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 is a characterized sequence-specific TF that binds the AuxRE motif; the generic parent "DNA binding" should be sharpened to a sequence-specific DNA-binding term. The molecular function as an activator is captured separately by the DNA-binding transcription factor activity annotation. Proposed replacements: sequence-specific double-stranded 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. file:ARATH/ARF5/ARF5-deep-research-falcon.md containing a B3 subdomain that recognizes AuxREs, plus additional DBD substructures that enable dimerization and cooperative binding
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. 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. file:ARATH/ARF5/ARF5-deep-research-falcon.md translating auxin levels into transcriptional outputs at AuxRE-containing cis-regulatory elements
GO:0006355 regulation of DNA-templated transcription	IEA GO_REF:0000002	ACCEPT	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. 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. file:ARATH/ARF5/ARF5-deep-research-falcon.md a terminal effector of the nuclear auxin pathway (NAP), translating auxin levels into transcriptional outputs
GO:0009725 response to hormone	IEA GO_REF:0000002	MARK AS OVER ANNOTATED	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: Too general for a protein with a well-defined and specific auxin role; the specific auxin terms (response to auxin, auxin-activated signaling pathway) are preferred. 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...	REMOVE	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 generic "protein binding" term is uninformative; the informative molecular function is the PB1-domain–mediated binding of an Aux/IAA co-repressor, captured by the proposed NEW GO:0019904 "protein domain specific binding" annotation. (Aux/IAA proteins lack a DNA-binding domain, so GO:0140297 "DNA-binding transcription factor binding" is not appropriate here.) Reason: Bare "protein binding" provides no functional information and is superseded by the more specific GO:0019904 "protein domain specific binding" annotation. 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 ...	REMOVE	Summary: IntAct interaction (with IAA19/O24409 and others). ARF5 binds Aux/IAA co-repressor proteins through a PB1-domain–specific interaction (its C-terminal PB1/domain III-IV). Generic "protein binding" is uninformative and is replaced by the specific GO:0019904 "protein domain specific binding" annotation. Reason: Uninformative generic term; the meaningful function (PB1-domain–mediated binding of Aux/IAA co-repressors) is captured by GO:0019904. Supporting Evidence: PMID:14729917 Domains III and IV of Aux/IAA proteins serve as protein–protein interaction domains that promote both homodimerization and heterodimerization between members of the Aux/IAA and ARF families
GO:0005515 protein binding	IPI PMID:16236149 Tissue-specific expression of stabilized SOLITARY-ROOT/IAA14...	REMOVE	Summary: IntAct interaction with IAA14/SOLITARY-ROOT (Q38832), an Aux/IAA co-repressor. Generic "protein binding" is uninformative; the functional molecular function is PB1-domain–mediated binding of an Aux/IAA co-repressor, captured by GO:0019904 "protein domain specific binding". Reason: Bare "protein binding" term replaced by the specific GO:0019904. Supporting Evidence: PMID:16236149 IAA14 interacted with ARF7 and ARF19 in yeasts.
GO:0005515 protein binding	IPI PMID:21734647 The auxin signalling network translates dynamic input into r...	REMOVE	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. Generic "protein binding" is uninformative and is superseded by GO:0019904. Reason: Uninformative; replaced by specific GO:0019904 "protein domain specific binding" annotation. 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...	REMOVE	Summary: Split-luciferase interactome showing ARF5 interacts with many Aux/IAA proteins and dimerizes with other ARFs. Generic "protein binding" is uninformative; the meaningful function (PB1-domain–mediated binding of Aux/IAA co-repressors and ARF dimerization) is captured by GO:0019904 and GO:0042802. Reason: Bare "protein binding" replaced by more specific terms. 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.	REMOVE	Summary: IntAct interaction with IAA1 (P49677). This is the early identification of IAA24 (=ARF5) as similar to ARF1 that heterodimerizes with Aux/IAA proteins. Generic "protein binding" is uninformative; the functional PB1-domain–mediated binding to Aux/IAA co-repressors is captured by GO:0019904. Reason: Uninformative generic term; replaced by GO:0019904. 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/MP homodimerizes (self-interaction; IntAct P93024-P93024). Homodimerization of the DNA-binding domain is functionally important, generating cooperative binding to paired AuxRE sites that is critical for in vivo function. This specific term is informative and retained. 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. 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. 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. 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. file:ARATH/ARF5/ARF5-deep-research-falcon.md For MP/ARF5, homodimerization is described as required for promoter binding and in vivo specificity.
