COP1 (CONSTITUTIVE PHOTOMORPHOGENIC 1) is a central E3 ubiquitin-protein ligase that functions as a master negative regulator of photomorphogenesis in Arabidopsis thaliana. The protein features a modular domain architecture: an N-terminal RING-finger domain (essential for E3 ligase activity and zinc coordination), a central coiled-coil domain (mediating homodimerization and protein interactions), and C-terminal WD40 repeats (forming beta-propeller structures for substrate recognition). In darkness, COP1 is predominantly nuclear localized in discrete subnuclear compartments where it accepts ubiquitin from E2 enzymes via thioester bonds and directly transfers it to target substrates. Key targets include light-responsive transcription factors (HY5, HYH, LAF1, CIP7, UNE10/PIF8, PCH1, PCHL) and regulatory proteins (MYB21), leading to their ubiquitination and subsequent 26S proteasomal degradation to maintain etiolation. Upon light exposure, COP1 undergoes dynamic nucleocytoplasmic relocalization to the cytoplasm, reducing nuclear repressive activity and allowing stabilization of photomorphogenic regulators. COP1 functions in higher-order complexes with SPA proteins (SPA1-4), which modulate substrate repertoire and catalytic kinetics. Light exposure promotes COP1-SPA1 complex dissociation, reducing catalytic efficiency. COP1 activity is further regulated by suppressors (CSU1, CSU2) and the SUMO E3 ligase SIZ1. The protein participates in multiple light signaling pathways including red/far-red light perception, shade avoidance, and UV-B responses, with secondary functions in circadian clock entrainment, flowering time control, and secondary metabolism regulation. COP1 represents a key molecular switch with conserved function across eukaryotes, integrating environmental light cues with developmental programs through precise post-translational control.
Definition: The formation of higher-order protein complexes containing COP1 and SPA proteins that modulate substrate repertoire and catalytic kinetics of the E3 ubiquitin ligase activity
Justification: COP1 functions in complexes with SPA proteins to regulate substrate specificity and enzymatic kinetics, representing a specific type of E3 ligase complex assembly. The parent is the assembly branch (GO:0065003 protein-containing complex assembly); the previously listed GO:0043161 is a catabolic process term and is the wrong ontological branch for a complex-assembly term.
Parent term: protein-containing complex assembly
Supporting Evidence:
Definition: The process by which proteins undergo dynamic subcellular relocalization between nucleus and cytoplasm in response to light stimuli to modulate their functional activity
Justification: COP1's light-dependent relocalization from nucleus to cytoplasm represents a specific mechanism of light-responsive protein regulation
Parent term: cellular response to light stimulus
Supporting Evidence:
Definition: A COP1-dependent process in which the RING E3 ligase ubiquitinates the Polycomb-associated PHD protein VIL1 (VIN3-LIKE 1) in darkness, targeting it for proteasomal degradation and thereby limiting VIL1/PRC2-dependent H3K27me3 deposition and repressive chromatin loop formation at growth-promoting genes.
Justification: A 2024 study (Wang et al., PNAS 2024, PMID:38349881, "COP1 controls light-dependent chromatin remodeling") established VIL1 as a direct COP1 substrate, connecting COP1 to Polycomb-associated chromatin regulation. The evidence is quantitative (3,368 VIL1-dependent H3K27me3-enriched loci; H3K27me3 significantly higher in cop1-4 with P = 3.8e-7; dark-induced VIL1 degradation blocked by bortezomib). This chromatin-remodeling role is not captured by any existing annotation.
Parent term: chromatin remodeling
Supporting Evidence:
Definition: A COP1-dependent process in which the RING E3 ligase ubiquitinates and degrades the plant-specific spliceosomal component DCS1, modulating light-regulated intron retention and nuclear detainment of intron-retained transcripts of light-signaling genes.
Justification: A 2024 study (Zhou et al., Nat Commun 2024, PMID:38879536, "Light regulates nuclear detainment of intron-retained transcripts through COP1-spliceosome to modulate photomorphogenesis") showed COP1 controls spliceosome activity via COP1-dependent ubiquitination and degradation of DCS1, affecting 1,594 COP1-responsive intron-retention events. This RNA-processing role expands COP1 function beyond transcription-factor turnover and is not captured by any existing annotation.
Parent term: regulation of mRNA splicing, via spliceosome
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: COP1 is a well-characterized E3 ubiquitin ligase that targets key photomorphogenesis regulators (HY5, HYH, LAF1, CIP7, UNE10/PIF8, PCH1, PCHL) for ubiquitination and subsequent proteasomal degradation in darkness. This IBA annotation accurately captures COP1's core biological function. Reason: This process annotation correctly represents COP1's primary mechanism of action - mediating proteasome-dependent degradation of substrates through ubiquitination. Well-supported by extensive literature including studies showing COP1 targets HY5, HYH, LAF1 and other transcription factors for degradation. Supporting Evidence: PMID:10839542 Targeted destabilization of HY5 during light-regulated development of Arabidopsis PMID:26474641 COP1-Mediated Degradation of HY5 during Arabidopsis Seedling Development file:ARATH/COP1/COP1-deep-research-manual.md See deep research file for comprehensive analysis |
| GO:0061630 ubiquitin protein ligase activity | IBA GO_REF:0000033 | ACCEPT | Summary: COP1 functions as an E3 ubiquitin-protein ligase with a characteristic RING-finger domain that is essential for catalytic activity. It accepts ubiquitin from E2 enzymes and transfers it to target substrates like HY5, HYH, and other photomorphogenesis regulators. Reason: This molecular function annotation accurately describes COP1's core enzymatic activity. COP1 contains a RING-finger domain required for E3 ligase activity and has been experimentally demonstrated to have ubiquitin ligase activity against multiple substrates. Supporting Evidence: PMID:15705947 COP1 exhibits ubiquitin ligase activity toward HFR1 in vitro PMID:29087315 COP1), a well-known E3 ubiquitin ligase, functions as a central repressor of seedling photomorphogenesis file:ARATH/COP1/COP1-deep-research-falcon.md COP1 is an **E3 ubiquitin ligase (EC 2.3.2.27)**. Its biochemical role is to facilitate transfer of ubiquitin from an E2 enzyme to specific substrate proteins (often transcription factors or regulatory proteins), typically marking them for proteasomal degradation. