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Hinge VR, Chavhan RL, Kale SP, Suprasanna P, Kadam US. Engineering Resistance Against Viruses in Field Crops Using CRISPR- Cas9. Curr Genomics 2021; 22:214-231. [PMID: 34975291 PMCID: PMC8640848 DOI: 10.2174/1389202922666210412102214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/29/2021] [Accepted: 02/24/2021] [Indexed: 12/26/2022] Open
Abstract
Food security is threatened by various biotic stresses that affect the growth and production of agricultural crops. Viral diseases have become a serious concern for crop plants as they incur huge yield losses. The enhancement of host resistance against plant viruses is a priority for the effective management of plant viral diseases. However, in the present context of the climate change scenario, plant viruses are rapidly evolving, resulting in the loss of the host resistance mechanism. Advances in genome editing techniques, such as CRISPR-Cas9 [clustered regularly interspaced palindromic repeats-CRISPR-associated 9], have been recognized as promising tools for the development of plant virus resistance. CRISPR-Cas9 genome editing tool is widely preferred due to high target specificity, simplicity, efficiency, and reproducibility. CRISPR-Cas9 based virus resistance in plants has been successfully achieved by gene targeting and cleaving the viral genome or altering the plant genome to enhance plant innate immunity. In this article, we have described the CRISPR-Cas9 system, mechanism of plant immunity against viruses and highlighted the use of the CRISPR-Cas9 system to engineer virus resistance in plants. We also discussed prospects and challenges on the use of CRISPR-Cas9-mediated plant virus resistance in crop improvement.
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Affiliation(s)
- Vidya R Hinge
- 1Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology, Latur; Vasantrao Naik Marathwada Krishi Vidyapeeth (VNMKV), Parbhani 431 402, India; 2USAID-BIRAC International Project, School of Life Sciences, S.R.T.M.U., Nanded, India; 3Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India; 4Max Planck Institute of Molecular Plant Physiology, Potsdam- Golm, 14476, Germany
| | - Rahul L Chavhan
- 1Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology, Latur; Vasantrao Naik Marathwada Krishi Vidyapeeth (VNMKV), Parbhani 431 402, India; 2USAID-BIRAC International Project, School of Life Sciences, S.R.T.M.U., Nanded, India; 3Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India; 4Max Planck Institute of Molecular Plant Physiology, Potsdam- Golm, 14476, Germany
| | - Sandeep P Kale
- 1Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology, Latur; Vasantrao Naik Marathwada Krishi Vidyapeeth (VNMKV), Parbhani 431 402, India; 2USAID-BIRAC International Project, School of Life Sciences, S.R.T.M.U., Nanded, India; 3Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India; 4Max Planck Institute of Molecular Plant Physiology, Potsdam- Golm, 14476, Germany
| | - Penna Suprasanna
- 1Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology, Latur; Vasantrao Naik Marathwada Krishi Vidyapeeth (VNMKV), Parbhani 431 402, India; 2USAID-BIRAC International Project, School of Life Sciences, S.R.T.M.U., Nanded, India; 3Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India; 4Max Planck Institute of Molecular Plant Physiology, Potsdam- Golm, 14476, Germany
| | - Ulhas S Kadam
- 1Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology, Latur; Vasantrao Naik Marathwada Krishi Vidyapeeth (VNMKV), Parbhani 431 402, India; 2USAID-BIRAC International Project, School of Life Sciences, S.R.T.M.U., Nanded, India; 3Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India; 4Max Planck Institute of Molecular Plant Physiology, Potsdam- Golm, 14476, Germany
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Rousseau E, Tamisier L, Fabre F, Simon V, Szadkowski M, Bouchez O, Zanchetta C, Girardot G, Mailleret L, Grognard F, Palloix A, Moury B. Impact of genetic drift, selection and accumulation level on virus adaptation to its host plants. MOLECULAR PLANT PATHOLOGY 2018; 19:2575-2589. [PMID: 30074299 PMCID: PMC6638063 DOI: 10.1111/mpp.12730] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The efficiency of plant major resistance genes is limited by the emergence and spread of resistance-breaking mutants. Modulation of the evolutionary forces acting on pathogen populations constitutes a promising way to increase the durability of these genes. We studied the effect of four plant traits affecting these evolutionary forces on the rate of resistance breakdown (RB) by a virus. Two of these traits correspond to virus effective population sizes (Ne ) at either plant inoculation or during infection. The third trait corresponds to differential selection exerted by the plant on the virus population. Finally, the fourth trait corresponds to within-plant virus accumulation (VA). These traits were measured experimentally on Potato virus Y (PVY) inoculated to a set of 84 pepper doubled-haploid lines, all carrying the same pvr23 resistance gene, but having contrasting genetic backgrounds. The lines showed extensive variation for the rate of pvr23 RB by PVY and for the four other traits of interest. A generalized linear model showed that three of these four traits, with the exception of Ne at inoculation, and several pairwise interactions between them had significant effects on RB. RB increased with increasing values of Ne during plant infection or VA. The effect of differential selection was more complex because of a strong interaction with VA. When VA was high, RB increased as the differential selection increased. An opposite relationship between RB and differential selection was observed when VA was low. This study provides a framework to select plants with appropriate virus evolution-related traits to avoid or delay RB.
