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    EDM2 ENHANCED DOWNY MILDEW 2 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 835632, updated on 14-Nov-2024

    Summary

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    Official Symbol
    EDM2
    Official Full Name
    ENHANCED DOWNY MILDEW 2
    Primary source
    TAIR:AT5G55390
    Locus tag
    AT5G55390
    See related
    Araport:AT5G55390
    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
    ENHANCED DOWNY MILDEW 2; MTE17.10; MTE17_10
    Summary
    Encodes EDM2 (enhanced downy mildew 2). The predicted protein bears typical features of transcriptional regulators. EDM2 contains two putative bipartite nuclear localization signals (NLS) two zinc-finger-like motifs, a Proline-rich region and a large aspartic acid-rich region. Both zinc-finger-like stretches resemble the PHD (plant homeodomain) finger motif. Mutations in EDM2 comprise RPP7 mediated resistance against Hyaloperonospora parasitica isolate Hiks1 (HpHiks1). EDM2 may function as a direct or indirect regulator of RPP7 expression.
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    Genomic context

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    See EDM2 in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    18
    Sequence:
    Chromosome: 5; NC_003076.8 (22447937..22454805, complement)

    Chromosome 5 - NC_003076.8Genomic Context describing neighboring genes Neighboring gene MBOAT (membrane bound O-acyl transferase) family protein Neighboring gene MBOAT (membrane bound O-acyl transferase) family protein Neighboring gene MBOAT (membrane bound O-acyl transferase) family protein Neighboring gene miscRNA Neighboring gene Actin binding Calponin homology (CH) domain-containing 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 Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression. Lai Y, et al. PLoS Genet, 2020 Sep. PMID 32925902, Free PMC Article
    2. Mutations in EDM2 selectively affect silencing states of transposons and induce plant developmental plasticity. Tsuchiya T, et al. Sci Rep, 2013. PMID 23609044, Free PMC Article
    3. EDM2 is required for RPP7-dependent disease resistance in Arabidopsis and affects RPP7 transcript levels. Eulgem T, et al. Plant J, 2007 Mar. PMID 17253987
    4. Genome-wide distribution and functions of the AAE complex in epigenetic regulation in Arabidopsis. Zhang YZ, et al. J Integr Plant Biol, 2021 Apr. PMID 33438356
    5. Demethylation of ERECTA receptor genes by IBM1 histone demethylase affects stomatal development. Wang Y, et al. Development, 2016 Dec 1. PMID 27697902, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Growth deficiency and enhanced basal immunity in Arabidopsis thaliana mutants of EDM2, EDM3 and IBM2 are genetically interlinked.
      Title: Growth deficiency and enhanced basal immunity in Arabidopsis thaliana mutants of EDM2, EDM3 and IBM2 are genetically interlinked.
    2. The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression.
      Title: The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression.
    3. The authors show that both ibm1 and edm2 mutants display defects in production of stomatal lineage cells, which is linked to DNA hypermethylation of the ERECTA family genes, including ER, ERL1 and ERL2 Stomatal phenotypes and DNA methylation levels of ER genes in ibm1 and edm2 mutants are restored by mutations in the genes encoding the histone methyltransferase KYP and DNA methyltransferase CMT3.
      Title: Demethylation of ERECTA receptor genes by IBM1 histone demethylase affects stomatal development.
    4. EDM2 promotes IBM1 distal polyadenylation and regulates genome DNA methylation
      Title: Arabidopsis EDM2 promotes IBM1 distal polyadenylation and regulates genome DNA methylation patterns.
    5. EDM2 promotes vegetative leaf growth and leaf pavement cell morphology, and is modulated by WNK8.
      Title: Co-option of EDM2 to distinct regulatory modules in Arabidopsis thaliana development.
    6. The role of EDM2 in plant immunity is limited and does not include a function in basal defense. EDM2 acts upstream of the floral repressor FLC and downstream of WNK8 to affect floral transition.
      Title: The Arabidopsis defense component EDM2 affects the floral transition in an FLC-dependent manner.
    7. In edm2 mutants both constitutive and Hyaloperonospora parasitica isolate Hiks1-induced RPP7 transcript levels are reduced, suggesting that EDM2 is either a direct or an indirect regulator of RPP7 expression.
      Title: EDM2 is required for RPP7-dependent disease resistance in Arabidopsis and affects RPP7 transcript levels.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    NM_124921.5

