7v6b | pdb_00007v6b
Structure of the Dicer-2-R2D2 heterodimer
Structural highlights
FunctionDCR2_DROME Double-stranded RNA (dsRNA) endoribonuclease which cleaves endogenous (endo), exogenous (exo), and viral dsRNAs to produce short interfering RNAs (siRNAs) (PubMed:15066283, PubMed:16554838, PubMed:18953338, PubMed:19635780, PubMed:21419681, PubMed:23063653, PubMed:24009507, PubMed:24488111, PubMed:25891075, PubMed:27872309, PubMed:28416567, PubMed:28874570, PubMed:29040648, PubMed:29317541, PubMed:29550490, PubMed:32843367, PubMed:34257295, PubMed:34590626, PubMed:35768513). The generated siRNAs then mediate gene silencing, also called RNA interference (RNAi), by controlling the elimination of endogenous transcripts from mobile and repetitive DNA elements of the genome as well as exogenous RNA of viral origin (PubMed:15066283, PubMed:16554838, PubMed:18953338, PubMed:21419681, PubMed:23063653, PubMed:24009507, PubMed:24488111, PubMed:27872309, PubMed:28416567, PubMed:28874570, PubMed:29040648, PubMed:29317541, PubMed:29550490, PubMed:32843367, PubMed:34257295, PubMed:34590626, PubMed:35768513). Also acts in an RNAi-independent manner to activate translation through cytoplasmic polyadenylation (PubMed:29317541). As well as its role in dsRNA processing, essential in several steps of the siRNA biogenesis pathway, including siRNA loading into the Argonaute 2 (AGO2)-containing RNA-induced silencing complex (siRISC), length-dependent dicing and guide strand selection for target silencing by the siRISC (PubMed:15066283, PubMed:15550672, PubMed:21245036, PubMed:21419681, PubMed:26257286, PubMed:27872309, PubMed:28416567, PubMed:34590626, PubMed:35768503). Cleaves dsRNAs into siRNAs that are predominantly around twenty-one nucleotides in length (PubMed:15066283, PubMed:21419681, PubMed:23063653, PubMed:24488111, PubMed:27872309, PubMed:28416567, PubMed:28874570, PubMed:29269422, PubMed:29550490, PubMed:32843367, PubMed:34257295, PubMed:35768513). Displays a preference for binding and processing blunt termini (BLT), likely non-self dsRNAs, over dsRNAs with 2 nucleotides 3' overhanging (3'ovr) termini, which are typically the structure of endogenous dsRNAs (PubMed:25891075, PubMed:29269422, PubMed:29550490, PubMed:32843367, PubMed:34257295, PubMed:34590626). According to many reports, the cleavage reaction mode of the enzyme changes according to the termini of the dsRNA substrate (PubMed:21419681, PubMed:25891075, PubMed:28416567, PubMed:29269422, PubMed:32843367, PubMed:34590626). BLT dsRNAs undergo an ATP-dependent processive reaction whereby multiple siRNAs of heterogeneous sizes are produced before the enzyme dissociates (PubMed:21419681, PubMed:25891075, PubMed:28416567, PubMed:29269422, PubMed:29550490, PubMed:32843367, PubMed:34590626). In contrast, dsRNAs with 3'ovr termini, which are typically the structure of endogenous dsRNAs, undergo ATP-independent, distributive cleavage whereby the enzyme dissociates after each cleavage to produce siRNAs of around 22 nucleotides (PubMed:25891075, PubMed:29269422, PubMed:32843367, PubMed:34590626). However, according to another report, the mode of cleavage reaction is not affected by the terminal structures of the dsRNAs substrates (PubMed:34257295). This report suggests that the enzyme is able to initiate processive cleavage of both BLT and 3'ovr dsRNA substrates, and only rarely initiates distributive cleavage (PubMed:34257295). During dsRNA processing and AGO2-loading, requires association with dsRNA-binding accessory proteins loqs isoform PD (loqs-PD) and r2d2 (PubMed:15550672, PubMed:21245036, PubMed:24009507, PubMed:28416567, PubMed:28874570, PubMed:29040648, PubMed:29550490). Functions with r2d2 to form the siRNA-mediated RISC loading complex (siRLC) which is responsible for Ago2-loading of endo- and exo-siRNAs (PubMed:15550672, PubMed:21245036, PubMed:28416567, PubMed:35768503). Interaction with loqs-PD increases initial binding to dsRNA substrates and promotes processing of a subset of endo- and exo-dsRNAs (PubMed:21245036, PubMed:24009507, PubMed:28874570, PubMed:29040648, PubMed:29550490, PubMed:34257295). In the absence of r2d2, may also form an alternative siRLC with loqs-PD to load siRNAs into the siRISC (PubMed:21245036). Function with loqs-PD allows the dicer enzyme to cleave endogenous dsRNA templates independently of their termini, and is required for ATP-dependent processing of a subset of siRNAs but is not required for antiviral RNAi (PubMed:24009507, PubMed:25891075, PubMed:29269422, PubMed:29550490, PubMed:32843367, PubMed:34590626). This suggests that the enzyme's intrinsic termini preferences function in viral defense, while function with loqs-PD allows processing of endogenous dsRNAs with diverse termini (PubMed:29269422, PubMed:32843367). However, according to another report the mode of cleavage reaction is not affected by the presence or absence of loqs-PD (PubMed:34257295). Loaded siRNAs serve as a guide to direct the siRISC to complementary RNAs to degrade them or prevent their translation (PubMed:15066283). The siRLC plays an important role in the ATP-dependent asymmetry sensing of the duplex, and is therefore also responsible for the selection of the strand that ultimately acts as the guide siRNA for the siRISC (PubMed:29040648, PubMed:35768503). Thermodynamically asymmetric siRNAs are preoriented in the siRLC by either the dsRNA-binding r2d2 protein, or the loqs-PD protein in the alternative siRLC, which preferentially bind to the most thermodynamically stable strand prior to loading onto AGO2 (PubMed:15550672, PubMed:29040648, PubMed:35768503). Both r2d2 and Dcr-2 also initiate unwinding of the siRNA duplex, at which point the heterodimer is exchanged by AGO2 (PubMed:15550672). The strand that was bound by r2d2 is discarded while the one that was bound by Dcr-2 is loaded onto Ago2 and serves as guide to direct the siRISC to complementary RNAs to degrade them or prevent their translation (PubMed:15550672). Independently of its role in RNAi, acts with the cytoplasmic poly(A) polymerase wisp to promote cytoplasmic polyadenylation and translational activation of certain messenger RNAs including r2d2 and toll (Tl) transcripts (PubMed:26601278, PubMed:29317541). Consequently it is involved in the post-transcriptional regulation of the Toll immune signaling pathway and promoting resistance to fungal and viral infections (PubMed:26601278, PubMed:29317541). As an RNA-binding protein, likely functions in cytoplasmic polyadenylation by recruiting the poly(A) RNA polymerase wisp to target mRNAs (PubMed:26601278, PubMed:29317541).[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] Publication Abstract from PubMedIn flies, Argonaute2 (Ago2) and small interfering RNA (siRNA) form an RNA-induced silencing complex to repress viral transcripts(1). 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 orientation(2-5). 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. Structure of the Dicer-2-R2D2 heterodimer bound to a small RNA duplex.,Yamaguchi S, Naganuma M, Nishizawa T, Kusakizako T, Tomari Y, Nishimasu H, Nureki O Nature. 2022 Jul;607(7918):393-398. doi: 10.1038/s41586-022-04790-2. Epub 2022 , Jun 29. PMID:35768503[26] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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