Arabidopsis thaliana CRY1 encodes cryptochrome-1, a soluble blue/UV-A light photoreceptor in the cryptochrome/photolyase superfamily. CRY1 binds FAD in a photolyase-homology region and uses blue-light-driven flavin photoredox and conformational changes to form signaling-competent oligomers. Activated CRY1 acts in the nucleus and cytoplasm to regulate photomorphogenesis, hypocotyl and petiole growth, circadian outputs, stomatal behavior, stress responses, and gene expression, chiefly through partner interactions including COP1/SPA, PIF4/PIF5, HY5-linked pathways, and FIP37-mediated m6A regulation. Despite its photolyase-like fold, Arabidopsis CRY1 has no DNA photolyase activity.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0009414 response to water deprivation | IGI PMID:16093319 From The Cover: A role for Arabidopsis cryptochromes and COP... | MARK AS OVER ANNOTATED | Summary: Water-deprivation response reflects altered stomatal aperture and water loss rather than a primary CRY1 function. Reason: The direct evidence is that CRY1/CRY2 regulate blue-light stomatal opening and water loss. Calling CRY1 a water-deprivation response gene overstates an indirect physiological consequence. Supporting Evidence: PMID:16093319 The Drought Tolerance Observed for the cry1 cry2 Mutant Correlates with the Reduced Blue Light-Induced Stomatal Opening. |
| GO:0009416 response to light stimulus | IMP PMID:36508461 A role for brassinosteroid signalling in decision-making pro... | MODIFY | Summary: Response to light stimulus is too broad for CRY1, whose direct evidence is blue/UV-A photoreception. Reason: The original cached abstract does not verify a CRY1-specific light-response claim, and the term is too broad in any case. The supported CRY1 biology should be represented by blue-light response/signaling terms. Proposed replacements: response to blue light blue light signaling pathway Supporting Evidence: PMID:36508461 The accessible abstract describes a BIN2 light/water screen, but does not mention CRY1. |
| GO:0009583 detection of light stimulus | IMP PMID:20668058 Cryptochrome as a sensor of the blue/green ratio of natural ... | ACCEPT | Summary: detection of light stimulus matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:20668058 Cryptochrome as a sensor of the blue/green ratio of natural radiation in Arabidopsis. |
| GO:0009637 response to blue light | IMP PMID:12324610 Arabidopsis Mutants Lacking Blue Light-Dependent Inhibition ... | ACCEPT | Summary: response to blue light matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:12324610 Hypocotyl elongation is not inhibited in the mutant seedlings by continuous blue light. |
| GO:0009638 phototropism | IMP PMID:32554507 Low Blue Light Enhances Phototropism by Releasing Cryptochro... | KEEP AS NON CORE | Summary: phototropism is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:32554507 Low Blue Light Enhances Phototropism by Releasing Cryptochrome1-Mediated Inhibition of PIF4 Expression. |
| GO:0009640 photomorphogenesis | IMP PMID:12324610 Arabidopsis Mutants Lacking Blue Light-Dependent Inhibition ... | ACCEPT | Summary: photomorphogenesis matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:12324610 Hypocotyl elongation is not inhibited in the mutant seedlings by continuous blue light. |
| GO:0009785 blue light signaling pathway | TAS PMID:10364413 Arabidopsis contains at least four independent blue-light-ac... | ACCEPT | Summary: blue light signaling pathway matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:10364413 In summary, our results support the conclusion that the blue-light photoreceptors cry1, cry2, nph1, and zeaxanthin (the likely photoreceptor chromophore for blue-light-induced stomatal opening) all activate genetically separable pathways and that Arabidopsis must contain at least four different photoreceptors and signal transduction pathways. |
| GO:0010075 regulation of meristem growth | IGI PMID:18424613 Distinct light-initiated gene expression and cell cycle prog... | KEEP AS NON CORE | Summary: regulation of meristem growth is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:18424613 phytochromes and cryptochromes play largely redundant roles |
| GO:0010118 stomatal movement | IGI PMID:16093319 From The Cover: A role for Arabidopsis cryptochromes and COP... | KEEP AS NON CORE | Summary: Stomatal movement is a supported non-core output of CRY1 blue-light signaling. Reason: CRY1/CRY2 influence blue-light stomatal opening, but this physiological output is downstream of the core photoreceptor/signaling role. Supporting Evidence: PMID:16093319 These results indicate that CRY functions additively with PHOT in mediating blue light-induced stomatal opening and that COP1 is a repressor of stomatal opening and likely acts downstream of CRY and PHOT signaling pathways. |
| GO:0010343 singlet oxygen-mediated programmed cell death | IMP PMID:17075038 Cryptochrome-1-dependent execution of programmed cell death ... | KEEP AS NON CORE | Summary: singlet oxygen-mediated programmed cell death is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:17075038 Cryptochrome-1-dependent execution of programmed cell death induced by singlet oxygen. |
| GO:0010468 regulation of gene expression | IMP PMID:32554507 Low Blue Light Enhances Phototropism by Releasing Cryptochro... | MODIFY | Summary: Regulation of gene expression is too broad for the CRY1/PIF4 phototropism evidence. Reason: The cited work supports CRY1 control of PIF4 expression in low-blue-light phototropism, so response to blue light and phototropism capture the evidence more specifically than general gene-expression regulation. Proposed replacements: response to blue light phototropism Supporting Evidence: PMID:32554507 Low Blue Light Enhances Phototropism by Releasing Cryptochrome1-Mediated Inhibition of PIF4 Expression. |
| GO:0010617 circadian regulation of calcium ion oscillation | IMP PMID:17982000 Distinct light and clock modulation of cytosolic free Ca2+ o... | KEEP AS NON CORE | Summary: circadian regulation of calcium ion oscillation is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:17982000 Our data demonstrate that in Arabidopsis seedlings, the circadian oscillation of [Ca 2+ ] cyt is regulated by red and blue light through CRY1, CRY2, PHYB, and, possibly, PHYA. |
