PRR5

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0000160 phosphorelay signal transduction system	IEA GO_REF:0000002	REMOVE	Summary: InterPro2GO mapping from the response-regulator receiver domain (IPR001789). PRR5 is a pseudo-response regulator: its N-terminal pseudo-receiver domain lacks the conserved phospho-accepting aspartate, and no His-to-Asp phosphotransfer to any PRR has been demonstrated. Reason: Domain-based mapping that ignores the defining loss of the phosphorylatable Asp in pseudo-receivers. The PRR family acts as clock transcriptional repressors, not as phosphorelay components; the inference is contradicted on biological grounds. Supporting Evidence: PMID:20233950 Here, we demonstrate that PRR9, PRR7, and PRR5 act as transcriptional repressors of CCA1 and LHY.
GO:0003677 DNA binding	IDA PMID:32165445 Pseudo Response Regulators Regulate Photoperiodic Hypocotyl ...	ACCEPT	Summary: PRRs, including PRR5, directly bind the PIF4 and PIF5 promoters (EMSA/ChIP) to repress them (Li et al. 2020). Together with CCT-dependent promoter association, this supports DNA binding. Reason: Experimentally supported DNA binding; the core MF is captured by the repressor term. Supporting Evidence: PMID:32165445 PRRs directly bind the promoters of PHYTOCHROME-INTERACTING FACTOR4 (PIF4) and PIF5 to repress their expression PMID:23027938 PRR5 associates with target DNA through binding at the CCT motif in vivo
GO:0003677 DNA binding	IPI PMID:20233950 PSEUDO-RESPONSE REGULATORS 9, 7, and 5 are transcriptional r...	ACCEPT	Summary: Annotation reflects ChIP association of PRR5 with the CCA1 and LHY promoters (WITH = the target loci). PRR promoter binding is mediated by the CCT motif, shown directly for PRR5. Reason: DNA (promoter) binding is a correct, if general, description; core function is captured with the more specific repressor term. Supporting Evidence: PMID:20233950 PRR9, PRR7, and PRR5 associate with the CCA1 and LHY promoters in vivo, coincident with the timing of decreased CCA1 and LHY expression PMID:23027938 PRR5 associates with target DNA through binding at the CCT motif in vivo
GO:0003677 DNA binding	IPI PMID:20233950 PSEUDO-RESPONSE REGULATORS 9, 7, and 5 are transcriptional r...	ACCEPT	Summary: Annotation reflects ChIP association of PRR5 with the CCA1 and LHY promoters (WITH = the target loci). PRR promoter binding is mediated by the CCT motif, shown directly for PRR5. Reason: DNA (promoter) binding is a correct, if general, description; core function is captured with the more specific repressor term. Supporting Evidence: PMID:20233950 PRR9, PRR7, and PRR5 associate with the CCA1 and LHY promoters in vivo, coincident with the timing of decreased CCA1 and LHY expression PMID:23027938 PRR5 associates with target DNA through binding at the CCT motif in vivo
GO:0003700 DNA-binding transcription factor activity	IBA GO_REF:0000033	MODIFY	Summary: PAINT inference of DNA-binding transcription factor activity. PRR5 associates with target promoters through its C-terminal CCT domain and represses transcription (CCA1, LHY and output genes); the activity is specifically repressive. Reason: The function is sound but the more informative child term DNA-binding transcription repressor activity (RNA polymerase II-specific), matching the TOC1 review, captures the experimentally demonstrated repressor activity. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN008123536 · PANTHER:PTN008123536 SUPPORTS TRANSFER Node-level DNA-binding transcription factor activity is sound for the PRR clade; the PRR5/7/9 activity is specifically repressive, so the child term is preferred. Proposed replacements: DNA-binding transcription repressor activity, RNA polymerase II-specific Supporting Evidence: PMID:20233950 Here, we demonstrate that PRR9, PRR7, and PRR5 act as transcriptional repressors of CCA1 and LHY. PMID:23027938 PRR5 associates with target DNA through binding at the CCT motif in vivo
GO:0005515 protein binding	IPI PMID:20407420 PRR5 regulates phosphorylation, nuclear import and subnuclea...	MODIFY	Summary: PRR5 and TOC1 interact through their conserved N-terminal pseudo-receiver domains, in vitro and in vivo. The heterotypic oligomerization has a demonstrated function, enhancing TOC1 nuclear accumulation and phosphorylation. Reason: Protein binding is uninformative; protein heterodimerization activity describes the functional PRR5-TOC1 heteromer. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:20407420 we find that both proteins interact in vitro and in vivo through their conserved N-termini PMID:20407420 TOC1-PRR5 oligomerization enhances TOC1 nuclear accumulation two-fold, most likely through enhanced nuclear import