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: COP1 is primarily nuclear localized in darkness where it executes its function as a repressor of photomorphogenesis. Multiple experimental studies confirm nuclear localization through IDA evidence, making this IEA annotation redundant but correct. Reason: While this is a computational prediction, COP1 nuclear localization is strongly supported by experimental evidence from multiple IDA annotations in this dataset and extensive literature. The annotation is accurate. Supporting Evidence: PMID:26474641 SHW1 promotes COP1-mediated degradation of HY5 through enhanced ubiquitylation in the darkness PMID:19061637 COP1 acts as a RING-type E3 ubiquitin-ligase that mediates ubiquitination and targeted degradation of positive regulators of light signal transduction in dark conditions file:ARATH/COP1/COP1-deep-research-falcon.md COP1 functions prominently in the **nucleus** in darkness, where it targets nuclear substrates for ubiquitination. COP1 contains a **bipartite nuclear localization signal (NLS)** and an **N-terminal cytoplasmic localization signal**, enabling **light-regulated nucleocytoplasmic partitioning**. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: COP1 does translocate to the cytoplasm upon light exposure as part of its regulation mechanism, but this is a secondary, light-induced localization rather than its primary functional location. The annotation is technically correct but represents non-core function. Reason: While COP1 can be found in the cytoplasm, particularly under light conditions, its primary and functionally important localization is nuclear. The cytoplasmic localization represents a regulatory mechanism to inactivate COP1 rather than a site of its primary function. Supporting Evidence: file:ARATH/COP1/COP1-deep-research-falcon.md a key current model is that **COP1 is excluded/depleted from the nucleus in light**, permitting VIL1 accumulation; in darkness, **COP1 accumulates in the nucleus and ubiquitinates VIL1**, reducing loop formation and altering repression at growth genes. |
| GO:0008270 zinc ion binding | IEA GO_REF:0000043 | ACCEPT | Summary: COP1 contains a RING-finger domain at its N-terminus that coordinates zinc ions, which is essential for its E3 ubiquitin ligase activity. This computational prediction is biochemically accurate. Reason: The RING-finger domain is a defining structural feature of COP1 that requires zinc coordination for proper folding and catalytic activity. This annotation correctly captures an essential molecular function. Supporting Evidence: PMID:11080276 deletion of the COP1 amino terminus including the Ring-finger domain abolished COP1 function |
| GO:0009585 red, far-red light phototransduction | IEA GO_REF:0000043 | MODIFY | Summary: GO:0009585 is defined as the sequence of reactions that convert absorbed red/far-red photons into a molecular signal - i.e. the phototransduction step carried out by photoreceptors such as phytochromes. COP1 is not a photoreceptor and does not perform phototransduction; it acts downstream as a repressor within the red/far-red light signaling pathway. The downstream role is correctly captured by GO:0010017 (red or far-red light signaling pathway), which is also annotated. Reason: The keyword-mapped phototransduction term overstates COP1's role. COP1 operates downstream of photoreceptors in the light signaling pathway rather than transducing the photon signal itself. The more appropriate term is the red or far-red light signaling pathway (GO:0010017), already present in this annotation set. Proposed replacements: red or far-red light signaling pathway Supporting Evidence: PMID:31732705 phyA-mediated inhibition of COP1/SPAs leading to the stabilization of PIF8 in far-red light file:ARATH/COP1/COP1-deep-research-falcon.md UV-B involves COP1 interaction with UVR8 in a pathway that supports HY5 stabilization, and COP1/SPA can cooperate with phytochromes in regulating PIF stability in light signaling. |
| GO:0010017 red or far-red light signaling pathway | IEA GO_REF:0000043 | ACCEPT | Summary: This annotation is very similar to GO:0009585 and captures COP1's role in red/far-red light signaling pathways. COP1 negatively regulates photomorphogenesis by targeting light-responsive factors for degradation in these pathways. Reason: While similar to the previous annotation, this term specifically refers to the signaling pathway rather than transduction. COP1 is a key negative regulator in red/far-red light signaling pathways through its interaction with phytochrome signaling components. Supporting Evidence: PMID:11461903 SPA1 function in the phyA signaling pathway PMID:31732705 phyA-mediated inhibition of COP1/SPAs leading to the stabilization of PIF8 in far-red light |
| GO:0016740 transferase activity | IEA GO_REF:0000043 | MARK AS OVER ANNOTATED | Summary: While technically correct since E3 ligases transfer ubiquitin, this annotation is too general and uninformative. COP1's transferase activity is specifically ubiquitin-protein transferase activity, which is better captured by more specific terms already annotated. Reason: This term is overly broad and doesn't provide meaningful functional information. The more specific ubiquitin-protein transferase activity (GO:0004842) and ubiquitin protein ligase activity (GO:0061630) terms better capture COP1's specific molecular function. Proposed replacements: ubiquitin-protein transferase activity ubiquitin protein ligase activity |
| GO:0042802 identical protein binding | IEA GO_REF:0000117 | ACCEPT | Summary: COP1 forms homodimers through its coiled-coil domain, which is essential for its full ubiquitination activity. This computational prediction accurately captures COP1's homodimerization capability. Reason: COP1 homodimerization is well-documented and functionally important for its E3 ligase activity. The coiled-coil domain mediates this interaction, making this annotation accurate. |
| GO:0046872 metal ion binding | IEA GO_REF:0000043 | MARK AS OVER ANNOTATED | Summary: COP1's RING-finger domain binds zinc ions, which is captured more specifically by the zinc ion binding annotation (GO:0008270). This broader term is accurate but less informative. Reason: While correct, this annotation is too general when the more specific zinc ion binding term already captures COP1's metal coordination function. The specific term provides more meaningful functional information. Proposed replacements: zinc ion binding |
