PHYB (PHYTOCHROME B, also known as HY3/OOP1) is the predominant red/far-red light photoreceptor in Arabidopsis that functions as a master regulator of photomorphogenesis, thermomorphogenesis, and circadian entrainment. The protein exists as a homodimer with a modular architecture comprising an N-terminal photosensory module (PSM) containing PAS, GAF, and PHY domains, and a C-terminal output module (OPM) carrying two PAS domains and a histidine kinase-related domain (HKRD) that lacks residues critical to histidine kinase activity. PHYB undergoes reversible photoconversion between the inactive cytoplasmic Pr form (red light-absorbing) and the active nuclear Pfr form (far-red light-absorbing) through conformational changes in its covalently-attached linear tetrapyrrole chromophore. Upon red light activation, the Pfr form rapidly translocates to the nucleus where it assembles into discrete nuclear photobodies and interacts with Phytochrome Interacting Factors (PIFs) including PIF3, PIF4, PIF5, and PIF8 to regulate gene expression. Key structural features include an N-terminal extension (NTE) essential for nuclear localization and transcriptional activity, and a light-sensing knot crucial for PIF binding specificity. PHYB functions as a thermal integrator, associating with target gene promoters in a temperature-dependent manner to control thermomorphogenic responses through PIF4-mediated transcriptional repression. The protein exhibits negative autoregulation of its own expression and controls diverse developmental processes including de-etiolation, hypocotyl elongation, flowering time, stomatal regulation, and circadian phase control. Additionally, PHYB destabilizes specific PIFs (like UNE10/PIF8) in response to red light and coordinates complex signaling networks through interactions with co-regulators, chromatin remodeling factors, and post-translational modification enzymes.
Definition: The formation of discrete nuclear foci containing photoactivated phytochrome and associated signaling proteins that serve as platforms for light-responsive transcriptional regulation
Justification: PHYB forms specialized nuclear photobodies upon light activation - discrete subnuclear foci that coordinate light signaling. This represents a unique nuclear organization not captured by existing GO terms
Parent term: protein-containing complex assembly
Supporting Evidence:
Definition: The reversible light-induced conformational change in a photoreceptor protein between distinct photoactive forms that differ in their absorption spectra and signaling activities
Justification: PHYB undergoes reversible photoconversion between Pr and Pfr forms - a unique light-sensing mechanism that represents the fundamental basis of phytochrome signal transduction
Parent term: response to light stimulus
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000155 phosphorelay sensor kinase activity | IEA GO_REF:0000002 | REMOVE | Summary: InterPro2GO mapping from the histidine kinase domain signature. Plant phytochromes carry a C-terminal histidine kinase-related domain (HKRD) that lacks residues critical to histidine kinase activity, so PHYB does not autophosphorylate on histidine or pass a phosphate to an aspartate. Both the GO definition of phosphorelay sensor kinase activity and that of phosphorelay signal transduction system require that His-to-Asp phosphotransfer. Reason: An electronic domain-to-function mapping contradicted by the known divergence of the plant phytochrome HKRD. Reconciled with the retired duplicate review genes/ARATH/P14713 (same protein), which had KEEP_AS_NON_CORE; this file previously had ACCEPT, supported only by a photosensory-module crystal structure quote that does not address kinase activity. Neither verdict fits once the missing catalytic residues are taken into account. Supporting Evidence: PMID:19286967 plant phys have unique C termini that contain two PAS domains and a region homologous to two-component histidine kinases but lacking residues critical to HK activity |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: Nuclear localization is a core function of PHYB. IEA annotation based on UniProt subcellular location mapping is well-supported by extensive experimental evidence for light-dependent nuclear translocation. Reason: Nuclear localization is fundamental to PHYB function. While IEA evidence, this is strongly supported by experimental studies and represents a core cellular component. Supporting Evidence: PMID:10225946 Light-dependent translocation of a phytochrome B-GFP fusion protein to the nucleus file:ARATH/PHYB/PHYB-deep-research-falcon.md In dark-grown seedlings, PHYB is described as largely **cytosolic and inactive**; red light induces formation of the Pfr state and promotes **nuclear accumulation**, a prerequisite for photobody assembly and much of downstream signaling. |
| GO:0005654 nucleoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: PHYB localizes to nucleoplasm upon light activation as part of its nuclear translocation and signaling function. This is a valid cellular component annotation supported by experimental evidence. Reason: Nucleoplasm localization is accurate for light-activated PHYB and represents a more specific nuclear compartment than general nucleus term. Supporting Evidence: PMID:10225946 Light-dependent translocation of a phytochrome B-GFP fusion protein to the nucleus |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: PHYB is present in cytoplasm in its dark-adapted Pr form and undergoes light-dependent translocation to nucleus upon activation. Cytoplasmic localization is fundamental to PHYB function and trafficking. Reason: Cytoplasmic localization is well-established for dark-adapted PHYB (Pr form). Essential part of light-dependent shuttling mechanism between cytoplasm and nucleus. Supporting Evidence: PMID:10225946 Light-dependent translocation of a phytochrome B-GFP fusion protein to the nucleus |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | ACCEPT | Summary: Regulation of DNA-templated transcription is a core biological process for PHYB. Through interactions with PIFs and association with promoters, PHYB regulates transcription of light-responsive genes. Reason: Transcriptional regulation is a fundamental biological process for PHYB function. Well-supported by extensive evidence for PHYB role in regulating gene expression through PIF interactions. Supporting Evidence: PMID:10466729 The phytochrome photoreceptor family directs plant gene expression by switching between biologically inactive and active conformers in response to the sequential absorption of red and farred photons |
| GO:0007165 signal transduction | IEA GO_REF:0000002 | ACCEPT | Summary: Signal transduction is a fundamental biological process for PHYB as a photoreceptor. PHYB transduces light signals into cellular responses through light-dependent nuclear import, photobody formation, and interactions with PIF transcription factors that it inactivates or destabilizes. The InterPro HKRD signature cited as a supporting entity reflects domain homology only; it does not imply His-to-Asp phosphorelay (see the GO:0000155 REMOVE rows). Reason: Signal transduction is the core biological process that defines PHYB function as a photoreceptor. Well-supported by extensive evidence for light signal transduction mechanisms. Supporting Evidence: PMID:10466729 The phytochrome photoreceptor family directs plant gene expression by switching between biologically inactive and active conformers in response to the sequential absorption of red and farred photons |
| GO:0009584 detection of visible light | IEA GO_REF:0000002 | ACCEPT | Summary: Light detection is a core function of PHYB as a photoreceptor, specifically detecting red and far-red light in the visible spectrum. This is well-supported by its function as the primary red light photoreceptor in Arabidopsis. Reason: Detection of visible light is a fundamental biological process in which PHYB acts as the sensor. Specifically detects red (660-670nm) and far-red (720-740nm) light through phytochromobilin chromophore. Supporting Evidence: PMID:23321421 Phytochromes ( phys ) encompass a diverse collection of biliproteins that enable cellular light perception by photoconverting between a red-light-absorbing ground state (Pr) and a far-red light-absorbing active state (Pfr) |
| GO:0010018 far-red light signaling pathway | IEA GO_REF:0000108 | KEEP AS NON CORE | Summary: PHYB participates in far-red light signaling, particularly in the photoconversion from Pfr back to Pr state upon far-red illumination. However, PHYA is typically the dominant far-red photoreceptor, making this a secondary function for PHYB. Reason: While PHYB does respond to far-red light (Pfr to Pr conversion), PHYA is the primary far-red photoreceptor. This represents a secondary function rather than core PHYB activity. Supporting Evidence: PMID:23321421 Phytochromes ( phys ) encompass a diverse collection of biliproteins that enable cellular light perception by photoconverting between a red-light-absorbing ground state (Pr) and a far-red light-absorbing active state (Pfr) |
| GO:0016607 nuclear speck | IEA GO_REF:0000044 | ACCEPT | Summary: PHYB localizes to nuclear speckles upon light activation, forming distinct subnuclear structures called photobodies. These nuclear speckles are important for PHYB function and interactions with signaling partners. Reason: Nuclear speck localization is well-documented for activated PHYB. These structures (photobodies) are functionally important for light signaling and protein interactions. Supporting Evidence: PMID:23321421 A collection of phyB mutants was generated affecting the bilin-binding pocket that altered photochemistry, thermal stability, and/or nuclear localization patterns [...] the effects of this panel of thermal reversion mutants support the hypothesis that such bodies serve as reservoirs of photoactivated phyB |
| GO:0017006 protein-tetrapyrrole linkage | IEA GO_REF:0000002 | MODIFY | Summary: PHYB contains a covalently-linked phytochromobilin chromophore (tetrapyrrole) that is essential for light perception. However, the more specific term protein-phytochromobilin linkage better describes this interaction. Reason: While accurate, the more specific term GO:0017012 (protein-phytochromobilin linkage) better describes the specific tetrapyrrole (phytochromobilin) that PHYB binds. Proposed replacements: protein-phytochromobilin linkage Supporting Evidence: PMID:24982198 phytochromobilin chromophore |
| GO:0042802 identical protein binding | IEA GO_REF:0000117 | ACCEPT | Summary: PHYB forms homodimers as demonstrated by crystal structure studies. This identical protein binding (homodimerization) is a core structural feature essential for PHYB function and is well-established experimentally. Reason: Homodimerization is a fundamental structural feature of PHYB confirmed by crystal structures and biochemical studies. Essential for proper protein function and signaling. Supporting Evidence: PMID:24982198 The PhyB PSM crystallized as a head-to-head dimer |
