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

Gene ID: 816538, updated on 18-Sep-2024

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_003071.7Genomic Context describing neighboring genes Neighboring gene uncharacterized protein Neighboring gene NEP-interacting protein, putative (DUF239) Neighboring gene E3 ubiquitin ligase SCF complex subunit SKP1/ASK1 family protein Neighboring gene CLIP-associated protein Neighboring gene RNI-like superfamily protein Neighboring gene low-molecular-weight cysteine-rich 60

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. Genome-wide analysis of genes targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during seed germination in Arabidopsis. Oh E, et al. Plant Cell, 2009 Feb. PMID 19244139, Free PMC Article
  2. PIF1 directly and indirectly regulates chlorophyll biosynthesis to optimize the greening process in Arabidopsis. Moon J, et al. Proc Natl Acad Sci U S A, 2008 Jul 8. PMID 18591656, Free PMC Article
  3. PIL5 represses floral transition in Arabidopsis under long day conditions. Wu M, et al. Biochem Biophys Res Commun, 2018 May 15. PMID 29588173
  4. PIF1 is regulated by light-mediated degradation through the ubiquitin-26S proteasome pathway to optimize photomorphogenesis of seedlings in Arabidopsis. Shen H, et al. Plant J, 2005 Dec. PMID 16359394
  5. Light activates the degradation of PIL5 protein to promote seed germination through gibberellin in Arabidopsis. Oh E, et al. Plant J, 2006 Jul. PMID 16740147

See all (52) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. The PIF1-miR408-PLANTACYANIN repression cascade regulates light-dependent seed germination.
    Title: The PIF1-miR408-PLANTACYANIN repression cascade regulates light-dependent seed germination.
  3. 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.
  4. 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.
  5. 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.
  6. PIL5 is involved in floral transition interacting with flowering integrators and gibberellic acid.
    Title: PIL5 represses floral transition in Arabidopsis under long day conditions.
  7. 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.
  8. 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.
  9. 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.
  10. the transcriptional cascade consisting of PIF1/PIF3, HY5, and BBX23 controls photomorphogenesis.
    Title: A PIF1/PIF3-HY5-BBX23 Transcription Factor Cascade Affects Photomorphogenesis.
Submit: New GeneRIF Correction See all GeneRIFs (36)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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NM_001202630.2
NM_001335663.1
NM_001335664.1
NM_001335665.1
NM_001335666.1
NM_001335667.1
NM_001335668.1

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

  1. NC_003071.7 Reference assembly

    Range
    8704024..8707009 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. 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

  3. 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

  4. NM_001335665.1 → NP_001323903.1  phytochrome interacting factor 3-like 5 [Arabidopsis thaliana]

    Status: REVIEWED

    UniProtKB/TrEMBL
    A0A5S9WZN4

  5. 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

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

    Status: REVIEWED

    UniProtKB/TrEMBL
    A0A5S9WZN4

  7. 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

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

    Status: REVIEWED

    UniProtKB/TrEMBL
    A0A1P8AYE4
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8GZM7.1

Gene LinkOut

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