| GO:0061630 ubiquitin protein ligase activity | IEA GO_REF:0000120 | ACCEPT | Summary: This is a duplicate annotation of the same GO term (GO:0061630) already annotated with IBA evidence. The IBA annotation provides stronger phylogenetic evidence than this computational prediction. Reason: While redundant with the IBA annotation, this computational prediction is accurate for COP1's core function as an E3 ubiquitin ligase. Both annotations can coexist as they represent different types of evidence. Supporting Evidence: PMID:29087315 COP1), a well-known E3 ubiquitin ligase, functions as a central repressor of seedling photomorphogenesis |
| GO:0005515 protein binding | IPI PMID:10488108 The RING finger motif of photomorphogenic repressor COP1 spe... | REMOVE | Summary: This is one of many redundant protein binding annotations. COP1 does bind proteins as part of its function, but the generic term provides no meaningful functional information. Reason: This is a redundant annotation among 35+ protein binding annotations. Removing to reduce redundancy and improve annotation quality. COP1's functional protein interactions are better captured by more specific terms already present in the annotation set. Supporting Evidence: PMID:10488108 The RING finger motif of photomorphogenic repressor COP1 specifically interacts with the RING-H2 motif of a novel Arabidopsis protein. |
| GO:0005515 protein binding | IPI PMID:10990463 HY5 stability and activity in arabidopsis is regulated by ph... | REMOVE | Summary: This is one of many redundant protein binding annotations that provides no additional functional information beyond what is already captured by specific molecular function terms. Reason: Redundant annotation. COP1's protein interactions are adequately represented by more specific and informative molecular function terms. Removing to improve annotation quality. Supporting Evidence: PMID:10990463 HY5 stability and activity in arabidopsis is regulated by phosphorylation in its COP1 binding domain. |
| GO:0005515 protein binding | IPI PMID:11226162 Identification of a structural motif that confers specific i... | REMOVE | Summary: Another redundant protein binding annotation in a set of 35+ such annotations. Generic protein binding provides no meaningful functional insight. Reason: Redundant annotation providing no additional functional information. COP1's specific protein interactions are better captured by existing specific molecular function terms. Supporting Evidence: PMID:11226162 Identification of a structural motif that confers specific interaction with the WD40 repeat domain of Arabidopsis COP1. |
| GO:0005515 protein binding | IPI PMID:11461903 The phytochrome A-specific signaling intermediate SPA1 inter... | REMOVE | Summary: This annotation represents COP1-SPA1 interaction but the generic protein binding term is uninformative compared to more specific molecular function terms. Reason: Redundant annotation. The COP1-SPA interaction is functionally captured by the E3 ligase activity annotations and complex formation terms. Generic protein binding adds no value. Supporting Evidence: PMID:11461903 2001 Jul 18. The phytochrome A-specific signaling intermediate SPA1 interacts directly with COP1, a constitutive repressor of light signaling in Arabidopsis. |
| GO:0005515 protein binding | IPI PMID:11509693 Direct interaction of Arabidopsis cryptochromes with COP1 in... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:11509693 Aug 16. Direct interaction of Arabidopsis cryptochromes with COP1 in light control development. |
| GO:0005515 protein binding | IPI PMID:11752373 The signaling mechanism of Arabidopsis CRY1 involves direct ... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:11752373 The signaling mechanism of Arabidopsis CRY1 involves direct interaction with COP1. |
| GO:0005515 protein binding | IPI PMID:11877375 Arabidopsis COP10 is a ubiquitin-conjugating enzyme variant ... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:11877375 Arabidopsis COP10 is a ubiquitin-conjugating enzyme variant that acts together with COP1 and the COP9 signalosome in repressing photomorphogenesis. |
| GO:0005515 protein binding | IPI PMID:12023303 Two interacting bZIP proteins are direct targets of COP1-med... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:12023303 Two interacting bZIP proteins are direct targets of COP1-mediated control of light-dependent gene expression in Arabidopsis. |
| GO:0005515 protein binding | IPI PMID:12028569 Biochemical evidence for ubiquitin ligase activity of the Ar... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:12028569 Biochemical evidence for ubiquitin ligase activity of the Arabidopsis COP1 interacting protein 8 (CIP8). |
| GO:0005515 protein binding | IPI PMID:12827204 LAF1 ubiquitination by COP1 controls photomorphogenesis and ... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:12827204 LAF1 ubiquitination by COP1 controls photomorphogenesis and is stimulated by SPA1. |
| GO:0005515 protein binding | IPI PMID:12887588 The SPA1-like proteins SPA3 and SPA4 repress photomorphogene... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:12887588 The SPA1-like proteins SPA3 and SPA4 repress photomorphogenesis in the light. |
| GO:0005515 protein binding | IPI PMID:14597662 The COP1-SPA1 interaction defines a critical step in phytoch... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:14597662 The COP1-SPA1 interaction defines a critical step in phytochrome A-mediated regulation of HY5 activity. |
| GO:0005515 protein binding | IPI PMID:15741320 HFR1 is targeted by COP1 E3 ligase for post-translational pr... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:15741320 HFR1 is targeted by COP1 E3 ligase for post-translational proteolysis during phytochrome A signaling. |
| GO:0005515 protein binding | IPI PMID:16339850 Arabidopsis CONSTANS-LIKE3 is a positive regulator of red li... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:16339850 Arabidopsis CONSTANS-LIKE3 is a positive regulator of red light signaling and root growth. |
| GO:0005515 protein binding | IPI PMID:16844902 Arabidopsis CULLIN4 Forms an E3 Ubiquitin Ligase with RBX1 a... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:16844902 Jul 14. Arabidopsis CULLIN4 Forms an E3 Ubiquitin Ligase with RBX1 and the CDD Complex in Mediating Light Control of Development. |
| GO:0005515 protein binding | IPI PMID:17699755 Independent and interdependent functions of LAF1 and HFR1 in... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:17699755 Independent and interdependent functions of LAF1 and HFR1 in phytochrome A signaling. |
| GO:0005515 protein binding | IPI PMID:18296627 COP1-mediated ubiquitination of CONSTANS is implicated in cr... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:18296627 COP1-mediated ubiquitination of CONSTANS is implicated in cryptochrome regulation of flowering in Arabidopsis. |
