ARF5

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0003677 DNA binding	IEA GO_REF:0000002	MODIFY	Summary: ARF5/MP binds DNA via its N-terminal B3-type DNA-binding domain (UniProt DNA_BIND 158-260), recognizing auxin response elements. While correct, the bare "DNA binding" term is less informative than the sequence-specific DNA-binding transcription factor activity that is independently annotated and well supported for this protein. Reason: ARF5 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:24485461 We show that ARF DNA-binding domains also homodimerize to generate cooperative DNA binding, which is critical for in vivo ARF5/MP function.
GO:0005634 nucleus	IEA GO_REF:0000120	ACCEPT	Summary: ARF5/MP is a nuclear transcription factor; UniProt curates the subcellular location as Nucleus and the cloned protein contains functional nuclear localization signals. Nuclear localization is required for its function as a transcriptional regulator. Reason: ARF5/MP is a nuclear transcription factor; UniProt curates the subcellular location as Nucleus and the cloned protein contains functional nuclear localization signals. Nuclear localization is required for its function as a transcriptional regulator. Supporting Evidence: PMID:9482737 The predicted protein product contains functional nuclear localization sequences and a DNA binding domain highly similar to a domain shown to bind to control elements of auxin inducible promoters.
GO:0006355 regulation of DNA-templated transcription	IEA GO_REF:0000002	MODIFY	Summary: ARF5/MP regulates transcription of auxin-responsive target genes. This broad process term is consistent with its role as a transcriptional activator that binds AuxREs and activates targets such as DRN, LFY and ANT. Acceptable as a general BP, though the more specific auxin-activated signaling pathway better captures its biology. Reason: ARF5 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:19369397 MP binds in vivo to two AuxRE-spanning fragments in the DRN promoter, and that MP is required for expression of DRN in cotyledon tips.
GO:0009725 response to hormone	IEA GO_REF:0000002	MODIFY	Summary: This generic "response to hormone" term derives from an InterPro2GO mapping. ARF5 functions specifically in auxin response; the broad parent term over-annotates relative to the specific response to auxin / auxin-activated signaling pathway that is well established. Reason: Auxin-responsive transcription is demonstrated for ARF5; refine the hormone-response parent rather than calling a true general claim over-annotation. Proposed replacements: response to auxin Supporting Evidence: PMID:12101120 Developmental responses to the plant hormone auxin are thought to be mediated by interacting pairs from two protein families
GO:0005515 protein binding	IPI PMID:12101120 The Arabidopsis BODENLOS gene encodes an auxin response prot...	MODIFY	Summary: This interaction is the ARF5/MP-BODENLOS(IAA12) heterodimer, a functionally important interaction in which the Aux/IAA co-repressor IAA12 inhibits MP during root meristem initiation. The binding claim is retained with a functional partner-class refinement. Reason: The reported interaction concerns an Aux/IAA transcriptional corepressor. Its independently established regulatory role supports corepressor binding; refine bare protein binding rather than removing a claim for which an informative partner class is known. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:12101120 BODENLOS and MONOPTEROS interact in the yeast two-hybrid assay and the two genes are coexpressed in early embryogenesis, suggesting that BODENLOS inhibits MONOPTEROS action in root meristem initiation.
GO:0005515 protein binding	IPI PMID:14729917 MASSUGU2 encodes Aux/IAA19, an auxin-regulated protein that ...	MODIFY	Summary: ARF5 C-terminal interaction domain binds IAA19 and additional Aux/IAA proteins in the yeast two-hybrid experiments of PMID:14729917, Figure 9B, bars 12–17. Reason: Retain transcription corepressor binding. The recovered full Results directly identify ARF5 CTD–IAA19 binding and additional Aux/IAA interactions, improving on a family-general domain quotation. The paper also notes that yeast interaction capacity need not predict overlap of native developmental phenotypes. Proposed replacements: transcription corepressor binding Supporting Evidence: file:publications/url_https___pmc.ncbi.nlm.nih.gov_articles_PMC341911_.md ARF5 CTD interacted with IAA19 as strongly as did ARF7 CTD
GO:0005515 protein binding	IPI PMID:16236149 Tissue-specific expression of stabilized SOLITARY-ROOT/IAA14...	MODIFY	Summary: IntAct interaction with IAA14/SOLITARY-ROOT (Q38832), an Aux/IAA co-repressor. The binding claim is retained with a functional partner-class refinement. Reason: The reported interaction concerns an Aux/IAA transcriptional corepressor. Its independently established regulatory role supports corepressor binding; refine bare protein binding rather than removing a claim for which an informative partner class is known. PMID:16236149 foregrounds ARF7/ARF19, so its abstract alone does not independently reconstruct the ARF5 pair assayed by the curator. The retained ARF5 binding-class claim is independently grounded by BODENLOS/IAA12 (PMID:12101120), rather than treating the title/abstract as proof of a wrong target. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:12101120 BODENLOS and MONOPTEROS interact in the yeast two-hybrid assay
