PHYA

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0009416 response to light stimulus	IMP PMID:36508461 A role for brassinosteroid signalling in decision-making pro...	MODIFY	Summary: The original cached abstract describes a light and water limitation decision-making screen but does not provide PHYA-specific support. The essence that PHYA responds to light is correct, but the term is too broad for this gene; PHYA should be captured with far-red signaling/response terms already present in the GOA. Reason: Replace the generic process with PHYA's specific and well-supported far-red light response/signaling role. Proposed replacements: response to far red light far-red light signaling pathway Supporting Evidence: PMID:36508461 combined light and water withdrawal PMID:21969386 PHYA is responsible for the far-red high-irradiance response file:ARATH/PHYA/PHYA-deep-research-falcon.md Arabidopsis phytochrome A (phyA; PHYA, UniProt P14712) is a red/far-red
GO:0009630 gravitropism	IMP PMID:15695459 The roles of phytochromes in elongation and gravitropism of ...	KEEP AS NON CORE	Summary: The cited paper directly assayed phyA, phyB, phyD and phyAB mutant roots for gravitropic curvature and found defects in phyAB double (and phyB) mutants, indicating a redundant PHYA contribution; the phyA single mutant alone was not the supported driver in this or a second root orientation paper. Reason: The cited study explicitly tested phyA-containing mutants for root gravitropism, so the curator's IMP is grounded in the paper and should not be overruled from the abstract; the phyAB double-mutant defect supports a redundant PHYA contribution to red-light modulation of gravitropic curvature. This is a modulatory, partially redundant role rather than a core PHYA function, so it is kept as non-core. Supporting Evidence: PMID:15695459 roots of phytochrome mutants of Arabidopsis (phyA, phyB, phyD and PMID:14686433 phyB and phyAB (but not phyA) were inhibited
GO:0009638 phototropism	IMP PMID:14686433 Phytochromes play a role in phototropism and gravitropism in...	KEEP AS NON CORE	Summary: Root phototropism is experimentally supported: phyA and phyB single mutants were impaired in red-light-based root phototropism, and phyA also contributed to blue-light negative phototropism. This is a valid light-dependent phenotype, but not the core molecular function of PHYA. Reason: Supported organismal response downstream of PHYA photoreceptor signaling, but secondary to the core far-red photoreceptor/signaling role. Supporting Evidence: PMID:14686433 phyA and phyB mediate the positive red-light-based photoresponse
GO:0009640 photomorphogenesis	IMP PMID:21969386 Missense mutation in the amino terminus of phytochrome A dis...	ACCEPT	Summary: PHYA is a major Arabidopsis photomorphogenesis photoreceptor under far-red and very-low-fluence conditions. The phyA-5 N-terminal mutant reduces PHYA nuclear import and correspondingly reduces hypocotyl and cotyledon responses under far-red light. Reason: Photomorphogenesis is a direct, central biological output of PHYA photoreceptor signaling. Supporting Evidence: PMID:21969386 hyposensitivity to continuous low-intensity far-red light
GO:0010161 red light signaling pathway	IMP PMID:17076805 phyA dominates in transduction of red-light signals to rapid...	KEEP AS NON CORE	Summary: PHYA has a measurable early role in red-light-induced gene expression during de-etiolation, even though PHYA's defining action mode is far-red HIR/VLFR rather than the main red-light responses dominated by PHYB. Reason: Red-light signaling is supported but is secondary to PHYA's core far-red and very-low-fluence signaling functions. Supporting Evidence: PMID:17076805 phyA has a quantitatively dominant role in Rc-induced expression