| GO:0042803 protein homodimerization activity | IEA GO_REF:0000002 | ACCEPT | Summary: PHYB homodimerization activity is well-established and fundamental to its structure and function. Crystal structures demonstrate that PHYB forms stable homodimers, and this activity is essential for proper photoreceptor function. Reason: Homodimerization activity is a core molecular function of PHYB, confirmed by structural studies and essential for photoreceptor activity. This is more specific than generic protein binding. Supporting Evidence: PMID:24982198 The PhyB PSM crystallized as a head-to-head dimer with strong structural homology to its bacterial relatives |
| GO:0005515 protein binding | IPI PMID:10348744 PKS1, a substrate phosphorylated by phytochrome that modulat... | REMOVE | Summary: Generic protein binding annotation supported by protein-protein interaction evidence. However, this contributes to the extensive redundancy of similar PHYB protein binding annotations. Reason: Generic protein binding annotation that adds to the redundancy of numerous similar PHYB interaction terms without providing specific functional information. Supporting Evidence: PMID:10348744 PKS1, a substrate phosphorylated by phytochrome that modulates light signaling in Arabidopsis |
| GO:0005515 protein binding | IPI PMID:10466729 Binding of phytochrome B to its nuclear signalling partner P... | MODIFY | Summary: This annotation is based on the landmark study demonstrating light-dependent binding of PHYB to PIF3. This represents a core regulatory interaction where light-activated PHYB binds to PIF transcription factors. However, the generic protein binding term is less informative than specific transcription factor binding. Note that PHYB itself is not a DNA-binding transcription factor; it binds PIF transcription factors, so the informative replacement is transcription factor binding (GO:0008134), not DNA-binding transcription factor activity. Reason: While the interaction is fundamental, generic protein binding is less informative. PHYB does not bind DNA directly as a transcription factor; rather, photoactivated PHYB binds the bHLH PIF transcription factors. The informative molecular function is therefore transcription factor binding (GO:0008134). Proposed replacements: transcription factor binding Supporting Evidence: PMID:10466729 Full-length photoactive phytochrome B binds PIF3 in vitro only upon light-induced conversion to its active form file:ARATH/PHYB/PHYB-deep-research-falcon.md A central mechanism is **direct binding** of photoactivated PHYB to PIF transcription factors (e.g., PIF1/3/4/5/7) via PIF recognition motifs (e.g., APB motifs) |
| GO:0005515 protein binding | IPI PMID:10995393 HFR1 encodes an atypical bHLH protein that acts in phytochro... | REMOVE | Summary: Generic protein binding annotation supported by protein-protein interaction evidence. However, given the numerous similar annotations for PHYB protein interactions, this adds redundancy without functional specificity. Reason: One of many generic protein binding annotations that adds redundancy without providing specific functional information. The specific interactions are better captured by other terms. Supporting Evidence: PMID:10995393 HFR1/PIF3 complex and PIF3 homodimer bound preferentially to the Pfr form of both phytochromes |
| GO:0005515 protein binding | IPI PMID:11069292 Phytochrome B binds with greater apparent affinity than phyt... | REMOVE | Summary: This study demonstrates PHYB binding to PIF3 with greater affinity than PHYA, establishing PHYB as the primary PIF3 interactor. However, generic protein binding is less informative than the specific transcriptional regulatory function. Reason: While this represents an important PIF3 interaction study, the generic protein binding annotation is redundant with multiple other similar annotations and lacks functional specificity. Supporting Evidence: PMID:11069292 Phytochrome B binds with greater apparent affinity than phytochrome A to the basic helix-loop-helix factor PIF3 |
| GO:0005515 protein binding | IPI PMID:11089975 Functional interaction of phytochrome B and cryptochrome 2. | REMOVE | Summary: Generic protein binding annotation that adds to the redundancy of similar annotations. Multiple protein binding terms for PHYB interactions provide limited functional insight compared to more specific interaction terms. Reason: Redundant generic protein binding annotation that does not provide specific functional information beyond what is captured by other binding and interaction terms. Supporting Evidence: PMID:11089975 PhyB interacts directly with cry2 as observed in co-immunoprecipitation experiments |
| GO:0005515 protein binding | IPI PMID:11691995 Interaction of the response regulator ARR4 with phytochrome ... | REMOVE | Summary: This study demonstrated PHYB interaction with ARR4, a response regulator in light signaling. However, the generic protein binding term contributes to annotation redundancy. Reason: Generic protein binding for ARR4 interaction. The specific regulatory function in light signaling is better captured by signaling process terms rather than generic binding. Supporting Evidence: PMID:11691995 Interaction of the response regulator ARR4 with phytochrome B in modulating red light signaling |
| GO:0005515 protein binding | IPI PMID:12006496 PIF4, a phytochrome-interacting bHLH factor, functions as a ... | REMOVE | Summary: Generic protein binding annotation that contributes to the extensive redundancy of similar PHYB interaction annotations. Lacks functional specificity compared to more detailed interaction terms. Reason: Another redundant generic protein binding annotation that provides no additional functional information beyond the numerous other similar annotations for PHYB. Supporting Evidence: PMID:12006496 PIF4, a phytochrome-interacting bHLH factor, functions as a negative regulator of phytochrome B signaling in Arabidopsis. |
| GO:0005515 protein binding | IPI PMID:15155879 Constitutive photomorphogenesis 1 and multiple photoreceptor... | REMOVE | Summary: This study demonstrated PHYB interaction with COP1 and PIF3 in the regulation of PIF3 degradation. While functionally important, the generic protein binding term is less informative than specific regulatory interaction terms. Reason: Generic protein binding for important PIF3/COP1 interactions. The specific regulatory mechanism is better captured by other process-specific annotations rather than generic binding. Supporting Evidence: PMID:15155879 Constitutive photomorphogenesis 1 and multiple photoreceptors control degradation of phytochrome interacting factor 3 |
| GO:0005515 protein binding | IPI PMID:15273290 Heterodimerization of type II phytochromes in Arabidopsis. | REMOVE | Summary: This study demonstrated heterodimerization between PHYB and other phytochrome family members (PHYC, PHYD, PHYE). This protein binding represents an important regulatory mechanism, but the generic term is less informative than the specific heterodimerization activity. Reason: Generic protein binding annotation for heterodimerization with other phytochromes. The homodimerization activity annotation (GO:0042803) already captures dimerization function more specifically. Supporting Evidence: PMID:15273290 Heterodimerization of type II phytochromes in Arabidopsis |
| GO:0005515 protein binding | IPI PMID:15448264 Phytochrome-interacting factor 1 is a critical bHLH regulato... | REMOVE | Summary: This study showed PHYB interaction with PIF1, a critical transcription factor in light signaling. PIF1 is one of the key regulatory targets of PHYB that controls chlorophyll biosynthesis and photomorphogenesis. Reason: Generic protein binding for functionally important PIF1 interaction. The specific transcriptional regulatory relationship is already captured by other annotations and this adds little functional information. Supporting Evidence: PMID:15448264 Phytochrome-interacting factor 1 is a critical bHLH regulator of chlorophyll biosynthesis |
| GO:0005515 protein binding | IPI PMID:15486100 A novel molecular recognition motif necessary for targeting ... | REMOVE | Summary: Generic protein binding annotation adding to the redundancy of multiple similar PHYB interaction terms. Does not provide specific functional insight beyond other binding annotations. Reason: Redundant generic protein binding annotation that contributes to over-annotation without providing specific functional information about PHYB interactions. Supporting Evidence: PMID:15486100 PIF5 and PIF6, that specifically bind phyB in the Pfr form |
| GO:0005515 protein binding | IPI PMID:15486102 PIL5, a phytochrome-interacting basic helix-loop-helix prote... | REMOVE | Summary: Another generic protein binding annotation that adds to the extensive redundancy of similar PHYB interaction terms without providing specific functional details. Reason: Redundant protein binding annotation that provides no additional functional information beyond the numerous other similar annotations for PHYB protein interactions. Supporting Evidence: PMID:15486102 PIL5, a phytochrome-interacting basic helix-loop-helix protein, is a key negative regulator of seed germination in Arabidopsis thaliana |
| GO:0005515 protein binding | IPI PMID:18728185 Genetically encoded photoswitching of actin assembly through... | REMOVE | Summary: Generic protein binding annotation that contributes to the over-annotation of PHYB with multiple similar interaction terms lacking functional specificity. Reason: Generic protein binding that adds redundancy without specific functional information. The numerous similar annotations provide diminishing returns for functional annotation. Supporting Evidence: PMID:18728185 Genetically encoded photoswitching of actin assembly through the Cdc42-WASP-Arp2/3 complex pathway |
| GO:0005515 protein binding | IPI PMID:19286967 Obligate heterodimerization of Arabidopsis phytochromes C an... | REMOVE | Summary: Generic protein binding annotation for PHYB interactions. Given the extensive number of similar annotations, this contributes to over-annotation without providing specific functional insights. Reason: Redundant generic protein binding annotation. The specific molecular functions and biological processes are better captured by more functionally informative terms. Supporting Evidence: PMID:19286967 Obligate heterodimerization of Arabidopsis phytochromes C and E and interaction with the PIF3 basic helix-loop-helix transcription factor. |
| GO:0005515 protein binding | IPI PMID:21928113 Dimerization and blue light regulation of PIF1 interacting b... | REMOVE | Summary: Generic protein binding annotation that adds to the redundancy of numerous similar PHYB interaction annotations without providing functional specificity. Reason: Redundant protein binding annotation contributing to over-annotation. The functional significance of PHYB interactions is better captured by specific molecular function and biological process terms. Supporting Evidence: PMID:21928113 Dimerization and blue light regulation of PIF1 interacting bHLH proteins in Arabidopsis |