| 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: anthocyanin-containing compound metabolic process is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:17217468 downstream of cryptochrome 1 (CRY1) at the level of transcript accumulation |
| GO:0046777 protein autophosphorylation | IDA PMID:12846824 Novel ATP-binding and autophosphorylation activity associate... | KEEP AS NON CORE | Summary: protein autophosphorylation is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: CRY1 autophosphorylation is experimentally supported, but its in vivo regulatory significance and light dependence are less central than CRY1 photoreceptor activity. Supporting Evidence: PMID:12846824 autophosphorylation activity associated with Arabidopsis cry1 protein |
| GO:0051510 regulation of unidimensional cell growth | IMP PMID:12324610 Arabidopsis Mutants Lacking Blue Light-Dependent Inhibition ... | ACCEPT | Summary: regulation of unidimensional cell growth matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:12324610 Hypocotyl elongation is not inhibited in the mutant seedlings by continuous blue light. |
| GO:2000652 regulation of secondary cell wall biogenesis | IDA PMID:30242037 Blue Light Regulates Secondary Cell Wall Thickening via MYC2... | KEEP AS NON CORE | Summary: regulation of secondary cell wall biogenesis is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:30242037 CRY1 overexpression led to enhanced SCW formation. |
| GO:0003904 deoxyribodipyrimidine photo-lyase activity | IBA GO_REF:0000033 | REMOVE | Summary: Photolyase activity is not supported for Arabidopsis CRY1. Reason: CRY1 is in the cryptochrome/photolyase superfamily, but Arabidopsis CRY1 is a cryptochrome photoreceptor and published summaries state that cryptochromes lack photolyase DNA repair activity. The PANTHER family includes true photolyases, making this IBA transfer over-propagated. OpenScientist independently classified the assignment as refuted family over-annotation: CRY1 retains the photolyase fold and cofactors but lacks the DNA repair catalytic activity that defines this term. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE PSEUDO OR SUBACTIVITY LOSS WRONG ORTHOLOG OR PARALOG Sources checked: PANTHER:PTN000155848 · PANTHER photolyase/cryptochrome source node SUPPORTS SOURCE BUT NOT TARGET The source node includes true photolyases that support GO:0003904, but CRY1 is in the cryptochrome branch and lacks detectable DNA photolyase repair activity. UniProtKB:P00914 · E. coli DNA photolyase SUPPORTS SOURCE BUT NOT TARGET P00914 is a bona fide deoxyribodipyrimidine photolyase source, but CRY1 has diverged into a blue-light photoreceptor. SGD:S000005913 · yeast PHR1 photolyase SUPPORTS SOURCE BUT NOT TARGET Yeast PHR1 supports the photolyase activity in the mixed family, whereas Arabidopsis CRY1 is a cryptochrome photoreceptor. Supporting Evidence: PMID:11752373 lack photolyase activity file:interpro/panther/PTHR11455/PTHR11455-notes.md The family contains both cryptochromes and photolyases; subfamilies separate circadian cryptochromes from repair enzymes. file:interpro/panther/PTHR11455/PTHR11455-entries.csv Q43125,Cryptochrome-1,protein,3702,Arabidopsis thaliana,...,PTHR11455:SF50,CRYPTOCHROME-1 file:ARATH/CRY1/CRY1-hypotheses/function-hypothesis-go-0003904/openscientist.md The seed hypothesis is **refuted as a family over-annotation.** Arabidopsis CRY1 does not have deoxyribodipyrimidine photo-lyase activity. |
| GO:0004672 protein kinase activity | IDA PMID:12846824 Novel ATP-binding and autophosphorylation activity associate... | KEEP AS NON CORE | Summary: protein kinase activity is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: AtCRY1 autokinase activity is experimentally supported in vitro, but the primary evolved molecular function is blue-light photoreceptor signaling. Supporting Evidence: PMID:12846824 autophosphorylation activity associated with Arabidopsis cry1 protein |
| GO:0005515 protein binding | IPI PMID:11509693 Direct interaction of Arabidopsis cryptochromes with COP1 in... | REMOVE | Summary: Generic protein binding from PMID:11509693 records a real CRY1 interaction but is not informative as a GO molecular function. Reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition, PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein binding. Supporting Evidence: PMID:11509693 photoactivated cryptochromes repress COP1 activity through a direct |
| GO:0005515 protein binding | IPI PMID:11752373 The signaling mechanism of Arabidopsis CRY1 involves direct ... | REMOVE | Summary: Generic protein binding from PMID:11752373 records a real CRY1 interaction but is not informative as a GO molecular function. Reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition, PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein binding. Supporting Evidence: PMID:11752373 Here we show that Arabidopsis cryptochrome 1 (CRY1) and its C-terminal domain (CCT1) interacted strongly with the COP1 protein. |
| GO:0005515 protein binding | IPI PMID:21511871 Arabidopsis cryptochrome 1 interacts with SPA1 to suppress C... | REMOVE | Summary: Generic protein binding from PMID:21511871 records a real CRY1 interaction but is not informative as a GO molecular function. Reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition, PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein binding. Supporting Evidence: PMID:21511871 CRY1-SPA1 interaction suppresses the SPA1-COP1 interaction |
| GO:0005515 protein binding | IPI PMID:21511872 Blue-light-dependent interaction of cryptochrome 1 with SPA1... | REMOVE | Summary: Generic protein binding from PMID:21511872 records a real CRY1 interaction but is not informative as a GO molecular function. Reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition, PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein binding. Supporting Evidence: PMID:21511872 CRY1 interacts physically with SPA1 in a blue-light-dependent manner. |
| GO:0005515 protein binding | IPI PMID:22577138 Light-dependent, dark-promoted interaction between Arabidops... | REMOVE | Summary: Generic protein binding from PMID:22577138 records a real CRY1 interaction but is not informative as a GO molecular function. Reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition, PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein binding. Supporting Evidence: PMID:22577138 CRY1), a UV-A/blue photoreceptor. |