GO:0010201 response to continuous far red light stimulus by the high-irradiance response system	IMP PMID:9351250 The VLF loci, polymorphic between ecotypes Landsberg erecta ...	ACCEPT	Summary: Continuous far-red high-irradiance response is one of the defining PHYA action modes. The cited genetic dissection shows HIR responses under continuous far-red light absent in phyA mutants. Reason: FR-HIR is a core PHYA biological process. Supporting Evidence: PMID:9351250 Under continuous far-red light, HIR of etiolated seedlings were absent
GO:0010203 response to very low fluence red light stimulus	IMP PMID:9351250 The VLF loci, polymorphic between ecotypes Landsberg erecta ...	ACCEPT	Summary: Very-low-fluence response is another defining PHYA action mode. The cited study reports that the VLFR phase is absent in phyA mutants. Reason: VLFR is a core PHYA signaling response. Supporting Evidence: PMID:9351250 The first phase, i.e. the VLFR, was absent
GO:0017148 negative regulation of translation	IMP PMID:22232680 Phytochrome regulates translation of mRNA in the cytosol.	MARK AS OVER ANNOTATED	Summary: The cited study supports cytosolic translational regulation by phytochromes through PNT1/PORA mRNA, but the cached text emphasizes phyB recruitment and only says PHYA is presumed. This is plausible phytochrome-family biology but not a strong PHYA-specific or core annotation. Reason: The term overstates PHYA-specific direct evidence and should not be treated as a core function of PHYA. Supporting Evidence: PMID:22232680 phyB, and presumably phyA too
GO:0046685 response to arsenic-containing substance	IMP PMID:17335514 Identification of an arsenic tolerant double mutant with a t...	KEEP AS NON CORE	Summary: Loss of PHYA increases arsenic tolerance, indicating genetic crosstalk with arsenic stress responses. This is experimentally supported but is a peripheral stress phenotype rather than PHYA's conserved photoreceptor function. Reason: Retain as a non-core phenotype-level annotation. Supporting Evidence: PMID:17335514 PHYA negatively regulates a pathway conferring arsenic tolerance
GO:0000155 phosphorelay sensor kinase activity	IEA GO_REF:0000002	MODIFY	Summary: PHYA contains a histidine-kinase-like output region, but the experimentally supported Arabidopsis molecular activity is protein kinase activity toward signaling partners such as FHY1, not a bacterial-style phosphorelay sensor kinase activity. Reason: The domain-derived phosphorelay term is too specific and mechanistically misleading for plant PHYA. Proposed replacements: protein kinase activity Supporting Evidence: PMID:19208901 recombinant phyA is able to robustly phosphorylate FHY1 file:interpro/panther/PTHR47876/PTHR47876-metadata.yaml The phytochrome family consists of regulatory photoreceptors
GO:0000155 phosphorelay sensor kinase activity	IBA GO_REF:0000033	MODIFY	Summary: The phylogenetic inference similarly overprojects the ancestral histidine-kinase-like architecture to phosphorelay sensor kinase activity. PHYA's supported output is photoreceptor signaling with protein kinase activity, not a phosphorelay sensor kinase. Reason: Replace with the experimentally supported protein kinase term. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE PSEUDO OR SUBACTIVITY LOSS Sources checked: PANTHER:PTN000703785 · phytochrome/two-component kinase node SUPPORTS SOURCE BUT NOT TARGET The phosphorelay sensor kinase IBD is seeded by bacterial two-component sensor kinases and non-seed-plant phytochrome-like kinases; seed-plant phytochromes carry a degenerate histidine-kinase-related domain and act as serine/threonine kinases, so the His-kinase term does not transfer. Proposed replacements: protein kinase activity Supporting Evidence: PMID:19208901 recombinant phyA is able to robustly phosphorylate FHY1 file:interpro/panther/PTHR47876/PTHR47876-entries.csv P14712,Phytochrome A,protein,3702,Arabidopsis thaliana
GO:0003729 mRNA binding	HDA PMID:27729395 In Planta Determination of the mRNA-Binding Proteome of Arab...	MARK AS OVER ANNOTATED	Summary: The source is an important high-throughput mRNA-protein capture study, but the cached article text does not expose PHYA-specific capture or a mechanistic RNA-binding role. PHYA's domain architecture and primary literature support photoreceptor signaling, not direct mRNA binding. Reason: A high-throughput candidate RNA-binding call should not be retained as a core molecular function without PHYA-specific validation. Supporting Evidence: PMID:27729395 we captured more than 700 proteins
