8yih

Structural highlights

Function

DCR2_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]}

References

1. ↑ Lee YS, Nakahara K, Pham JW, Kim K, He Z, Sontheimer EJ, Carthew RW. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell. 2004 Apr 2;117(1):69-81. PMID:15066283 doi:10.1016/s0092-8674(04)00261-2
2. ↑ Tomari Y, Matranga C, Haley B, Martinez N, Zamore PD. A protein sensor for siRNA asymmetry. Science. 2004 Nov 19;306(5700):1377-80. PMID:15550672 doi:10.1126/science.1102755
3. ↑ Galiana-Arnoux D, Dostert C, Schneemann A, Hoffmann JA, Imler JL. Essential function in vivo for Dicer-2 in host defense against RNA viruses in drosophila. Nat Immunol. 2006 Jun;7(6):590-7. PMID:16554838 doi:10.1038/ni1335
4. ↑ Deddouche S, Matt N, Budd A, Mueller S, Kemp C, Galiana-Arnoux D, Dostert C, Antoniewski C, Hoffmann JA, Imler JL. The DExD/H-box helicase Dicer-2 mediates the induction of antiviral activity in drosophila. Nat Immunol. 2008 Dec;9(12):1425-32. PMID:18953338 doi:10.1038/ni.1664
5. ↑ Zhou R, Czech B, Brennecke J, Sachidanandam R, Wohlschlegel JA, Perrimon N, Hannon GJ. Processing of Drosophila endo-siRNAs depends on a specific Loquacious isoform. RNA. 2009 Oct;15(10):1886-95. PMID:19635780 doi:10.1261/rna.1611309
6. ↑ Hartig JV, Förstemann K. Loqs-PD and R2D2 define independent pathways for RISC generation in Drosophila. Nucleic Acids Res. 2011 May;39(9):3836-51. PMID:21245036 doi:10.1093/nar/gkq1324
7. ↑ Cenik ES, Fukunaga R, Lu G, Dutcher R, Wang Y, Tanaka Hall TM, Zamore PD. Phosphate and R2D2 restrict the substrate specificity of Dicer-2, an ATP-driven ribonuclease. Mol Cell. 2011 Apr 22;42(2):172-84. PMID:21419681 doi:10.1016/j.molcel.2011.03.002
8. ↑ Fukunaga R, Han BW, Hung JH, Xu J, Weng Z, Zamore PD. Dicer partner proteins tune the length of mature miRNAs in flies and mammals. Cell. 2012 Oct 26;151(3):533-46. PMID:23063653 doi:10.1016/j.cell.2012.09.027
9. ↑ Marques JT, Wang JP, Wang X, de Oliveira KP, Gao C, Aguiar ER, Jafari N, Carthew RW. Functional specialization of the small interfering RNA pathway in response to virus infection. PLoS Pathog. 2013;9(8):e1003579. PMID:24009507 doi:10.1371/journal.ppat.1003579
10. ↑ Fukunaga R, Colpan C, Han BW, Zamore PD. Inorganic phosphate blocks binding of pre-miRNA to Dicer-2 via its PAZ domain. EMBO J. 2014 Feb 18;33(4):371-84. PMID:24488111 doi:10.1002/embj.201387176
11. ↑ Sinha NK, Trettin KD, Aruscavage PJ, Bass BL. Drosophila dicer-2 cleavage is mediated by helicase states that are modulated by Loquacious-PD. Mol Cell. 2015 May 7;58(3):406-17. PMID:25891075 doi:10.1016/j.molcel.2015.03.012
12. ↑ Liang C, Wang Y, Murota Y, Liu X, Smith D, Siomi MC, Liu Q. TAF11 Assembles the RISC Loading Complex to Enhance RNAi Efficiency. Mol Cell. 2015 Sep 3;59(5):807-18. PMID:26257286 doi:10.1016/j.molcel.2015.07.006
13. ↑ Wang Z, Wu D, Liu Y, Xia X, Gong W, Qiu Y, Yang J, Zheng Y, Li J, Wang YF, Xiang Y, Hu Y, Zhou X. Drosophila Dicer-2 has an RNA interference-independent function that modulates Toll immune signaling. Sci Adv. 2015 Oct 16;1(9):e1500228. PMID:26601278 doi:10.1126/sciadv.1500228