| GO:0005515 protein binding | IPI PMID:26596765 TCP2 positively regulates HY5/HYH and photomorphogenesis in ... | REMOVE | Summary: Generic protein binding from PMID:26596765 records a real CRY1 interaction but is not informative as a GO molecular function. Reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition, PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein binding. Supporting Evidence: PMID:26596765 TCP2 physically interacts with CRY1 |
| GO:0005515 protein binding | IPI PMID:26724867 Cryptochromes Interact Directly with PIFs to Control Plant G... | REMOVE | Summary: Generic protein binding from PMID:26724867 records a real CRY1 interaction but is not informative as a GO molecular function. Reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition, PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein binding. Supporting Evidence: PMID:26724867 CRY1 and CRY2 perceive |
| GO:0005515 protein binding | IPI PMID:32661061 Photoexcited Cryptochrome2 Interacts Directly with TOE1 and ... | REMOVE | Summary: Generic protein binding from PMID:32661061 records a real CRY1 interaction but is not informative as a GO molecular function. Reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition, PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein binding. Supporting Evidence: PMID:32661061 CRY1 and CRY2 physically interact with TOE1 and TOE2 in a BL-dependent manner. |
| GO:0005515 protein binding | IPI PMID:9651577 The CRY1 blue light photoreceptor of Arabidopsis interacts w... | REMOVE | Summary: Generic protein binding from PMID:9651577 records a real CRY1 interaction but is not informative as a GO molecular function. Reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition, PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein binding. Supporting Evidence: PMID:9651577 The CRY1 blue light photoreceptor of Arabidopsis interacts with phytochrome A in vitro. |
| GO:0005524 ATP binding | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: ATP binding is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: ATP binding is a supported biochemical property that affects CRY1 conformation and flavin photochemistry, but it is accessory to photoreceptor signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Binding to ATP mediates conformational changes which facilitate flavin binding. |
| GO:0005524 ATP binding | IDA PMID:12846824 Novel ATP-binding and autophosphorylation activity associate... | KEEP AS NON CORE | Summary: ATP binding is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: ATP binding is a supported biochemical property that affects CRY1 conformation and flavin photochemistry, but it is accessory to photoreceptor signaling. Supporting Evidence: PMID:12846824 autophosphorylation activity associated with Arabidopsis cry1 protein |
| GO:0005524 ATP binding | IDA PMID:17073458 Analysis of autophosphorylating kinase activities of Arabido... | KEEP AS NON CORE | Summary: ATP binding is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: ATP binding is a supported biochemical property that affects CRY1 conformation and flavin photochemistry, but it is accessory to photoreceptor signaling. Supporting Evidence: PMID:17073458 AtCry1, which contains near stoichiometric |
| GO:0005524 ATP binding | IDA PMID:19327354 Conformational change induced by ATP binding correlates with... | KEEP AS NON CORE | Summary: ATP binding is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: ATP binding is a supported biochemical property that affects CRY1 conformation and flavin photochemistry, but it is accessory to photoreceptor signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Binding to ATP mediates conformational changes which facilitate flavin binding. |
| GO:0009882 blue light photoreceptor activity | IEA GO_REF:0000002 | ACCEPT | Summary: blue light photoreceptor activity matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Photoreceptor that mediates primarily blue light inhibition of hypocotyl elongation. file:ARATH/CRY1/CRY1-deep-research-falcon.md nucleo-cytoplasmic blue/UV-A photoreceptor |
| GO:0009882 blue light photoreceptor activity | IDA PMID:30242037 Blue Light Regulates Secondary Cell Wall Thickening via MYC2... | ACCEPT | Summary: blue light photoreceptor activity matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:8953250 CRY1 is a flavin-type blue type receptor of Arabidopsis PMID:30242037 CRY1 overexpression led to enhanced SCW formation. |
| GO:0009882 blue light photoreceptor activity | IMP PMID:8953250 Arabidopsis cryptochrome 1 is a soluble protein mediating bl... | ACCEPT | Summary: blue light photoreceptor activity matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:8953250 CRY1 is a flavin-type blue type receptor of Arabidopsis |
| GO:0016301 kinase activity | IDA PMID:17073458 Analysis of autophosphorylating kinase activities of Arabido... | MODIFY | Summary: Kinase activity is supported only as CRY1 autokinase activity and should be stated more specifically. Reason: The biochemical evidence is for protein autophosphorylation/autokinase activity of AtCRY1. Protein kinase activity is the more specific molecular-function term than generic kinase activity. Proposed replacements: protein kinase activity Supporting Evidence: PMID:17073458 AtCry1, which contains near stoichiometric |
| GO:0042802 identical protein binding | IPI PMID:15805487 N-terminal domain-mediated homodimerization is required for ... | MODIFY | Summary: Identical protein binding captures CRY1 self-association but the specific homodimerization term is better. Reason: The evidence concerns CRY1 homodimerization, and GO:0042803 directly states this activity whereas identical protein binding is less precise. Proposed replacements: protein homodimerization activity Supporting Evidence: PMID:15805487 N-terminal domain-mediated homodimerization is required for photoreceptor activity of Arabidopsis CRYPTOCHROME 1. |
| GO:0042803 protein homodimerization activity | IEA GO_REF:0000117 | ACCEPT | Summary: protein homodimerization activity matches the core CRY1 photoreceptor/signaling role. Reason: CRY1 homodimerization/oligomerization is an activation mechanism required for photoreceptor signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subunit: Homodimer. |