GO:0004672 protein kinase activity	IDA PMID:19208901 Phytochrome A mediates rapid red light-induced phosphorylati...	ACCEPT	Summary: Direct in vitro kinase assays show recombinant PHYA phosphorylates FHY1, and the phosphorylation event depends on functional PHYA in seedlings. This is a supported molecular activity of PHYA, although its biological context is regulatory photoreceptor signaling rather than metabolism. Reason: Experimental evidence directly supports PHYA protein kinase activity toward FHY1. Supporting Evidence: PMID:19208901 recombinant phyA is able to robustly phosphorylate FHY1
GO:0005515 protein binding	IPI PMID:10348744 PKS1, a substrate phosphorylated by phytochrome that modulat...	MARK AS OVER ANNOTATED	Summary: PKS1 binding is supported and biologically relevant to phytochrome signaling, but GO:0005515 is too generic to describe PHYA function. Reason: Generic protein binding should not be retained as a core PHYA MF. Supporting Evidence: PMID:10348744 A phytochrome binding protein, PKS1
GO:0005515 protein binding	IPI PMID:10524631 Phytochrome signalling is mediated through nucleoside diphos...	MARK AS OVER ANNOTATED	Summary: NDPK2 interaction with activated phytochrome is supported, but this annotation captures only a generic interaction instead of PHYA's photoreceptor signaling output. Reason: Generic protein binding is less informative than pathway-specific PHYA annotations. Supporting Evidence: PMID:10524631 preferentially binds to the red-light-activated form of phytochrome
GO:0005515 protein binding	IPI PMID:10995393 HFR1 encodes an atypical bHLH protein that acts in phytochro...	MARK AS OVER ANNOTATED	Summary: HFR1 acts in the phyA pathway but the paper states that HFR1 did not bind phyA or phyB directly in the tested assay. The generic protein binding annotation is therefore not appropriate as a PHYA molecular function. Reason: Evidence supports pathway participation more than a direct PHYA binding function captured by GO:0005515. Supporting Evidence: PMID:10995393 HFR1 did not bind either phyA or B
GO:0005515 protein binding	IPI PMID:11069292 Phytochrome B binds with greater apparent affinity than phyt...	MARK AS OVER ANNOTATED	Summary: PHYA-PIF3 binding is supported, but this specific signaling interaction should not be summarized as a core generic protein-binding activity. Reason: The relevant biology is PHYA phototransduction through PIF regulation, not generic protein binding. Supporting Evidence: PMID:11069292 phyA also binds selectively and reversibly to PIF3
GO:0005515 protein binding	IPI PMID:12006496 PIF4, a phytochrome-interacting bHLH factor, functions as a ...	MARK AS OVER ANNOTATED	Summary: PIF4 is primarily a phyB signaling factor and shows little affinity for phyA. Any PHYA interaction here is weak or indirect, making generic protein binding an over-annotation. Reason: The cited evidence argues against a strong PHYA-PIF4 binding annotation. Supporting Evidence: PMID:12006496 but has little affinity for phyA
GO:0005515 protein binding	IPI PMID:15155879 Constitutive photomorphogenesis 1 and multiple photoreceptor...	MARK AS OVER ANNOTATED	Summary: PIF3 interaction with phyA/phyB is part of early light signaling, but GO:0005515 remains an uninformative annotation relative to phototransduction and PIF degradation outputs. Reason: Generic protein binding overstates the molecular function and obscures the specific photoreceptor signaling mechanism. Supporting Evidence: PMID:15155879 promotes interaction of phytochrome A (phyA) and phyB
