1
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Zhang J, Zhan C, Fan J, Wu D, Zhang R, Wu D, Chen X, Lu Y, Li M, Lin M, Gong J, Jiang D. Structural insights into double-stranded RNA recognition and transport by SID-1. Nat Struct Mol Biol 2024; 31:1095-1104. [PMID: 38664565 DOI: 10.1038/s41594-024-01276-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 03/14/2024] [Indexed: 07/20/2024]
Abstract
RNA uptake by cells is critical for RNA-mediated gene interference (RNAi) and RNA-based therapeutics. In Caenorhabditis elegans, RNAi is systemic as a result of SID-1-mediated double-stranded RNA (dsRNA) across cells. Despite the functional importance, the underlying mechanisms of dsRNA internalization by SID-1 remain elusive. Here we describe cryogenic electron microscopy structures of SID-1, SID-1-dsRNA complex and human SID-1 homologs SIDT1 and SIDT2, elucidating the structural basis of dsRNA recognition and import by SID-1. The homodimeric SID-1 homologs share conserved architecture, but only SID-1 possesses the molecular determinants within its extracellular domains for distinguishing dsRNA from single-stranded RNA and DNA. We show that the removal of the long intracellular loop between transmembrane helix 1 and 2 attenuates dsRNA uptake and systemic RNAi in vivo, suggesting a possible endocytic mechanism of SID-1-mediated dsRNA internalization. Our study provides mechanistic insights into dsRNA internalization by SID-1, which may facilitate the development of dsRNA applications based on SID-1.
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Affiliation(s)
- Jiangtao Zhang
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Chunhua Zhan
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Junping Fan
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing, China
| | - Dian Wu
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ruixue Zhang
- Key Laboratory of Agricultural Microbiome (MARA), Biotechnology Research Institute, Chinese Academy Agricultural Sciences, Beijing, China
| | - Di Wu
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinyao Chen
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ying Lu
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ming Li
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Min Lin
- Food Laboratory of Zhongyuan, College of Agriculture, Henan University, Kaifeng, Henan, China
| | - Jianke Gong
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Daohua Jiang
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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2
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Yoshida K, Suehiro Y, Dejima K, Yoshina S, Mitani S. Distinct pathways for export of silencing RNA in Caenorhabditis elegans systemic RNAi. iScience 2023; 26:108067. [PMID: 37854694 PMCID: PMC10579535 DOI: 10.1016/j.isci.2023.108067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/08/2023] [Accepted: 09/25/2023] [Indexed: 10/20/2023] Open
Abstract
Dietary supplied double-stranded RNA (dsRNA) can trigger RNA interference (RNAi) systemically in some animals, including the nematode Caenorhabditis elegans. Although this phenomenon has been utilized as a major tool for gene silencing in C. elegans, how cells spread the silencing RNA throughout the organism is largely unknown. Here, we identify two novel systemic RNAi-related factors, REXD-1 and TBC-3, and show that these two factors together with SID-5 act redundantly to promote systemic spreading of dsRNA. Animals that are defective in all REXD-1, TBC-3, and SID-5 functions show strong deficiency in export of dsRNA from intestinal cells, whereas cellular uptake and processing of dsRNA and general secretion events other than dsRNA secretion are still functional in the triple mutant animals. Our findings reveal pathways that specifically regulate the export of dsRNA in parallel, implying the importance of spreading RNA molecules for intercellular communication in organisms.
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Affiliation(s)
- Keita Yoshida
- Department of Physiology, Tokyo Women’s Medical University School of Medicine, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Yuji Suehiro
- Department of Physiology, Tokyo Women’s Medical University School of Medicine, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Katsufumi Dejima
- Department of Physiology, Tokyo Women’s Medical University School of Medicine, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Sawako Yoshina
- Department of Physiology, Tokyo Women’s Medical University School of Medicine, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Shohei Mitani
- Department of Physiology, Tokyo Women’s Medical University School of Medicine, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
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3
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Dejima K, Imae R, Suehiro Y, Yoshida K, Mitani S. An endomembrane zinc transporter negatively regulates systemic RNAi in Caenorhabditis elegans. iScience 2023; 26:106930. [PMID: 37305693 PMCID: PMC10250833 DOI: 10.1016/j.isci.2023.106930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/18/2023] [Accepted: 05/16/2023] [Indexed: 06/13/2023] Open
Abstract
Double-stranded RNA (dsRNA) regulates gene expression in a sequence-dependent manner. In Caenorhabditis elegans, dsRNA spreads through the body and leads to systemic RNA silencing. Although several genes involved in systemic RNAi have been genetically identified, molecules that mediate systemic RNAi remain largely unknown. Here, we identified ZIPT-9, a C. elegans homolog of ZIP9/SLC39A9, as a broad-spectrum negative regulator of systemic RNAi. We showed that RSD-3, SID-3, and SID-5 genetically act in parallel for efficient RNAi, and that zipt-9 mutants suppress the RNAi defects of all the mutants. Analysis of a complete set of deletion mutants for SLC30 and SLC39 family genes revealed that only zipt-9 mutants showed altered RNAi activity. Based on these results and our analysis using transgenic Zn2+ reporters, we propose that ZIPT-9-dependent Zn2+ homeostasis, rather than overall cytosolic Zn2+, modulates systemic RNAi activity. Our findings reveal a previously unknown function of zinc transporters in negative RNAi regulation.
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Affiliation(s)
- Katsufumi Dejima
- Department of Physiology, Tokyo Women’s Medical University School of Medicine, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Rieko Imae
- Department of Physiology, Tokyo Women’s Medical University School of Medicine, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Yuji Suehiro
- Department of Physiology, Tokyo Women’s Medical University School of Medicine, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Keita Yoshida
- Department of Physiology, Tokyo Women’s Medical University School of Medicine, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Shohei Mitani
- Department of Physiology, Tokyo Women’s Medical University School of Medicine, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
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4
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Geens E, Van de Walle P, Caroti F, Jelier R, Steuwe C, Schoofs L, Temmerman L. Yolk-deprived Caenorhabditis elegans secure brood size at the expense of competitive fitness. Life Sci Alliance 2023; 6:e202201675. [PMID: 37059473 PMCID: PMC10105328 DOI: 10.26508/lsa.202201675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 04/16/2023] Open
Abstract
Oviparous animals support reproduction via the incorporation of yolk as a nutrient source into the eggs. In Caenorhabditis elegans, however, yolk proteins seem dispensable for fecundity, despite constituting the vast majority of the embryonic protein pool and acting as carriers for nutrient-rich lipids. Here, we used yolk protein-deprived C. elegans mutants to gain insight into the traits that may yet be influenced by yolk rationing. We show that massive yolk provisioning confers a temporal advantage during embryogenesis, while also increasing early juvenile body size and promoting competitive fitness. Opposite to species that reduce egg production under yolk deprivation, our results indicate that C. elegans relies on yolk as a fail-safe to secure offspring survival, rather than to maintain offspring numbers.
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Affiliation(s)
- Ellen Geens
- Department of Biology, KU Leuven, Leuven, Belgium
| | | | - Francesca Caroti
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Rob Jelier
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Christian Steuwe
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
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5
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Gaeta AL, Nourse JB, Willicott K, McKay LE, Keogh CM, Peter K, Russell SN, Hamamichi S, Berkowitz LA, Caldwell KA, Caldwell GA. Systemic RNA Interference Defective (SID) genes modulate dopaminergic neurodegeneration in C. elegans. PLoS Genet 2022; 18:e1010115. [PMID: 35984862 PMCID: PMC9432717 DOI: 10.1371/journal.pgen.1010115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 08/31/2022] [Accepted: 08/01/2022] [Indexed: 02/02/2023] Open
Abstract
The fine-tuning of gene expression is critical for all cellular processes; aberrations in this activity can lead to pathology, and conversely, resilience. As their role in coordinating organismal responses to both internal and external factors have increasingly come into focus, small non-coding RNAs have emerged as an essential component to disease etiology. Using Systemic RNA interference Defective (SID) mutants of the nematode Caenorhabditis elegans, deficient in gene silencing, we examined the potential consequences of dysfunctional epigenomic regulation in the context of Parkinson's disease (PD). Specifically, the loss of either the sid-1 or sid-3 genes, which encode a dsRNA transporter and an endocytic regulatory non-receptor tyrosine kinase, respectively, conferred neuroprotection to dopaminergic (DA) neurons in an established transgenic C. elegans strain wherein overexpression of human α-synuclein (α-syn) from a chromosomally integrated multicopy transgene causes neurodegeneration. We further show that knockout of a specific microRNA, mir-2, attenuates α-syn neurotoxicity; suggesting that the native targets of mir-2-dependent gene silencing represent putative neuroprotective modulators. In support of this, we demonstrated that RNAi knockdown of multiple mir-2 targets enhanced α-syn-induced DA neurodegeneration. Moreover, we demonstrate that mir-2 overexpression originating in the intestine can induce neurodegeneration of DA neurons, an effect that was reversed by pharmacological inhibition of SID-3 activity. Interestingly, sid-1 mutants retained mir-2-induced enhancement of neurodegeneration. Transcriptomic analysis of α-syn animals with and without a sid-1 mutation revealed 27 differentially expressed genes with human orthologs related to a variety of diseases, including PD. Among these was pgp-8, encoding a P-glycoprotein-related ABC transporter. Notably, sid-1; pgp-8 double mutants abolished the neurodegeneration resulting from intestinal mir-2 overexpression. This research positions known regulators of small RNA-dependent gene silencing within a framework that facilitates mechanistic evaluation of epigenetic responses to exogenous and endogenous factors influencing DA neurodegeneration, revealing a path toward new targets for therapeutic intervention of PD.
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Affiliation(s)
- Anthony L. Gaeta
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - J. Brucker Nourse
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Karolina Willicott
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Luke E. McKay
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Candice M. Keogh
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Kylie Peter
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Shannon N. Russell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Shusei Hamamichi
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Laura A. Berkowitz
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Kim A. Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
- Center for Convergent Bioscience and Medicine, The University of Alabama, Tuscaloosa, Alabama, United States of America
- Alabama Research Institute on Aging, The University of Alabama, Tuscaloosa, Alabama, United States of America
- Departments of Neurology and Neurobiology, Center for Neurodegeneration and Experimental Therapeutics, Nathan Shock Center of Excellence for Basic Research in the Biology of Aging, University of Alabama at Birmingham, Heersink School of Medicine, Birmingham, Alabama, United States of America
| | - Guy A. Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America
- Center for Convergent Bioscience and Medicine, The University of Alabama, Tuscaloosa, Alabama, United States of America
- Departments of Neurology and Neurobiology, Center for Neurodegeneration and Experimental Therapeutics, Nathan Shock Center of Excellence for Basic Research in the Biology of Aging, University of Alabama at Birmingham, Heersink School of Medicine, Birmingham, Alabama, United States of America
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6
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Phillips CM, Updike DL. Germ granules and gene regulation in the Caenorhabditis elegans germline. Genetics 2022; 220:6541922. [PMID: 35239965 PMCID: PMC8893257 DOI: 10.1093/genetics/iyab195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 10/10/2021] [Indexed: 01/27/2023] Open
Abstract
The transparency of Caenorhabditis elegans provides a unique window to observe and study the function of germ granules. Germ granules are specialized ribonucleoprotein (RNP) assemblies specific to the germline cytoplasm, and they are largely conserved across Metazoa. Within the germline cytoplasm, they are positioned to regulate mRNA abundance, translation, small RNA production, and cytoplasmic inheritance to help specify and maintain germline identity across generations. Here we provide an overview of germ granules and focus on the significance of more recent observations that describe how they further demix into sub-granules, each with unique compositions and functions.
