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    PHYA phytochrome A [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 837483, updated on 18-Sep-2024

    Summary

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    Official Symbol
    PHYA
    Official Full Name
    phytochrome A
    Primary source
    TAIR:AT1G09570
    Locus tag
    AT1G09570
    See related
    Araport:AT1G09570
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Arabidopsis thaliana (ecotype: Columbia)
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
    Also known as
    ELONGATED HYPOCOTYL 8; F14J9.23; F14J9_23; FAR RED ELONGATED 1; FAR RED ELONGATED HYPOCOTYL 2; FHY2; FRE1; HY8; phytochrome A
    Summary
    Light-labile cytoplasmic red/far-red light photoreceptor involved in the regulation of photomorphogenesis. It exists in two inter-convertible forms: Pr and Pfr (active) and functions as a dimer.The N terminus carries a single tetrapyrrole chromophore, and the C terminus is involved in dimerization. It is the sole photoreceptor mediating the FR high irradiance response (HIR). Major regulator in red-light induction of phototropic enhancement. Involved in the regulation of de-etiolation. Involved in gravitropism and phototropism. Requires FHY1 for nuclear accumulation.
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    Genomic context

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    See PHYA in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    6
    Sequence:
    Chromosome: 1; NC_003070.9 (3095160..3100819, complement)

    Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene Pectinacetylesterase family protein Neighboring gene germin-like protein 5 Neighboring gene calcium uniporter-like protein (DUF607) Neighboring gene emp24/gp25L/p24 family/GOLD family protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003070.9

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Light-induced degradation of phyA is promoted by transfer of the photoreceptor into the nucleus. Debrieux D, et al. Plant Mol Biol, 2010 Aug. PMID 20473552
    2. Phytochrome A antagonizes PHYTOCHROME INTERACTING FACTOR 1 to prevent over-activation of photomorphogenesis. Krzymuski M, et al. Mol Plant, 2014 Sep. PMID 25009301
    3. In response to partial plant shading, the lack of phytochrome A does not directly induce leaf senescence but alters the fine-tuning of chlorophyll biosynthesis. Brouwer B, et al. J Exp Bot, 2014 Jul. PMID 24604733, Free PMC Article
    4. Transcriptional programs related to phytochrome A function in Arabidopsis seed germination. Ibarra SE, et al. Mol Plant, 2013 Jul. PMID 23292879
    5. Arabidopsis phytochrome a is modularly structured to integrate the multiple features that are required for a highly sensitized phytochrome. Oka Y, et al. Plant Cell, 2012 Jul. PMID 22843485, Free PMC Article

