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Oliver JE, Rotenberg D, Agosto-Shaw K, McInnes HA, Lahre KA, Mulot M, Adkins S, Whitfield AE. Multigenic Hairpin Transgenes in Tomato Confer Resistance to Multiple Orthotospoviruses Including Sw-5 Resistance-Breaking Tomato Spotted Wilt Virus. PHYTOPATHOLOGY 2024; 114:1137-1149. [PMID: 37856697 DOI: 10.1094/phyto-07-23-0256-kc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Tomato spotted wilt virus (TSWV) and related thrips-borne orthotospoviruses are a threat to food and ornamental crops. Orthotospoviruses have the capacity for rapid genetic change by genome segment reassortment and mutation. Genetic resistance is one of the most effective strategies for managing orthotospoviruses, but there are multiple examples of resistance gene breakdown. Our goal was to develop effective multigenic, broad-spectrum resistance to TSWV and other orthotospoviruses. The most conserved sequences for each open reading frame (ORF) of the TSWV genome were identified, and comparison with other orthotospoviruses revealed sequence conservation within virus clades; some overlapped with domains with well-documented biological functions. We made six hairpin constructs, each of which incorporated sequences matching portions of all five ORFs. Tomato plants expressing the hairpin transgene were challenged with TSWV by thrips and leaf-rub inoculation, and four constructs provided strong protection against TSWV in foliage and fruit. To determine if the hairpin constructs provided protection against other emerging orthotospoviruses, we challenged the plants with tomato chlorotic spot virus and resistance-breaking TSWV and found that the same constructs also provided resistance to these related viruses. Antiviral hairpin constructs are an effective way to protect plants from multiple orthotospoviruses and are an important strategy in the fight against resistance-breaking TSWV and emerging viruses. Targeting of all five viral ORFs is expected to increase the durability of resistance, and combining them with other resistance genes could further extend the utility of this disease control strategy. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Jonathan E Oliver
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66502
| | - Dorith Rotenberg
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
| | - Karolyn Agosto-Shaw
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
| | - Holly A McInnes
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
| | - Kirsten A Lahre
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
| | - Michaël Mulot
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
| | - Scott Adkins
- U.S. Department of Agriculture-Agricultural Research Service-USHRL, Fort Pierce, FL 34945
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
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2
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Mesel F, Zhao M, García B, Simón‐Mateo C, García J. Targeting of genomic and negative-sense strands of viral RNA contributes to antiviral resistance mediated by artificial miRNAs and promotes the emergence of complex viral populations. MOLECULAR PLANT PATHOLOGY 2022; 23:1640-1657. [PMID: 35989243 PMCID: PMC9562735 DOI: 10.1111/mpp.13258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/07/2022] [Accepted: 07/16/2022] [Indexed: 05/27/2023]
Abstract
Technology based on artificial small RNAs, including artificial microRNAs (amiRNAs), exploits natural RNA silencing mechanisms to achieve silencing of endogenous genes or pathogens. This technology has been successfully employed to generate resistance against different eukaryotic viruses. However, information about viral RNA molecules effectively targeted by these small RNAs is rather conflicting, and factors contributing to the selection of virus mutants escaping the antiviral activity of virus-specific small RNAs have not been studied in detail. In this work, we transformed Nicotiana benthamiana plants with amiRNA constructs designed against the potyvirus plum pox virus (PPV), a positive-sense RNA virus, and obtained lines highly resistant to PPV infection and others showing partial resistance. These lines have allowed us to verify that amiRNA directed against genomic RNA is more efficient than amiRNA targeting its complementary strand. However, we also provide evidence that the negative-sense RNA strand is cleaved by the amiRNA-guided RNA silencing machinery. Our results show that the selection pressure posed by the amiRNA action on both viral RNA strands causes an evolutionary explosion that results in the emergence of a broad range of virus variants, which can further expand in the presence, and even in the absence, of antiviral challenges.
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Affiliation(s)
- Frida Mesel
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB‐CSIC)Campus Universidad Autónoma de MadridMadridSpain
| | - Mingmin Zhao
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB‐CSIC)Campus Universidad Autónoma de MadridMadridSpain
- College of Horticulture and Plant ProtectionInner Mongolia Agricultural UniversityHohhotChina
| | - Beatriz García
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB‐CSIC)Campus Universidad Autónoma de MadridMadridSpain
| | - Carmen Simón‐Mateo
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB‐CSIC)Campus Universidad Autónoma de MadridMadridSpain
| | - Juan Antonio García
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB‐CSIC)Campus Universidad Autónoma de MadridMadridSpain
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3
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Innate immune pathways act synergistically to constrain RNA virus evolution in Drosophila melanogaster. Nat Ecol Evol 2022; 6:565-578. [PMID: 35273366 PMCID: PMC7612704 DOI: 10.1038/s41559-022-01697-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 12/14/2021] [Indexed: 02/05/2023]
Abstract
Host-pathogen interactions impose recurrent selective pressures that lead to constant adaptation and counter-adaptation in both competing species. Here, we sought to study this evolutionary arms-race and assessed the impact of the innate immune system on viral population diversity and evolution, using Drosophila melanogaster as model host and its natural pathogen Drosophila C virus (DCV). We isogenized eight fly genotypes generating animals defective for RNAi, Imd and Toll innate immune pathways as well as pathogen sensing and gut renewal pathways. Wild-type or mutant flies were then orally infected with DCV, and the virus was serially passaged ten times via reinfection in naïve flies. Viral population diversity was studied after each viral passage by high-throughput sequencing, and infection phenotypes were assessed at the beginning and at the end of the evolution experiment. We found that the absence of any of the various immune pathways studied increased viral genetic diversity while attenuating virulence. Strikingly, these effects were observed in a range of host factors described as having mainly antiviral or antibacterial functions. Together, our results indicate that the innate immune system as a whole, and not specific antiviral defense pathways in isolation, generally constrains viral diversity and evolution.