GO:0005515 protein binding	IPI PMID:15448264 Phytochrome-interacting factor 1 is a critical bHLH regulato...	MARK AS OVER ANNOTATED	Summary: PIF1 interaction with photoactivated phyA/phyB supports a real signaling interaction, but the annotation should not be treated as a core generic binding function. Reason: Use the PHYA photoreceptor/signaling annotations rather than generic protein binding. Supporting Evidence: PMID:15448264 PIF1 interacts specifically with the photoactivated conformer
GO:0005515 protein binding	IPI PMID:16332538 Nuclear accumulation of the phytochrome A photoreceptor requ...	MARK AS OVER ANNOTATED	Summary: FHY1 directly interacts with PHYA and is essential for PHYA nuclear accumulation. The interaction is important, but GO:0005515 is too generic for a core function. Reason: The specific supported biology is FHY1-dependent PHYA nuclear import. Supporting Evidence: PMID:16332538 FHY1 physically interacts with phyA
GO:0005515 protein binding	IPI PMID:16861711 FHY1 and FHL act together to mediate nuclear accumulation of...	MARK AS OVER ANNOTATED	Summary: FHY1/FHL interaction with PHYA is supported and functionally important for nuclear accumulation, but generic protein binding is not an informative PHYA function term. Reason: Keep the interaction in the evidence narrative, not as a core MF. Supporting Evidence: PMID:16861711 FHL and phyA interact with each other
GO:0005515 protein binding	IPI PMID:18722184 Arabidopsis COP1/SPA1 complex and FHY1/FHY3 associate with d...	MARK AS OVER ANNOTATED	Summary: PHYA association with FHY1/FHY3 and COP1/SPA complexes depends on phosphorylation state and regulates signaling flux. GO:0005515 is too generic for this regulatory mechanism. Reason: Specific complex switching is better described in curation text than by generic protein binding. Supporting Evidence: PMID:18722184 underphosphorylated phyA predominantly associates with
GO:0005515 protein binding	IPI PMID:19208901 Phytochrome A mediates rapid red light-induced phosphorylati...	MARK AS OVER ANNOTATED	Summary: PHYA directly interacts with FHY1/FHL and phosphorylates FHY1, but the generic binding term should not be used as a core molecular function. Reason: The mechanistically informative terms are protein kinase activity and far-red photoreceptor signaling. Supporting Evidence: PMID:19208901 FHY1 and FHL directly interact with phyA
GO:0005515 protein binding	IPI PMID:19286967 Obligate heterodimerization of Arabidopsis phytochromes C an...	MARK AS OVER ANNOTATED	Summary: PHYA interaction with PIF3 after red light is supported, but the term protein binding is too general and redundant with the phototransduction model. Reason: Treat this as evidence for signaling pathway mechanics rather than a separate core MF. Supporting Evidence: PMID:19286967 phyA, phyB, phyC, and phyD interact in vivo
GO:0005515 protein binding	IPI PMID:19482971 FAR-RED ELONGATED HYPOCOTYL1 and FHY1-LIKE associate with th...	MARK AS OVER ANNOTATED	Summary: PHYA/FHY1/FHL/LAF1/HFR1 complexes are supported and important for hypocotyl inhibition in far-red light. The core annotation should capture far-red signaling and photomorphogenesis, not generic protein binding. Reason: Generic binding is redundant and less informative than PHYA signaling process annotations. Supporting Evidence: PMID:19482971 phyA, FHY1, FHL, LAF1, and HFR1
GO:0005515 protein binding	IPI PMID:21884939 Photoconversion and nuclear trafficking cycles determine phy...	MARK AS OVER ANNOTATED	Summary: PHYA-FHY1/FHL nuclear import complex dynamics explain PHYA far-red response properties. This is real pathway biology, but GO:0005515 is a generic over-annotation. Reason: The specific role is nuclear trafficking and far-red signal decoding. Supporting Evidence: PMID:21884939 phyA-FHY1/FHL nuclear import complex
GO:0005515 protein binding	IPI PMID:21969386 Missense mutation in the amino terminus of phytochrome A dis...	MARK AS OVER ANNOTATED	Summary: The phyA-5 mutation weakens binding to FHY1/FHL and impairs nuclear import. This validates the interaction but not generic protein binding as a core function. Reason: Specific PHYA-FHY1/FHL import biology is already captured by localization and far-red signaling reviews. Supporting Evidence: PMID:21969386 weakened binding affinity of the mutant photoreceptor
