UFO

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0000151 ubiquitin ligase complex	IBA GO_REF:0000033	MODIFY	Summary: Part of ubiquitin ligase complex inferred by PAINT (node PTN008706702, seeded by UFO itself and rice APO1). Reason: Correct; UFO forms an SCF(UFO) complex in vivo, so the more specific SCF ubiquitin ligase complex term applies. UFO appearing in its own WITH/FROM reflects its experimental grounding. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN008706702 · UFO/APO1/FIM node SUPPORTS TRANSFER Seeded by UFO itself and rice APO1; the complex membership transfers correctly, only the granularity is improvable. Proposed replacements: SCF ubiquitin ligase complex Supporting Evidence: PMID:12724534 We show that UNUSUAL FLORAL ORGANS (UFO) forms a SCF(UFO) complex, which is associated with CSN in vivo.
GO:0000151 ubiquitin ligase complex	IPI PMID:10607296 The UNUSUAL FLORAL ORGANS gene of Arabidopsis thaliana is an...	MODIFY	Summary: Part of ubiquitin ligase complex (IPI with ASK1/SKP1A). Reason: UFO binds ASK1 through its F-box; the SCF ubiquitin ligase complex term is more specific and is supported by in vivo complex data. Proposed replacements: SCF ubiquitin ligase complex Supporting Evidence: PMID:10607296 we show here that UFO is an F-box protein that interacts with Arabidopsis SKP1-like proteins, both in the yeast two-hybrid system and in vitro.
GO:0004842 ubiquitin-protein transferase activity	IBA GO_REF:0000033	MODIFY	Summary: Ubiquitin-protein transferase activity inferred by PAINT (PTN001281291, seeded by UFO). Reason: An F-box protein is the substrate-recognition subunit of an SCF E3; it does not itself transfer ubiquitin (the RING subunit RBX1 and the E2 do). Assigning the catalytic E3 activity to the adaptor subunit is a complex-activity transfer. The adaptor activity term is the appropriate MF. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: ROLE CONFLATION Sources checked: PANTHER:PTN001281291 · UFO F-box node SUPPORTS SOURCE BUT NOT TARGET Node seeded by UFO's own IMP for ubiquitin-protein transferase activity; the seed itself conflates the SCF complex's catalytic activity with the F-box adaptor subunit. Proposed replacements: ubiquitin-like ligase-substrate adaptor activity Supporting Evidence: PMID:10607296 we show here that UFO is an F-box protein that interacts with Arabidopsis SKP1-like proteins, both in the yeast two-hybrid system and in vitro.
GO:0004842 ubiquitin-protein transferase activity	IMP PMID:18287201 An Arabidopsis F-box protein acts as a transcriptional co-fa...	REMOVE	Summary: Ubiquitin-protein transferase activity (IMP) from the study of UFO as a LEAFY cofactor. Reason: The paper shows proteasome activity is needed for LFY-dependent AP3 activation, which is consistent with UFO acting in an SCF-dependent pathway, but it shows neither UFO catalysing ubiquitin transfer (an F-box protein is the substrate receptor; RBX1 and the E2 perform the transfer) nor UFO adaptor activity toward a substrate. Later work found the F-box connection to ubiquitination mostly dispensable for UFO-LFY function. The F-box substrate-adaptor activity (GO:1990756) is instead carried by the ASK-binding IPI rows, so this IMP row is removed rather than modified. Supporting Evidence: PMID:18287201 Moreover, chemical or genetic disruption of proteasome activity compromises LFY-dependent AP3 activation, indicating that protein degradation is required to promote LFY activity. PMID:36732360 Here we show in transient assays and stable transgenic plants that the connection to ubiquitination pathways suggested by the UFO F-box domain is mostly dispensable.
GO:0005515 protein binding	IPI PMID:10607296 The UNUSUAL FLORAL ORGANS gene of Arabidopsis thaliana is an...	MODIFY	Summary: Protein binding (IPI) recorded with UniProtKB:P43291 from the paper identifying UFO as an F-box protein. Reason: The interaction partner is an Arabidopsis SKP1-like (ASK) protein bound through the UFO F-box; this is the substrate-adaptor role of an F-box protein within an SCF complex, which ubiquitin-like ligase-substrate adaptor activity describes better than protein binding. Note: P43291 is SnRK2.4/SRK2A, a kinase that also carries the synonym 'ASK1'; the paper describes binding to SKP1-like proteins (ASK1 = SKP1A, Q39255), so the WITH/FROM accession appears to be a synonym mis-mapping. The UFO binding activity itself is not in doubt. Proposed replacements: ubiquitin-like ligase-substrate adaptor activity Supporting Evidence: PMID:10607296 we show here that UFO is an F-box protein that interacts with Arabidopsis SKP1-like proteins, both in the yeast two-hybrid system and in vitro.