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4
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Carbonell A, Lisón P, Daròs J. Multi-targeting of viral RNAs with synthetic trans-acting small interfering RNAs enhances plant antiviral resistance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:720-737. [PMID: 31350772 PMCID: PMC6899541 DOI: 10.1111/tpj.14466] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/10/2019] [Accepted: 07/12/2019] [Indexed: 05/15/2023]
Abstract
RNA interference (RNAi)-based tools are used in multiple organisms to induce antiviral resistance through the sequence-specific degradation of target RNAs by complementary small RNAs. In plants, highly specific antiviral RNAi-based tools include artificial microRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs). syn-tasiRNAs have emerged as a promising antiviral tool allowing for the multi-targeting of viral RNAs through the simultaneous expression of several syn-tasiRNAs from a single precursor. Here, we compared in tomato plants the effects of an amiRNA construct expressing a single amiRNA and a syn-tasiRNA construct expressing four different syn-tasiRNAs against Tomato spotted wilt virus (TSWV), an economically important pathogen affecting tomato crops worldwide. Most of the syn-tasiRNA lines were resistant to TSWV, whereas the majority of the amiRNA lines were susceptible and accumulated viral progenies with mutations in the amiRNA target site. Only the two amiRNA lines with higher amiRNA accumulation were resistant, whereas resistance in syn-tasiRNA lines was not exclusive of lines with high syn-tasiRNA accumulation. Collectively, these results suggest that syn-tasiRNAs induce enhanced antiviral resistance because of the combined silencing effect of each individual syn-tasiRNA, which minimizes the possibility that the virus simultaneously mutates all different target sites to fully escape each syn-tasiRNA.
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Affiliation(s)
- Alberto Carbonell
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas‐Universitat Politècnica de València46022ValenciaSpain
| | - Purificación Lisón
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas‐Universitat Politècnica de València46022ValenciaSpain
| | - José‐Antonio Daròs
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas‐Universitat Politècnica de València46022ValenciaSpain
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5
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Clarke EL, Sundararaman SA, Seifert SN, Bushman FD, Hahn BH, Brisson D. swga: a primer design toolkit for selective whole genome amplification. Bioinformatics 2018; 33:2071-2077. [PMID: 28334194 PMCID: PMC5870857 DOI: 10.1093/bioinformatics/btx118] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/24/2017] [Indexed: 02/04/2023] Open
Abstract
Motivation Population genomic analyses are often hindered by difficulties in obtaining sufficient numbers of genomes for analysis by DNA sequencing. Selective whole-genome amplification (SWGA) provides an efficient approach to amplify microbial genomes from complex backgrounds for sequence acquisition. However, the process of designing sets of primers for this method has many degrees of freedom and would benefit from an automated process to evaluate the vast number of potential primer sets. Results Here, we present swga, a program that identifies primer sets for SWGA and evaluates them for efficiency and selectivity. We used swga to design and test primer sets for the selective amplification of Wolbachia pipientis genomic DNA from infected Drosophila melanogaster and Mycobacterium tuberculosis from human blood. We identify primer sets that successfully amplify each against their backgrounds and describe a general method for using swga for arbitrary targets. In addition, we describe characteristics of primer sets that correlate with successful amplification, and present guidelines for implementation of SWGA to detect new targets. Availability and Implementation Source code and documentation are freely available on https://www.github.com/eclarke/swga. The program is implemented in Python and C and licensed under the GNU Public License. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Erik L Clarke
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Sesh A Sundararaman
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA.,Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Beatrice H Hahn
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA.,Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dustin Brisson
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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7
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Pooggin MM. RNAi-mediated resistance to viruses: a critical assessment of methodologies. Curr Opin Virol 2017; 26:28-35. [PMID: 28753441 DOI: 10.1016/j.coviro.2017.07.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 07/05/2017] [Accepted: 07/11/2017] [Indexed: 01/07/2023]
Abstract
In plants, RNA interference (RNAi)-based antiviral defense is mediated by multigenic families of Dicer-like enzymes generating small interfering (si)RNAs from double-stranded RNA (dsRNA) produced during replication and/or transcription of RNA and DNA viruses, and Argonaute enzymes binding viral siRNAs and targeting viral RNA and DNA for siRNA-directed posttranscriptional and transcriptional silencing. Successful viruses are able to suppress or evade the production or action of viral siRNAs. In antiviral biotech approaches based on RNAi, transgenic expression or non-transgenic delivery of dsRNA cognate to a target virus pre-activates or boosts the natural plant antiviral defenses. Design of more effective antiviral RNAi strategies requires better understanding of viral siRNA biogenesis and viral anti-silencing strategies in virus-infected plants.
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8
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Kinoti WM, Constable FE, Nancarrow N, Plummer KM, Rodoni B. Analysis of intra-host genetic diversity of Prunus necrotic ringspot virus (PNRSV) using amplicon next generation sequencing. PLoS One 2017; 12:e0179284. [PMID: 28632759 PMCID: PMC5478126 DOI: 10.1371/journal.pone.0179284] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 05/08/2017] [Indexed: 12/28/2022] Open
Abstract
PCR amplicon next generation sequencing (NGS) analysis offers a broadly applicable and targeted approach to detect populations of both high- or low-frequency virus variants in one or more plant samples. In this study, amplicon NGS was used to explore the diversity of the tripartite genome virus, Prunus necrotic ringspot virus (PNRSV) from 53 PNRSV-infected trees using amplicons from conserved gene regions of each of PNRSV RNA1, RNA2 and RNA3. Sequencing of the amplicons from 53 PNRSV-infected trees revealed differing levels of polymorphism across the three different components of the PNRSV genome with a total number of 5040, 2083 and 5486 sequence variants observed for RNA1, RNA2 and RNA3 respectively. The RNA2 had the lowest diversity of sequences compared to RNA1 and RNA3, reflecting the lack of flexibility tolerated by the replicase gene that is encoded by this RNA component. Distinct PNRSV phylo-groups, consisting of closely related clusters of sequence variants, were observed in each of PNRSV RNA1, RNA2 and RNA3. Most plant samples had a single phylo-group for each RNA component. Haplotype network analysis showed that smaller clusters of PNRSV sequence variants were genetically connected to the largest sequence variant cluster within a phylo-group of each RNA component. Some plant samples had sequence variants occurring in multiple PNRSV phylo-groups in at least one of each RNA and these phylo-groups formed distinct clades that represent PNRSV genetic strains. Variants within the same phylo-group of each Prunus plant sample had ≥97% similarity and phylo-groups within a Prunus plant sample and between samples had less ≤97% similarity. Based on the analysis of diversity, a definition of a PNRSV genetic strain was proposed. The proposed definition was applied to determine the number of PNRSV genetic strains in each of the plant samples and the complexity in defining genetic strains in multipartite genome viruses was explored.