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Affiliation(s)
- Carolyn M Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA,Corresponding author: (C.M.P.); (D.L.U.)
| | - Dustin L Updike
- The Mount Desert Island Biological Laboratory, Bar Harbor, ME 04672, USA,Corresponding author: (C.M.P.); (D.L.U.)
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7
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Chen X, Rechavi O. Plant and animal small RNA communications between cells and organisms. Nat Rev Mol Cell Biol 2022; 23:185-203. [PMID: 34707241 PMCID: PMC9208737 DOI: 10.1038/s41580-021-00425-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2021] [Indexed: 01/09/2023]
Abstract
Since the discovery of eukaryotic small RNAs as the main effectors of RNA interference in the late 1990s, diverse types of endogenous small RNAs have been characterized, most notably microRNAs, small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs). These small RNAs associate with Argonaute proteins and, through sequence-specific gene regulation, affect almost every major biological process. Intriguing features of small RNAs, such as their mechanisms of amplification, rapid evolution and non-cell-autonomous function, bestow upon them the capacity to function as agents of intercellular communications in development, reproduction and immunity, and even in transgenerational inheritance. Although there are many types of extracellular small RNAs, and despite decades of research, the capacity of these molecules to transmit signals between cells and between organisms is still highly controversial. In this Review, we discuss evidence from different plants and animals that small RNAs can act in a non-cell-autonomous manner and even exchange information between species. We also discuss mechanistic insights into small RNA communications, such as the nature of the mobile agents, small RNA signal amplification during transit, signal perception and small RNA activity at the destination.
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Affiliation(s)
- Xuemei Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA.
| | - Oded Rechavi
- Department of Neurobiology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel. .,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
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8
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Choudhary C, Meghwanshi KK, Shukla N, Shukla JN. Innate and adaptive resistance to RNAi: a major challenge and hurdle to the development of double stranded RNA-based pesticides. 3 Biotech 2021; 11:498. [PMID: 34881161 PMCID: PMC8595431 DOI: 10.1007/s13205-021-03049-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/31/2021] [Indexed: 10/19/2022] Open
Abstract
RNA interference (RNAi) is a post-transcriptional gene silencing process where short interfering RNAs degrade targeted mRNA. Exploration of gene function through reverse genetics is the major achievement of RNAi discovery. Besides, RNAi can be used as a potential strategy for the control of insect pests. This has led to the idea of developing RNAi-based pesticides. Differential RNAi efficiency in the different insect orders is the biggest biological obstacle in developing RNAi-based pesticides. dsRNA stability, the sensitivity of core RNAi machinery, uptake of dsRNA and amplification and spreading of the RNAi signal are the key factors responsible for RNAi efficiency in insects. This review discusses the physiological and adaptive factors responsible for reduced RNAi in insects that pose a major challenge in developing dsRNA- based pesticides.
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Affiliation(s)
- Chhavi Choudhary
- Department of Biotechnology, Central University of Rajasthan, NH-8, Bandarsindri, Distt. Ajmer, Kishangarh, Rajasthan 305817 India
| | - Keshav Kumar Meghwanshi
- Department of Biotechnology, Central University of Rajasthan, NH-8, Bandarsindri, Distt. Ajmer, Kishangarh, Rajasthan 305817 India
| | - Nidhi Shukla
- Birla Institute of Scientific Research, Statue Circle, Prithviraj Rd, C-Scheme, Jaipur, Rajasthan 302001 India
| | - Jayendra Nath Shukla
- Department of Biotechnology, Central University of Rajasthan, NH-8, Bandarsindri, Distt. Ajmer, Kishangarh, Rajasthan 305817 India
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9
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Abstract
More than a century ago, August Weissman defined a distinction between the germline (responsible for propagating heritable information from generation to generation) and the perishable soma. A central motivation for this distinction was to argue against the inheritance of acquired characters, as the germline was partly defined by its protection from external conditions. However, recent decades have seen an explosion of studies documenting the intergenerational and transgenerational effects of environmental conditions, forcing a re-evaluation of how external signals are sensed by, or communicated to, the germline epigenome. Here, motivated by the centrality of small RNAs in paradigms of epigenetic inheritance, we review across species the myriad examples of intercellular RNA trafficking from nurse cells or somatic tissues to developing gametes.
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10
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Charlesworth AG, Seroussi U, Lehrbach NJ, Renaud MS, Sundby AE, Molnar RI, Lao RX, Willis AR, Woock JR, Aber MJ, Diao AJ, Reinke AW, Ruvkun G, Claycomb JM. Two isoforms of the essential C. elegans Argonaute CSR-1 differentially regulate sperm and oocyte fertility. Nucleic Acids Res 2021; 49:8836-8865. [PMID: 34329465 PMCID: PMC8421154 DOI: 10.1093/nar/gkab619] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 07/01/2021] [Accepted: 07/19/2021] [Indexed: 01/09/2023] Open
Abstract
The Caenorhabditis elegans genome encodes nineteen functional Argonaute proteins that use 22G-RNAs, 26G-RNAs, miRNAs or piRNAs to regulate target transcripts. Only one Argonaute is essential under normal laboratory conditions: CSR-1. While CSR-1 has been studied widely, nearly all studies have overlooked the fact that the csr-1 locus encodes two isoforms. These isoforms differ by an additional 163 amino acids present in the N-terminus of CSR-1a. Using CRISPR-Cas9 genome editing to introduce GFP::3xFLAG into the long (CSR-1a) and short (CSR-1b) isoforms, we found that CSR-1a is expressed during spermatogenesis and in several somatic tissues, including the intestine. CSR-1b is expressed constitutively in the germline. small RNA sequencing of CSR-1 complexes shows that they interact with partly overlapping sets of 22G-RNAs. Phenotypic analyses reveal that the essential functions of csr-1 described in the literature coincide with CSR-1b, while CSR-1a plays tissue specific functions. During spermatogenesis, CSR-1a integrates into an sRNA regulatory network including ALG-3, ALG-4 and WAGO-10 that is necessary for fertility at 25°C. In the intestine, CSR-1a silences immunity and pathogen-responsive genes, and its loss results in improved survival from the pathogen Pseudomonas aeruginosa. Our findings functionally distinguish the CSR-1 isoforms and highlight the importance of studying each AGO isoform independently.
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Affiliation(s)
| | - Uri Seroussi
- Department of Molecular Genetics, University of Toronto Toronto, ON M5S 1A8 Canada
| | - Nicolas J Lehrbach
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Mathias S Renaud
- Department of Molecular Genetics, University of Toronto Toronto, ON M5S 1A8 Canada
| | - Adam E Sundby
- Department of Molecular Genetics, University of Toronto Toronto, ON M5S 1A8 Canada
| | - Ruxandra I Molnar
- Department of Molecular Genetics, University of Toronto Toronto, ON M5S 1A8 Canada
| | - Robert X Lao
- Department of Molecular Genetics, University of Toronto Toronto, ON M5S 1A8 Canada
| | - Alexandra R Willis
- Department of Molecular Genetics, University of Toronto Toronto, ON M5S 1A8 Canada
| | - Jenna R Woock
- Department of Molecular Genetics, University of Toronto Toronto, ON M5S 1A8 Canada
| | - Matthew J Aber
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Annette J Diao
- Department of Molecular Genetics, University of Toronto Toronto, ON M5S 1A8 Canada
| | - Aaron W Reinke
- Department of Molecular Genetics, University of Toronto Toronto, ON M5S 1A8 Canada
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto Toronto, ON M5S 1A8 Canada
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11
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Nganso BT, Sela N, Soroker V. A genome-wide screening for RNAi pathway proteins in Acari. BMC Genomics 2020; 21:791. [PMID: 33183236 PMCID: PMC7659050 DOI: 10.1186/s12864-020-07162-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 10/19/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND RNA interference (RNAi) is a highly conserved, sequence-specific gene silencing mechanism present in Eukaryotes. Three RNAi pathways are known, namely micro-RNA (miRNA), piwi-interacting RNA (piRNA) and short interfering RNA (siRNA). However, little knowledge exists about the proteins involved in these pathways in Acari. Moreover, variable successes has been obtained in gene knockdown via siRNA pathway in their functional genomics and management. We hypothesized that the clue may be in the variability of the composition and the efficacy of siRNA machinery among Acari. RESULTS Both comparative genomic analyses and domain annotation suggest that all the analyzed species have homologs of putative core proteins that mediate cleaving of targeted genes via the three RNAi pathways. We identified putative homologs of Caenorhabditis elegans RNA-dependent RNA polymerase (RdRP) protein in all species though no secondary Argonaute homologs that operate with this protein in siRNA amplification mechanism were found, suggesting that the siRNA amplification mechanism present in Acari may be distinct from that described in C. elegans. Moreover, the genomes of these species do not encode homologs of C. elegans systemic RNAi defective-1 (Sid-1) protein that mediate silencing of the mRNA target throughout the treated organisms suggesting that the phenomena of systemic RNAi that has been reported in some Acari species probably occur through a different mechanism. However, homologs of putative RNAi spreading defective-3 (Rsd-3) protein and scavenger receptors namely Eater and SR-CI that mediate endocytosis cellular update of dsRNA in C. elegans and Drosophila melanogaster were found in Acari genomes. This result suggests that cellular dsRNA uptake in Acari is endocytosis-dependent. Detailed phylogenetic analyses of core RNAi pathway proteins in the studied species revealed that their evolution is compatible with the proposed monophyletic evolution of this group. CONCLUSIONS Our analyses have revealed the potential activity of all three pathways in Acari. Still, much experimental work remains to be done to confirm the mechanisms behind these pathways in particular those that govern systemic/parental RNAi and siRNA amplification in Acari. Disclosure of these mechanisms will facilitate the development of new and specific management tools for the harmful species and enrichment of the beneficial species.
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Affiliation(s)
- Beatrice T Nganso
- Institute of Plant Protection, Agricultural Research Organization, the Volcani Center, P.O.B 15159, 7505101, Rishon leZion, Israel
| | - Noa Sela
- Institute of Plant Protection, Agricultural Research Organization, the Volcani Center, P.O.B 15159, 7505101, Rishon leZion, Israel
| | - Victoria Soroker
- Institute of Plant Protection, Agricultural Research Organization, the Volcani Center, P.O.B 15159, 7505101, Rishon leZion, Israel.
