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    PIF4 phytochrome interacting factor 4 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 818903, updated on 18-Sep-2024

    Summary

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    Official Symbol
    PIF4
    Official Full Name
    phytochrome interacting factor 4
    Primary source
    TAIR:AT2G43010
    Locus tag
    AT2G43010
    See related
    Araport:AT2G43010
    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
    AtPIF4; MFL8.13; MFL8_13; phytochrome interacting factor 4; SRL2
    Summary
    Isolated as a semidominant mutation defective in red -light responses. Encodes a nuclear localized bHLH protein that interacts with active PhyB protein. Negatively regulates phyB mediated red light responses. Involved in shade avoidance response. Protein abundance is negatively regulated by PhyB.
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    Genomic context

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    See PIF4 in Genome Data Viewer
    Location:
    chromosome: 2
    Exon count:
    6
    Sequence:
    Chromosome: 2; NC_003071.7 (17886101..17889087)

    Chromosome 2 - NC_003071.7Genomic Context describing neighboring genes Neighboring gene GDSL-like Lipase/Acylhydrolase superfamily protein Neighboring gene NAC domain containing protein 42 Neighboring gene ncRNA Neighboring gene polyamine oxidase 2 Neighboring gene Ribosomal protein L3 family protein

    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. Atmospheric nitrogen dioxide suppresses the activity of phytochrome interacting factor 4 to suppress hypocotyl elongation. Takahashi M, et al. Planta, 2024 Jul 3. PMID 38958765, Free PMC Article
    2. Phytochrome-interacting factor 4 (PIF4) regulates auxin biosynthesis at high temperature. Franklin KA, et al. Proc Natl Acad Sci U S A, 2011 Dec 13. PMID 22123947, Free PMC Article
    3. PIF4-induced BR synthesis is critical to diurnal and thermomorphogenic growth. Martínez C, et al. EMBO J, 2018 Dec 3. PMID 30389669, Free PMC Article
    4. Transcription factor PIF4 controls the thermosensory activation of flowering. Kumar SV, et al. Nature, 2012 Mar 21. PMID 22437497, Free PMC Article
    5. The epidermis coordinates thermoresponsive growth through the phyB-PIF4-auxin pathway. Kim S, et al. Nat Commun, 2020 Feb 26. PMID 32103019, Free PMC Article

    See all (106) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Atmospheric nitrogen dioxide suppresses the activity of phytochrome interacting factor 4 to suppress hypocotyl elongation.
      Title: Atmospheric nitrogen dioxide suppresses the activity of phytochrome interacting factor 4 to suppress hypocotyl elongation.
    2. Histone methylation readers MRG1/2 interact with PIF4 to promote thermomorphogenesis in Arabidopsis.
      Title: Histone methylation readers MRG1/2 interact with PIF4 to promote thermomorphogenesis in Arabidopsis.
    3. The heat response regulators HSFA1s promote Arabidopsis thermomorphogenesis via stabilizing PIF4 during the day.
      Title: The heat response regulators HSFA1s promote Arabidopsis thermomorphogenesis via stabilizing PIF4 during the day.
    4. Transcription factors KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4 regulate long intergenic noncoding RNAs expressed in Arabidopsis roots.
      Title: Transcription factors KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4 regulate long intergenic noncoding RNAs expressed in Arabidopsis roots.
    5. PHYTOCHROME INTERACTING FACTOR 4 regulates microtubule organization to mediate high temperature-induced hypocotyl elongation in Arabidopsis.
      Title: PHYTOCHROME INTERACTING FACTOR 4 regulates microtubule organization to mediate high temperature-induced hypocotyl elongation in Arabidopsis.
    6. The Mediator complex subunit MED25 interacts with HDA9 and PIF4 to regulate thermomorphogenesis.
      Title: The Mediator complex subunit MED25 interacts with HDA9 and PIF4 to regulate thermomorphogenesis.
    7. The Arabidopsis Phytoglobin 2 mediates phytochrome B (phyB) light signaling responses during somatic embryogenesis.
      Title: The Arabidopsis Phytoglobin 2 mediates phytochrome B (phyB) light signaling responses during somatic embryogenesis.
    8. Guard cell activity of PIF4 and HY5 control transpiration.
      Title: Guard cell activity of PIF4 and HY5 control transpiration.
    9. FLS2-RBOHD-PIF4 Module Regulates Plant Response to Drought and Salt Stress.
      Title: FLS2-RBOHD-PIF4 Module Regulates Plant Response to Drought and Salt Stress.
    10. PIF4-PAP1 interaction affects MYB-bHLH-WD40 complex formation and anthocyanin accumulation in Arabidopsis.
      Title: PIF4-PAP1 interaction affects MYB-bHLH-WD40 complex formation and anthocyanin accumulation in Arabidopsis.
    Submit: New GeneRIF Correction See all GeneRIFs (79)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    NM_001337009.1
    NM_129862.3
    NM_180050.1