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Affiliation(s)
- Wycliff M. Kinoti
- Agriculture Victoria, AgriBio, La Trobe University, Melbourne, VIC, Australia
- School of Applied Systems Biology, AgriBio, La Trobe University, Melbourne, VIC, Australia
| | - Fiona E. Constable
- Agriculture Victoria, AgriBio, La Trobe University, Melbourne, VIC, Australia
| | - Narelle Nancarrow
- Agriculture Victoria, AgriBio, La Trobe University, Melbourne, VIC, Australia
| | - Kim M. Plummer
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Melbourne, VIC, Australia
| | - Brendan Rodoni
- Agriculture Victoria, AgriBio, La Trobe University, Melbourne, VIC, Australia
- School of Applied Systems Biology, AgriBio, La Trobe University, Melbourne, VIC, Australia
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9
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Deep sequencing for discovery and evolutionary analysis of plant viruses. Virus Res 2016; 239:82-86. [PMID: 27876625 DOI: 10.1016/j.virusres.2016.11.019] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/18/2016] [Indexed: 11/21/2022]
Abstract
The advent of next generation sequencing (NGS), or deep sequencing, has allowed great advances to be made in discovery, diagnostics, and evolutionary studies in plant viruses. Various methods have been used for enrichment for virus-specific nucleic acids, each of which have some drawbacks. Many novel viruses have been discovered in plants by NGS technologies, and there is a good deal of promise for more comprehensive studies in virus evolution. However, each aspect of using NGS has its caveats that need to be considered, and there is still a need for better tools of analysis, as well as method for validation of sequence variation.
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10
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Hillung J, Cuevas JM, Elena SF. Evaluating the within-host fitness effects of mutations fixed during virus adaptation to different ecotypes of a new host. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0292. [PMID: 26150658 DOI: 10.1098/rstb.2014.0292] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The existence of genetic variation for resistance in host populations is assumed to be essential to the spread of an emerging virus. Models predict that the rate of spread slows down with the increasing frequency and higher diversity of resistance alleles in the host population. We have been using the experimental pathosystem Arabidopsis thaliana-tobacco etch potyvirus (TEV) to explore the interplay between genetic variation in host's susceptibility and virus diversity. We have recently shown that TEV populations evolving in A. thaliana ecotypes that differ in susceptibility to infection gained within-host fitness, virulence and infectivity in a manner compatible with a gene-for-gene model of host-parasite interactions: hard-to-infect ecotypes were infected by generalist viruses, whereas easy-to-infect ecotypes were infected by every virus. We characterized the genomes of the evolved viruses and found cases of host-driven convergent mutations. To gain further insights in the mechanistic basis of this gene-for-gene model, we have generated all viral mutations individually as well as in specific combinations and tested their within-host fitness effects across ecotypes. Most of these mutations were deleterious or neutral in their local ecotype and only a very reduced number had a host-specific beneficial effect. We conclude that most of the mutations fixed during the evolution experiment were so by drift or by selective sweeps along with the selected driver mutation. In addition, we evaluated the ruggedness of the underlying adaptive fitness landscape and found that mutational effects were mostly multiplicative, with few cases of significant epistasis.
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Affiliation(s)
- Julia Hillung
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València 46022, Spain
| | - José M Cuevas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València 46022, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València 46022, Spain The Santa Fe Institute, Santa Fe, NM 87501, USA
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11
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Abstract
Despite having very limited coding capacity, RNA viruses are able to withstand challenge of antiviral drugs, cause epidemics in previously exposed human populations, and, in some cases, infect multiple host species. They are able to achieve this by virtue of their ability to multiply very rapidly, coupled with their extraordinary degree of genetic heterogeneity. RNA viruses exist not as single genotypes, but as a swarm of related variants, and this genomic diversity is an essential feature of their biology. RNA viruses have a variety of mechanisms that act in combination to determine their genetic heterogeneity. These include polymerase fidelity, error-mitigation mechanisms, genomic recombination, and different modes of genome replication. RNA viruses can vary in their ability to tolerate mutations, or “genetic robustness,” and several factors contribute to this. Finally, there is evidence that some RNA viruses exist close to a threshold where polymerase error rate has evolved to maximize the possible sequence space available, while avoiding the accumulation of a lethal load of deleterious mutations. We speculate that different viruses have evolved different error rates to complement the different “life-styles” they possess.
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Affiliation(s)
- J.N. Barr
- University of Leeds, Leeds, United Kingdom
| | - R. Fearns
- Boston University School of Medicine, Boston, MA, United States
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12
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Multiple virus resistance using artificial trans-acting siRNAs. J Virol Methods 2015; 228:16-20. [PMID: 26562057 DOI: 10.1016/j.jviromet.2015.11.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 11/05/2015] [Accepted: 11/06/2015] [Indexed: 11/24/2022]
Abstract
Plant TAS gene encoded trans-acting siRNAs (ta-siRNAs) regulate the expression of target mRNAs by guiding their cleavage at the sequence complementary region as microRNAs. Since one TAS transcript is cleaved into multiple ta-siRNAs in a phased manner, TAS genes may be engineered to express multiple artificial ta-siRNAs (ata-siRNAs) that target multiple viruses at several distinct genomic positions. To test this hypothesis, the Arabidopsis TAS3a gene was engineered to express ata-siRNAs targeting the genome of Turnip mosaic virus (TuMV) and Cucumber mosaic virus (CMV). Transgenic Arabidopsis thaliana plants expressing these ata-siRNAs showed high level of resistance to both viruses. These results suggest that plant TAS genes can be modified to express artificial ta-siRNAs to confer multiple virus resistance and could have broad applications for future development in virus resistance strategies.