| GO:0005515 protein binding | IPI PMID:22904146 The phytochrome-interacting vascular plant one-zinc finger1 ... | REMOVE | Summary: This study demonstrated PHYB interactions with VOZ1 and VOZ2 transcription factors in flowering regulation. However, the generic protein binding term is less informative than the specific flowering regulation process. Reason: Generic protein binding for VOZ1/VOZ2 interactions related to flowering. The specific biological process (flowering regulation) captures the functional significance better than generic binding. Supporting Evidence: PMID:22904146 The phytochrome-interacting VASCULAR PLANT ONE-ZINC FINGER1 and VOZ2 redundantly regulate flowering in Arabidopsis |
| GO:0005515 protein binding | IPI PMID:9845368 PIF3, a phytochrome-interacting factor necessary for normal ... | REMOVE | Summary: This is the original study that identified PIF3 as a phytochrome-interacting factor and established the fundamental PHYB-PIF3 interaction that is central to light signaling. This represents a core regulatory interaction. Reason: While this is a foundational study for PHYB-PIF interactions, the generic protein binding annotation is already captured multiple times and adds redundancy without functional specificity. Supporting Evidence: PMID:9845368 PIF3, a phytochrome-interacting factor necessary for normal photoinduced signal transduction, is a novel basic helix-loop-helix protein |
| GO:0042802 identical protein binding | IPI PMID:15273290 Heterodimerization of type II phytochromes in Arabidopsis. | ACCEPT | Summary: While this study focused on heterodimerization with other phytochromes, PHYB homodimerization is well-established from other evidence. Reason: Although this specific study emphasized heterodimerization, PHYB homodimerization (identical protein binding) is well-established and essential for its function, supported by multiple studies including structural evidence. Supporting Evidence: PMID:15273290 six myc (myc6)-phyB coprecipitates phyC-phyE; and myc6-phyD coprecipitates phyB and phyE |
| GO:0042802 identical protein binding | IPI PMID:19286967 Obligate heterodimerization of Arabidopsis phytochromes C an... | ACCEPT | Summary: Identical protein binding (homodimerization) is well-established for PHYB and supported by multiple studies including crystal structure evidence. This represents a fundamental structural feature. Reason: Homodimerization is well-established for PHYB and essential for its function. This annotation provides specific evidence for identical protein binding beyond the structural studies. Supporting Evidence: PMID:19286967 Obligate heterodimerization of Arabidopsis phytochromes C and E and interaction with the PIF3 basic helix-loop-helix transcription factor |
| GO:0005515 protein binding | IPI PMID:35222493 SWELLMAP 2, a phyB-Interacting Splicing Factor, Negatively R... | REMOVE | Summary: This study demonstrated PHYB interaction with SMP2 (SWELLMAP 2), a splicing factor that regulates photomorphogenesis. While functionally important, the generic protein binding term is less informative. Reason: Generic protein binding for SMP2 interaction. The specific regulatory function in splicing and photomorphogenesis is better captured by process-specific terms rather than generic binding. Supporting Evidence: PMID:35222493 SWELLMAP 2, a phyB-interacting splicing factor, negatively regulates seedling photomorphogenesis in Arabidopsis |
| GO:0005634 nucleus | IDA PMID:35222493 SWELLMAP 2, a phyB-Interacting Splicing Factor, Negatively R... | ACCEPT | Summary: Nuclear localization demonstrated by direct experimental evidence (IDA). This study shows PHYB nuclear localization and its role in splicing regulation. Supports the well-established nuclear function of light-activated PHYB. Reason: Direct experimental evidence (IDA) for nuclear localization, which is a core function of activated PHYB. This is one of several IDA annotations confirming nuclear localization. Supporting Evidence: PMID:35222493 SWELLMAP 2, a phyB-interacting splicing factor, negatively regulates seedling photomorphogenesis in Arabidopsis |
| GO:0009416 response to light stimulus | IDA PMID:35222493 SWELLMAP 2, a phyB-Interacting Splicing Factor, Negatively R... | ACCEPT | Summary: Response to light stimulus is fundamental to PHYB function as a photoreceptor. Direct experimental evidence supports this core biological process. However, more specific light response terms may be more informative. Reason: Response to light stimulus is a fundamental biological process for PHYB with strong experimental support. While more specific terms exist, this captures the essential light responsiveness. Supporting Evidence: PMID:35222493 SWELLMAP 2, a phyB-interacting splicing factor, negatively regulates seedling photomorphogenesis |
| GO:0005515 protein binding | IPI PMID:36282917 SWAP1-SFPS-RRC1 splicing factor complex modulates pre-mRNA s... | REMOVE | Summary: This study showed PHYB interaction with SWAP1 in splicing regulation. However, the generic protein binding annotation is less informative than the specific splicing regulatory function. Reason: Generic protein binding for SWAP1 interaction in splicing regulation. The specific functional role is better captured by splicing-related process terms rather than generic binding. Supporting Evidence: PMID:36282917 SWAP1-SFPS-RRC1 splicing factor complex modulates pre-mRNA splicing to promote photomorphogenesis in Arabidopsis |
| GO:0005515 protein binding | IPI PMID:28760995 SPF45-related splicing factor for phytochrome signaling prom... | REMOVE | Summary: This study demonstrated PHYB interaction with DRT111/RSN2/SFPS, a splicing factor involved in photomorphogenesis regulation. While functionally important, the generic binding term is less informative. Reason: Generic protein binding for splicing factor interaction. The specific regulatory function in pre-mRNA splicing and photomorphogenesis is better captured by process-specific annotations. Supporting Evidence: PMID:28760995 SPF45-related splicing factor for phytochrome signaling promotes photomorphogenesis by regulating pre-mRNA splicing in Arabidopsis |
| GO:0005634 nucleus | IDA PMID:28760995 SPF45-related splicing factor for phytochrome signaling prom... | ACCEPT | Summary: Nuclear localization demonstrated by direct experimental evidence in the context of PHYB interaction with splicing factors. Supports the well-established nuclear function of light-activated PHYB. Reason: Direct experimental evidence for nuclear localization. This is a fundamental cellular component for PHYB function and is consistently supported across multiple studies. Supporting Evidence: PMID:28760995 In response to light, SFPS-RFP (red fluorescent protein) colocalizes with phyB-GFP in photobodies |
| GO:0009416 response to light stimulus | IDA PMID:28760995 SPF45-related splicing factor for phytochrome signaling prom... | ACCEPT | Summary: Response to light stimulus is a fundamental biological process for PHYB as a photoreceptor. Direct experimental evidence supports this core function, although more specific light response terms are available. Reason: Response to light stimulus is a core biological process for PHYB with direct experimental support. While general, it captures the essential light responsiveness of the photoreceptor. Supporting Evidence: PMID:28760995 which directly interacts with the photoreceptor phytochrome B (phyB) |
| GO:0005634 nucleus | IDA PMID:29263319 PCH1 and PCHL promote photomorphogenesis in plants by contro... | ACCEPT | Summary: Nuclear localization demonstrated by direct experimental evidence. This study showed PHYB interaction with PCH1 and PCHL in nuclear photobodies, supporting nuclear function. Reason: Direct experimental evidence for nuclear localization in the context of photobody formation and protein interactions. Consistent with established PHYB nuclear function. Supporting Evidence: PMID:29263319 the homologous phyB-binding proteins PCH1 and PCHL suppress phyB dark reversion |
| GO:0005515 protein binding | IPI PMID:29263319 PCH1 and PCHL promote photomorphogenesis in plants by contro... | REMOVE | Summary: This study demonstrated PHYB interaction with PCH1 and PCHL proteins that control dark reversion. While functionally important, the generic protein binding term adds to annotation redundancy. Reason: Generic protein binding for PCH1/PCHL interactions. The specific functional role in dark reversion and photomorphogenesis is better captured by process-specific terms. Supporting Evidence: PMID:29263319 the homologous phyB-binding proteins PCH1 and PCHL suppress phyB dark reversion |
| GO:0005515 protein binding | IPI PMID:31732705 PHYTOCHROME INTERACTING FACTOR8 Inhibits Phytochrome A-Media... | REMOVE | Summary: This study demonstrated PHYB interaction with UNE10/PIF8 in the regulation of far-red light responses. While functionally important, the generic protein binding term is less informative than specific regulatory functions. Reason: Generic protein binding for UNE10/PIF8 interaction. The specific role in far-red light signaling and PIF regulation is better captured by transcriptional regulatory terms. Supporting Evidence: PMID:31732705 PHYTOCHROME INTERACTING FACTOR8 inhibits phytochrome a-mediated far-red light responses in Arabidopsis |
| GO:0009266 response to temperature stimulus | IMP PMID:30635559 Daytime temperature is sensed by phytochrome B in Arabidopsi... | ACCEPT | Summary: PHYB functions as a thermosensor that integrates temperature and light information. This study demonstrates that PHYB senses daytime temperature and regulates thermomorphogenic responses through HEMERA. Reason: PHYB itself is the temperature sensor: temperature-dependent thermal reversion of its active Pfr state sets the level of signaling, so this is a direct function of the photoreceptor rather than a downstream consequence. Reconciled with the retired duplicate review genes/ARATH/P14713 (same protein), which had ACCEPT; adopted over this file's earlier KEEP_AS_NON_CORE. Supporting Evidence: PMID:30635559 Daytime temperature is sensed by phytochrome B in Arabidopsis through a transcriptional activator HEMERA |
| GO:0005829 cytosol | IDA PMID:36401805 Phytochrome B regulates reactive oxygen signaling during abi... | ACCEPT | Summary: Cytosol localization is demonstrated by direct experimental evidence. PHYB is present in cytosol in its dark-adapted state and this represents a more specific cytoplasmic compartment than general cytoplasm annotation. Reason: Cytosol is a specific cytoplasmic compartment where PHYB resides in darkness. Direct experimental evidence supports this localization and it represents more specific localization than general cytoplasm. Supporting Evidence: PMID:36401805 phyB can regulate ROS production during stress even if it is restricted to the cytosol |
| GO:0009416 response to light stimulus | IMP PMID:36508461 A role for brassinosteroid signalling in decision-making pro... | ACCEPT | Summary: Response to light stimulus is a fundamental biological process for PHYB as a photoreceptor. Experimental evidence supports this core function in light perception and signaling. Reason: Response to light stimulus is a core biological process for PHYB with experimental support. While general, it captures the essential light responsiveness of the photoreceptor. Supporting Evidence: PMID:36508461 A role for brassinosteroid signalling in decision-making processes in the Arabidopsis seedling |
