PHYD phytochrome D [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: PHYD
Official Full Name: phytochrome D
Primary source: TAIR:AT4G16250
Locus tag: AT4G16250
See related: Araport:AT4G16250
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: DL4165C; FCAALL.323; phytochrome D; PHYTOCHROME D
Summary: Encodes a phytochrome photoreceptor with a function similar to that of phyB that absorbs the red/far-red part of the light spectrum and is involved in light responses. It cannot compensate for phyB loss in Arabidopsis but can substitute for tobacco phyB in vivo.
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Genomic context

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See PHYD in Genome Data Viewer

Location:: chromosome: 4

Exon count:: 4

Sequence:: Chromosome: 4; NC_003075.7 (9195247..9199840, complement)

Chromosome 4 - NC_003075.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003075.7

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A functional PHYD gene is required for the germination of seeds that experienced high temperature, and ABA- and GA-related gene expression during and after pre-incubation at high temperatures was altered in a phyD mutant. The level of PHYD mRNA increased in seeds pre-incubated at high temperature and that this increase correlates with efficient removal of the germination repressor PIL5.
Title: PHYD prevents secondary dormancy establishment of seeds exposed to high temperature and is associated with lower PIL5 accumulation.
Surprisingly, none of the phytochromes alone conferred a photoperiodic response. Although phyE and phyB were the strongest repressors of flowering, both phyB and phyC were needed to confer a flowering response to photoperiod. Thus, a specific combination of phytochromes is required to detect changes in photoperiod
Title: Bottom-up Assembly of the Phytochrome Network.
LRB1 (LIGHT-RESPONSE BTB1) and LRB2 (LIGHT-RESPONSE BTB2) are involved in many developmental processes mediated by phyB and phyD.
Title: The light-response BTB1 and BTB2 proteins assemble nuclear ubiquitin ligases that modify phytochrome B and D signaling in Arabidopsis.
The expression of 35S:NtPHYB:GFP and 35S:AtPHYB:GFP complemented the tobacco hgl2 and Arabidopsis phyB-9 mutations, whereas the 35S:AtPHYD:GFP only rescued the hgl2 mutant
Title: Analysis of the function of the photoreceptors phytochrome B and phytochrome D in Nicotiana plumbaginifolia and Arabidopsis thaliana.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

NM_117721.2

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
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 protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IEA Inferred from Electronic Annotation more info
enables red or far-red light photoreceptor activity	IGI Inferred from Genetic Interaction 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 red or far-red light signaling pathway	IGI Inferred from Genetic Interaction 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

Component	Evidence Code	Pubs
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 D

NP_193360.1

phytochrome D (PHYD); 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 B (TAIR:AT2G18790.1); Has 26426 Blast hits to 26152 proteins in 3833 species: Archae - 221; Bacteria - 20797; Metazoa - 4; Fungi - 482; Plants - 3855; Viruses - 5; Other Eukaryotes - 1062 (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_003075.7 Reference assembly

Range

9195247..9199840 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_117721.2 → NP_193360.1 phytochrome D [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_193360.1

Status: REVIEWED

UniProtKB/Swiss-Prot

O23472, P42497

UniProtKB/TrEMBL

A0A5S9XT15, A0A654FPT9, Q5G878, Q5G885, Q5G887

Conserved Domains (4) summary

COG4251
Location:97 → 618

COG4251; Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]

PRK09303
Location:913 → 1128

PRK09303; histidine kinase

cd16932
Location:1042 → 1153

HATPase_Phy-like; Histidine kinase-like ATPase domain of plant phytochromes similar to Arabidopsis thaliana Phytochrome A, B, C, D and E

pfam00989
Location:658 → 774

PAS; PAS fold