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Hong WS, Shpak M, Townsend JP. Inferring the Origin of Metastases from Cancer Phylogenies. Cancer Res 2015; 75:4021-5. [PMID: 26260528 PMCID: PMC4833389 DOI: 10.1158/0008-5472.can-15-1889] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 08/04/2015] [Indexed: 01/06/2023]
Abstract
Determining the evolutionary history of metastases is a key problem in cancer biology. Several recent studies have presented inferences regarding the origin of metastases based on phylogenies of cancer lineages. Many of these studies have concluded that the observed monophyly of metastatic subclones favored metastasis-to-metastasis spread ("a metastatic cascade" rather than parallel metastases from the primary tumor). In this article, we argue that identifying a monophyletic clade of metastatic subclones does not provide sufficient evidence to unequivocally establish a history of metastatic cascades. In the absence of a complete phylogeny of the subclones within the primary tumor, a scenario of parallel metastatic events from the primary tumor is an equally plausible interpretation. Future phylogenetic studies on the origin of metastases should obtain a complete phylogeny of subclones within the primary tumor. This complete phylogeny may be obtainable by ultra-deep sequencing and phasing of large sections or by targeted sequencing of many small, spatially heterogeneous sections, followed by phylogenetic reconstruction using well-established molecular evolutionary models. In addition to resolving the evolutionary history of metastases, a complete phylogeny of subclones within the primary tumor facilitates the identification of driver mutations by application of phylogeny-based tests of natural selection.
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Affiliation(s)
| | - Max Shpak
- NeuroTexas Institute, St. David's Medical Center, Austin, Texas. Center for Systems and Synthetic Biology, University of Texas, Austin, Texas. Fresh Pond Research Institute, Cambridge, Massachusetts.
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut. Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut. Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut
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14
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Presloid JB, Novella IS. RNA Viruses and RNAi: Quasispecies Implications for Viral Escape. Viruses 2015; 7:3226-40. [PMID: 26102581 PMCID: PMC4488735 DOI: 10.3390/v7062768] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 06/04/2015] [Accepted: 06/17/2015] [Indexed: 12/16/2022] Open
Abstract
Due to high mutation rates, populations of RNA viruses exist as a collection of closely related mutants known as a quasispecies. A consequence of error-prone replication is the potential for rapid adaptation of RNA viruses when a selective pressure is applied, including host immune systems and antiviral drugs. RNA interference (RNAi) acts to inhibit protein synthesis by targeting specific mRNAs for degradation and this process has been developed to target RNA viruses, exhibiting their potential as a therapeutic against infections. However, viruses containing mutations conferring resistance to RNAi were isolated in nearly all cases, underlining the problems of rapid viral evolution. Thus, while promising, the use of RNAi in treating or preventing viral diseases remains fraught with the typical complications that result from high specificity of the target, as seen in other antiviral regimens.
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Affiliation(s)
- John B Presloid
- Department of Medical Microbiology and Immunology, College of Medicine, The University of Toledo, 3055 Arlington Avenue, Toledo, OH 43614, USA.
| | - Isabel S Novella
- Department of Medical Microbiology and Immunology, College of Medicine, The University of Toledo, 3055 Arlington Avenue, Toledo, OH 43614, USA.
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15
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Ilardi V, Tavazza M. Biotechnological strategies and tools for Plum pox virus resistance: trans-, intra-, cis-genesis, and beyond. FRONTIERS IN PLANT SCIENCE 2015; 6:379. [PMID: 26106397 PMCID: PMC4458569 DOI: 10.3389/fpls.2015.00379] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/12/2015] [Indexed: 05/19/2023]
Abstract
Plum pox virus (PPV) is the etiological agent of sharka, the most devastating and economically important viral disease affecting Prunus species. It is widespread in most stone fruits producing countries even though eradication and quarantine programs are in place. The development of resistant cultivars and rootstocks remains the most ecologically and economically suitable approach to achieve long-term control of sharka disease. However, the few PPV resistance genetic resources found in Prunus germplasm along with some intrinsic biological features of stone fruit trees pose limits for efficient and fast breeding programs. This review focuses on an array of biotechnological strategies and tools, which have been used, or may be exploited to confer PPV resistance. A considerable number of scientific studies clearly indicate that robust and predictable resistance can be achieved by transforming plant species with constructs encoding intron-spliced hairpin RNAs homologous to conserved regions of the PPV genome. In addition, we discuss how recent advances in our understanding of PPV biology can be profitably exploited to develop viral interference strategies. In particular, genetic manipulation of host genes by which PPV accomplishes its infection cycle already permits the creation of intragenic resistant plants. Finally, we review the emerging genome editing technologies based on ZFN, TALEN and CRISPR/Cas9 engineered nucleases and how the knockout of host susceptibility genes will open up next generation of PPV resistant plants.
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Affiliation(s)
- Vincenza Ilardi
- Centro di Ricerca per la Patologia Vegetale, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Rome, Italy
| | - Mario Tavazza
- UTAGRI Centro Ricerche Casaccia, Agenzia Nazionale per le Nuove Tecnologie, l’Energia e lo Sviluppo Economico Sostenibile, Rome, Italy
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16
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Bordería AV, Isakov O, Moratorio G, Henningsson R, Agüera-González S, Organtini L, Gnädig NF, Blanc H, Alcover A, Hafenstein S, Fontes M, Shomron N, Vignuzzi M. Group Selection and Contribution of Minority Variants during Virus Adaptation Determines Virus Fitness and Phenotype. PLoS Pathog 2015; 11:e1004838. [PMID: 25941809 PMCID: PMC4420505 DOI: 10.1371/journal.ppat.1004838] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Accepted: 03/27/2015] [Indexed: 11/19/2022] Open
Abstract
Understanding how a pathogen colonizes and adapts to a new host environment is a primary aim in studying emerging infectious diseases. Adaptive mutations arise among the thousands of variants generated during RNA virus infection, and identifying these variants will shed light onto how changes in tropism and species jumps can occur. Here, we adapted Coxsackie virus B3 to a highly permissive and less permissive environment. Using deep sequencing and bioinformatics, we identified a multi-step adaptive process to adaptation involving residues in the receptor footprints that correlated with receptor availability and with increase in virus fitness in an environment-specific manner. We show that adaptation occurs by selection of a dominant mutation followed by group selection of minority variants that together, confer the fitness increase observed in the population, rather than selection of a single dominant genotype.