| GO:0042803 protein homodimerization activity | IPI PMID:15805487 N-terminal domain-mediated homodimerization is required for ... | ACCEPT | Summary: protein homodimerization activity matches the core CRY1 photoreceptor/signaling role. Reason: CRY1 homodimerization/oligomerization is an activation mechanism required for photoreceptor signaling. Supporting Evidence: PMID:15805487 N-terminal domain-mediated homodimerization is required for photoreceptor activity of Arabidopsis CRYPTOCHROME 1. |
| GO:0071949 FAD binding | IEA GO_REF:0000117 | ACCEPT | Summary: FAD binding matches the core CRY1 photoreceptor/signaling role. Reason: FAD binding is central to CRY1 blue-light absorption and flavin photoredox signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Name=FAD; Binds 1 FAD per subunit. |
| GO:0071949 FAD binding | IDA PMID:17073458 Analysis of autophosphorylating kinase activities of Arabido... | ACCEPT | Summary: FAD binding matches the core CRY1 photoreceptor/signaling role. Reason: FAD binding is central to CRY1 blue-light absorption and flavin photoredox signaling. Supporting Evidence: PMID:17073458 AtCry1, which contains near stoichiometric |
| GO:0140517 protein-RNA adaptor activity | IPI PMID:36305219 The blue light receptor CRY1 interacts with FIP37 to promote... | KEEP AS NON CORE | Summary: protein-RNA adaptor activity is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The CRY1-FIP37 interaction supports a specific adaptor role in blue-light m6A regulation, but this appears to be a specialized signaling branch rather than the primary CRY1 molecular function. Supporting Evidence: PMID:36305219 CRY1 physically interacted with FIP37 |
| GO:0007623 circadian rhythm | IEP PMID:11743105 Circadian clock-regulated expression of phytochrome and cryp... | KEEP AS NON CORE | Summary: circadian rhythm is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:11743105 display circadian oscillations under constant conditions |
| GO:0009266 response to temperature stimulus | IMP PMID:30635559 Daytime temperature is sensed by phytochrome B in Arabidopsi... | KEEP AS NON CORE | Summary: response to temperature stimulus is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:30635559 the PHYB-dependent hypocotyl thermoresponse is masked by CRY1 |
| GO:0009414 response to water deprivation | IEA GO_REF:0000117 | MARK AS OVER ANNOTATED | Summary: Water-deprivation response reflects altered stomatal aperture and water loss rather than a primary CRY1 function. Reason: The direct evidence is that CRY1/CRY2 regulate blue-light stomatal opening and water loss. Calling CRY1 a water-deprivation response gene overstates an indirect physiological consequence. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses. |
| GO:0009416 response to light stimulus | IEP PMID:11743105 Circadian clock-regulated expression of phytochrome and cryp... | MODIFY | Summary: Response to light stimulus is too broad for CRY1, whose direct evidence is blue/UV-A photoreception. Reason: This IEP row reflects light/circadian regulation of CRY1 expression, while the gene-product function is better captured by direct blue-light response and blue-light signaling terms. Proposed replacements: response to blue light blue light signaling pathway Supporting Evidence: PMID:11743105 display circadian oscillations under constant conditions |
| GO:0009416 response to light stimulus | IMP PMID:15751956 Role of structural plasticity in signal transduction by the ... | MODIFY | Summary: Response to light stimulus is too broad for CRY1, whose direct evidence is blue/UV-A photoreception. Reason: CRY1 is a blue/UV-A photoreceptor. The broad parent term loses the relevant spectral and signaling specificity. Proposed replacements: response to blue light blue light signaling pathway Supporting Evidence: PMID:15751956 light-dependent conformational change in the C-terminal domain of Arabidopsis |
| GO:0009416 response to light stimulus | IDA PMID:21467031 Light-activated cryptochrome reacts with molecular oxygen to... | MODIFY | Summary: Response to light stimulus is too broad for CRY1, whose direct evidence is blue/UV-A photoreception. Reason: CRY1 is a blue/UV-A photoreceptor. The broad parent term loses the relevant spectral and signaling specificity. Proposed replacements: response to blue light blue light signaling pathway Supporting Evidence: PMID:21467031 Light-activated cryptochrome reacts with molecular oxygen to form a flavin-superoxide radical pair. |
| GO:0009637 response to blue light | IMP PMID:12857830 Second positive phototropism results from coordinated co-act... | ACCEPT | Summary: response to blue light matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:12857830 phototropins and cryptochromes function |
| GO:0009637 response to blue light | IMP PMID:21511871 Arabidopsis cryptochrome 1 interacts with SPA1 to suppress C... | ACCEPT | Summary: response to blue light matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:21511871 CRY1-SPA1 interaction suppresses the SPA1-COP1 interaction |
| GO:0009637 response to blue light | IDA PMID:21511872 Blue-light-dependent interaction of cryptochrome 1 with SPA1... | ACCEPT | Summary: response to blue light matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:21511872 CRY1 interacts physically with SPA1 in a blue-light-dependent manner. |
| GO:0009637 response to blue light | IMP PMID:22147516 Phototropins but not cryptochromes mediate the blue light-sp... | ACCEPT | Summary: response to blue light matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:22147516 effects of cry on stomatal conductance are largely indirect |
| GO:0009637 response to blue light | IMP PMID:23511208 Network balance via CRY signalling controls the Arabidopsis ... | ACCEPT | Summary: response to blue light matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:23511208 Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures. |
| GO:0009637 response to blue light | IMP PMID:25721730 The CNT1 Domain of Arabidopsis CRY1 Alone Is Sufficient to M... | ACCEPT | Summary: response to blue light matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:25721730 The CNT1 Domain of Arabidopsis CRY1 Alone Is Sufficient to Mediate Blue Light Inhibition of Hypocotyl Elongation. |