GO:0005515 protein binding	IPI PMID:22895253 Photoactivated phytochromes interact with HEMERA and promote...	MARK AS OVER ANNOTATED	Summary: PHYA can directly interact with HEMERA/HMR as part of early phytochrome signaling and photobody/PIF-degradation machinery. This is functionally important but too generic as GO:0005515. Reason: The specific output is photomorphogenesis establishment, not generic protein binding. Supporting Evidence: PMID:22895253 HMR is another direct binding partner of both phyA and phyB
GO:0005515 protein binding	IPI PMID:31732705 PHYTOCHROME INTERACTING FACTOR8 Inhibits Phytochrome A-Media...	MARK AS OVER ANNOTATED	Summary: The PIF8 study emphasizes weak or absent direct PIF8 binding to PHYA, while PHYA indirectly stabilizes PIF8 through COP1 inhibition in far-red light. This does not support a useful generic PHYA protein-binding function. Reason: Pathway regulation is supported, but generic direct protein binding is not a strong PHYA annotation here. Supporting Evidence: PMID:31732705 only very weakly, if at all, with that of phyA
GO:0005515 protein binding	IPI PMID:9845368 PIF3, a phytochrome-interacting factor necessary for normal ...	MARK AS OVER ANNOTATED	Summary: PIF3 was identified as a phytochrome-interacting factor and binds PHYA domains, but GO:0005515 is not a sufficiently informative core MF for PHYA. Reason: The interaction supports PHYA signaling to photoregulated genes rather than a standalone protein-binding function. Supporting Evidence: PMID:9845368 PIF3 binds to wild-type C-terminal domains of both phyA
GO:0009881 photoreceptor activity	IEA GO_REF:0000002	MODIFY	Summary: PHYA is unquestionably a photoreceptor, but this parent term is less informative than the existing PHYA-specific far-red and red/far-red photoreceptor terms. Reason: Replace the broad photoreceptor term with the more specific far-red light photoreceptor activity. Proposed replacements: far-red light photoreceptor activity Supporting Evidence: file:ARATH/PHYA/PHYA-uniprot.txt Regulatory photoreceptor which exists in two forms
GO:0009883 red or far-red light photoreceptor activity	TAS PMID:8400877 Arabidopsis HY8 locus encodes phytochrome A.	KEEP AS NON CORE	Summary: PHYA is a red/far-red reversible phytochrome photoreceptor. This term is true but broader than the more specific far-red light photoreceptor activity that captures PHYA's distinguishing role. Reason: Retain as an accurate broad molecular activity, while treating far-red light photoreceptor activity as the core MF. Supporting Evidence: PMID:8400877 hy8 long hypocotyl mutants of Arabidopsis
GO:0031516 far-red light photoreceptor activity	IMP PMID:21969386 Missense mutation in the amino terminus of phytochrome A dis...	ACCEPT	Summary: PHYA is responsible for far-red high-irradiance and very-low-fluence responses, and the phyA-5 mutation disrupts far-red nuclear import and signaling. This is the best specific MF term for PHYA. Reason: Far-red photoreceptor activity is the core molecular function of PHYA. Supporting Evidence: PMID:21969386 PHYA is responsible for the far-red high-irradiance response
GO:0042802 identical protein binding	IEA GO_REF:0000117	MODIFY	Summary: PHYA homodimerization is well supported, but identical protein binding is a less precise way to represent that property. Reason: Use the more informative homodimerization term. Proposed replacements: protein homodimerization activity Supporting Evidence: file:ARATH/PHYA/PHYA-uniprot.txt SUBUNIT: Homodimer.
GO:0042802 identical protein binding	IPI PMID:10348744 PKS1, a substrate phosphorylated by phytochrome that modulat...	MODIFY	Summary: PHYA dimerization is real, but identical protein binding should be replaced by protein homodimerization activity. Reason: Homodimerization is the precise interpretation. Proposed replacements: protein homodimerization activity Supporting Evidence: file:ARATH/PHYA/PHYA-uniprot.txt SUBUNIT: Homodimer.