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Affiliation(s)
- Antonio V. Bordería
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
- Institut Pasteur, International Group for Data Analysis, Paris, France
| | - Ofer Isakov
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gonzalo Moratorio
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
| | - Rasmus Henningsson
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
- Institut Pasteur, International Group for Data Analysis, Paris, France
- Centre for Mathematical Sciences, Lund University, Lund, Sweden
| | | | - Lindsey Organtini
- Division of Infectious Diseases, Pennsylvania State College of Medicine, Hershey, Pennsylvania, United States of America
| | - Nina F. Gnädig
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
| | - Hervé Blanc
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
| | - Andrés Alcover
- Institut Pasteur, Lymphocyte Cell Biology Unit, CNRS URA 1960, Paris, France
| | - Susan Hafenstein
- Division of Infectious Diseases, Pennsylvania State College of Medicine, Hershey, Pennsylvania, United States of America
| | - Magnus Fontes
- Institut Pasteur, International Group for Data Analysis, Paris, France
- Centre for Mathematical Sciences, Lund University, Lund, Sweden
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Marco Vignuzzi
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
- * E-mail:
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17
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Orton RJ, Wright CF, Morelli MJ, King DJ, Paton DJ, King DP, Haydon DT. Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data. BMC Genomics 2015; 16:229. [PMID: 25886445 PMCID: PMC4425905 DOI: 10.1186/s12864-015-1456-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 03/09/2015] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND RNA viruses have high mutation rates and exist within their hosts as large, complex and heterogeneous populations, comprising a spectrum of related but non-identical genome sequences. Next generation sequencing is revolutionising the study of viral populations by enabling the ultra deep sequencing of their genomes, and the subsequent identification of the full spectrum of variants within the population. Identification of low frequency variants is important for our understanding of mutational dynamics, disease progression, immune pressure, and for the detection of drug resistant or pathogenic mutations. However, the current challenge is to accurately model the errors in the sequence data and distinguish real viral variants, particularly those that exist at low frequency, from errors introduced during sequencing and sample processing, which can both be substantial. RESULTS We have created a novel set of laboratory control samples that are derived from a plasmid containing a full-length viral genome with extremely limited diversity in the starting population. One sample was sequenced without PCR amplification whilst the other samples were subjected to increasing amounts of RT and PCR amplification prior to ultra-deep sequencing. This enabled the level of error introduced by the RT and PCR processes to be assessed and minimum frequency thresholds to be set for true viral variant identification. We developed a genome-scale computational model of the sample processing and NGS calling process to gain a detailed understanding of the errors at each step, which predicted that RT and PCR errors are more likely to occur at some genomic sites than others. The model can also be used to investigate whether the number of observed mutations at a given site of interest is greater than would be expected from processing errors alone in any NGS data set. After providing basic sample processing information and the site's coverage and quality scores, the model utilises the fitted RT-PCR error distributions to simulate the number of mutations that would be observed from processing errors alone. CONCLUSIONS These data sets and models provide an effective means of separating true viral mutations from those erroneously introduced during sample processing and sequencing.
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Affiliation(s)
- Richard J Orton
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, United Kingdom.
- Medical Research Council-University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, United Kingdom.
| | | | - Marco J Morelli
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia at the IFOM-IEO Campus, Via Adamello 16, Milano, 20139, Italy.
| | - David J King
- Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK.
| | - David J Paton
- Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK.
| | - Donald P King
- Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK.
| | - Daniel T Haydon
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, United Kingdom.
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18
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Isakov O, Bordería AV, Golan D, Hamenahem A, Celniker G, Yoffe L, Blanc H, Vignuzzi M, Shomron N. Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum. ACTA ACUST UNITED AC 2015; 31:2141-50. [PMID: 25701575 PMCID: PMC4481840 DOI: 10.1093/bioinformatics/btv101] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 02/11/2015] [Indexed: 12/22/2022]
Abstract
Motivation: The study of RNA virus populations is a challenging task. Each population of RNA virus is composed of a collection of different, yet related genomes often referred to as mutant spectra or quasispecies. Virologists using deep sequencing technologies face major obstacles when studying virus population dynamics, both experimentally and in natural settings due to the relatively high error rates of these technologies and the lack of high performance pipelines. In order to overcome these hurdles we developed a computational pipeline, termed ViVan (Viral Variance Analysis). ViVan is a complete pipeline facilitating the identification, characterization and comparison of sequence variance in deep sequenced virus populations. Results: Applying ViVan on deep sequenced data obtained from samples that were previously characterized by more classical approaches, we uncovered novel and potentially crucial aspects of virus populations. With our experimental work, we illustrate how ViVan can be used for studies ranging from the more practical, detection of resistant mutations and effects of antiviral treatments, to the more theoretical temporal characterization of the population in evolutionary studies. Availability and implementation: Freely available on the web at http://www.vivanbioinfo.org Contact: nshomron@post.tau.ac.il Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ofer Isakov
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
| | - Antonio V Bordería
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
| | - David Golan
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
| | - Amir Hamenahem
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
| | - Gershon Celniker
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
| | - Liron Yoffe
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
| | - Hervé Blanc
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
| | - Marco Vignuzzi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
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19