| GO:0005515 protein binding | IPI PMID:18388858 Arabidopsis COP1 shapes the temporal pattern of CO accumulat... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:18388858 Arabidopsis COP1 shapes the temporal pattern of CO accumulation conferring a photoperiodic flowering response. |
| GO:0005515 protein binding | IPI PMID:18397371 CRY1 inhibits COP1-mediated degradation of BIT1, a MYB trans... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:18397371 2008 Apr 4. CRY1 inhibits COP1-mediated degradation of BIT1, a MYB transcription factor, to activate blue light-dependent gene expression in Arabidopsis. |
| GO:0005515 protein binding | IPI PMID:18552200 Arabidopsis DDB1-CUL4 ASSOCIATED FACTOR1 forms a nuclear E3 ... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:18552200 Arabidopsis DDB1-CUL4 ASSOCIATED FACTOR1 forms a nuclear E3 ubiquitin ligase with DDB1 and CUL4 that is involved in multiple plant developmental processes. |
| GO:0005515 protein binding | IPI PMID:18812498 Biochemical characterization of Arabidopsis complexes contai... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:18812498 Biochemical characterization of Arabidopsis complexes containing CONSTITUTIVELY PHOTOMORPHOGENIC1 and SUPPRESSOR OF PHYA proteins in light control of plant development. |
| GO:0005515 protein binding | IPI PMID:19165148 Interaction of COP1 and UVR8 regulates UV-B-induced photomor... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:19165148 Interaction of COP1 and UVR8 regulates UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis. |
| GO:0005515 protein binding | IPI PMID:20624951 Cryptochrome 2 and phototropin 2 regulate resistance protein... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:20624951 Cryptochrome 2 and phototropin 2 regulate resistance protein-mediated viral defense by negatively regulating an E3 ubiquitin ligase. |
| GO:0005515 protein binding | IPI PMID:21041653 Negative feedback regulation of UV-B-induced photomorphogene... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:21041653 Negative feedback regulation of UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis. |
| GO:0005515 protein binding | IPI PMID:21798944 Evidence for network evolution in an Arabidopsis interactome... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:21798944 Evidence for network evolution in an Arabidopsis interactome map. |
| GO:0005515 protein binding | IPI PMID:7753789 Arabidopsis COP1 protein specifically interacts in vitro wit... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:7753789 Arabidopsis COP1 protein specifically interacts in vitro with a cytoskeleton-associated protein, CIP1. |
| GO:0005515 protein binding | IPI PMID:9659918 Molecular interaction between COP1 and HY5 defines a regulat... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:9659918 Molecular interaction between COP1 and HY5 defines a regulatory switch for light control of Arabidopsis development. |
| GO:0005515 protein binding | IPI PMID:9755158 Functional dissection of Arabidopsis COP1 reveals specific r... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:9755158 Functional dissection of Arabidopsis COP1 reveals specific roles of its three structural modules in light control of seedling development. |
| GO:0042802 identical protein binding | IPI PMID:17551013 Imaging protein interactions with bioluminescence resonance ... | ACCEPT | Summary: COP1 forms homodimers through its coiled-coil domain, which is essential for its full ubiquitination activity. This computational prediction accurately captures COP1's homodimerization capability. Reason: COP1 homodimerization is well-documented and functionally important for its E3 ligase activity. The coiled-coil domain mediates this interaction, making this annotation accurate. Supporting Evidence: PMID:17551013 Imaging protein interactions with bioluminescence resonance energy transfer (BRET) in plant and mammalian cells and tissues. |
| GO:0042802 identical protein binding | IPI PMID:18812498 Biochemical characterization of Arabidopsis complexes contai... | ACCEPT | Summary: COP1 forms homodimers through its coiled-coil domain, which is essential for its full ubiquitination activity. This computational prediction accurately captures COP1's homodimerization capability. Reason: COP1 homodimerization is well-documented and functionally important for its E3 ligase activity. The coiled-coil domain mediates this interaction, making this annotation accurate. Supporting Evidence: PMID:18812498 Biochemical characterization of Arabidopsis complexes containing CONSTITUTIVELY PHOTOMORPHOGENIC1 and SUPPRESSOR OF PHYA proteins in light control of plant development. |
| GO:0042802 identical protein binding | IPI PMID:9755158 Functional dissection of Arabidopsis COP1 reveals specific r... | ACCEPT | Summary: COP1 forms homodimers through its coiled-coil domain, which is essential for its full ubiquitination activity. This computational prediction accurately captures COP1's homodimerization capability. Reason: COP1 homodimerization is well-documented and functionally important for its E3 ligase activity. The coiled-coil domain mediates this interaction, making this annotation accurate. Supporting Evidence: PMID:9755158 Functional dissection of Arabidopsis COP1 reveals specific roles of its three structural modules in light control of seedling development. |
| GO:0005515 protein binding | IPI PMID:32061894 PCH1 and PCHL Directly Interact with PIF1, Promote Its Degra... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:32061894 2020 Feb 13. PCH1 and PCHL Directly Interact with PIF1, Promote Its Degradation, and Inhibit Its Transcriptional Function during Photomorphogenesis. |
| GO:0016567 protein ubiquitination | IEA GO_REF:0000041 | ACCEPT | Summary: COP1 mediates protein ubiquitination as part of its core function as an E3 ubiquitin ligase. This annotation accurately captures the biological process that COP1 directly catalyzes through its E3 ligase activity. Reason: This annotation correctly represents the core biological process that COP1 performs - ubiquitinating target proteins for proteasomal degradation. This is COP1's primary mechanism of action in regulating photomorphogenesis. Supporting Evidence: PMID:29087315 COP1), a well-known E3 ubiquitin ligase, functions as a central repressor of seedling photomorphogenesis |
| GO:0005515 protein binding | IPI PMID:31732705 PHYTOCHROME INTERACTING FACTOR8 Inhibits Phytochrome A-Media... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:31732705 PHYTOCHROME INTERACTING FACTOR8 Inhibits Phytochrome A-Mediated Far-Red Light Responses in Arabidopsis. |