| GO:0009637 response to blue light | IDA PMID:25728686 Blue-light dependent reactive oxygen species formation by Ar... | ACCEPT | Summary: response to blue light matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:25728686 Blue-light dependent reactive oxygen species formation by Arabidopsis cryptochrome. |
| GO:0009637 response to blue light | IMP PMID:26313597 Cellular metabolites modulate in vivo signaling of Arabidops... | ACCEPT | Summary: response to blue light matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:26313597 These pathways are potentiated by metabolites in the intracellular |
| GO:0009637 response to blue light | IMP PMID:8528277 Mutations throughout an Arabidopsis blue-light photoreceptor... | ACCEPT | Summary: response to blue light matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:8528277 CRY1 was originally defined as the photoreceptor responsible for blue-light-mediated inhibition |
| GO:0009637 response to blue light | IMP PMID:9733523 Genetic interactions between phytochrome A, phytochrome B, a... | ACCEPT | Summary: response to blue light matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:9733523 cry1 activity in a phyAphyB mutant |
| GO:0009637 response to blue light | IMP PMID:9765547 Two genetically separable phases of growth inhibition induce... | ACCEPT | Summary: response to blue light matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:9765547 High fluence-rate blue light (BL) rapidly inhibits hypocotyl growth |
| GO:0009638 phototropism | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: phototropism is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses. |
| GO:0009638 phototropism | IMP PMID:12857830 Second positive phototropism results from coordinated co-act... | KEEP AS NON CORE | Summary: phototropism is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:12857830 phototropins and cryptochromes function |
| GO:0009638 phototropism | IMP PMID:8528277 Mutations throughout an Arabidopsis blue-light photoreceptor... | KEEP AS NON CORE | Summary: phototropism is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:8528277 CRY1 was originally defined as the photoreceptor responsible for blue-light-mediated inhibition |
| GO:0009644 response to high light intensity | IMP PMID:22786870 The CRYPTOCHROME1-dependent response to excess light is medi... | KEEP AS NON CORE | Summary: response to high light intensity is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:22786870 components of the cry1-mediated photoprotective response |
| GO:0009646 response to absence of light | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: response to absence of light is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses. |
| GO:0009646 response to absence of light | IMP PMID:22855128 cry1 and GPA1 signaling genetically interact in hook opening... | KEEP AS NON CORE | Summary: response to absence of light is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:22855128 While studying blue light-independent effects of cryptochrome 1 (cry1) photoreceptor, we observed premature opening of the hook in cry1 mutants grown in complete darkness |
| GO:0009785 blue light signaling pathway | IEA GO_REF:0000002 | ACCEPT | Summary: blue light signaling pathway matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses. |
| GO:0009785 blue light signaling pathway | IEA GO_REF:0000117 | ACCEPT | Summary: blue light signaling pathway matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses. |
| GO:0009791 post-embryonic development | IEA GO_REF:0000117 | MODIFY | Summary: post-embryonic development is a broad developmental consequence of CRY1 light signaling. Reason: The evidence supports CRY1 regulation of photomorphogenesis and light-dependent growth, not a generic role in overall development. Proposed replacements: photomorphogenesis response to blue light Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses. |
| GO:0010075 regulation of meristem growth | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: regulation of meristem growth is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses. |
| GO:0010114 response to red light | IMP PMID:9733523 Genetic interactions between phytochrome A, phytochrome B, a... | KEEP AS NON CORE | Summary: response to red light is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:9733523 cry1 activity in a phyAphyB mutant |
| GO:0010117 photoprotection | IMP PMID:22786870 The CRYPTOCHROME1-dependent response to excess light is medi... | KEEP AS NON CORE | Summary: photoprotection is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:22786870 components of the cry1-mediated photoprotective response |
| GO:0010118 stomatal movement | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: Stomatal movement is a supported non-core output of CRY1 blue-light signaling. Reason: CRY1/CRY2 influence blue-light stomatal opening, but this physiological output is downstream of the core photoreceptor/signaling role. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses. |
| GO:0010118 stomatal movement | IMP PMID:22147516 Phototropins but not cryptochromes mediate the blue light-sp... | KEEP AS NON CORE | Summary: Stomatal movement is retained as a non-core CRY1 output, with this study supporting an indirect ABA-linked effect on conductance. Reason: The paper argues cry effects on stomatal conductance are largely indirect rather than direct blue-light stomatal photoreception, so the term should not be treated as core CRY1 function. Supporting Evidence: PMID:22147516 effects of cry on stomatal conductance are largely indirect |
| GO:0010218 response to far red light | IMP PMID:9733523 Genetic interactions between phytochrome A, phytochrome B, a... | KEEP AS NON CORE | Summary: response to far red light is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:9733523 cry1 activity in a phyAphyB mutant |
| GO:0010244 response to low fluence blue light stimulus by blue low-fluence system | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: response to low fluence blue light stimulus by blue low-fluence system is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses. |
| GO:0010244 response to low fluence blue light stimulus by blue low-fluence system | IMP PMID:19558423 Differential petiole growth in Arabidopsis thaliana: photoco... | KEEP AS NON CORE | Summary: response to low fluence blue light stimulus by blue low-fluence system is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Reduced hyponastic growth (differential growth-driven upward leaf movement) in low blue light fluence. |
