Double-Stranded RNA Binding Protein, Staufen, Is Required for the Initiation of Rnai in Coleopteran Insects

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Double-Stranded RNA Binding Protein, Staufen, Is Required for the Initiation of Rnai in Coleopteran Insects Double-stranded RNA binding protein, Staufen, is required for the initiation of RNAi in coleopteran insects June-Sun Yoona, Kanakachari Mogilicherlaa, Dhandapani Gurusamya, Xien Chena, Shankar C. R. R. Chereddya, and Subba Reddy Pallia,1 aDepartment of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY 40546 Edited by Lynn M. Riddiford, University of Washington, Friday Harbor, WA, and approved July 6, 2018 (received for review May 31, 2018) RNA interference (RNAi) is being used to develop methods to the main contributors to differential RNAi efficiency among control pests and disease vectors. RNAi is robust and systemic in insects (13–16). Recent studies identified dsRNA digestion by coleopteran insects but is quite variable in other insects. The dsRNases and entrapment of dsRNA in endosomes as the major determinants of efficient RNAi in coleopterans, as well as its potential contributors to RNAi recalcitrance in lepidopteran insects and mechanisms of resistance, are not known. RNAi screen identified a cell lines (17). Whether or not any coleopteran insect-specific double-stranded RNA binding protein (StaufenC) as a major player in proteins contribute to robust RNAi in these insects is not known. RNAi. StaufenC homologs have been identified in only coleopteran Cells defend themselves from dsRNAs from many sources insects. Experiments in two coleopteran insects, Leptinotarsa decem- (e.g., viruses). The enzyme Dicer-2 cleaves dsRNAs to small lineata and Tribolium castaneum, showed the requirement of interfering RNAs (siRNAs), which are then incorporated into an StaufenC for RNAi, especially for processing of double-stranded RNA RNA-induced silencing complex, bind to complementary (dsRNA) to small interfering RNA. RNAi-resistant cells were selected by mRNAs, and interfere with their translation (18, 19). Key pro- exposing L. decemlineata, Lepd-SL1 cells to the inhibitor of apoptosis 1 teins including Dicer-2, R2D2, Loquacious (Loqs), and Argo- dsRNA for multiple generations. The resistant cells showed lower levels nautes involved in RNAi pathway have been identified (20–22). of StaufenC expression compared with its expression in susceptible However, the difference in composition and function of silencing cells. These studies showed that coleopteran-specific StaufenC is re- complexes between insects in which RNAi works efficiently (e.g., quired for RNAi and is a potential target for RNAi resistance. The data coleopterans) and those in which RNAi does not work efficiently included in this article will help improve RNAi in noncoleopteran insects (e.g., lepidopterans) remains unknown. and manage RNAi resistance in coleopteran insects. Staufen was discovered in Drosophila melanogaster in a screen for maternal effect mutations (23). Molecular genetic studies Tribolium | Leptinotarsa | RNAi efficiency | resistance | siRNA have shown that D. melanogaster Staufen is required to localize mRNAs in oocytes and neuroblasts (24, 25). Human and mouse xposure of cells to double-stranded RNA (dsRNA) causes Staufen homologs were identified and the human staufen gene Etarget-specific gene silencing known as RNA interference codes for two proteins (Stau1 and Stau2) with differences in the (RNAi). RNAi was discovered in the nematode, Caenorhabditis elegans, and was subsequently observed in most eukaryotes in- Significance cluding humans, plants, and insects (1). dsRNAs synthesized in vitro or in microorganisms (including bacteria, yeast, and algae) or plants The RNA interference (RNAi) discovered in nematodes has have been used to achieve gene silencing in insects (2–4). RNAi- contributed to major advances in basic and applied sciences. aided gene silencing methods helped to determine functions of RNAi-based methods are being developed for controlling pests genes identified by the genome, transcriptome, and proteome se- and disease vectors. RNAi is highly efficient and systemic in quencing and advance our understanding of the molecular basis of coleopteran insects, but not in other insects. The lower effi- many developmental and physiological processes including insect ciency of RNAi in economically important insects and concerns development, reproduction, behavior, and communication (5, 6). about resistance development are hindering the widespread RNAi technology is being employed to develop methods to control use of this technology. To address these problems, a RNAi- crop pests as well as vectors that transmit deadly diseases affecting sensitive Colorado potato beetle, Leptinotarsa decemlineata, humans, animals, and plants (2–4, 7, 8). RNAi is also used to and a cell line derived from this insect were used to identify a identify target sites for insecticide development, as well as to dsRNA-binding protein, StaufenC, as a major contributor to manage insecticide resistance in pests and disease vectors (7–9). RNAi and its resistance. Interestingly, StaufenC homologs are The US Environmental Protection Agency recently