GO:0005515 protein binding	IPI PMID:10607296 The UNUSUAL FLORAL ORGANS gene of Arabidopsis thaliana is an...	MODIFY	Summary: Protein binding (IPI) with ASK2/SKP1B. Reason: The interaction partner is an Arabidopsis SKP1-like (ASK) protein bound through the UFO F-box; this is the substrate-adaptor role of an F-box protein within an SCF complex, which ubiquitin-like ligase-substrate adaptor activity describes better than protein binding. Proposed replacements: ubiquitin-like ligase-substrate adaptor activity Supporting Evidence: PMID:10607296 we show here that UFO is an F-box protein that interacts with Arabidopsis SKP1-like proteins, both in the yeast two-hybrid system and in vitro.
GO:0005515 protein binding	IPI PMID:12169662 The F-box subunit of the SCF E3 complex is encoded by a dive...	MODIFY	Summary: Protein binding (IPI) with ASK11 from the Arabidopsis F-box superfamily study. Reason: The interaction partner is an Arabidopsis SKP1-like (ASK) protein bound through the UFO F-box; this is the substrate-adaptor role of an F-box protein within an SCF complex, which ubiquitin-like ligase-substrate adaptor activity describes better than protein binding. Proposed replacements: ubiquitin-like ligase-substrate adaptor activity Supporting Evidence: PMID:12169662 These interactions were similar to that of the BD-UFO/AD-ASK1 combination, which was used as the control Skp/F-box protein pair
GO:0005515 protein binding	IPI PMID:12169662 The F-box subunit of the SCF E3 complex is encoded by a dive...	MODIFY	Summary: Protein binding (IPI) with ASK1/SKP1A from the F-box superfamily study. Reason: The interaction partner is an Arabidopsis SKP1-like (ASK) protein bound through the UFO F-box; this is the substrate-adaptor role of an F-box protein within an SCF complex, which ubiquitin-like ligase-substrate adaptor activity describes better than protein binding. Proposed replacements: ubiquitin-like ligase-substrate adaptor activity Supporting Evidence: PMID:12169662 These interactions were similar to that of the BD-UFO/AD-ASK1 combination, which was used as the control Skp/F-box protein pair
GO:0005515 protein binding	IPI PMID:12169662 The F-box subunit of the SCF E3 complex is encoded by a dive...	MODIFY	Summary: Protein binding (IPI) with ASK2/SKP1B from the F-box superfamily study. Reason: The interaction partner is an Arabidopsis SKP1-like (ASK) protein bound through the UFO F-box; this is the substrate-adaptor role of an F-box protein within an SCF complex, which ubiquitin-like ligase-substrate adaptor activity describes better than protein binding. Proposed replacements: ubiquitin-like ligase-substrate adaptor activity
GO:0005515 protein binding	IPI PMID:12724534 The COP9 signalosome interacts with SCF UFO and participates...	MODIFY	Summary: Protein binding (IPI) with ASK1 from the COP9 signalosome / SCF(UFO) study. Reason: The interaction partner is an Arabidopsis SKP1-like (ASK) protein bound through the UFO F-box; this is the substrate-adaptor role of an F-box protein within an SCF complex, which ubiquitin-like ligase-substrate adaptor activity describes better than protein binding. Proposed replacements: ubiquitin-like ligase-substrate adaptor activity Supporting Evidence: PMID:12724534 We show that UNUSUAL FLORAL ORGANS (UFO) forms a SCF(UFO) complex, which is associated with CSN in vivo.
GO:0005515 protein binding	IPI PMID:12795696 Protein interaction analysis of SCF ubiquitin E3 ligase subu...	MODIFY	Summary: Protein binding (IPI) with ASK11 from the SCF subunit interaction analysis. Reason: The interaction partner is an Arabidopsis SKP1-like (ASK) protein bound through the UFO F-box; this is the substrate-adaptor role of an F-box protein within an SCF complex, which ubiquitin-like ligase-substrate adaptor activity describes better than protein binding. Proposed replacements: ubiquitin-like ligase-substrate adaptor activity Supporting Evidence: PMID:12795696 Analysis of the protein interaction profiles involving the products of all three gene families suggests a functional distinction between ASK proteins in that selected members of the protein family interact generally while others interact more specifically with members of the F-box protein family.
GO:0005515 protein binding	IPI PMID:12795696 Protein interaction analysis of SCF ubiquitin E3 ligase subu...	MODIFY	Summary: Protein binding (IPI) with ASK1 from the SCF subunit interaction analysis. Reason: The interaction partner is an Arabidopsis SKP1-like (ASK) protein bound through the UFO F-box; this is the substrate-adaptor role of an F-box protein within an SCF complex, which ubiquitin-like ligase-substrate adaptor activity describes better than protein binding. Proposed replacements: ubiquitin-like ligase-substrate adaptor activity