| GO:0005515 protein binding | IPI PMID:28735869 DHU1 negatively regulates UV-B signaling via its direct inte... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:28735869 DHU1 negatively regulates UV-B signaling via its direct interaction with COP1 and RUP1. |
| GO:0005515 protein binding | IPI PMID:29087315 COP1 mediates dark-specific degradation of microtubule-assoc... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:29087315 COP1 mediates dark-specific degradation of microtubule-associated protein WDL3 in regulating Arabidopsis hypocotyl elongation. |
| GO:0061630 ubiquitin protein ligase activity | IDA PMID:29087315 COP1 mediates dark-specific degradation of microtubule-assoc... | ACCEPT | Summary: This is high-quality experimental evidence (IDA) directly demonstrating COP1's ubiquitin ligase activity. The paper reports an in vitro ubiquitination assay in which COP1 directly ubiquitinates its substrate WDL3, supporting COP1's core molecular function. Reason: Excellent experimental evidence for COP1's primary molecular function. IDA evidence provides the strongest support for ubiquitin ligase activity, which is COP1's defining enzymatic activity for targeting photomorphogenic regulators. Supporting Evidence: PMID:29087315 COP1 directly ubiquitinates WDL3 in vitro and that WDL3 protein is degraded in WT seedlings but is abundant in the cop1 mutant in the dark |
| GO:0005515 protein binding | IPI PMID:9668129 Role of a COP1 interactive protein in mediating light-regula... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:9668129 Role of a COP1 interactive protein in mediating light-regulated gene expression in arabidopsis. |
| GO:0004842 ubiquitin-protein transferase activity | IMP PMID:26474641 Short Hypocotyl in White Light1 Interacts with Elongated Hyp... | ACCEPT | Summary: This experimental annotation provides direct evidence for COP1's E3 ubiquitin ligase activity. The IMP evidence shows COP1's role in ubiquitin transfer, which is its core molecular function for targeting substrates like HY5 for degradation. Reason: This is high-quality experimental evidence (IMP) directly demonstrating COP1's ubiquitin-protein transferase activity, which is synonymous with its E3 ligase function. This annotation captures COP1's core enzymatic mechanism. Supporting Evidence: PMID:26474641 SHW1 promotes COP1-mediated degradation of HY5 through enhanced ubiquitylation in the darkness |
| GO:0005515 protein binding | IPI PMID:26474641 Short Hypocotyl in White Light1 Interacts with Elongated Hyp... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:26474641 Oct 16. Short Hypocotyl in White Light1 Interacts with Elongated Hypocotyl5 (HY5) and Constitutive Photomorphogenic1 (COP1) and Promotes COP1-Mediated Degradation of HY5 during Arabidopsis Seedling Development. |
| GO:0005634 nucleus | IDA PMID:26474641 Short Hypocotyl in White Light1 Interacts with Elongated Hyp... | ACCEPT | Summary: COP1 is predominantly nuclear localized in darkness where it executes its function as a repressor of photomorphogenesis. This experimental evidence confirms COP1's nuclear localization. Reason: Strong experimental support for COP1's nuclear localization, which is essential for its function as a nuclear E3 ligase regulating photomorphogenic transcription factors. Supporting Evidence: PMID:26474641 SHW1 promotes COP1-mediated degradation of HY5 through enhanced ubiquitylation in the darkness |
| GO:0005515 protein binding | IPI PMID:22535582 BZS1, a B-box protein, promotes photomorphogenesis downstrea... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:22535582 BZS1, a B-box protein, promotes photomorphogenesis downstream of both brassinosteroid and light signaling pathways. |
| GO:0016604 nuclear body | IDA PMID:23647163 COP1 re-accumulates in the nucleus under shade. | ACCEPT | Summary: COP1 has been shown to localize to discrete nuclear bodies or foci within the nucleus. This represents a more specific subcellular localization than general nuclear localization. Reason: This annotation provides experimentally supported evidence for COP1's organization into distinct nuclear compartments, which may be functionally relevant for its E3 ligase activity and substrate targeting. Supporting Evidence: PMID:23647163 COP1 accumulates in the nucleus under natural or simulated shade |
| GO:0005515 protein binding | IPI PMID:22988111 C-terminal region of the UV-B photoreceptor UVR8 initiates s... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:22988111 C-terminal region of the UV-B photoreceptor UVR8 initiates signaling through interaction with the COP1 protein. |
| GO:0005634 nucleus | IDA PMID:19061637 COP1 and ELF3 control circadian function and photoperiodic f... | ACCEPT | Summary: COP1 is predominantly nuclear localized in darkness where it executes its function as a repressor of photomorphogenesis. This experimental evidence confirms COP1's nuclear localization. Reason: Strong experimental support for COP1's nuclear localization, which is essential for its function as a nuclear E3 ligase regulating photomorphogenic transcription factors. Supporting Evidence: PMID:19061637 COP1 acts as a RING-type E3 ubiquitin-ligase |
| GO:0009649 entrainment of circadian clock | IMP PMID:21395889 Functional interaction of the circadian clock and UV RESISTA... | KEEP AS NON CORE | Summary: COP1 has been implicated in circadian clock regulation through its control of light signaling pathways that influence clock entrainment. This represents a secondary but validated function linking light perception to circadian regulation. Reason: While COP1 does influence circadian rhythms through its role in light signaling, this is a secondary consequence of its primary photomorphogenic regulatory function rather than a core function. The IMP evidence supports this connection but it's not COP1's primary role. Supporting Evidence: PMID:21395889 UV RESISTANCE LOCUS 8 (UVR8) and CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) are required |