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Affiliation(s)
- Elsa Rousseau
- Pathologie VégétaleINRA84140MontfavetFrance
- Université Côte d'Azur, Inria, INRA, CNRS, Sorbonne UniversitéBiocore TeamSophia AntipolisFrance
- Université Côte d'Azur, INRA, CNRS, ISAFrance
- Present address:
IBM Almaden Research CenterSan Jose, CA 95120–6099USA
| | - Lucie Tamisier
- Pathologie VégétaleINRA84140MontfavetFrance
- GAFL, INRA84140MontfavetFrance
- Present address:
Université de Liège, Terra‐Gembloux Agro-Bio Tech, PlantPathology Laboratory, Passage des Déportés2, GemblouxBelgium, 5030
| | | | - Vincent Simon
- Pathologie VégétaleINRA84140MontfavetFrance
- UMR BFPINRA33882Villenave d'OrnonFrance
| | | | - Olivier Bouchez
- INRAGeT‐PlaGe, US 1426, Genotoul, 31326 Castanet‐TolosanFrance
| | | | | | - Ludovic Mailleret
- Université Côte d'Azur, Inria, INRA, CNRS, Sorbonne UniversitéBiocore TeamSophia AntipolisFrance
- Université Côte d'Azur, INRA, CNRS, ISAFrance
| | - Frederic Grognard
- Université Côte d'Azur, Inria, INRA, CNRS, Sorbonne UniversitéBiocore TeamSophia AntipolisFrance
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Time-Sampled Population Sequencing Reveals the Interplay of Selection and Genetic Drift in Experimental Evolution of Potato Virus Y. J Virol 2017; 91:JVI.00690-17. [PMID: 28592544 PMCID: PMC5533922 DOI: 10.1128/jvi.00690-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 05/28/2017] [Indexed: 11/20/2022] Open
Abstract
RNA viruses are one of the fastest-evolving biological entities. Within their hosts, they exist as genetically diverse populations (i.e., viral mutant swarms), which are sculpted by different evolutionary mechanisms, such as mutation, natural selection, and genetic drift, and also the interactions between genetic variants within the mutant swarms. To elucidate the mechanisms that modulate the population diversity of an important plant-pathogenic virus, we performed evolution experiments with Potato virus Y (PVY) in potato genotypes that differ in their defense response against the virus. Using deep sequencing of small RNAs, we followed the temporal dynamics of standing and newly generated variations in the evolving viral lineages. A time-sampled approach allowed us to (i) reconstruct theoretical haplotypes in the starting population by using clustering of single nucleotide polymorphisms' trajectories and (ii) use quantitative population genetics approaches to estimate the contribution of selection and genetic drift, and their interplay, to the evolution of the virus. We detected imprints of strong selective sweeps and narrow genetic bottlenecks, followed by the shift in frequency of selected haplotypes. Comparison of patterns of viral evolution in differently susceptible host genotypes indicated possible diversifying evolution of PVY in the less-susceptible host (efficient in the accumulation of salicylic acid).IMPORTANCE High diversity of within-host populations of RNA viruses is an important aspect of their biology, since they represent a reservoir of genetic variants, which can enable quick adaptation of viruses to a changing environment. This study focuses on an important plant virus, Potato virus Y, and describes, at high resolution, temporal changes in the structure of viral populations within different potato genotypes. A novel and easy-to-implement computational approach was established to cluster single nucleotide polymorphisms into viral haplotypes from very short sequencing reads. During the experiment, a shift in the frequency of selected viral haplotypes was observed after a narrow genetic bottleneck, indicating an important role of the genetic drift in the evolution of the virus. On the other hand, a possible case of diversifying selection of the virus was observed in less susceptible host genotypes.
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Hong JS, Ju HJ. The Plant Cellular Systems for Plant Virus Movement. THE PLANT PATHOLOGY JOURNAL 2017; 33:213-228. [PMID: 28592941 PMCID: PMC5461041 DOI: 10.5423/ppj.rw.09.2016.0198] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 11/05/2016] [Accepted: 11/13/2016] [Indexed: 05/24/2023]
Abstract
Plasmodesmata (PDs) are specialized intercellular channels that facilitate the exchange of various molecules, including sugars, ribonucleoprotein complexes, transcription factors, and mRNA. Their diameters, estimated to be 2.5 nm in the neck region, are too small to transfer viruses or viral genomes. Tobacco mosaic virus and Potexviruses are the most extensively studied viruses. In viruses, the movement protein (MP) is responsible for the PD gating that allows the intercellular movement of viral genomes. Various host factors interact with MP to regulate complicated mechanisms related to PD gating. Virus replication and assembly occur in viral replication complex (VRC) with membrane association, especially in the endoplasmic reticulum. VRC have a highly organized structure and are highly regulated by interactions among the various host factors, proteins encoded by the viral genome, and the viral genome. Virus trafficking requires host machineries, such as the cytoskeleton and the secretory systems. MP facilitates the virus replication and movement process. Despite the current level of understanding of virus movement, there are still many unknown and complex interactions between virus replication and virus movement. While numerous studies have been conducted to understand plant viruses with regards to cell-to-cell movement and replication, there are still many knowledge gaps. To study these interactions, adequate research tools must be used such as molecular, and biochemical techniques. Without such tools, virologists will not be able to gain an accurate or detailed understanding of the virus infection process.
