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    PCL1 Homeodomain-like superfamily protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 823817, updated on 18-Sep-2024

    Summary

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    Official Symbol
    PCL1
    Official Full Name
    Homeodomain-like superfamily protein
    Primary source
    TAIR:AT3G46640
    Locus tag
    AT3G46640
    See related
    Araport:AT3G46640
    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
    LUX; LUX ARRHYTHMO; PHYTOCLOCK 1
    Summary
    Encodes a myb family transcription factor with a single Myb DNA-binding domain (type SHAQKYF) that is unique to plants and is essential for circadian rhythms, specifically for transcriptional regulation within the circadian clock. LUX is required for normal rhythmic expression of multiple clock outputs in both constant light and darkness. It is coregulated with TOC1 and seems to be repressed by CCA1 and LHY by direct binding of these proteins to the evening element in the LUX promoter.
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    Genomic context

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    See PCL1 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    3
    Sequence:
    Chromosome: 3; NC_003074.8 (17183042..17186959)

    Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene ncRNA Neighboring gene zinc finger (C3HC4-type RING finger) family protein Neighboring gene DCL protein (DUF3223) Neighboring gene UDP-Glycosyltransferase superfamily protein Neighboring gene ncRNA Neighboring gene UDP-glucosyl transferase 76E12 Neighboring gene uncharacterized protein Neighboring gene ncRNA

    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. LUX ARRHYTHMO mediates crosstalk between the circadian clock and defense in Arabidopsis. Zhang C, et al. Nat Commun, 2019 Jun 11. PMID 31186426, Free PMC Article
    2. LUX ARRHYTHMO encodes a nighttime repressor of circadian gene expression in the Arabidopsis core clock. Helfer A, et al. Curr Biol, 2011 Jan 25. PMID 21236673, Free PMC Article
    3. LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms. Hazen SP, et al. Proc Natl Acad Sci U S A, 2005 Jul 19. PMID 16006522, Free PMC Article
    4. Transcriptional regulation of LUX by CBF1 mediates cold input to the circadian clock in Arabidopsis. Chow BY, et al. Curr Biol, 2014 Jul 7. PMID 24954045, Free PMC Article
    5. The ELF4-ELF3-LUX complex links the circadian clock to diurnal control of hypocotyl growth. Nusinow DA, et al. Nature, 2011 Jul 13. PMID 21753751, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. mutations in the core clock component LUX ARRHYTHMO (LUX) disrupt circadian regulation of stomata under free running and Pseudomonas syringae challenge conditions as well as defense signaling mediated by salicylic and jasmonic acid, leading to compromised disease resistance.
      Title: LUX ARRHYTHMO mediates crosstalk between the circadian clock and defense in Arabidopsis.
    2. Data identified proteins that associate with the evening complex composed of EARLY FLOWERING 4 (ELF4), EARLY FLOWERING 3 (ELF3), and LUX ARRHYTHMO (LUX).
      Title: Identification of Evening Complex Associated Proteins in Arabidopsis by Affinity Purification and Mass Spectrometry.
    3. Transcriptional regulation of LUX by CBF1 mediates cold input to the circadian clock in Arabidopsis.
      Title: Transcriptional regulation of LUX by CBF1 mediates cold input to the circadian clock in Arabidopsis.
    4. Transcriptional co-regulators PRR9, PRR7 and PRR5 inhibit morning loops LHY and CCA1 expression by binding to their promoters.
      Title: A Bayesian approach for parameter estimation in the extended clock gene circuit of Arabidopsis thaliana.
    5. identification of a protein complex composed of the proteins encoded by EARLY FLOWERING 3 (ELF3), ELF4 and the transcription-factor-encoding gene LUX ARRHYTHMO (LUX; also known as PHYTOCLOCK 1)--that directly regulates plant growth
      Title: The ELF4-ELF3-LUX complex links the circadian clock to diurnal control of hypocotyl growth.
    6. The in vitro Dna-binding specificity of LUX, its role in the expression of PRR9, and its feedback properties are reported.
      Title: LUX ARRHYTHMO encodes a nighttime repressor of circadian gene expression in the Arabidopsis core clock.
    7. The PCL1 gene is the clock oscillator gene essential to the generation of clock oscillation in the higher plant. [PCL1]
      Title: PHYTOCLOCK 1 encoding a novel GARP protein essential for the Arabidopsis circadian clock.
    8. LUX ARRHYTHMO (LUX) encodes a Myb domain protein essential for circadian rhythms. [LUX]
      Title: LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    NM_001035746.2
    NM_001339273.1
    NM_114531.3