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Deep sequencing of virus-derived small interfering RNAs and RNA from viral particles shows highly similar mutational landscapes of a plant virus population. J Virol 2015; 89:4760-9. [PMID: 25673712 DOI: 10.1128/jvi.03685-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 02/04/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED RNA viruses exist within a host as a population of mutant sequences, often referred to as quasispecies. Within a host, sequences of RNA viruses constitute several distinct but interconnected pools, such as RNA packed in viral particles, double-stranded RNA, and virus-derived small interfering RNAs. We aimed to test if the same representation of within-host viral population structure could be obtained by sequencing different viral sequence pools. Using ultradeep Illumina sequencing, the diversity of two coexisting Potato virus Y sequence pools present within a plant was investigated: RNA isolated from viral particles and virus-derived small interfering RNAs (the derivatives of a plant RNA silencing mechanism). The mutational landscape of the within-host virus population was highly similar between both pools, with no notable hotspots across the viral genome. Notably, all of the single-nucleotide polymorphisms with a frequency of higher than 1.6% were found in both pools. Some unique single-nucleotide polymorphisms (SNPs) with very low frequencies were found in each of the pools, with more of them occurring in the small RNA (sRNA) pool, possibly arising through genetic drift in localized virus populations within a plant and the errors introduced during the amplification of silencing signal. Sequencing of the viral particle pool enhanced the efficiency of consensus viral genome sequence reconstruction. Nonhomologous recombinations were commonly detected in the viral particle pool, with a hot spot in the 3' untranslated and coat protein regions of the genome. We stress that they present an important but often overlooked aspect of virus population diversity. IMPORTANCE This study is the most comprehensive whole-genome characterization of a within-plant virus population to date and the first study comparing diversity of different pools of viral sequences within a host. We show that both virus-derived small RNAs and RNA from viral particles could be used for diversity assessment of within-plant virus population, since they show a highly congruent portrayal of the virus mutational landscape within a plant. The study is an important baseline for future studies of virus population dynamics, for example, during the adaptation to a new host. The comparison of the two virus sequence enrichment techniques, sequencing of virus-derived small interfering RNAs and RNA from purified viral particles, shows the strength of the latter for the detection of recombinant viral genomes and reconstruction of complete consensus viral genome sequence.
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20
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Bedhomme S, Hillung J, Elena SF. Emerging viruses: why they are not jacks of all trades? Curr Opin Virol 2014; 10:1-6. [PMID: 25467278 DOI: 10.1016/j.coviro.2014.10.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 10/27/2014] [Accepted: 10/28/2014] [Indexed: 12/21/2022]
Abstract
In order to limit the impact of the recent pandemics ignited by viral host jumps, it is necessary to better understand the ecological and evolutionary factors influencing the early steps of emergence and the interactions between them. Antagonistic pleiotropy, that is, the negative fitness effect in the primary host of mutations allowing the infection of and the multiplication in a new host, has long been thought to be the main limitation to the evolution of generalist viruses and thus to emergence. However, the accumulation of experimental examples contradicting the hypothesis of antagonistic pleiotropy has highlighted the importance of other factors such as the epistasis between mutations increasing the adaptation to a new host. Epistasis is pervasive in viruses, affects the shape of the adaptive landscape and consequently the accessibility of evolutionary pathways. Finally, recent studies have gone steps further in the complexity of viral fitness determinism and stressed the potential importance of the epistatic pleiotropy and of the impact of host living conditions.
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Affiliation(s)
- Stéphanie Bedhomme
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, 46022 Valencia, Spain.
| | - Julia Hillung
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, 46022 Valencia, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, 46022 Valencia, Spain; The Santa Fe Institute, Santa Fe, NM 87501, USA
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21
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Abstract
Viruses are common agents of plant infectious diseases. During last decades, worldwide agriculture production has been compromised by a series of epidemics caused by new viruses that spilled over from reservoir species or by new variants of classic viruses that show new pathogenic and epidemiological properties. Virus emergence has been generally associated with ecological change or with intensive agronomical practices. However, the complete picture is much more complex since the viral populations constantly evolve and adapt to their new hosts and vectors. This chapter puts emergence of plant viruses into the framework of evolutionary ecology, genetics, and epidemiology. We will stress that viral emergence begins with the stochastic transmission of preexisting genetic variants from the reservoir to the new host, whose fate depends on their fitness on each hosts, followed by adaptation to new hosts or vectors, and finalizes with an efficient epidemiological spread.
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Affiliation(s)
- Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Campus UPV, València, Spain; The Santa Fe Institute, Santa Fe, New Mexico, USA
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas, UPM-INIA, and ETSI Agrónomos, UPM, Campus de Montegancedo, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas, UPM-INIA, and ETSI Agrónomos, UPM, Campus de Montegancedo, Madrid, Spain.
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22
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Hillung J, Cuevas JM, Valverde S, Elena SF. Experimental evolution of an emerging plant virus in host genotypes that differ in their susceptibility to infection. Evolution 2014; 68:2467-80. [PMID: 24889935 DOI: 10.1111/evo.12458] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 05/16/2014] [Indexed: 01/02/2023]
Abstract
This study evaluates the extent to which genetic differences among host individuals from the same species condition the evolution of a plant RNA virus. We performed a threefold replicated evolution experiment in which Tobacco etch potyvirus isolate At17b (TEV-At17b), adapted to Arabidopsis thaliana ecotype Ler-0, was serially passaged in five genetically heterogeneous ecotypes of A. thaliana. After 15 passages we found that evolved viruses improved their fitness, showed higher infectivity and stronger virulence in their local host ecotypes. The genome of evolved lineages was sequenced and putative adaptive mutations identified. Host-driven convergent mutations have been identified. Evidences supported selection for increased translational efficiency. Next, we sought for the specificity of virus adaptation by infecting all five ecotypes with all 15 evolved virus populations. We found that some ecotypes were more permissive to infection than others, and that some evolved virus isolates were more specialist/generalist than others. The bipartite network linking ecotypes with evolved viruses was significantly nested but not modular, suggesting that hard-to-infect ecotypes were infected by generalist viruses whereas easy-to-infect ecotypes were infected by all viruses, as predicted by a gene-for-gene model of infection.