GO:0005515 protein binding	IPI PMID:31899321 Nuclear Localized O-Fucosyltransferase SPY Facilitates PRR5 ...	REMOVE	Summary: Interaction with the O-fucosyltransferase SPINDLY, of which PRR5 is a substrate. PRR5 is the acted-upon partner, and generic protein binding adds no functional information. Reason: Uninformative protein-binding term; the relationship is enzyme (SPY) to substrate (PRR5). Supporting Evidence: PMID:31899321 PRR5 can be O-fucosylated by SPY in planta
GO:0005634 nucleus	EXP PMID:31899321 Nuclear Localized O-Fucosyltransferase SPY Facilitates PRR5 ...	ACCEPT	Summary: PRR5 is a nuclear protein that interacts with and is O-fucosylated by nuclear-localized SPINDLY (Wang et al. 2020). Reason: Consistent experimental nuclear localization. Supporting Evidence: PMID:31899321 PRR5 can be O-fucosylated by SPY in planta
GO:0005634 nucleus	IBA GO_REF:0000033	ACCEPT	Summary: PRR5 is a nuclear clock repressor; nuclear localization of the PRR proteins is experimentally established. Reason: Consistent with experimental localization of PRR family members. Supporting Evidence: PMID:18562312 Each PRR protein examined is nuclear-localized
GO:0005634 nucleus	IDA PMID:20407420 PRR5 regulates phosphorylation, nuclear import and subnuclea...	ACCEPT	Summary: PRR5 is nuclear localized and recruits TOC1 to subnuclear foci (Wang et al. 2010). Reason: Direct experimental localization. Supporting Evidence: PMID:20407420 Both TOC1 and a closely related protein, PRR5, are nuclear localized
GO:0005634 nucleus	IEA GO_REF:0000044	ACCEPT	Summary: UniProt subcellular-location mapping to nucleus; consistent with experimental data for PRR proteins. Reason: Correct, redundant with experimental and IBA support. Supporting Evidence: PMID:18562312 Each PRR protein examined is nuclear-localized
GO:0005634 nucleus	ISM GO_REF:0000122	ACCEPT	Summary: AtSubP prediction of nuclear localization; consistent with experimental data. Reason: Correct prediction, supported experimentally. Supporting Evidence: PMID:18562312 Each PRR protein examined is nuclear-localized
GO:0006355 regulation of DNA-templated transcription	IBA GO_REF:0000033	ACCEPT	Summary: PRR5 regulates transcription of clock and clock-output genes by promoter-bound repression. Reason: Correct, though the more specific negative regulation term (also annotated, IDA) better describes the activity. Supporting Evidence: PMID:20233950 Here, we demonstrate that PRR9, PRR7, and PRR5 act as transcriptional repressors of CCA1 and LHY.
GO:0006355 regulation of DNA-templated transcription	TAS PMID:12068096 Two-component signal transduction pathways in Arabidopsis.	ACCEPT	Summary: Traceable author statement from a two-component signalling review; the transcriptional-regulator role is now experimentally established (PRRs repress CCA1/LHY). Reason: Correct in substance; superseded by the IDA negative-regulation annotation. Supporting Evidence: PMID:20233950 Here, we demonstrate that PRR9, PRR7, and PRR5 act as transcriptional repressors of CCA1 and LHY.
GO:0007623 circadian rhythm	IBA GO_REF:0000033	ACCEPT	Summary: PRR5 is a component of the plant circadian oscillator: PRR9/PRR7/PRR5 act sequentially through the day as repressors of CCA1/LHY, and prr mutants alter period or become arrhythmic. Reason: Core function strongly supported by genetics and molecular data. Supporting Evidence: PMID:15767265 PRR9/PRR7/PRR5 together act as period-controlling factors PMID:20233950 the repressor activities of PRR9, PRR7, and PRR5 on the CCA1 and LHY promoter regions constitute the molecular mechanism that accounts for the role of these proteins in the feedback loop of the circadian clock
GO:0007623 circadian rhythm	IEA GO_REF:0000117	ACCEPT	Summary: ARBA electronic annotation to circadian rhythm; consistent with the experimental clock role. Reason: Correct, redundant with experimental support. Supporting Evidence: PMID:15767265 PRR9/PRR7/PRR5 together act as period-controlling factors
