BIN2-mediated phosphorylation of ... | MODIFY | Summary: ARF7 interaction with the Aux/IAA repressor IAA19. Aux/IAAs bind the ARF7 C-terminal PB1 domain and repress ARF7 until auxin triggers their degradation. Reason: Generic protein binding is uninformative. Aux/IAA proteins act as transcriptional co-repressors of ARF activators (recruiting TOPLESS), so the ARF7 side of this interaction is transcription corepressor binding. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:24362628 BIN2-mediated phosphorylation of ARF7 and ARF19 suppresses their interaction with AUX/IAAs PMID:24706860 In the absence of auxin, ARF transcription factors are repressed by interaction with AUXIN/INDOLE 3-ACETIC ACID (Aux/IAA) proteins |
| GO:0005515 protein binding | IPI PMID:24362628 A secreted peptide acts on BIN2-mediated phosphorylation of ... | MODIFY | Summary: ARF7 interaction with the Aux/IAA repressor IAA1. Aux/IAAs bind the ARF7 C-terminal PB1 domain and repress ARF7 until auxin triggers their degradation. Reason: Generic protein binding is uninformative. Aux/IAA proteins act as transcriptional co-repressors of ARF activators (recruiting TOPLESS), so the ARF7 side of this interaction is transcription corepressor binding. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:24362628 BIN2-mediated phosphorylation of ARF7 and ARF19 suppresses their interaction with AUX/IAAs PMID:24706860 In the absence of auxin, ARF transcription factors are repressed by interaction with AUXIN/INDOLE 3-ACETIC ACID (Aux/IAA) proteins |
| GO:0005515 protein binding | IPI PMID:24362628 A secreted peptide acts on BIN2-mediated phosphorylation of ... | MODIFY | Summary: ARF7 interaction with the Aux/IAA repressor IAA3. Aux/IAAs bind the ARF7 C-terminal PB1 domain and repress ARF7 until auxin triggers their degradation. Reason: Generic protein binding is uninformative. Aux/IAA proteins act as transcriptional co-repressors of ARF activators (recruiting TOPLESS), so the ARF7 side of this interaction is transcription corepressor binding. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:24362628 BIN2-mediated phosphorylation of ARF7 and ARF19 suppresses their interaction with AUX/IAAs PMID:24706860 In the absence of auxin, ARF transcription factors are repressed by interaction with AUXIN/INDOLE 3-ACETIC ACID (Aux/IAA) proteins |
| GO:0005515 protein binding | IPI PMID:24362628 A secreted peptide acts on BIN2-mediated phosphorylation of ... | MODIFY | Summary: ARF7 interaction with the Aux/IAA repressor IAA14. Aux/IAAs bind the ARF7 C-terminal PB1 domain and repress ARF7 until auxin triggers their degradation. Reason: Generic protein binding is uninformative. Aux/IAA proteins act as transcriptional co-repressors of ARF activators (recruiting TOPLESS), so the ARF7 side of this interaction is transcription corepressor binding. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:24362628 BIN2-mediated phosphorylation of ARF7 and ARF19 suppresses their interaction with AUX/IAAs PMID:24706860 In the absence of auxin, ARF transcription factors are repressed by interaction with AUXIN/INDOLE 3-ACETIC ACID (Aux/IAA) proteins |
| GO:0005515 protein binding | IPI PMID:24362628 A secreted peptide acts on BIN2-mediated phosphorylation of ... | MODIFY | Summary: ARF7 interacts with and is phosphorylated by the GSK3-like kinase BIN2, which weakens ARF7-Aux/IAA binding and potentiates ARF7 transcriptional output during lateral root development. Reason: Replace generic protein binding with protein kinase binding (ARF7 is a BIN2 substrate). Proposed replacements: protein kinase binding Supporting Evidence: PMID:24362628 BIN2-mediated phosphorylation of ARF7 and ARF19 suppresses their interaction with AUX/IAAs |
| GO:0005515 protein binding | IPI PMID:29184030 Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD ... | MODIFY | Summary: ARF7 interacts with the histone H3K36 methyltransferase ATXR2 and recruits it to LBD promoters during callus formation. Reason: Replace generic protein binding with histone methyltransferase binding, consistent with the ARF19 review. 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: ARF7 interacts with the histone H3K36 methyltransferase ATXR2 and recruits it to LBD promoters during callus formation. Reason: Replace generic protein binding with histone methyltransferase binding, consistent with the ARF19 review. 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:29923261 JMJ30-mediated demethylation of H3K9me3 drives tissue identi... | MODIFY | Summary: ARF7 interacts with the H3K9me3 demethylase JMJ30, forming an ARF-JMJ30 complex that activates LBD16/LBD29 during leaf-to-callus transition. Reason: Replace generic protein binding with enzyme binding, consistent with the ARF19 review (no specific histone demethylase binding term exists). 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 |
