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Xia J, Peng R, Fei S, Awais MM, Lai W, Huang Y, Wu H, Yu Y, Liang L, Swevers L, Sun J, Feng M. Systematic analysis of innate immune-related genes in the silkworm: Application to antiviral research. INSECT SCIENCE 2024. [PMID: 38571329 DOI: 10.1111/1744-7917.13363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 02/21/2024] [Accepted: 03/01/2024] [Indexed: 04/05/2024]
Abstract
The silkworm, a crucial model organism of the Lepidoptera, offers an excellent platform for investigating the molecular mechanisms underlying the innate immune response of insects toward pathogens. Over the years, researchers worldwide have identified numerous immune-related genes in silkworms. However, these identified silkworm immune genes are not well classified and not well known to the scientific community. With the availability of the latest genome data of silkworms and the extensive research on silkworm immunity, it has become imperative to systematically categorize the immune genes of silkworms with different database IDs. In this study, we present a meticulous organization of prevalent immune-related genes in the domestic silkworm, using the SilkDB 3.0 database as a reliable source for updated gene information. Furthermore, utilizing the available data, we classify the collected immune genes into distinct categories: pattern recognition receptors, classical immune pathways, effector genes and others. In-depth data analysis has enabled us to predict some potential antiviral genes. Subsequently, we performed antiviral experiments on selected genes, exploring their impact on Bombyx mori nucleopolyhedrovirus replication. The outcomes of this research furnish novel insights into the immune genes of the silkworm, consequently fostering advancements in the field of silkworm immunity research by establishing a comprehensive classification and functional understanding of immune-related genes in the silkworm. This study contributes to the broader understanding of insect immune responses and opens up new avenues for future investigations in the domain of host-pathogen interactions.
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Affiliation(s)
- Junming Xia
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Ruoxuan Peng
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Shigang Fei
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Mian Muhammad Awais
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Wenxuan Lai
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yigui Huang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Hailin Wu
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yue Yu
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Lingying Liang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Luc Swevers
- Insect Molecular Genetics and Biotechnology, National Center for Scientific Research Demokritos, Institute of Biosciences and Applications, Athens, Greece
| | - Jingchen Sun
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Min Feng
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
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2
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Koh C, Saleh MC. Translating mosquito viromes into vector management strategies. Trends Parasitol 2024; 40:10-20. [PMID: 38065789 DOI: 10.1016/j.pt.2023.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 01/06/2024]
Abstract
Mosquitoes are best known for transmitting human and animal viruses. However, they also harbour mosquito-specific viruses (MSVs) as part of their microbiota. These are a group of viruses whose diversity and prevalence overshadow their medically relevant counterparts. Although metagenomics sequencing has remarkably accelerated the discovery of these viruses, what we know about them is often limited to sequence information, leaving much of their fundamental biology to be explored. Understanding the biology and ecology of MSVs can enlighten our knowledge of virus-virus interactions and lead to new innovations in the management of mosquito-borne viral diseases. We retrace the history of their discovery and discuss research milestones that would line the path from mosquito virome knowledge to vector management strategies.
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Affiliation(s)
- Cassandra Koh
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France.
| | - Maria-Carla Saleh
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
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3
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Kim H, Masuta C. VIGS as a strategy to reverse aphid wing induction by Y-satellite RNA of cucumber mosaic virus. FEBS Open Bio 2023; 13:2005-2019. [PMID: 37596957 PMCID: PMC10626274 DOI: 10.1002/2211-5463.13697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/02/2023] [Accepted: 08/17/2023] [Indexed: 08/21/2023] Open
Abstract
Y-satellite RNA (Y-sat) of cucumber mosaic virus upregulates the expression of the aphid ABCG4 gene, which promotes aphid wing formation. We used ABCG4 virus-induced gene silencing (VIGS) to prevent the wing-induction mechanism of Y-sat and thus inhibited aphid wing formation. Of the aphids on plants with VIGS of ABCG4, only about 30% had wings, and 60-70% of the winged aphids were small and likely impaired in flying ability. In addition, we showed that double-stranded RNAs (dsRNAs) and small RNAs were transferred from the plant to the aphid to adequately silence aphid genes. Supplying ABCG4 dsRNA by VIGS to aphids is thus a potential strategy to inhibit aphid wing formation.
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Affiliation(s)
- Hangil Kim
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Chikara Masuta
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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4
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Khalifa ME, MacDiarmid RM. Molecular Characterization of Two Totiviruses from the Commensal Yeast Geotrichum candidum. Viruses 2023; 15:2150. [PMID: 38005831 PMCID: PMC10674808 DOI: 10.3390/v15112150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/16/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
Mycoviruses can infect many of the major taxa of fungi including yeasts. Mycoviruses in the yeast fungus Geotrichum candidum are not well studied with only three G. candidum-associated viral species characterized to date, all of which belong to the Totiviridae genus Totivirus. In this study, we report the molecular characteristics of another two totiviruses co-infecting isolate Gc6 of G. candidum. The two totiviruses were tentatively named Geotrichum candidum totivirus 2 isolate Gc6 (GcTV2-Gc6) and Geotrichum candidum totivirus 4 isolate Gc6 (GcTV4-Gc6). Both viruses have the typical genome organization of totiviruses comprising two ORFs encoding capsid protein (CP) and RNA-dependent RNA polymerase (RdRp) at the N and C termini, respectively. The genomes of GcTV2-Gc6 and GcTV4-Gc6 are 4592 and 4530 bp long, respectively. Both viruses contain the-frameshifting elements and their proteins could be expressed as a single fusion protein. GcTV2-Gc6 is closely related to a totivirus isolated from the same host whereas GcTV4-Gc6 is related to insect-associated totiviruses. The phylogenetic analysis indicated that GcTV2-Gc6 and GcTV4-Gc6 belong to two different sister clades, I-A and I-B, respectively. It is interesting that all viruses identified from G. candidum belong to the genus Totivirus; however, this might be due to the lack of research reporting the characterization of mycoviruses from this fungal host. It is possible that the RNA interference (RNAi) mechanism cannot actively suppress totivirus accumulation in G. candidum Gc6.
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Affiliation(s)
- Mahmoud E. Khalifa
- Botany and Microbiology Department, Faculty of Science, Damietta University, Damietta 34517, Egypt;
| | - Robin M. MacDiarmid
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1025, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
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5
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Osborne CJ, Cohnstaedt LW, Silver KS. Outlook on RNAi-Based Strategies for Controlling Culicoides Biting Midges. Pathogens 2023; 12:1251. [PMID: 37887767 PMCID: PMC10610143 DOI: 10.3390/pathogens12101251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023] Open
Abstract
Culicoides are small biting midges with the capacity to transmit important livestock pathogens around much of the world, and their impacts on animal welfare are likely to expand. Hemorrhagic diseases resulting from Culicoides-vectored viruses, for example, can lead to millions of dollars in economic damages for producers. Chemical insecticides can reduce Culicoides abundance but may not suppress population numbers enough to prevent pathogen transmission. These insecticides can also cause negative effects on non-target organisms and ecosystems. RNA interference (RNAi) is a cellular regulatory mechanism that degrades mRNA and suppresses gene expression. Studies have examined the utility of this mechanism for insect pest control, and with it, have described the hurdles towards producing, optimizing, and applying these RNAi-based products. These methods hold promise for being highly specific and environmentally benign when compared to chemical insecticides and are more transient than engineering transgenic insects. Given the lack of available control options for Culicoides, RNAi-based products could be an option to treat large areas with minimal environmental impact. In this study, we describe the state of current Culicoides control methods, successes and hurdles towards using RNAi for pest control, and the necessary research required to bring an RNAi-based control method to fruition for Culicoides midges.
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Affiliation(s)
- Cameron J. Osborne
- Department of Entomology, College of Agriculture, Kansas State University, Manhattan, KS 66506, USA;
| | - Lee W. Cohnstaedt
- Foreign Arthropod-Borne Animal Diseases Research Unit, National Bio- and Agro-Defense Facility, Agricultural Research Service, United Stated Department of Agriculture, Manhattan, KS 66502, USA
| | - Kristopher S. Silver
- Department of Entomology, College of Agriculture, Kansas State University, Manhattan, KS 66506, USA;
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Merkling SH, Crist AB, Henrion-Lacritick A, Frangeul L, Couderc E, Gausson V, Blanc H, Bergman A, Baidaliuk A, Romoli O, Saleh MC, Lambrechts L. Multifaceted contributions of Dicer2 to arbovirus transmission by Aedes aegypti. Cell Rep 2023; 42:112977. [PMID: 37573505 DOI: 10.1016/j.celrep.2023.112977] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 06/20/2023] [Accepted: 07/28/2023] [Indexed: 08/15/2023] Open
Abstract
Arthropod-borne viruses (arboviruses) transmitted by Aedes aegypti mosquitoes are an increasing threat to global health. The small interfering RNA (siRNA) pathway is considered the main antiviral immune pathway of insects, but its effective impact on arbovirus transmission is surprisingly poorly understood. Here, we use CRISPR-Cas9-mediated gene editing in vivo to mutate Dicer2, a gene encoding the RNA sensor and key component of the siRNA pathway. The loss of Dicer2 enhances early viral replication and systemic viral dissemination of four medically significant arboviruses (chikungunya, Mayaro, dengue, and Zika viruses) representing two viral families. However, Dicer2 mutants and wild-type mosquitoes display overall similar levels of vector competence. In addition, Dicer2 mutants undergo significant virus-induced mortality during infection with chikungunya virus. Together, our results define a multifaceted role for Dicer2 in the transmission of arboviruses by Ae. aegypti mosquitoes and pave the way for further mechanistic investigations.
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Affiliation(s)
- Sarah Hélène Merkling
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Insect-Virus Interactions Unit, 75015 Paris, France
| | - Anna Beth Crist
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Insect-Virus Interactions Unit, 75015 Paris, France
| | - Annabelle Henrion-Lacritick
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
| | - Lionel Frangeul
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
| | - Elodie Couderc
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Insect-Virus Interactions Unit, 75015 Paris, France; Sorbonne Université, Collège Doctoral, 75005 Paris, France
| | - Valérie Gausson
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
| | - Hervé Blanc
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
| | - Alexander Bergman
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Insect-Virus Interactions Unit, 75015 Paris, France
| | - Artem Baidaliuk
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Insect-Virus Interactions Unit, 75015 Paris, France; Sorbonne Université, Collège Doctoral, 75005 Paris, France
| | - Ottavia Romoli
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
| | - Maria-Carla Saleh
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France.
| | - Louis Lambrechts
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Insect-Virus Interactions Unit, 75015 Paris, France.
