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    PHYB phytochrome B [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 816394, updated on 8-Oct-2024

    Summary

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    Official Symbol
    PHYB
    Official Full Name
    phytochrome B
    Primary source
    TAIR:AT2G18790
    Locus tag
    AT2G18790
    See related
    Araport:AT2G18790
    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
    HY3; MSF3.17; MSF3_17; OOP1; OUT OF PHASE 1; phytochrome B; PHYTOCHROME B
    Summary
    Red/far-red photoreceptor involved in the regulation of de-etiolation. Exists in two inter-convertible forms: Pr and Pfr (active). Involved in the light-promotion of seed germination and in the shade avoidance response. Promotes seedling etiolation in both the presence and absence of phytochrome A. Overexpression results in etiolation under far-red light. Accumulates in the nucleus after exposure to far red light. The phosphorylation state of the Ser-86 residue of the phytochrome B molecule alters dark reversion of the molecule.
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    Genomic context

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    See PHYB in Genome Data Viewer
    Location:
    chromosome: 2
    Exon count:
    3
    Sequence:
    Chromosome: 2; NC_003071.7 (8139756..8144461)

    Chromosome 2 - NC_003071.7Genomic Context describing neighboring genes Neighboring gene P-loop containing nucleoside triphosphate hydrolases superfamily protein Neighboring gene F-box and associated interaction domains-containing protein Neighboring gene xyloglucan endotransglucosylase/hydrolase 21 Neighboring gene B3 domain protein (DUF313)

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003071.7

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Phytochromes function as thermosensors in Arabidopsis. Jung JH, et al. Science, 2016 Nov 18. PMID 27789797
    2. Phytochrome B promotes branching in Arabidopsis by suppressing auxin signaling. Krishna Reddy S, et al. Plant Physiol, 2014 Mar. PMID 24492336, Free PMC Article
    3. A red and far-red light receptor mutation confers resistance to the herbicide glyphosate. Sharkhuu A, et al. Plant J, 2014 Jun. PMID 24654847, Free PMC Article
    4. phytochrome B Is required for light-mediated systemic control of stomatal development. Casson SA, et al. Curr Biol, 2014 Jun 2. PMID 24835461, Free PMC Article
    5. Crystal structure of the photosensing module from a red/far-red light-absorbing plant phytochrome. Burgie ES, et al. Proc Natl Acad Sci U S A, 2014 Jul 15. PMID 24982198, Free PMC Article