    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 histone reader activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables methylated histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within defense response to fungus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in epigenetic regulation of gene expression IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within epigenetic regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in epigenetic regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in leaf pavement cell development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of heterochromatin formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of defense response to oomycetes IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of flower development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of flower development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of defense response IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of leaf development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of post-transcriptional gene silencing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in stomatal lineage progression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in transposable element silencing by heterochromatin formation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in transposable element silencing by heterochromatin formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within vegetative to reproductive phase transition of meristem IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in vegetative to reproductive phase transition of meristem IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in heterochromatin IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  
    part_of protein-containing complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ENHANCED DOWNY MILDEW 2
    NP_001190545.1
    • ENHANCED DOWNY MILDEW 2 (EDM2); CONTAINS InterPro DOMAIN/s: Zinc finger, PHD-type (InterPro:IPR001965), Zinc finger, FYVE/PHD-type (InterPro:IPR011011); BEST Arabidopsis thaliana protein match is: EDM2-like protein1 (TAIR:AT5G48090.1).
    NP_200350.2
    • ENHANCED DOWNY MILDEW 2 (EDM2); CONTAINS InterPro DOMAIN/s: Zinc finger, PHD-type (InterPro:IPR001965), Zinc finger, FYVE/PHD-type (InterPro:IPR011011); BEST Arabidopsis thaliana protein match is: EDM2-like protein1 (TAIR:AT5G48090.1); Has 807 Blast hits to 790 proteins in 126 species: Archae - 0; Bacteria - 19; Metazoa - 421; Fungi - 75; Plants - 194; Viruses - 2; Other Eukaryotes - 96 (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
      22447937..22454805 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001345123.1 → NP_001332152.1  ENHANCED DOWNY MILDEW 2 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      F4K3G5, Q9FJ71
      UniProtKB/TrEMBL
      A0A178UPD6, A0A7G2FH10
      Conserved Domains (4) summary
      cd15565
      Location:284 → 349
      PHD2_NSD; PHD finger 2 found in nuclear receptor-binding SET domain-containing (NSD) proteins
      cd15566
      Location:351 → 416
      PHD3_NSD; PHD finger 3 found in nuclear receptor-binding SET domain-containing (NSD) proteins
      pfam12047
      Location:20 → 140
      DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain
      cl22851
      Location:225 → 278
      PHD_SF; PHD finger superfamily

    2. NM_001203616.2 → NP_001190545.1  ENHANCED DOWNY MILDEW 2 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001190545.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      F4K3G5, Q9FJ71
      UniProtKB/TrEMBL
      A0A178UPD6, A0A7G2FH10
      Conserved Domains (4) summary
      cd15565
      Location:284 → 349
      PHD2_NSD; PHD finger 2 found in nuclear receptor-binding SET domain-containing (NSD) proteins
      cd15566
      Location:351 → 416
      PHD3_NSD; PHD finger 3 found in nuclear receptor-binding SET domain-containing (NSD) proteins
      pfam12047
      Location:20 → 140
      DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain
      cl22851
      Location:225 → 278
      PHD_SF; PHD finger superfamily

    3. NM_124921.5 → NP_200350.2  ENHANCED DOWNY MILDEW 2 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_200350.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      F4K3G5, Q9FJ71
      UniProtKB/TrEMBL
      A0A178UPD6, A0A7G2FH10
      Conserved Domains (4) summary
      cd15565
      Location:284 → 349
      PHD2_NSD; PHD finger 2 found in nuclear receptor-binding SET domain-containing (NSD) proteins
      cd15566
      Location:351 → 416
      PHD3_NSD; PHD finger 3 found in nuclear receptor-binding SET domain-containing (NSD) proteins
      pfam12047
      Location:20 → 140
      DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain
      cl22851
      Location:225 → 278
      PHD_SF; PHD finger superfamily
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    F4K3G5.1

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