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7
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Airs PM, Kudrna KE, Lubinski B, Phanse Y, Bartholomay LC. A Comparative Analysis of RNAi Trigger Uptake and Distribution in Mosquito Vectors of Disease. INSECTS 2023; 14:556. [PMID: 37367372 DOI: 10.3390/insects14060556] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/28/2023]
Abstract
In mosquitoes, the utilization of RNAi for functional genetics is widespread, usually mediated through introduced double-stranded RNAs (dsRNAs) with sequence identity to a gene of interest. However, RNAi in mosquitoes is often hampered by inconsistencies in target gene knockdown between experimental setups. While the core RNAi pathway is known to function in most mosquito strains, the uptake and biodistribution of dsRNAs across different mosquito species and life stages have yet to be extensively explored as a source of variation in RNAi experiments. To better understand mosquito-RNAi dynamics, the biodistribution of a dsRNA to a heterologous gene, LacZ (iLacZ), was tracked following various routes of exposure in the larval and adult stages of Aedes aegypti, Anopheles gambiae, and Culex pipiens. iLacZ was largely limited to the gut lumen when exposed per os, or to the cuticle when topically applied, but spread through the hemocoel when injected. Uptake of dsRNA was noted in a subset of cells including: hemocytes, pericardial cells of the dorsal vessel, ovarian follicles, and ganglia of the ventral nerve cord. These cell types are all known to undergo phagocytosis, pinocytosis, or both, and as such may actively take up RNAi triggers. In Ae. aegypti, iLacZ was detected for up to one week post exposure by Northern blotting, but uptake and degradation drastically differed across tissues. The results presented here reveal that the uptake of RNAi triggers is distinct and specific to the cell type in vivo.
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Affiliation(s)
- Paul M Airs
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Katherine E Kudrna
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Bailey Lubinski
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yashdeep Phanse
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lyric C Bartholomay
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
- Midwest Center of Excellence for Vector-Borne Diseases, University of Wisconsin-Madison, Madison, WI 53706, USA
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8
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An Ascovirus Utilizes Different Types of Host Larval Regulated Cell Death Mechanisms To Produce and Release Vesicles. J Virol 2023; 97:e0156622. [PMID: 36533952 PMCID: PMC9888208 DOI: 10.1128/jvi.01566-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Ascoviruses are insect-specific viruses that are thought to utilize the cellular apoptotic processes of host larvae to produce numerous virion-containing vesicles. In this study, we monitored the in vivo infection processes of Heliothis virescens ascovirus 3h (HvAV-3h) to illustrate the regulated cell death (RCD) of host cells. Transmission electron microscopic observations did not reveal any morphological markers of apoptosis in the fat bodies or hemocytes of HvAV-3h-infected Helicoverpa armigera or Spodoptera exigua larvae. However, several hemocytes showed the morphological criteria for necrosis and/or pyroptosis. Further in vitro biochemical tests were performed to confirm the RCD type of host cells after infection with HvAV-3h. Different morphological characteristics were found between the early (prior to 24 hours post-infection, [hpi]) and later (48 to 120 hpi) stages in both HvAV-3h infected larval fat bodies and hemocytes. In the early stages, the virions could only be found in several adipohemocytes, and the fat bodies were cleaving their contained lipid inclusions into small lipid dots. In the later stage, both fat bodies and hemocytes were filled with numerous virions. According to the morphological characteristics of HvAV-3h infected larval fat bodies or hemocytes, the pathogenic characteristics and infection patterns of HvAV-3h in the host larvae were described, and the systematic pathogenic mode of ascovirus infection was refined in this study. This study details the complete infection process of ascoviruses, which provides insights into the relationship between a pathogenesis of an insect virus and the RCD of different host tissues at different stages of infection. IMPORTANCE Viruses and other pathogens can interrupt host cellular apoptosis to gain benefits, such as sufficient resources and a stable environment that enables them to complete their replication and assembly. It is unusual for viruses to code proteins with homology to caspases, which are commonly recognized as apoptosis regulators. Ascoviruses are insect viruses with special cytopathology, and they have been hypothesized to induce apoptosis in their host larvae via coding a caspase-like protein. This enables them to utilize the process of cellular apoptosis to facilitate vesicle formation and replication. However, our previous studies revealed different trends. The fat bodies and hemocytes of Heliothis virescens ascovirus 3h (HvAV-3h)-infected larvae did not show any morphological markers of apoptosis but did display necrosis and/or pyroptosis morphological characteristics. The pathogenic characteristics and infection patterns of HvAV-3h in the host larvae were described, which can help us understand the relationship between the pathogenesis of an insect virus and host RCD.
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9
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A Tale of Two Lobsters—Transcriptomic Analysis Reveals a Potential Gap in the RNA Interference Pathway in the Tropical Rock Lobster Panulirus ornatus. Int J Mol Sci 2022; 23:ijms231911752. [PMID: 36233053 PMCID: PMC9569428 DOI: 10.3390/ijms231911752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 11/25/2022] Open
Abstract
RNA interference (RNAi) has been widely utilised in many invertebrate models since its discovery, and in a majority of instances presents as a highly efficient and potent gene silencing mechanism. This is emphasized in crustaceans with almost all taxa having the capacity to trigger effective silencing, with a notable exception in the spiny lobsters where repeated attempts at dsRNA induced RNAi have demonstrated extremely ineffective gene knockdown. A comparison of the core RNAi machinery in transcriptomic data from spiny lobsters (Panulirus ornatus) and the closely related slipper lobsters (Thenus australiensis, where silencing is highly effective) revealed that both lobsters possess all proteins involved in the small interfering and microRNA pathways, and that there was little difference at both the sequence and domain architecture level. Comparing the expression of these genes however demonstrated that T. australiensis had significantly higher expression in the transcripts encoding proteins which directly interact with dsRNA when compared to P. ornatus, validated via qPCR. These results suggest that low expression of the core RNAi genes may be hindering the silencing response in P. ornatus, and suggest that it may be critical to enhance the expression of these genes to induce efficient silencing in spiny lobsters.
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10
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Torri A, Jaeger J, Pradeu T, Saleh MC. The origin of RNA interference: Adaptive or neutral evolution? PLoS Biol 2022; 20:e3001715. [PMID: 35767561 PMCID: PMC9275709 DOI: 10.1371/journal.pbio.3001715] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/12/2022] [Indexed: 11/30/2022] Open
Abstract
The origin of RNA interference (RNAi) is usually explained by a defense-based hypothesis, in which RNAi evolved as a defense against transposable elements (TEs) and RNA viruses and was already present in the last eukaryotic common ancestor (LECA). However, since RNA antisense regulation and double-stranded RNAs (dsRNAs) are ancient and widespread phenomena, the origin of defensive RNAi should have occurred in parallel with its regulative functions to avoid imbalances in gene regulation. Thus, we propose a neutral evolutionary hypothesis for the origin of RNAi in which qualitative system drift from a prokaryotic antisense RNA gene regulation mechanism leads to the formation of RNAi through constructive neutral evolution (CNE). We argue that RNAi was already present in the ancestor of LECA before the need for a new defense system arose and that its presence helped to shape eukaryotic genomic architecture and stability. Where does RNA interference come from? This Essay describes a new step-by-step evolutionary model of how RNA interference might have originated in early eukaryotes through neutral events from the molecular machinery present in prokaryotes.
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Affiliation(s)
- Alessandro Torri
- Virus & RNA interference Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Université Paris Cité, Paris, France
- * E-mail: (AT); (M-CS)
| | | | - Thomas Pradeu
- ImmunoConcEpT, CNRS UMR 5164, University of Bordeaux, Bordeaux, France
- Institut d’histoire et de philosophie des sciences et des techniques, CNRS UMR 8590, Pantheon-Sorbonne University, Paris, France
| | - Maria-Carla Saleh
- Virus & RNA interference Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Université Paris Cité, Paris, France
- * E-mail: (AT); (M-CS)
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11
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Yan Y, Ham BK. The Mobile Small RNAs: Important Messengers for Long-Distance Communication in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:928729. [PMID: 35783973 PMCID: PMC9247610 DOI: 10.3389/fpls.2022.928729] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/25/2022] [Indexed: 06/06/2023]
Abstract
Various species of small RNAs (sRNAs), notably microRNAs and small interfering RNAs (siRNAs), have been characterized as the major effectors of RNA interference in plants. Growing evidence supports a model in which sRNAs move, intercellularly, systemically, and between cross-species. These non-coding sRNAs can traffic cell-to-cell through plasmodesmata (PD), in a symplasmic manner, as well as from source to sink tissues, via the phloem, to trigger gene silencing in their target cells. Such mobile sRNAs function in non-cell-autonomous communication pathways, to regulate various biological processes, such as plant development, reproduction, and plant defense. In this review, we summarize recent progress supporting the roles of mobile sRNA in plants, and discuss mechanisms of sRNA transport, signal amplification, and the plant's response, in terms of RNAi activity, within the recipient tissues. We also discuss potential research directions and their likely impact on engineering of crops with traits for achieving food security.
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Affiliation(s)
- Yan Yan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Byung-Kook Ham
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
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12
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Hernández-Pelegrín L, Llopis-Giménez Á, Crava CM, Ortego F, Hernández-Crespo P, Ros VID, Herrero S. Expanding the Medfly Virome: Viral Diversity, Prevalence, and sRNA Profiling in Mass-Reared and Field-Derived Medflies. Viruses 2022; 14:v14030623. [PMID: 35337030 PMCID: PMC8955247 DOI: 10.3390/v14030623] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 12/04/2022] Open
Abstract
The Mediterranean fruit fly (medfly), Ceratitis capitata, is an agricultural pest of a wide range of fruits. The advent of high-throughput sequencing has boosted the discovery of RNA viruses infecting insects. In this article, we aim to characterize the RNA virome and viral sRNA profile of medfly. By means of transcriptome mining, we expanded the medfly RNA virome to 13 viruses, including two novel positive ssRNA viruses and the first two novel dsRNA viruses reported for medfly. Our analysis across multiple laboratory-reared and field-collected medfly samples showed the presence of a core RNA virome comprised of Ceratitis capitata iflavirus 2 and Ceratitis capitata negev-like virus 1. Furthermore, field-collected flies showed a higher viral diversity in comparison to the laboratory-reared flies. Based on the small RNA sequencing, we detected small interfering RNAs mapping to all the viruses present in each sample, except for Ceratitis capitata nora virus. Although the identified RNA viruses do not cause obvious symptoms in medflies, the outcome of their interaction may still influence the medfly’s fitness and ecology, becoming either a risk or an opportunity for mass-rearing and SIT applications.
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Affiliation(s)
- Luis Hernández-Pelegrín
- Department of Genetics and University Institute of Biotechnology and Biomedicine (BIOTECMED), Universitat de València, 46100 Valencia, Spain; (L.H.-P.); (Á.L.-G.); (C.M.C.)
