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    HD1 histone deacetylase 1 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 829969, updated on 18-Sep-2024

    Summary

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    Official Symbol
    HD1
    Official Full Name
    histone deacetylase 1
    Primary source
    TAIR:AT4G38130
    Locus tag
    AT4G38130
    See related
    Araport:AT4G38130
    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
    ARABIDOPSIS HISTONE DEACETYLASE 1; ARABIDOPSIS HISTONE DEACETYLASE 19; ATHD1; ATHDA19; ATRPD3A; F20D10.250; F20D10_250; HDA1; HDA19; HISTONE DEACETYLASE; histone deacetylase 1; HISTONE DEACETYLASE 19; HISTONE DEACETYLASE19; RPD3A
    Summary
    Encodes a histone deacetylase that enhances AtERF7-mediated transcriptional repression. Binds SIM3 and ERF7. Expressed in the nucleus in most tissues examined and throughout the life of the plant. Involved in jasmonic acid and ethylene dependent pathogen resistance. The sequence in GenBank has 17 AG dinucleotide repeats missing, which is also missing in Ler shotgun sequence from Cereon. Although it is annotated to be in Columbia, the GB sequence is probably not of Columbia origin. Plays a role in embryogenesis as mutants grown at higher temperatures display abnormalities in the organization of the root and shoot. Plant lines expressing an RNAi construct targeted against HDA19 shows some resistance to agrobacterium-mediated root transformation.
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    Genomic context

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    See HD1 in Genome Data Viewer
    Location:
    chromosome: 4
    Exon count:
    8
    Sequence:
    Chromosome: 4; NC_003075.7 (17896278..17899509, complement)

    Chromosome 4 - NC_003075.7Genomic Context describing neighboring genes Neighboring gene exportin-4 protein Neighboring gene CURVATURE THYLAKOID 1D-like protein Neighboring gene ARM repeat superfamily protein Neighboring gene RING/U-box superfamily protein Neighboring gene Pentatricopeptide repeat (PPR) superfamily protein Neighboring gene Mitochondrial transcription termination factor family protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003075.7

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. HISTONE DEACETYLASE19 Controls Ovule Number Determination and Transmitting Tract Differentiation. Manrique S, et al. Plant Physiol, 2024 Mar 29. PMID 38060625, Free PMC Article
    2. HDA19 is required for the repression of salicylic acid biosynthesis and salicylic acid-mediated defense responses in Arabidopsis. Choi SM, et al. Plant J, 2012 Jul. PMID 22381007
    3. Arabidopsis thaliana histone deacetylase 1 (AtHD1) is localized in euchromatic regions and demonstrates histone deacetylase activity in vitro. Fong PM, et al. Cell Res, 2006 May. PMID 16699543, Free PMC Article
    4. The Distinct Roles of Class I and II RPD3-Like Histone Deacetylases in Salinity Stress Response. Ueda M, et al. Plant Physiol, 2017 Dec. PMID 29018096, Free PMC Article
    5. HISTONE DEACETYLASE19 is involved in jasmonic acid and ethylene signaling of pathogen response in Arabidopsis. Zhou C, et al. Plant Cell, 2005 Apr. PMID 15749761, Free PMC Article

