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Review
. 2023 Jul 5;24(7):e57215.
doi: 10.15252/embr.202357215. Epub 2023 Jun 13.

Dicer structure and function: conserved and evolving features

David Zapletal  1   2 , Karel Kubicek  1   3 , Petr Svoboda  3 , Richard Stefl  1   2
Affiliations
Review

Dicer structure and function: conserved and evolving features

David Zapletal et al. EMBO Rep. .

Abstract

RNase III Dicer produces small RNAs guiding sequence-specific regulations, with important biological roles in eukaryotes. Major Dicer-dependent mechanisms are RNA interference (RNAi) and microRNA (miRNA) pathways, which employ distinct types of small RNAs. Small interfering RNAs (siRNAs) for RNAi are produced by Dicer from long double-stranded RNA (dsRNA) as a pool of different small RNAs. In contrast, miRNAs have specific sequences because they are precisely cleaved out from small hairpin precursors. Some Dicer homologs efficiently generate both, siRNAs and miRNAs, while others are adapted for biogenesis of one small RNA type. Here, we review the wealth of recent structural analyses of animal and plant Dicers, which have revealed how different domains and their adaptations contribute to substrate recognition and cleavage in different organisms and pathways. These data imply that siRNA generation was Dicer's ancestral role and that miRNA biogenesis relies on derived features. While the key element of functional divergence is a RIG-I-like helicase domain, Dicer-mediated small RNA biogenesis also documents the impressive functional versatility of the dsRNA-binding domain.

Keywords: Dicer; dsRBD; helicase; miRNA; siRNA.

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Conflict of interest statement

The authors declare that they have no conflict of interest.