| GO:0010244 response to low fluence blue light stimulus by blue low-fluence system | IEP PMID:26724867 Cryptochromes Interact Directly with PIFs to Control Plant G... | KEEP AS NON CORE | Summary: response to low fluence blue light stimulus by blue low-fluence system is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:26724867 CRY1 and CRY2 perceive |
| GO:0010310 regulation of hydrogen peroxide metabolic process | IDA PMID:25728686 Blue-light dependent reactive oxygen species formation by Ar... | KEEP AS NON CORE | Summary: regulation of hydrogen peroxide metabolic process is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:25728686 Blue-light dependent reactive oxygen species formation by Arabidopsis cryptochrome. |
| GO:0010617 circadian regulation of calcium ion oscillation | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: circadian regulation of calcium ion oscillation is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses. |
| GO:0032922 circadian regulation of gene expression | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: circadian regulation of gene expression is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses. |
| GO:0042752 regulation of circadian rhythm | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: regulation of circadian rhythm is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses. |
| GO:0042752 regulation of circadian rhythm | IMP PMID:23511208 Network balance via CRY signalling controls the Arabidopsis ... | KEEP AS NON CORE | Summary: regulation of circadian rhythm is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:23511208 Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures. |
| GO:0043153 entrainment of circadian clock by photoperiod | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: entrainment of circadian clock by photoperiod is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses. |
| GO:0046283 anthocyanin-containing compound metabolic process | IMP PMID:8528277 Mutations throughout an Arabidopsis blue-light photoreceptor... | KEEP AS NON CORE | Summary: anthocyanin-containing compound metabolic process is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:8528277 CRY1 was originally defined as the photoreceptor responsible for blue-light-mediated inhibition |
| GO:0046777 protein autophosphorylation | IDA PMID:17073458 Analysis of autophosphorylating kinase activities of Arabido... | KEEP AS NON CORE | Summary: protein autophosphorylation is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: CRY1 autophosphorylation is experimentally supported, but its in vivo regulatory significance and light dependence are less central than CRY1 photoreceptor activity. Supporting Evidence: PMID:17073458 AtCry1, which contains near stoichiometric |
| GO:0048580 regulation of post-embryonic development | IEA GO_REF:0000117 | MODIFY | Summary: regulation of post-embryonic development is a broad developmental consequence of CRY1 light signaling. Reason: The evidence supports CRY1 regulation of photomorphogenesis and light-dependent growth, not a generic role in overall development. Proposed replacements: photomorphogenesis response to blue light Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses. |
| GO:0048731 system development | IEA GO_REF:0000117 | MODIFY | Summary: system development is a broad developmental consequence of CRY1 light signaling. Reason: The evidence supports CRY1 regulation of photomorphogenesis and light-dependent growth, not a generic role in overall development. Proposed replacements: photomorphogenesis response to blue light Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses. |
| GO:0060918 auxin transport | IMP PMID:20133010 Arabidopsis cryptochrome-1 restrains lateral roots growth by... | KEEP AS NON CORE | Summary: auxin transport is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:20133010 Arabidopsis CRY1 restrains lateral roots growth by inhibiting auxin transport. |
| GO:0071000 response to magnetism | IDA PMID:22421133 Magnetically sensitive light-induced reactions in cryptochro... | KEEP AS NON CORE | Summary: response to magnetism is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:22421133 Magnetically sensitive light-induced reactions in cryptochrome are consistent with its proposed role as a magnetoreceptor. |
| GO:0071000 response to magnetism | IMP PMID:26095447 Suppression of Arabidopsis flowering by near-null magnetic f... | KEEP AS NON CORE | Summary: response to magnetism is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:26095447 The effect of near-null magnetic field on Arabidopsis flowering is associated with CRY. |
| GO:0072387 flavin adenine dinucleotide metabolic process | ISS GO_REF:0000024 | MODIFY | Summary: FAD photochemistry in CRY1 supports cofactor binding and photoreceptor function, not FAD metabolic process. Reason: CRY1 binds FAD and undergoes flavin photoreduction during blue-light signaling, but there is no evidence that CRY1 is part of FAD biosynthesis, degradation, or cofactor metabolism as a biological process. Proposed replacements: FAD binding blue light photoreceptor activity Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Blue-light absorbing flavoprotein that activates reversible flavin photoreduction. |
| GO:0072387 flavin adenine dinucleotide metabolic process | IEA GO_REF:0000117 | MODIFY | Summary: FAD photochemistry in CRY1 supports cofactor binding and photoreceptor function, not FAD metabolic process. Reason: CRY1 binds FAD and undergoes flavin photoreduction during blue-light signaling, but there is no evidence that CRY1 is part of FAD biosynthesis, degradation, or cofactor metabolism as a biological process. Proposed replacements: FAD binding blue light photoreceptor activity Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Blue-light absorbing flavoprotein that activates reversible flavin photoreduction. |