- Laboratory of Virology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands;
| | - Ángel Llopis-Giménez
- Department of Genetics and University Institute of Biotechnology and Biomedicine (BIOTECMED), Universitat de València, 46100 Valencia, Spain; (L.H.-P.); (Á.L.-G.); (C.M.C.)
| | - Cristina Maria Crava
- Department of Genetics and University Institute of Biotechnology and Biomedicine (BIOTECMED), Universitat de València, 46100 Valencia, Spain; (L.H.-P.); (Á.L.-G.); (C.M.C.)
| | - Félix Ortego
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain; (F.O.); (P.H.-C.)
| | - Pedro Hernández-Crespo
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain; (F.O.); (P.H.-C.)
| | - Vera I. D. Ros
- Laboratory of Virology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands;
| | - Salvador Herrero
- Department of Genetics and University Institute of Biotechnology and Biomedicine (BIOTECMED), Universitat de València, 46100 Valencia, Spain; (L.H.-P.); (Á.L.-G.); (C.M.C.)
- Correspondence: ; Tel.: +34-963-54-30-06
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Japanese Encephalitis Virus Interaction with Mosquitoes: A Review of Vector Competence, Vector Capacity and Mosquito Immunity. Pathogens 2022; 11:pathogens11030317. [PMID: 35335641 PMCID: PMC8953304 DOI: 10.3390/pathogens11030317] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 02/01/2023] Open
Abstract
Japanese encephalitis virus (JEV) is a mosquito-borne zoonotic flavivirus and a major cause of human viral encephalitis in Asia. We provide an overview of the knowledge on vector competence, vector capacity, and immunity of mosquitoes in relation to JEV. JEV has so far been detected in more than 30 mosquito species. This does not necessarily mean that these species contribute to JEV transmission under field conditions. Therefore, vector capacity, which considers vector competence, as well as environmental, behavioral, cellular, and biochemical variables, needs to be taken into account. Currently, 17 species can be considered as confirmed vectors for JEV and 10 other species as potential vectors. Culex tritaeniorhynchus and Culex annulirostris are considered primary JEV vectors in endemic regions. Culex pipiens and Aedes japonicus could be considered as potentially important vectors in the case of JEV introduction in new regions. Vector competence is determined by various factors, including vector immunity. The available knowledge on physical and physiological barriers, molecular pathways, antimicrobial peptides, and microbiome is discussed in detail. This review highlights that much remains to be studied about vector immunity against JEV in order to identify novel strategies to reduce JEV transmission by mosquitoes.
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14
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Cheng CX, Alvin Tan MJ, Chan KWK, Watanabe S, Wang S, Choy MM, Manuel M, Victorio CBL, Ong J, Reolo M, Chacko AM, Vasudevan SG. In Vitro and In Vivo Stability of P884T, a Mutation that Relocalizes Dengue Virus 2 Non-structural Protein 5. ACS Infect Dis 2021; 7:3277-3291. [PMID: 34735113 DOI: 10.1021/acsinfecdis.1c00441] [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] [Indexed: 12/27/2022]
Abstract
Dengue virus (DENV) non-structural protein 5 (NS5) is critical for viral RNA synthesis within endoplasmic reticulum (ER)-derived replication complexes in the cytoplasm; however a proportion of NS5 is known to be localized to the nucleus of infected cells. The importance of nuclear DENV NS5 on viral replication and pathogenesis is still unclear. We recently discovered a nuclear localization signal (NLS) residing in the C-terminal 18 amino acid (Cter18) region of DENV NS5 and that a single NS5 P884T amino acid substitution adjacent to the NLS is sufficient to relocalize a significant proportion of DENV2 NS5 from the nucleus to the cytoplasm of infected cells. Here, in vitro studies show that the DENV2 NS5 P884T mutant replicates similarly to the parental wild-type infectious clone-derived virus while inducing a greater type I interferon and inflammatory cytokine response, in a manner independent of NS5's ability to degrade STAT2 or regulate SAT1 splicing. In both AG129 mouse and Aedes aegypti mosquito infection models, the P884T virus exhibits lower levels of viral replication only at early timepoints. Intriguingly, there appears to be a tendency for selection pressure to revert to the wild-type proline in P884T-infected Ae. aegypti, in agreement with the high conservation of the proline at this position of NS5 in DENV2, 3, and 4. These results suggest that the predominant nuclear localization of DENV NS5, while not required for viral RNA replication, may play a role in pathogenesis and modulation of the host immune response and contribute to viral fitness in the mosquito host.
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Affiliation(s)
- Colin X. Cheng
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Min Jie Alvin Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Kitti W. K. Chan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Satoru Watanabe
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Sai Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Milly M. Choy
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Menchie Manuel
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Carla B. L. Victorio
- Laboratory for Translational and Molecular Imaging, Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Joanne Ong
- Laboratory for Translational and Molecular Imaging, Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Marie Reolo
- Laboratory for Translational and Molecular Imaging, Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Ann-Marie Chacko
- Laboratory for Translational and Molecular Imaging, Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Subhash G. Vasudevan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
- Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, NUS, 5 Science Drive 2, Singapore 117545, Singapore
- Institute for Glycomics, Griffith University, Southport 4222, Australia
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15
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Mehlhorn S, Hunnekuhl VS, Geibel S, Nauen R, Bucher G. Establishing RNAi for basic research and pest control and identification of the most efficient target genes for pest control: a brief guide. Front Zool 2021; 18:60. [PMID: 34863212 PMCID: PMC8643023 DOI: 10.1186/s12983-021-00444-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/04/2021] [Indexed: 11/14/2022] Open
Abstract
RNA interference (RNAi) has emerged as a powerful tool for knocking-down gene function in diverse taxa including arthropods for both basic biological research and application in pest control. The conservation of the RNAi mechanism in eukaryotes suggested that it should-in principle-be applicable to most arthropods. However, practical hurdles have been limiting the application in many taxa. For instance, species differ considerably with respect to efficiency of dsRNA uptake from the hemolymph or the gut. Here, we review some of the most frequently encountered technical obstacles when establishing RNAi and suggest a robust procedure for establishing this technique in insect species with special reference to pests. Finally, we present an approach to identify the most effective target genes for the potential control of agricultural and public health pests by RNAi.
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Affiliation(s)
- Sonja Mehlhorn
- Crop Science Division, Bayer AG, R&D, Pest Control, Alfred-Nobel-Straße 50, 40789, Monheim, Germany
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany
| | - Vera S Hunnekuhl
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany
| | - Sven Geibel
- Crop Science Division, Bayer AG, R&D, Pest Control, Alfred-Nobel-Straße 50, 40789, Monheim, Germany
| | - Ralf Nauen
- Crop Science Division, Bayer AG, R&D, Pest Control, Alfred-Nobel-Straße 50, 40789, Monheim, Germany
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany.
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16
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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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17
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Parisot N, Vargas-Chávez C, Goubert C, Baa-Puyoulet P, Balmand S, Beranger L, Blanc C, Bonnamour A, Boulesteix M, Burlet N, Calevro F, Callaerts P, Chancy T, Charles H, Colella S, Da Silva Barbosa A, Dell'Aglio E, Di Genova A, Febvay G, Gabaldón T, Galvão Ferrarini M, Gerber A, Gillet B, Hubley R, Hughes S, Jacquin-Joly E, Maire J, Marcet-Houben M, Masson F, Meslin C, Montagné N, Moya A, Ribeiro de Vasconcelos AT, Richard G, Rosen J, Sagot MF, Smit AFA, Storer JM, Vincent-Monegat C, Vallier A, Vigneron A, Zaidman-Rémy A, Zamoum W, Vieira C, Rebollo R, Latorre A, Heddi A. The transposable element-rich genome of the cereal pest Sitophilus oryzae. BMC Biol 2021; 19:241. [PMID: 34749730 PMCID: PMC8576890 DOI: 10.1186/s12915-021-01158-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/27/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions. RESULTS We sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino acids required for insect development and cuticle biosynthesis. CONCLUSIONS Here we present the genome of an agricultural pest beetle, which may act as a foundation for pest control. In addition, S. oryzae may be a useful model for endosymbiosis, and studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.
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Affiliation(s)
- Nicolas Parisot
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Carlos Vargas-Chávez
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Institute for Integrative Systems Biology (I2SySBio), Universitat de València and Spanish Research Council (CSIC), València, Spain
- Present Address: Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Clément Goubert
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, New York, 14853, USA
- Present Address: Human Genetics, McGill University, Montreal, QC, Canada
| | | | - Séverine Balmand
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Louis Beranger
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Caroline Blanc
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Aymeric Bonnamour
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Matthieu Boulesteix
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
| | - Nelly Burlet
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
| | - Federica Calevro
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Patrick Callaerts
- Department of Human Genetics, Laboratory of Behavioral and Developmental Genetics, KU Leuven, University of Leuven, B-3000, Leuven, Belgium
| | - Théo Chancy
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Hubert Charles
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- ERABLE European Team, INRIA, Rhône-Alpes, France
| | - Stefano Colella
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: LSTM, Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, CIRAD, INRAE, SupAgro, Univ Montpellier, Montpellier, France
| | - André Da Silva Barbosa
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Elisa Dell'Aglio
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Alex Di Genova
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
- ERABLE European Team, INRIA, Rhône-Alpes, France
- Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile
| | - Gérard Febvay
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Toni Gabaldón
- Life Sciences, Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Mechanisms of Disease, Institute for Research in Biomedicine (IRB), Barcelona, Spain
- Institut Catalan de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Alexandra Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Benjamin Gillet
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Lyon, France
| | | | - Sandrine Hughes
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Lyon, France
| | - Emmanuelle Jacquin-Joly
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Justin Maire
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Florent Masson
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Camille Meslin
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Nicolas Montagné
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Andrés Moya
- Institute for Integrative Systems Biology (I2SySBio), Universitat de València and Spanish Research Council (CSIC), València, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), València, Spain
| | | | - Gautier Richard
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653, Le Rheu, France
| | - Jeb Rosen
- Institute for Systems Biology, Seattle, WA, USA
| | - Marie-France Sagot
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
- ERABLE European Team, INRIA, Rhône-Alpes, France
| | | | | | | | - Agnès Vallier
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Aurélien Vigneron
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: Department of Evolutionary Ecology, Institute for Organismic and Molecular Evolution, Johannes Gutenberg University, 55128, Mainz, Germany
| | - Anna Zaidman-Rémy
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Waël Zamoum
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France.
- ERABLE European Team, INRIA, Rhône-Alpes, France.
| | - Rita Rebollo
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France.
| | - Amparo Latorre
- Institute for Integrative Systems Biology (I2SySBio), Universitat de València and Spanish Research Council (CSIC), València, Spain.
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), València, Spain.
| | - Abdelaziz Heddi
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France.