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12
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Manage KI, Rogers AK, Wallis DC, Uebel CJ, Anderson DC, Nguyen DAH, Arca K, Brown KC, Cordeiro Rodrigues RJ, de Albuquerque BF, Ketting RF, Montgomery TA, Phillips CM. A tudor domain protein, SIMR-1, promotes siRNA production at piRNA-targeted mRNAs in C. elegans. eLife 2020; 9:56731. [PMID: 32338603 PMCID: PMC7255803 DOI: 10.7554/elife.56731] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 04/24/2020] [Indexed: 02/06/2023] Open
Abstract
piRNAs play a critical role in the regulation of transposons and other germline genes. In Caenorhabditis elegans, regulation of piRNA target genes is mediated by the mutator complex, which synthesizes high levels of siRNAs through the activity of an RNA-dependent RNA polymerase. However, the steps between mRNA recognition by the piRNA pathway and siRNA amplification by the mutator complex are unknown. Here, we identify the Tudor domain protein, SIMR-1, as acting downstream of piRNA production and upstream of mutator complex-dependent siRNA biogenesis. Interestingly, SIMR-1 also localizes to distinct subcellular foci adjacent to P granules and Mutator foci, two phase-separated condensates that are the sites of piRNA-dependent mRNA recognition and mutator complex-dependent siRNA amplification, respectively. Thus, our data suggests a role for multiple perinuclear condensates in organizing the piRNA pathway and promoting mRNA regulation by the mutator complex. In the biological world, a process known as RNA interference helps cells to switch genes on and off and to defend themselves against harmful genetic material. This mechanism works by deactivating RNA sequences, the molecular templates cells can use to create proteins. Overall, RNA interference relies on the cell creating small RNA molecules that can target and inhibit the harmful RNA sequences that need to be silenced. More precisely, in round worms such as Caenorhabditis elegans, RNA interference happens in two steps. First, primary small RNAs identify the target sequences, which are then combatted by newly synthetised, secondary small RNAs. A number of proteins are also involved in both steps of the process. RNA interference is particularly important to preserve fertility, guarding sex cells against ‘rogue’ segments of genetic information that could be passed on to the next generation. In future sex cells, the proteins involved in RNA interference cluster together, forming a structure called a germ granule. Yet, little is known about the roles and identity of these proteins. To fill this knowledge gap, Manage et al. focused on the second stage of the RNA interference pathway in the germ granules of C. elegans, examining the molecules that physically interact with a key protein. This work revealed a new protein called SIMR-1. Looking into the role of SIMR-1 showed that the protein is required to amplify secondary small RNAs, but not to identify target sequences. However, it only promotes the creation of secondary small RNAs if a specific subtype of primary small RNAs have recognized the target RNAs for silencing. Further experiments also showed that within the germ granule, SIMR-1 is present in a separate substructure different from any compartment previously identified. This suggests that each substep of the RNA interference process takes place at a different location in the granule. In both C. elegans and humans, disruptions in the RNA interference pathway can lead to conditions such as cancer or infertility. Dissecting the roles of the proteins involved in this process in roundworms may help to better grasp how this process unfolds in mammals, and how it could be corrected in the case of disease.
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Affiliation(s)
- Kevin I Manage
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Alicia K Rogers
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Dylan C Wallis
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Celja J Uebel
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Dorian C Anderson
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Dieu An H Nguyen
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Katerina Arca
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Kristen C Brown
- Department of Biology, Colorado State University, Fort Collins, United States.,Cell and Molecular Biology Program, Colorado State University, Fort Collins, United States
| | - Ricardo J Cordeiro Rodrigues
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Mainz, Germany.,International PhD Programme on Gene Regulation, Epigenetics, and Genome Stability, Mainz, Germany
| | | | - René F Ketting
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Mainz, Germany
| | - Taiowa A Montgomery
- Department of Biology, Colorado State University, Fort Collins, United States
| | - Carolyn Marie Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
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13
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Dias NP, Cagliari D, Dos Santos EA, Smagghe G, Jurat-Fuentes JL, Mishra S, Nava DE, Zotti MJ. Insecticidal Gene Silencing by RNAi in the Neotropical Region. NEOTROPICAL ENTOMOLOGY 2020; 49:1-11. [PMID: 31749122 DOI: 10.1007/s13744-019-00722-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 09/22/2019] [Indexed: 06/10/2023]
Abstract
Insecticidal gene silencing by RNA interference (RNAi) involves a post-transcriptional mechanism with great potential for insect control. Here, we aim to summarize the progress on RNAi research toward control of insect pests in the Neotropical region and discuss factors determining its efficacy and prospects for pest management. We include an overview of the available RNAi information for Neotropical pests in the Lepidoptera, Coleoptera, Diptera, and Hemiptera orders. Emphasis is put on significant findings in the use of RNAi against relevant Neotropical pests, including diamondback moth (Plutella xylostella L.), Asian citrus psyllid (Diaphorina citri Kuwayama), and the cotton boll weevil (Anthonomus grandis Boheman). We also examine the main factors involved in insecticidal RNAi efficiency and major advances to improve screening of lethal genes, formulation, and delivery. Few studies detail resistance mechanisms to RNAi, demonstrating a need for more research. Advances in formulation, delivery, and resistance management tools for insecticidal RNAi in the Neotropics can provide a basis for efficient field application.
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Affiliation(s)
- N P Dias
- Dept of Crop Protection, Federal Univ of Pelotas, Pelotas, Brazil.
| | - D Cagliari
- Dept of Crop Protection, Federal Univ of Pelotas, Pelotas, Brazil
| | - E A Dos Santos
- Dept of Crop Protection, Federal Univ of Pelotas, Pelotas, Brazil
| | - G Smagghe
- Dept of Plants and Crops, Ghent Univ, Ghent, Belgium
| | - J L Jurat-Fuentes
- Dept of Entomology and Plant Pathology, The Univ of Tennessee, Knoxville, USA
| | - S Mishra
- Dept of Entomology and Plant Pathology, The Univ of Tennessee, Knoxville, USA
| | - D E Nava
- Entomology Lab, EmbrapaClima Temperado, Pelotas, Brasil
| | - M J Zotti
- Dept of Crop Protection, Federal Univ of Pelotas, Pelotas, Brazil.
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14
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De-Souza EA, Camara H, Salgueiro WG, Moro RP, Knittel TL, Tonon G, Pinto S, Pinca APF, Antebi A, Pasquinelli AE, Massirer KB, Mori MA. RNA interference may result in unexpected phenotypes in Caenorhabditis elegans. Nucleic Acids Res 2019; 47:3957-3969. [PMID: 30838421 PMCID: PMC6486631 DOI: 10.1093/nar/gkz154] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 02/20/2019] [Accepted: 03/01/2019] [Indexed: 12/19/2022] Open
Abstract
RNA interference (RNAi) is a valuable technique to determine gene function. In Caenorhabditis elegans, RNAi can be achieved by feeding worms bacteria carrying a plasmid expressing double-stranded RNA (dsRNA) targeting a gene of interest. The most commonly used plasmid vector for this purpose is L4440. However, it has been noticed that sequences within L4440 may elicit unspecific effects. Here, we provide a comprehensive characterization of these effects and their mechanisms and describe new unexpected phenotypes uncovered by the administration of unspecific exogenous dsRNA. An example involves dsRNA produced by the multiple cloning site (MCS) of L4440, which shares complementary sequences with some widely used reporter vectors and induces partial transgene silencing via the canonical and antiviral RNAi pathway. Going beyond transgene silencing, we found that the reduced embryonic viability of mir-35-41(gk262) mutants is partially reversed by exogenous dsRNA via a mechanism that involves canonical RNAi. These results indicate cross-regulation between different small RNA pathways in C. elegans to regulate embryonic viability. Recognition of the possible unspecific effects elicited by RNAi vectors is important for rigorous interpretation of results from RNAi-based experiments.
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Affiliation(s)
- Evandro A De-Souza
- Program in Molecular Biology, Federal University of São Paulo, São Paulo 04044-020, Brazil.,Program in Molecular Biology and Biotechnology, Instituto de Bioquímica Médica Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Henrique Camara
- Program in Molecular Biology, Federal University of São Paulo, São Paulo 04044-020, Brazil.,Department of Biochemistry and Tissue Biology, University of Campinas, Campinas, São Paulo 13083-862, Brazil.,Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Willian G Salgueiro
- Department of Biochemistry and Tissue Biology, University of Campinas, Campinas, São Paulo 13083-862, Brazil.,Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Raíssa P Moro
- Department of Biochemistry and Tissue Biology, University of Campinas, Campinas, São Paulo 13083-862, Brazil.,Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Thiago L Knittel
- Department of Biochemistry and Tissue Biology, University of Campinas, Campinas, São Paulo 13083-862, Brazil.,Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Guilherme Tonon
- Department of Biochemistry and Tissue Biology, University of Campinas, Campinas, São Paulo 13083-862, Brazil.,Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Silas Pinto
- Program in Molecular Biology, Federal University of São Paulo, São Paulo 04044-020, Brazil.,Department of Biochemistry and Tissue Biology, University of Campinas, Campinas, São Paulo 13083-862, Brazil.,Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Ana Paula F Pinca
- Program in Molecular Biology, Federal University of São Paulo, São Paulo 04044-020, Brazil
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing, Cologne 50931, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Amy E Pasquinelli
- Division of Biology, University of California, San Diego, La Jolla, California 92093-0349, USA
| | - Katlin B Massirer
- Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo 13083-970, Brazil.,Center for Molecular Biology and Genetic Engineering, University of Campinas, CBMEG-UNICAMP, Campinas, São Paulo 13083-875, Brazil.,The Structural Genomics Consortium - UNICAMP, University of Campinas, Campinas, São Paulo 13083-875, Brazil
| | - Marcelo A Mori
- Program in Molecular Biology, Federal University of São Paulo, São Paulo 04044-020, Brazil.,Department of Biochemistry and Tissue Biology, University of Campinas, Campinas, São Paulo 13083-862, Brazil.,Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo 13083-970, Brazil
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15
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Weiser NE, Kim JK. Multigenerational Regulation of the Caenorhabditis elegans Chromatin Landscape by Germline Small RNAs. Annu Rev Genet 2019; 53:289-311. [PMID: 31150586 DOI: 10.1146/annurev-genet-112618-043505] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In animals, small noncoding RNAs that are expressed in the germline and transmitted to progeny control gene expression to promote fertility. Germline-expressed small RNAs, including endogenous small interfering RNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs), drive the repression of deleterious transcripts such as transposons, repetitive elements, and pseudogenes. Recent studies have highlighted an important role for small RNAs in transgenerational epigenetic inheritance via regulation of heritable chromatin marks; therefore, small RNAs are thought to convey an epigenetic memory of genomic self and nonself elements. Small RNA pathways are highly conserved in metazoans and have been best described for the model organism Caenorhabditis elegans. In this review, we describe the biogenesis, regulation, and function of C. elegans endo-siRNAs and piRNAs, along with recent insights into how these distinct pathways are integrated to collectively regulate germline gene expression, transgenerational epigenetic inheritance, and ultimately, animal fertility.
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Affiliation(s)
- Natasha E Weiser
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - John K Kim
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA;
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16
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Huang X, Xu CL, Yang SH, Li JY, Wang HL, Zhang ZX, Chen C, Xie H. Life-stage specific transcriptomes of a migratory endoparasitic plant nematode, Radopholus similis elucidate a different parasitic and life strategy of plant parasitic nematodes. Sci Rep 2019; 9:6277. [PMID: 31000750 PMCID: PMC6472380 DOI: 10.1038/s41598-019-42724-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 04/02/2019] [Indexed: 01/21/2023] Open
Abstract
Radopholus similis is an important migratory endoparasitic nematode, severely harms banana, citrus and many other commercial crops. Little is known about the molecular mechanism of infection and pathogenesis of R. similis. In this study, 64761 unigenes were generated from eggs, juveniles, females and males of R. similis. 11443 unigenes showed significant expression difference among these four life stages. Genes involved in host parasitism, anti-host defense and other biological processes were predicted. There were 86 and 102 putative genes coding for cell wall degrading enzymes and antioxidase respectively. The amount and type of putative parasitic-related genes reported in sedentary endoparasitic plant nematodes are variable from those of migratory parasitic nematodes on plant aerial portion. There were no sequences annotated to effectors in R. similis, involved in feeding site formation of sedentary endoparasites nematodes. This transcriptome data provides a new insight into the parasitic and pathogenic molecular mechanisms of the migratory endoparasitic nematodes. It also provides a broad idea for further research on R. similis.