| GO:0072387 flavin adenine dinucleotide metabolic process | IDA PMID:21467031 Light-activated cryptochrome reacts with molecular oxygen to... | MODIFY | Summary: FAD photochemistry in CRY1 supports cofactor binding and photoreceptor function, not FAD metabolic process. Reason: CRY1 binds FAD and undergoes flavin photoreduction during blue-light signaling, but there is no evidence that CRY1 is part of FAD biosynthesis, degradation, or cofactor metabolism as a biological process. Proposed replacements: FAD binding blue light photoreceptor activity Supporting Evidence: PMID:21467031 Light-activated cryptochrome reacts with molecular oxygen to form a flavin-superoxide radical pair. |
| GO:0072387 flavin adenine dinucleotide metabolic process | IDA PMID:25157750 ATP binding and aspartate protonation enhance photoinduced e... | MODIFY | Summary: FAD photochemistry in CRY1 supports cofactor binding and photoreceptor function, not FAD metabolic process. Reason: CRY1 binds FAD and undergoes flavin photoreduction during blue-light signaling, but there is no evidence that CRY1 is part of FAD biosynthesis, degradation, or cofactor metabolism as a biological process. Proposed replacements: FAD binding blue light photoreceptor activity Supporting Evidence: PMID:25157750 ATP binding and aspartate protonation enhance photoinduced electron transfer in plant cryptochrome. |
| GO:0072387 flavin adenine dinucleotide metabolic process | IMP PMID:26313597 Cellular metabolites modulate in vivo signaling of Arabidops... | MODIFY | Summary: FAD photochemistry in CRY1 supports cofactor binding and photoreceptor function, not FAD metabolic process. Reason: CRY1 binds FAD and undergoes flavin photoreduction during blue-light signaling, but there is no evidence that CRY1 is part of FAD biosynthesis, degradation, or cofactor metabolism as a biological process. Proposed replacements: FAD binding blue light photoreceptor activity Supporting Evidence: PMID:26313597 These pathways are potentiated by metabolites in the intracellular |
| GO:0099402 plant organ development | IMP PMID:25721730 The CNT1 Domain of Arabidopsis CRY1 Alone Is Sufficient to M... | MODIFY | Summary: plant organ development is a broad developmental consequence of CRY1 light signaling. Reason: The evidence supports CRY1 regulation of photomorphogenesis and light-dependent growth, not a generic role in overall development. Proposed replacements: photomorphogenesis response to blue light Supporting Evidence: PMID:25721730 The CNT1 Domain of Arabidopsis CRY1 Alone Is Sufficient to Mediate Blue Light Inhibition of Hypocotyl Elongation. |
| GO:1900426 positive regulation of defense response to bacterium | IMP PMID:20053798 CRYPTOCHROME 1 is implicated in promoting R protein-mediated... | KEEP AS NON CORE | Summary: positive regulation of defense response to bacterium is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Promotes systemic acquired resistance (SAR) and PR gene expression triggered by P.syringae. |
| GO:1901332 negative regulation of lateral root development | IMP PMID:20133010 Arabidopsis cryptochrome-1 restrains lateral roots growth by... | KEEP AS NON CORE | Summary: negative regulation of lateral root development is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:20133010 Arabidopsis CRY1 restrains lateral roots growth by inhibiting auxin transport. |
| GO:1901371 regulation of leaf morphogenesis | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: regulation of leaf morphogenesis is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses. |
| GO:1901371 regulation of leaf morphogenesis | IMP PMID:19558423 Differential petiole growth in Arabidopsis thaliana: photoco... | KEEP AS NON CORE | Summary: regulation of leaf morphogenesis is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Reduced hyponastic growth (differential growth-driven upward leaf movement) in low blue light fluence. |
| GO:1901529 positive regulation of anion channel activity | IMP PMID:9765547 Two genetically separable phases of growth inhibition induce... | KEEP AS NON CORE | Summary: positive regulation of anion channel activity is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:9765547 High fluence-rate blue light (BL) rapidly inhibits hypocotyl growth |
| GO:1901672 positive regulation of systemic acquired resistance | IMP PMID:20053798 CRYPTOCHROME 1 is implicated in promoting R protein-mediated... | KEEP AS NON CORE | Summary: positive regulation of systemic acquired resistance is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Promotes systemic acquired resistance (SAR) and PR gene expression triggered by P.syringae. |
| GO:1902347 response to strigolactone | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: response to strigolactone is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses. |
| GO:1902347 response to strigolactone | IMP PMID:24126495 Strigolactone-regulated hypocotyl elongation is dependent on... | KEEP AS NON CORE | Summary: response to strigolactone is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:24126495 Strigolactone-regulated hypocotyl elongation is dependent on cryptochrome and phytochrome signaling pathways. |
| GO:1902448 positive regulation of shade avoidance | IMP PMID:21457375 Cryptochrome 1 and phytochrome B control shade-avoidance res... | KEEP AS NON CORE | Summary: positive regulation of shade avoidance is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:21457375 These responses to blue light attenuation required the UV-A/blue light photoreceptor cry1. |
| GO:2000377 regulation of reactive oxygen species metabolic process | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: regulation of reactive oxygen species metabolic process is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses. |
| GO:2000377 regulation of reactive oxygen species metabolic process | IDA PMID:25728686 Blue-light dependent reactive oxygen species formation by Ar... | KEEP AS NON CORE | Summary: regulation of reactive oxygen species metabolic process is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:25728686 Blue-light dependent reactive oxygen species formation by Arabidopsis cryptochrome. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: nucleus matches the core CRY1 photoreceptor/signaling role. Reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body accumulation during photomorphogenic signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present in nuclear bodies. |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: nucleus matches the core CRY1 photoreceptor/signaling role. Reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body accumulation during photomorphogenic signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present in nuclear bodies. |