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18
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Interactions of the Insect-Specific Palm Creek Virus with Zika and Chikungunya Viruses in Aedes Mosquitoes. Microorganisms 2021; 9:microorganisms9081652. [PMID: 34442731 PMCID: PMC8402152 DOI: 10.3390/microorganisms9081652] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 11/17/2022] Open
Abstract
Palm Creek virus (PCV) is an insect-specific flavivirus that can interfere with the replication of mosquito-borne flaviviruses in Culex mosquitoes, thereby potentially reducing disease transmission. We examined whether PCV could interfere with arbovirus replication in Aedes (Ae.) aegypti and Ae. albopictus mosquitoes, major vectors for many prominent mosquito-borne viral diseases. We infected laboratory colonies of Ae. aegypti and Ae. albopictus with PCV to evaluate infection dynamics. PCV infection was found to persist to at least 21 days post-infection and could be detected in the midguts and ovaries. We then assayed for PCV-arbovirus interference by orally challenging PCV-infected mosquitoes with Zika and chikungunya viruses. For both arboviruses, PCV infection had no effect on infection and transmission rates, indicating limited potential as a method of intervention for Aedes-transmitted arboviruses. We also explored the hypothesis that PCV-arbovirus interference is mediated by the small interfering RNA pathway in silico. Our findings indicate that RNA interference is unlikely to underlie the mechanism of arbovirus inhibition and emphasise the need for empirical examination of individual pairs of insect-specific viruses and arboviruses to fully understand their impact on arbovirus transmission.
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19
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Spadar A, Phelan JE, Benavente ED, Campos M, Gomez LF, Mohareb F, Clark TG, Campino S. Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus. Parasit Vectors 2021; 14:332. [PMID: 34174947 PMCID: PMC8235865 DOI: 10.1186/s13071-021-04828-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 06/07/2021] [Indexed: 12/15/2022] Open
Abstract
Mosquitoes of the genus Aedes are the main vectors of many viruses, e.g. dengue and Zika, which affect millions of people each year and for which there are limited treatment options. Understanding how Aedes mosquitoes tolerate high viral loads may lead to better disease control strategies. Elucidating endogenous viral elements (EVEs) within vector genomes may give exploitable biological insights. Previous studies have reported the presence of a large number of EVEs in Aedes genomes. Here we investigated if flavivirus EVEs are conserved across populations and different Aedes species by using ~ 500 whole genome sequence libraries from Aedes aegypti and Aedes albopictus, sourced from colonies and field mosquitoes across continents. We found that nearly all flavivirus EVEs in the Ae. aegypti reference genome originate from four separate putative viral integration events, and that they are highly conserved across geographically diverse samples. By contrast, flavivirus EVEs in the Ae. albopictus reference genome originate from up to nine distinct integration events and show low levels of conservation, even within samples from narrow geographical ranges. Our analysis suggests that flaviviruses integrated as long sequences and were subsequently fragmented and shuffled by transposable elements. Given that EVEs of Ae. aegypti and Ae. albopictus belong to different phylogenetic clades and have very differing levels of conservation, they may have different evolutionary origins and potentially different functional roles.
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Affiliation(s)
- Anton Spadar
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Jody E Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Ernest Diez Benavente
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Monica Campos
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Lara Ferrero Gomez
- Unidade de Ciências da Natureza, da Vida e do Ambiente, Universidade Jean Piaget de Cabo Verde, Praia, Cabo Verde
| | - Fady Mohareb
- School of Water, Energy and Environment, Cranfield University, Bedford, UK
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK.
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
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20
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Wang K, Cheng H, Chen J, Zhu G, Tang P, Han Z. Chimeric Double-Stranded RNAs Could Act as Tailor-Made Pesticides for Controlling Storage Insects. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:6166-6171. [PMID: 34039005 DOI: 10.1021/acs.jafc.1c00853] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Double-stranded RNA (dsRNA), the unique trigger of RNA interference, could be used as potential pesticides for the management of storage insects. High species specificity greatly improves the biosafety of dsRNAs. However, there are usually more than one insect species in real circumstances. In this study, we present a new strategy that broadens the control spectrum of a formulation using single dsRNA fragments. First, effective target genes were selected for each insect pest, here including Rhyzopertha dominica and Blattella germanica. Then, a template was prepared by conjugating various fragments from each of the selected genes. With this template, a piece of chimeric dsRNA was synthesized, and, thus, regional complementary specificity for genes from different insects was harnessed. Finally, injection treatments with this chimeric dsRNA demonstrated that each gene was selectively silenced, and the insects of both species were effectively killed by continuously feeding the chimeric dsRNA. Meanwhile, the results also demonstrated that the toxicity of chimeric dsRNA for non-target organisms, including Zophobas atratus and Periplaneta americana, could be low. This is the first description of a single dsRNA fragment accurately targeting several pest species, and the method provides promise of novel tailor-made biopesticides in the future management of storage insects.
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Affiliation(s)
- Kangxu Wang
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, Jiangsu 210023, People's Republic of China
| | - Hong Cheng
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, Jiangsu 210023, People's Republic of China
| | - Jiasheng Chen
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Guanheng Zhu
- School of Agriculture, Sun Yat-Sen University, Shenzhen, Guangdong 518107, People's Republic of China
| | - Peian Tang
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, Jiangsu 210023, People's Republic of China
| | - Zhaojun Han
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
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21
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Flynt AS. Insecticidal RNA interference, thinking beyond long dsRNA. PEST MANAGEMENT SCIENCE 2021; 77:2179-2187. [PMID: 33078549 PMCID: PMC8048086 DOI: 10.1002/ps.6147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 05/07/2023]
Abstract
Over 20 years ago double-stranded RNA (dsRNA) was described as the trigger of RNAi interference (RNAi)-based gene silencing. This paradigm has held since, especially for insect biopesticide technologies where dsRNAs, similar to those described in 1998, are used to inhibit gene expression. In the intervening years, investigation of RNAi pathways has revealed the small RNA effectors of RNAi are diverse and rapidly evolving. The rich biology of insect small RNAs suggests potential to use multiple RNAi modes for manipulating gene expression. By exploiting different RNAi pathways, the menu of options for pest control can be expanded and could lead to better tailored solutions. Fortunately, basic delivery strategies used for dsRNA such as direct application or transgenic expression will translate well between RNAs transiting different RNAi pathways. Importantly, further engineering of RNAi-based biopesticides may provide an opportunity to address dsRNA insensitivity seen in some pests. Characterization of RNAi pathways unique to target species will be indispensable to this end and may require thinking beyond long dsRNA. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Alex S Flynt
- Cellular and Molecular Biology, University of Southern Mississippi, Hattiesburg, MS, USA
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22
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Rozen-Gagnon K, Gu M, Luna JM, Luo JD, Yi S, Novack S, Jacobson E, Wang W, Paul MR, Scheel TKH, Carroll T, Rice CM. Argonaute-CLIP delineates versatile, functional RNAi networks in Aedes aegypti, a major vector of human viruses. Cell Host Microbe 2021; 29:834-848.e13. [PMID: 33794184 DOI: 10.1016/j.chom.2021.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/20/2021] [Accepted: 03/04/2021] [Indexed: 02/07/2023]
Abstract
Argonaute (AGO) proteins bind small RNAs to silence complementary RNA transcripts, and they are central to RNA interference (RNAi). RNAi is critical for regulation of gene expression and antiviral defense in Aedes aegypti mosquitoes, which transmit Zika, chikungunya, dengue, and yellow fever viruses. In mosquitoes, AGO1 mediates miRNA interactions, while AGO2 mediates siRNA interactions. We applied AGO-crosslinking immunoprecipitation (AGO-CLIP) for both AGO1 and AGO2, and we developed a universal software package for CLIP analysis (CLIPflexR), identifying 230 small RNAs and 5,447 small RNA targets that comprise a comprehensive RNAi network map in mosquitoes. RNAi network maps predicted expression levels of small RNA targets in specific tissues. Additionally, this resource identified unexpected, context-dependent AGO2 target preferences, including endogenous viral elements and 3'UTRs. Finally, contrary to current thinking, mosquito AGO2 repressed imperfect targets. These findings expand our understanding of small RNA networks and have broad implications for the study of antiviral RNAi.
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Affiliation(s)
- Kathryn Rozen-Gagnon
- Laboratory of Virology and Infectious Disease, the Rockefeller University, New York, NY 10065, USA.
| | - Meigang Gu
- Laboratory of Virology and Infectious Disease, the Rockefeller University, New York, NY 10065, USA
| | - Joseph M Luna
- Laboratory of Virology and Infectious Disease, the Rockefeller University, New York, NY 10065, USA
| | - Ji-Dung Luo
- Bioinformatics Resource Center, the Rockefeller University, New York, NY 10065, USA
| | - Soon Yi
- Laboratory of Virology and Infectious Disease, the Rockefeller University, New York, NY 10065, USA
| | - Sasha Novack
- Laboratory of Virology and Infectious Disease, the Rockefeller University, New York, NY 10065, USA
| | - Eliana Jacobson
- Laboratory of Virology and Infectious Disease, the Rockefeller University, New York, NY 10065, USA
| | - Wei Wang
- Bioinformatics Resource Center, the Rockefeller University, New York, NY 10065, USA
| | - Matthew R Paul
- Bioinformatics Resource Center, the Rockefeller University, New York, NY 10065, USA
| | - Troels K H Scheel
- Laboratory of Virology and Infectious Disease, the Rockefeller University, New York, NY 10065, USA; Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, DK-2650 Hvidovre, Denmark; Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Thomas Carroll
- Bioinformatics Resource Center, the Rockefeller University, New York, NY 10065, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, the Rockefeller University, New York, NY 10065, USA.
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23
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Marconcini M, Pischedda E, Houé V, Palatini U, Lozada-Chávez N, Sogliani D, Failloux AB, Bonizzoni M. Profile of Small RNAs, vDNA Forms and Viral Integrations in Late Chikungunya Virus Infection of Aedes albopictus Mosquitoes. Viruses 2021; 13:553. [PMID: 33806250 PMCID: PMC8066115 DOI: 10.3390/v13040553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/07/2021] [Accepted: 03/23/2021] [Indexed: 12/11/2022] Open
Abstract
The Asian tiger mosquito Aedes albopictus is contributing to the (re)-emergence of Chikungunya virus (CHIKV). To gain insights into the molecular underpinning of viral persistence, which renders a mosquito a life-long vector, we coupled small RNA and whole genome sequencing approaches on carcasses and ovaries of mosquitoes sampled 14 days post CHIKV infection and investigated the profile of small RNAs and the presence of vDNA fragments. Since Aedes genomes harbor nonretroviral Endogenous Viral Elements (nrEVEs) which confers tolerance to cognate viral infections in ovaries, we also tested whether nrEVEs are formed after CHIKV infection. We show that while small interfering (si)RNAs are evenly distributed along the full viral genome, PIWI-interacting (pi)RNAs mostly arise from a ~1000 bp window, from which a unique vDNA fragment is identified. CHIKV infection does not result in the formation of new nrEVEs, but piRNAs derived from existing nrEVEs correlate with differential expression of an endogenous transcript. These results demonstrate that all three RNAi pathways contribute to the homeostasis during the late stage of CHIKV infection, but in different ways, ranging from directly targeting the viral sequence to regulating the expression of mosquito transcripts and expand the role of nrEVEs beyond immunity against cognate viruses.