GO:0007623 circadian rhythm	IMP PMID:12461138 Aberrant expression of the Arabidopsis circadian-regulated A...	ACCEPT	Summary: Constitutive PRR5 expression alters free-running rhythms of CCA1, LHY, TOC1 and other clock genes (Sato et al. 2002). Reason: Genetic (overexpression) evidence for a clock role; consistent with later loss-of-function data. Supporting Evidence: PMID:12461138 free-running rhythms were considerably altered for certain circadian-regulated genes
GO:0007623 circadian rhythm	IMP PMID:14634148 Comparative genetic studies on the APRR5 and APRR7 genes bel...	ACCEPT	Summary: aprr5 mutation alters the free-running period of clock-controlled genes including CCA1 and TOC1. Reason: Direct genetic evidence; core. Supporting Evidence: PMID:14634148 the period of free-running rhythms of certain clock-controlled genes including CCA1 and APRR1/TOC1 in constant white light
GO:0007623 circadian rhythm	TAS PMID:11100772 Circadian waves of expression of the APRR1/TOC1 family of ps...	ACCEPT	Summary: Matsushika et al. 2000 described the sequential 'circadian waves' of PRR9->PRR7->PRR5->PRR3->TOC1 transcripts and proposed a clock role, since confirmed genetically. Reason: Author statement now fully supported by later genetic and molecular studies. Supporting Evidence: PMID:11100772 these members of the APRR1/TOC1 family are together all involved in an as yet unknown mechanism underlying the Arabidopsis circadian clock
GO:0009414 response to water deprivation	IEP PMID:41566362 Genome-Wide Association Study Pinpoints Novel Genes Regulati...	MARK AS OVER ANNOTATED	Summary: Expression-pattern annotation from a GWAS of seedling root growth under PEG-simulated drought (Marik et al. 2026). The cached abstract does not mention PRR5, and the full text is not available in the cache. The specific basis of the annotation (an expression change or a GWAS association) cannot be seen, and the cited study's focus is on other loci. Reason: An expression-level (IEP) or GWAS-association signal does not establish that PRR5 itself functions in a water-deprivation response; this is the same standard applied to the ELF3 auxin/ABA IEP rows in this review. In addition, the candidate genes the study validated by reverse genetics are listed explicitly in the abstract and PRR5 is not among them (quoted below). The full text is not cached, so the exact basis of the TAIR row could not be inspected; the over-annotation call rests on the evidence-type argument plus the visible candidate list, not on unseen data. PRR5's established role is as a clock transcriptional repressor. Supporting Evidence: PMID:41566362 Reverse genetic evaluation using T-DNA insertion knockout/knockdown mutants confirmed the involvement of candidate genes: AT1G06690 (PLP pathway), AT4G26990, RBP45C (stress granules), ACD55.5 (protein folding), PCMP-A4 (AT1G14470; RNA editing), SKS6, ANAC094 (cell wall remodelling) and INCENP (cell cycle), with seedling drought tolerance.
GO:0009640 photomorphogenesis	IMP PMID:14634148 Comparative genetic studies on the APRR5 and APRR7 genes bel...	KEEP AS NON CORE	Summary: aprr5 mutants show altered red-light sensitivity during early photomorphogenesis (Yamamoto et al. 2003). Reason: Genetic evidence supports involvement, but via clock/output repression rather than a direct photomorphogenic activity. Supporting Evidence: PMID:14634148 red light sensitivity of seedlings during the early photomorphogenesis
GO:0009736 cytokinin-activated signaling pathway	IEA GO_REF:0000002	REMOVE	Summary: InterPro2GO mapping (IPR045279, ARR-like family) transferring cytokinin signalling from type-B ARR relatives. There is no evidence that PRR5 participates in cytokinin perception or signalling; its function is in the circadian oscillator. Reason: Family-level over-propagation from type-B ARRs; pseudo-response regulators lack the phospho-accepting Asp needed for cytokinin phosphorelay and have no reported cytokinin role. Supporting Evidence: PMID:20233950 Here, we demonstrate that PRR9, PRR7, and PRR5 act as transcriptional repressors of CCA1 and LHY.
GO:0010017 red or far-red light signaling pathway	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: prr mutants are hyposensitive to red light during de-etiolation, so PRR5 acts in red-light-regulated seedling development. This is likely an indirect consequence of clock/PIF-target repression rather than a direct phytochrome signalling activity. Reason: Supported phenotypically; retained as non-core because the protein's direct activity is clock transcriptional repression. Supporting Evidence: PMID:15767265 hyposensitivity (or blind) to red light in the photomorphogenic responses
