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    PIF3 phytochrome interacting factor 3 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 837479, updated on 18-Sep-2024

    Summary

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    Official Symbol
    PIF3
    Official Full Name
    phytochrome interacting factor 3
    Primary source
    TAIR:AT1G09530
    Locus tag
    AT1G09530
    See related
    Araport:AT1G09530
    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
    F14J9.19; F14J9_19; PAP3; PHOTOCURRENT 1; phytochrome interacting factor 3; PHYTOCHROME INTERACTING FACTOR 3; PHYTOCHROME-ASSOCIATED PROTEIN 3; POC1; purple acid phosphatase 3
    Summary
    Transcription factor interacting with photoreceptors phyA and phyB. Forms a ternary complex in vitro with G-box element of the promoters of LHY, CCA1. Acts as a negative regulator of phyB signalling. It degrades rapidly after irradiation of dark grown seedlings in a process controlled by phytochromes. Does not play a significant role in controlling light input and function of the circadian clockwork. Binds to G- and E-boxes, but not to other ACEs. Binds to anthocyanin biosynthetic genes in a light- and HY5-independent fashion. PIF3 function as a transcriptional activator can be functionally and mechanistically separated from its role in repression of PhyB mediated processes.
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    Genomic context

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    See PIF3 in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    8
    Sequence:
    Chromosome: 1; NC_003070.9 (3075768..3079654)

    Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene NAD(P)-binding Rossmann-fold superfamily protein Neighboring gene uncharacterized protein Neighboring gene ncRNA Neighboring gene myb domain protein 61

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003070.9

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. PIF3 is a repressor of chloroplast development. Stephenson PG, et al. Proc Natl Acad Sci U S A, 2009 May 5. PMID 19380736, Free PMC Article
    2. Integration of Ethylene and Light Signaling Affects Hypocotyl Growth in Arabidopsis. Yu Y, et al. Front Plant Sci, 2017. PMID 28174592, Free PMC Article
    3. Functional characterization of phytochrome interacting factor 3 for the Arabidopsis thaliana circadian clockwork. Viczián A, et al. Plant Cell Physiol, 2005 Oct. PMID 16055924
    4. DELLA-mediated PIF degradation contributes to coordination of light and gibberellin signalling in Arabidopsis. Li K, et al. Nat Commun, 2016 Jun 10. PMID 27282989, Free PMC Article
    5. PIF3 is a negative regulator of the CBF pathway and freezing tolerance in Arabidopsis. Jiang B, et al. Proc Natl Acad Sci U S A, 2017 Aug 8. PMID 28739888, Free PMC Article

    See all (97) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Discovery of a second-site nia2 mutation in the background of multiple Arabidopsis PIF-related mutants containing the pif3-3 allele.
      Title: Discovery of a second-site nia2 mutation in the background of multiple Arabidopsis PIF-related mutants containing the pif3-3 allele.
    2. 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.
    3. PIF3 is phosphorylated by MAPK to modulate plant immunity.
      Title: PIF3 is phosphorylated by MAPK to modulate plant immunity.
    4. 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.
    5. Direct photoresponsive inhibition of a p53-like transcription activation domain in PIF3 by Arabidopsis phytochrome B.
      Title: Direct photoresponsive inhibition of a p53-like transcription activation domain in PIF3 by Arabidopsis phytochrome B.
    6. SUMOylation of PHYTOCHROME INTERACTING FACTOR 3 promotes photomorphogenesis in Arabidopsis thaliana.
      Title: SUMOylation of PHYTOCHROME INTERACTING FACTOR 3 promotes photomorphogenesis in Arabidopsis thaliana.
    7. Cold-Induced CBF-PIF3 Interaction Enhances Freezing Tolerance by Stabilizing the phyB Thermosensor in Arabidopsis.
      Title: Cold-Induced CBF-PIF3 Interaction Enhances Freezing Tolerance by Stabilizing the phyB Thermosensor in Arabidopsis.
    8. Phytochrome B Induces Intron Retention and Translational Inhibition of PHYTOCHROME-INTERACTING FACTOR3.
      Title: Phytochrome B Induces Intron Retention and Translational Inhibition of PHYTOCHROME-INTERACTING FACTOR3.
    9. phyB and AGB1 antagonistically regulate PIF3 stability by dynamically interacting with each other and PIF3
      Title: Phytochrome B and AGB1 Coordinately Regulate Photomorphogenesis by Antagonistically Modulating PIF3 Stability in Arabidopsis.
    10. MPK6 was activated by red light, and the cotyledon opening angle in red light was reduced in mpk6 seedlings. MKK10, a MAPKK whose function is currently unclear, appears to act as a kinase upstream of MPK6 in regulating cotyledon opening. Activation of MPK6 by MKK10 led to the phosphorylation of PIF3 and accelerated its turnover in transgenic seedlings.
      Title: Arabidopsis MKK10-MPK6 mediates red-light-regulated opening of seedling cotyledons through phosphorylation of PIF3.
    Submit: New GeneRIF Correction See all GeneRIFs (44)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    NM_001331836.1
    NM_001331837.1
    NM_001331839.1
    NM_100824.3
    NM_179295.3