GO:0042802 identical protein binding	IPI PMID:15273290 Heterodimerization of type II phytochromes in Arabidopsis.	MODIFY	Summary: The dimerization evidence supports the more specific homodimerization/phytochrome-dimer property rather than the generic identical protein binding term. Reason: Replace identical protein binding with homodimerization. Proposed replacements: protein homodimerization activity Supporting Evidence: PMID:15273290 all five of the Arabidopsis phytochromes are present in seedlings as dimers
GO:0042802 identical protein binding	IPI PMID:19286967 Obligate heterodimerization of Arabidopsis phytochromes C an...	MODIFY	Summary: PHYA is described as a homodimer in the phytochrome dimerization study. Identical protein binding is therefore too generic. Reason: Use protein homodimerization activity. Proposed replacements: protein homodimerization activity Supporting Evidence: PMID:19286967 phyA is present only as a homodimer
GO:0042803 protein homodimerization activity	IEA GO_REF:0000002	KEEP AS NON CORE	Summary: PHYA functions as a phytochrome dimer and UniProt summarizes it as a homodimer. This structural property is valid, but is secondary to PHYA's core photoreceptor activity. Reason: Retain as an accurate non-core molecular property. Supporting Evidence: file:ARATH/PHYA/PHYA-uniprot.txt SUBUNIT: Homodimer.
GO:0000160 phosphorelay signal transduction system	IEA GO_REF:0000108	REMOVE	Summary: This process is inferred from the rejected phosphorelay sensor kinase activity annotation. PHYA's histidine-kinase-like region and PANTHER family context support plant phytochrome photoreceptor signaling, not a bacterial-type phosphorelay signal transduction system. Reason: The biological process follows from an inappropriate electronic MF inference and should not be retained for PHYA. Supporting Evidence: file:interpro/panther/PTHR47876/PTHR47876-metadata.yaml Plant Phytochrome Photoreceptors
GO:0006355 regulation of DNA-templated transcription	IEA GO_REF:0000002	ACCEPT	Summary: PHYA regulates transcriptional programs indirectly through PIF factors, COP1/SPA-associated regulators, and PHYA/FHY1/FHL/LAF1/HFR1 complexes. Although PHYA is not a DNA-binding transcription factor, regulation of gene expression is a central downstream output of its photoreceptor signaling. Reason: Retain as a core biological output of PHYA phototransduction, with the caveat that the molecular function is photoreceptor/kinase activity rather than direct DNA binding. Supporting Evidence: PMID:17076805 phyA has a quantitatively dominant role in Rc-induced expression PMID:19482971 culminating in alterations in gene expression
GO:0007165 signal transduction	IEA GO_REF:0000002	MODIFY	Summary: PHYA is a signal-transducing photoreceptor, but the generic signal transduction term is less specific than far-red light signaling pathway and red/far-red phototransduction terms. Reason: Use PHYA-specific light signaling process terms. Proposed replacements: far-red light signaling pathway red, far-red light phototransduction Supporting Evidence: PMID:19208901 key regulatory mechanism in phyA signaling
GO:0009409 response to cold	IEP PMID:23708772 Phytochrome-interacting factors have both shared and distinc...	MARK AS OVER ANNOTATED	Summary: UniProt/GOA attribute a cold-response expression annotation to this PIF review, but the cached full text available here does not contain PHYA-specific cold evidence or PHYA expression data (the cached copy is abstract-only and the PMC full text could not be retrieved). The paper is a PIF-focused review that compared public expression data for responses to various stimuli; the same reference supplies parallel IEP rows (heat, cold, auxin, ABA) for PIF1. Whatever the underlying data, an IEP row of this kind records transcript responsiveness in a meta-analysis, not a role for PHYA in cold responses. Reason: Expression-level responsiveness from a review-level meta-analysis does not establish PHYA participation in a cold response; PHYA function is far-red/red photoreception. Not removed because the underlying expression observation may well be correct. Supporting Evidence: PMID:23708772 responses to various stimuli