| GO:0005634 nucleus | IDA PMID:10221900 Cryptochromes: blue light receptors for plants and animals. | ACCEPT | Summary: nucleus matches the core CRY1 photoreceptor/signaling role. Reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body accumulation during photomorphogenic signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present in nuclear bodies. |
| GO:0005634 nucleus | HDA PMID:15610358 High-throughput protein localization in Arabidopsis using Ag... | ACCEPT | Summary: nucleus matches the core CRY1 photoreceptor/signaling role. Reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body accumulation during photomorphogenic signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present in nuclear bodies. |
| GO:0005634 nucleus | EXP PMID:18003924 Separate functions for nuclear and cytoplasmic cryptochrome ... | ACCEPT | Summary: nucleus matches the core CRY1 photoreceptor/signaling role. Reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body accumulation during photomorphogenic signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present in nuclear bodies. |
| GO:0005634 nucleus | IDA PMID:26724867 Cryptochromes Interact Directly with PIFs to Control Plant G... | ACCEPT | Summary: nucleus matches the core CRY1 photoreceptor/signaling role. Reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body accumulation during photomorphogenic signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present in nuclear bodies. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: cytoplasm matches the core CRY1 photoreceptor/signaling role. Reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body accumulation during photomorphogenic signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present in nuclear bodies. |
| GO:0005737 cytoplasm | IEA GO_REF:0000117 | ACCEPT | Summary: cytoplasm matches the core CRY1 photoreceptor/signaling role. Reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body accumulation during photomorphogenic signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present in nuclear bodies. |
| GO:0005737 cytoplasm | IDA PMID:18003924 Separate functions for nuclear and cytoplasmic cryptochrome ... | ACCEPT | Summary: cytoplasm matches the core CRY1 photoreceptor/signaling role. Reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body accumulation during photomorphogenic signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present in nuclear bodies. |
| GO:0005829 cytosol | HDA PMID:28887381 Global Analysis of Membrane-associated Protein Oligomerizati... | UNDECIDED | Summary: Cytosol localization is plausible for CRY1 but the high-throughput dataset support is not accessible in the cached text. Reason: CRY1 has independent cytoplasm evidence, but this specific HDA cytosol assertion cannot be checked from the accessible publication text. The cached full text of PMID:28887381 is a global protein-correlation profiling study that nowhere names CRY1 or At4g08920; the per-protein localization calls live in its supplementary tables, which are not in the cache, so no supporting quotation can be given here. |
| GO:0016604 nuclear body | IEA GO_REF:0000117 | ACCEPT | Summary: nuclear body matches the core CRY1 photoreceptor/signaling role. Reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body accumulation during photomorphogenic signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present in nuclear bodies. |
| GO:0016604 nuclear body | IDA PMID:21511872 Blue-light-dependent interaction of cryptochrome 1 with SPA1... | ACCEPT | Summary: nuclear body matches the core CRY1 photoreceptor/signaling role. Reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body accumulation during photomorphogenic signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present in nuclear bodies. |
| GO:0016605 PML body | IEA GO_REF:0000044 | MODIFY | Summary: PML body is an animal-centric mapping; the plant evidence supports CRY1 nuclear bodies. Reason: Arabidopsis CRY1 is reported in nuclear bodies. PML body is too specific for plant CRY1 and should be replaced by nuclear body. Proposed replacements: nuclear body Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present in nuclear bodies. |
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Download this section (compressed HTML)Q: Which CRY1 phosphorylation sites or kinase-active residues are required in vivo for blue-light signaling, given conflicting in vitro reports on light-stimulated autokinase activity?
Suggested experts: Bouly JP, Sancar A, Ahmad M
Q: How much of the CRY1 stomatal and water-loss phenotype is direct guard-cell signaling versus indirect ABA or developmental acclimation?
Suggested experts: Mao J, Boccalandro HE, Casal JJ
Q: Should plant CRY1 nuclear bodies be represented only as nuclear bodies rather than PML bodies in GO-derived mappings?
Suggested experts: Lian HL, Yang HQ
Experiment: Complement cry1 mutants with native-promoter CRY1 phosphorylation-site and kinase-impaired variants, then assay hypocotyl inhibition, SPA/COP1 association, HY5 stability, and FAD photoreduction kinetics under matched blue-light fluence.
Hypothesis: CRY1 autophosphorylation is required for a subset of photomorphogenic outputs but not for initial FAD photoreduction.
Type: native-promoter rescue with phosphosite mutagenesis
Experiment: Express CRY1 specifically in guard cells versus mesophyll/epidermal tissues in a cry1 cry2 background and measure stomatal aperture, ABA abundance, transpiration, and photosynthesis after acute and acclimated blue-light treatments.
Hypothesis: CRY1 regulation of stomatal conductance is partly indirect through ABA and long-term acclimation rather than direct blue-light guard-cell photoreception.
Type: cell-type-specific complementation and physiology
Experiment: Combine CRY1-FIP37 interaction-defective CRY1 alleles with m6A profiling and RNA decay measurements under blue light to separate FIP37-dependent RNA regulation from COP1/SPA-dependent proteostasis outputs.
Hypothesis: The CRY1-FIP37 branch controls a defined subset of m6A-modified PIF and photomorphogenesis transcripts.
Type: interaction-mutant m6A profiling
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