14. ↑ Kandasamy SK, Fukunaga R. Phosphate-binding pocket in Dicer-2 PAZ domain for high-fidelity siRNA production. Proc Natl Acad Sci U S A. 2016 Dec 6;113(49):14031-14036. PMID:27872309 doi:10.1073/pnas.1612393113
15. ↑ Kandasamy SK, Zhu L, Fukunaga R. The C-terminal dsRNA-binding domain of Drosophila Dicer-2 is crucial for efficient and high-fidelity production of siRNA and loading of siRNA to Argonaute2. RNA. 2017 Jul;23(7):1139-1153. PMID:28416567 doi:10.1261/rna.059915.116
16. ↑ Trettin KD, Sinha NK, Eckert DM, Apple SE, Bass BL. Loquacious-PD facilitates Drosophila Dicer-2 cleavage through interactions with the helicase domain and dsRNA. Proc Natl Acad Sci U S A. 2017 Sep 19;114(38):E7939-E7948. PMID:28874570 doi:10.1073/pnas.1707063114
17. ↑ Tants JN, Fesser S, Kern T, Stehle R, Geerlof A, Wunderlich C, Juen M, Hartlmuller C, Bottcher R, Kunzelmann S, Lange O, Kreutz C, Forstemann K, Sattler M. Molecular basis for asymmetry sensing of siRNAs by the Drosophila Loqs-PD/Dcr-2 complex in RNA interference. Nucleic Acids Res. 2017 Oct 13. doi: 10.1093/nar/gkx886. PMID:29040648 doi:http://dx.doi.org/10.1093/nar/gkx886
18. ↑ Sinha NK, Iwasa J, Shen PS, Bass BL. Dicer uses distinct modules for recognizing dsRNA termini. Science. 2017 Dec 21. pii: science.aaq0921. doi: 10.1126/science.aaq0921. PMID:29269422 doi:http://dx.doi.org/10.1126/science.aaq0921
19. ↑ Coll O, Guitart T, Villalba A, Papin C, Simonelig M, Gebauer F. Dicer-2 promotes mRNA activation through cytoplasmic polyadenylation. RNA. 2018 Apr;24(4):529-539. PMID:29317541 doi:10.1261/rna.065417.117
20. ↑ Fukunaga R. Loquacious-PD removes phosphate inhibition of Dicer-2 processing of hairpin RNAs into siRNAs. Biochem Biophys Res Commun. 2018 Apr 15;498(4):1022-1027. PMID:29550490 doi:10.1016/j.bbrc.2018.03.108
21. ↑ Donelick HM, Talide L, Bellet M, Aruscavage PJ, Lauret E, Aguiar ERGR, Marques JT, Meignin C, Bass BL. In vitro studies provide insight into effects of Dicer-2 helicase mutations in Drosophila melanogaster. RNA. 2020 Dec;26(12):1847-1861. PMID:32843367 doi:10.1261/rna.077289.120
22. ↑ Naganuma M, Tadakuma H, Tomari Y. Single-molecule analysis of processive double-stranded RNA cleavage by Drosophila Dicer-2. Nat Commun. 2021 Jul 13;12(1):4268. PMID:34257295 doi:10.1038/s41467-021-24555-1
23. ↑ Jonely M, Singh RK, Donelick HM, Bass BL, Noriega R. Loquacious-PD regulates the terminus-dependent molecular recognition of Dicer-2 toward double-stranded RNA. Chem Commun (Camb). 2021 Oct 19;57(83):10879-10882. PMID:34590626 doi:10.1039/d1cc03843e
24. ↑ Yamaguchi S, Naganuma M, Nishizawa T, Kusakizako T, Tomari Y, Nishimasu H, Nureki O. 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. PMID:35768503 doi:http://dx.doi.org/10.1038/s41586-022-04790-2
25. ↑ Su S, Wang J, Deng T, Yuan X, He J, Liu N, Li X, Huang Y, Wang HW, Ma J. Structural insights into dsRNA processing by Drosophila Dicer-2-Loqs-PD. Nature. 2022 Jul;607(7918):399-406. doi: 10.1038/s41586-022-04911-x. Epub 2022, Jun 29. PMID:35768513 doi:http://dx.doi.org/10.1038/s41586-022-04911-x