GO:0005515 protein binding	IPI PMID:21734647 The auxin signalling network translates dynamic input into r...	MODIFY	Summary: From the large-scale Aux/IAA-ARF interactome at the shoot apex. ARF5 is one of the ARF activators that interacts with Aux/IAA co-repressors. The binding claim is retained with a functional partner-class refinement. Reason: The reported interaction concerns an Aux/IAA transcriptional corepressor. Its independently established regulatory role supports corepressor binding; refine bare protein binding rather than removing a claim for which an informative partner class is known. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:21734647 the Aux/IAA repressors form heterodimers with the ARF transcription factors
GO:0005515 protein binding	IPI PMID:22096563 Large-scale protein-protein interaction analysis in Arabidop...	MODIFY	Summary: Split-luciferase interactome showing ARF5 interacts with many Aux/IAA proteins and dimerizes with other ARFs. The binding claim is retained with a functional partner-class refinement. Reason: The reported interaction concerns an Aux/IAA transcriptional corepressor. Its independently established regulatory role supports corepressor binding; refine bare protein binding rather than removing a claim for which an informative partner class is known. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:22096563 the transcription activator ARF5 stood out among the tested ARFs to interact with 10 Aux/IAA proteins
GO:0005515 protein binding	IPI PMID:9342315 Protein-protein interactions among the Aux/IAA proteins.	MODIFY	Summary: IntAct interaction with IAA1 (P49677). This is the early identification of IAA24 (=ARF5) as similar to ARF1 that heterodimerizes with Aux/IAA proteins. The binding claim is retained with a functional partner-class refinement. Reason: The reported interaction concerns an Aux/IAA transcriptional corepressor. Its independently established regulatory role supports corepressor binding; refine bare protein binding rather than removing a claim for which an informative partner class is known. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:9342315 The new member IAA24 has similarity to ARF1, a transcription factor that binds to an auxin response element.
GO:0042802 identical protein binding	IPI PMID:14729917 MASSUGU2 encodes Aux/IAA19, an auxin-regulated protein that ...	ACCEPT	Summary: ARF5 self-association is retained. PMID:14729917 uses C-terminal interaction-domain constructs in yeast; independent PMID:24485461 establishes the distinct DNA-binding-domain homodimer and cooperative DNA recognition. These assays support self-binding without conflating their domain interfaces. Reason: Retain the reported ARF5 self-interaction. The interaction screen and the independently characterized DNA-binding-domain homodimer (PMID:24485461) support the same broad self-binding claim; the latter does not establish that the screen measured the same domain interface. Supporting Evidence: PMID:24485461 We show that ARF DNA-binding domains also homodimerize to generate cooperative DNA binding, which is critical for in vivo ARF5/MP function.
GO:0042802 identical protein binding	IPI PMID:21734647 The auxin signalling network translates dynamic input into r...	ACCEPT	Summary: ARF5/MP self-interaction (homodimerization) detected in the shoot-apex interactome. Functionally meaningful for cooperative AuxRE binding; retained. Reason: Retain the reported ARF5 self-interaction. The interaction screen and the independently characterized DNA-binding-domain homodimer (PMID:24485461) support the same broad self-binding claim; the latter does not establish that the screen measured the same domain interface. Supporting Evidence: PMID:24485461 ARF1 and ARF5 homodimers, however, differ in spacing tolerated between binding sites.
GO:0042802 identical protein binding	IPI PMID:22096563 Large-scale protein-protein interaction analysis in Arabidop...	ACCEPT	Summary: ARF5/MP homodimerization confirmed by split-luciferase complementation (ARF-ARF dimerization). Functionally relevant for cooperative DNA binding; retained. Reason: Retain the reported ARF5 self-interaction. The interaction screen and the independently characterized DNA-binding-domain homodimer (PMID:24485461) support the same broad self-binding claim; the latter does not establish that the screen measured the same domain interface. Supporting Evidence: PMID:22096563 a ubiquitous occurrence of ARF dimerization in plant cells