| GO:0009408 response to heat | IMP PMID:36401805 Phytochrome B regulates reactive oxygen signaling during abi... | KEEP AS NON CORE | Summary: PHYB functions as a thermosensor and mediates heat stress responses in plants. This represents an important physiological function where PHYB integrates temperature and light signals for stress adaptation. Reason: Heat response is an important but secondary function of PHYB. While experimentally supported, temperature sensing represents an additional role beyond the core photoreceptor function. Supporting Evidence: PMID:36401805 Phytochrome B regulates reactive oxygen signaling during abiotic and biotic stress in plants. |
| GO:0009409 response to cold | IMP PMID:36401805 Phytochrome B regulates reactive oxygen signaling during abi... | KEEP AS NON CORE | Summary: PHYB mediates cold stress responses as part of its thermosensing function. Temperature sensing represents an additional role for PHYB beyond light perception in environmental adaptation. Reason: Cold response is a secondary function of PHYB related to its thermosensing capabilities. While important for plant adaptation, this represents a non-core function compared to light perception. Supporting Evidence: PMID:36401805 Phytochrome B regulates reactive oxygen signaling during abiotic and biotic stress in plants. |
| GO:0009643 photosynthetic acclimation | IMP PMID:36401805 Phytochrome B regulates reactive oxygen signaling during abi... | KEEP AS NON CORE | Summary: PHYB contributes to photosynthetic acclimation by regulating light-responsive genes involved in photosynthetic apparatus. This represents a downstream consequence of PHYB light signaling. Reason: Photosynthetic acclimation is a downstream consequence of PHYB light signaling rather than a core function. While important for plant physiology, it represents a secondary process. Supporting Evidence: PMID:36401805 Phytochrome B regulates reactive oxygen signaling during abiotic and biotic stress in plants. |
| GO:0042742 defense response to bacterium | IMP PMID:36401805 Phytochrome B regulates reactive oxygen signaling during abi... | KEEP AS NON CORE | Summary: PHYB influences plant defense responses to bacterial pathogens, likely through modulation of light-regulated defense genes. This represents a secondary role in plant immunity. Reason: Defense response to bacteria is a secondary function of PHYB. While experimentally supported, pathogen defense represents a pleiotropic effect rather than core photoreceptor function. Supporting Evidence: PMID:36401805 phyB is also required for ROS accumulation in response to heat, wounding, cold, and bacterial infection |
| GO:0005515 protein binding | IPI PMID:24127609 PHYTOCHROME-DEPENDENT LATE-FLOWERING accelerates flowering t... | REMOVE | Summary: This study demonstrated PHYB interaction with PHL (PHYTOCHROME-DEPENDENT LATE-FLOWERING) in flowering time regulation. While functionally important, the generic binding term is less informative. Reason: Generic protein binding for PHL interaction in flowering regulation. The specific developmental function is better captured by flowering regulation process terms. Supporting Evidence: PMID:24127609 PHYTOCHROME-DEPENDENT LATE-FLOWERING accelerates flowering through physical interactions with phytochrome B and CONSTANS |
| GO:0005634 nucleus | IDA PMID:24127609 PHYTOCHROME-DEPENDENT LATE-FLOWERING accelerates flowering t... | ACCEPT | Summary: Nuclear localization demonstrated by direct experimental evidence in the context of flowering regulation and PHL interaction. Consistent with established PHYB nuclear function. Reason: Direct experimental evidence for nuclear localization in flowering regulatory context. Supports the well-established nuclear function of light-activated PHYB. Supporting Evidence: PMID:24127609 PHYTOCHROME-DEPENDENT LATE-FLOWERING accelerates flowering through physical interactions with phytochrome B and CONSTANS |
| GO:0009266 response to temperature stimulus | IMP PMID:27789797 Phytochromes function as thermosensors in Arabidopsis. | ACCEPT | Summary: This landmark study demonstrated that PHYB functions as a thermosensor, integrating temperature and light information for plant development. Reason: PHYB itself is the temperature sensor: temperature-dependent thermal reversion of its active Pfr state sets the level of signaling, so this is a direct function of the photoreceptor rather than a downstream consequence. Reconciled with the retired duplicate review genes/ARATH/P14713 (same protein), which had ACCEPT; adopted over this file's earlier KEEP_AS_NON_CORE. Supporting Evidence: PMID:27789797 Phytochromes function as thermosensors in Arabidopsis file:ARATH/PHYB/PHYB-deep-research-falcon.md PHYB is also an **ambient-temperature sensor** because active Pfr undergoes **temperature-dependent thermal reversion** back to Pr |
| GO:0043565 sequence-specific DNA binding | IDA PMID:27789797 Phytochromes function as thermosensors in Arabidopsis. | MODIFY | Summary: This study demonstrates that PHYB associates with promoters of target genes in a temperature-dependent manner. However, PHYB typically works through protein-protein interactions with PIFs rather than direct sequence-specific DNA binding. Reason: While PHYB associates with promoters, it typically functions through protein interactions with PIFs rather than direct sequence-specific DNA binding. Promoter-specific chromatin binding is more accurate; that term is already carried by its own ACCEPTed IDA row from the same paper, so this row is redundant with it once modified. Proposed replacements: promoter-specific chromatin binding Supporting Evidence: PMID:27789797 phytochrome B (phyB) directly associates with the promoters of key target genes in a temperature-dependent manner |
| GO:0045892 negative regulation of DNA-templated transcription | IDA PMID:27789797 Phytochromes function as thermosensors in Arabidopsis. | ACCEPT | Summary: PHYB can negatively regulate transcription through its interactions with PIFs and direct association with promoters. This study shows temperature-dependent transcriptional repression, representing an important regulatory mechanism. Reason: Direct experimental evidence for transcriptional repression activity. PHYB functions as both positive and negative regulator of transcription depending on target genes and conditions. Supporting Evidence: PMID:27789797 Phytochrome null plants display a constitutive warm-temperature response, and consistent with this, we show in this background that the warm-temperature transcriptome becomes derepressed at low temperatures |
| GO:1990841 promoter-specific chromatin binding | IDA PMID:27789797 Phytochromes function as thermosensors in Arabidopsis. | ACCEPT | Summary: Promoter-specific chromatin binding is demonstrated by direct experimental evidence showing PHYB association with target gene promoters. This represents a more accurate description of PHYB transcriptional regulation mechanism than generic DNA binding. Reason: Direct experimental evidence for promoter-specific chromatin binding, which accurately describes how PHYB regulates transcription through chromatin association rather than direct DNA sequence recognition. Supporting Evidence: PMID:27789797 phytochrome B (phyB) directly associates with the promoters of key target genes in a temperature-dependent manner |
| GO:0005515 protein binding | IPI PMID:26724867 Cryptochromes Interact Directly with PIFs to Control Plant G... | REMOVE | Summary: This study demonstrated PHYB interactions with PIF4 and PIF5 in blue light responses. While functionally significant, the generic protein binding term contributes to annotation redundancy. Reason: Generic protein binding for PIF4/PIF5 interactions. The specific regulatory functions in light signaling are better captured by transcriptional and signaling process terms. Supporting Evidence: PMID:26724867 Cryptochromes interact directly with PIFs to control plant growth in limiting blue light |
| GO:0010244 response to low fluence blue light stimulus by blue low-fluence system | IDA PMID:26724867 Cryptochromes Interact Directly with PIFs to Control Plant G... | KEEP AS NON CORE | Summary: This study showed PHYB involvement in blue light responses through interactions with PIFs under low blue light conditions. While PHYB primarily responds to red light, it can modulate blue light signaling. Reason: Blue light response is a secondary function for PHYB. While experimentally supported, red light perception is the primary function, and CRY1/CRY2 are the main blue light photoreceptors. Supporting Evidence: PMID:26724867 Cryptochromes interact directly with PIFs to control plant growth in limiting blue light |
| GO:0005515 protein binding | IPI PMID:22577138 Light-dependent, dark-promoted interaction between Arabidops... | REMOVE | Summary: This study demonstrated light-dependent interaction between CRY1 and PHYB, showing cross-talk between different photoreceptor systems. However, the generic binding term is less informative. Reason: Generic protein binding for CRY1 interaction. The specific photoreceptor cross-talk and signaling integration is better captured by light signaling process terms. Supporting Evidence: PMID:22577138 Light-dependent, dark-promoted interaction between Arabidopsis cryptochrome 1 and phytochrome B proteins |
| GO:0005515 protein binding | IPI PMID:26120968 High-level expression and phosphorylation of phytochrome B m... | REMOVE | Summary: This study demonstrated PHYB protein interactions in the context of flowering regulation. However, the generic protein binding term adds to the extensive redundancy of similar annotations. Reason: Generic protein binding annotation for flowering-related interactions. The specific developmental function is better captured by flowering regulation process terms rather than generic binding. Supporting Evidence: PMID:26120968 the light-activated Pfr form of phyB [...] inhibits the function of the COP1-SPA1 complex by direct interactions |
| GO:2000028 regulation of photoperiodism, flowering | IMP PMID:26120968 High-level expression and phosphorylation of phytochrome B m... | KEEP AS NON CORE | Summary: PHYB regulates flowering time through photoperiodism pathways, particularly by modulating the expression of flowering time genes in response to light quality and duration. This is an important developmental process controlled by PHYB. Reason: Flowering regulation is an important but secondary function of PHYB. While well-supported experimentally, photomorphogenesis and direct light signaling are more fundamental to PHYB core function. Supporting Evidence: PMID:26120968 High-level expression and phosphorylation of phytochrome B modulates flowering time in Arabidopsis |