Figures

Figure 1
Figure 1. Dicer architecture
(A) Domain organization of selected Dicer and Dicer‐like proteins across eukaryotic kingdoms. Animal proteins are in a black font, fungi in brown, plants in green, and Protista in blue. Abbreviations of species names: H.s.—Homo sapiens, D.m.—Drosophila melanogaster, C.e.—Caenorhabditis elegans, N.v.—Nematostella vectensis (sea anemone), A.q.—Amphimedon queenslandica (sponge), N.c.—Neurospora crassa (red bread mold), S.t.—Sporotrichum thermophile (thermophilic fungus), S.p.—Schizosaccharomyces pombe (fission yeast), K.p.—Kluyveromyces polysporus, A.t.—Arabidopsis thaliana, D.d.—Dictyostelium discoideum (slime mold), T.t.—Tetrahymena thermophila, G.i.—Giardia intestinalis, and N.g.—Naegleria gruberi. Schemes were built based on domain annotations in Genbank, conserved domain search, sequence alignments, and inspection of AlphaFold predictions (Varadi et al, 2022). (B) Exploded and normal views of mammalian Dicer [PDB ID: 7YZ4] architecture depicting the key structural modules (Zapletal et al, 2022). (C) Comparison of the folds of the PAZ domain of S. pombe (gray fold) and H. sapiens (green fold). The red connector helix was retained in the fold to indicate orientation of the fold relative to the rest of Dicer. S. pombe fold is based on AlphaFold (Varadi et al, 2022), for the human Dicer a published structure [PDB ID: 5ZAM] was used (Liu et al, 2018). (D) A ribbon model of Dicer of Giardia intestinalis based on its crystal structure [PDB ID: 2FFL] (MacRae et al, 2006). This Dicer represents a simpler variant lacking the base and the C‐terminal dsRBD. (E) A ribbon model of the full architecture of Dicer‐2 of Drosophila melanogaster [PDB ID: 7W0B] (Su et al, 2022).
Figure 2
Figure 2. Dicer substrates and principles of their dicing
(A) Schematic representation of origins of different dsRNA substrates and their key features. Genomic transcripts producing dsRNA can originate from repetitive transcripts in pathways protecting genome integrity, or from genic sequences in pathways regulating gene expression. (B) Two modes of substrate processing. In the processive mode, Dicer is dicing long dsRNA molecules in a set of consecutive dicing where ATP‐dependent activity of the helicase domain “feeds” the substrate into Dicer. In the distributive mode, Dicer performs a single cleavage and then binds a new substrate. (C) Variability of lengths of pre‐miRNAs in human, C. elegans, D. melanogaster and A. thaliana. Pre‐miRNA lengths were estimated for miRNAs having both mature miRNA strands annotated in the miRBase (Kozomara et al, 2019). The curve was smoothed by calculating average length for five adjacent miRNAs, points in the graph correspond to the central size of the five. (D) Several examples of murine mirtrons and miRNA stem‐loop miRNA precursors from the sponge Amphimedon and slime mold Dictyostelium. Stem‐loop structures were obtained from miRBase (Kozomara et al, 2019). Annotated mature miRNAs are highlighted in red font when on the ascending strand (5p miRNA) and blue font when on descending strand (3p miRNA).
Figure 3
Figure 3. Substrate recognition and dicing by Dicer
(A) Substrate recognition and threading of dsRNA substrate through the helicase domain exemplified on Drosophila Dicer‐2 (PDB IDs: 7W0B, 7W0A [monomer], and 7W0E) (Su et al, 2022). (B) Substrate recognition involving PAZ domain exemplified by miRNA recognition by mouse Dicer‐1 (PDB ID: 7YZ4, 7YYM, and 7YYN) (Zapletal et al, 2022). In the dicing state, the helicase becomes flexible and its precise position cannot be determined. (C) Overlay of the dicing state of human Dicer‐1 (in yellow) and Drosophila Dicer–1 (in magenta; PDB IDs: 7XW2 and 8DG7) (Jouravleva et al, ; Lee et al, 2023b). (D) Dicing states of human, murine and Arabidopsis Dicers (PDB IDs: 7XW2, 7YYN, and 7VG2; Wang et al, ; Zapletal et al, ; Lee et al, 2023b). Position of the helicase domain in these dicing states was not determined.
Figure 4
Figure 4. Different modes of RNA binding by dsRBD in substrate selection, dicing, and substrate release by Dicer
(A) Overview of Dicer cofactors that contain dsRBD. (B) In pre‐dicing state, the internal dsRBD of mouse Dicer unusually uses its β‐sheet surface to recognize RNA (Zapletal et al, ; PDB ID: 7YYM). (C) In dicing state, the internal dsRBD of mouse Dicer utilizes its α‐helical face for RNA recognition (Zapletal et al, ; PDB ID: 7YYN). (D) TABRB2 dsRBD1 and 2 bind the central region of pre‐miRNA (Zapletal et al, ; PDB ID: 7ZPK). (E) Dicer‐1 dsRBD and Loqs‐PB dsRBD encircle the RNA and lock it in the catalytic site (Jouravleva et al, ; PDB ID: 8DFV). (F) While Dicer–2 releases the substrate, R2D2 asymmetrically recognizes the end of the siRNA duplex with the higher base‐pairing stability (PDB ID: 7V6C). dDcr‐1, Drosophila Dicer–1; dDcr–2, Drosophila Dicer–2; mDicer, murine Dicer1.
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References

    1. Aderounmu AM, Aruscavage PJ, Kolaczkowski B, Bass BL (2023) Ancestral protein reconstruction reveals evolutionary events governing variation in Dicer helicase function. Elife 12: e85120 - PMC - PubMed
    1. Bartel DP (2018) Metazoan microRNAs. Cell 173: 20–51 - PMC - PubMed
    1. Bass BL, Hurst SR, Singer JD (1994) Binding properties of newly identified Xenopus proteins containing dsRNA‐binding motifs. Curr Biol 4: 301–314 - PubMed
    1. Bernstein E, Caudy AA, Hammond SM, Hannon GJ (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409: 363–366 - PubMed
    1. Blaszczyk J, Gan J, Tropea JE, Court DL, Waugh DS, Ji X (2004) Noncatalytic assembly of ribonuclease III with double‐stranded RNA. Structure 12: 457–466 - PubMed