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    RDR6 RNA-dependent RNA polymerase 6 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 824112, updated on 18-Sep-2024

    Summary

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    Official Symbol
    RDR6
    Official Full Name
    RNA-dependent RNA polymerase 6
    Primary source
    TAIR:AT3G49500
    Locus tag
    AT3G49500
    See related
    Araport:AT3G49500
    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
    AtRDR6; RNA-dependent RNA polymerase 6; SDE1; SGS2; SILENCING DEFECTIVE 1; SUPPRESSOR OF GENE SILENCING 2
    Summary
    Encodes RNA-dependent RNA polymerase. Involved in trans-acting siRNA and other siRNA biogenesis. Required for post-transcriptional gene silencing and natural virus resistance.
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    Genomic context

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    See RDR6 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    3
    Sequence:
    Chromosome: 3; NC_003074.8 (18348974..18353673, complement)

    Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene nascent polypeptide-associated complex subunit alpha-like protein 2 Neighboring gene F-box/FBD/LRR protein Neighboring gene uncharacterized protein Neighboring gene F-box family protein Neighboring gene F-box and associated interaction domains-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. The Arabidopsis miR472-RDR6 silencing pathway modulates PAMP- and effector-triggered immunity through the post-transcriptional control of disease resistance genes. Boccara M, et al. PLoS Pathog, 2014 Jan. PMID 24453975, Free PMC Article
    2. Biochemical activities of Arabidopsis RNA-dependent RNA polymerase 6. Curaba J, et al. J Biol Chem, 2008 Feb 8. PMID 18063577, Free PMC Article
    3. Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis. Cuperus JT, et al. Nat Struct Mol Biol, 2010 Aug. PMID 20562854, Free PMC Article
    4. RNA-dependent RNA polymerase 6 is required for efficient hpRNA-induced gene silencing in plants. Harmoko R, et al. Mol Cells, 2013 Mar. PMID 23456296, Free PMC Article
    5. The initiation of epigenetic silencing of active transposable elements is triggered by RDR6 and 21-22 nucleotide small interfering RNAs. Nuthikattu S, et al. Plant Physiol, 2013 May. PMID 23542151, Free PMC Article

    See all (35) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A small peptide inhibits siRNA amplification in plants by mediating autophagic degradation of SGS3/RDR6 bodies.
      Title: A small peptide inhibits siRNA amplification in plants by mediating autophagic degradation of SGS3/RDR6 bodies.
    2. Synergy between the anthocyanin and RDR6/SGS3/DCL4 siRNA pathways expose hidden features of Arabidopsis carbon metabolism.
      Title: Synergy between the anthocyanin and RDR6/SGS3/DCL4 siRNA pathways expose hidden features of Arabidopsis carbon metabolism.
    3. CHH and CHG methylation coincides spatially and temporally with RDR6-dependent products derived from the central and 3' regions of the coding sequence, and requires the components of the RNA-directed DNA methylation pathway NRPE1, DRD1 and DRM2, but not CLSY1, NRPD1, RDR2 or DCL3, suggesting that RDR6-dependent products, namely long dsRNAs and/or siRNAs, trigger post-transcriptional gene-dependent DNA methylation.
      Title: Post-transcriptional gene silencing triggers dispensable DNA methylation in gene body in Arabidopsis.
    4. DCL2- and RDR6-dependent transitive silencing of SMXL4 and SMXL5 in Arabidopsis dcl4 mutants causes defective phloem transport and carbohydrate over-accumulation
      Title: DCL2- and RDR6-dependent transitive silencing of SMXL4 and SMXL5 in Arabidopsis dcl4 mutants causes defective phloem transport and carbohydrate over-accumulation.
    5. This expression-dependent RdDM mechanism functions through RNAi degradation of transposable element mRNAs into small RNAs guided by the RNA-dependent RNA polymerase 6 (RDR6) protein and is therefore referred to as RDR6-RdDM.We identified a new mechanism of expression-dependent RdDM, which functions through DICER-LIKE3 (DCL3) but bypasses the requirement of both RNA polymerase IV and RDR6 (termed DCL3-RdDM).
      Title: Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation.
    6. The results show that the expression of VPg alone, independent of viral infection, is sufficient to induce the degradation of SGS3 and its intimate partner, RDR6.
      Title: The Potyvirus Silencing Suppressor Protein VPg Mediates Degradation of SGS3 via Ubiquitination and Autophagy Pathways.
    7. Mungbean yellow mosaic Indian virus AC2 interferes with the biogenesis of siRNA by interacting and blocking the RDR6 activity.
      Title: Mungbean yellow mosaic Indian virus encoded AC2 protein suppresses RNA silencing by inhibiting Arabidopsis RDR6 and AGO1 activities.
    8. Data show that the lethality of decapping mutants is suppressed by impairing RNA-dependent RNA polymerase 6 (RDR6) activity.
      Title: In plants, decapping prevents RDR6-dependent production of small interfering RNAs from endogenous mRNAs.
    9. The Arabidopsis miR472-RDR6 silencing pathway modulates PAMP- and effector-triggered immunity through the post-transcriptional control of disease resistance genes.
      Title: The Arabidopsis miR472-RDR6 silencing pathway modulates PAMP- and effector-triggered immunity through the post-transcriptional control of disease resistance genes.
    10. RDR6-RdDM functions to recognize active Polymerase II-derived Transposable element (TE) mRNA transcripts to both trigger and correctively reestablish TE methylation and epigenetic silencing.
      Title: The initiation of epigenetic silencing of active transposable elements is triggered by RDR6 and 21-22 nucleotide small interfering RNAs.
    Submit: New GeneRIF Correction See all GeneRIFs (24)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    NM_001339424.1
    NM_001339425.1
    NM_001339426.1
    NM_114810.3