    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 
    Process Evidence Code Pubs
    involved_in circadian rhythm IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within circadian rhythm IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of circadian rhythm 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 
    acts_upstream_of_or_within regulation of gene expression 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
    Homeodomain-like superfamily protein
    NP_001030823.1
    • PHYTOCLOCK 1 (PCL1); CONTAINS InterPro DOMAIN/s: Homeodomain-like (InterPro:IPR009057), Myb, DNA-binding (InterPro:IPR014778), Myb-like DNA-binding domain, SHAQKYF class (InterPro:IPR006447), HTH transcriptional regulator, Myb-type, DNA-binding (InterPro:IPR017930), Homeodomain-related (InterPro:IPR012287); BEST Arabidopsis thaliana protein match is: Homeodomain-like superfamily protein (TAIR:AT5G59570.1); 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_001319698.1
    • PHYTOCLOCK 1 (PCL1); CONTAINS InterPro DOMAIN/s: Myb, DNA-binding (InterPro:IPR014778), Homeodomain-like (InterPro:IPR009057), Homeodomain-related (InterPro:IPR012287), Myb-like DNA-binding domain, SHAQKYF class (InterPro:IPR006447), HTH transcriptional regulator, Myb-type, DNA-binding (InterPro:IPR017930); BEST Arabidopsis thaliana protein match is: Homeodomain-like superfamily protein (TAIR:AT5G59570.1).
    NP_190248.1
    • PHYTOCLOCK 1 (PCL1); CONTAINS InterPro DOMAIN/s: Homeodomain-like (InterPro:IPR009057), Myb, DNA-binding (InterPro:IPR014778), Myb-like DNA-binding domain, SHAQKYF class (InterPro:IPR006447), HTH transcriptional regulator, Myb-type, DNA-binding (InterPro:IPR017930), Homeodomain-related (InterPro:IPR012287); BEST Arabidopsis thaliana protein match is: Homeodomain-like superfamily protein (TAIR:AT5G59570.1); Has 1709 Blast hits to 1707 proteins in 80 species: Archae - 0; Bacteria - 29; Metazoa - 20; Fungi - 11; Plants - 1622; Viruses - 0; Other Eukaryotes - 27 (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
      17183042..17186959
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_114531.3 → NP_190248.1  Homeodomain-like superfamily protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_190248.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      B9DI71, Q9SNB4
      UniProtKB/TrEMBL
      A0A5S9XII7, A0A654FDC6, A0A7G2EQR8
      Conserved Domains (2) summary
      TIGR01557
      Location:144 → 197
      myb_SHAQKYF; myb-like DNA-binding domain, SHAQKYF class
      PLN03162
      Location:60 → 229
      PLN03162; golden-2 like transcription factor; Provisional

    2. NM_001339273.1 → NP_001319698.1  Homeodomain-like superfamily protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A7G2EQR8, F4J959

    3. NM_001035746.2 → NP_001030823.1  Homeodomain-like superfamily protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001030823.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      B9DI71, Q9SNB4
      UniProtKB/TrEMBL
      A0A5S9XII7, A0A654FDC6, A0A7G2EQR8
      Conserved Domains (2) summary
      TIGR01557
      Location:144 → 197
      myb_SHAQKYF; myb-like DNA-binding domain, SHAQKYF class
      PLN03162
      Location:60 → 229
      PLN03162; golden-2 like transcription factor; Provisional
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9SNB4.1

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