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DME HhH-GPD base excision DNA repair family protein [ Arabidopsis thaliana (thale cress) ]

Gene ID: 830335, updated on 18-Sep-2024

Summary

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Official Symbol
DME
Official Full Name
HhH-GPD base excision DNA repair family protein
Primary source
TAIR:AT5G04560
Locus tag
AT5G04560
See related
Araport:AT5G04560
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
AT5G04570; AT5G04580; DEMETER; T32M21.160; T32M21_160
Summary
Encodes a DNA glycosylase DEMETER (DME). Responsible for endosperm maternal-allele-specific hypomethylation at the MEDEA (MEA) gene. DME can excise 5-methylcytosine in vitro and when expressed in E. coli. DME establishes MEA imprinting by removing 5-methylcytosine to activate the maternal allele.
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Genomic context

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See DME in Genome Data Viewer
Location:
chromosome: 5
Exon count:
20
Sequence:
Chromosome: 5; NC_003076.8 (1309099..1318520)

Chromosome 5 - NC_003076.8Genomic Context describing neighboring genes Neighboring gene Myotubularin-like phosphatases II superfamily Neighboring gene type-1 restriction enzyme mjaxp r protein (DUF668) Neighboring gene sulfite reductase Neighboring gene RNA-binding (RRM/RBD/RNP motifs) family protein Neighboring gene S-adenosyl-L-methionine-dependent methyltransferases superfamily protein

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_003076.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. The DME demethylase regulates sporophyte gene expression, cell proliferation, differentiation, and meristem resurrection. Kim S, et al. Proc Natl Acad Sci U S A, 2021 Jul 20. PMID 34266952, Free PMC Article
  2. DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in arabidopsis. Choi Y, et al. Cell, 2002 Jul 12. PMID 12150995
  3. DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation. Gehring M, et al. Cell, 2006 Feb 10. PMID 16469697, Free PMC Article
  4. Identification of putative Arabidopsis DEMETER target genes by GeneChip analysis. Ohr H, et al. Biochem Biophys Res Commun, 2007 Dec 28. PMID 17964287, Free PMC Article
  5. Function of the DEMETER DNA glycosylase in the Arabidopsis thaliana male gametophyte. Schoft VK, et al. Proc Natl Acad Sci U S A, 2011 May 10. PMID 21518889, Free PMC Article

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Two imprinted genes primed by DEMETER in the central cell and activated by WRKY10 in the endosperm.
    Title: Two imprinted genes primed by DEMETER in the central cell and activated by WRKY10 in the endosperm.
  2. The DME demethylase regulates sporophyte gene expression, cell proliferation, differentiation, and meristem resurrection.
    Title: The DME demethylase regulates sporophyte gene expression, cell proliferation, differentiation, and meristem resurrection.
  3. DME contributes to DNA demethylase activity and susceptibility to Fusarium oxysporum infection.
    Title: DEMETER plays a role in DNA demethylation and disease response in somatic tissues of Arabidopsis.
  4. DME and ROS1 have a significant 5-hydroxymethylcytosine (5hmC) excision activity in vitro, although the study detected no 5hmC in Arabidopsis, suggesting that it is very unlikely for plants to utilize 5hmC as a DNA demethylation intermediate.
    Title: Excision of 5-hydroxymethylcytosine by DEMETER family DNA glycosylases.
  5. Histone H1 is involved in DME-mediated DNA methylation and gene regulation at imprinted loci.
    Title: Histone H1 affects gene imprinting and DNA methylation in Arabidopsis.
  6. Active DNA demethylation by DEMETER requires SSRP1 function through a distinctly different process from direct DNA methylation control.
    Title: HMG domain containing SSRP1 is required for DNA demethylation and genomic imprinting in Arabidopsis.
  7. DME is active and demethylates similar genes and transposons in the genomes of the vegetative and central cells in the male and female gametophytes
    Title: Function of the DEMETER DNA glycosylase in the Arabidopsis thaliana male gametophyte.
  8. Analyses indicate that AtLIG1 acts downstream of DME. The removal of methylated cytosine residues by DME involves the creation of DNA single-strand breaks and our results suggest that AtLIG1 repairs these breaks.
    Title: DNA LIGASE I exerts a maternal effect on seed development in Arabidopsis thaliana.
  9. control DNA methylation in Arabidopsis thaliana.[review]
    Title: [Mechanisms to control DNA methylation in Arabidopsis thaliana].
  10. Gene ontology analysis identified three molecular functions enriched in the DME-inducible RNA list: DNA or RNA binding, kinase activity, and transcription factor activity.
    Title: Identification of putative Arabidopsis DEMETER target genes by GeneChip analysis.
Submit: New GeneRIF Correction See all GeneRIFs (12)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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NM_001085058.2
NM_120538.2