| GO:0017012 protein-phytochromobilin linkage | IDA PMID:24982198 Crystal structure of the photosensing module from a red/far-... | ACCEPT | Summary: Protein-phytochromobilin linkage is a fundamental structural feature of PHYB essential for photoreceptor function. The covalent attachment of phytochromobilin chromophore to Cys357 is well-characterized by crystal structure and biochemical studies. Reason: Phytochromobilin linkage is essential for PHYB photoreceptor activity. Direct experimental evidence from crystal structure studies confirms this critical post-translational modification. Supporting Evidence: PMID:24982198 phytochromobilin chromophore |
| GO:0042803 protein homodimerization activity | IDA PMID:24982198 Crystal structure of the photosensing module from a red/far-... | ACCEPT | Summary: Homodimerization activity is demonstrated by direct experimental evidence from crystal structure studies. PHYB forms stable homodimers which is essential for proper photoreceptor function and signal transduction. Reason: Direct experimental evidence (IDA) from crystal structure confirming homodimerization. This is a fundamental molecular function of PHYB essential for its activity as a photoreceptor. Supporting Evidence: PMID:24982198 The PhyB PSM crystallized as a head-to-head dimer with strong structural homology to its bacterial relatives |
| GO:0005515 protein binding | IPI PMID:22895253 Photoactivated phytochromes interact with HEMERA and promote... | REMOVE | Summary: This study demonstrated PHYB interaction with PTAC12/HMR/PAP5 (HEMERA) that promotes photomorphogenesis. While functionally important, the generic protein binding term is less informative. Reason: Generic protein binding for HEMERA interaction. The specific regulatory function in photomorphogenesis is better captured by process-specific terms rather than generic binding. Supporting Evidence: PMID:22895253 Photoactivated phytochromes interact with HEMERA and promote its accumulation to establish photomorphogenesis in Arabidopsis |
| GO:0005829 cytosol | IDA PMID:23321421 Structure-guided engineering of plant phytochrome B with alt... | ACCEPT | Summary: Cytosol localization is well-established for PHYB in its dark-adapted state, though this specific citation may not be ideal. Reason: PHYB is present in the cytosol in its dark-adapted state before light-induced nuclear translocation. This is well-supported by other evidence even if this specific publication focuses more on nuclear localization patterns. Supporting Evidence: PMID:23321421 A collection of phyB mutants was generated affecting the bilin-binding pocket that altered photochemistry, thermal stability, and/or nuclear localization patterns |
| GO:0009640 photomorphogenesis | IMP PMID:23321421 Structure-guided engineering of plant phytochrome B with alt... | ACCEPT | Summary: Photomorphogenesis is the core biological process that PHYB regulates. As the primary red light photoreceptor, PHYB controls light-dependent developmental processes including hypocotyl elongation, cotyledon expansion, and chloroplast development. This is a fundamental PHYB function. Reason: Photomorphogenesis is the primary biological process that PHYB controls as the main red light photoreceptor. This represents the core developmental function with strong experimental support. Supporting Evidence: PMID:23321421 phyB, the dominant isoform in light-grown plants |
| GO:0016604 nuclear body | IDA PMID:23321421 Structure-guided engineering of plant phytochrome B with alt... | ACCEPT | Summary: Nuclear body formation (photobodies) is a characteristic feature of light-activated PHYB. These structures are important for PHYB signaling and represent concentrated sites of PHYB accumulation and potentially degradation. Reason: Nuclear body formation is a well-characterized feature of activated PHYB with direct experimental evidence. These photobodies are functionally important for PHYB signaling and regulation. Supporting Evidence: PMID:23321421 A collection of phyB mutants was generated affecting the bilin-binding pocket that altered photochemistry, thermal stability, and/or nuclear localization patterns |
| GO:0031516 far-red light photoreceptor activity | IDA PMID:23321421 Structure-guided engineering of plant phytochrome B with alt... | ACCEPT | Summary: Far-red light photoreceptor activity is demonstrated by direct experimental evidence. PHYB absorbs far-red light in its Pfr state and undergoes photoreversion to Pr. This is a core molecular function of PHYB photoreceptor activity. Reason: Far-red light photoreceptor activity is a core molecular function of PHYB, supported by direct experimental evidence. Essential for the Pfr to Pr photoconversion cycle. Supporting Evidence: PMID:23321421 Structure-guided engineering of plant phytochrome B with altered photochemistry and light signaling |
| GO:0031517 red light photoreceptor activity | IDA PMID:23321421 Structure-guided engineering of plant phytochrome B with alt... | ACCEPT | Summary: Red light photoreceptor activity is the primary and most fundamental molecular function of PHYB. Direct experimental evidence confirms PHYB as the dominant red light photoreceptor in Arabidopsis. This is the core defining activity of PHYB. Reason: Red light photoreceptor activity is the most fundamental and well-characterized molecular function of PHYB. This is the primary activity that defines PHYB function in plants. Supporting Evidence: PMID:23321421 Arabidopsis (Arabidopsis thaliana) phyB, the dominant isoform in light-grown plants, as the example |
| GO:0005515 protein binding | IPI PMID:23371951 Arabidopsis phytochrome B promotes SPA1 nuclear accumulation... | REMOVE | Summary: Generic protein binding annotation that contributes to the extensive redundancy of similar PHYB interaction terms. This adds limited functional information beyond other binding annotations. Reason: Generic protein binding annotation that contributes to over-annotation without providing specific functional insights beyond the numerous other similar terms for PHYB interactions. Supporting Evidence: PMID:23371951 Arabidopsis phytochrome B promotes SPA1 nuclear accumulation to repress photomorphogenesis under far-red light. |
| GO:0005634 nucleus | IDA PMID:23371951 Arabidopsis phytochrome B promotes SPA1 nuclear accumulation... | ACCEPT | Summary: Nuclear localization is a core function of PHYB demonstrated by direct experimental evidence. Light-dependent nuclear translocation is fundamental to PHYB transcriptional regulatory function. Reason: Direct experimental evidence for nuclear localization. Nuclear function is fundamental to PHYB signaling mechanism and represents a core subcellular localization. Supporting Evidence: PMID:23371951 Arabidopsis phytochrome B promotes SPA1 nuclear accumulation to repress photomorphogenesis under far-red light |
| GO:0010218 response to far red light | IMP PMID:23371951 Arabidopsis phytochrome B promotes SPA1 nuclear accumulation... | ACCEPT | Summary: PHYB responds to far-red light through photoconversion from Pfr back to Pr state. This is part of the normal photoconversion cycle and represents a core photoreceptor function. Reason: Far-red light response is integral to PHYB photoconversion cycle (Pfr to Pr). This represents a fundamental aspect of PHYB photoreceptor function with experimental support. Supporting Evidence: PMID:23371951 phyB predominantly regulates light responses in red light |
| GO:0016604 nuclear body | IDA PMID:23371951 Arabidopsis phytochrome B promotes SPA1 nuclear accumulation... | ACCEPT | Summary: Nuclear body formation (photobodies) demonstrated by direct experimental evidence. These structures are characteristic of light-activated PHYB and important for signaling and regulation. Reason: Direct experimental evidence for nuclear body formation. Photobodies are a well-characterized feature of activated PHYB and functionally important for signaling. Supporting Evidence: file:ARATH/PHYB/PHYB-deep-research-perplexity-lite.md These are dynamic nuclear bodies where PHYB interacts with various signaling proteins and transcription factors PMID:23371951 Arabidopsis phytochrome B promotes SPA1 nuclear accumulation to repress photomorphogenesis under far-red light. |
| GO:0006325 chromatin organization | IMP PMID:20935177 Photoreceptors CRYTOCHROME2 and phytochrome B control chroma... | KEEP AS NON CORE | Summary: PHYB influences chromatin organization through its association with promoters and regulation of gene expression. This represents an important mechanism for transcriptional control. Reason: Chromatin organization is an important but secondary function of PHYB. While involved in transcriptional regulation, this represents a downstream consequence of primary photoreceptor signaling. Supporting Evidence: PMID:20935177 Phytochrome B also controls light-induced chromatin organization |
| GO:0010148 transpiration | IMP PMID:19363093 Phytochrome B enhances photosynthesis at the expense of wate... | KEEP AS NON CORE | Summary: PHYB influences transpiration through regulation of stomatal development and aperture. This represents a physiological consequence of PHYB light signaling rather than a core function. Reason: Transpiration regulation is a downstream physiological consequence of PHYB signaling. While important for plant physiology, it represents a secondary effect rather than core photoreceptor function. Supporting Evidence: PMID:19363093 Increased stomata density resulted in increased transpiration per unit leaf area |
| GO:0010374 stomatal complex development | IMP PMID:19363093 Phytochrome B enhances photosynthesis at the expense of wate... | KEEP AS NON CORE | Summary: PHYB regulates stomatal development as part of its control over photomorphogenesis and light-responsive development. This represents an important developmental process under PHYB control. Reason: Stomatal development is an important but secondary developmental function of PHYB. While experimentally supported, it represents a specific developmental outcome rather than core photoreceptor function. Supporting Evidence: PMID:19363093 phyB promoted the expression of FAMA and TOO MANY MOUTHS genes involved in the regulation of stomata development in young leaves |
| GO:0015979 photosynthesis | IMP PMID:19363093 Phytochrome B enhances photosynthesis at the expense of wate... | KEEP AS NON CORE | Summary: PHYB influences photosynthesis through regulation of chloroplast development and photosynthetic gene expression. This represents a downstream consequence of PHYB light signaling. Reason: Photosynthesis regulation is a downstream consequence of PHYB signaling rather than a direct function. While important for plant physiology, PHYB affects photosynthesis indirectly through developmental regulation. Supporting Evidence: PMID:19363093 phyB promoted photosynthesis rates only at high fluence rates of photosynthetically active radiation |
| GO:0009867 jasmonic acid mediated signaling pathway | IMP PMID:19251652 Ecological modulation of plant defense via phytochrome contr... | KEEP AS NON CORE | Summary: PHYB participates in jasmonic acid signaling pathways, likely through modulation of hormone-responsive gene expression. This represents cross-talk between light and hormone signaling. Reason: Jasmonic acid signaling represents cross-talk between light and hormone pathways. While experimentally supported, this is a secondary signaling function rather than core photoreceptor activity. Supporting Evidence: PMID:19251652 phytochrome inactivation by FR caused a strong reduction of plant sensitivity to jasmonates |