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Affiliation(s)
- Xin Huang
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, College of Agriculture, South China Agricultural University, Guangzhou, People's Republic of China
| | - Chun-Ling Xu
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, College of Agriculture, South China Agricultural University, Guangzhou, People's Republic of China
| | - Si-Hua Yang
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, College of Agriculture, South China Agricultural University, Guangzhou, People's Republic of China
| | - Jun-Yi Li
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, College of Agriculture, South China Agricultural University, Guangzhou, People's Republic of China
| | - Hong-Le Wang
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, College of Agriculture, South China Agricultural University, Guangzhou, People's Republic of China
| | - Zi-Xu Zhang
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, College of Agriculture, South China Agricultural University, Guangzhou, People's Republic of China
| | - Chun Chen
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, College of Agriculture, South China Agricultural University, Guangzhou, People's Republic of China
| | - Hui Xie
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, College of Agriculture, South China Agricultural University, Guangzhou, People's Republic of China.
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17
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Dulovic A, Streit A. RNAi-mediated knockdown of daf-12 in the model parasitic nematode Strongyloides ratti. PLoS Pathog 2019; 15:e1007705. [PMID: 30925161 PMCID: PMC6457571 DOI: 10.1371/journal.ppat.1007705] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/10/2019] [Accepted: 03/13/2019] [Indexed: 01/27/2023] Open
Abstract
The gene daf-12 has long shown to be involved in the dauer pathway in Caenorhabditis elegans (C. elegans). Due to the similarities of the dauer larvae of C. elegans and infective larvae of certain parasitic nematodes such as Strongyloides spp., this gene has also been suspected to be involved in the development of infective larvae. Previous research has shown that the application of dafachronic acid, the steroid hormone ligand of DAF-12 in C. elegans, affects the development of infective larvae and metabolism in Strongyloides. However, a lack of tools for either forward or reverse genetics within Strongyloides has limited studies of gene function within these important parasites. After determining whether Strongyloides had the requisite proteins for RNAi, we developed and report here the first successful RNAi by soaking protocol for Strongyloides ratti (S. ratti) and use this protocol to study the functions of daf-12 within S. ratti. Suppression of daf-12 in S. ratti severely impairs the formation of infective larvae of the direct cycle and redirects development towards the non-infective (non-dauer) free-living life cycle. Further, daf-12(RNAi) S. ratti produce slightly but significantly fewer offspring and these offspring are developmentally delayed or incapable of completing their development to infective larvae (L3i). Whilst the successful daf-12(RNAi) L3i are still able to infect a new host, the resulting infection is less productive and shorter lived. Further, daf-12 knockdown affects metabolism in S. ratti resulting in a shift from aerobic towards anaerobic fat metabolism. Finally, daf-12(RNAi) S. ratti have reduced tolerance of temperature stress.
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Affiliation(s)
- Alex Dulovic
- Department of Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Baden-Württemberg, Germany
| | - Adrian Streit
- Department of Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Baden-Württemberg, Germany
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18
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Liposome-based transfection enhances RNAi and CRISPR-mediated mutagenesis in non-model nematode systems. Sci Rep 2019; 9:483. [PMID: 30679624 PMCID: PMC6345965 DOI: 10.1038/s41598-018-37036-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 11/28/2018] [Indexed: 11/09/2022] Open
Abstract
Nematodes belong to one of the most diverse animal phyla. However, functional genomic studies in nematodes, other than in a few species, have often been limited in their reliability and success. Here we report that by combining liposome-based technology with microinjection, we were able to establish a wide range of genomic techniques in the newly described nematode genus Auanema. The method also allowed heritable changes in dauer larvae of Auanema, despite the immaturity of the gonad at the time of the microinjection. As proof of concept for potential functional studies in other nematode species, we also induced RNAi in the free-living nematode Pristionchus pacificus and targeted the human parasite Strongyloides stercoralis.
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19
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Marr EJ, Wright HW, Sargison ND, Nisbet AJ, Burgess STG. Gene silencing by RNA interference in the ectoparasitic mite, Psoroptes ovis. Vet Res 2018; 49:112. [PMID: 30382906 PMCID: PMC6211577 DOI: 10.1186/s13567-018-0608-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/24/2018] [Indexed: 11/10/2022] Open
Abstract
The presence of components of the RNA interference (RNAi) pathway in Psoroptes ovis, an ectoparasitic mite responsible for psoroptic mange, was investigated through interrogation of the P. ovis genome. Homologues of transcripts representing critical elements for achieving effective RNAi in the mite, Tetranychus urticae and the model organisms Caenorhabditis elegans and Drosophila melanogaster were identified and, following the development of a non-invasive immersion method of double stranded RNA delivery, gene silencing by RNAi was successfully demonstrated in P. ovis. Significant reductions in transcript levels were achieved for three target genes which encode the Group 2 allergen (Pso o 2), mu-class glutathione S-transferase (PoGST-mu1) and beta-tubulin (Poβtub). This is the first demonstration of RNAi in P. ovis and provides a mechanism for mining transcriptomic and genomic datasets for novel control targets against this economically important ectoparasite.
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Affiliation(s)
- Edward J Marr
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Edinburgh, EH26 0PZ, Scotland, UK.,Institute of Immunology and Infection Research, The King's Buildings, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, Scotland, UK
| | - Harry W Wright
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Edinburgh, EH26 0PZ, Scotland, UK
| | - Neil D Sargison
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Roslin, Midlothian, EH25 9RG, Scotland, UK
| | - Alasdair J Nisbet
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Edinburgh, EH26 0PZ, Scotland, UK
| | - Stewart T G Burgess
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Edinburgh, EH26 0PZ, Scotland, UK.
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20
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Transgene-Assisted Genetic Screen Identifies rsd-6 and Novel Genes as Key Components of Antiviral RNA Interference in Caenorhabditis elegans. J Virol 2018; 92:JVI.00416-18. [PMID: 29950414 PMCID: PMC6096818 DOI: 10.1128/jvi.00416-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/16/2018] [Indexed: 12/21/2022] Open
Abstract
RNA interference (RNAi) is a widespread antiviral mechanism triggered by virus-produced double-stranded RNAs (dsRNAs). In Caenorhabditis elegans, antiviral RNAi involves a RIG-I-like RNA helicase, termed DRH-1 (dicer related RNA helicase 1), that is not required for classical RNAi triggered by artificial dsRNA. Currently, whether antiviral RNAi in C. elegans involves novel factors that are dispensable for classical RNAi remains an open question. To address this question, we designed and carried out a genetic screen that aims to identify novel genes involved in worm antiviral RNAi. By introducing extra copies of known antiviral RNAi genes into the reporter worms, we managed to reject alleles derived from 4 known antiviral RNAi genes, including the DRH-1 coding gene, during the screen. Our genetic screen altogether identified 25 alleles, which were assigned to 11 candidate genes and 2 known antiviral RNAi genes through genetic complementation tests. Using a mapping-by-sequencing strategy, we identified one of the candidate genes as rsd-6, a gene that helps maintain genome integrity through an endogenous gene-silencing pathway but was not known to be required for antiviral RNAi. More importantly, we found that two of the candidate genes are required for antiviral RNAi targeting Orsay virus, a natural viral pathogen of C. elegans, but dispensable for classical RNAi. Since drh-1 is so far the only antiviral RNAi gene not required for classical RNAi, we believe that our genetic screen led to identification of novel worm genes that may target virus-specific features to function in RNAi.IMPORTANCE In nematode worms, drh-1 detects virus-produced double-stranded RNA (dsRNA), thereby specifically contributing to antiviral RNA silencing. To identify drh-1-like genes with dedicated function in antiviral RNAi, we recently carried out a genetic screen that was designed to automatically reject all alleles derived from 4 known antiviral silencing genes, including drh-1 Of the 11 candidate genes identified, we found two of them to be required for antiviral silencing targeting a natural viral pathogen of C. elegans but not for classical RNA silencing triggered by artificial dsRNA. We believe that these two genes are novel components of worm antiviral RNAi, considering the fact that drh-1 is the only known antiviral RNAi gene that is dispensable for classical RNAi. This genetic screen also identified rsd-6, a gene that maintains genome integrity under unfavorable conditions, as a key regulator of worm antiviral silencing, demonstrating an interplay between antiviral immunity and genome integrity maintenance.
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21
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Rechavi O, Lev I. Principles of Transgenerational Small RNA Inheritance in Caenorhabditis elegans. Curr Biol 2018; 27:R720-R730. [PMID: 28743023 DOI: 10.1016/j.cub.2017.05.043] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Examples of transgenerational inheritance of environmental responses are rapidly accumulating. In Caenorhabditis elegans nematodes, such heritable information transmits across generations in the form of RNA-dependent RNA polymerase-amplified small RNAs. Regulatory small RNAs enable sequence-specific gene regulation, and unlike chromatin modifications, can move between tissues, and escape from immediate germline reprogramming. In this review, we discuss the path that small RNAs take from the soma to the germline, and elaborate on the mechanisms that maintain or erase parental small RNA responses after a specific number of generations. We focus on the intricate interactions between heritable small RNAs and histone modifications, deposited on specific loci. A trace of heritable chromatin marks, in particular trimethylation of histone H3 lysine 9, is deposited on RNAi-targeted loci. However, how these modifications regulate RNAi or small RNA inheritance was until recently unclear. Integrating the very latest literature, we suggest that changes to histone marks may instigate transgenerational gene regulation indirectly, by affecting the biogenesis of heritable small RNAs. Inheritance of small RNAs could spread adaptive ancestral responses.
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Affiliation(s)
- Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School for Neuroscience, Tel Aviv University, Tel Aviv, Israel 69978.
| | - Itamar Lev
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School for Neuroscience, Tel Aviv University, Tel Aviv, Israel 69978.
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22
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Peng Y, Wang K, Fu W, Sheng C, Han Z. Biochemical Comparison of dsRNA Degrading Nucleases in Four Different Insects. Front Physiol 2018; 9:624. [PMID: 29892232 PMCID: PMC5985623 DOI: 10.3389/fphys.2018.00624] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/08/2018] [Indexed: 12/21/2022] Open
Abstract
Double stranded RNAs (dsRNA) degrading nuclease is responsible for the rapid degradation of dsRNA molecules, and thus accounts for variations in RNA interference (RNAi) efficacy among insect species. Here, the biochemical properties and tissue-specific activities of dsRNA degrading nucleases in four insects (Spodoptera litura, Locusta migratoria, Periplaneta americana, and Zophobas atratus) from different orders were characterized using a modified assay method. The results revealed that all insect dsRNA degrading nucleases tested showed high activity in alkaline environments at optimal Mg2+ concentrations and elevated temperatures. We also found that enzymes from different insects varied in terms of their optimal reaction conditions and kinetic parameters. Whole body enzyme activity differed dramatically between insect species, although enzymes with higher substrate affinities (lower Km) were usually balanced by a smaller Vmax to maintain a proper level of degradative capacity. Furthermore, enzyme activities varied significantly between the four tested tissues (whole body, gut, hemolymph, and carcass) of the insect species. All the insects tested showed several hundred-fold higher dsRNA degrading activity in their gut than in other tissues. Reaction environment analysis demonstrated that physiological conditions in the prepared gut fluid and serum of different insects were not necessarily optimal for dsRNA degrading nuclease activity. Our data describe the biochemical characteristics and tissue distributions of dsRNA degrading activities in various insects, not only explaining why oral delivery of dsRNA often produces lower RNAi effects than injection of dsRNA, but also suggesting that dsRNA-degrading activities are regulated by physiological conditions. These results allow for a better understanding of the properties of dsRNA degrading nucleases, and will aid in the development of successful RNAi strategies in insects.