    See all (189) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. RACK1 links phyB and BES1 to coordinate brassinosteroid-dependent root meristem development.
      Title: RACK1 links phyB and BES1 to coordinate brassinosteroid-dependent root meristem development.
    2. Modulation of warm temperature-sensitive growth using a phytochrome B dark reversion variant, phyB[G515E], in Arabidopsis and rice.
      Title: Modulation of warm temperature-sensitive growth using a phytochrome B dark reversion variant, phyB[G515E], in Arabidopsis and rice.
    3. The PHYB-FOF2-VOZ2 module functions to fine-tune flowering in response to changes in light quality by modulating FLC expression in Arabidopsis.
      Title: The PHYB-FOF2-VOZ2 module functions to fine-tune flowering in response to changes in light quality by modulating FLC expression in Arabidopsis.
    4. A cytosol-tethered YHB variant of phytochrome B retains photomorphogenic signaling activity.
      Title: A cytosol-tethered YHB variant of phytochrome B retains photomorphogenic signaling activity.
    5. Modulation of starch synthesis in Arabidopsis via phytochrome B-mediated light signal transduction.
      Title: Modulation of starch synthesis in Arabidopsis via phytochrome B-mediated light signal transduction.
    6. Distinguishing individual photobodies using Oligopaints reveals thermo-sensitive and -insensitive phytochrome B condensation at distinct subnuclear locations.
      Title: Distinguishing individual photobodies using Oligopaints reveals thermo-sensitive and -insensitive phytochrome B condensation at distinct subnuclear locations.
    7. FAR-RED INSENSITIVE 219 and phytochrome B corepress shade avoidance via modulating nuclear speckle formation.
      Title: FAR-RED INSENSITIVE 219 and phytochrome B corepress shade avoidance via modulating nuclear speckle formation.
    8. The Arabidopsis Phytoglobin 2 mediates phytochrome B (phyB) light signaling responses during somatic embryogenesis.
      Title: The Arabidopsis Phytoglobin 2 mediates phytochrome B (phyB) light signaling responses during somatic embryogenesis.
    9. Epidermal phyB requires RRC1 to promote light responses by activating the circadian rhythm.
      Title: Epidermal phyB requires RRC1 to promote light responses by activating the circadian rhythm.
    10. The Arabidopsis endosperm is a temperature-sensing tissue that implements seed thermoinhibition through phyB.
      Title: The Arabidopsis endosperm is a temperature-sensing tissue that implements seed thermoinhibition through phyB.
    Submit: New GeneRIF Correction See all GeneRIFs (116)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    NM_127435.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables far-red light photoreceptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables phosphorelay sensor kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables promoter-specific chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables red light photoreceptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables red or far-red light photoreceptor activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within abscisic acid metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within chromatin organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within circadian regulation of calcium ion oscillation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in defense response to bacterium IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in detection of visible light IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within entrainment of circadian clock IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within gravitropism IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in hydrogen peroxide mediated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within jasmonic acid mediated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within photomorphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within photosynthesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in photosynthetic acclimation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within phototropism IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein-phytochromobilin linkage IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within red light signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of defense response IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of photoperiodism, flowering IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of seed germination IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within response to cold IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to cold IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within response to far red light IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to heat IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within response to light stimulus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to low fluence blue light stimulus by blue low-fluence system IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within response to low fluence red light stimulus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to temperature stimulus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within stomatal complex development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within transpiration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol 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 B
    NP_179469.1
    • phytochrome B (PHYB); 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), Phytochrome chromophore binding site (InterPro:IPR013516), Signal transduction histidine kinase, subgroup 1, dimerisation/phosphoacceptor domain (InterPro:IPR003661), GAF (InterPro:IPR003018); BEST Arabidopsis thaliana protein match is: phytochrome D (TAIR:AT4G16250.1); Has 25059 Blast hits to 24774 proteins in 3701 species: Archae - 266; Bacteria - 19279; Metazoa - 9; Fungi - 493; Plants - 3930; Viruses - 5; Other Eukaryotes - 1077 (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_003071.7 Reference assembly

      Range
      8139756..8144461
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001335612.1 → NP_001325249.1  phytochrome B [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178VXX1, A0A1P8B2L0, A0A384KZ81, Q5G8A3
      Conserved Domains (4) summary
      smart00388
      Location:928 → 991
      HisKA; His Kinase A (phosphoacceptor) domain
      COG4251
      Location:95 → 614
      COG4251; Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]
      pfam00989
      Location:654 → 770
      PAS; PAS fold
      cl00075
      Location:1038 → 1088
      HATPase; Histidine kinase-like ATPase domain

    2. NM_127435.4 → NP_179469.1  phytochrome B [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_179469.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      P14713, Q6S4P0
      UniProtKB/TrEMBL
      A0A178W0V4, B0FWI9
      Conserved Domains (4) summary
      COG4251
      Location:95 → 614
      COG4251; Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]
      cd16932
      Location:1038 → 1149
      HATPase_Phy-like; Histidine kinase-like ATPase domain of plant phytochromes similar to Arabidopsis thaliana Phytochrome A, B, C, D and E
      cl30606
      Location:912 → 1134
      KdpD; K+-sensing histidine kinase KdpD [Signal transduction mechanisms]
      pfam00989
      Location:654 → 770
      PAS; PAS fold
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P14713.1

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