GO:0042802 identical protein binding	IPI PMID:24485461 Structural basis for DNA binding specificity by the auxin-de...	ACCEPT	Summary: Crystal structures demonstrate that the ARF5/MP DNA-binding domain homodimerizes, and that this homodimerization generates cooperative DNA binding required in vivo. This is a structurally and functionally validated self-interaction; retained as informative. Reason: Crystal structures demonstrate that the ARF5/MP DNA-binding domain homodimerizes, and that this homodimerization generates cooperative DNA binding required in vivo. This is a structurally and functionally validated self-interaction; retained as informative. Supporting Evidence: PMID:24485461 We show that ARF DNA-binding domains also homodimerize to generate cooperative DNA binding, which is critical for in vivo ARF5/MP function.
GO:0005515 protein binding	IPI PMID:26460543 Auxin-regulated chromatin switch directs acquisition of flow...	MODIFY	Summary: MP binds and recruits SWI/SNF remodeling ATPases during activation of flower-primordium regulators (PMID:26460543). Reason: BRAHMA/SPLAYED are transcriptional chromatin coregulators recruited by MP at target loci in PMID:26460543. The demonstrated recruitment mechanism supports transcription coregulator binding, without assigning ATPase catalysis to MP. Proposed replacements: transcription coregulator binding Supporting Evidence: PMID:26460543 the MONOPTEROS transcription factor recruits SWI/SNF chromatin remodeling ATPases to increase accessibility of the DNA for induction of key regulators of flower primordium initiation
GO:0000976 transcription cis-regulatory region binding	IDA PMID:19369397 DORNROSCHEN is a direct target of the auxin response factor ...	ACCEPT	Summary: ChIP demonstrates that MP binds in vivo to AuxRE-containing fragments in the DORNROSCHEN (DRN) promoter, directly establishing cis-regulatory region binding. Strong direct experimental support; this is a core molecular function of ARF5. Reason: ChIP demonstrates that MP binds in vivo to AuxRE-containing fragments in the DORNROSCHEN (DRN) promoter, directly establishing cis-regulatory region binding. Strong direct experimental support; this is a core molecular function of ARF5. Supporting Evidence: PMID:19369397 Chromatin immunoprecipitation experiments show that MP binds in vivo to two AuxRE-spanning fragments in the DRN promoter, and that MP is required for expression of DRN in cotyledon tips.
GO:0000976 transcription cis-regulatory region binding	IPI PMID:25533953 An Arabidopsis gene regulatory network for secondary cell wa...	ACCEPT	Summary: In a yeast one-hybrid gene regulatory network for secondary cell wall synthesis, ARF5 was found among transcription factors binding promoter fragments (e.g. IRX14/AT1G71930). Consistent with ARF5 binding cis-regulatory regions of target promoters. Retained as it supports the AuxRE/promoter binding molecular function, though this particular network role is peripheral. Reason: In a yeast one-hybrid gene regulatory network for secondary cell wall synthesis, ARF5 was found among transcription factors binding promoter fragments (e.g. IRX14/AT1G71930). Consistent with ARF5 binding cis-regulatory regions of target promoters. Retained as it supports the AuxRE/promoter binding molecular function, though this particular network role is peripheral. Supporting Evidence: PMID:25533953 a protein-DNA network between Arabidopsis thaliana transcription factors and secondary cell wall metabolic genes
GO:0005634 nucleus	ISM GO_REF:0000122	ACCEPT	Summary: Computational (AtSubP) prediction of nuclear localization, consistent with experimental evidence that MP carries functional NLSs and acts as a nuclear transcription factor. Accepted as a correct location. Reason: Computational (AtSubP) prediction of nuclear localization, consistent with experimental evidence that MP carries functional NLSs and acts as a nuclear transcription factor. Accepted as a correct location. Supporting Evidence: PMID:9482737 The predicted protein product contains functional nuclear localization sequences
GO:0009793 embryo development ending in seed dormancy	IGI PMID:17553903 AMP1 and MP antagonistically regulate embryo and meristem de...	KEEP AS NON CORE	Summary: mp/arf5 mutants have severe embryo patterning defects, and MP acts antagonistically with AMP1 in embryo development. This is a genuine but downstream developmental role of this pleiotropic regulator rather than its core molecular activity. Reason: ARF5 is developmentally pleiotropic; embryo development is a downstream consequence of its transcriptional-activator function, retained as non-core. Supporting Evidence: PMID:17553903 mutations in MONOPTEROS (MP/ARF5) result in severe patterning defects during embryonic and postembryonic development
GO:0006355 regulation of DNA-templated transcription	IEP PMID:21478855 Auxin triggers a genetic switch.	MODIFY	Summary: MP controls transcription, including autoregulation of its own expression and that of its inhibitor BODENLOS, with auxin acting as a threshold trigger. Supports the broad transcription-regulation process. This duplicates the IEA GO:0006355 annotation, which is acceptable. Reason: ARF5 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:21478855 the Arabidopsis ARF protein MONOPTEROS (MP) controls its own expression and the expression of its AUX/IAA inhibitor BODENLOS (BDL)