| GO:0009640 photomorphogenesis | IGI PMID:20061554 Arabidopsis CULLIN4-damaged DNA binding protein 1 interacts ... | ACCEPT | Summary: Photomorphogenesis is COP1's central biological process - it acts as a negative regulator, repressing photomorphogenesis in darkness by targeting light-responsive transcription factors for degradation. This IGI evidence supports COP1's core regulatory role. Reason: This annotation captures COP1's most important biological function. COP1 is a key negative regulator of photomorphogenesis, ensuring proper light-regulated development by controlling the stability of photomorphogenic factors. Supporting Evidence: PMID:20061554 CUL4-DDB1-COP1-SPA E3 ligase complexes may mediate the repression of photomorphogenesis PMID:10201077 The role of COP1 in repression of Arabidopsis photomorphogenic development file:ARATH/COP1/COP1-deep-research-falcon.md COP1 is a “central switch” of global light-responsive gene expression by promoting the turnover of multiple nuclear positive regulators of photomorphogenesis, including the bZIP transcription factor **HY5** (direct COP1 substrate). |
| GO:0010100 negative regulation of photomorphogenesis | IGI PMID:10201077 The role of COP1 in repression of Arabidopsis photomorphogen... | NEW | Summary: COP1's defining biological role is the negative regulation (repression) of photomorphogenesis. The existing GOA annotations use the generic parent term photomorphogenesis (GO:0009640), but COP1 acts specifically as a repressor that maintains skotomorphogenesis in darkness by degrading positive regulators of photomorphogenesis. This more precise term is proposed as a NEW core annotation. Reason: COP1 is universally described as the central repressor of photomorphogenesis; the negative regulation term (GO:0010100) captures the directionality of its role more precisely than the generic photomorphogenesis term and represents its core biological process. Supporting Evidence: PMID:10201077 The role of COP1 in repression of Arabidopsis photomorphogenic development file:ARATH/COP1/COP1-deep-research-falcon.md COP1 is a “central switch” of global light-responsive gene expression by promoting the turnover of multiple nuclear positive regulators of photomorphogenesis, including the bZIP transcription factor **HY5** (direct COP1 substrate). |
| GO:0010119 regulation of stomatal movement | IGI PMID:16093319 From The Cover: A role for Arabidopsis cryptochromes and COP... | KEEP AS NON CORE | Summary: COP1's role in stomatal movement regulation is likely indirect through its effects on light signaling pathways that influence stomatal responses. This represents a downstream consequence of COP1's primary light signaling function. Reason: While the IGI evidence supports some connection between COP1 and stomatal regulation, this is a peripheral function that likely results from COP1's broader role in light signaling rather than being a direct, core function. Supporting Evidence: PMID:16093319 COP1 is a repressor of stomatal opening and likely acts downstream of CRY and PHOT signaling pathways |
| GO:0005515 protein binding | IPI PMID:15705947 Light regulates COP1-mediated degradation of HFR1, a transcr... | MARK AS OVER ANNOTATED | Summary: While COP1 does interact with proteins as part of its regulatory function, the generic "protein binding" term provides little functional insight. More specific molecular function terms would be more informative. Reason: According to curation guidelines, "protein binding" doesn't provide meaningful functional information. This is a heterodimeric interaction; where COP1 ubiquitinates the partner the function is better captured by "ubiquitin protein ligase activity" (GO:0061630). Note that "identical protein binding" (GO:0042802) is NOT an appropriate replacement here because it denotes homodimerization/self-association, not this heterodimeric interaction. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:15705947 Light regulates COP1-mediated degradation of HFR1, a transcription factor essential for light signaling in Arabidopsis. |
| GO:0080008 Cul4-RING E3 ubiquitin ligase complex | ISS PMID:18223036 Characterization of Arabidopsis and rice DWD proteins and th... | KEEP AS NON CORE | Summary: COP1's canonical and best-characterized active form is the COP1/SPA RING E3 ligase complex. However, COP1/SPA additionally connects to a CUL4-DDB1-RBX1 scaffold, so association with a CUL4-RING E3 module is supported by current literature. This is a peripheral/accessory complex membership rather than COP1's core catalytic configuration. Reason: Earlier review treated COP1 as strictly a standalone RING E3 and called for removal, but authoritative reviews describe COP1/SPA connecting to a CUL4-DDB1-RBX1 scaffold to form a multimeric E3 ligase module. The annotation is therefore retained as non-core, since COP1's primary mode is the COP1/SPA complex while CUL4-DDB1 association is an accessory configuration. Supporting Evidence: PMID:18812498 The four endogenous SPA proteins can form stable complexes with COP1 in vivo PMID:18223036 Characterization of Arabidopsis and rice DWD proteins and their roles as substrate receptors for CUL4-RING E3 ubiquitin ligases. file:ARATH/COP1/COP1-deep-research-falcon.md COP1 associates with **SPA proteins** to form COP1/SPA complexes and connects to a **CUL4–DDB1–RBX1** scaffold, creating a multimeric E3 ligase module that supports substrate ubiquitylation in light signaling. |
| GO:0006281 DNA repair | IMP PMID:18434413 The Arabidopsis COP9 signalosome is essential for G2 phase p... | MARK AS OVER ANNOTATED | Summary: PMID:18434413 characterizes the COP9 signalosome (CSN), a multi-subunit deneddylase complex that is a distinct entity from COP1 (a RING E3 ubiquitin ligase). The paper shows that csn mutants undergo DNA damage and G2 arrest; its abstract also explicitly reports DNA damage in cop1 mutants, alongside csn, cullin4 and det1 mutants, so the cop1 mutant was directly assayed in this study. Reason: This is not a mis-attribution - the abstract explicitly states that DNA damage is apparent in cop1 mutants, so the curator's IMP has direct support and cannot be overruled from the abstract-only cache. However, DNA damage accumulating in a mutant of a CRL-pathway component is most parsimoniously an indirect consequence of impaired cullin-RING ligase regulation rather than evidence that COP1 itself functions in DNA repair, so the broad DNA repair process term likely over-annotates COP1; it is not a core function. Supporting Evidence: PMID:18434413 DNA damage is also apparent in mutants of the NEDD8 conjugation pathway and in mutants of the E3 ligase subunits CULLIN4, COP1 and DET1, which share phenotypes with csn mutants. |
| GO:0004842 ubiquitin-protein transferase activity | IDA PMID:15705947 Light regulates COP1-mediated degradation of HFR1, a transcr... | ACCEPT | Summary: This is another experimental annotation (IDA) demonstrating COP1's core ubiquitin-protein transferase activity, providing additional direct evidence for its E3 ligase function beyond the IMP annotation with the same term. Reason: High-quality experimental evidence (IDA) for COP1's core molecular function. This annotation represents direct demonstration of COP1's ubiquitin-protein transferase activity, which is essential for its role in photomorphogenesis regulation. Supporting Evidence: PMID:15705947 COP1 exhibits ubiquitin ligase activity toward HFR1 in vitro |