GO:0005515 protein binding	IPI PMID:26460543 Auxin-regulated chromatin switch directs acquisition of flow...	REMOVE	Summary: This TAIR annotation captures the interaction of MP with the SWI/SNF chromatin-remodeling ATPases BRAHMA (BRM, AT2G46020) and SPLAYED (SYD, AT2G28290). MP physically interacts with and recruits these remodelers to target loci to open chromatin for activation. Generic "protein binding" is uninformative; the functional partner class here is a chromatin-remodeling ATPase. Removed in favor of a more informative description in core functions. Reason: Bare "protein binding" gives no functional information; the meaningful interaction (recruitment of SWI/SNF remodelers) is documented in the review and reflected in the activator function captured elsewhere. 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. 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. 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. 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.	ACCEPT	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. 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...	ACCEPT	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. 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...	ACCEPT	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. 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). 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. 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 file:ARATH/ARF5/ARF5-deep-research-falcon.md MP/ARF5 is a nuclear auxin-dependent transcriptional activator that binds AuxREs and drives developmental gene programs.
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...	ACCEPT	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. 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: NEW annotation. ARF5/MP binds Aux/IAA repressor proteins through a PB1-domain–mediated interaction: the C-terminal PB1 (domain III/IV) domain of ARF5 binds the PB1 domain of Aux/IAA proteins. Documented partners include BODENLOS/IAA12 (PMID:12101120), IAA17/AXR3 (PMID:11283339) and IAA19 plus other Aux/IAAs (PMID:22096563, PMID:21734647). Aux/IAA proteins are transcriptional co-repressors that lack a DNA-binding domain, so the partner-specific term GO:0140297 "DNA-binding transcription factor binding" is not appropriate; the PB1-domain–specific interaction is instead captured by GO:0019904 "protein domain specific binding". This informative molecular function replaces the multiple generic GO:0005515 "protein binding" annotations and captures the specific interaction class (Aux/IAA co-repressor binding) through which ARF5 activity is gated by auxin. 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. file:ARATH/ARF5/ARF5-deep-research-falcon.md a C-terminal PB1 domain for ARF–ARF and ARF–Aux/IAA interactions
GO:0009734 auxin-activated signaling pathway	IMP PMID:26460543 Auxin-regulated chromatin switch directs acquisition of flow...	NEW	Summary: NEW annotation. ARF5/MP is the transcriptional effector of the nuclear auxin-activated signaling pathway: auxin triggers degradation of Aux/IAA repressors bound to MP, releasing MP to activate target genes (including via recruitment of SWI/SNF chromatin remodelers). This process is captured by the UniProt keyword "Auxin signaling pathway" (GO:0009734, IEA:UniProtKB-KW in the UniProt record) and is the defining biological process for ARF5. 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 file:ARATH/ARF5/ARF5-deep-research-falcon.md Increased auxin promotes TIR1/AFB-mediated Aux/IAA degradation, releasing MP/ARF5 to activate transcription

Gene Description

Proposed New Ontology Terms

transcription factor activity sequestered by Aux/IAA repressor

Existing Annotations Review

Core Functions

Sequence-specific DNA-binding transcriptional activator that binds auxin response elements (AuxREs; TGTCTC) in target-gene promoters and activates their transcription; the DNA-binding domain homodimerizes to bind paired AuxRE sites cooperatively, which is required for in vivo function.

References

Suggested Questions for Experts

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Notes

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