Gene Ontology Provided by TAIR

Function Evidence Code Pubs
enables DNA N-glycosylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA N-glycosylase activity ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
enables DNA demethylase activity IEA
Inferred from Electronic Annotation
more info
  
enables DNA-(apurinic or apyrimidinic site) endonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables SUMO binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in base-excision repair IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within embryo development ending in seed dormancy IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within epigenetic programming in the endosperm IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within epigenetic regulation of gene expression IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in nucleus ISM
Inferred from Sequence Model
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
located_in polar nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
HhH-GPD base excision DNA repair family protein
NP_001078527.1
  • DEMETER (DME); CONTAINS InterPro DOMAIN/s: DNA glycosylase (InterPro:IPR011257), Endonuclease III-like, iron-sulphur cluster loop motif (InterPro:IPR003651), HhH-GPD domain (InterPro:IPR003265); BEST Arabidopsis thaliana protein match is: demeter-like 1 (TAIR:AT2G36490.1); Has 3806 Blast hits to 3649 proteins in 1364 species: Archae - 237; Bacteria - 2338; Metazoa - 256; Fungi - 124; Plants - 347; Viruses - 0; Other Eukaryotes - 504 (source: NCBI BLink).
NP_196076.2
  • DEMETER (DME); CONTAINS InterPro DOMAIN/s: DNA glycosylase (InterPro:IPR011257), Endonuclease III-like, iron-sulphur cluster loop motif (InterPro:IPR003651), HhH-GPD domain (InterPro:IPR003265); BEST Arabidopsis thaliana protein match is: demeter-like 1 (TAIR:AT2G36490.1); Has 3638 Blast hits to 3482 proteins in 1335 species: Archae - 238; Bacteria - 2315; Metazoa - 178; Fungi - 96; Plants - 343; Viruses - 0; Other Eukaryotes - 468 (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_003076.8 Reference assembly

    Range
    1309099..1318520
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001342781.1 → NP_001331593.1  HhH-GPD base excision DNA repair family protein [Arabidopsis thaliana]

    Status: REVIEWED

    UniProtKB/TrEMBL
    A0A7G2F8C8

  2. NM_001085058.2 → NP_001078527.1  HhH-GPD base excision DNA repair family protein [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_001078527.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    Q1WEY5, Q84TL4, Q8LK56, Q9LZ67, Q9LZ68, Q9LZ69
    UniProtKB/TrEMBL
    A0A178UGU0, A0A5S9Y1N6, A0A654FYG5
    Conserved Domains (4) summary
    smart00478
    Location:1474 → 1626
    ENDO3c; endonuclease III
    pfam01101
    Location:299 → 375
    HMG14_17; HMG14 and HMG17
    pfam15628
    Location:1877 → 1978
    RRM_DME; RRM in Demeter
    pfam15629
    Location:1843 → 1874
    Perm-CXXC; Permuted single zf-CXXC unit

  3. NM_120538.2 → NP_196076.2  HhH-GPD base excision DNA repair family protein [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_196076.2

    Status: REVIEWED

    UniProtKB/TrEMBL
    A0A7G2F8C8
    Conserved Domains (4) summary
    smart00478
    Location:1216 → 1368
    ENDO3c; endonuclease III
    pfam01101
    Location:41 → 117
    HMG14_17; HMG14 and HMG17
    pfam15628
    Location:1619 → 1720
    RRM_DME; RRM in Demeter
    pfam15629
    Location:1585 → 1616
    Perm-CXXC; Permuted single zf-CXXC unit
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8LK56.2

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