| GO:0005515 protein binding | IPI PMID:9342315 Protein-protein interactions among the Aux/IAA proteins. | MODIFY | Summary: ARF7 interaction with the Aux/IAA repressor IAA1. (In this early study ARF7 was identified as the "IAA" family member IAA23/IAA25 in an IAA1 two-hybrid screen.) Aux/IAAs bind the ARF7 C-terminal PB1 domain and repress ARF7 until auxin triggers their degradation. Reason: Generic protein binding is uninformative. Aux/IAA proteins act as transcriptional co-repressors of ARF activators (recruiting TOPLESS), so the ARF7 side of this interaction is transcription corepressor binding. 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:24706860 In the absence of auxin, ARF transcription factors are repressed by interaction with AUXIN/INDOLE 3-ACETIC ACID (Aux/IAA) proteins |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: ARF7 is nuclear in root cells where it regulates transcription; localization is cell-type dependent. Reason: Figure 1 of PMID:17259263 visualizes ARF7-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:0005634 nucleus | IDA PMID:17259263 ARF7 and ARF19 regulate lateral root formation via direct ac... | ACCEPT | Summary: ARF7 is nuclear in root cells where it regulates transcription; localization is cell-type dependent. Reason: Figure 1 of PMID:17259263 visualizes ARF7-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:0005634 nucleus | IDA PMID:29184030 Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD ... | ACCEPT | Summary: ARF7 is nuclear in root cells where it regulates transcription; localization is cell-type dependent. Reason: Figure 1 of PMID:17259263 visualizes ARF7-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:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: ARF7 is nuclear in root cells where it regulates transcription; localization is cell-type dependent. Reason: Figure 1 of PMID:17259263 visualizes ARF7-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:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: ARF7 is nuclear in root cells where it regulates transcription; localization is cell-type dependent. Reason: Figure 1 of PMID:17259263 visualizes ARF7-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: Regulation of DNA-templated transcription inferred for ARFs. Reason: ARF7 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 ARF7. 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:10810148 we report that NPH4 encodes the auxin-regulated transcriptional activator ARF7 |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | MODIFY | Summary: Regulation of DNA-templated transcription via InterPro. Reason: ARF7 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:10810148 we report that NPH4 encodes the auxin-regulated transcriptional activator ARF7 |
| GO:0006355 regulation of DNA-templated transcription | TAS PMID:10318972 Activation and repression of transcription by auxin-response... | MODIFY | Summary: ARFs bind AuxREs and activate or repress transcription of early auxin response genes. Reason: ARF7 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:10318972 Auxin-response factors (ARFs) bind with specificity to TGTCTC auxin-response elements (AuxREs) PMID:10318972 Four ARFs function as activators and contain glutamine-rich activation domains |
| GO:0009630 gravitropism | TAS PMID:15923351 AUXIN RESPONSE FACTOR7 restores the expression of auxin-resp... | KEEP AS NON CORE | Summary: arf7 (nph4) and arf7 arf19 mutants show abnormal hypocotyl and root gravitropism. Reason: Tropic growth is a physiological output of ARF7-dependent auxin-induced transcription. 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 and abnormal gravitropism in both hypocotyl and root |
| GO:0009638 phototropism | IMP PMID:10364413 Arabidopsis contains at least four independent blue-light-ac... | KEEP AS NON CORE | Summary: nph4 (arf7) seedlings are aphototropic (conditionally; phototropism is restored by ethylene). Reason: ARF7/NPH4 is required for differential growth underlying hypocotyl phototropism; a downstream output of auxin-induced transcription. Supporting Evidence: PMID:10810148 Here, we describe isolation of the NPH4 gene of Arabidopsis, which is conditionally required for differential growth responses of aerial tissues PMID:10810148 Maximal recovery of phototropism in nph4 seedlings was observed over a range of ACC concentrations similar to that required for inhibition of phototropism in the wild type |