GO:0005515 protein binding	IPI PMID:12795696 Protein interaction analysis of SCF ubiquitin E3 ligase subu...	MODIFY	Summary: Protein binding (IPI) with ASK2 from the SCF subunit interaction analysis. Reason: The interaction partner is an Arabidopsis SKP1-like (ASK) protein bound through the UFO F-box; this is the substrate-adaptor role of an F-box protein within an SCF complex, which ubiquitin-like ligase-substrate adaptor activity describes better than protein binding. Proposed replacements: ubiquitin-like ligase-substrate adaptor activity
GO:0005515 protein binding	IPI PMID:12826617 The F-box-containing protein UFO and AGAMOUS participate in ...	MODIFY	Summary: Protein binding (IPI) with ASK1 from the study of UFO in petal development. Reason: The interaction partner is an Arabidopsis SKP1-like (ASK) protein bound through the UFO F-box; this is the substrate-adaptor role of an F-box protein within an SCF complex, which ubiquitin-like ligase-substrate adaptor activity describes better than protein binding. Proposed replacements: ubiquitin-like ligase-substrate adaptor activity Supporting Evidence: PMID:12826617 The gene encodes an F-box-containing protein, UFO, which interacts physically and genetically with the Skp1 homolog, ASK1.
GO:0005515 protein binding	IPI PMID:15749712 Cullins 3a and 3b assemble with members of the broad complex...	MODIFY	Summary: Protein binding (IPI) with ASK1 from the CUL3/BTB E3 paper (UFO-ASK1 likely used as a reference F-box/SKP1 pair). Reason: The interaction partner is an Arabidopsis SKP1-like (ASK) protein bound through the UFO F-box; this is the substrate-adaptor role of an F-box protein within an SCF complex, which ubiquitin-like ligase-substrate adaptor activity describes better than protein binding. The full text was not available locally; the curator's assignment is retained. Proposed replacements: ubiquitin-like ligase-substrate adaptor activity
GO:0005515 protein binding	IPI PMID:18287201 An Arabidopsis F-box protein acts as a transcriptional co-fa...	MODIFY	Summary: Protein binding (IPI) with LEAFY, shown in vitro and in vivo. Reason: The UFO-LFY interaction recruits UFO to the AP3 promoter, so binding to a DNA-binding transcription factor is the informative MF; this underlies UFO's transcription coactivator activity. Proposed replacements: DNA-binding transcription factor binding Supporting Evidence: PMID:18287201 Here, we show that UFO physically interacts with LFY both in vitro and in vivo, and this interaction is necessary to recruit UFO to the AP3 promoter.
GO:0005515 protein binding	IPI PMID:23166809 A comprehensive analysis of interaction and localization of ...	MODIFY	Summary: Protein binding (IPI) with ASK1 from the large-scale ASK-FBX interaction study. Reason: The interaction partner is an Arabidopsis SKP1-like (ASK) protein bound through the UFO F-box; this is the substrate-adaptor role of an F-box protein within an SCF complex, which ubiquitin-like ligase-substrate adaptor activity describes better than protein binding. Proposed replacements: ubiquitin-like ligase-substrate adaptor activity Supporting Evidence: PMID:23166809 The Arabidopsis SKP-LIKE (ASK) proteins are also members of a family and some of them interact with FBX proteins directly.
GO:0005515 protein binding	IPI PMID:23166809 A comprehensive analysis of interaction and localization of ...	MODIFY	Summary: Protein binding (IPI) with ASK2 from the large-scale ASK-FBX interaction study. Reason: The interaction partner is an Arabidopsis SKP1-like (ASK) protein bound through the UFO F-box; this is the substrate-adaptor role of an F-box protein within an SCF complex, which ubiquitin-like ligase-substrate adaptor activity describes better than protein binding. Proposed replacements: ubiquitin-like ligase-substrate adaptor activity Supporting Evidence: PMID:23166809 The Arabidopsis SKP-LIKE (ASK) proteins are also members of a family and some of them interact with FBX proteins directly.
GO:0005634 nucleus	IEA GO_REF:0000044	ACCEPT	Summary: Nucleus from UniProt subcellular location. Reason: UFO is recruited with LFY to the AP3 promoter and forms a LFY-UFO-DNA complex, which requires nuclear localization. Supporting Evidence: PMID:18287201 Here, we show that UFO physically interacts with LFY both in vitro and in vivo, and this interaction is necessary to recruit UFO to the AP3 promoter.
GO:0006355 regulation of DNA-templated transcription	IBA GO_REF:0000033	ACCEPT	Summary: Regulation of DNA-templated transcription inferred by PAINT (PTN008706702; UFO and rice APO1). Reason: Consistent with UFO's cofactor role in LFY-dependent transcription and with the proposed deep conservation of the LFY-UFO complex; UFO in its own WITH/FROM is expected, not circular. Supporting Evidence: PMID:36732360 Finally, we propose that this complex might have a deep evolutionary origin, largely predating flowering plants.