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Affiliation(s)
| | | | | | | | - Zhaojun Han
- The Agricultural Ministry Key Laboratory of Monitoring and Management of Plant Diseases and Insects, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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23
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Clarke EK, Rivera Gomez KA, Mustachi Z, Murph MC, Schvarzstein M. Manipulation of Ploidy in Caenorhabditis elegans. J Vis Exp 2018. [PMID: 29608173 PMCID: PMC5931776 DOI: 10.3791/57296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Mechanisms that involve whole genome polyploidy play important roles in development and evolution; also, an abnormal generation of tetraploid cells has been associated with both the progression of cancer and the development of drug resistance. Until now, it has not been feasible to easily manipulate the ploidy of a multicellular animal without generating mostly sterile progeny. Presented here is a simple and rapid protocol for generating tetraploid Caenorhabditis elegans animals from any diploid strain. This method allows the user to create a bias in chromosome segregation during meiosis, ultimately increasing ploidy in C. elegans. This strategy relies on the transient reduction of expression of the rec-8 gene to generate diploid gametes. A rec-8 mutant produces diploid gametes that can potentially produce tetraploids upon fertilization. This tractable scheme has been used to generate tetraploid strains carrying mutations and chromosome rearrangements to gain insight into chromosomal dynamics and interactions during pairing and synapsis in meiosis. This method is efficient for generating stable tetraploid strains without genetic markers, can be applied to any diploid strain, and can be used to derive triploid C. elegans. This straightforward method is useful for investigating other fundamental biological questions relevant to genome instability, gene dosage, biological scaling, extracellular signaling, adaptation to stress, development of resistance to drugs, and mechanisms of speciation.
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Affiliation(s)
- Erlyana K Clarke
- Brooklyn College, Biology Department, City University of New York
| | - Katherine A Rivera Gomez
- Brooklyn College, Biology Department, City University of New York; The Graduate Center, Biology Department, City University of New York
| | - Zaki Mustachi
- Brooklyn College, Biology Department, City University of New York
| | - Mikaela C Murph
- Brooklyn College, Biology Department, City University of New York; Advanced Science Research Center, City University of New York
| | - Mara Schvarzstein
- Brooklyn College, Biology Department, City University of New York; The Graduate Center, Biology Department, City University of New York; Advanced Science Research Center, City University of New York;
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24
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Abstract
In the nematode Caenorhabditis elegans, RNA interference (RNAi) triggered by double-stranded RNA (dsRNA) spreads systemically to cause gene silencing throughout the organism and its progeny. We confirm that Caenorhabditis nematode SID-1 orthologs have dsRNA transport activity and demonstrate that the SID-1 paralog CHUP-1 does not transport dsRNA. Sequence comparison of these similar proteins, in conjunction with analysis of loss-of-function missense alleles, identifies several conserved 2–7 amino acid microdomains within the extracellular domain (ECD) that are important for dsRNA transport. Among these missense alleles, we identify and characterize a sid-1 allele, qt95, which causes tissue-specific silencing defects most easily explained as a systemic RNAi export defect. However, we conclude from genetic and biochemical analyses that sid-1(qt95) disrupts only import, and speculate that the apparent export defect is caused by the cumulative effect of sequentially impaired dsRNA import steps. Thus, consistent with previous studies, we fail to detect a requirement for sid-1 in dsRNA export, but demonstrate for the first time that SID-1 functions in the intestine to support environmental RNAi (eRNAi).
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25
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Palominos MF, Verdugo L, Gabaldon C, Pollak B, Ortíz-Severín J, Varas MA, Chávez FP, Calixto A. Transgenerational Diapause as an Avoidance Strategy against Bacterial Pathogens in Caenorhabditis elegans. mBio 2017; 8:e01234-17. [PMID: 29018118 PMCID: PMC5635688 DOI: 10.1128/mbio.01234-17] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 08/30/2017] [Indexed: 12/22/2022] Open
Abstract
The dynamic response of organisms exposed to environmental pathogens determines their survival or demise, and the outcome of this interaction depends on the host's susceptibility and pathogen-dependent virulence factors. The transmission of acquired information about the nature of a pathogen to progeny may ensure effective defensive strategies for the progeny's survival in adverse environments. Environmental RNA interference (RNAi) is a systemic and heritable mechanism and has recently been linked to antibacterial and antifungal defenses in both plants and animals. Here, we report that the second generation of Caenorhabditis elegans living on pathogenic bacteria can avoid bacterial infection by entering diapause in an RNAi pathway-dependent mechanism. Furthermore, we demonstrate that the information encoding this survival strategy is transgenerationally transmitted to the progeny via the maternal germ line.IMPORTANCE Bacteria vastly influence physiology and behavior, and yet, the specific mechanisms by which they cause behavioral changes in hosts are not known. We use C. elegans as a host and the bacteria they eat to understand how microbes trigger a behavioral change that helps animals to survive. We found that animals faced with an infection for two generations could enter a hibernationlike state, arresting development by forming dauer larvae. Dauers have closed mouths and effectively avoid infection. Animals accumulate information that is transgenerationally transmitted to the next generations to form dauers. This work gives insight on how bacteria communicate in noncanonical ways with their hosts, resulting in long-lasting effects providing survival strategies to the community.
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Affiliation(s)
- M Fernanda Palominos
- Centro Interdisciplinario de Neurociencia de Valparaíso (CINV), Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
| | - Lidia Verdugo
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Carolaing Gabaldon
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Bernardo Pollak
- Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Javiera Ortíz-Severín
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Macarena A Varas
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Francisco P Chávez
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Andrea Calixto
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- Centro Interdisciplinario de Neurociencia de Valparaíso (CINV), Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
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26
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Fontenla S, Rinaldi G, Smircich P, Tort JF. Conservation and diversification of small RNA pathways within flatworms. BMC Evol Biol 2017; 17:215. [PMID: 28893179 PMCID: PMC5594548 DOI: 10.1186/s12862-017-1061-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 09/05/2017] [Indexed: 02/04/2023] Open
Abstract
Background Small non-coding RNAs, including miRNAs, and gene silencing mediated by RNA interference have been described in free-living and parasitic lineages of flatworms, but only few key factors of the small RNA pathways have been exhaustively investigated in a limited number of species. The availability of flatworm draft genomes and predicted proteomes allowed us to perform an extended survey of the genes involved in small non-coding RNA pathways in this phylum. Results Overall, findings show that the small non-coding RNA pathways are conserved in all the analyzed flatworm linages; however notable peculiarities were identified. While Piwi genes are amplified in free-living worms they are completely absent in all parasitic species. Remarkably all flatworms share a specific Argonaute family (FL-Ago) that has been independently amplified in different lineages. Other key factors such as Dicer are also duplicated, with Dicer-2 showing structural differences between trematodes, cestodes and free-living flatworms. Similarly, a very divergent GW182 Argonaute interacting protein was identified in all flatworm linages. Contrasting to this, genes involved in the amplification of the RNAi interfering signal were detected only in the ancestral free living species Macrostomum lignano. We here described all the putative small RNA pathways present in both free living and parasitic flatworm lineages. Conclusion These findings highlight innovations specifically evolved in platyhelminths presumably associated with novel mechanisms of gene expression regulation mediated by small RNA pathways that differ to what has been classically described in model organisms. Understanding these phylum-specific innovations and the differences between free living and parasitic species might provide clues to adaptations to parasitism, and would be relevant for gene-silencing technology development for parasitic flatworms that infect hundreds of million people worldwide. Electronic supplementary material The online version of this article (10.1186/s12862-017-1061-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Santiago Fontenla
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UDELAR), Gral. Flores 2125, CP11800, Montevideo, MVD, Uruguay
| | - Gabriel Rinaldi
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Pablo Smircich
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UDELAR), Gral. Flores 2125, CP11800, Montevideo, MVD, Uruguay.,Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Jose F Tort
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UDELAR), Gral. Flores 2125, CP11800, Montevideo, MVD, Uruguay.
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Fishilevich E, Vélez AM, Storer NP, Li H, Bowling AJ, Rangasamy M, Worden SE, Narva KE, Siegfried BD. RNAi as a management tool for the western corn rootworm, Diabrotica virgifera virgifera. PEST MANAGEMENT SCIENCE 2016; 72:1652-1663. [PMID: 27218412 DOI: 10.1002/ps.4324] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 04/27/2016] [Accepted: 05/13/2016] [Indexed: 06/05/2023]
Abstract
The western corn rootworm (WCR), Diabrotica virgifera virgifera, is the most important pest of corn in the US Corn Belt. Economic estimates indicate that costs of control and yield loss associated with WCR damage exceed $US 1 billion annually. Historically, corn rootworm management has been extremely difficult because of its ability to evolve resistance to both chemical insecticides and cultural control practices. Since 2003, the only novel commercialized developments in rootworm management have been transgenic plants expressing Bt insecticidal proteins. Four transgenic insecticidal proteins are currently registered for rootworm management, and field resistance to proteins from the Cry3 family highlights the importance of developing traits with new modes of action. One of the newest approaches for controlling rootworm pests involves RNA interference (RNAi). This review describes the current understanding of the RNAi mechanisms in WCR and the use of this technology for WCR management. Further, the review addresses ecological risk assessment of RNAi and insect resistance management of RNAi for corn rootworm. © 2016 Society of Chemical Industry.
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Affiliation(s)
| | - Ana M Vélez
- Department of Entomology, University of Nebraska, Lincoln, NE, USA
| | | | | | | | | | | | | | - Blair D Siegfried
- Entomology and Nematology Department, University of Florida, Gainesville, FL, USA
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Imae R, Dejima K, Kage-Nakadai E, Arai H, Mitani S. Endomembrane-associated RSD-3 is important for RNAi induced by extracellular silencing RNA in both somatic and germ cells of Caenorhabditis elegans. Sci Rep 2016; 6:28198. [PMID: 27306325 PMCID: PMC4910058 DOI: 10.1038/srep28198] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 06/01/2016] [Indexed: 12/25/2022] Open
Abstract
RNA silencing signals in C. elegans spread among cells, leading to RNAi
throughout the body. During systemic spread of RNAi, membrane trafficking is thought
to play important roles. Here, we show that RNAi Spreading Defective-3
(rsd-3), which encodes a homolog of epsinR, a conserved ENTH (epsin
N-terminal homology) domain protein, generally participates in cellular uptake of
silencing RNA. RSD-3 is previously thought to be involved in systemic RNAi only in
germ cells, but we isolated several deletion alleles of rsd-3, and found that
these mutants are defective in the spread of silencing RNA not only into germ cells
but also into somatic cells. RSD-3 is ubiquitously expressed, and intracellularly
localized to the trans-Golgi network (TGN) and endosomes. Tissue-specific
rescue experiments indicate that RSD-3 is required for importing silencing RNA into
cells rather than exporting from cells. Structure/function analysis showed that the
ENTH domain alone is sufficient, and membrane association of the ENTH domain is
required, for RSD-3 function in systemic RNAi. Our results suggest that endomembrane
trafficking through the TGN and endosomes generally plays an important role in
cellular uptake of silencing RNA.
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Affiliation(s)
- Rieko Imae
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Katsufumi Dejima
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Eriko Kage-Nakadai
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Hiroyuki Arai
- Graduate School of Pharmaceutical Science, University of Tokyo, Tokyo, Japan
| | - Shohei Mitani
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan.,Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo, Japan
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29
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Arur S. Context-dependent regulation of Dicer activity and small RNA production: Implications to oocyte-to-embryo transition. WORM 2016; 4:e1086062. [PMID: 27123367 PMCID: PMC4826148 DOI: 10.1080/21624054.2015.1086062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 08/05/2015] [Accepted: 08/17/2015] [Indexed: 12/26/2022]
Abstract
Cellular and molecular mechanisms that suppress small RNAs in oocytes while maintaining them in zygotes remain unknown. Signal-mediated regulation of small RNA biogenesis pathway is emerging as a theme for regulating small RNA production. We recently reported that ERK-mediated phosphorylation of Dicer, a central player in small RNA biogenesis, induced Dicer to move from the cytoplasm to the nucleus. Dicer phosphorylation inhibited its function, e.g., the production of 26G endo-siRNAs in the female germline. Moreover, our findings showed that the inhibition of Dicer function was necessary for normal progression of meiosis I and oogenesis, and that Dicer function had to be restored before fertilization for normal progression of embryogenesis. Thus, extracellular signal-dependent inhibition and then reactivation of Dicer is essential for oocyte-to-embryo transition. Strikingly, signal-induced Dicer translocation from the cytoplasm to nucleus is evolutionarily conserved from worm, flies, mice to humans thereby suggesting the ERK-mediated control of Dicer activity may be a generalized mechanism for regulating small RNA biogenesis.