approved present in only coleopteran insects and are essential for effi- transgenic corn plants expressing dsRNA for the control of Western cient RNAi response and its resistance in these insects. corn rootworm in the United States (https://www.regulations.gov/ docket?D=EPA-HQ-OPP-2014-0293). Author contributions: J.S.Y., K.M., and S.R.P. designed research; J.S.Y., K.M., D.G., X.C., and S.C.R.R.C. performed research; J.S.Y., K.M., D.G., X.C., S.C.R.R.C., and S.R.P. analyzed RNAi efficiency is variable among insects tested so far. RNAi data; and J.S.Y. and S.R.P. wrote the paper. works very well and is systemic in beetles (Coleoptera), including The authors declare no conflict of interest. the red flour beetle (Tribolium castaneum), Colorado potato This article is a PNAS Direct Submission. beetle (Leptinotarsa decemlineata), and Western corn rootworm – This open access article is distributed under Creative Commons Attribution-NonCommercial- (Diabrotica virgifera virgifera)(710). In contrast, RNAi works NoDerivatives License 4.0 (CC BY-NC-ND). poorly in moths and butterflies belonging to the order Lepi- Data deposition: The sequence reported in this paper has been deposited in the GenBank doptera (11, 12). Differences in digestion of dsRNA by en- database (accession no. SRP150964). dogenous dsRNases (dsRNA endonucleases), in transport of 1To whom correspondence should be addressed. Email: [email protected]. dsRNA into cells and trafficking within cells, in processing of This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. dsRNA to siRNA, and in expression of RNAi genes and com- 1073/pnas.1809381115/-/DCSupplemental. position of proteins coded by these genes have been identified as Published online July 30, 2018. 8334–8339 | PNAS | August 14, 2018 | vol. 115 | no. 33 www.pnas.org/cgi/doi/10.1073/pnas.1809381115 Downloaded by guest on October 1, 2021 N-terminal end (26). Staufen1 is the mammalian homolog of D. melanogaster Staufen and is thought to function in mRNA transport, translational control, and mRNA decay (27–29). The staufen protein contains multiple double-stranded RNA binding domains, and some of them are shown to bind dsRNA (26, 30). Insects have developed resistance to almost all synthetic chem- icals used for their control, resulting in a constant battle between humans and insects. It is possible that insects will develop resistance to RNAi-based technologies as well. L. decemlineata has developed resistance to almost all synthetic chemicals used for its control withinashortperiodof2–3 y after their introduction (31). There- fore, L. decemlineata could be a good model insect to study po- tential RNAi resistance. Resistance in dsRNA-treated insects might be developed by the selection of individuals with modification in genes coding for proteins functioning in the RNAi pathway. Al- Fig. 1. Coleopteran-specific StauC is a major contributor to RNAi pathway. ternatively, insects might develop resistance to dsRNAs by selection (A) Phenotypes of cells exposed to dsGFP or dsStauC followed by exposure to of individuals with mutations in the dsRNA target sites. Information second dsRNA (dsGFP or dsIAP). The Lepd-SL1 cells were exposed to the first on potential mechanisms of RNAi resistance is needed to make dsRNA (dsGFP or dsStauC) for 48 h, followed by the treatment with the progress in the widespread use of RNAi for controlling insect pests second dsRNA (dsGFP or dsIAP). Photographs were taken at 24 h after and disease vectors. We used L. decemlineata and a cell line derived treatment with the second dsRNA. The arrow points to the cells undergoing from this insect to identify proteins required for RNAi in co- apoptosis. (B) Comparison of processing of dsRNA to siRNA in Lepd-SL1 cells leopteran insects, as well as to study potential mechanisms of RNAi exposed to dsGFP (control) or dsStauC. The Lepd-SL1 cells seeded in six-well plates were incubated with dsGFP or dsStauC for 24 or 48 h. Then, the cells resistance. were exposed to 1.6 million cpm 32P-labeled dsGFP. At 48 h after the addi- Results tion of the second dsRNA, the cells were harvested, and total RNA was iso- lated and the RNA containing 2,000 cpm was resolved on 16% acrylamide- StauC Is a Major Contributor to RNAi. In a recent study, we screened urea gel. The gel was dried and analyzed using a phosphorImager. The first 50 genes in Lepd-SL1 cells and identified five genes (Argonaute- lane shows GFP dsRNA used as a marker, and the last lane shows dsRNA 1, Argonaute-2a, Argonaute-2b, Aubergine, and vha16) that are processed to siRNA in Lepd-SL1 cells used as a marker for siRNA. The arrows essential for RNAi (32). In these experiments, when Lepd-SL1 point to dsRNA and siRNA bands. (C) Phylogenetic tree of dsRNA-binding cells were exposed to StaufenC (named as StauC because of its proteins. Major clusters of proteins include Staufen (mammalian Stau1 and presence only in coleopteran insects) dsRNA for 24 h, followed Stau2, and insect Staufens from 10 insect orders, and coleopteran StaufenC), insect dsRNA binding proteins (R2D2 and Loquacious), and mammalian RNA by a second dsRNA targeting the gene coding for inhibitor of binding protein (TRBP2).
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