GO:0009584 detection of visible light	IEA GO_REF:0000002	ACCEPT	Summary: PHYA detects red/far-red visible light through phytochromobilin-dependent Pr/Pfr photoconversion. The term is broad but accurate as a core process upstream of PHYA signaling. Reason: Visible-light detection is inherent to PHYA photoreceptor activity. Supporting Evidence: PMID:18722184 photoconversion between the red light
GO:0009585 red, far-red light phototransduction	IEA GO_REF:0000002	ACCEPT	Summary: PHYA converts red/far-red light perception into intracellular signaling, including nuclear import and PIF/COP1/FHY pathway regulation. This term accurately captures the phototransduction process. Reason: Red/far-red phototransduction is a core PHYA process. Supporting Evidence: PMID:19208901 red/far-red light reversible phosphorylation
GO:0010018 far-red light signaling pathway	IEA GO_REF:0000108	ACCEPT	Summary: Far-red signaling is the central pathway in which PHYA acts; PHYA-FHY1/FHL nuclear import and downstream transcriptional complexes explain the far-red response. Reason: Far-red signaling is a core PHYA biological process. Supporting Evidence: PMID:21884939 initiating responses in far-red light
GO:0010218 response to far red light	IDA PMID:19482971 FAR-RED ELONGATED HYPOCOTYL1 and FHY1-LIKE associate with th...	ACCEPT	Summary: The PHYA/FHY1/FHL/LAF1/HFR1 complex evidence and far-red hypocotyl phenotypes support PHYA's direct role in far-red light response. Reason: Response to far-red light is a core PHYA process. Supporting Evidence: PMID:19482971 phyA plays a major role in seedling deetiolation
GO:0017006 protein-tetrapyrrole linkage	IEA GO_REF:0000002	KEEP AS NON CORE	Summary: PHYA contains a covalently linked phytochromobilin tetrapyrrole chromophore, which is essential for photoconversion. This is a valid biochemical property/maturation feature, but not the primary signaling function itself. Reason: Retain as a non-core property required for photoreceptor function. Supporting Evidence: file:ARATH/PHYA/PHYA-uniprot.txt Contains one covalently linked phytochromobilin chromophore.
GO:0005634 nucleus	IDA PMID:12119377 Missense mutation in the PAS2 domain of phytochrome A impair...	ACCEPT	Summary: PHYA-GFP translocates from cytosol to nucleus under continuous far-red light, and subnuclear localization affects HIR signaling. Nuclear localization is central to PHYA signaling output. Reason: Light-dependent nuclear accumulation is a core PHYA localization. Supporting Evidence: PMID:12119377 normal translocation from the cytosol to the nucleus
GO:0005634 nucleus	IDA PMID:21969386 Missense mutation in the amino terminus of phytochrome A dis...	ACCEPT	Summary: The phyA-5 study shows that reduced nuclear import causes impaired low-fluence far-red signaling, confirming the functional importance of PHYA nuclear localization. Reason: Nuclear localization is required for effective PHYA signaling. Supporting Evidence: PMID:21969386 reduced nuclear import of phyA-5
GO:0005654 nucleoplasm	IEA GO_REF:0000044	ACCEPT	Summary: UniProt subcellular mapping includes PHYA in the nucleoplasm after light-dependent nuclear translocation. This is compatible with the experimentally supported nuclear signaling site. Reason: Nucleoplasmic localization is an appropriate specific nuclear component for light-activated PHYA. Supporting Evidence: file:ARATH/PHYA/PHYA-uniprot.txt Nucleus, nucleoplasm
GO:0005737 cytoplasm	IEA GO_REF:0000044	ACCEPT	Summary: PHYA is cytoplasmic in darkness and forms the pool from which light induces nuclear import. Cytoplasm is therefore a valid core localization for the dark and trafficking states. Reason: Cytoplasmic localization is an experimentally and UniProt-supported PHYA localization. Supporting Evidence: file:ARATH/PHYA/PHYA-uniprot.txt Cytoplasmic in darkness