| GO:0009723 response to ethylene | IGI PMID:16461383 A role for auxin response factor 19 in auxin and ethylene si... | KEEP AS NON CORE | Summary: arf7 and arf19 mutants have ethylene-insensitive root phenotypes; ARF7/ARF19 integrate auxin and ethylene signals. Reason: Ethylene responses in roots are largely mediated via auxin; this is a contextual, non-core role. Supporting Evidence: PMID:16461383 ARF19 and ARF7 not only participate in auxin signaling, but also play a critical role in ethylene responses in Arabidopsis (Arabidopsis thaliana) roots |
| GO:0009725 response to hormone | IEA GO_REF:0000002 | MODIFY | Summary: Response to hormone from InterPro mapping. Reason: ARF7 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 ARF7 an ethylene receptor. Proposed replacements: response to auxin response to ethylene 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 | IBA GO_REF:0000033 | ACCEPT | Summary: Response to auxin inferred for the ARF7/ARF19 subclade. Reason: Core context; ARF7 mediates auxin-induced gene expression. 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:10810148 The NPH4 locus encodes the auxin response factor ARF7, a con... | ACCEPT | Summary: arf7/nph4 mutants have impaired auxin-induced gene expression and reduced auxin responsiveness. Reason: Direct genetic evidence. 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:15659631 Functional genomic analysis of the AUXIN RESPONSE FACTOR gen... | ACCEPT | Summary: arf7/nph4 mutants have impaired auxin-induced gene expression and reduced auxin responsiveness. Reason: Direct genetic evidence. 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/nph4 mutants have impaired auxin-induced gene expression and reduced auxin responsiveness. Reason: Direct genetic evidence. 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:0009785 blue light signaling pathway | IMP PMID:10364413 Arabidopsis contains at least four independent blue-light-ac... | KEEP AS NON CORE | Summary: ARF7/NPH4 contributes to the transcriptional branch controlling blue-light-directed hypocotyl bending, while the stomatal response is separable. Reason: GO:0009785 includes molecular signaling downstream of blue-light perception, not only photoreceptors. PMID:10364413 finds normal stomatal opening in nph4, which does not exclude the phototropic branch. Native NPH4 cloning and differential-growth experiments (PMID:10810148) identify ARF7 as the conditional auxin-responsive transcriptional effector of this output. Retain this context-specific light-signaling involvement without claiming blue-light sensing or participation in every blue-light response. Supporting Evidence: PMID:10810148 Originally identified by their dramatically reduced phototropic responses PMID:10364413 The stomatal responses of light-grown mutant plants |
| GO:0010311 lateral root formation | IBA GO_REF:0000033 | ACCEPT | Summary: Lateral root formation inferred for the ARF7/ARF19 subclade. 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:0010311 lateral root formation | IGI PMID:17259263 ARF7 and ARF19 regulate lateral root formation via direct ac... | ACCEPT | Summary: arf7 arf19 double mutants are severely impaired in lateral root formation; ARF7/ARF19 directly activate LBD16/LBD29. 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 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:0040008 regulation of growth | TAS PMID:10810148 The NPH4 locus encodes the auxin response factor ARF7, a con... | KEEP AS NON CORE | Summary: NPH4/ARF7 is a conditional regulator of differential growth in aerial tissues. Reason: Regulation of growth is a broad physiological output of ARF7 activity. Supporting Evidence: PMID:10810148 Here, we describe isolation of the NPH4 gene of Arabidopsis, which is conditionally required for differential growth responses of aerial tissues |
| GO:0045893 positive regulation of DNA-templated transcription | IMP PMID:15923351 AUXIN RESPONSE FACTOR7 restores the expression of auxin-resp... | ACCEPT | Summary: Auxin-responsive reporter and endogenous gene expression is lost in nph4/arf7 protoplasts and restored by ARF7 in an auxin-dependent manner. Reason: Direct evidence that ARF7 positively regulates transcription; core activity. Supporting Evidence: PMID:15923351 Expression of the reporter and natural genes was restored in an auxin-dependent manner when protoplasts were transfected with a 35S:ARF7 effector gene, encoding a full-length ARF7 protein |