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Affiliation(s)
- Michele Marconcini
- Department of Biology and Biotechnology, University of Pavia, via Ferrata, 27100 Pavia, Italy; (M.M.); (E.P.); (U.P.); (N.L.-C.); (D.S.)
| | - Elisa Pischedda
- Department of Biology and Biotechnology, University of Pavia, via Ferrata, 27100 Pavia, Italy; (M.M.); (E.P.); (U.P.); (N.L.-C.); (D.S.)
| | - Vincent Houé
- Arbovirus and Insect Vectors Unit, Department of Virology, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France; (V.H.); (A.-B.F.)
| | - Umberto Palatini
- Department of Biology and Biotechnology, University of Pavia, via Ferrata, 27100 Pavia, Italy; (M.M.); (E.P.); (U.P.); (N.L.-C.); (D.S.)
| | - Nabor Lozada-Chávez
- Department of Biology and Biotechnology, University of Pavia, via Ferrata, 27100 Pavia, Italy; (M.M.); (E.P.); (U.P.); (N.L.-C.); (D.S.)
| | - Davide Sogliani
- Department of Biology and Biotechnology, University of Pavia, via Ferrata, 27100 Pavia, Italy; (M.M.); (E.P.); (U.P.); (N.L.-C.); (D.S.)
| | - Anna-Bella Failloux
- Arbovirus and Insect Vectors Unit, Department of Virology, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France; (V.H.); (A.-B.F.)
| | - Mariangela Bonizzoni
- Department of Biology and Biotechnology, University of Pavia, via Ferrata, 27100 Pavia, Italy; (M.M.); (E.P.); (U.P.); (N.L.-C.); (D.S.)
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24
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Arraes FBM, Martins-de-Sa D, Noriega Vasquez DD, Melo BP, Faheem M, de Macedo LLP, Morgante CV, Barbosa JARG, Togawa RC, Moreira VJV, Danchin EGJ, Grossi-de-Sa MF. Dissecting protein domain variability in the core RNA interference machinery of five insect orders. RNA Biol 2020; 18:1653-1681. [PMID: 33302789 DOI: 10.1080/15476286.2020.1861816] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
RNA interference (RNAi)-mediated gene silencing can be used to control specific insect pest populations. Unfortunately, the variable efficiency in the knockdown levels of target genes has narrowed the applicability of this technology to a few species. Here, we examine the current state of knowledge regarding the miRNA (micro RNA) and siRNA (small interfering RNA) pathways in insects and investigate the structural variability at key protein domains of the RNAi machinery. Our goal was to correlate domain variability with mechanisms affecting the gene silencing efficiency. To this end, the protein domains of 168 insect species, encompassing the orders Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera, were analysed using our pipeline, which takes advantage of meticulous structure-based sequence alignments. We used phylogenetic inference and the evolutionary rate coefficient (K) to outline the variability across domain regions and surfaces. Our results show that four domains, namely dsrm, Helicase, PAZ and Ribonuclease III, are the main contributors of protein variability in the RNAi machinery across different insect orders. We discuss the potential roles of these domains in regulating RNAi-mediated gene silencing and the role of loop regions in fine-tuning RNAi efficiency. Additionally, we identified several order-specific singularities which indicate that lepidopterans have evolved differently from other insect orders, possibly due to constant coevolution with plants and viruses. In conclusion, our results highlight several variability hotspots that deserve further investigation in order to improve the application of RNAi technology in the control of insect pests.
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Affiliation(s)
| | - Diogo Martins-de-Sa
- Departamento De Biologia Celular, Universidade De Brasília, Brasília-DF, Brazil
| | - Daniel D Noriega Vasquez
- Plant-Pest Molecular Interaction Laboratory (LIMPP), Brasilia, Brasília-DF, Brazil.,Catholic University of Brasília, Brasília-DF, Brazil
| | - Bruno Paes Melo
- Plant-Pest Molecular Interaction Laboratory (LIMPP), Brasilia, Brasília-DF, Brazil.,Viçosa University, UFV, Viçosa-MG, Brazil
| | - Muhammad Faheem
- Plant-Pest Molecular Interaction Laboratory (LIMPP), Brasilia, Brasília-DF, Brazil.,Department of Biological Sciences, National University of Medical Sciences, Punjab, Pakistan
| | | | - Carolina Vianna Morgante
- Plant-Pest Molecular Interaction Laboratory (LIMPP), Brasilia, Brasília-DF, Brazil.,Embrapa Semiarid, Petrolina-PE, Brazil.,National Institute of Science and Technology, Jakarta Embrapa-Brazil
| | | | - Roberto Coiti Togawa
- Plant-Pest Molecular Interaction Laboratory (LIMPP), Brasilia, Brasília-DF, Brazil
| | - Valdeir Junio Vaz Moreira
- Biotechnology Center, Brazil.,Plant-Pest Molecular Interaction Laboratory (LIMPP), Brasilia, Brasília-DF, Brazil.,Departamento De Biologia Celular, Universidade De Brasília, Brasília-DF, Brazil
| | - Etienne G J Danchin
- National Institute of Science and Technology, Jakarta Embrapa-Brazil.,INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Maria Fatima Grossi-de-Sa
- Plant-Pest Molecular Interaction Laboratory (LIMPP), Brasilia, Brasília-DF, Brazil.,Catholic University of Brasília, Brasília-DF, Brazil.,National Institute of Science and Technology, Jakarta Embrapa-Brazil
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25
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Donelick HM, Talide L, Bellet M, Aruscavage PJ, Lauret E, Aguiar ERGR, Marques JT, Meignin C, Bass BL. In vitro studies provide insight into effects of Dicer-2 helicase mutations in Drosophila melanogaster. RNA (NEW YORK, N.Y.) 2020; 26:1847-1861. [PMID: 32843367 PMCID: PMC7668257 DOI: 10.1261/rna.077289.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 08/20/2020] [Indexed: 05/03/2023]
Abstract
In vitro, Drosophila melanogaster Dicer-2 (Dcr-2) uses its helicase domain to initiate processing of dsRNA with blunt (BLT) termini, and its Platform•PAZ domain to initiate processing of dsRNA with 3' overhangs (ovrs). To understand the relationship of these in vitro observations to roles of Dcr-2 in vivo, we compared in vitro effects of two helicase mutations to their impact on production of endogenous and viral siRNAs in flies. Consistent with the importance of the helicase domain in processing BLT dsRNA, both point mutations eliminated processing of BLT, but not 3'ovr, dsRNA in vitro. However, the mutations had different effects in vivo. A point mutation in the Walker A motif of the Hel1 subdomain, G31R, largely eliminated production of siRNAs in vivo, while F225G, located in the Hel2 subdomain, showed reduced levels of endogenous siRNAs, but did not significantly affect virus-derived siRNAs. In vitro assays monitoring dsRNA cleavage, dsRNA binding, ATP hydrolysis, and binding of the accessory factor Loquacious-PD provided insight into the different effects of the mutations on processing of different sources of dsRNA in flies. Our in vitro studies suggest effects of the mutations in vivo relate to their effects on ATPase activity, dsRNA binding, and interactions with Loquacious-PD. Our studies emphasize the importance of future studies to characterize dsRNA termini as they exist in Drosophila and other animals.
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Affiliation(s)
- Helen M Donelick
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Loïc Talide
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg, France
| | - Matthieu Bellet
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg, France
| | - P Joseph Aruscavage
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Emilie Lauret
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg, France
| | - Eric R G R Aguiar
- Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
| | - Joao T Marques
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg, France
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, CEP 31270-901, Brazil
| | - Carine Meignin
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg, France
| | - Brenda L Bass
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, USA
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26
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Environmental RNA interference in two-spotted spider mite, Tetranychus urticae, reveals dsRNA processing requirements for efficient RNAi response. Sci Rep 2020; 10:19126. [PMID: 33154461 PMCID: PMC7644771 DOI: 10.1038/s41598-020-75682-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 10/16/2020] [Indexed: 12/13/2022] Open
Abstract
Comprehensive understanding of pleiotropic roles of RNAi machinery highlighted the conserved chromosomal functions of RNA interference. The consequences of the evolutionary variation in the core RNAi pathway genes are mostly unknown, but may lead to the species-specific functions associated with gene silencing. The two-spotted spider mite, Tetranychus urticae, is a major polyphagous chelicerate pest capable of feeding on over 1100 plant species and developing resistance to pesticides used for its control. A well annotated genome, susceptibility to RNAi and economic importance, make T. urticae an excellent candidate for development of an RNAi protocol that enables high-throughput genetic screens and RNAi-based pest control. Here, we show that the length of the exogenous dsRNA critically determines its processivity and ability to induce RNAi in vivo. A combination of the long dsRNAs and the use of dye to trace the ingestion of dsRNA enabled the identification of genes involved in membrane transport and 26S proteasome degradation as sensitive RNAi targets. Our data demonstrate that environmental RNAi can be an efficient reverse genetics and pest control tool in T. urticae. In addition, the species-specific properties together with the variation in the components of the RNAi machinery make T. urticae a potent experimental system to study the evolution of RNAi pathways.
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27
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Deep Sequencing of Small RNAs in the Whitefly Bemisia tabaci Reveals Novel MicroRNAs Potentially Associated with Begomovirus Acquisition and Transmission. INSECTS 2020; 11:insects11090562. [PMID: 32842525 PMCID: PMC7564577 DOI: 10.3390/insects11090562] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/21/2020] [Accepted: 08/21/2020] [Indexed: 11/17/2022]
Abstract
Summary The whitefly (Bemisia tabaci), a notorious insect vector, transmits hundreds of viruses causing serious yield losses in a diverse food and fiber crops including beans, cassava, cotton, cucurbits, pepper, sweet potato and tomato, and results in billions of U.S. dollars of economic losses annually worldwide. To investigate the molecular mechanisms regulating gene expression in whitefly that is associated with begomovirus transmission, we conducted small RNA sequencing and compared the microRNA (miRNA) profiles between viruliferous whiteflies feeding on tomato plants infected with a begomovirus, tomato yellow leaf curl virus (TYLCV), and those whiteflies feeding on uninfected plants. We uncovered a comprehensive microRNA genetic regulatory system in whiteflies that may be involved in virus acquisition and transmission. Interestingly, correlating the expression profile of miRNAs and their target transcript expression in our earlier transcriptome study, we found miRNA expression was inversely correlated with predicted target gene expression in over 50% of all cases. This fundamental understanding will help identify new target sequences that could be used to improve RNA interference technology for whitefly control. These analyses could also serve as a model to study gene regulation in other systems involving arthropod transmission of viruses to plants and animals. Abstract The whitefly Bemisia tabaci (Gennadius) is a notorious insect vector that transmits hundreds of plant viruses, affecting food and fiber crops worldwide, and results in the equivalent of billions of U.S. dollars in crop loss annually. To gain a better understanding of the mechanism in virus transmission, we conducted deep sequencing of small RNAs on the whitefly B. tabaci MEAM1 (Middle East-Asia Minor 1) that fed on tomato plants infected with tomato yellow leaf curl virus (TYLCV). Overall, 160 miRNAs were identified, 66 of which were conserved and 94 were B. tabaci-specific. Among the B. tabaci-specific miRNAs, 67 were newly described in the present study. Two miRNAs, with predicted targets encoding a nuclear receptor (Bta05482) and a very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 2 (Bta10702), respectively, were differentially expressed in whiteflies that fed on TYLCV-infected versus uninfected plants. To better understand the regulatory effects of identified miRNAs and their target genes, we correlated expression profiles of miRNAs and their target transcripts and found that, interestingly, miRNA expression was inversely correlated with the expression of ~50% of the predicted target genes. These analyses could serve as a model to study gene regulation in other systems involving arthropod transmission of viruses to plants and animals.