| GO:0048573 photoperiodism, flowering | IMP PMID:18388858 Arabidopsis COP1 shapes the temporal pattern of CO accumulat... | KEEP AS NON CORE | Summary: COP1 regulates flowering time through its control of light signaling pathways that influence photoperiodic responses. This is a well-documented secondary function of COP1 linking light perception to developmental timing. Reason: While COP1 does influence flowering time through its role in light signaling and regulation of transcription factors like CONSTANS, this is a secondary consequence of its primary photomorphogenic function rather than a core activity. Supporting Evidence: PMID:18388858 COP1 contributes to day length perception by reducing the abundance of CO during the night and thereby delaying flowering under SDs |
| GO:0009641 shade avoidance | IMP PMID:8205001 Genetic and molecular analysis of an allelic series of cop1 ... | KEEP AS NON CORE | Summary: Shade avoidance is one of many light-regulated developmental programs influenced by COP1. COP1 re-accumulates in the nucleus under shade and modulates the stability of light-signaling factors, but shade avoidance is a downstream pleiotropic developmental output rather than COP1's core molecular/biochemical function. Reason: For this highly pleiotropic gene, shade avoidance is a downstream physiological consequence of COP1's core activity (RING E3 ligase / repression of photomorphogenesis), not a core function in itself. Retained as non-core to reflect the experimental link while keeping the core annotation set focused on the E3 ligase and photomorphogenesis repression roles. Supporting Evidence: PMID:8205001 Genetic and molecular analysis of an allelic series of cop1 mutants suggests functional roles for the multiple protein domains PMID:23647163 COP1 accumulates in the nucleus under natural or simulated shade |
| GO:0046283 anthocyanin-containing compound metabolic process | IMP PMID:17217468 HY5 is a point of convergence between cryptochrome and cytok... | KEEP AS NON CORE | Summary: COP1 regulates anthocyanin biosynthesis through its control of light-responsive transcription factors involved in secondary metabolism. This represents a secondary function linking light signaling to pigment production. Reason: While COP1 does influence anthocyanin metabolism through its regulation of transcription factors, this is a downstream consequence of its primary light signaling function rather than a core activity. Supporting Evidence: PMID:17217468 As both cryptochrome and cytokinin signalling pathways increase HY5 protein levels, and as HY5 binds to the promoters of anthocyanin biosynthetic enzymes to stimulate gene expression, it is concluded that the regulation of HY5 protein stability represents a point of convergence between cryptochrome and cytokinin signalling pathways. |
| GO:0005634 nucleus | IDA PMID:16829591 CONSTITUTIVELY PHOTOMORPHOGENIC1 is required for the UV-B re... | ACCEPT | Summary: This provides additional experimental evidence (IDA) for COP1's nuclear localization, reinforcing the multiple lines of evidence showing COP1's primary localization in the nucleus where it executes its E3 ligase function. Reason: Strong experimental support for COP1's nuclear localization, which is essential for its function as a nuclear E3 ligase regulating photomorphogenic transcription factors. Multiple IDA annotations confirm this key cellular localization. Supporting Evidence: PMID:16829591 COP1 functions as an E3 ubiquitin ligase |
| GO:0009963 positive regulation of flavonoid biosynthetic process | IMP PMID:16829591 CONSTITUTIVELY PHOTOMORPHOGENIC1 is required for the UV-B re... | KEEP AS NON CORE | Summary: COP1 influences flavonoid biosynthesis through its regulation of light-responsive gene expression. This is related to its role in secondary metabolism regulation downstream of light signaling. Reason: Flavonoid regulation is a secondary consequence of COP1's primary function in light signaling. While experimentally supported, this represents a downstream metabolic effect rather than core function. Supporting Evidence: PMID:16829591 in the cop1-4 mutant, flavonoid accumulation and genome-wide expression changes in response to UV-B are blocked to a large extent |
| GO:0010224 response to UV-B | IMP PMID:16829591 CONSTITUTIVELY PHOTOMORPHOGENIC1 is required for the UV-B re... | ACCEPT | Summary: COP1 participates in UV-B light responses as part of its broader role in light quality perception and signaling. UV-B responses are an extension of COP1's light signaling functions. Reason: UV-B response is directly related to COP1's core function in light perception and signaling. This annotation captures an important aspect of COP1's role in responding to different light qualities. Supporting Evidence: PMID:16829591 COP1 is a critical positive regulator of responses to low levels of UV-B |
| GO:0000152 nuclear ubiquitin ligase complex | TAS PMID:10839542 Targeted destabilization of HY5 during light-regulated devel... | ACCEPT | Summary: COP1 functions as part of nuclear ubiquitin ligase complexes, often in association with SPA proteins, to target substrates for degradation in the nucleus. This accurately describes COP1's functional complex organization. Reason: This annotation correctly captures COP1's cellular organization as a nuclear ubiquitin ligase complex. COP1 functions with partner proteins like SPA1-4 to form active ubiquitin ligase complexes in the nucleus. Supporting Evidence: PMID:10839542 Targeted destabilization of HY5 during light-regulated development of Arabidopsis. |
| GO:0005634 nucleus | IDA PMID:11080276 Modular domain structure of Arabidopsis COP1. Reconstitution... | ACCEPT | Summary: COP1 is predominantly nuclear localized in darkness where it executes its function as a repressor of photomorphogenesis. This experimental evidence confirms COP1's nuclear localization. Reason: Strong experimental support for COP1's nuclear localization, which is essential for its function as a nuclear E3 ligase regulating photomorphogenic transcription factors. Supporting Evidence: PMID:11080276 The Arabidopsis COP1 protein functions as a developmental regulator, in part by repressing photomorphogenesis in darkness [...] site-directed mutations in the single nuclear localization signal of COP1 were partially compensated by high-level transgene expression |