| GO:0048366 leaf development | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Leaf development inferred for the ARF7/ARF19 subclade. Reason: arf7 arf19 shows reduced leaf cell expansion; developmental output. Supporting Evidence: PMID:15960621 they cause several phenotypes including a drastic decrease in lateral and adventitious root formation and a decrease in leaf cell expansion |
| GO:0048366 leaf development | IGI PMID:15960621 NPH4/ARF7 and ARF19 promote leaf expansion and auxin-induced... | KEEP AS NON CORE | Summary: arf7 arf19 mutants show decreased leaf cell expansion. Reason: Developmental output of ARF7/ARF19 auxin signalling. Supporting Evidence: PMID:15960621 they cause several phenotypes including a drastic decrease in lateral and adventitious root formation and a decrease in leaf cell expansion PMID:15960621 These results indicate that auxin induces lateral roots and leaf expansion by activating NPH4/ARF7 and ARF19 |
| GO:0048527 lateral root development | IGI PMID:15960621 NPH4/ARF7 and ARF19 promote leaf expansion and auxin-induced... | MODIFY | Summary: arf7 arf19 mutants show drastic reduction of lateral and adventitious roots. 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 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: Callus formation inferred for the ARF7/ARF19 subclade. Reason: Supported by arf7 arf19 callus defects; output of LBD activation. Supporting Evidence: PMID:29184030 Leaf explants from arf7-1arf19-2 double mutants were defective in callus formation |
| GO:1990110 callus formation | IMP PMID:29184030 Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD ... | KEEP AS NON CORE | Summary: arf7-1 arf19-2 leaf explants are defective in callus formation; ARF7/ARF19 recruit ATXR2 to LBD promoters. Reason: Developmental/regenerative output of the core activity. Supporting Evidence: PMID:29184030 Leaf explants from arf7-1arf19-2 double mutants were defective in callus formation PMID:29184030 ATXR2 was recruited to LBD promoters by the transcription factors AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 |
| GO:0001216 DNA-binding transcription activator activity | IMP PMID:15923351 AUXIN RESPONSE FACTOR7 restores the expression of auxin-resp... | NEW | Summary: NEW annotation. ARF7 is a Q-rich activator ARF that binds AuxREs and activates transcription: ARF7 restores auxin-responsive reporter and endogenous gene expression in arf7 (nph4-1) null protoplasts, and directly activates LBD16/LBD29. Reason: More specific and informative than the existing DNA-binding transcription factor activity (ISS) annotation, and directly supported by experiments on ARF7. Supporting Evidence: PMID:15923351 Expression of the reporter and natural genes was restored in an auxin-dependent manner when protoplasts were transfected with a 35S:ARF7 effector gene, encoding a full-length ARF7 protein 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:10810148 we report that NPH4 encodes the auxin-regulated transcriptional activator ARF7 |
| GO:0009734 auxin-activated signaling pathway | IMP PMID:15659631 Functional genomic analysis of the AUXIN RESPONSE FACTOR gen... | NEW | Summary: NEW annotation. ARF7 is the transcriptional effector of nuclear auxin signalling: it binds AuxREs and is released from Aux/IAA repression when auxin triggers Aux/IAA degradation; auxin-induced gene expression is severely impaired in arf7 mutants. Reason: ARF7 performs the transcriptional-activation step of the pathway, so it participates in (not merely responds to) auxin-activated signalling; GOA currently has only response to auxin for ARF7. 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 PMID:24706860 In the absence of auxin, ARF transcription factors are repressed by interaction with AUXIN/INDOLE 3-ACETIC ACID (Aux/IAA) proteins |
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Download this section (compressed HTML)Q: How does partitioning of ARF7 into cytoplasmic condensates interact with Aux/IAA-mediated repression in determining tissue-specific auxin competence?
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 annotated as GO:0019899 enzyme binding)?
Experiment: Genome-wide ARF7 DAP-seq/ChIP-seq in lateral root founder cells with and without auxin, combined with Aux/IAA (IAA14) stabilization, to separate auxin-dependent from constitutive ARF7 occupancy.
Hypothesis: ARF7 occupies AuxREs constitutively and auxin acts primarily by removing Aux/IAA-TPL repression.
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