| GO:0031347 regulation of defense response | IMP PMID:19251652 Ecological modulation of plant defense via phytochrome contr... | KEEP AS NON CORE | Summary: PHYB regulates plant defense responses through modulation of defense-related gene expression and hormone signaling. This represents a secondary regulatory function. Reason: Defense response regulation is a secondary function of PHYB related to its pleiotropic effects on gene expression. While important for plant fitness, this represents a non-core function. Supporting Evidence: PMID:19251652 phytochrome inactivation by FR caused a strong reduction of plant sensitivity to jasmonates, which are key regulators of plant immunity |
| 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: PHYB influences circadian regulation of calcium oscillations as part of its role in circadian clock input. This represents a specific aspect of circadian regulation. Reason: Circadian calcium regulation is a secondary function related to PHYB role in circadian entrainment. While experimentally supported, it represents a specific downstream circadian effect. Supporting Evidence: PMID:17982000 Red light signaling is mediated by PHYTOCHROME B (PHYB) |
| GO:0010161 red light signaling pathway | IMP PMID:17076805 phyA dominates in transduction of red-light signals to rapid... | ACCEPT | Summary: Red light signaling pathway is the core biological process that defines PHYB function. As the primary red light photoreceptor, PHYB is central to this pathway that controls photomorphogenesis and light-responsive gene expression. Reason: Red light signaling is the core biological process for PHYB function. In this study phyA dominates early red-light-responsive gene expression and phyB has a minor role when phyA is present, but phyB assumes a larger role in its absence and phyA and phyB together account for nearly all red-light responsiveness of these genes; phyB mutants were assayed directly. Supporting Evidence: PMID:17076805 phyA and phyB combined are responsible for the full extent of Rc responsiveness of 96% of these genes |
| GO:0009687 abscisic acid metabolic process | IMP PMID:17010113 Regulation of hormone metabolism in Arabidopsis seeds: phyto... | KEEP AS NON CORE | Summary: PHYB influences abscisic acid metabolism through regulation of ABA-related genes. This represents cross-talk between light and hormone signaling pathways. Reason: ABA metabolism regulation is a secondary function related to hormone signaling cross-talk. While experimentally supported, this represents an indirect effect rather than core photoreceptor function. Supporting Evidence: PMID:17010113 PHYB-mediated regulation of ABA metabolism |
| GO:0010029 regulation of seed germination | IMP PMID:17010113 Regulation of hormone metabolism in Arabidopsis seeds: phyto... | KEEP AS NON CORE | Summary: PHYB regulates seed germination through light perception and signaling pathways that control germination responses. This is an important developmental process under PHYB control. Reason: Seed germination regulation is an important but secondary developmental function of PHYB. While biologically significant, it represents a specific developmental outcome rather than core photoreceptor function. Supporting Evidence: PMID:17010113 ABA metabolism (both biosynthesis and inactivation) was phytochrome-regulated in an opposite fashion to GA metabolism during photoreversible seed germination |
| GO:0005634 nucleus | IDA PMID:10225946 Light-dependent translocation of a phytochrome B-GFP fusion ... | ACCEPT | Summary: This is a landmark study demonstrating light-dependent nuclear translocation of PHYB using GFP fusion proteins. Direct experimental evidence for nuclear localization fundamental to PHYB function. Reason: Direct experimental evidence (IDA) from a foundational study showing light-dependent nuclear translocation. Nuclear localization is essential for PHYB transcriptional regulatory function. Supporting Evidence: PMID:10225946 the phyB-GFP fusion protein was localized to the nucleus in light grown tissues |
| GO:0005634 nucleus | IDA PMID:15823535 Regulation of phytochrome B nuclear localization through lig... | ACCEPT | Summary: Nuclear localization demonstrated by direct experimental evidence. Consistent with the well-established nuclear function of light-activated PHYB in gene regulation. Reason: Direct experimental evidence for nuclear localization. Nuclear function is fundamental to PHYB signaling mechanism and well-supported across multiple studies. Supporting Evidence: PMID:15823535 Regulation of phytochrome B nuclear localization through light-dependent unmasking of nuclear-localization signals |
| GO:0009409 response to cold | IMP PMID:12148528 Light signalling mediated by phytochrome plays an important ... | KEEP AS NON CORE | Summary: PHYB mediates cold responses through light signaling pathways that interact with cold-responsive gene expression. This study showed PHYB role in cold-induced gene expression. Reason: Cold response is a secondary environmental response function of PHYB. While experimentally supported, temperature sensing represents an additional role beyond core light perception. Supporting Evidence: PMID:12148528 Light signalling mediated by phytochrome plays an important role in cold-induced gene expression |
| GO:0009630 gravitropism | IMP PMID:15695459 The roles of phytochromes in elongation and gravitropism of ... | KEEP AS NON CORE | Summary: PHYB influences gravitropic responses through interactions with gravity sensing pathways. This represents cross-talk between light and gravity signaling systems. Reason: Gravitropism is a secondary function representing cross-talk between light and gravity sensing. While experimentally supported, this is not a core photoreceptor function. Supporting Evidence: PMID:15695459 phytochromes play in gravitropism and elongation of roots |
| GO:0009638 phototropism | IMP PMID:14686433 Phytochromes play a role in phototropism and gravitropism in... | KEEP AS NON CORE | Summary: PHYB contributes to phototropic responses through modulation of light directional growth responses. This represents interaction between different light sensing pathways. Reason: Phototropism is primarily mediated by phototropins, with PHYB playing a modulatory role. While experimentally supported, this represents a secondary function rather than core PHYB activity. Supporting Evidence: PMID:14686433 Phytochromes play a role in phototropism and gravitropism in Arabidopsis roots |
| GO:0009649 entrainment of circadian clock | IMP PMID:12177480 The out of phase 1 mutant defines a role for PHYB in circadi... | KEEP AS NON CORE | Summary: PHYB plays an important role in circadian clock entrainment by providing light input to reset circadian rhythms. This study shows altered circadian timing in phyB mutants, demonstrating its role in circadian regulation. Reason: Circadian entrainment is an important but secondary function of PHYB. While well-supported, it represents a downstream consequence of light perception rather than the core photoreceptor function. Supporting Evidence: PMID:12177480 The out of phase 1 mutant defines a role for PHYB in circadian phase control in Arabidopsis |
| GO:0009883 red or far-red light photoreceptor activity | IMP PMID:12177480 The out of phase 1 mutant defines a role for PHYB in circadi... | ACCEPT | Summary: Red or far-red light photoreceptor activity is the most fundamental molecular function of PHYB. This annotation captures the core photoreceptor activity with experimental evidence. Reason: This is the most fundamental molecular function of PHYB - red/far-red light photoreceptor activity. Represents the core defining activity with strong experimental support. Supporting Evidence: PMID:12177480 The out of phase 1 mutant defines a role for PHYB in circadian phase control in Arabidopsis |
| GO:0010202 response to low fluence red light stimulus | IMP PMID:9351250 The VLF loci, polymorphic between ecotypes Landsberg erecta ... | ACCEPT | Summary: Response to low fluence red light is a specific and important aspect of PHYB photoreceptor function. PHYB shows high sensitivity to low fluence red light, which is critical for detecting light quality changes. Reason: Low fluence red light response is a specific and important aspect of PHYB photoreceptor function. This represents a key characteristic of PHYB sensitivity and signaling with experimental support. Supporting Evidence: PMID:9351250 The VLF loci, polymorphic between ecotypes Landsberg erecta and Columbia, dissect two branches of phytochrome A signal transduction that correspond to very-low-fluence and high-irradiance responses |
| GO:0000155 phosphorelay sensor kinase activity | IBA GO_REF:0000033 | REMOVE | Summary: IBA from PTN000703785, a deep histidine kinase node. Plant phytochromes carry a C-terminal histidine kinase-related domain (HKRD) that lacks residues critical to histidine kinase activity, so PHYB does not autophosphorylate on histidine or pass a phosphate to an aspartate. Both the GO definition of phosphorelay sensor kinase activity and that of phosphorelay signal transduction system require that His-to-Asp phosphotransfer. Reason: The function is real at the node but was lost in the plant phytochrome lineage: target-specific divergence (loss of HK catalytic residues) is documented, so the propagation does not apply to PHYB. Propagation Review Root cause: PROPAGATION BAD Failure modes: PSEUDO OR SUBACTIVITY LOSS Sources checked: PANTHER:PTN000703785 · histidine kinase superfamily node SUPPORTS SOURCE BUT NOT TARGET The GO:0000155 IBD at this deep node is seeded only by canonical two-component histidine kinases (E. coli, S. pombe, Dictyostelium, Arabidopsis cytokinin/ethylene-pathway HKs); no phytochrome is among the seeds, and the plant phytochrome clade lost the catalytic residues. Supporting Evidence: PMID:19286967 plant phys have unique C termini that contain two PAS domains and a region homologous to two-component histidine kinases but lacking residues critical to HK activity |