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Affiliation(s)
- Julia Hillung
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Campus UPV CPI 8E, C/Ingeniero Fausto Elio s/n, 46022, València, Spain
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23
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Non-coding RNAs in crop genetic modification: considerations and predictable environmental risk assessments (ERA). Mol Biotechnol 2014; 55:87-100. [PMID: 23381873 DOI: 10.1007/s12033-013-9648-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Of late non-coding RNAs (ncRNAs)-mediated gene silencing is an influential tool deliberately deployed to negatively regulate the expression of targeted genes. In addition to the widely employed small interfering RNA (siRNA)-mediated gene silencing approach, other variants like artificial miRNA (amiRNA), miRNA mimics, and artificial transacting siRNAs (tasiRNAs) are being explored and successfully deployed in developing non-coding RNA-based genetically modified plants. The ncRNA-based gene manipulations are typified with mobile nature of silencing signals, interference from viral genome-derived suppressor proteins, and an obligation for meticulous computational analysis to prevaricate any inadvertent effects. In a broad sense, risk assessment inquiries for genetically modified plants based on the expression of ncRNAs are competently addressed by the environmental risk assessment (ERA) models, currently in vogue, designed for the first generation transgenic plants which are based on the expression of heterologous proteins. Nevertheless, transgenic plants functioning on the foundation of ncRNAs warrant due attention with respect to their unique attributes like off-target or non-target gene silencing effects, small RNAs (sRNAs) persistence, food and feed safety assessments, problems in detection and tracking of sRNAs in food, impact of ncRNAs in plant protection measures, effect of mutations etc. The role of recent developments in sequencing techniques like next generation sequencing (NGS) and the ERA paradigm of the different countries in vogue are also discussed in the context of ncRNA-based gene manipulations.
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24
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Ramesh SV, Ratnaparkhe MB, Kumawat G, Gupta GK, Husain SM. Plant miRNAome and antiviral resistance: a retrospective view and prospective challenges. Virus Genes 2014; 48:1-14. [PMID: 24445902 DOI: 10.1007/s11262-014-1038-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 01/12/2014] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNAs) are small regulatory RNAs that play a defining role in post-transcriptional gene silencing of eukaryotes by either mRNA cleavage or translational inhibition. Plant miRNAs have been implicated in innumerable growth and developmental processes that extend beyond their ability to respond to biotic and abiotic stresses. Active in an organism's immune defence response, host miRNAs display a propensity to target viral genomes. During viral invasion, these virus-targeting miRNAs can be identified by their altered expression. All the while, pathogenic viruses, as a result of their long-term interaction with plants, have been evolving viral suppressors of RNA silencing (VSRs), as well as viral-encoded miRNAs as a counter-defence strategy. However, the gene silencing attribute of miRNAs has been ingeniously manipulated to down-regulate the expression of any gene of interest, including VSRs, in artificial miRNA (amiRNA)-based transgenics. Since we currently have a better understanding of the intricacies of miRNA-mediated gene regulation in plant-virus interactions, the majority of miRNAs manipulated to confer antiviral resistance to date are in plants. This review will share the insights gained from the studies of plant-virus combat and from the endeavour to manipulate miRNAs, including prospective challenges in the context of the evolutionary dynamics of the viral genome. Next generation sequencing technologies and bioinformatics analysis will further delineate the molecular details of host-virus interactions. The need for appropriate environmental risk assessment principles specific to amiRNA-based virus resistance is also discussed.
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Affiliation(s)
- Shunmugiah Veluchamy Ramesh
- Directorate of Soybean Research, Indian Council of Agricultural Research (ICAR), Khandwa Road, Indore, 452001, Madhya Pradesh, India,
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25
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The role of innate immunity in conditioning mosquito susceptibility to West Nile virus. Viruses 2013; 5:3142-70. [PMID: 24351797 PMCID: PMC3967165 DOI: 10.3390/v5123142] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 11/13/2013] [Accepted: 12/09/2013] [Indexed: 01/02/2023] Open
Abstract
Arthropod-borne viruses (arboviruses) represent an emerging threat to human and livestock health globally. In particular, those transmitted by mosquitoes present the greatest challenges to disease control efforts. An understanding of the molecular basis for mosquito innate immunity to arbovirus infection is therefore critical to investigations regarding arbovirus evolution, virus-vector ecology, and mosquito vector competence. In this review, we discuss the current state of understanding regarding mosquito innate immunity to West Nile virus. We draw from the literature with respect to other virus-vector pairings to attempt to draw inferences to gaps in our knowledge about West Nile virus and relevant vectors.
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26
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Wang H, Xie J, Shreeve TG, Ma J, Pallett DW, King LA, Possee RD. Sequence recombination and conservation of Varroa destructor virus-1 and deformed wing virus in field collected honey bees (Apis mellifera). PLoS One 2013; 8:e74508. [PMID: 24058580 PMCID: PMC3776811 DOI: 10.1371/journal.pone.0074508] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 08/02/2013] [Indexed: 12/23/2022] Open
Abstract
We sequenced small (s) RNAs from field collected honeybees (Apis mellifera) and bumblebees (Bombuspascuorum) using the Illumina technology. The sRNA reads were assembled and resulting contigs were used to search for virus homologues in GenBank. Matches with Varroadestructor virus-1 (VDV1) and Deformed wing virus (DWV) genomic sequences were obtained for A. mellifera but not B. pascuorum. Further analyses suggested that the prevalent virus population was composed of VDV-1 and a chimera of 5’-DWV-VDV1-DWV-3’. The recombination junctions in the chimera genomes were confirmed by using RT-PCR, cDNA cloning and Sanger sequencing. We then focused on conserved short fragments (CSF, size > 25 nt) in the virus genomes by using GenBank sequences and the deep sequencing data obtained in this study. The majority of CSF sites confirmed conservation at both between-species (GenBank sequences) and within-population (dataset of this study) levels. However, conserved nucleotide positions in the GenBank sequences might be variable at the within-population level. High mutation rates (Pi>10%) were observed at a number of sites using the deep sequencing data, suggesting that sequence conservation might not always be maintained at the population level. Virus-host interactions and strategies for developing RNAi treatments against VDV1/DWV infections are discussed.