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Affiliation(s)
- Swathi Arur
- Department of Genetics; UT MD Anderson Cancer Center ; Houston, TX USA
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30
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Jose AM. Movement of regulatory RNA between animal cells. Genesis 2015; 53:395-416. [PMID: 26138457 PMCID: PMC4915348 DOI: 10.1002/dvg.22871] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 06/28/2015] [Accepted: 06/29/2015] [Indexed: 12/12/2022]
Abstract
Recent studies suggest that RNA can move from one cell to another and regulate genes through specific base-pairing. Mechanisms that modify or select RNA for secretion from a cell are unclear. Secreted RNA can be stable enough to be detected in the extracellular environment and can enter the cytosol of distant cells to regulate genes. Mechanisms that import RNA into the cytosol of an animal cell can enable uptake of RNA from many sources including other organisms. This role of RNA is akin to that of steroid hormones, which cross cell membranes to regulate genes. The potential diagnostic use of RNA in human extracellular fluids has ignited interest in understanding mechanisms that enable the movement of RNA between animal cells. Genetic model systems will be essential to gain more confidence in proposed mechanisms of RNA transport and to connect an extracellular RNA with a specific biological function. Studies in the worm C. elegans and in other animals have begun to reveal parts of this novel mechanism of cell-to-cell communication. Here, I summarize the current state of this nascent field, highlight the many unknowns, and suggest future directions.
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Affiliation(s)
- Antony M Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland
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31
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Shimizu T, Yaegashi H, Ito T, Kanematsu S. Systemic RNA interference is not triggered by locally-induced RNA interference in a plant pathogenic fungus, Rosellinia necatrix. Fungal Genet Biol 2015; 76:27-35. [PMID: 25677378 DOI: 10.1016/j.fgb.2015.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 01/23/2015] [Accepted: 02/03/2015] [Indexed: 01/28/2023]
Abstract
The white root rot fungus, Rosellinia necatrix, damages a wide range of fruit trees. R. necatrix is known to host a variety of mycoviruses, and several of these have potential as biological control agents. RNA interference (RNAi) is a fungal defense mechanism against viral infection, and it is therefore important to understand the RNAi amplification and transmission systems in R. necatrix for effective use of mycoviruses in disease control. In this study, we describe an intriguing RNAi signal transmission phenomenon in R. necatrix. In R. necatrix transformants with autonomously replicating vectors carrying a hairpin structure to induce RNAi, the gene silencing effect was distributed locally and unevenly, based on the vector distribution. This indicates that R. necatrix has no mechanism to propagate silencing signals systemically, unlike Caenorhabditis elegans and Arabidopsis thaliana. Furthermore, the expression of RNA-dependent RNA polymerase homologs was not upregulated during RNAi induction, suggesting that silencing signals are not amplified at sufficient levels to induce systemic RNAi in R. necatrix. Our results also suggest that, in addition to hairpin-induced RNAi, there is either a 5' transitive RNAi or quelling-like gene silencing system in R. necatrix. This is the first study demonstrating that systemic RNAi is not induced by local RNAi in fungi.
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Affiliation(s)
- Takeo Shimizu
- Apple Research Division, Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NARO), 92-24 Nabeyashiki, Shimokuriyagawa, Morioka, Iwate 020-0123, Japan
| | - Hajime Yaegashi
- Apple Research Division, Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NARO), 92-24 Nabeyashiki, Shimokuriyagawa, Morioka, Iwate 020-0123, Japan
| | - Tsutae Ito
- Apple Research Division, Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NARO), 92-24 Nabeyashiki, Shimokuriyagawa, Morioka, Iwate 020-0123, Japan
| | - Satoko Kanematsu
- Apple Research Division, Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NARO), 92-24 Nabeyashiki, Shimokuriyagawa, Morioka, Iwate 020-0123, Japan.
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32
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Nagy AI, Vázquez-Manrique RP, Lopez M, Christov CP, Sequedo MD, Herzog M, Herlihy AE, Bodak M, Gatsi R, Baylis HA. IP3 signalling regulates exogenous RNAi in Caenorhabditis elegans. EMBO Rep 2015; 16:341-50. [PMID: 25608529 DOI: 10.15252/embr.201439585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
RNA interference (RNAi) is a widespread and widely exploited phenomenon. Here, we show that changing inositol 1,4,5-trisphosphate (IP3) signalling alters RNAi sensitivity in Caenorhabditis elegans. Reducing IP3 signalling enhances sensitivity to RNAi in a broad range of genes and tissues. Conversely up-regulating IP3 signalling decreases sensitivity. Tissue-specific rescue experiments suggest IP3 functions in the intestine. We also exploit IP3 signalling mutants to further enhance the sensitivity of RNAi hypersensitive strains. These results demonstrate that conserved cell signalling pathways can modify RNAi responses, implying that RNAi responses may be influenced by an animal's physiology or environment.
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Affiliation(s)
- Anikó I Nagy
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Rafael P Vázquez-Manrique
- Research Group in Molecular, Cellular and Genomic Biomedicine, Health Research Institute-La Fe, Valencia, Spain Centre for Biomedical Network Research on Rare Diseases (CIBERER), Valencia, Spain
| | - Marie Lopez
- Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - María Dolores Sequedo
- Research Group in Molecular, Cellular and Genomic Biomedicine, Health Research Institute-La Fe, Valencia, Spain Centre for Biomedical Network Research on Rare Diseases (CIBERER), Valencia, Spain
| | - Mareike Herzog
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Anna E Herlihy
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Maxime Bodak
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Roxani Gatsi
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Howard A Baylis
- Department of Zoology, University of Cambridge, Cambridge, UK
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Zhao C, Alvarez Gonzales MA, Poland TM, Mittapalli O. Core RNAi machinery and gene knockdown in the emerald ash borer (Agrilus planipennis). JOURNAL OF INSECT PHYSIOLOGY 2015; 72:70-78. [PMID: 25541004 DOI: 10.1016/j.jinsphys.2014.12.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/11/2014] [Accepted: 12/12/2014] [Indexed: 06/04/2023]
Abstract
The RNA interference (RNAi) technology has been widely used in insect functional genomics research and provides an alternative approach for insect pest management. To understand whether the emerald ash borer (Agrilus planipennis), an invasive and destructive coleopteran insect pest of ash tree (Fraxinus spp.), possesses a strong RNAi machinery that is capable of degrading target mRNA as a response to exogenous double-stranded RNA (dsRNA) induction, we identified three RNAi pathway core component genes, Dicer-2, Argonaute-2 and R2D2, from the A. planipennis genome sequence. Characterization of these core components revealed that they contain conserved domains essential for the proteins to function in the RNAi pathway. Phylogenetic analyses showed that they are closely related to homologs derived from other coleopteran species. We also delivered the dsRNA fragment of AplaScrB-2, a β-fructofuranosidase-encoding gene horizontally acquired by A. planipennis as we reported previously, into A. planipennis adults through microinjection. Quantitative real-time PCR analysis on the dsRNA-treated beetles demonstrated a significantly decreased gene expression level of AplaScrB-2 appearing on day 2 and lasting until at least day 6. This study is the first record of RNAi applied in A. planipennis.
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Affiliation(s)
- Chaoyang Zhao
- Department of Entomology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691, USA
| | - Miguel A Alvarez Gonzales
- Department of Entomology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691, USA
| | - Therese M Poland
- U.S. Forest Service, Northern Research Station, East Lansing, MI 48823, USA
| | - Omprakash Mittapalli
- Department of Entomology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691, USA.
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34
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Luo Y, Wang X, Yu D, Kang L. The SID-1 double-stranded RNA transporter is not required for systemic RNAi in the migratory locust. RNA Biol 2014; 9:663-71. [DOI: 10.4161/rna.19986] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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35
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Caenorhabditis elegans RSD-2 and RSD-6 promote germ cell immortality by maintaining small interfering RNA populations. Proc Natl Acad Sci U S A 2014; 111:E4323-31. [PMID: 25258416 DOI: 10.1073/pnas.1406131111] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Germ cells are maintained in a pristine non-aging state as they proliferate over generations. Here, we show that a novel function of the Caenorhabditis elegans RNA interference proteins RNAi spreading defective (RSD)-2 and RSD-6 is to promote germ cell immortality at high temperature. rsd mutants cultured at high temperatures became progressively sterile and displayed loss of small interfering RNAs (siRNAs) that target spermatogenesis genes, simple repeats, and transposons. Desilencing of spermatogenesis genes occurred in late-generation rsd mutants, although defective spermatogenesis was insufficient to explain the majority of sterility. Increased expression of repetitive loci occurred in both germ and somatic cells of late-generation rsd mutant adults, suggesting that desilencing of many heterochromatic segments of the genome contributes to sterility. Nuclear RNAi defective (NRDE)-2 promotes nuclear silencing in response to exogenous double-stranded RNA, and our data imply that RSD-2, RSD-6, and NRDE-2 function in a common transgenerational nuclear silencing pathway that responds to endogenous siRNAs. We propose that RSD-2 and RSD-6 promote germ cell immortality at stressful temperatures by maintaining transgenerational epigenetic inheritance of endogenous siRNA populations that promote genome silencing.
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36
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Sarkies P, Miska EA. Small RNAs break out: the molecular cell biology of mobile small RNAs. Nat Rev Mol Cell Biol 2014; 15:525-35. [DOI: 10.1038/nrm3840] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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37
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Miyata K, Ramaseshadri P, Zhang Y, Segers G, Bolognesi R, Tomoyasu Y. Establishing an in vivo assay system to identify components involved in environmental RNA interference in the western corn rootworm. PLoS One 2014; 9:e101661. [PMID: 25003334 PMCID: PMC4086966 DOI: 10.1371/journal.pone.0101661] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 06/09/2014] [Indexed: 12/14/2022] Open
Abstract
The discovery of environmental RNA interference (RNAi), in which gene expression is suppressed via feeding with double-stranded RNA (dsRNA) molecules, opened the door to the practical application of RNAi-based techniques in crop pest management. The western corn rootworm (WCR, Diabrotica virgifera virgifera) is one of the most devastating corn pests in North America. Interestingly, WCR displays a robust environmental RNAi response, raising the possibility of applying an RNAi-based pest management strategy to this pest. Understanding the molecular mechanisms involved in the WCR environmental RNAi process will allow for determining the rate limiting steps involved with dsRNA toxicity and potential dsRNA resistance mechanisms in WCR. In this study, we have established a two-step in vivo assay system, which allows us to evaluate the involvement of genes in environmental RNAi in WCR. We show that laccase 2 and ebony, critical cuticle pigmentation/tanning genes, can be used as marker genes in our assay system, with ebony being a more stable marker to monitor RNAi activity. In addition, we optimized the dsRNA dose and length for the assay, and confirmed that this assay system is sensitive to detect well-known RNAi components such as Dicer-2 and Argonaute-2. We also evaluated two WCR sid1- like (sil) genes with this assay system. This system will be useful to quickly survey candidate systemic RNAi genes in WCR, and also will be adaptable for a genome-wide RNAi screening to give us an unbiased view of the environmental/systemic RNAi pathway in WCR.