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28
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Liu S, Coates BS, Bonning BC. Endogenous viral elements integrated into the genome of the soybean aphid, Aphis glycines. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 123:103405. [PMID: 32534986 DOI: 10.1016/j.ibmb.2020.103405] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 05/12/2020] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
Sequence analysis of the genomic DNA isolated from four biotypes of the soybean aphid, Aphis glycines (AG), revealed that in addition to the commonly observed retrovirus-related retrotransposons, viral sequences derived from multiple RNA and DNA viruses have integrated into the genome. Notably, sequences of more than 60 nudiviral genes were identified from de novo assembled DNA contigs, and mapped to assembled genomic scaffolds of AG, indicating that an ancient nudivirus, named Aphis glycines endogenous nudivirus (AgENV), had integrated into the AG genome. Furthermore, sequences derived from a similar endogenous nudivirus, Melanaphis sacchari endogenous nudivirus (MsENV), were identified from the genomic scaffolds of the sugarcane aphid, Melanaphis sacchari. Analysis of transcriptome and small RNA sequence data derived from AG did not provide evidence for transcription of the integrated AgENV genes. Hence, the genes of AgENV may be present as pseudogenes. Phylogenetic analysis based on nudivirus core genes indicated that these aphid ENVs belong to the genus Alphanudivirus.
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Affiliation(s)
- Sijun Liu
- Department of Entomology, Iowa State University, Ames, IA, 50011, USA
| | - Brad S Coates
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, Ames, IA, 50011, USA
| | - Bryony C Bonning
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, 32611, USA.
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29
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Nitschko V, Kunzelmann S, Fröhlich T, Arnold GJ, Förstemann K. Trafficking of siRNA precursors by the dsRBD protein Blanks in Drosophila. Nucleic Acids Res 2020; 48:3906-3921. [PMID: 32025726 PMCID: PMC7144943 DOI: 10.1093/nar/gkaa072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 01/21/2020] [Accepted: 02/03/2020] [Indexed: 01/03/2023] Open
Abstract
RNA interference targets aberrant transcripts with cognate small interfering RNAs, which derive from double-stranded RNA precursors. Several functional screens have identified Drosophila blanks/lump (CG10630) as a facilitator of RNAi, yet its molecular function has remained unknown. The protein carries two dsRNA binding domains (dsRBD) and blanks mutant males have a spermatogenesis defect. We demonstrate that blanks selectively boosts RNAi triggered by dsRNA of nuclear origin. Blanks binds dsRNA via its second dsRBD in vitro, shuttles between nucleus and cytoplasm and the abundance of siRNAs arising at many sites of convergent transcription is reduced in blanks mutants. Since features of nascent RNAs - such as introns and transcription beyond the polyA site – contribute to the small RNA pool, we propose that Blanks binds dsRNA formed by cognate nascent RNAs in the nucleus and fosters its export to the cytoplasm for dicing. We refer to the resulting small RNAs as blanks exported siRNAs (bepsiRNAs). While bepsiRNAs were fully dependent on RNA binding to the second dsRBD of blanks in transgenic flies, male fertility was not. This is consistent with a previous report that linked fertility to the first dsRBD of Blanks. The role of blanks in spermatogenesis appears thus unrelated to its role in dsRNA export.
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Affiliation(s)
- Volker Nitschko
- Genzentrum & Department Biochemie, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Stefan Kunzelmann
- Genzentrum & Department Biochemie, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Thomas Fröhlich
- Laboratory of Functional Genome Analysis, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Georg J Arnold
- Laboratory of Functional Genome Analysis, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Klaus Förstemann
- Genzentrum & Department Biochemie, Ludwig-Maximilians-Universität, 81377 München, Germany
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30
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González-González A, Wayne ML. Immunopathology and immune homeostasis during viral infection in insects. Adv Virus Res 2020; 107:285-314. [PMID: 32711732 DOI: 10.1016/bs.aivir.2020.06.001] [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] [Indexed: 12/27/2022]
Abstract
Organisms clear infections by mounting an immune response that is normally turned off once the pathogens have been cleared. However, sometimes this immune response is not properly or timely arrested, resulting in the host damaging itself. This immune dysregulation may be referred to as immunopathology. While our knowledge of immune and metabolic pathways in insects, particularly in response to viral infections, is growing, little is known about the mechanisms that regulate this immune response and hence little is known about immunopathology in this important and diverse group of organisms. In this chapter we focus both on documenting the molecular mechanisms described involved in restoring immune homeostasis in insects after viral infections and on identifying potential mechanisms for future investigation. We argue that learning about the immunopathological consequences of an improperly regulated immune response in insects will benefit both insect and human health.
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Affiliation(s)
| | - Marta L Wayne
- Department of Biology, University of Florida, Gainesville, FL, United States
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31
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Torri A, Mongelli V, Mondotte JA, Saleh MC. Viral Infection and Stress Affect Protein Levels of Dicer 2 and Argonaute 2 in Drosophila melanogaster. Front Immunol 2020; 11:362. [PMID: 32194567 PMCID: PMC7065269 DOI: 10.3389/fimmu.2020.00362] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/14/2020] [Indexed: 12/21/2022] Open
Abstract
The small interfering RNA (siRNA) pathway of Drosophila melanogaster, mainly characterized by the activity of the enzymes Dicer 2 (Dcr-2) and Argonaute 2 (Ago-2), has been described as the major antiviral immune response. Several lines of evidence demonstrated its pivotal role in conferring resistance against viral infections at cellular and systemic level. However, only few studies have addressed the regulation and induction of this system upon infection and knowledge on stability and turnover of the siRNA pathway core components transcripts and proteins remains scarce. In the current work, we explore whether the siRNA pathway is regulated following viral infection in D. melanogaster. After infecting different fly strains with two different viruses and modes of infection, we observed changes in Dcr-2 and Ago-2 protein concentrations that were not related with changes in gene expression. This response was observed either upon viral infection or upon stress-related experimental procedure, indicating a bivalent function of the siRNA system operating as a general gene regulation rather than a specific antiviral system.
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Affiliation(s)
- Alessandro Torri
- Viruses and RNA Interference Unit, CNRS Unité Mixte de Recherche, Institut Pasteur, Paris, France
| | - Vanesa Mongelli
- Viruses and RNA Interference Unit, CNRS Unité Mixte de Recherche, Institut Pasteur, Paris, France
| | - Juan A Mondotte
- Viruses and RNA Interference Unit, CNRS Unité Mixte de Recherche, Institut Pasteur, Paris, France
| | - Maria-Carla Saleh
- Viruses and RNA Interference Unit, CNRS Unité Mixte de Recherche, Institut Pasteur, Paris, France
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32
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Merkling SH, Raquin V, Dabo S, Henrion-Lacritick A, Blanc H, Moltini-Conclois I, Frangeul L, Varet H, Saleh MC, Lambrechts L. Tudor-SN Promotes Early Replication of Dengue Virus in the Aedes aegypti Midgut. iScience 2020; 23:100870. [PMID: 32059176 PMCID: PMC7054812 DOI: 10.1016/j.isci.2020.100870] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/24/2019] [Accepted: 01/24/2020] [Indexed: 01/15/2023] Open
Abstract
Diseases caused by mosquito-borne viruses have been on the rise for the last decades, and novel methods aiming to use laboratory-engineered mosquitoes that are incapable of carrying viruses have been developed to reduce pathogen transmission. This has stimulated efforts to identify optimal target genes that are naturally involved in mosquito antiviral defenses or required for viral replication. Here, we investigated the role of a member of the Tudor protein family, Tudor-SN, upon dengue virus infection in the mosquito Aedes aegypti. Tudor-SN knockdown reduced dengue virus replication in the midgut of Ae. aegypti females. In immunofluorescence assays, Tudor-SN localized to the nucleolus in both Ae. aegypti and Aedes albopictus cells. A reporter assay and small RNA profiling demonstrated that Tudor-SN was not required for RNA interference function in vivo. Collectively, these results defined a novel proviral role for Tudor-SN upon early dengue virus infection of the Ae. aegypti midgut.
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Affiliation(s)
- Sarah Hélène Merkling
- Institut Pasteur, Insect-Virus Interactions Unit, UMR2000, CNRS, 75015 Paris, France
| | - Vincent Raquin
- Institut Pasteur, Insect-Virus Interactions Unit, UMR2000, CNRS, 75015 Paris, France
| | - Stéphanie Dabo
- Institut Pasteur, Insect-Virus Interactions Unit, UMR2000, CNRS, 75015 Paris, France
| | | | - Hervé Blanc
- Institut Pasteur, Viruses and RNA Interference Unit, UMR3569, CNRS, 75015 Paris, France
| | | | - Lionel Frangeul
- Institut Pasteur, Viruses and RNA Interference Unit, UMR3569, CNRS, 75015 Paris, France
| | - Hugo Varet
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756, CNRS, Paris, France; Plate-forme Technologique Biomics - Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, Paris, France
| | - Maria-Carla Saleh
- Institut Pasteur, Viruses and RNA Interference Unit, UMR3569, CNRS, 75015 Paris, France.
| | - Louis Lambrechts
- Institut Pasteur, Insect-Virus Interactions Unit, UMR2000, CNRS, 75015 Paris, France.
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Yang L, Tian Y, Peng YY, Niu J, Wang JJ. Expression Dynamics of Core RNAi Machinery Genes in Pea Aphids Upon Exposure to Artificially Synthesized dsRNA and miRNAs. INSECTS 2020; 11:insects11020070. [PMID: 31973072 PMCID: PMC7074054 DOI: 10.3390/insects11020070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/14/2020] [Accepted: 01/18/2020] [Indexed: 01/01/2023]
Abstract
The pea aphid is an important pest of vegetables and causes serious losses worldwide. RNA interference (RNAi) is an effective pest control tool, and three sub-pathways have been described: The miRNA pathway, siRNA pathway, and piRNA pathway. A large number of genes in miRNA pathway and piRNA pathway are found to be expanded. To study the roles of these genes, the expression of 25 core RNAi genes was screened in spatiotemporal samples, artificially synthesized dsRNA and miRNA treated samples. The 25 genes were all expressed during different development stages and in different tissues. In dsRNA-treated samples and miRNA-treated samples, the expressions of genes in these three pathways were induced, especially the expanded genes. This suggests a complex network of RNAi core genes in the three sub-pathways. Treatment of miRNA seems to induce gene expression in a dosage-dependent manner. These results increase our knowledge of the siRNA pathway and related factors from RNAi pathway in aphids and promote the use of RNAi for the control of aphid pests.
