PHYB phytochrome B [Arabidopsis thaliana (thale cress)] - Gene

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_003071.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003071.7

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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

MASC_STS15697 (e-PCR)
- UniSTS:258820

NM_127435.4

Supported by ESTs:

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

NC_003071.7 Reference assembly

Range

8139756..8144461

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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