    See all (44) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. HISTONE DEACETYLASE19 Controls Ovule Number Determination and Transmitting Tract Differentiation.
      Title: HISTONE DEACETYLASE19 Controls Ovule Number Determination and Transmitting Tract Differentiation.
    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. S-Nitrosylation of the histone deacetylase HDA19 stimulates its activity to enhance plant stress tolerance in Arabidopsis.
      Title: S-Nitrosylation of the histone deacetylase HDA19 stimulates its activity to enhance plant stress tolerance in Arabidopsis.
    4. HDA19 is required for cellular patterning of root epidermis and cortex.HDA19 binds to the SCR promoter and SCR target genes and affects their expression.
      Title: Histone Deacetylase HDA19 Affects Root Cortical Cell Fate by Interacting with SCARECROW.
    5. These results suggested that integrating activation of Brassinosteroid (BR)-signaling pathways with the formation of the protein complex containing BES1/BZR1 and TPL-HDA19 via the EAR motif was important in fine-tuning BR-related gene networks in plants.
      Title: Transcriptional network regulation of the brassinosteroid signaling pathway by the BES1-TPL-HDA19 co-repressor complex.
    6. This work therefore identifies a new role for FD in reproductive patterning, as FD regulates IM function together with HDA19 in an age-dependent fashion.
      Title: HISTONE DEACETYLASE 19 and the flowering time gene FD maintain reproductive meristem identity in an age-dependent manner.
    7. These results reveal the presence of an MSI1-HDA19 complex that fine-tunes abscissic acid signaling in Arabidopsis.
      Title: The WD40 Domain Protein MSI1 Functions in a Histone Deacetylase Complex to Fine-Tune Abscisic Acid Signaling.
    8. SCL15 acts as an HDA19-associated regulator to repress embryonic traits in seedlings.
      Title: SCARECROW-LIKE15 interacts with HISTONE DEACETYLASE19 and is essential for repressing the seed maturation programme.
    9. HDC1 is a ubiquitously expressed nuclear protein that interacts with at least two deacetylases (HDA6 and HDA19), promotes histone deacetylation, and attenuates derepression of genes under water stress.
      Title: Histone deacetylase complex1 expression level titrates plant growth and abscisic acid sensitivity in Arabidopsis.
    10. HDA19 and HSL1 may act together to repress seed maturation gene expression during germination. HDA19 and HSL1 may play a vital role during embryogenesis.
      Title: HISTONE DEACETYLASE19 interacts with HSL1 and participates in the repression of seed maturation genes in Arabidopsis seedlings.
    Submit: New GeneRIF Correction See all GeneRIFs (18)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    NM_001085042.1
    NM_119974.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables histone deacetylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone deacetylase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone deacetylase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables histone deacetylase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within DNA-mediated transformation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within defense response to bacterium IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within jasmonic acid and ethylene-dependent systemic resistance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of response to salt stress IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of stem cell population maintenance IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of multicellular organismal development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of Sin3-type complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of histone deacetylase complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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
    histone deacetylase 1
    NP_001078511.1
    • histone deacetylase 1 (HD1); CONTAINS InterPro DOMAIN/s: Histone deacetylase (InterPro:IPR003084), Histone deacetylase superfamily (InterPro:IPR000286); BEST Arabidopsis thaliana protein match is: histone deacetylase 6 (TAIR:AT5G63110.1); Has 8759 Blast hits to 8549 proteins in 1452 species: Archae - 219; Bacteria - 3192; Metazoa - 1525; Fungi - 536; Plants - 478; Viruses - 0; Other Eukaryotes - 2809 (source: NCBI BLink).
    NP_195526.1
    • histone deacetylase 1 (HD1); CONTAINS InterPro DOMAIN/s: Histone deacetylase (InterPro:IPR003084), Histone deacetylase superfamily (InterPro:IPR000286); BEST Arabidopsis thaliana protein match is: histone deacetylase 6 (TAIR:AT5G63110.1); Has 8765 Blast hits to 8554 proteins in 1452 species: Archae - 219; Bacteria - 3185; Metazoa - 1529; Fungi - 558; Plants - 480; Viruses - 0; Other Eukaryotes - 2794 (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_003075.7 Reference assembly

      Range
      17896278..17899509 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_119974.4 → NP_195526.1  histone deacetylase 1 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_195526.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      O22446, Q0WWG3, Q9SZL3
      UniProtKB/TrEMBL
      A0A178UVX8, A0A5S9XZQ1
      Conserved Domains (1) summary
      cl17011
      Location:17 → 395
      Arginase_HDAC; Arginase-like and histone-like hydrolases

    2. NM_001085042.1 → NP_001078511.1  histone deacetylase 1 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001078511.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A8MSD0
      Conserved Domains (2) summary
      PTZ00063
      Location:16 → 407
      PTZ00063; histone deacetylase; Provisional
      cl17011
      Location:17 → 395
      Arginase_HDAC; Arginase-like and histone-like hydrolases
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O22446.2

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