PSEUDO-RESPONSE REGULATOR 9 (PRR9, APRR9) is a nuclear transcriptional repressor of the Arabidopsis circadian oscillator and the earliest-phased member of the PRR1/TOC1 family, whose transcripts peak sequentially through the day (PRR9, PRR7, PRR5, PRR3, TOC1). PRR9 has an N-terminal pseudo-receiver domain, which resembles a two-component receiver but lacks the phospho-accepting aspartate, and a C-terminal CCT domain that mediates promoter association. Its expression is rapidly induced by light via phytochrome signalling and is directly repressed at night by the evening complex (LUX/ELF3/ELF4). In the morning PRR9 binds the CCA1 and LHY promoters, together with PRR7 and PRR5, and represses them by recruiting TOPLESS/TPR corepressors and histone deacetylase (HDA6). This forms the daytime negative arm of the CCA1/LHY-PRR feedback loop. prr9 mutants have a lengthened period, and prr9 prr7 prr5 triple mutants are arrhythmic in continuous light. PRR9 also represses clock-output genes, contributing to photoperiodic flowering (via CDF1/CO) and to red-light responses during seedling de-etiolation.
| 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). PRR9 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 | IPI PMID:20233950 PSEUDO-RESPONSE REGULATORS 9, 7, and 5 are transcriptional r... | ACCEPT | Summary: Annotation reflects ChIP association of PRR9 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 PRR9 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. PRR9 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:14634162 Characterization of the APRR9 pseudo-response regulator belo... | REMOVE | Summary: Yeast two-hybrid interaction of PRR9 with TOC1/PRR1 (Ito et al. 2003). The interaction may be real, but generic protein binding conveys no functional information and its physiological role has not been established. Reason: Uninformative protein-binding term (removal does not dispute the reported interaction). Supporting Evidence: PMID:14634162 The APRR9 protein is capable of interacting with APRR1/TOC1, suggesting a hetrodimer formation between these cognate family members. |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | REMOVE | Summary: High-throughput CrY2H-seq interactions of PRR9 with B-box proteins BBX18/BBX19. Generic protein binding from a screen; no functional MF can be inferred. Reason: Uninformative protein-binding term from a large-scale Y2H screen. |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | REMOVE | Summary: High-throughput CrY2H-seq interactions of PRR9 with B-box proteins BBX18/BBX19. Generic protein binding from a screen; no functional MF can be inferred. Reason: Uninformative protein-binding term from a large-scale Y2H screen. |
| GO:0005515 protein binding | IPI PMID:32612234 Extensive signal integration by the phytohormone protein net... | REMOVE | Summary: Binary Y2H interactions of PRR9 with NF-YC2/NF-YC4 from the phytohormone interactome map. Generic protein binding; no more informative activity is demonstrated in this study. Reason: Uninformative protein-binding term from a systematic Y2H map. |
| GO:0005515 protein binding | IPI PMID:32612234 Extensive signal integration by the phytohormone protein net... | REMOVE | Summary: Binary Y2H interactions of PRR9 with NF-YC2/NF-YC4 from the phytohormone interactome map. Generic protein binding; no more informative activity is demonstrated in this study. Reason: Uninformative protein-binding term from a systematic Y2H map. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: PRR9 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 | 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: PRR9 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: PRR9 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:15767265 PSEUDO-RESPONSE REGULATORS, PRR9, PRR7 and PRR5, together pl... | ACCEPT | Summary: prr9 single and higher-order mutants alter free-running period; the prr9 prr7 prr5 triple mutant is arrhythmic in continuous light. Reason: Direct genetic evidence for a clock role; core. Supporting Evidence: PMID:15767265 PRR9/PRR7/PRR5 together act as period-controlling factors |
| 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:0007623 circadian rhythm | TAS PMID:12068096 Two-component signal transduction pathways in Arabidopsis. | ACCEPT | Summary: Review-based statement of a circadian role; correct and supported by primary data. Reason: Correct; redundant with experimental annotations. Supporting Evidence: PMID:15767265 PRR9/PRR7/PRR5 together act as period-controlling factors |
| 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 PRR9 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 PRR9 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:0010017 red or far-red light signaling pathway | IMP PMID:16891401 Functional profiling reveals that only a small number of phy... | KEEP AS NON CORE | Summary: Functional profiling of rapidly phytochrome-induced genes (Khanna et al. 2006) included PRR9; PRR9 is a phy-induced early-response gene, and PIL1 is needed for its light induction. A role in red/far-red seedling responses is plausible but secondary to its clock function. Reason: Light-signalling involvement is supported (PRR9 is phytochrome-induced and prr mutants are red-light hyposensitive) but is not the core activity. Supporting Evidence: PMID:16891401 PIL1 is necessary for normal maximum PRR9 expression upon first exposure of dark-grown seedlings to light PMID:14634162 A phytochrome-mediated signaling pathway(s) activates the transcription of APRR9 |
| 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 PRR9 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 |
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Download this section (compressed HTML)Q: Does PRR9 bind DNA directly through its CCT domain with its own sequence specificity, or is its promoter occupancy partly dependent on heterodimerization with other PRRs or DNA-binding partners?
Q: How is the specificity of the PRR9-TPL-HDA6 repressor complex for CCA1/LHY versus output-gene promoters determined across the day?
Experiment: In vitro DNA-binding (EMSA/DAP-seq) of purified PRR9 CCT domain alone and with PRR7/PRR5, compared with ChIP-seq occupancy in prr7 prr5 backgrounds.
Hypothesis: PRR9 binds G-box-like motifs directly through its CCT domain, independently of other PRRs.
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