| GO:0000160 phosphorelay signal transduction system | IBA GO_REF:0000033 | REMOVE | Summary: IBA from PTN000703785, a deep histidine kinase node. Plant phytochromes carry a C-terminal histidine kinase-related domain (HKRD) that lacks residues critical to histidine kinase activity, so PHYB does not autophosphorylate on histidine or pass a phosphate to an aspartate. Both the GO definition of phosphorelay sensor kinase activity and that of phosphorelay signal transduction system require that His-to-Asp phosphotransfer. Reason: PHYB signals by light-dependent interaction with and destabilization of PIF transcription factors, not by a His-Asp phosphorelay; the node-level function does not apply to the plant phytochrome clade. This replaces the earlier IEA (GO_REF:0000108) row for the same term, which is no longer in GOA and had been ACCEPTed here (KEEP_AS_NON_CORE in the retired P14713 duplicate). Propagation Review Root cause: PROPAGATION BAD Failure modes: PSEUDO OR SUBACTIVITY LOSS Sources checked: PANTHER:PTN000703785 · histidine kinase superfamily node SUPPORTS SOURCE BUT NOT TARGET The GO:0000160 IBD at this deep node is seeded only by canonical two-component histidine kinases (E. coli, S. pombe, Dictyostelium, Arabidopsis cytokinin/ethylene-pathway HKs); no phytochrome is among the seeds, and the plant phytochrome clade lost the catalytic residues. Supporting Evidence: PMID:19286967 plant phys have unique C termini that contain two PAS domains and a region homologous to two-component histidine kinases but lacking residues critical to HK activity |
| GO:0005515 protein binding | IPI PMID:12006496 PIF4, a phytochrome-interacting bHLH factor, functions as a ... | REMOVE | Summary: Generic protein binding annotation that contributes to the extensive redundancy of similar PHYB interaction annotations. Lacks functional specificity compared to more detailed interaction terms. Reason: Per-partner GOA row (with UniProtKB:Q8W2F3-2) newly split out from the existing row for the same paper. The interaction is not in doubt, but under the GO:0005515 policy a bare protein binding row carries no functional information, so a newly reviewed row is REMOVEd, consistent with the sibling row for this paper. Supporting Evidence: PMID:12006496 PIF4, a phytochrome-interacting bHLH factor, functions as a negative regulator of phytochrome B signaling in Arabidopsis. |
| GO:0005515 protein binding | IPI PMID:15273290 Heterodimerization of type II phytochromes in Arabidopsis. | REMOVE | Summary: This study demonstrated heterodimerization between PHYB and other phytochrome family members (PHYC, PHYD, PHYE). This protein binding represents an important regulatory mechanism, but the generic term is less informative than the specific heterodimerization activity. Reason: Per-partner GOA row (with UniProtKB:P42497) newly split out from the existing row for the same paper. The interaction is not in doubt, but under the GO:0005515 policy a bare protein binding row carries no functional information, so a newly reviewed row is REMOVEd, consistent with the sibling row for this paper. Supporting Evidence: PMID:15273290 Heterodimerization of type II phytochromes in Arabidopsis |
| GO:0005515 protein binding | IPI PMID:15273290 Heterodimerization of type II phytochromes in Arabidopsis. | REMOVE | Summary: This study demonstrated heterodimerization between PHYB and other phytochrome family members (PHYC, PHYD, PHYE). This protein binding represents an important regulatory mechanism, but the generic term is less informative than the specific heterodimerization activity. Reason: Per-partner GOA row (with UniProtKB:P42498) newly split out from the existing row for the same paper. The interaction is not in doubt, but under the GO:0005515 policy a bare protein binding row carries no functional information, so a newly reviewed row is REMOVEd, consistent with the sibling row for this paper. Supporting Evidence: PMID:15273290 Heterodimerization of type II phytochromes in Arabidopsis |
| GO:0005515 protein binding | IPI PMID:15448264 Phytochrome-interacting factor 1 is a critical bHLH regulato... | REMOVE | Summary: This study showed PHYB interaction with PIF1, a critical transcription factor in light signaling. PIF1 is one of the key regulatory targets of PHYB that controls chlorophyll biosynthesis and photomorphogenesis. Reason: Per-partner GOA row (with UniProtKB:Q8GZM7) newly split out from the existing row for the same paper. The interaction is not in doubt, but under the GO:0005515 policy a bare protein binding row carries no functional information, so a newly reviewed row is REMOVEd, consistent with the sibling row for this paper. Supporting Evidence: PMID:15448264 Phytochrome-interacting factor 1 is a critical bHLH regulator of chlorophyll biosynthesis |
| GO:0005515 protein binding | IPI PMID:15448264 Phytochrome-interacting factor 1 is a critical bHLH regulato... | REMOVE | Summary: This study showed PHYB interaction with PIF1, a critical transcription factor in light signaling. PIF1 is one of the key regulatory targets of PHYB that controls chlorophyll biosynthesis and photomorphogenesis. Reason: Per-partner GOA row (with UniProtKB:Q8W2F3-2) newly split out from the existing row for the same paper. The interaction is not in doubt, but under the GO:0005515 policy a bare protein binding row carries no functional information, so a newly reviewed row is REMOVEd, consistent with the sibling row for this paper. Supporting Evidence: PMID:15448264 Phytochrome-interacting factor 1 is a critical bHLH regulator of chlorophyll biosynthesis |
| GO:0005515 protein binding | IPI PMID:15486100 A novel molecular recognition motif necessary for targeting ... | REMOVE | Summary: Generic protein binding annotation adding to the redundancy of multiple similar PHYB interaction terms. Does not provide specific functional insight beyond other binding annotations. Reason: Per-partner GOA row (with UniProtKB:Q8W2F3-2) newly split out from the existing row for the same paper. The interaction is not in doubt, but under the GO:0005515 policy a bare protein binding row carries no functional information, so a newly reviewed row is REMOVEd, consistent with the sibling row for this paper. Supporting Evidence: PMID:15486100 PIF5 and PIF6, that specifically bind phyB in the Pfr form |
| GO:0005515 protein binding | IPI PMID:15486102 PIL5, a phytochrome-interacting basic helix-loop-helix prote... | REMOVE | Summary: Another generic protein binding annotation that adds to the extensive redundancy of similar PHYB interaction terms without providing specific functional details. Reason: Per-partner GOA row (with UniProtKB:Q8GZM7) newly split out from the existing row for the same paper. The interaction is not in doubt, but under the GO:0005515 policy a bare protein binding row carries no functional information, so a newly reviewed row is REMOVEd, consistent with the sibling row for this paper. Supporting Evidence: PMID:15486102 PIL5, a phytochrome-interacting basic helix-loop-helix protein, is a key negative regulator of seed germination in Arabidopsis thaliana |
| GO:0005515 protein binding | IPI PMID:19286967 Obligate heterodimerization of Arabidopsis phytochromes C an... | REMOVE | Summary: Generic protein binding annotation for PHYB interactions. Given the extensive number of similar annotations, this contributes to over-annotation without providing specific functional insights. Reason: Per-partner GOA row (with UniProtKB:P14714) newly split out from the existing row for the same paper. The interaction is not in doubt, but under the GO:0005515 policy a bare protein binding row carries no functional information, so a newly reviewed row is REMOVEd, consistent with the sibling row for this paper. Supporting Evidence: PMID:19286967 Obligate heterodimerization of Arabidopsis phytochromes C and E and interaction with the PIF3 basic helix-loop-helix transcription factor. |
| GO:0005515 protein binding | IPI PMID:19286967 Obligate heterodimerization of Arabidopsis phytochromes C an... | REMOVE | Summary: Generic protein binding annotation for PHYB interactions. Given the extensive number of similar annotations, this contributes to over-annotation without providing specific functional insights. Reason: Per-partner GOA row (with UniProtKB:P42497) newly split out from the existing row for the same paper. The interaction is not in doubt, but under the GO:0005515 policy a bare protein binding row carries no functional information, so a newly reviewed row is REMOVEd, consistent with the sibling row for this paper. Supporting Evidence: PMID:19286967 Obligate heterodimerization of Arabidopsis phytochromes C and E and interaction with the PIF3 basic helix-loop-helix transcription factor. |
| GO:0005515 protein binding | IPI PMID:19286967 Obligate heterodimerization of Arabidopsis phytochromes C an... | REMOVE | Summary: Generic protein binding annotation for PHYB interactions. Given the extensive number of similar annotations, this contributes to over-annotation without providing specific functional insights. Reason: Per-partner GOA row (with UniProtKB:P42498) newly split out from the existing row for the same paper. The interaction is not in doubt, but under the GO:0005515 policy a bare protein binding row carries no functional information, so a newly reviewed row is REMOVEd, consistent with the sibling row for this paper. Supporting Evidence: PMID:19286967 Obligate heterodimerization of Arabidopsis phytochromes C and E and interaction with the PIF3 basic helix-loop-helix transcription factor. |
| GO:0005515 protein binding | IPI PMID:21928113 Dimerization and blue light regulation of PIF1 interacting b... | REMOVE | Summary: Generic protein binding annotation that adds to the redundancy of numerous similar PHYB interaction annotations without providing functional specificity. Reason: Per-partner GOA row (with UniProtKB:Q8GZM7) newly split out from the existing row for the same paper. The interaction is not in doubt, but under the GO:0005515 policy a bare protein binding row carries no functional information, so a newly reviewed row is REMOVEd, consistent with the sibling row for this paper. Supporting Evidence: PMID:21928113 Dimerization and blue light regulation of PIF1 interacting bHLH proteins in Arabidopsis |
| GO:0005515 protein binding | IPI PMID:22904146 The phytochrome-interacting vascular plant one-zinc finger1 ... | REMOVE | Summary: This study demonstrated PHYB interactions with VOZ1 and VOZ2 transcription factors in flowering regulation. However, the generic protein binding term is less informative than the specific flowering regulation process. Reason: Per-partner GOA row (with UniProtKB:Q9SGQ0) newly split out from the existing row for the same paper. The interaction is not in doubt, but under the GO:0005515 policy a bare protein binding row carries no functional information, so a newly reviewed row is REMOVEd, consistent with the sibling row for this paper. Supporting Evidence: PMID:22904146 The phytochrome-interacting VASCULAR PLANT ONE-ZINC FINGER1 and VOZ2 redundantly regulate flowering in Arabidopsis |
| GO:0005515 protein binding | IPI PMID:22904146 The phytochrome-interacting vascular plant one-zinc finger1 ... | REMOVE | Summary: This study demonstrated PHYB interactions with VOZ1 and VOZ2 transcription factors in flowering regulation. However, the generic protein binding term is less informative than the specific flowering regulation process. Reason: Per-partner GOA row (with UniProtKB:Q9SLB9) newly split out from the existing row for the same paper. The interaction is not in doubt, but under the GO:0005515 policy a bare protein binding row carries no functional information, so a newly reviewed row is REMOVEd, consistent with the sibling row for this paper. Supporting Evidence: PMID:22904146 The phytochrome-interacting VASCULAR PLANT ONE-ZINC FINGER1 and VOZ2 redundantly regulate flowering in Arabidopsis |