GO:0005737 cytoplasm	IDA PMID:12119377 Missense mutation in the PAS2 domain of phytochrome A impair...	ACCEPT	Summary: The cited PHYA localization paper describes PHYA moving from cytosol to nucleus under far-red light, supporting cytoplasmic localization before nuclear import. Reason: Cytoplasm is a real PHYA localization state. Supporting Evidence: PMID:12119377 translocation from the cytosol to the nucleus
GO:0005737 cytoplasm	EXP PMID:15707897 Phytochrome-specific type 5 phosphatase controls light signa...	ACCEPT	Summary: UniProt maps the PMID:15707897 evidence to cytoplasm and nucleus for PHYA/PAPP5-regulated signaling. The broader PHYA literature also supports a dark cytoplasmic pool. Reason: Cytoplasm is an accepted PHYA localization. Supporting Evidence: file:ARATH/PHYA/PHYA-uniprot.txt Cytoplasm {ECO:0000269\|PubMed:15707897
GO:0005737 cytoplasm	EXP PMID:21969386 Missense mutation in the amino terminus of phytochrome A dis...	ACCEPT	Summary: The phyA-5 study directly links impaired nuclear import with cytoplasmic retention under low-Pfr conditions. Reason: Cytoplasmic localization is experimentally supported. Supporting Evidence: PMID:21969386 phyA-5 Pfr is stranded in the cytoplasm
GO:0005886 plasma membrane	ISM GO_REF:0000122	REMOVE	Summary: The AtSubP plasma membrane prediction conflicts with the curated experimental model in which PHYA is a soluble cytoplasmic/nuclear photoreceptor. No PHYA plasma membrane localization evidence was found in the reviewed sources. Reason: Unsupported computational localization prediction. Supporting Evidence: file:ARATH/PHYA/PHYA-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm
GO:0009507 chloroplast	ISM GO_REF:0000122	REMOVE	Summary: The AtSubP chloroplast prediction is not supported by PHYA literature or UniProt. PHYA regulates chloroplast-related gene expression and PORA abundance indirectly, but the photoreceptor itself is curated as cytoplasmic/nuclear rather than chloroplast-localized. Reason: Unsupported computational localization prediction. Supporting Evidence: file:ARATH/PHYA/PHYA-uniprot.txt Cytoplasmic in darkness, but translocated to the nucleus
GO:0016604 nuclear body	IDA PMID:16332538 Nuclear accumulation of the phytochrome A photoreceptor requ...	ACCEPT	Summary: FHY1-dependent nuclear accumulation and colocalization support PHYA localization to light-induced nuclear bodies/photobodies. Reason: Nuclear bodies are a core PHYA signaling localization after illumination. Supporting Evidence: PMID:16332538 FHY1 and phyA colocalize in planta
GO:0016604 nuclear body	IDA PMID:21969386 Missense mutation in the amino terminus of phytochrome A dis...	ACCEPT	Summary: The phyA-5 study monitors PHYA-YFP nuclear import and subnuclear localization, supporting light-induced nuclear-body localization. Reason: Nuclear body/photobody localization is experimentally supported. Supporting Evidence: PMID:21969386 formation of the FHY1/FHL/PHYA
GO:0016607 nuclear speck	IEA GO_REF:0000044	ACCEPT	Summary: UniProt maps PHYA to nuclear speckles, reflecting the experimentally observed light-induced subnuclear bodies associated with signaling and degradation. Reason: Nuclear speckle is a supported specific nuclear localization. Supporting Evidence: file:ARATH/PHYA/PHYA-uniprot.txt Nucleus speckle
GO:0016607 nuclear speck	EXP PMID:15707897 Phytochrome-specific type 5 phosphatase controls light signa...	ACCEPT	Summary: UniProt cites PMID:15707897 for PHYA nuclear speckle localization in the PAPP5 signaling context. This is consistent with other PHYA photobody evidence. Reason: Nuclear speckle localization is retained as a supported PHYA component. Supporting Evidence: file:ARATH/PHYA/PHYA-uniprot.txt Nucleus speckle {ECO:0000269\|PubMed:15707897}

Gene Description

Existing Annotations Review

Core Functions

PHYA also has regulatory protein kinase activity in the light-signaling pathway, shown most directly by recombinant PHYA phosphorylation of FHY1. This activity is interpreted as part of the photoreceptor signaling module rather than as phosphorelay sensor kinase activity.

References

Suggested Questions for Experts

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📚 Additional Documentation

Notes

PHYA (P14712) curation notes

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