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables RNA-dependent RNA polymerase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within RNAi-mediated antiviral immune response IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within carpel development IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within defense response to virus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within gynoecium development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within leaf development IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    NOT involved_in miRNA processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within post-transcriptional gene silencing TAS
    Traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of_or_within recognition of pollen IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulatory ncRNA-mediated gene silencing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within siRNA processing IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within siRNA processing TAS
    Traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of_or_within ta-siRNA processing 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
    RNA-dependent RNA polymerase 6
    NP_190519.1
    • RNA-dependent RNA polymerase 6 (RDR6); CONTAINS InterPro DOMAIN/s: RNA-dependent RNA polymerase, eukaryotic-type (InterPro:IPR007855); BEST Arabidopsis thaliana protein match is: RNA-dependent RNA polymerase 1 (TAIR:AT1G14790.1); Has 633 Blast hits to 609 proteins in 113 species: Archae - 0; Bacteria - 0; Metazoa - 73; Fungi - 284; Plants - 204; Viruses - 2; Other Eukaryotes - 70 (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
      18348974..18353673 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001339423.1 → NP_001327617.1  RNA-dependent RNA polymerase 6 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      A0A1I9LSW2, Q9LKP0, Q9SG02
      UniProtKB/TrEMBL
      A0A7G2ETS9

    2. NM_114810.3 → NP_190519.1  RNA-dependent RNA polymerase 6 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_190519.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      A0A1I9LSW2, Q9LKP0, Q9SG02
      UniProtKB/TrEMBL
      A0A7G2ETS9
      Conserved Domains (2) summary
      pfam05183
      Location:424 → 940
      RdRP; RNA dependent RNA polymerase
      cl17169
      Location:68 → 112
      RRM_SF; RNA recognition motif (RRM) superfamily

    3. NM_001339426.1 → NP_001327620.1  RNA-dependent RNA polymerase 6 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      A0A1I9LSW2, Q9LKP0, Q9SG02
      UniProtKB/TrEMBL
      A0A7G2ETS9

    4. NM_001339425.1 → NP_001327619.1  RNA-dependent RNA polymerase 6 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      A0A1I9LSW2, Q9LKP0, Q9SG02
      UniProtKB/TrEMBL
      A0A7G2ETS9

    5. NM_001339424.1 → NP_001327618.1  RNA-dependent RNA polymerase 6 [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      A0A1I9LSW2, Q9LKP0, Q9SG02
      UniProtKB/TrEMBL
      A0A7G2ETS9
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9SG02.1

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