    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 ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    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 sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transcription cis-regulatory region binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    NOT involved_in circadian rhythm IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within de-etiolation 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_or_within positive regulation of anthocyanin metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within red or far-red light signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of DNA-templated transcription TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of photosynthesis, light reaction IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of plant organ morphogenesis IMP
    Inferred from Mutant Phenotype
    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 ethylene IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in response to heat IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within response to red or far red light IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to salt IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in response to water-immersion restraint stress IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within signal transduction TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in unidimensional cell growth IMP
    Inferred from Mutant Phenotype
    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
    NP_001318964.1
    • phytochrome interacting factor 3 (PIF3); 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-like 1 (TAIR:AT2G46970.1); Has 4326 Blast hits to 4310 proteins in 315 species: Archae - 0; Bacteria - 2; Metazoa - 732; Fungi - 183; Plants - 3377; Viruses - 7; Other Eukaryotes - 25 (source: NCBI BLink).
    NP_001318965.1
    • phytochrome interacting factor 3 (PIF3); 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-like 1 (TAIR:AT2G46970.1); Has 4326 Blast hits to 4310 proteins in 315 species: Archae - 0; Bacteria - 2; Metazoa - 732; Fungi - 183; Plants - 3377; Viruses - 7; Other Eukaryotes - 25 (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_003070.9 Reference assembly

      Range
      3075768..3079654
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001331838.1 → NP_001322700.1  phytochrome interacting factor 3 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      A5Y7A2, A5Y7A3, A5Y7A4, A5Y7A5, A5Y7A6, A5Y7A7, A5Y7A8, A5Y7A9, A5Y7B0, A5Y7B1, A5Y7B2, A5Y7B3, A5Y7B4, A5Y7B5, A5Y7B6, O80536, Q9SBC5
      UniProtKB/TrEMBL
      A0A178W5U6, A0A5S9TG51, A0A654EA77
      Conserved Domains (1) summary
      cd11445
      Location:343 → 405
      bHLH_AtPIF_like; basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting factors (PIFs) and similar proteins

    2. NM_001331837.1 → NP_001318965.1  phytochrome interacting factor 3 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      A5Y7A2, A5Y7A3, A5Y7A4, A5Y7A5, A5Y7A6, A5Y7A7, A5Y7A8, A5Y7A9, A5Y7B0, A5Y7B1, A5Y7B2, A5Y7B3, A5Y7B4, A5Y7B5, A5Y7B6, O80536, Q9SBC5
      UniProtKB/TrEMBL
      A0A178W5U6, A0A5S9TG51, A0A654EA77
      Conserved Domains (1) summary
      cd11445
      Location:343 → 405
      bHLH_AtPIF_like; basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting factors (PIFs) and similar proteins

    3. NM_001331836.1 → NP_001318964.1  phytochrome interacting factor 3 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      A5Y7A2, A5Y7A3, A5Y7A4, A5Y7A5, A5Y7A6, A5Y7A7, A5Y7A8, A5Y7A9, A5Y7B0, A5Y7B1, A5Y7B2, A5Y7B3, A5Y7B4, A5Y7B5, A5Y7B6, O80536, Q9SBC5
      UniProtKB/TrEMBL
      A0A178W5U6, A0A5S9TG51, A0A654EA77
      Conserved Domains (1) summary
      cd11445
      Location:343 → 405
      bHLH_AtPIF_like; basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting factors (PIFs) and similar proteins

    4. NM_001331839.1 → NP_001322701.1  phytochrome interacting factor 3 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      A5Y7A2, A5Y7A3, A5Y7A4, A5Y7A5, A5Y7A6, A5Y7A7, A5Y7A8, A5Y7A9, A5Y7B0, A5Y7B1, A5Y7B2, A5Y7B3, A5Y7B4, A5Y7B5, A5Y7B6, O80536, Q9SBC5
      UniProtKB/TrEMBL
      A0A178W5U6, A0A5S9TG51, A0A654EA77
      Conserved Domains (1) summary
      cd11445
      Location:343 → 405
      bHLH_AtPIF_like; basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting factors (PIFs) and similar proteins

    5. NM_179295.3 → NP_849626.1  phytochrome interacting factor 3 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_849626.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      A5Y7A2, A5Y7A3, A5Y7A4, A5Y7A5, A5Y7A6, A5Y7A7, A5Y7A8, A5Y7A9, A5Y7B0, A5Y7B1, A5Y7B2, A5Y7B3, A5Y7B4, A5Y7B5, A5Y7B6, O80536, Q9SBC5
      UniProtKB/TrEMBL
      A0A178W5U6, A0A5S9TG51, A0A654EA77
      Conserved Domains (1) summary
      cd11445
      Location:343 → 405
      bHLH_AtPIF_like; basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting factors (PIFs) and similar proteins

    6. NM_100824.3 → NP_172424.1  phytochrome interacting factor 3 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_172424.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      A5Y7A2, A5Y7A3, A5Y7A4, A5Y7A5, A5Y7A6, A5Y7A7, A5Y7A8, A5Y7A9, A5Y7B0, A5Y7B1, A5Y7B2, A5Y7B3, A5Y7B4, A5Y7B5, A5Y7B6, O80536, Q9SBC5
      UniProtKB/TrEMBL
      A0A178W5U6, A0A5S9TG51, A0A654EA77
      Conserved Domains (1) summary
      cd11445
      Location:343 → 405
      bHLH_AtPIF_like; basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting factors (PIFs) and similar proteins
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O80536.1

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