| GO:0009647 skotomorphogenesis | TAS PMID:11080276 Modular domain structure of Arabidopsis COP1. Reconstitution... | ACCEPT | Summary: Skotomorphogenesis (etiolated growth in darkness) is the developmental program that COP1 actively promotes by repressing photomorphogenic factors. This is a core biological process that COP1 regulates. Reason: COP1 is a key positive regulator of skotomorphogenesis, maintaining the etiolated state in darkness by degrading photomorphogenic transcription factors. This annotation accurately captures COP1's role in dark-grown development. Supporting Evidence: PMID:11080276 Modular domain structure of Arabidopsis COP1. Reconstitution of activity by fragment complementation and mutational analysis of a nuclear localization signal in planta |
| GO:0010119 regulation of stomatal movement | IMP PMID:16093319 From The Cover: A role for Arabidopsis cryptochromes and COP... | KEEP AS NON CORE | Summary: COP1's role in stomatal movement regulation is likely indirect through its effects on light signaling pathways that influence stomatal responses. This represents a downstream consequence of COP1's primary light signaling function. Reason: While the IMP evidence supports some connection between COP1 and stomatal regulation, this is a peripheral function that likely results from COP1's broader role in light signaling rather than being a direct, core function. Supporting Evidence: PMID:16093319 COP1 is a repressor of stomatal opening and likely acts downstream of CRY and PHOT signaling pathways |
| GO:0005634 nucleus | IMP PMID:10480941 A novel motif mediates the targeting of the Arabidopsis COP1... | ACCEPT | Summary: COP1 is predominantly nuclear localized in darkness where it executes its function as a repressor of photomorphogenesis. This experimental evidence confirms COP1's nuclear localization. Reason: Strong experimental support for COP1's nuclear localization, which is essential for its function as a nuclear E3 ligase regulating photomorphogenic transcription factors. Supporting Evidence: PMID:10480941 A novel motif mediates the targeting of the Arabidopsis COP1 protein to subnuclear foci |
| GO:0009640 photomorphogenesis | TAS PMID:10201077 The role of COP1 in repression of Arabidopsis photomorphogen... | ACCEPT | Summary: Photomorphogenesis is COP1's central biological process - it acts as a negative regulator, repressing photomorphogenesis in darkness by targeting light-responsive transcription factors for degradation. This TAS evidence supports COP1's core regulatory role. Reason: This annotation captures COP1's most important biological function. COP1 is a key negative regulator of photomorphogenesis, ensuring proper light-regulated development by controlling the stability of photomorphogenic factors. Supporting Evidence: PMID:10201077 The role of COP1 in repression of Arabidopsis photomorphogenic development |
| GO:0009640 photomorphogenesis | TAS PMID:11080276 Modular domain structure of Arabidopsis COP1. Reconstitution... | ACCEPT | Summary: Photomorphogenesis is COP1's central biological process - it acts as a negative regulator, repressing photomorphogenesis in darkness by targeting light-responsive transcription factors for degradation. This TAS evidence supports COP1's core regulatory role. Reason: This annotation captures COP1's most important biological function. COP1 is a key negative regulator of photomorphogenesis, ensuring proper light-regulated development by controlling the stability of photomorphogenic factors. Supporting Evidence: PMID:11080276 COP1 consists of two modules, an amino terminal module conferring a basal function during development and a carboxyl terminal module conferring repression of photomorphogenesis |
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Download this section (compressed HTML)Q: What are the molecular mechanisms governing COP1's light-dependent nucleocytoplasmic shuttling and how do different light qualities affect this process?
Suggested experts: Plant photobiology researchers, Nuclear transport specialists
Q: How does the COP1-SPA complex achieve substrate specificity and what determines the kinetics of different substrate ubiquitination?
Suggested experts: Ubiquitin ligase specialists, Plant protein degradation researchers
Q: What are the structural determinants in the WD40 domain that enable recognition of diverse transcription factor substrates?
Suggested experts: Structural biologists working on WD40 domains, E3 ligase structure-function researchers
Q: How does COP1 coordinate with other regulatory pathways beyond light signaling to integrate multiple environmental and developmental cues?
Suggested experts: Plant systems biology researchers, Circadian clock specialists
Experiment: Generate COP1 mutants with altered nuclear localization signals and test their subcellular localization using live-cell imaging under different light conditions. Use mass spectrometry to identify light-dependent phosphorylation or other modifications that regulate nuclear transport. Test interaction with importins and exportins using co-immunoprecipitation.
Hypothesis: COP1 nucleocytoplasmic shuttling involves specific nuclear export and import signals that are regulated by light-induced post-translational modifications
Experiment: Generate COP1-SPA chimeric proteins and test their substrate specificity using in vitro ubiquitination assays with purified transcription factor substrates (HY5, LAF1, PCH1). Use hydrogen-deuterium exchange mass spectrometry to map conformational changes in COP1 upon SPA binding.
Hypothesis: Different SPA proteins confer distinct substrate specificities to COP1 complexes through allosteric regulation of the WD40 domain
Experiment: Use super-resolution microscopy to map COP1 subnuclear distribution in relation to transcriptionally active chromatin regions. Combine ChIP-seq for COP1 with ATAC-seq to correlate COP1 occupancy with chromatin accessibility changes upon light exposure. Test whether COP1 targets are preferentially degraded at specific chromatin sites.
Hypothesis: COP1 subnuclear localization and substrate accessibility are regulated by light-dependent chromatin organization changes
Experiment: Use single-molecule FRET to monitor conformational dynamics of full-length COP1 in the presence and absence of substrates and SPA proteins. Generate domain deletion and substitution mutants to test the importance of inter-domain communication for catalytic activity. Perform hydrogen-deuterium exchange to map allosteric networks.
Hypothesis: COP1 E3 ligase activity is regulated by a conformational switch mechanism involving the RING-coiled coil-WD40 domain architecture
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