GO:0009908 flower development	IGI PMID:17553903 AMP1 and MP antagonistically regulate embryo and meristem de...	KEEP AS NON CORE	Summary: MP is required for flower primordium initiation and flower development; mp and auxin pathway mutants form characteristic flowerless "pin" inflorescences. This is a real downstream developmental role of this pleiotropic transcription factor. Reason: Downstream developmental process of a pleiotropic regulator; retained as non-core. Supporting Evidence: PMID:26460543 In the absence of auxin or MP, shoot apices cannot initiate flower primordia and give rise to characteristic 'naked pin' inflorescences
GO:0010305 leaf vascular tissue pattern formation	IGI PMID:17553903 AMP1 and MP antagonistically regulate embryo and meristem de...	KEEP AS NON CORE	Summary: MP is required for proper vascular patterning, including leaf venation; mp mutants show distorted vascular strands in all organs. A genuine role, kept as a non-core downstream developmental output of ARF5's transcriptional activity in provascular tissues. Reason: Specific downstream developmental patterning role; non-core relative to the molecular activator function. Supporting Evidence: PMID:8904808 the vascular strands in all analyzed organs are distorted
GO:0048364 root development	IGI PMID:17553903 AMP1 and MP antagonistically regulate embryo and meristem de...	KEEP AS NON CORE	Summary: MP is essential for root meristem initiation during embryogenesis (mp mutants fail to form hypocotyl/radicle and root meristem). A bona fide developmental role, kept as non-core for this pleiotropic factor. Reason: Downstream developmental process; non-core. Supporting Evidence: PMID:12101120 monopteros mutants lacking activating ARF5 and the auxin-insensitive mutant bodenlos fail to initiate the root meristem during early embryogenesis
GO:0048507 meristem development	IGI PMID:17553903 AMP1 and MP antagonistically regulate embryo and meristem de...	KEEP AS NON CORE	Summary: MP carves out meristematic niches by locally overcoming AMP1-dependent differentiation, antagonistically regulating meristem development. A genuine downstream developmental role of this pleiotropic regulator. Reason: Downstream developmental process; non-core. Supporting Evidence: PMID:17553903 auxin-derived positional information through MP carves out meristematic niches by locally overcoming a general differentiation-promoting activity involving AMP1
GO:0003700 DNA-binding transcription factor activity	ISS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a...	MODIFY	Summary: ARF5/MP is a sequence-specific DNA-binding transcription factor (B3 family) that acts as a transcriptional activator at AuxREs. This is a core molecular function, strongly supported by structural, biochemical and genetic data. Reason: ARF5 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:24485461 Auxin regulates numerous plant developmental processes by controlling gene expression via a family of functionally distinct DNA-binding auxin response factors (ARFs)
GO:0003700 DNA-binding transcription factor activity	ISS PMID:9482737 The Arabidopsis gene MONOPTEROS encodes a transcription fact...	MODIFY	Summary: The cloning of MP established it as a transcription factor with a DNA binding domain similar to auxin-promoter-binding domains and functional NLSs. Core molecular function; duplicate of the other GO:0003700 annotations, which is acceptable. Reason: ARF5 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:9482737 a DNA binding domain highly similar to a domain shown to bind to control elements of auxin inducible promoters
GO:0005634 nucleus	ISS PMID:9482737 The Arabidopsis gene MONOPTEROS encodes a transcription fact...	ACCEPT	Summary: MP localizes to the nucleus; the protein contains functional nuclear localization signals. Consistent with its role as a transcription factor. Accepted location (duplicate of the IEA/ISM nucleus annotations). Reason: MP localizes to the nucleus; the protein contains functional nuclear localization signals. Consistent with its role as a transcription factor. Accepted location (duplicate of the IEA/ISM nucleus annotations). Supporting Evidence: PMID:9482737 The predicted protein product contains functional nuclear localization sequences
GO:0009733 response to auxin	IEP PMID:11283339 IAA17/AXR3: biochemical insight into an auxin mutant phenoty...	ACCEPT	Summary: ARF5/MP is a central effector of auxin response: it binds auxin response elements and, when released from Aux/IAA repression upon auxin perception, activates auxin-responsive target genes. Core to its biology; auxin response / auxin-activated signaling is its defining process. Reason: ARF5/MP is a central effector of auxin response: it binds auxin response elements and, when released from Aux/IAA repression upon auxin perception, activates auxin-responsive target genes. Core to its biology; auxin response / auxin-activated signaling is its defining process. Supporting Evidence: PMID:11283339 the ARFs are capable of binding synthetic and natural auxin responsive promoter elements through a VP1-B3 DNA binding domain located at their N termini