    See all (125) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PHYTOCHROME A controls the DNA damage response and cell death tolerance within the Arabidopsis root meristem.
      Title: PHYTOCHROME A controls the DNA damage response and cell death tolerance within the Arabidopsis root meristem.
    2. The structure of Arabidopsis phytochrome A reveals topological and functional diversification among the plant photoreceptor isoforms.
      Title: The structure of Arabidopsis phytochrome A reveals topological and functional diversification among the plant photoreceptor isoforms.
    3. Mutual upregulation of HY5 and TZP in mediating phytochrome A signaling.
      Title: Mutual upregulation of HY5 and TZP in mediating phytochrome A signaling.
    4. Phytochrome A elevates plant circadian-clock components to suppress shade avoidance in deep-canopy shade.
      Title: Phytochrome A elevates plant circadian-clock components to suppress shade avoidance in deep-canopy shade.
    5. Arabidopsis FHY1 and FHY1-LIKE Are Not Required for Phytochrome A Signal Transduction in the Nucleus.
      Title: Arabidopsis FHY1 and FHY1-LIKE Are Not Required for Phytochrome A Signal Transduction in the Nucleus.
    6. Phytochrome A inhibits shade avoidance responses under strong shade through repressing the brassinosteroid pathway in Arabidopsis.
      Title: Phytochrome A inhibits shade avoidance responses under strong shade through repressing the brassinosteroid pathway in Arabidopsis.
    7. Reversible SUMOylation of FHY1 Regulates Phytochrome A Signaling in Arabidopsis.
      Title: Reversible SUMOylation of FHY1 Regulates Phytochrome A Signaling in Arabidopsis.
    8. Regulation of Sugar and Storage Oil Metabolism by Phytochrome during De-etiolation.
      Title: Regulation of Sugar and Storage Oil Metabolism by Phytochrome during De-etiolation.
    9. These results identify TZP as a positive regulator of phytochrome A (phyA) signaling required for phosphorylation of the phyA photoreceptor, thus suggesting an important role of phosphorylated phyA in inducing the FR light response.
      Title: TANDEM ZINC-FINGER/PLUS3 Is a Key Component of Phytochrome A Signaling.
    10. Three sites in the hinge region of Arabidopsis phyA (i.e., S590, T593, and S602) are essential in regulating phyA function. Mutating all three of these sites to either alanines or aspartic acids impaired phyA function, changed the interactions of mutant phyA with FHY1 and FHL, and delayed the degradation of mutant phyA upon light exposure.
      Title: Hinge region of Arabidopsis phyA plays an important role in regulating phyA function.
    Submit: New GeneRIF Correction See all GeneRIFs (70)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    NM_001123784.1
    NM_001331840.1
    NM_001331841.1
    NM_001331842.1
    NM_001331843.1
    NM_100828.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables far-red light photoreceptor activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables mRNA binding HDA PubMed 
    enables phosphorelay sensor kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein histidine kinase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein homodimerization activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein kinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables red or far-red light photoreceptor activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in detection of visible light IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within gravitropism IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of translation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within photomorphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within phototropism IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within red light signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in red, far-red light phototransduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within response to arsenic-containing substance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to cold IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within response to continuous far red light stimulus by the high-irradiance response system IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to far red light IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within response to far red light ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    acts_upstream_of_or_within response to light stimulus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within response to very low fluence red light stimulus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chloroplast ISM
    Inferred from Sequence Model
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    phytochrome A
    NP_001117256.1
    • phytochrome A (PHYA); CONTAINS InterPro DOMAIN/s: PAC motif (InterPro:IPR001610), Phytochrome, central region (InterPro:IPR013515), Signal transduction histidine kinase, core (InterPro:IPR005467), PAS fold (InterPro:IPR013767), PAS (InterPro:IPR000014), Phytochrome chromophore attachment domain (InterPro:IPR016132), ATPase-like, ATP-binding domain (InterPro:IPR003594), PAS fold-2 (InterPro:IPR013654), Phytochrome (InterPro:IPR001294), Signal transduction histidine kinase, subgroup 1, dimerisation/phosphoacceptor domain (InterPro:IPR003661), Phytochrome chromophore binding site (InterPro:IPR013516), GAF (InterPro:IPR003018); BEST Arabidopsis thaliana protein match is: phytochrome B (TAIR:AT2G18790.1); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink).
    NP_172428.1
    • phytochrome A (PHYA); CONTAINS InterPro DOMAIN/s: Phytochrome, central region (InterPro:IPR013515), Signal transduction histidine kinase, core (InterPro:IPR005467), PAS fold (InterPro:IPR013767), PAS (InterPro:IPR000014), Phytochrome chromophore attachment domain (InterPro:IPR016132), ATPase-like, ATP-binding domain (InterPro:IPR003594), PAS fold-2 (InterPro:IPR013654), Phytochrome A/B/C/D/E (InterPro:IPR012129), Phytochrome (InterPro:IPR001294), Signal transduction histidine kinase, subgroup 1, dimerisation/phosphoacceptor domain (InterPro:IPR003661), Phytochrome chromophore binding site (InterPro:IPR013516), GAF (InterPro:IPR003018); BEST Arabidopsis thaliana protein match is: phytochrome C (TAIR:AT5G35840.1); Has 30353 Blast hits to 29854 proteins in 3804 species: Archae - 337; Bacteria - 24139; Metazoa - 4; Fungi - 596; Plants - 4116; Viruses - 7; Other Eukaryotes - 1154 (source: NCBI BLink).