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Affiliation(s)
- Li Yang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Yuan Tian
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Yuan-Yuan Peng
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jinzhi Niu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
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Abstract
The RNA interference (RNAi) triggered by short/small interfering RNA (siRNA) was discovered in nematodes and found to function in most living organisms. RNAi has been widely used as a research tool to study gene functions and has shown great potential for the development of novel pest management strategies. RNAi is highly efficient and systemic in coleopterans but highly variable or inefficient in many other insects. Differences in double-stranded RNA (dsRNA) degradation, cellular uptake, inter- and intracellular transports, processing of dsRNA to siRNA, and RNA-induced silencing complex formation influence RNAi efficiency. The basic dsRNA delivery methods include microinjection, feeding, and soaking. To improve dsRNA delivery, various new technologies, including cationic liposome-assisted, nanoparticle-enabled, symbiont-mediated, and plant-mediated deliveries, have been developed. Major challenges to widespread use of RNAi in insect pest management include variable RNAi efficiency among insects, lack of reliable dsRNA delivery methods, off-target and nontarget effects, and potential development of resistance in insect populations.
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Affiliation(s)
- Kun Yan Zhu
- Department of Entomology, Kansas State University, Manhattan, Kansas 66506, USA;
| | - Subba Reddy Palli
- Department of Entomology, University of Kentucky, Lexington, Kentucky 40546, USA;
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Santos D, Mingels L, Vogel E, Wang L, Christiaens O, Cappelle K, Wynant N, Gansemans Y, Van Nieuwerburgh F, Smagghe G, Swevers L, Vanden Broeck J. Generation of Virus- and dsRNA-Derived siRNAs with Species-Dependent Length in Insects. Viruses 2019; 11:v11080738. [PMID: 31405199 PMCID: PMC6723321 DOI: 10.3390/v11080738] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/07/2019] [Accepted: 08/08/2019] [Indexed: 01/01/2023] Open
Abstract
Double-stranded RNA (dsRNA) molecules of viral origin trigger a post-transcriptional gene-silencing mechanism called RNA interference (RNAi). Specifically, virally derived dsRNA is recognized and cleaved by the enzyme Dicer2 into short interfering RNAs (siRNAs), which further direct sequence-specific RNA silencing, ultimately silencing replication of the virus. Notably, RNAi can also be artificially triggered by the delivery of gene-specific dsRNA, thereby leading to endogenous gene silencing. This is a widely used technology that holds great potential to contribute to novel pest control strategies. In this regard, research efforts have been set to find methods to efficiently trigger RNAi in the field. In this article, we demonstrate the generation of dsRNA- and/or virus-derived siRNAs—the main RNAi effectors—in six insect species belonging to five economically important orders (Lepidoptera, Orthoptera, Hymenoptera, Coleoptera, and Diptera). In addition, we describe that the siRNA length distribution is species-dependent. Taken together, our results reveal interspecies variability in the (antiviral) RNAi mechanism in insects and show promise to contribute to future research on (viral-based) RNAi-triggering mechanisms in this class of animals.
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Affiliation(s)
- Dulce Santos
- Research Group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, 3000 Leuven, Belgium.
| | - Lina Mingels
- Research Group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, 3000 Leuven, Belgium
| | - Elise Vogel
- Research Group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, 3000 Leuven, Belgium
| | - Luoluo Wang
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Olivier Christiaens
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Kaat Cappelle
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Niels Wynant
- Research Group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, 3000 Leuven, Belgium
| | - Yannick Gansemans
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Luc Swevers
- Insect Molecular Genetics and Biotechnology Group, Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos", 15310 Athens, Greece
| | - Jozef Vanden Broeck
- Research Group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, 3000 Leuven, Belgium
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Flynn PJ, Moreau CS. Assessing the Diversity of Endogenous Viruses Throughout Ant Genomes. Front Microbiol 2019; 10:1139. [PMID: 31191479 PMCID: PMC6540820 DOI: 10.3389/fmicb.2019.01139] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/06/2019] [Indexed: 12/22/2022] Open
Abstract
Endogenous viral elements (EVEs) can play a significant role in the evolution of their hosts and have been identified in animals, plants, and fungi. Additionally, EVEs potentially provide an important snapshot of the evolutionary frequency of viral infection. The purpose of this study is to take a comparative host-centered approach to EVE discovery in ant genomes to better understand the relationship of EVEs to their ant hosts. Using a comprehensive bioinformatic pipeline, we screened all nineteen published ant genomes for EVEs. Once the EVEs were identified, we assessed their phylogenetic relationships to other closely related exogenous viruses. A diverse group of EVEs were discovered in all screened ant host genomes and in many cases are similar to previously identified exogenous viruses. EVEs similar to ssRNA viral proteins are the most common viral lineage throughout the ant hosts, which is potentially due to more chronic infection or more effective endogenization of certain ssRNA viruses in ants. In addition, both EVEs similar to viral glycoproteins and retrovirus-derived proteins are also abundant throughout ant genomes, suggesting their tendency to endogenize. Several of these newly discovered EVEs are found to be potentially functional within the genome. The discovery and analysis of EVEs is essential in beginning to understand viral–ant interactions over evolutionary time.
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Affiliation(s)
- Peter J Flynn
- Committee on Evolutionary Biology, The University of Chicago, Chicago, IL, United States.,Department of Science and Education, Integrative Research Center, Field Museum of Natural History, Chicago, IL, United States
| | - Corrie S Moreau
- Department of Science and Education, Integrative Research Center, Field Museum of Natural History, Chicago, IL, United States.,Departments of Entomology and Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States
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Ding BY, Yang L, Peng YY, Chang TY, Ye C, Shang F, Niu J, Wang JJ. RNA-sequencing of a citrus bud-feeder, Podagricomela weisei (Coleoptera: Chrysomelidae), reveals xenobiotic metabolism/core RNAi machinery-associated genes and conserved miRNAs. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 29:339-350. [PMID: 30682656 DOI: 10.1016/j.cbd.2019.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 11/15/2022]
Abstract
The citrus leaf-mining beetle, Podagricomela weisei Heikertinger, is an important citrus pest that ingests the mesophyll and new shoots. The mechanism underlying the xenobiotic metabolism of P. weisei is not well understood, in part because of a lack of available genomic and transcriptomic data, which has hampered the development of novel pest management approaches [e.g., RNA interference (RNAi)]. In this study, we completed the deep sequencing of the P. weisei transcriptome to identify factors potentially involved in xenobiotic metabolism and the core RNAi machinery. The sequencing of the P. weisei transcriptome generated >27 million clean reads, ultimately yielding 90,410 unigenes with an N50 of 1065 bp. The unigenes were used as queries to search the Nr database, which revealed that 21,847 unigenes were homologous to known genes in various species. Transcripts encoding genes involved in xenobiotic metabolism were identified, including genes encoding cytochrome P450 monooxygenase (P450, 47 unigenes), glutathione S-transferase (GST, 12 unigenes), esterase (EST, 25 unigenes), and the ATP-binding cassette transporter (ABC transporter, 32 unigenes). A parallel sequencing of small RNAs detected 30 conserved miRNAs, with the most abundant being Pwe-miR-1-3p, with an expression level reaching 517,996 reads in the prepared library, followed by Pwe-miR-8-3p (149,402 reads). Genes encoding components of the miRNA, siRNA, and piRNA pathways were also identified, and the results indicated that P. weisei possesses only one of each gene in all three pathways. In summary, this is the first detailed analysis of the transcriptome and small RNAs of P. weisei. The datasets presented herein may form the basis for future molecular characterizations of P. weisei as well as the development of enhanced pest control strategies.
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Affiliation(s)
- Bi-Yue Ding
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Li Yang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Yuan-Yuan Peng
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Teng-Yu Chang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Chao Ye
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Feng Shang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jinzhi Niu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
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Cooper AM, Silver K, Zhang J, Park Y, Zhu KY. Molecular mechanisms influencing efficiency of RNA interference in insects. PEST MANAGEMENT SCIENCE 2019; 75:18-28. [PMID: 29931761 DOI: 10.1002/ps.5126] [Citation(s) in RCA: 164] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 06/13/2018] [Accepted: 06/15/2018] [Indexed: 05/21/2023]
Abstract
RNA interference (RNAi) is an endogenous, sequence-specific gene-silencing mechanism elicited by small RNA molecules. RNAi is a powerful reverse genetic tool, and is currently being utilized for managing insects and viruses. Widespread implementation of RNAi-based pest management strategies is currently hindered by inefficient and highly variable results when different insect species, strains, developmental stages, tissues, and genes are targeted. Mechanistic studies have shown that double-stranded ribonucleases (dsRNases), endosomal entrapment, deficient function of the core machinery, and inadequate immune stimulation contribute to limited RNAi efficiency. However, a comprehensive understanding of the molecular mechanisms limiting RNAi efficiency remains elusive. Recent advances in dsRNA stability in physiological tissues, dsRNA internalization into cells, the composition and function of the core RNAi machinery, as well as small-interfering RNA/double-stranded RNA amplification and spreading mechanisms are reviewed to establish a global understanding of the obstacles impeding wider understanding of RNAi mechanisms in insects. © 2018 Society of Chemical Industry.
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Affiliation(s)
| | - Kristopher Silver
- Department of Entomology, Kansas State University, Manhattan, KS, USA
| | - Jianzhen Zhang
- Department of Entomology, Kansas State University, Manhattan, KS, USA
- Institute of Applied Biology, Shanxi University, Taiyuan, China
| | - Yoonseong Park
- Department of Entomology, Kansas State University, Manhattan, KS, USA
| | - Kun Yan Zhu
- Department of Entomology, Kansas State University, Manhattan, KS, USA
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39
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Pooggin MM. Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization. Front Microbiol 2018; 9:2779. [PMID: 30524398 PMCID: PMC6256188 DOI: 10.3389/fmicb.2018.02779] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/30/2018] [Indexed: 11/13/2022] Open
Abstract
RNA interference (RNAi)-based antiviral defense generates small interfering RNAs that represent the entire genome sequences of both RNA and DNA viruses as well as viroids and viral satellites. Therefore, deep sequencing and bioinformatics analysis of small RNA population (small RNA-ome) allows not only for universal virus detection and genome reconstruction but also for complete virome reconstruction in mixed infections. Viral infections (like other stress factors) can also perturb the RNAi and gene silencing pathways regulating endogenous gene expression and repressing transposons and host genome-integrated endogenous viral elements which can potentially be released from the genome and contribute to disease. This review describes the application of small RNA-omics for virus detection, virome reconstruction and antiviral defense characterization in cultivated and non-cultivated plants. Reviewing available evidence from a large and ever growing number of studies of naturally or experimentally infected hosts revealed that all families of land plant viruses, their satellites and viroids spawn characteristic small RNAs which can be assembled into contigs of sufficient length for virus, satellite or viroid identification and for exhaustive reconstruction of complex viromes. Moreover, the small RNA size, polarity and hotspot profiles reflect virome interactions with the plant RNAi machinery and allow to distinguish between silent endogenous viral elements and their replicating episomal counterparts. Models for the biogenesis and functions of small interfering RNAs derived from all types of RNA and DNA viruses, satellites and viroids as well as endogenous viral elements are presented and discussed.
