PSEUDO-RESPONSE REGULATOR 7 (PRR7, APRR7) is a nuclear transcriptional repressor of the Arabidopsis circadian oscillator. Its transcript and protein peak from midday into the afternoon, after PRR9 and before PRR5/TOC1. Like other PRRs, it has an N-terminal pseudo-receiver domain, which lacks the phospho-accepting aspartate, and a C-terminal CCT domain that mediates promoter association. PRR7 binds the CCA1 and LHY promoters and represses them together with PRR9 and PRR5, recruiting TOPLESS/TPR corepressors. This forms part of the daytime negative arm of the CCA1/LHY-PRR feedback loop. PRR7 also directly represses many morning-expressed output genes, including master regulators of growth, light signalling and abiotic-stress responses. prr7 mutants have a lengthened period and an altered clock phase, prr5 prr7 double mutants are nearly arrhythmic, and PRR7 is needed for clock entrainment by sugars (its promoter is a target of the sugar-responsive bZIP63) and for red/far-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). PRR7 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 PRR7 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 PRR7 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. PRR7 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:30078562 Circadian Entrainment in Arabidopsis by the Sugar-Responsive... | REMOVE | Summary: Annotation from Frank et al. 2018 with bZIP63 (AT5G28770) in WITH. The study's central finding is that bZIP63 regulates PRR7 transcription by binding its promoter, which is a regulatory relationship upstream of PRR7 rather than a binding activity of the PRR7 protein. Generic protein binding is uninformative in any case. Reason: Uninformative protein-binding term; the documented relationship is bZIP63 acting on the PRR7 gene. Supporting Evidence: PMID:30078562 the transcription factor BASIC LEUCINE ZIPPER63 (bZIP63) regulates the circadian oscillator gene PSEUDO RESPONSE REGULATOR7 (PRR7) to change the circadian phase in response to sugars |
| GO:0005515 protein binding | IPI PMID:32612234 Extensive signal integration by the phytohormone protein net... | REMOVE | Summary: Binary Y2H interaction from the phytohormone interactome map. Generic protein binding; no more informative activity can be derived. Reason: Uninformative protein-binding term from a systematic Y2H map. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: PRR7 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:14563930 Arabidopsis PSEUDO-RESPONSE REGULATOR7 is a signaling interm... | ACCEPT | Summary: PRR7-GUS fusion localizes to the nucleus (Kaczorowski & Quail 2003). Reason: Direct experimental localization consistent with function as a transcriptional repressor. Supporting Evidence: PMID:14563930 A PRR7-beta-glucuronidase fusion protein localized to the nucleus |
| 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:0005739 mitochondrion | HDA PMID:14671022 Experimental analysis of the Arabidopsis mitochondrial prote... | MARK AS OVER ANNOTATED | Summary: PRR7 was detected in a large LC-MS/MS mitochondrial proteome (416 proteins). The authors note that only about half the set is predicted to be mitochondrial. PRR7 is a nuclear clock transcriptional repressor (nuclear localization shown by GUS fusion), so the mitochondrial call most likely reflects co-purification. Reason: A single high-throughput organellar proteomics detection is at odds with the well-established nuclear function and localization; not representative of PRR7 biology. Supporting Evidence: PMID:14563930 A PRR7-beta-glucuronidase fusion protein localized to the nucleus |
| GO:0006355 regulation of DNA-templated transcription | IBA GO_REF:0000033 | ACCEPT | Summary: PRR7 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: PRR7 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:15695441 The Arabidopsis pseudo-response regulators, PRR5 and PRR7, c... | ACCEPT | Summary: prr5 prr7 double mutants are severely perturbed in free-running rhythms in LL and DD, appearing arrhythmic or very short period. Reason: Direct genetic evidence for a clock role; core. Supporting Evidence: PMID:15695441 we propose for the first time that PRR5 and PRR7 coordinately (or synergistically) play essential clock-associated roles close to the central oscillator |
| 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: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 PRR7 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 PRR7 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:14563930 Arabidopsis PSEUDO-RESPONSE REGULATOR7 is a signaling interm... | KEEP AS NON CORE | Summary: prr7 mutants were isolated in a sensitized screen for reduced de-etiolation in red and far-red light, and PRR7 was proposed as a signalling intermediate in phytochrome-regulated gene expression. Reason: Experimentally supported light-signalling involvement, but secondary to the core clock repressor activity. Supporting Evidence: PMID:14563930 PRR7 functions as a signaling intermediate in the phytochrome-regulated gene expression responsible for both seedling deetiolation and phasing of the circadian clock in response to light |
| 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 PRR7 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: Which features of the PRR7 middle region (between the pseudo-receiver and CCT domains) determine its distinct target set and phase relative to PRR9 and PRR5?
Q: Is PRR7 protein turnover regulated by a dedicated E3 ligase, given that ZTL targets TOC1 and PRR5 but apparently not PRR7?
Experiment: Domain-swap of PRR7 and PRR5 middle regions followed by ChIP-seq and period analysis in prr5 prr7 backgrounds.
Hypothesis: Target and phase specificity among PRRs is encoded outside the CCT DNA-binding motif.
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