GO:0010114 response to red light	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: PRR5 mis-expression and loss alter red-light sensitivity of seedlings during de-etiolation. The effect is real but likely indirect, via clock control of light-signalling targets such as PIF4/PIF5. Reason: Phenotypically supported; secondary to core clock repressor function. Supporting Evidence: PMID:14634148 red light sensitivity of seedlings during the early photomorphogenesis
GO:0010114 response to red light	IEP PMID:17076805 phyA dominates in transduction of red-light signals to rapid...	KEEP AS NON CORE	Summary: Expression-pattern evidence: PRR5 is among genes whose transcript responds rapidly to continuous red light at the onset of de-etiolation (Tepperman et al. 2006 microarray profiling). Reason: Transcriptional responsiveness to red light is plausible for a clock gene, but it is an expression response rather than a function of the protein. Supporting Evidence: PMID:17076805 phyA has a quantitatively dominant role in Rc-induced expression of these early response genes
GO:0010218 response to far red light	IEP PMID:17076805 phyA dominates in transduction of red-light signals to rapid...	KEEP AS NON CORE	Summary: Expression-pattern evidence from the same light-profiling study; PRR5 transcript responds to light signals mediated largely by phyA. Reason: Expression response only; non-core. Supporting Evidence: PMID:17076805 phyA has a quantitatively dominant role in Rc-induced expression of these early response genes
GO:0043565 sequence-specific DNA binding	IBA GO_REF:0000033	ACCEPT	Summary: PAINT inference of sequence-specific DNA binding. PRR proteins bind target promoters via the CCT motif (shown directly for PRR5, with PRR7/PRR9 co-occupying the same targets); ChIP-seq peaks are enriched for G-box-like motifs. Reason: Consistent with CCT-mediated promoter association across the PRR5/7/9 clade. Supporting Evidence: PMID:23027938 PRR5 associates with target DNA through binding at the CCT motif in vivo PMID:23027938 ChIP-quantitative PCR assays indicated that PRR7 and PRR9 bind to the direct-targets of PRR5.
GO:0045892 negative regulation of DNA-templated transcription	IDA PMID:20233950 PSEUDO-RESPONSE REGULATORS 9, 7, and 5 are transcriptional r...	ACCEPT	Summary: Nakamichi et al. 2010 showed that PRR5 represses CCA1 and LHY promoter activity, confers repressor activity on a heterologous DNA-binding domain in transient assays, and associates with these promoters in vivo. Reason: Direct experimental demonstration of transcriptional repressor function; core. Supporting Evidence: PMID:20233950 Here, we demonstrate that PRR9, PRR7, and PRR5 act as transcriptional repressors of CCA1 and LHY. PMID:20233950 PRR9, PRR7, and PRR5 associate with the CCA1 and LHY promoters in vivo, coincident with the timing of decreased CCA1 and LHY expression
GO:0051170 import into nucleus	IDA PMID:20407420 PRR5 regulates phosphorylation, nuclear import and subnuclea...	KEEP AS NON CORE	Summary: PRR5-TOC1 oligomerization enhances TOC1 nuclear accumulation about two-fold, most likely by enhancing its nuclear import. PRR5 therefore promotes the nuclear import of a partner rather than mediating import as a transport component. Reason: Supported (acts_upstream_of_or_within), but describes a regulatory effect of PRR5 on TOC1 localization; the core activity remains transcriptional repression. Supporting Evidence: PMID:20407420 TOC1-PRR5 oligomerization enhances TOC1 nuclear accumulation two-fold, most likely through enhanced nuclear import

Gene Description

Existing Annotations Review

Core Functions

Afternoon/evening-phased transcriptional repressor of CCA1 and LHY. PRR5 binds target promoters through its CCT motif and recruits TOPLESS/TPR corepressors, acting with PRR9 and PRR7 in the negative arm of the CCA1/LHY-PRR feedback loop.

Directly represses clock-output transcription-factor genes for flowering time, hypocotyl elongation (PIF4/PIF5) and cold-stress responses, restricting their expression to the night and early morning.

Heterodimerizes with TOC1 through the conserved pseudo-receiver domains, promoting TOC1 phosphorylation, nuclear accumulation and recruitment to subnuclear foci.

References

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