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    PIL6 phytochrome interacting factor 3-like 6 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 825075, updated on 18-Sep-2024

    Summary

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    Official Symbol
    PIL6
    Official Full Name
    phytochrome interacting factor 3-like 6
    Primary source
    TAIR:AT3G59060
    Locus tag
    AT3G59060
    See related
    Araport:AT3G59060
    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
    phytochrome interacting factor 3-like 6; PHYTOCHROME-INTERACTING FACTOR 5; PIF5
    Summary
    Encodes a novel Myc-related bHLH transcription factor, which physically associated with APRR1/TOC1 and is a member of PIF3 transcription factor family. Involved in shade avoidance. Functions as negative regulator of PhyB. Protein levels are modulated by phytochrome B.
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    Genomic context

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    See PIL6 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    6
    Sequence:
    Chromosome: 3; NC_003074.8 (21827905..21830837, complement)

    Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene Tetratricopeptide repeat (TPR)-like superfamily protein Neighboring gene ncRNA Neighboring gene polyamine oxidase 3 Neighboring gene ncRNA Neighboring gene ncRNA Neighboring gene Cytochrome b561/ferric reductase transmembrane with DOMON related domain-containing protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003074.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. PHYTOCHROME-INTERACTING FACTOR 5 (PIF5) positively regulates dark-induced senescence and chlorophyll degradation in Arabidopsis. Zhang Y, et al. Plant Sci, 2015 Aug. PMID 26089152
    2. Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling. Hornitschek P, et al. Plant J, 2012 Sep. PMID 22536829
    3. Genomic analysis of circadian clock-, light-, and growth-correlated genes reveals PHYTOCHROME-INTERACTING FACTOR5 as a modulator of auxin signaling in Arabidopsis. Nozue K, et al. Plant Physiol, 2011 May. PMID 21430186, Free PMC Article
    4. PHYTOCHROME-INTERACTING FACTORS PIF4 and PIF5 are implicated in the regulation of hypocotyl elongation in response to blue light in Arabidopsis thaliana. Kunihiro A, et al. Biosci Biotechnol Biochem, 2010. PMID 21150090
    5. Phytochrome-interacting transcription factors PIF4 and PIF5 induce leaf senescence in Arabidopsis. Sakuraba Y, et al. Nat Commun, 2014 Aug 14. PMID 25119965

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PHYTOCHROME INTERACTING FACTORS PIF4 and PIF5 promote heat stress induced leaf senescence in Arabidopsis.
      Title: PHYTOCHROME INTERACTING FACTORS PIF4 and PIF5 promote heat stress induced leaf senescence in Arabidopsis.
    2. High Ambient Temperature Accelerates Leaf Senescence via PHYTOCHROME-INTERACTING FACTOR 4 and 5 in Arabidopsis.
      Title: High Ambient Temperature Accelerates Leaf Senescence via PHYTOCHROME-INTERACTING FACTOR 4 and 5 in Arabidopsis.
    3. Phytochrome interacting factors 4 and 5 regulate axillary branching via bud abscisic acid and stem auxin signalling.
      Title: Phytochrome interacting factors 4 and 5 regulate axillary branching via bud abscisic acid and stem auxin signalling.
    4. MYB30 Is a Key Negative Regulator of Arabidopsis Photomorphogenic Development That Promotes PIF4 and PIF5 Protein Accumulation in the Light.
      Title: MYB30 Is a Key Negative Regulator of Arabidopsis Photomorphogenic Development That Promotes PIF4 and PIF5 Protein Accumulation in the Light.
    5. Degradation of the transcription factors PIF4 and PIF5 under UV-B promotes UVR8-mediated inhibition of hypocotyl growth in Arabidopsis.
      Title: Degradation of the transcription factors PIF4 and PIF5 under UV-B promotes UVR8-mediated inhibition of hypocotyl growth in Arabidopsis.
    6. Binding of UV RESISTANCE LOCUS8 protein (UVR8) to COP1 E3 ligase (COP1) in UV-B disrupts stabilisation of PHYTOCHROME-INTERACTING FACTOR5 (PIF5) by COP1, providing a mechanism to rapidly lower PIF5 abundance in sunlight.
      Title: UVR8 disrupts stabilisation of PIF5 by COP1 to inhibit plant stem elongation in sunlight.
    7. 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.
    8. COG1 binds to the promoter regions of PIF4 and PIF5, and PIF4 and PIF5 bind to the promoter regions of key Brassinosteroid biosynthetic genes, such as DWF4 and BR6ox2, to directly promote their expression.
      Title: Brassinosteroid Biosynthesis Is Modulated via a Transcription Factor Cascade of COG1, PIF4, and PIF5.
    9. outline a novel phytochrome signaling mechanism by which TOPP4-mediated dephosphorylation of PIF5 attenuates phytochrome-dependent light responses
      Title: TOPP4 Regulates the Stability of PHYTOCHROME INTERACTING FACTOR5 during Photomorphogenesis in Arabidopsis.
    10. For growth under a canopy, where blue light is diminished, CRY1 and CRY2 perceive this change and respond by directly contacting two bHLH transcription factors, PIF4 and PIF5.
      Title: Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light.
    Submit: New GeneRIF Correction See all GeneRIFs (29)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    NM_001035812.2
    NM_001035813.2
    NM_115768.5
    NM_180690.2

