Structure of the Dicer-2-R2D2 heterodimer bound to a small RNA duplex

Nature. 2022 Jul;607(7918):393-398. doi: 10.1038/s41586-022-04790-2. Epub 2022 Jun 29.

Abstract

In flies, Argonaute2 (Ago2) and small interfering RNA (siRNA) form an RNA-induced silencing complex to repress viral transcripts1. The RNase III enzyme Dicer-2 associates with its partner protein R2D2 and cleaves long double-stranded RNAs to produce 21-nucleotide siRNA duplexes, which are then loaded into Ago2 in a defined orientation2-5. Here we report cryo-electron microscopy structures of the Dicer-2-R2D2 and Dicer-2-R2D2-siRNA complexes. R2D2 interacts with the helicase domain and the central linker of Dicer-2 to inhibit the promiscuous processing of microRNA precursors by Dicer-2. Notably, our structure represents the strand-selection state in the siRNA-loading process, and reveals that R2D2 asymmetrically recognizes the end of the siRNA duplex with the higher base-pairing stability, and the other end is exposed to the solvent and is accessible by Ago2. Our findings explain how R2D2 senses the thermodynamic asymmetry of the siRNA and facilitates the siRNA loading into Ago2 in a defined orientation, thereby determining which strand of the siRNA duplex is used by Ago2 as the guide strand for target silencing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Argonaute Proteins / metabolism
  • Base Pairing
  • Cryoelectron Microscopy*
  • Drosophila Proteins* / chemistry
  • Drosophila Proteins* / metabolism
  • Drosophila Proteins* / ultrastructure
  • Drosophila melanogaster / chemistry
  • Drosophila melanogaster / genetics
  • Drosophila melanogaster / metabolism
  • MicroRNAs / metabolism
  • Protein Multimerization
  • RNA Helicases* / chemistry
  • RNA Helicases* / metabolism
  • RNA Helicases* / ultrastructure
  • RNA Interference
  • RNA, Double-Stranded* / chemistry
  • RNA, Double-Stranded* / metabolism
  • RNA, Double-Stranded* / ultrastructure
  • RNA, Small Interfering* / chemistry
  • RNA, Small Interfering* / metabolism
  • RNA, Small Interfering* / ultrastructure
  • RNA-Binding Proteins* / chemistry
  • RNA-Binding Proteins* / metabolism
  • RNA-Binding Proteins* / ultrastructure
  • RNA-Induced Silencing Complex / metabolism
  • Ribonuclease III* / chemistry
  • Ribonuclease III* / metabolism
  • Ribonuclease III* / ultrastructure

Substances

  • AGO2 protein, Drosophila
  • Argonaute Proteins
  • Drosophila Proteins
  • MicroRNAs
  • R2D2 protein, Drosophila
  • RNA, Double-Stranded
  • RNA, Small Interfering
  • RNA-Binding Proteins
  • RNA-Induced Silencing Complex
  • DCR-2 protein, Drosophila
  • Ribonuclease III
  • RNA Helicases