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_003070.9 Reference assembly

      Range
      3095160..3100819 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_100828.4 → NP_172428.1  phytochrome A [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_172428.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      B3H6K9, P14712
      UniProtKB/TrEMBL
      A0A178W883, A0A5S9THJ0
      Conserved Domains (4) summary
      COG4251
      Location:79 → 586
      COG4251; Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]
      PRK15347
      Location:876 → 1098
      PRK15347; two component system sensor kinase
      cd16932
      Location:1006 → 1117
      HATPase_Phy-like; Histidine kinase-like ATPase domain of plant phytochromes similar to Arabidopsis thaliana Phytochrome A, B, C, D and E
      pfam00989
      Location:621 → 734
      PAS; PAS fold

    2. NM_001331841.1 → NP_001322909.1  phytochrome A [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      B3H6K9, P14712
      UniProtKB/TrEMBL
      A0A178W883, A0A5S9THJ0
      Conserved Domains (4) summary
      COG4251
      Location:79 → 586
      COG4251; Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]
      PRK15347
      Location:876 → 1098
      PRK15347; two component system sensor kinase
      cd16932
      Location:1006 → 1117
      HATPase_Phy-like; Histidine kinase-like ATPase domain of plant phytochromes similar to Arabidopsis thaliana Phytochrome A, B, C, D and E
      pfam00989
      Location:621 → 734
      PAS; PAS fold

    3. NM_001331840.1 → NP_001322906.1  phytochrome A [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1P8AVD9
      Conserved Domains (4) summary
      COG4251
      Location:83 → 590
      COG4251; Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]
      PRK15347
      Location:880 → 1102
      PRK15347; two component system sensor kinase
      cd16932
      Location:1010 → 1121
      HATPase_Phy-like; Histidine kinase-like ATPase domain of plant phytochromes similar to Arabidopsis thaliana Phytochrome A, B, C, D and E
      pfam00989
      Location:625 → 738
      PAS; PAS fold

    4. NM_001331843.1 → NP_001322907.1  phytochrome A [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      B3H6K9, P14712
      UniProtKB/TrEMBL
      A0A178W883, A0A5S9THJ0
      Conserved Domains (4) summary
      COG4251
      Location:79 → 586
      COG4251; Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]
      PRK15347
      Location:876 → 1098
      PRK15347; two component system sensor kinase
      cd16932
      Location:1006 → 1117
      HATPase_Phy-like; Histidine kinase-like ATPase domain of plant phytochromes similar to Arabidopsis thaliana Phytochrome A, B, C, D and E
      pfam00989
      Location:621 → 734
      PAS; PAS fold

    5. NM_001331842.1 → NP_001322908.1  phytochrome A [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      B3H6K9, P14712
      UniProtKB/TrEMBL
      A0A178W883, A0A5S9THJ0
      Conserved Domains (4) summary
      COG4251
      Location:79 → 586
      COG4251; Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]
      PRK15347
      Location:876 → 1098
      PRK15347; two component system sensor kinase
      cd16932
      Location:1006 → 1117
      HATPase_Phy-like; Histidine kinase-like ATPase domain of plant phytochromes similar to Arabidopsis thaliana Phytochrome A, B, C, D and E
      pfam00989
      Location:621 → 734
      PAS; PAS fold

    6. NM_001123784.1 → NP_001117256.1  phytochrome A [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001117256.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      P14712
      Conserved Domains (7) summary
      smart00065
      Location:111 → 296
      GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
      smart00387
      Location:899 → 1010
      HATPase_c; Histidine kinase-like ATPases
      smart00388
      Location:787 → 850
      HisKA; His Kinase A (phosphoacceptor) domain
      cd00130
      Location:521 → 627
      PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
      pfam00360
      Location:311 → 482
      PHY; Phytochrome region
      pfam00989
      Location:513 → 627
      PAS; PAS fold
      pfam08446
      Location:17 → 77
      PAS_2; PAS fold
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P14712.2

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