Structural Basis for Double-Stranded RNA Processing by Dicer

  title={Structural Basis for Double-Stranded RNA Processing by Dicer},
  author={Ian J. MacRae and Kaihong Zhou and Fei Li and Adrian Repic and Angela N. Brooks and William Zacheus Cande and Paul D. Adams and Jennifer A. Doudna},
  pages={195 - 198}
The specialized ribonuclease Dicer initiates RNA interference by cleaving double-stranded RNA (dsRNA) substrates into small fragments about 25 nucleotides in length. In the crystal structure of an intact Dicer enzyme, the PAZ domain, a module that binds the end of dsRNA, is separated from the two catalytic ribonuclease III (RNase III) domains by a flat, positively charged surface. The 65 angstrom distance between the PAZ and RNase III domains matches the length spanned by 25 base pairs of RNA… 

Structural determinants of RNA recognition and cleavage by Dicer

It is shown that the PAZ domain responsible for dsRNA end recognition confers this measuring ability through both its structural position and RNA-binding specificity, which explains how Dicer functions as a molecular ruler and provide a structural basis for modifying its activity in cells.

Structure of Dicer and mechanistic implications for RNAi.

Evidence is provided that Dicer is composed of three structurally rigid regions connected by flexible hinges and proposed that conformational flexibility facilitates dsRNA binding and processing and a model for the architecture of the RNA-induced silencing complex (RISC)-loading complex is proposed.

Short RNA duplexes guide sequence-dependent cleavage by human Dicer.

Examination of the structure of natural pre-microRNAs (pre-miRNAs) suggests that they may form bipartite substrates with complementary mRNA sequences, and thus induce seed-independent Dicer cleavage, which suggests a flexible mechanism for substrate selectivity that recognizes the overall shape of an RNA helix.

The mechanism of RNase III action: how dicer dices.

  • X. Ji
  • Biology, Chemistry
    Current topics in microbiology and immunology
  • 2008
The structure and function of Dicer is being elucidated, the structurally most complicated member of the Ribonuclease III family; bacterial RNase III is comparatively much simpler.

Coordinated activities of human dicer domains in regulatory RNA processing.

Ribonuclease III and the Role of Double-Stranded RNA Processing in Bacterial Systems

This review summarizes the current state of knowledge of RNase III, and relates the structural and mechanistic features of the endonuclease to its function in dsRNA-dependent gene expression and regulation.

Dicer uses distinct modules for recognizing dsRNA termini

Structures of a Drosophila Dicer protein reveal a previously unrecognized mechanism for optimizing antiviral defense and set the stage for the discovery of helicase-dependent functions in other Dicers.

A stepwise model for double‐stranded RNA processing by ribonuclease III

Three crystal structures of RNase III in complex with double‐stranded RNA are presented, demonstrating how Mg2+ is essential for the formation of a catalytically competent protein–RNA complex, and how conformational changes in both the substrate and the protein are critical elements for assembling the catalytic complex.

Structural basis for non-catalytic and catalytic activities of ribonuclease III.

  • X. Ji
  • Biology, Chemistry
    Acta crystallographica. Section D, Biological crystallography
  • 2006
The information revealed by the structures of bacterial RNase III provides insight into the mechanism of dsRNA processing by all members of the family.

The Inside-Out Mechanism of Dicers from Budding Yeasts




Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP

The purification and properties of a recombinant human Dicer are described and it is suggested that if ATP participates in the Dicer reaction in mammalian cells, it might be involved in product release needed for the multiple turnover of the enzyme.

Structure of the nuclease domain of ribonuclease III from M. tuberculosis at 2.1 Å

  • D. AkeyJ. Berger
  • Biology, Chemistry
    Protein science : a publication of the Protein Society
  • 2005
Although globally similar to other RNase III folds, this structure has some features not observed in previously reported models, including the presence of an additional metal ion near the catalytic site, as well as conserved secondary structural elements that are proposed to have functional roles in the recognition of dsRNAs.

Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain

It is proposed that PAZ might serve as an siRNA-end-binding module for siRNA transfer in the RNA silencing pathway, and as an anchoring site for the 3′ end of guide RNA within silencing effector complexes.

Intrinsic double-stranded-RNA processing activity of Escherichia coli ribonuclease III lacking the dsRNA-binding domain.

It is shown that a truncated form of Escherichia coli RNase III lacking the dsRBD (RNase III[DeltadsRBD]) can accurately cleave small processing substrates in vitro and supports an RNaseIII mechanism of action in which the catalytic domain can function independently of the dSRBD, is dsRNA-specific, and participates in cleavage site selection.

Role for a bidentate ribonuclease in the initiation step of RNA interference

Dicer is a member of the RNase III family of nucleases that specifically cleave double-stranded RNAs, and is evolutionarily conserved in worms, flies, plants, fungi and mammals, and has a distinctive structure, which includes a helicase domain and dualRNase III motifs.

RNA interference is mediated by 21- and 22-nucleotide RNAs.

It is demonstrated that 21- and 22-nt RNA fragments are the sequence-specific mediators of RNAi, and evidence that the direction of dsRNA processing determines whether sense or antisense target RNA can be cleaved by the siRNA-protein complex is provided.