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Affiliation(s)
- Hui Wang
- Centre for Ecology and Hydrology, Natural Environmental Research Council, Wallingford, Oxfordshire, United Kingdom
- * E-mail:
| | - Jiazheng Xie
- Beijing Genome Institute, Yantian District, Shenzhen, China
| | - Tim G. Shreeve
- Department of Biological and Medical Sciences, Oxford Brooks University, Oxford, United Kingdom
| | - Jinmin Ma
- Beijing Genome Institute, Yantian District, Shenzhen, China
| | - Denise W. Pallett
- Centre for Ecology and Hydrology, Natural Environmental Research Council, Wallingford, Oxfordshire, United Kingdom
| | - Linda A. King
- Department of Biological and Medical Sciences, Oxford Brooks University, Oxford, United Kingdom
| | - Robert D. Possee
- Centre for Ecology and Hydrology, Natural Environmental Research Council, Wallingford, Oxfordshire, United Kingdom
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27
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Martínez F, Elena SF, Daròs JA. Fate of artificial microRNA-mediated resistance to plant viruses in mixed infections. PHYTOPATHOLOGY 2013; 103:870-6. [PMID: 23617337 DOI: 10.1094/phyto-09-12-0233-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Artificial microRNAs (amiRNAs) are the expression products of engineered microRNA (miRNA) genes that efficiently and specifically downregulate RNAs that contain complementary sequences. Transgenic plants expressing high levels of one or more amiRNAs targeting particular sequences in the genomes of some RNA viruses have shown specific resistance to the corresponding virus. This is the case of the Arabidopsis thaliana transgenic line 12-4 expressing a high level of the amiR159-HC-Pro targeting 21 nucleotides in the Turnip mosaic virus (TuMV) (family Potyviridae) cistron coding for the viral RNA-silencing suppressor HC-Pro that is highly resistant to TuMV infection. In this study, we explored the fate of this resistance when the A. thaliana 12-4 plants are challenged with a second virus in addition to TuMV. The A. thaliana 12-4 plants maintained the resistance to TuMV when this virus was co-inoculated with Tobacco mosaic virus, Tobacco rattle virus (TRV), Cucumber mosaic virus (CMV), Turnip yellow mosaic virus, Cauliflower mosaic virus (CaMV), Lettuce mosaic virus, or Plum pox virus. However, when the plants were preinfected with these viruses, TuMV was able to co-infect 12-4 plants preinfected with TRV, CaMV, and, particularly, CMV. Therefore, preinfection by another virus jeopardizes the amiRNA-mediated resistance to TuMV.
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Affiliation(s)
- Fernando Martínez
- Instituto de Biologia Molecular y Celular de Plantas, Valencia, Spain
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28
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Lafforgue G, Martínez F, Niu QW, Chua NH, Daròs JA, Elena SF. Improving the effectiveness of artificial microRNA (amiR)-mediated resistance against Turnip mosaic virus by combining two amiRs or by targeting highly conserved viral genomic regions. J Virol 2013; 87:8254-6. [PMID: 23698292 PMCID: PMC3700214 DOI: 10.1128/jvi.00914-13] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 05/10/2013] [Indexed: 01/04/2023] Open
Abstract
A drawback of recent antiviral therapies based on the transgenic expression of artificial microRNAs (amiRs) is the ease with which viruses generate escape mutations. Here, we show two alternative strategies for improving the effectiveness of resistance in plants. First, we expressed two amiRs complementary to independent targets in the viral genome, and second, we designed amiRs complementary to highly conserved RNA motifs in the viral genome.
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Affiliation(s)
- Guillaume Lafforgue
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, València, Spain
| | - Fernando Martínez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, València, Spain
| | - Qi-Wen Niu
- Laboratory of Plant Biology, Rockefeller University, New York, New York, USA
| | - Nam-Hai Chua
- Laboratory of Plant Biology, Rockefeller University, New York, New York, USA
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, València, Spain
| | - Santiago F. Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, València, Spain
- The Santa Fe Institute, Santa Fe, New Mexico, USA
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29
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Grimm D, Dalmay T, van Rij RP. Everybody wins! Poland hosts thrilling competitions of viruses, RNAi and football teams. EMBO Rep 2012; 13:874-6. [PMID: 22986551 PMCID: PMC3463971 DOI: 10.1038/embor.2012.136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The ESF-EMBO conference on 'Antiviral RNAi: From Molecular Biology towards Applications' took place in June 2012 in Pultusk, Poland. It brought together scientists working at the interface of RNAi and virus infections in different organisms, covering the complete range from basic mechanisms of RNA silencing to RNAi-based antiviral therapy.
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Affiliation(s)
- Dirk Grimm
- Department of Infectious Diseases, Virology, Cluster of Excellence Cell Networks, Heidelberg University Hospital, Heidelberg, Germany.
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30
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Elena SF. RNA virus genetic robustness: possible causes and some consequences. Curr Opin Virol 2012; 2:525-30. [PMID: 22818515 DOI: 10.1016/j.coviro.2012.06.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 06/27/2012] [Indexed: 11/30/2022]
Abstract
In general terms, robustness is the capacity of biological systems to function in spite of genetic or environmental perturbations. The small and compacted genomes and high mutation rates of RNA viruses, as well as the ever-changing environments wherein they replicate, create the conditions for robustness to be advantageous. In this review, I will enumerate possible mechanisms by which viral populations may acquire robustness, distinguishing between mechanisms that are inherent to virus replication and population dynamics and those that result from the interaction with host factors. Then, I will move to review some evidences that RNA virus populations are robust indeed. Finally, I will comment on the implications of robustness for virus evolvability, the emergence of new viruses and the efficiency of lethal mutagenesis as an antiviral strategy.
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Affiliation(s)
- Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022 València, Spain.
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