HFR1 basic helix-loop-helix (bHLH) DNA-binding superfamily protein [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: HFR1
Official Full Name: basic helix-loop-helix (bHLH) DNA-binding superfamily protein
Primary source: TAIR:AT1G02340
Locus tag: AT1G02340
See related: Araport:AT1G02340
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: FBI1; LONG HYPOCOTYL IN FAR-RED; REDUCED PHYTOCHROME SIGNALING 1; REDUCED SENSITIVITY TO FAR-RED LIGHT 1; REP1; RSF1; T6A9.4; T6A9_4
Summary: Encodes a light-inducible, nuclear bHLH protein involved in phytochrome signaling. Mutants exhibit a long-hypocotyl phenotype only under far-red light but not under red light and are defective in other phytochrome A-related responses. Mutants also show blue light response defects. HFR1 interacts with COP1, co-localizes to the nuclear specks and is ubiquinated by COP1.
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Genomic context

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See HFR1 in Genome Data Viewer

Location:: chromosome: 1

Exon count:: 5

Sequence:: Chromosome: 1; NC_003070.9 (465616..467880, complement)

Chromosome 1 - NC_003070.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003070.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

results reveal a new mechanism for NO signals in modulating PHYB-mediated seed germination by repressing PIF1 expression at the transcriptional level as well as preventing PIF1 activity by stabilizing HFR1 protein.
Title: Nitric oxide promotes light-initiated seed germination by repressing PIF1 expression and stabilizing HFR1.
light inactivates DET1, elevating HFR1 to sequester PIF1's suppression on seed germination
Title: Arabidopsis DET1 degrades HFR1 but stabilizes PIF1 to precisely regulate seed germination.
HFR1 prevents PIF1 from binding to its target genes and antagonistically regulates PIF1-mediated gene expression. HFR1 and PIF1 are the major transcription regulators responsible for light-directed Transcriptome changes in seed germination.
Title: HFR1 sequesters PIF1 to govern the transcriptional network underlying light-initiated seed germination in Arabidopsis.
HY5 transmits phyA signals through an FHY1/FHL-independent pathway but it may also modulate FHY1/FHL signal through its interaction with HFR1 and LAF1.
Title: Three transcription factors, HFR1, LAF1 and HY5, regulate largely independent signaling pathways downstream of phytochrome A.
The HLH and the adjacent C-terminal domain are required for biological activity of HFR1.
Title: The shade avoidance syndrome in Arabidopsis: a fundamental role for atypical basic helix-loop-helix proteins as transcriptional cofactors.
OWL1 interacts with the basic helix-loop-helix HFR1 (LONG HYPOCOTYL IN FAR-RED) transcription factor. Both proteins are involved in the agravitropic response under far-red light.
Title: OWL1: an Arabidopsis J-domain protein involved in perception of very low light fluences.
HFR1, which is fine-tuned by cry1, is crucial for regulating global gene expression in cry1-mediated early blue light signaling.
Title: HFR1 is crucial for transcriptome regulation in the cryptochrome 1-mediated early response to blue light in Arabidopsis thaliana.
CKII-mediated phosphorylation represents an important post-translational modification influencing the stability and signaling activity of Arabidopsis HFR1
Title: Multisite phosphorylation of Arabidopsis HFR1 by casein kinase II and a plausible role in regulating its degradation rate.
in addition to their independent functions in phyA signaling, LAF1 and HFR1 also cooperate post-translationally to stabilize each other through inhibition of ubiquitination by COP1, thereby enhancing phyA photoresponses
Title: Independent and interdependent functions of LAF1 and HFR1 in phytochrome A signaling.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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NM_001331332.1

Supported by ESTs:

NM_100115.3

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein dimerization activity	IEA Inferred from Electronic Annotation more info
enables transcription cis-regulatory region binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription coregulator activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within abscisic acid-activated signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within blue light signaling pathway	TAS Traceable Author Statement more info	PubMed
acts_upstream_of_or_within red, far-red light phototransduction	TAS Traceable Author Statement more info	PubMed
involved_in response to abscisic acid	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to far red light	IDA Inferred from Direct Assay more info	PubMed
involved_in response to heat	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within response to light intensity	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to salt	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within signal transduction	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISM Inferred from Sequence Model more info
located_in nucleus	TAS Traceable Author Statement more info	PubMed

General protein information

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Preferred Names: basic helix-loop-helix (bHLH) DNA-binding superfamily protein

NP_563650.1

LONG HYPOCOTYL IN FAR-RED (HFR1); CONTAINS InterPro DOMAIN/s: Helix-loop-helix DNA-binding domain (InterPro:IPR001092), Helix-loop-helix DNA-binding (InterPro:IPR011598); BEST Arabidopsis thaliana protein match is: phytochrome interacting factor 3 (TAIR:AT1G09530.2); Has 1715 Blast hits to 1709 proteins in 90 species: Archae - 0; Bacteria - 0; Metazoa - 4; Fungi - 4; Plants - 1707; Viruses - 0; Other Eukaryotes - 0 (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_003070.9 Reference assembly

Range

465616..467880 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_100115.3 → NP_563650.1 basic helix-loop-helix (bHLH) DNA-binding superfamily protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_563650.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q8GZ25, Q9FE22, Q9FZ26

UniProtKB/TrEMBL

A0A5S9S689

Conserved Domains (1) summary

smart00353
Location:144 → 188

HLH; helix loop helix domain
NM_001331332.1 → NP_001323315.1 basic helix-loop-helix (bHLH) DNA-binding superfamily protein [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A178W6M2, A0A1P8AWQ4