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Affiliation(s)
- Keita Miyata
- Department of Biology, Miami University, Oxford, Ohio, United States of America
| | | | - Yuanji Zhang
- Biotechnology Division, Monsanto Company, Chesterfield, Missouri, United States of America
| | - Gerrit Segers
- Biotechnology Division, Monsanto Company, Chesterfield, Missouri, United States of America
| | - Renata Bolognesi
- Biotechnology Division, Monsanto Company, Chesterfield, Missouri, United States of America
| | - Yoshinori Tomoyasu
- Department of Biology, Miami University, Oxford, Ohio, United States of America
- * E-mail:
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Long OS, Benson JA, Kwak JH, Luke CJ, Gosai SJ, O'Reilly LP, Wang Y, Li J, Vetica AC, Miedel MT, Stolz DB, Watkins SC, Züchner S, Perlmutter DH, Silverman GA, Pak SC. A C. elegans model of human α1-antitrypsin deficiency links components of the RNAi pathway to misfolded protein turnover. Hum Mol Genet 2014; 23:5109-22. [PMID: 24838286 DOI: 10.1093/hmg/ddu235] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The accumulation of serpin oligomers and polymers within the endoplasmic reticulum (ER) causes cellular injury in patients with the classical form α1-antitrypsin deficiency (ATD). To better understand the cellular and molecular genetic aspects of this disorder, we generated transgenic C. elegans strains expressing either the wild-type (ATM) or Z mutant form (ATZ) of the human serpin fused to GFP. Animals secreted ATM, but retained polymerized ATZ within dilated ER cisternae. These latter animals also showed slow growth, smaller brood sizes and decreased longevity; phenotypes observed in ATD patients or transgenic mouse lines expressing ATZ. Similar to mammalian models, ATZ was disposed of by autophagy and ER-associated degradation pathways. Mutant strains defective in insulin signaling (daf-2) also showed a marked decrease in ATZ accumulation. Enhanced ATZ turnover was associated with the activity of two proteins central to systemic/exogenous (exo)-RNAi pathway: the dsRNA importer, SID-1 and the argonaute, RDE-1. Animals with enhanced exo-RNAi activity (rrf-3 mutant) phenocopied the insulin signaling mutants and also showed increased ATZ turnover. Taken together, these studies allude to the existence of a novel proteostasis pathway that mechanistically links misfolded protein turnover to components of the systemic RNAi machinery.
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Affiliation(s)
- Olivia S Long
- Departments of Pediatrics, Cell Biology, University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of UPMC and Magee Womens Hospital Research Institute, 4401 Penn Avenue, Pittsburgh, PA 15224, USA
| | - Joshua A Benson
- Departments of Pediatrics, Cell Biology, University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of UPMC and Magee Womens Hospital Research Institute, 4401 Penn Avenue, Pittsburgh, PA 15224, USA
| | - Joon Hyeok Kwak
- Departments of Pediatrics, Cell Biology, University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of UPMC and Magee Womens Hospital Research Institute, 4401 Penn Avenue, Pittsburgh, PA 15224, USA
| | - Cliff J Luke
- Departments of Pediatrics, Cell Biology, University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of UPMC and Magee Womens Hospital Research Institute, 4401 Penn Avenue, Pittsburgh, PA 15224, USA
| | - Sager J Gosai
- Departments of Pediatrics, Cell Biology, University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of UPMC and Magee Womens Hospital Research Institute, 4401 Penn Avenue, Pittsburgh, PA 15224, USA
| | - Linda P O'Reilly
- Departments of Pediatrics, Cell Biology, University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of UPMC and Magee Womens Hospital Research Institute, 4401 Penn Avenue, Pittsburgh, PA 15224, USA
| | - Yan Wang
- Departments of Pediatrics, Cell Biology, University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of UPMC and Magee Womens Hospital Research Institute, 4401 Penn Avenue, Pittsburgh, PA 15224, USA
| | - Jie Li
- Departments of Pediatrics, Cell Biology, University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of UPMC and Magee Womens Hospital Research Institute, 4401 Penn Avenue, Pittsburgh, PA 15224, USA
| | - Anne C Vetica
- Departments of Pediatrics, Cell Biology, University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of UPMC and Magee Womens Hospital Research Institute, 4401 Penn Avenue, Pittsburgh, PA 15224, USA
| | - Mark T Miedel
- Departments of Pediatrics, Cell Biology, University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of UPMC and Magee Womens Hospital Research Institute, 4401 Penn Avenue, Pittsburgh, PA 15224, USA
| | - Donna B Stolz
- Center for Biologic Imaging, University of Pittsburgh School of Medicine, 3500 Terrace Street, S233 BST, Pittsburgh, PA 15261, USA
| | - Simon C Watkins
- Center for Biologic Imaging, University of Pittsburgh School of Medicine, 3500 Terrace Street, S233 BST, Pittsburgh, PA 15261, USA
| | - Stephan Züchner
- Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - David H Perlmutter
- Departments of Pediatrics, Cell Biology, University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of UPMC and Magee Womens Hospital Research Institute, 4401 Penn Avenue, Pittsburgh, PA 15224, USA
| | - Gary A Silverman
- Departments of Pediatrics, Cell Biology, University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of UPMC and Magee Womens Hospital Research Institute, 4401 Penn Avenue, Pittsburgh, PA 15224, USA
| | - Stephen C Pak
- Departments of Pediatrics, Cell Biology, University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of UPMC and Magee Womens Hospital Research Institute, 4401 Penn Avenue, Pittsburgh, PA 15224, USA,
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Yang H, Vallandingham J, Shiu P, Li H, Hunter CP, Mak HY. The DEAD box helicase RDE-12 promotes amplification of RNAi in cytoplasmic foci in C. elegans. Curr Biol 2014; 24:832-8. [PMID: 24684930 DOI: 10.1016/j.cub.2014.01.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 11/20/2013] [Accepted: 01/03/2014] [Indexed: 11/26/2022]
Abstract
RNAi is a potent mechanism for downregulating gene expression. Conserved RNAi pathway components are found in animals, plants, fungi, and other eukaryotes. In C. elegans, the RNAi response is greatly amplified by the synthesis of abundant secondary small interfering RNAs (siRNAs). Exogenous double-stranded RNA is processed by Dicer and RDE-1/Argonaute into primary siRNA that guides target mRNA recognition. The RDE-10/RDE-11 complex and the RNA-dependent RNA polymerase RRF-1 then engage the target mRNA for secondary siRNA synthesis. However, the molecular link between primary siRNA production and secondary siRNA synthesis remains largely unknown. Furthermore, it is unclear whether the subcellular sites for target mRNA recognition and degradation coincide with sites where siRNA synthesis and amplification occur. In the C. elegans germline, cytoplasmic P granules at the nuclear pores and perinuclear Mutator foci contribute to target mRNA surveillance and siRNA amplification, respectively. We report that RDE-12, a conserved phenylalanine-glycine (FG) domain-containing DEAD box helicase, localizes in P granules and cytoplasmic foci that are enriched in RSD-6 but are excluded from the Mutator foci. Our results suggest that RDE-12 promotes secondary siRNA synthesis by orchestrating the recruitment of RDE-10 and RRF-1 to primary siRNA-targeted mRNA in distinct cytoplasmic compartments.
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Affiliation(s)
- Huan Yang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | | | - Philip Shiu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Hua Li
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Craig P Hunter
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ho Yi Mak
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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Cotton JA, Lilley CJ, Jones LM, Kikuchi T, Reid AJ, Thorpe P, Tsai IJ, Beasley H, Blok V, Cock PJA, den Akker SEV, Holroyd N, Hunt M, Mantelin S, Naghra H, Pain A, Palomares-Rius JE, Zarowiecki M, Berriman M, Jones JT, Urwin PE. The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. Genome Biol 2014; 15:R43. [PMID: 24580726 PMCID: PMC4054857 DOI: 10.1186/gb-2014-15-3-r43] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 03/03/2014] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Globodera pallida is a devastating pathogen of potato crops, making it one of the most economically important plant parasitic nematodes. It is also an important model for the biology of cyst nematodes. Cyst nematodes and root-knot nematodes are the two most important plant parasitic nematode groups and together represent a global threat to food security. RESULTS We present the complete genome sequence of G. pallida, together with transcriptomic data from most of the nematode life cycle, particularly focusing on the life cycle stages involved in root invasion and establishment of the biotrophic feeding site. Despite the relatively close phylogenetic relationship with root-knot nematodes, we describe a very different gene family content between the two groups and in particular extensive differences in the repertoire of effectors, including an enormous expansion of the SPRY domain protein family in G. pallida, which includes the SPRYSEC family of effectors. This highlights the distinct biology of cyst nematodes compared to the root-knot nematodes that were, until now, the only sedentary plant parasitic nematodes for which genome information was available. We also present in-depth descriptions of the repertoires of other genes likely to be important in understanding the unique biology of cyst nematodes and of potential drug targets and other targets for their control. CONCLUSIONS The data and analyses we present will be central in exploiting post-genomic approaches in the development of much-needed novel strategies for the control of G. pallida and related pathogens.
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Affiliation(s)
- James A Cotton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | | | - Laura M Jones
- Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Taisei Kikuchi
- Forestry and Forest Products Research Institute, Tsukuba, Japan
- Division of Parasitology, Department of Infectious Disease, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Adam J Reid
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Peter Thorpe
- Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, UK
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Isheng J Tsai
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
- Division of Parasitology, Department of Infectious Disease, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Helen Beasley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Vivian Blok
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Peter J A Cock
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Sebastian Eves-van den Akker
- Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, UK
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Nancy Holroyd
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Martin Hunt
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | | | - Hardeep Naghra
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
- Present address: School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Arnab Pain
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
- Present address: Computational Bioscience Research Center (CBRC), Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Juan E Palomares-Rius
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- Present address: Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Alameda del Obispo s/n Apdo 4084, 14080 Córdoba, Spain
| | - Magdalena Zarowiecki
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - John T Jones
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Peter E Urwin
- Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, UK
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Ni JT, Yang ZX, Yi YF. Construction of a eukaryotic expression vector containing shRNA targeting maspin. Shijie Huaren Xiaohua Zazhi 2014; 22:469-475. [DOI: 10.11569/wcjd.v22.i4.469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To construct a eukaryotic expression vector containing short hairpin RNA (shRNA) targeting the maspin gene.
METHODS: A shRNA targeting the maspin gene was ligated to the pGenesil-1.1 plasmid expressing green fluorescent protein. Recombinant maspin/pGenesil positive plasmid and YX/pGenesil negative plasmid were constructed. After recombinant plasmids were transfected into MKN-28 cells, RT-PCR and Western blot were performed to detect maspin mRNA and protein expression, respectively.
RESULTS: The recombinant plasmids were validated by gel electrophoresis and DNA sequence analysis. RT-PCR and Western blot analyses indicated that after successful transfection, both maspin mRNA and protein expression in the maspin/pGenesil group was dramatically down-regulated, compared with that in the YX/pGenesil group (0.127 ± 0.02 vs 0.510 ± 0.01, P < 0.05; 0.24 ± 0.10 vs 0.65 ± 0.09, P < 0.05).
CONCLUSION: The maspin shRNA recombinant plasmid has been constructed successfully. Transfection with the maspin shRNA recombinant plasmid could inhibit the expression of maspin mRNA and protein effectively in human gastric cancer cell line MKN-28.
