Ago hook and RNA helicase motifs underpin dual roles for SDE3 in antiviral defense and silencing of nonconserved intergenic regions

Mol Cell. 2012 Oct 12;48(1):109-20. doi: 10.1016/j.molcel.2012.07.028. Epub 2012 Aug 30.


In Arabidopsis thaliana, the putative RNA-helicase SDE3 assists posttranscriptional-gene-silencing (PTGS) amplification by RNA-dependent-RNA-polymerase-6 (RDR6). SDE3 homologs in Drosophila, worm and human contribute to silence viruses, transposons or recently duplicated genes but the underlying mechanisms remain largely unknown. Here, we demonstrate that SDE3 is present with the PTGS effectors AGO1 and AGO2 in higher-order protein complexes owing to a specialized GW-repeat-containing C-terminal domain. We uncover an essential contribution of the RNA-helicase activity and a facilitating role for AGO binding in SDE3 action, which occurs downstream of RDR6. We show that these biochemical properties underpin dual roles for SDE3 in antiviral defense and, unexpectedly, in transposon silencing via a hitherto unanticipated pathway that correlates with DNA methylation, suggesting a continuum of action between PTGS and chromatin-level silencing. We identified endogenous SDE3 targets corresponding to nonconserved intergenic regions, transposons and recently evolved pseudogenes, unraveling striking functional convergences among plant and metazoan SDE3 pathways.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Animals
  • Arabidopsis / genetics*
  • Arabidopsis / metabolism*
  • Arabidopsis / virology
  • Arabidopsis Proteins / chemistry*
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism*
  • Argonaute Proteins / chemistry
  • Argonaute Proteins / metabolism
  • Conserved Sequence
  • DNA Methylation
  • DNA, Intergenic / genetics*
  • DNA, Intergenic / metabolism
  • DNA, Plant / genetics*
  • DNA, Plant / metabolism
  • Humans
  • Models, Biological
  • Molecular Sequence Data
  • Protein Interaction Domains and Motifs
  • RNA Helicases / chemistry*
  • RNA Helicases / genetics
  • RNA Helicases / metabolism*
  • RNA Interference
  • RNA-Binding Proteins / chemistry
  • RNA-Binding Proteins / metabolism
  • RNA-Dependent RNA Polymerase / metabolism
  • Sequence Homology, Amino Acid


  • AGO1 protein, Arabidopsis
  • Arabidopsis Proteins
  • Argonaute Proteins
  • DNA, Intergenic
  • DNA, Plant
  • RNA-Binding Proteins
  • argonaute 2 protein, Arabidopsis
  • SDE3 protein, Arabidopsis
  • RDR6 protein, Arabidopsis
  • RNA-Dependent RNA Polymerase
  • RNA Helicases