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Affiliation(s)
- Mikhail M. Pooggin
- Institut National de la Recherche Agronomique, UMR BGPI, Montpellier, France
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40
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Monsanto-Hearne V, Johnson KN. miRNAs in Insects Infected by Animal and Plant Viruses. Viruses 2018; 10:E354. [PMID: 29970868 PMCID: PMC6071220 DOI: 10.3390/v10070354] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/29/2018] [Accepted: 06/29/2018] [Indexed: 12/13/2022] Open
Abstract
Viruses vectored by insects cause severe medical and agricultural burdens. The process of virus infection of insects regulates and is regulated by a complex interplay of biomolecules including the small, non-coding microRNAs (miRNAs). Considered an anomaly upon its discovery only around 25 years ago, miRNAs as a class have challenged the molecular central dogma which essentially typifies RNAs as just intermediaries in the flow of information from DNA to protein. miRNAs are now known to be common modulators or fine-tuners of gene expression. While recent years has seen an increased emphasis on understanding the role of miRNAs in host-virus associations, existing literature on the interaction between insects and their arthropod-borne viruses (arboviruses) is largely restricted to miRNA abundance profiling. Here we analyse the commonalities and contrasts between miRNA abundance profiles with different host-arbovirus combinations and outline a suggested pipeline and criteria for functional analysis of the contribution of miRNAs to the insect vector-virus interaction. Finally, we discuss the potential use of the model organism, Drosophila melanogaster, in complementing research on the role of miRNAs in insect vector-virus interaction.
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Affiliation(s)
- Verna Monsanto-Hearne
- School of Biological Sciences, The University of Queensland, Brisbane 4072, Australia.
| | - Karyn N Johnson
- School of Biological Sciences, The University of Queensland, Brisbane 4072, Australia.
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41
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Eng MW, Clemons A, Hill C, Engel R, Severson DW, Behura SK. Multifaceted functional implications of an endogenously expressed tRNA fragment in the vector mosquito Aedes aegypti. PLoS Negl Trop Dis 2018; 12:e0006186. [PMID: 29364883 PMCID: PMC5783352 DOI: 10.1371/journal.pntd.0006186] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 12/22/2017] [Indexed: 01/16/2023] Open
Abstract
The mosquito Aedes aegypti is the primary vector of human arboviral diseases caused by dengue, chikungunya and Zika viruses. Many studies have shown the potential roles of small RNA molecules such as microRNA, small interfering RNA and PIWI-interacting RNA in vector mosquitoes. The function of tRNA fragments (tRF), the newly discovered class of small RNAs, in mosquitoes is not known. In this study, we show that specific tRFs are expressed in significantly differential manner between males and females of Ae. aegypti strains. Specific tRFs also show differential response during developmental transition from larvae to adults, as well as after blood feeding of adult females. The expression pattern of tRFs upon blood feeding varied depending upon if the blood contained dengue virus, and also if the females were treated with antibiotic prior to feeding to cleanse of the gut bacteria. Our findings show that a single tRF derived from the precursor sequences of a tRNA-Gly was differentially expressed between males and females, developmental transitions and also upon blood feeding by females of two laboratory strains that vary in midgut susceptibility to dengue virus infection. The multifaceted functional implications of this specific tRF suggest that biogenesis of small regulatory molecules from a tRNA can have wide ranging effects on key aspects of Ae. aegypti vector biology. The mosquito Aedes aegypti is a major vector of arboviral diseases in subtropics and tropics. The confounding effects of immature development and adult microbiome on the ability of Ae. aegypti to transmit diseases (vector competence) have gained renewed attention in the recent years. However, the molecular nature of these links/ effects remains unknown. This is major gap in knowledge regarding how vector competence is regulated at molecular level, and how that regulation may be variable among different strains of this mosquito. In this study, we investigated expression of newly discovered class of small RNAs, called tRNA fragments (tRF) in Ae. aegypti strains. Based on small RNA sequencing and bioinformatics analyses, we show that tRFs are expressed in Ae. aegypti, and they are associated with significant changes in expression between males and females, during development stages, and post blood feeding responses. A single tRF showed association with sex-biased expression, developmental regulation and in response to blood meals between Moyo-S and Moyo-R strains that differ in midgut susceptibility to dengue virus. The findings of this study are expected to guide future research efforts directed toward examining detailed regulatory mechanisms of tRFs in vector competence of Ae. aegypti to disease transmission.
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Affiliation(s)
- Matthew W. Eng
- Department of Biological Sciences and Eck institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Anthony Clemons
- Department of Biological Sciences and Eck institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Casey Hill
- Department of Biological Sciences and Eck institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Roberta Engel
- Department of Biological Sciences and Eck institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - David W. Severson
- Department of Biological Sciences and Eck institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Susanta K. Behura
- Department of Biological Sciences and Eck institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
- * E-mail:
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42
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Whitfield ZJ, Dolan PT, Kunitomi M, Tassetto M, Seetin MG, Oh S, Heiner C, Paxinos E, Andino R. The Diversity, Structure, and Function of Heritable Adaptive Immunity Sequences in the Aedes aegypti Genome. Curr Biol 2017; 27:3511-3519.e7. [PMID: 29129531 DOI: 10.1016/j.cub.2017.09.067] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/29/2017] [Accepted: 09/29/2017] [Indexed: 12/22/2022]
Abstract
The Aedes aegypti mosquito transmits arboviruses, including dengue, chikungunya, and Zika virus. Understanding the mechanisms underlying mosquito immunity could provide new tools to control arbovirus spread. Insects exploit two different RNAi pathways to combat viral and transposon infection: short interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs) [1, 2]. Endogenous viral elements (EVEs) are sequences from non-retroviral viruses that are inserted into the mosquito genome and can act as templates for the production of piRNAs [3, 4]. EVEs therefore represent a record of past infections and a reservoir of potential immune memory [5]. The large-scale organization of EVEs has been difficult to resolve with short-read sequencing because they tend to integrate into repetitive regions of the genome. To define the diversity, organization, and function of EVEs, we took advantage of the contiguity associated with long-read sequencing to generate a high-quality assembly of the Ae. aegypti-derived Aag2 cell line genome, an important and widely used model system. We show EVEs are acquired through recombination with specific classes of long terminal repeat (LTR) retrotransposons and organize into large loci (>50 kbp) characterized by high LTR density. These EVE-containing loci have increased density of piRNAs compared to similar regions without EVEs. Furthermore, we detected EVE-derived piRNAs consistent with a targeted processing of persistently infecting virus genomes. We propose that comparisons of EVEs across mosquito populations may explain differences in vector competence, and further study of the structure and function of these elements in the genome of mosquitoes may lead to epidemiological interventions.
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Affiliation(s)
- Zachary J Whitfield
- Department of Microbiology and Immunology, University of California, San Francisco, 600 16(th) Street, GH-S572, UCSF Box 2280, San Francisco, CA 94143-2280, USA
| | - Patrick T Dolan
- Department of Microbiology and Immunology, University of California, San Francisco, 600 16(th) Street, GH-S572, UCSF Box 2280, San Francisco, CA 94143-2280, USA; Department of Biology, Stanford University, E200 Clark Center, 318 Campus Drive, Stanford, CA 94305, USA
| | - Mark Kunitomi
- Department of Microbiology and Immunology, University of California, San Francisco, 600 16(th) Street, GH-S572, UCSF Box 2280, San Francisco, CA 94143-2280, USA
| | - Michel Tassetto
- Department of Microbiology and Immunology, University of California, San Francisco, 600 16(th) Street, GH-S572, UCSF Box 2280, San Francisco, CA 94143-2280, USA
| | - Matthew G Seetin
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Steve Oh
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Cheryl Heiner
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Ellen Paxinos
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, 600 16(th) Street, GH-S572, UCSF Box 2280, San Francisco, CA 94143-2280, USA.
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43
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Göertz GP, Abbo SR, Fros JJ, Pijlman GP. Functional RNA during Zika virus infection. Virus Res 2017; 254:41-53. [PMID: 28864425 DOI: 10.1016/j.virusres.2017.08.015] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/28/2017] [Accepted: 08/28/2017] [Indexed: 12/24/2022]
Abstract
Zika virus (ZIKV; family Flaviviridae; genus Flavivirus) is a pathogenic mosquito-borne RNA virus that currently threatens human health in the Americas, large parts of Asia and occasionally elsewhere in the world. ZIKV infection is often asymptomatic but can cause severe symptoms including congenital microcephaly and Guillain-Barré syndrome. The positive single-stranded RNA genome of the mosquito-borne ZIKV requires effective replication in two evolutionary distinct hosts - mosquitoes and primates. In addition to some of the viral proteins, the ZIKV genomic RNA and functional RNAs produced thereof aid in the establishment of productive infection and the evasion of host cell antiviral responses. ZIKV has evolved to contain a nucleotide composition and RNA modifications, such as methylation and the formation of G-quadruplexes that allow effective replication in both hosts. Furthermore, a number of host factors interact with the viral genome to modulate RNA replication. Importantly, the ZIKV genome produces non-coding subgenomic flavivirus RNA (sfRNA) due to stalling of host 5'- 3' ribonucleases on viral RNA structures in the 3' untranslated region (UTR). This sfRNA (sfRNA) exerts important proviral functions such as antagonizing the innate interferon response and RNA interference. Here, we discuss the ZIKV genomic RNA and functional RNAs thereof to assess their significance during ZIKV infection. Understanding the details of the ZIKV infection cycle will aid in the development of effective antiviral strategies and safe vaccines.
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Affiliation(s)
- Giel P Göertz
- Laboratory of Virology, Wageningen University & Research, Wageningen, The Netherlands.
| | - Sandra R Abbo
- Laboratory of Virology, Wageningen University & Research, Wageningen, The Netherlands.
| | - Jelke J Fros
- Laboratory of Virology, Wageningen University & Research, Wageningen, The Netherlands; Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK.
| | - Gorben P Pijlman
- Laboratory of Virology, Wageningen University & Research, Wageningen, The Netherlands.
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