GO:0006355 regulation of DNA-templated transcription	IDA PMID:18287201 An Arabidopsis F-box protein acts as a transcriptional co-fa...	ACCEPT	Summary: Regulation of DNA-templated transcription (IDA) from UFO acting as a transcriptional co-factor at the AP3 promoter. Reason: UFO is recruited to the AP3 promoter via LFY, and a UFO-repressor-domain fusion reduces LFY activity in plants. Supporting Evidence: PMID:18287201 Furthermore, a transcriptional repressor domain fused to UFO reduces endogenous LFY activity in plants, supporting the idea that UFO acts as part of a transcriptional complex at the AP3 promoter.
GO:0006511 ubiquitin-dependent protein catabolic process	TAS PMID:11019805 Protein degradation in signaling.	KEEP AS NON CORE	Summary: Ubiquitin-dependent protein catabolic process (TAS) from a review of proteolysis in plant signalling. Reason: UFO is an SCF F-box subunit, and proteasome activity contributes to LFY-dependent AP3 activation, but no UFO substrate has been identified and the ubiquitination link is largely dispensable for its floral function. Retain as non-core. Supporting Evidence: PMID:11019805 Significant advances have recently revealed connections between proteolysis and hormone responses, light perception, environmental adaptation, and floral development.
GO:0009933 meristem structural organization	IMP PMID:10607296 The UNUSUAL FLORAL ORGANS gene of Arabidopsis thaliana is an...	KEEP AS NON CORE	Summary: Meristem structural organization (IMP); ufo mutants have altered growth and patterning of young floral primordia. Reason: UFO controls growth of young floral primordia and whorl patterning; a real phenotype, but secondary to its molecular role as a LEAFY cofactor. Supporting Evidence: PMID:10607296 Results from in situ hybridization using genes expressed early in floral development as probes indicate that UFO controls growth of young floral primordia.
GO:0016567 protein ubiquitination	IEA GO_REF:0000041	KEEP AS NON CORE	Summary: Protein ubiquitination (IEA from UniPathway). Reason: Generic F-box mapping; UFO can assemble an SCF complex but its ubiquitination role and substrates are not established and are largely dispensable for LFY cofactor activity. Supporting Evidence: PMID:36732360 Here we show in transient assays and stable transgenic plants that the connection to ubiquitination pathways suggested by the UFO F-box domain is mostly dispensable.
GO:0031146 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: SCF-dependent proteasomal ubiquitin-dependent protein catabolic process inferred by PAINT. Reason: Consistent with UFO being an SCF F-box subunit, but no degradation substrate is known; non-core relative to the transcriptional cofactor role.
GO:0031146 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	IGI PMID:15047903 Regulation of flower development in Arabidopsis by SCF compl...	KEEP AS NON CORE	Summary: SCF-dependent proteasomal protein catabolic process (IGI with CUL1). Reason: Genetic interaction between ufo and Atcul1 supports UFO acting through SCF complexes in flower development; the specific catabolic process is inferred rather than demonstrated. Supporting Evidence: PMID:15047903 Furthermore, the genetic interaction between UFO and AtCUL1 supports the idea that UFO regulates multiple aspects of flower development as a part of SCF complexes.
GO:0003713 transcription coactivator activity	IDA PMID:36732360 The F-box protein UFO controls flower development by redirec...	NEW	Summary: UFO forms an active transcriptional complex with LEAFY on DNA, redirecting LEAFY to new cis-elements; cryo-EM shows UFO contacting both LFY and DNA. Reason: Biochemical, genome-wide and structural data show UFO is a non-DNA-binding (on its own) cofactor that increases LFY-dependent activation at specific elements. This MF is not represented in GOA; existing transcription regulation BP annotations imply it. Supporting Evidence: PMID:36732360 we establish that UFO instead acts by forming an active transcriptional complex with LFY at newly discovered regulatory elements. PMID:18287201 These results define an unexpected role for an F-box protein in functioning as a DNA-associated transcriptional co-factor in regulating floral homeotic gene expression.

Gene Description

Existing Annotations Review

Core Functions

Transcriptional cofactor of LEAFY: UFO binds LEAFY and DNA, forming a LEAFY-UFO-DNA complex that redirects LEAFY to new cis-elements and activates region-specific floral targets such as APETALA3, thereby contributing to floral meristem identity and floral patterning downstream of LEAFY.

F-box substrate-adaptor subunit of an SCF(UFO) ubiquitin ligase that binds SKP1-like ASK proteins and associates with the COP9 signalosome; substrates are unknown and this activity is largely dispensable for the LEAFY cofactor function.

References

Suggested Questions for Experts

Suggested Experiments

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Notes

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