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Wynant N, Santos D, Vanden Broeck J. Biological mechanisms determining the success of RNA interference in insects. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 312:139-67. [PMID: 25262241 DOI: 10.1016/b978-0-12-800178-3.00005-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Insects constitute the largest group of animals on this planet, having a huge impact on our environment, as well as on our quality of life. RNA interference (RNAi) is a posttranscriptional gene silencing mechanism triggered by double-stranded (ds)RNA fragments. This process not only forms the basis of a widely used reverse genetics research method in many different eukaryotes but also holds great promise to contribute to the species-specific control of agricultural pests and to combat viral infections in beneficial and disease vectoring insects. However, in many economically important insect species, such as flies, mosquitoes, and caterpillars, systemic delivery of naked dsRNA does not trigger effective gene silencing. Although many components of the RNAi pathway have initially been deciphered in the fruit fly, Drosophila melanogaster, it will be of major importance to investigate this process in a wider variety of species, including dsRNA-sensitive insects such as locusts and beetles, to elucidate the factors responsible for the remarkable variability in RNAi efficiency, as observed in different insects. In this chapter, we review the current knowledge on the RNAi pathway, as well as the most recent insights into the mechanisms that might determine successful RNAi in insects.
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Affiliation(s)
- Niels Wynant
- Department of Animal Physiology and Neurobiology, KU Leuven, Naamsestraat, Leuven, Belgium.
| | - Dulce Santos
- Department of Animal Physiology and Neurobiology, KU Leuven, Naamsestraat, Leuven, Belgium
| | - Jozef Vanden Broeck
- Department of Animal Physiology and Neurobiology, KU Leuven, Naamsestraat, Leuven, Belgium
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Apone F, Ruggiero A, Tortora A, Tito A, Grimaldi MR, Arciello S, Andrenacci D, Di Lelio I, Colucci G. Targeting the diuretic hormone receptor to control the cotton leafworm, Spodoptera littoralis. JOURNAL OF INSECT SCIENCE (ONLINE) 2014; 14:87. [PMID: 25368043 PMCID: PMC4212857 DOI: 10.1093/jis/14.1.87] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 11/23/2012] [Indexed: 05/31/2023]
Abstract
The cotton leafworm, Spodoptera littoralis Boisduval (Lepidoptera: Noctuidae), is one of the most devastating pests of crops worldwide. Several types of treatments have been used against this pest, but many of them failed because of the rapid development of genetic resistance in the different insect populations. G protein coupled receptors have vital functions in most organisms, including insects; thus, they are appealing targets for species-specific pest control strategies. Among the insect G protein coupled receptors, the diuretic hormone receptors have several key roles in development and metabolism, but their importance in vivo and their potential role as targets of novel pest control strategies are largely unexplored. With the goal of using DHR genes as targets to control S. littoralis, we cloned a corticotropin-releasing factor-like binding receptor in this species and expressed the corresponding dsRNA in tobacco plants to knock down the receptor activity in vivo through RNA interference. We also expressed the receptor in mammalian cells to study its signaling pathways. The results indicate that this diuretic hormone receptor gene has vital roles in S. littoralis and represents an excellent molecular target to protect agriculturally-important plants from this pest.
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Affiliation(s)
- Fabio Apone
- Arterra BioSci., via Brin 69, 80142 Napoli, Italy
| | - Alessandra Ruggiero
- Arterra BioSci., via Brin 69, 80142 Napoli, Italy Current address: Center for Cardiovascular Genetics, The University of Texas Health Science Center, 6770 Bertner Street, Houston, TX 77030
| | | | | | | | | | - Davide Andrenacci
- Institute of Genetics and Biophysics, CNR, via Castellino 111, 80131 Napoli, Italy
| | - Ilaria Di Lelio
- Department of Entomology and Agricultural Zoology, University of Napoli, via Università 100, 80055 Portici (NA), Italy
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Marker genes for activation of the RNA interference (RNAi) pathway in the free-living nematode Caenorhabditis elegans and RNAi development in the ovine nematode Teladorsagia circumcincta. J Helminthol 2013; 89:208-16. [PMID: 24345514 DOI: 10.1017/s0022149x13000801] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The nematode Teladorsagia circumcincta is a major cause of parasitic gastroenteritis in sheep in temperate regions. The development of resistance to the major anthelmintic classes used for its control is a threat to small ruminant farming sustainability. Vaccination is a potential alternative control method for this nematode. Gene datasets can be exploited to identify potential vaccine candidates and these validated further by methods such as RNA interference (RNAi) prior to vaccine trials. Previous reports indicate that RNAi in parasitic nematodes is inconsistent and, to date, there are no internal controls that indicate activation of the RNAi pathway in response to double-stranded RNA (dsRNA). The present aims were to determine whether or not the transcription levels of potential marker genes in the RNAi pathway could indicate activation of the pathway in Caenorhabditis elegans and to develop an RNAi platform in T. circumcincta. In C. elegans, transcript levels of three candidate marker genes, Ce-dcr-1 (Dicer), Ce-ego-1 (Enhancer of Glp-One family member) and Ce-rsd-3 (RNAi Spreading Defective), were analysed and results indicated that activation of the pathway had no effect on transcript levels of these genes. In T. circumcincta, two vaccine candidate genes from the Activation-associated Secreted Protein (ASP) family were targets for knockdown. RNAi experiments showed successful silencing of both targets, although inconsistencies in efficacy were observed. After testing a number of parameters that might affect variability, it was found that the length of the storage period of the larvae plays an important role in the consistency of the RNAi results.
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New role for DCR-1/dicer in Caenorhabditis elegans innate immunity against the highly virulent bacterium Bacillus thuringiensis DB27. Infect Immun 2013; 81:3942-57. [PMID: 23918784 DOI: 10.1128/iai.00700-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacillus thuringiensis produces toxins that target invertebrates, including Caenorhabditis elegans. Virulence of Bacillus strains is often highly specific, such that B. thuringiensis strain DB27 is highly pathogenic to C. elegans but shows no virulence for another model nematode, Pristionchus pacificus. To uncover the underlying mechanisms of the differential responses of the two nematodes to B. thuringiensis DB27 and to reveal the C. elegans defense mechanisms against this pathogen, we conducted a genetic screen for C. elegans mutants resistant to B. thuringiensis DB27. Here, we describe a B. thuringiensis DB27-resistant C. elegans mutant that is identical to nasp-1, which encodes the C. elegans homolog of the nuclear-autoantigenic-sperm protein. Gene expression analysis indicated a substantial overlap between the genes downregulated in the nasp-1 mutant and targets of C. elegans dcr-1/Dicer, suggesting that dcr-1 is repressed in nasp-1 mutants, which was confirmed by quantitative PCR. Consistent with this, the nasp-1 mutant exhibits RNA interference (RNAi) deficiency and reduced longevity similar to those of a dcr-1 mutant. Building on these surprising findings, we further explored a potential role for dcr-1 in C. elegans innate immunity. We show that dcr-1 mutant alleles deficient in microRNA (miRNA) processing, but not those deficient only in RNAi, are resistant to B. thuringiensis DB27. Furthermore, dcr-1 overexpression rescues the nasp-1 mutant's resistance, suggesting that repression of dcr-1 determines the nasp-1 mutant's resistance. Additionally, we identified the collagen-encoding gene col-92 as one of the downstream effectors of nasp-1 that play an important role in resistance to DB27. Taken together, these results uncover a previously unknown role for DCR-1/Dicer in C. elegans antibacterial immunity that is largely associated with miRNA processing.
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RNAi for Insect Control: Current Perspective and Future Challenges. Appl Biochem Biotechnol 2013; 171:847-73. [DOI: 10.1007/s12010-013-0399-4] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 07/15/2013] [Indexed: 12/15/2022]
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Antiviral RNA silencing initiated in the absence of RDE-4, a double-stranded RNA binding protein, in Caenorhabditis elegans. J Virol 2013; 87:10721-9. [PMID: 23885080 DOI: 10.1128/jvi.01305-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Small interfering RNAs (siRNAs) processed from double-stranded RNA (dsRNA) of virus origins mediate potent antiviral defense through a process referred to as RNA interference (RNAi) or RNA silencing in diverse organisms. In the simple invertebrate Caenorhabditis elegans, the RNAi process is initiated by a single Dicer, which partners with the dsRNA binding protein RDE-4 to process dsRNA into viral siRNAs (viRNAs). Notably, in C. elegans this RNA-directed viral immunity (RDVI) also requires a number of worm-specific genes for its full antiviral potential. One such gene is rsd-2 (RNAi spreading defective 2), which was implicated in RDVI in our previous studies. In the current study, we first established an antiviral role by showing that rsd-2 null mutants permitted higher levels of viral RNA accumulation, and that this enhanced viral susceptibility was reversed by ectopic expression of RSD-2. We then examined the relationship of rsd-2 with other known components of RNAi pathways and established that rsd-2 functions in a novel pathway that is independent of rde-4 but likely requires the RNA-dependent RNA polymerase RRF-1, suggesting a critical role for RSD-2 in secondary viRNA biogenesis, likely through coordinated action with RRF-1. Together, these results suggest that RDVI in the single-Dicer organism C. elegans depends on the collective actions of both RDE-4-dependent and RDE-4-independent mechanisms to produce RNAi-inducing viRNAs. Our study reveals, for the first time, a novel siRNA-producing mechanism in C. elegans that bypasses the need for a dsRNA-binding protein.
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Abstract
Systemic RNAi, the intercellular spreading of RNAi silencing, requires SID-1 and SID-3 to import silencing signals in Caenorhabditis elegans. How are these signals exported? SID-5, an endosome-associated protein, is a candidate for the job.
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Affiliation(s)
- Christian E Rocheleau
- Division of Endocrinology and Metabolism, Department of Medicine, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Quebec H3A 0C7, Canada.
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Shreve JT, Shukle RH, Subramanyam S, Johnson AJ, Schemerhorn BJ, Williams CE, Stuart JJ. A genome-wide survey of small interfering RNA and microRNA pathway genes in a galling insect. JOURNAL OF INSECT PHYSIOLOGY 2013; 59:367-376. [PMID: 23232437 DOI: 10.1016/j.jinsphys.2012.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 11/28/2012] [Accepted: 11/30/2012] [Indexed: 06/01/2023]
Abstract
Deployment of resistance (R) genes is the most effective control for Hessian fly, Mayetiola destructor (Say); however, deployment of R genes results in an increased frequency of pest genotypes that display virulence to them. RNA interference (RNAi) is a useful reverse genetics tool for studying such insect virulence pathways, but requires a systemic phenotype, which is not found in all species. In an effort to correlate our observed weak RNAi phenotype in M. destructor with a genetic basis, we have aggregated and compared RNAi related genes across M. destructor, three other insect species, and the nematode Caenorhabditis elegans. We report here the annotation of the core genes in the small interfering RNA (siRNA) and microRNA (miRNA) pathways in M. destructor. While most of the miRNA pathway genes were highly conserved across the species studied, the siRNA pathway genes showed increased relative variability in comparison to the miRNA pathway. In particular, the Piwi/Argonaute/Zwille (PAZ) domain of Dicer-2 (DCR-2) had the least amount of sequence similarity of any domain among species surveyed, with a trend of increased conservation in those species with amenable systemic RNAi. A homolog of the systemic interference defective-1 (Sid-1) gene of C. elegans was also not annotated in the M. destructor genome. Indeed, it is of interest that a Sid-1 homolog has not been detected in any dipteran species to date. We hypothesize the sequence architecture of the PAZ domain in the M. destructor DCR-2 protein is related to reduced efficacy of this enzyme and this taken together with the lack of a Sid-1 homolog may account for the weak RNAi response observed to date in this species as well as other dipteran species.
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Affiliation(s)
- Jacob T Shreve
- Department of Entomology, Purdue University, West Lafayette, IN 47907, USA
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