PIL5 phytochrome interacting factor 3-like 5 [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: PIL5
Official Full Name: phytochrome interacting factor 3-like 5
Primary source: TAIR:AT2G20180
Locus tag: AT2G20180
See related: Araport:AT2G20180
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: PHY-INTERACTING FACTOR 1; phytochrome interacting factor 3-like 5; PIF1; T2G17.2; T2G17_2
Summary: Encodes a novel Myc-related bHLH transcription factor that has transcriptional activation activity in the dark. It is a key negative regulator of phytochrome-mediated seed germination and acts by inhibiting chlorophyll biosynthesis, light-mediated suppression of hypocotyl elongation and far-red light-mediated suppression of seed germination, and promoting negative gravitropism in hypocotyls. Light reduces this activity in a phy-dependent manner. The protein preferentially interacts with the Pfr forms of Phytochrome A (PhyA) and Phytochrome B (PhyB), is physically associated with APRR1/TOC1 and is degraded in red (R) and far-red (FR) light through the ubiquitin (ub)-26S proteasome pathway to optimize photomorphogenic development in Arabidopsis. It also negatively regulates GA3 oxidase expression.
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Genomic context

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See PIL5 in Genome Data Viewer

Location:: chromosome: 2

Exon count:: 9

Sequence:: Chromosome: 2; NC_003071.7 (8704024..8707009, complement)

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?

The PIF1/PIF3-MED25-HDA19 transcriptional repression complex regulates phytochrome signaling in Arabidopsis.
Title: The PIF1/PIF3-MED25-HDA19 transcriptional repression complex regulates phytochrome signaling in Arabidopsis.
The PIF1-miR408-PLANTACYANIN repression cascade regulates light-dependent seed germination.
Title: The PIF1-miR408-PLANTACYANIN repression cascade regulates light-dependent seed germination.
SPA1 acts as a serine/threonine kinase and directly phosphorylates PIF1 in vitro and in vivo.
Title: A phyB-PIF1-SPA1 kinase regulatory complex promotes photomorphogenesis in Arabidopsis.
Data suggest that canopy light represses polyamines accumulation through PIF1 while red light promotes polyamines accumulation. Canopy light also downregulates PIF1 levels, through phyA; however, PIF1 reaccumulates rapidly, which limits phyA-mediated germination.
Title: polyamine uptake transporter 2 (put2) and decaying seeds enhance phyA-mediated germination by overcoming PIF1 repression of germination.
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.
PIL5 is involved in floral transition interacting with flowering integrators and gibberellic acid.
Title: PIL5 represses floral transition in Arabidopsis under long day conditions.
The genetic, physiological, and biochemical evidence, when taken together, leads us to propose that PIF1 and CTG10 coexist, and even accumulate, in the nucleus in darkness, but that, following illumination, CTG10 assists in reducing PIF1 amounts, thus promoting the completion of seed germination and subsequent seedling development.
Title: KELCH F-BOX protein positively influences Arabidopsis seed germination by targeting PHYTOCHROME-INTERACTING FACTOR1.
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.
COP1 promotes the degradation of HFR1 under shade, thus increasing the ability of PIFs to control gene expression, increase auxin levels and promote stem growth.
Title: Convergence of CONSTITUTIVE PHOTOMORPHOGENESIS 1 and PHYTOCHROME INTERACTING FACTOR signalling during shade avoidance.
the transcriptional cascade consisting of PIF1/PIF3, HY5, and BBX23 controls photomorphogenesis.
Title: A PIF1/PIF3-HY5-BBX23 Transcription Factor Cascade Affects Photomorphogenesis.

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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_001202630.2

Supported by ESTs:

NM_001335663.1

Supported by ESTs:

NM_001335664.1

Supported by ESTs:

NM_001335665.1

Supported by ESTs:

NM_001335666.1

Supported by ESTs:

NM_001335667.1

Supported by ESTs:

NM_001335668.1

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables DNA-binding transcription factor activity	TAS Traceable Author Statement more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables phytochrome binding	IDA Inferred from Direct Assay 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

Process	Evidence Code	Pubs
acts_upstream_of_or_within chlorophyll biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within gibberellic acid mediated signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_negative_effect gibberellin biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heme biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative gravitropism	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative gravitropism	TAS Traceable Author Statement more info	PubMed
acts_upstream_of_or_within negative regulation of photomorphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of seed germination	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within negative regulation of seed germination	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within red light signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of photomorphogenesis	TAS Traceable Author Statement more info	PubMed
acts_upstream_of_or_within regulation of seed germination	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 auxin	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to cold	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to heat	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISM Inferred from Sequence Model more info

General protein information

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Preferred Names: phytochrome interacting factor 3-like 5

NP_001189559.1

phytochrome interacting factor 3-like 5 (PIL5); 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: basic helix-loop-helix (bHLH) DNA-binding superfamily protein (TAIR:AT4G28800.1).

NP_001318252.1

phytochrome interacting factor 3-like 5 (PIL5); 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: basic helix-loop-helix (bHLH) DNA-binding superfamily protein (TAIR:AT4G28800.1); Has 4736 Blast hits to 4693 proteins in 351 species: Archae - 0; Bacteria - 27; Metazoa - 921; Fungi - 265; Plants - 3401; Viruses - 2; Other Eukaryotes - 120 (source: NCBI BLink).

NP_849996.1

phytochrome interacting factor 3-like 5 (PIL5); 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: basic helix-loop-helix (bHLH) DNA-binding superfamily protein (TAIR:AT4G28800.1); Has 4635 Blast hits to 4615 proteins in 348 species: Archae - 0; Bacteria - 26; Metazoa - 878; Fungi - 251; Plants - 3376; Viruses - 2; Other Eukaryotes - 102 (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

8704024..8707009 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_179665.3 → NP_849996.1 phytochrome interacting factor 3-like 5 [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_849996.1

Status: REVIEWED

UniProtKB/TrEMBL

A0A5S9WZN4

Conserved Domains (1) summary

smart00353
Location:219 → 267

HLH; helix loop helix domain
NM_001335663.1 → NP_001318252.1 phytochrome interacting factor 3-like 5 [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/Swiss-Prot

Q0WQ83, Q3EBY0, Q8GZM7, Q9SL63

UniProtKB/TrEMBL

A0A5S9WZN4
NM_001202630.2 → NP_001189559.1 phytochrome interacting factor 3-like 5 [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_001189559.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q0WQ83, Q3EBY0, Q8GZM7, Q9SL63

UniProtKB/TrEMBL

A0A5S9WZN4

Conserved Domains (1) summary

smart00353
Location:290 → 338

HLH; helix loop helix domain
NM_001335665.1 → NP_001323903.1 phytochrome interacting factor 3-like 5 [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A5S9WZN4
NM_001335664.1 → NP_001323902.1 phytochrome interacting factor 3-like 5 [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/Swiss-Prot

Q0WQ83, Q3EBY0, Q8GZM7, Q9SL63

UniProtKB/TrEMBL

A0A5S9WZN4
NM_001335667.1 → NP_001323905.1 phytochrome interacting factor 3-like 5 [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A5S9WZN4
NM_001335666.1 → NP_001323904.1 phytochrome interacting factor 3-like 5 [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/Swiss-Prot

Q0WQ83, Q3EBY0, Q8GZM7, Q9SL63

UniProtKB/TrEMBL

A0A5S9WZN4
NM_001335668.1 → NP_001323901.1 phytochrome interacting factor 3-like 5 [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A1P8AYE4