GO:0009942 longitudinal axis specification	IMP PMID:8904808 Studies on the role of the Arabidopsis gene MONOPTEROS in va...	KEEP AS NON CORE	Summary: mp mutant embryos fail to initiate the hypocotyl/root (body) axis; MP is required for apical-basal axis formation in the early embryo. This is the classic mp loss-of-function phenotype and a well-supported downstream developmental role. Kept as non-core relative to the molecular activator function. Reason: Strongly supported developmental patterning role, but a downstream output of the transcriptional-activator activity in a pleiotropic gene. Supporting Evidence: PMID:8904808 The process depends on the activity of the gene MONOPTEROS (MP); mp mutant embryos fail to produce hypocotyl and radicle.
GO:0010051 xylem and phloem pattern formation	IMP PMID:8904808 Studies on the role of the Arabidopsis gene MONOPTEROS in va...	KEEP AS NON CORE	Summary: mp mutants show distorted vascular strands in all organs at all stages; MP is required for vascular tissue patterning and continuity. A well-supported downstream developmental role of this pleiotropic regulator. Reason: Genuine, strongly supported vascular patterning role; non-core relative to the molecular function. Supporting Evidence: PMID:8904808 the vascular strands in all analyzed organs are distorted
GO:0003700 DNA-binding transcription factor activity	TAS PMID:9482737 The Arabidopsis gene MONOPTEROS encodes a transcription fact...	MODIFY	Summary: Author-stated (TAS) assignment of DNA-binding transcription factor activity from the MP cloning paper. Core molecular function; duplicate of the ISS GO:0003700 annotations, which is acceptable. Reason: ARF5 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:9482737 The Arabidopsis gene MONOPTEROS encodes a transcription factor mediating embryo axis formation and vascular development.
GO:0019904 protein domain specific binding	IPI PMID:12101120 The Arabidopsis BODENLOS gene encodes an auxin response prot...	NEW	Summary: Existing proposed annotation retained: ARF5 binds Aux/IAA proteins through conserved C-terminal interaction domains, independently supported by domain-III perturbation in IAA17 and by BODENLOS binding. This domain-level property is distinct from the partner-role refinement of the existing bare-binding rows. Reason: Existing proposed annotation retained: ARF5 binds Aux/IAA proteins through conserved C-terminal interaction domains, independently supported by domain-III perturbation in IAA17 and by BODENLOS binding. This domain-level property is distinct from the partner-role refinement of the existing bare-binding rows. Supporting Evidence: PMID:12101120 BODENLOS and MONOPTEROS interact in the yeast two-hybrid assay and the two genes are coexpressed in early embryogenesis, suggesting that BODENLOS inhibits MONOPTEROS action in root meristem initiation. PMID:11283339 heterodimerization of the revertant forms of IAA17/AXR3 with IAA3/SHY2, another Aux/IAA protein, and ARF1 or ARF5/MP proteins is affected only by changes in domain III.
GO:0009734 auxin-activated signaling pathway	IMP PMID:26460543 Auxin-regulated chromatin switch directs acquisition of flow...	NEW	Summary: Existing proposed annotation retained: ARF5 executes the transcriptional output of nuclear auxin signaling, including recruitment of SWI/SNF remodelers after auxin sensing (PMID:26460543). This is active pathway participation, supported by primary evidence rather than a UniProt keyword. Reason: Existing proposed annotation retained: ARF5 executes the transcriptional output of nuclear auxin signaling, including recruitment of SWI/SNF remodelers after auxin sensing (PMID:26460543). This is active pathway participation, supported by primary evidence rather than a UniProt keyword. Supporting Evidence: PMID:26460543 Upon auxin sensing, the MONOPTEROS transcription factor recruits SWI/SNF chromatin remodeling ATPases to increase accessibility of the DNA for induction of key regulators of flower primordium initiation. PMID:21478855 auxin acting as a threshold-specific trigger by promoting the degradation of the inhibitor

Gene Description

Proposed New Ontology Terms

transcription factor activity sequestered by Aux/IAA repressor

Existing Annotations Review

Core Functions

Sequence-specific activator of AuxRE-containing target genes; DBD dimerization promotes cooperative recognition of paired sites and is important for native MP function.

Binds Aux/IAA corepressors through PB1-domain interactions, providing an auxin-sensitive regulatory interface. Direct BODENLOS binding and IAA17 domain perturbation support this role; interaction assays do not imply every partner recruits an identical repression complex.

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