    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 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 ethylene biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within red, far-red light phototransduction IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 mediated signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in response to brassinosteroid 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 low fluence blue light stimulus by blue low-fluence system IDA
    Inferred from Direct Assay
    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 6
    NP_001030889.1
    • phytochrome interacting factor 3-like 6 (PIL6); FUNCTIONS IN: DNA binding, sequence-specific DNA binding transcription factor activity; INVOLVED IN: red, far-red light phototransduction, ethylene biosynthetic process, circadian rhythm; LOCATED IN: nucleus; EXPRESSED IN: 18 plant structures; EXPRESSED DURING: 10 growth stages; 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 4 (TAIR:AT2G43010.1); Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798; Bacteria - 22429; Metazoa - 974; Fungi - 991; Plants - 531; Viruses - 0; Other Eukaryotes - 9610 (source: NCBI BLink).
    NP_001030890.1
    • phytochrome interacting factor 3-like 6 (PIL6); FUNCTIONS IN: DNA binding, sequence-specific DNA binding transcription factor activity; INVOLVED IN: red, far-red light phototransduction, ethylene biosynthetic process, circadian rhythm; LOCATED IN: nucleus; EXPRESSED IN: 18 plant structures; EXPRESSED DURING: 10 growth stages; 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 4 (TAIR:AT2G43010.1); Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798; Bacteria - 22429; Metazoa - 974; Fungi - 991; Plants - 531; Viruses - 0; Other Eukaryotes - 9610 (source: NCBI BLink).
    NP_191465.3
    • phytochrome interacting factor 3-like 6 (PIL6); FUNCTIONS IN: DNA binding, sequence-specific DNA binding transcription factor activity; INVOLVED IN: red, far-red light phototransduction, ethylene biosynthetic process, circadian rhythm; LOCATED IN: nucleus; EXPRESSED IN: 18 plant structures; EXPRESSED DURING: 10 growth stages; 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 4 (TAIR:AT2G43010.1); Has 4555 Blast hits to 4547 proteins in 305 species: Archae - 0; Bacteria - 0; Metazoa - 974; Fungi - 129; Plants - 3421; Viruses - 0; Other Eukaryotes - 31 (source: NCBI BLink).
    NP_851021.1
    • phytochrome interacting factor 3-like 6 (PIL6); FUNCTIONS IN: DNA binding, sequence-specific DNA binding transcription factor activity; INVOLVED IN: red, far-red light phototransduction, ethylene biosynthetic process, circadian rhythm; LOCATED IN: nucleus; EXPRESSED IN: 18 plant structures; EXPRESSED DURING: 10 growth stages; 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 4 (TAIR:AT2G43010.1); Has 4578 Blast hits to 4570 proteins in 308 species: Archae - 0; Bacteria - 0; Metazoa - 987; Fungi - 138; Plants - 3423; Viruses - 0; Other Eukaryotes - 30 (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_003074.8 Reference assembly

      Range
      21827905..21830837 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_115768.5 → NP_191465.3  phytochrome interacting factor 3-like 6 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_191465.3

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q84LH8, Q8RXG4, Q8S3D7, Q9LYT0
      UniProtKB/TrEMBL
      A0A178VFB8, A0A5S9XMU6, B9DH29
      Conserved Domains (1) summary
      cd11445
      Location:256 → 318
      bHLH_AtPIF_like; basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting factors (PIFs) and similar proteins

    2. NM_001035813.2 → NP_001030890.1  phytochrome interacting factor 3-like 6 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001030890.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q84LH8, Q8RXG4, Q8S3D7, Q9LYT0
      UniProtKB/TrEMBL
      A0A178VFB8, A0A5S9XMU6, B9DH29
      Conserved Domains (1) summary
      cd11445
      Location:256 → 318
      bHLH_AtPIF_like; basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting factors (PIFs) and similar proteins

    3. NM_001035812.2 → NP_001030889.1  phytochrome interacting factor 3-like 6 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001030889.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q84LH8, Q8RXG4, Q8S3D7, Q9LYT0
      UniProtKB/TrEMBL
      A0A178VFB8, A0A5S9XMU6, B9DH29
      Conserved Domains (1) summary
      cd11445
      Location:256 → 318
      bHLH_AtPIF_like; basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting factors (PIFs) and similar proteins

    4. NM_180690.2 → NP_851021.1  phytochrome interacting factor 3-like 6 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_851021.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A7G2EW66
      Conserved Domains (1) summary
      smart00353
      Location:262 → 310
      HLH; helix loop helix domain
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q84LH8.1

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