    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 ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    enables promoter-specific chromatin 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
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within de-etiolation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within phototropism IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of thermomorphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within red light signaling pathway IGI
    Inferred from Genetic Interaction
    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 auxin biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of auxin biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of auxin mediated signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of plant organ morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    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 
    involved_in response to low fluence blue light stimulus by blue low-fluence system IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in response to salt IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within response to temperature stimulus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to temperature stimulus 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 4
    NP_565991.2
    • phytochrome interacting factor 4 (PIF4); 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 6 (TAIR:AT3G59060.1); Has 4545 Blast hits to 4539 proteins in 356 species: Archae - 0; Bacteria - 0; Metazoa - 939; Fungi - 192; Plants - 3373; Viruses - 2; Other Eukaryotes - 39 (source: NCBI BLink).
    NP_850381.1
    • phytochrome interacting factor 4 (PIF4); 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 6 (TAIR:AT3G59060.1); Has 4535 Blast hits to 4529 proteins in 355 species: Archae - 0; Bacteria - 0; Metazoa - 936; Fungi - 188; Plants - 3370; Viruses - 2; Other Eukaryotes - 39 (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
      17886101..17889087
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001337007.1 → NP_001323428.1  phytochrome interacting factor 4 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1P8AX01, A0A7G2EDM5, D5JZM7

    2. NM_001337008.1 → NP_001323427.1  phytochrome interacting factor 4 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178VYH3, A0A1P8AX62, A0A384LFY4, A0A7G2EDM5, D5JZM7
      Conserved Domains (1) summary
      cd11445
      Location:257 → 314
      bHLH_AtPIF_like; basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting factors (PIFs) and similar proteins

    3. NM_129862.3 → NP_565991.2  phytochrome interacting factor 4 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_565991.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      A5Y7D4, A5Y7D5, A5Y7D6, A5Y7D7, A5Y7D8, A5Y7D9, A5Y7E0, A5Y7E1, A5Y7E2, A5Y7E3, A5Y7E4, A5Y7E5, A5Y7E6, A5Y7E7, Q8W2F3, Q9C5I8, Q9SKX6
      UniProtKB/TrEMBL
      A0A654F1E9, A0A7G2EDM5, B9DFT8, D5JZM7
      Conserved Domains (1) summary
      cd11445
      Location:257 → 314
      bHLH_AtPIF_like; basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting factors (PIFs) and similar proteins

    4. NM_180050.1 → NP_850381.1  phytochrome interacting factor 4 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_850381.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A7G2EDM5, D5JZM7, F4IQ51
      Conserved Domains (1) summary
      smart00353
      Location:263 → 311
      HLH; helix loop helix domain

    5. NM_001337009.1 → NP_001323426.1  phytochrome interacting factor 4 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1P8AX08, A0A7G2EDM5, D5JZM7
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8W2F3.1

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