| GO:0005515 protein binding | IPI PMID:26724867 Cryptochromes Interact Directly with PIFs to Control Plant G... | REMOVE | Summary: This study demonstrated PHYB interactions with PIF4 and PIF5 in blue light responses. While functionally significant, the generic protein binding term contributes to annotation redundancy. Reason: Per-partner GOA row (with UniProtKB:Q8W2F3) newly split out from the existing row for the same paper. The interaction is not in doubt, but under the GO:0005515 policy a bare protein binding row carries no functional information, so a newly reviewed row is REMOVEd, consistent with the sibling row for this paper. Supporting Evidence: PMID:26724867 Cryptochromes interact directly with PIFs to control plant growth in limiting blue light |
| GO:0005515 protein binding | IPI PMID:29263319 PCH1 and PCHL promote photomorphogenesis in plants by contro... | REMOVE | Summary: This study demonstrated PHYB interaction with PCH1 and PCHL proteins that control dark reversion. While functionally important, the generic protein binding term adds to annotation redundancy. Reason: Per-partner GOA row (with UniProtKB:Q84V03) newly split out from the existing row for the same paper. The interaction is not in doubt, but under the GO:0005515 policy a bare protein binding row carries no functional information, so a newly reviewed row is REMOVEd, consistent with the sibling row for this paper. Supporting Evidence: PMID:29263319 the homologous phyB-binding proteins PCH1 and PCHL suppress phyB dark reversion |
| GO:0005515 protein binding | IPI PMID:36282917 SWAP1-SFPS-RRC1 splicing factor complex modulates pre-mRNA s... | REMOVE | Summary: This study showed PHYB interaction with SWAP1 in splicing regulation. However, the generic protein binding annotation is less informative than the specific splicing regulatory function. Reason: Per-partner GOA row (with UniProtKB:O49570) newly split out from the existing row for the same paper. The interaction is not in doubt, but under the GO:0005515 policy a bare protein binding row carries no functional information, so a newly reviewed row is REMOVEd, consistent with the sibling row for this paper. Supporting Evidence: PMID:36282917 SWAP1-SFPS-RRC1 splicing factor complex modulates pre-mRNA splicing to promote photomorphogenesis in Arabidopsis |
| GO:0005737 cytoplasm | EXP PMID:15707897 Phytochrome-specific type 5 phosphatase controls light signa... | ACCEPT | Summary: Experimental localization of PHYB to the cytoplasm, where the inactive Pr form resides in darkness. The cached record for PMID:15707897 is abstract-only and the abstract is about PAPP5 dephosphorylation of Pfr-phytochromes, so the localization data cannot be checked here. Reason: The location is well established for PHYB (see the IEA and IDA rows for the same compartments), so the curator's experimental annotation is accepted without the full text. |
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | REMOVE | Summary: IBA from PTN000703785, seeded by membrane-anchored two-component histidine kinases (E. coli sensor kinases, Arabidopsis AHK3 and CKI1). PHYB is soluble and localizes to the cytoplasm and nucleus. Reason: The seeds are membrane-bound because of their transmembrane sensor domains, which plant phytochromes do not have; there is no evidence that PHYB is at the plasma membrane. Propagation Review Root cause: PROPAGATION BAD Failure modes: COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN000703785 · histidine kinase superfamily node SUPPORTS SOURCE BUT NOT TARGET Plasma membrane IBD seeded by transmembrane sensor histidine kinases; the soluble plant phytochrome clade does not share the membrane anchor. |
| GO:0005886 plasma membrane | ISM GO_REF:0000122 | REMOVE | Summary: AtSubP prediction of plasma membrane localization. PHYB is a soluble protein that shuttles between cytoplasm and nucleus; there is no experimental evidence for plasma membrane localization. Reason: Adopted from the retired duplicate review genes/ARATH/P14713, which reviewed this row (it was absent from this file's older GOA snapshot): the ISM prediction has no experimental support and conflicts with the established cytoplasm/nucleus localization. |
| GO:0006979 response to oxidative stress | IMP PMID:36401805 Phytochrome B regulates reactive oxygen signaling during abi... | KEEP AS NON CORE | Summary: phyB mutants are impaired in ROS accumulation and signaling in response to several abiotic and biotic stresses. GOA now records this paper as response to oxidative stress, replacing the earlier hydrogen peroxide mediated signaling pathway row. Reason: Experimentally supported but downstream of PHYB's photoreceptor role; kept non-core, matching the verdict on the retired GO:0071588 row for the same paper. Supporting Evidence: PMID:36401805 phyB is also required for ROS accumulation in response to heat, wounding, cold, and bacterial infection |
| GO:0009585 red, far-red light phototransduction | IEA GO_REF:0000002 | ACCEPT | Summary: Red, far-red light phototransduction is the core biological process that defines PHYB function. This represents the primary process by which PHYB detects and transduces red/far-red light signals into cellular responses. Reason: This is the most fundamental biological process for PHYB - red/far-red light phototransduction. Represents the core function that distinguishes PHYB from other photoreceptors. (Carried over from the GO_REF:0000120 row for the same term, which GOA now supplies via GO_REF:0000002.) Supporting Evidence: PMID:10466729 The phytochrome photoreceptor family directs plant gene expression by switching between biologically inactive and active conformers in response to the sequential absorption of red and farred photons file:ARATH/PHYB/PHYB-deep-research-falcon.md PHYB exists in two interconvertible forms: - **Pr**: inactive state. - **Pfr**: active state produced by red light; far-red light drives reversion. The biologically active **Pfr** accumulates in the nucleus and is associated with downstream signaling, including photobody formation and transcriptional regulation. |
| GO:0009638 phototropism | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: PAINT places phototropism at the plant phytochrome node PTN005179043, seeded by PHYA and PHYB. Reason: Matches the KEEP_AS_NON_CORE verdict on the IMP phototropism row (PMID:14686433): phototropism is driven by phototropins, and PHYB has a modulatory role. |
| GO:0009881 photoreceptor activity | IEA GO_REF:0000002 | ACCEPT | Summary: Photoreceptor activity is the fundamental molecular function of PHYB. As the primary red light photoreceptor in Arabidopsis, this annotation correctly captures the core activity of the protein. Reason: Photoreceptor activity is the most fundamental molecular function of PHYB. Well-established as the predominant red light photoreceptor controlling photomorphogenesis in Arabidopsis. (Carried over from the GO_REF:0000120 row for the same term, which GOA now supplies via GO_REF:0000002.) Supporting Evidence: PMID:24982198 Many aspects of plant photomorphogenesis are controlled by the phytochrome (Phy) family of bilin-containing photoreceptors that detect red and far-red light file:ARATH/PHYB/PHYB-deep-research-falcon.md PHYB is a **red/far-red photoreceptor** that reversibly interconverts between inactive **Pr** and active **Pfr** states. |
| GO:0016607 nuclear speck | EXP PMID:15707897 Phytochrome-specific type 5 phosphatase controls light signa... | ACCEPT | Summary: Experimental localization of PHYB to the nuclear speckles (photobodies) formed by photoactivated Pfr. The cached record for PMID:15707897 is abstract-only and the abstract is about PAPP5 dephosphorylation of Pfr-phytochromes, so the localization data cannot be checked here. Reason: The location is well established for PHYB (see the IEA and IDA rows for the same compartments), so the curator's experimental annotation is accepted without the full text. |
| GO:0031516 far-red light photoreceptor activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT places far-red light photoreceptor activity at the plant phytochrome node PTN005179043, seeded by PHYA (AT1G09570) and PHYB itself (AT2G18790). Reason: Consistent with the ACCEPTed IDA row for the same term (PMID:23321421). PHYB appearing among the seeds reflects its own experimental annotation, as expected for an IBD-derived IBA. |
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Download this section (compressed HTML)Q: What are the precise molecular mechanisms governing photobody assembly and disassembly kinetics in different light conditions?
Suggested experts: Plant photobiology researchers, Protein complex assembly specialists
Q: How do different phosphorylation sites on PHYB differentially regulate PIF interaction specificity and nuclear body formation?
Suggested experts: Plant protein modification experts, Phytochrome signaling researchers
Q: The plant HKRD lacks residues required for histidine kinase activity; does the OPM support the Ser/Thr protein kinase activity that has been proposed, but not firmly established, for plant phytochromes, and if so what are its structural determinants and in vivo substrates?
Suggested experts: Structural biologists, Plant kinase researchers
Q: How does the PSM-OPM inter-domain communication regulate light-dependent conformational changes?
Suggested experts: Protein conformational dynamics researchers, Phytochrome structural biologists
Experiment: Generate phosphomimetic and phosphodeficient mutants of key PHYB phosphorylation sites and analyze nuclear body formation using live-cell imaging under different light conditions. Compare photobody dynamics, size, and PIF sequestration capacity.
Hypothesis: PHYB phosphorylation status controls the formation and dissolution of nuclear photobodies
Experiment: Use FRET-based biosensors with fluorophores positioned in PSM and OPM domains to monitor real-time conformational changes during red/far-red light treatments. Combine with hydrogen-deuterium exchange mass spectrometry to map conformational flexibility.
Hypothesis: The PSM and OPM domains undergo conformational coupling during Pr-to-Pfr photoconversion
Experiment: Generate PHYB mutants defective in the proposed Ser/Thr kinase activity and analyze genome-wide chromatin accessibility changes using ATAC-seq and RNA-seq under different light conditions. Compare with wild-type PHYB to identify kinase-dependent vs. kinase-independent functions.
Hypothesis: If the Ser/Thr protein kinase activity proposed for plant phytochromes is real (histidine kinase activity is excluded by the HKRD sequence), it contributes to PHYB-dependent chromatin organization and gene expression regulation
Experiment: Use single-molecule tracking and fluorescence recovery after photobleaching (FRAP) to measure binding kinetics of different PIF proteins to PHYB photobodies. Correlate binding dynamics with transcriptional output of PIF target genes.
Hypothesis: Different PIF family members have distinct binding affinities and residence times with PHYB in photobodies
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