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Affiliation(s)
- Jin-Sung Hong
- Department of Applied Biology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Ho-Jong Ju
- Department of Agricultural Biology, College of Agricultural Life Science, Chonbuk National University, Jeonju 54896, Korea
- Plant Medicinal Research Center, College of Agricultural Life Science, Chonbuk National University, Jeonju 54896, Korea
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5
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Willemsen A, Zwart MP, Higueras P, Sardanyés J, Elena SF. Predicting the Stability of Homologous Gene Duplications in a Plant RNA Virus. Genome Biol Evol 2016; 8:3065-3082. [PMID: 27604880 PMCID: PMC5633665 DOI: 10.1093/gbe/evw219] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2016] [Indexed: 01/03/2023] Open
Abstract
One of the striking features of many eukaryotes is the apparent amount of redundancy in coding and non-coding elements of their genomes. Despite the possible evolutionary advantages, there are fewer examples of redundant sequences in viral genomes, particularly those with RNA genomes. The factors constraining the maintenance of redundant sequences in present-day RNA virus genomes are not well known. Here, we use Tobacco etch virus, a plant RNA virus, to investigate the stability of genetically redundant sequences by generating viruses with potentially beneficial gene duplications. Subsequently, we tested the viability of these viruses and performed experimental evolution. We found that all gene duplication events resulted in a loss of viability or in a significant reduction in viral fitness. Moreover, upon analyzing the genomes of the evolved viruses, we always observed the deletion of the duplicated gene copy and maintenance of the ancestral copy. Interestingly, there were clear differences in the deletion dynamics of the duplicated gene associated with the passage duration and the size and position of the duplicated copy. Based on the experimental data, we developed a mathematical model to characterize the stability of genetically redundant sequences, and showed that fitness effects are not enough to predict genomic stability. A context-dependent recombination rate is also required, with the context being the duplicated gene and its position. Our results therefore demonstrate experimentally the deleterious nature of gene duplications in RNA viruses. Beside previously described constraints on genome size, we identified additional factors that reduce the likelihood of the maintenance of duplicated genes.
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Affiliation(s)
- Anouk Willemsen
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, València, Spain Present address: MIVEGEC (UMR CNRS 5290, IRD 224, UM), National Center for Scientific Research (CNRS), 911 Avenue Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France
| | - Mark P Zwart
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, València, Spain Present address: Institute of Theoretical Physics, University of Cologne, Zülpicher Straße 77, 50937 Cologne, Germany
| | - Pablo Higueras
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, València, Spain
| | - Josep Sardanyés
- ICREA Complex Systems Laboratory, Universitat Pompeu Fabra, Barcelona, Spain Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, València, Spain Instituto de Biología Integrativa y de Sistems (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, Parc Científic de la Universitat de València, Paterna, València, Spain The Santa Fe Institute, Santa Fe, New Mexico
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Borer ET, Laine AL, Seabloom EW. A Multiscale Approach to Plant Disease Using the Metacommunity Concept. ANNUAL REVIEW OF PHYTOPATHOLOGY 2016; 54:397-418. [PMID: 27296140 DOI: 10.1146/annurev-phyto-080615-095959] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Plant disease arises from the interaction of processes occurring at multiple spatial and temporal scales. With new tools such as next-generation sequencing, we are learning about the diversity of microbes circulating within and among plant populations and often coinhabiting host individuals. The proliferation of pathogenic microbes depends on single-species dynamics and multispecies interactions occurring within and among host cells, the spatial organization and genetic landscape of hosts, the frequency and mode of transmission among hosts and host populations, and the abiotic environmental context. Here, we examine empirical evidence from these multiple scales to assess the utility of metacommunity theory, a theoretical framework developed for free-living organisms to further our understanding of and assist in predicting plant-pathogen infection and spread. We suggest that deeper understanding of disease dynamics can arise through the application of this conceptual framework at scales ranging from individual cells to landscapes. In addition, we use this multiscale theoretical perspective to synthesize existing knowledge, generate novel hypotheses, and point toward promising future opportunities for the study of plant pathogens in natural populations.
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Affiliation(s)
- Elizabeth T Borer
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota 55108; ,
| | - Anna-Liisa Laine
- Centre of Excellence in Metapopulation Biology, Department of Biosciences, University of Helsinki, FI-00014, Finland;
| | - Eric W Seabloom
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota 55108; ,
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7
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Rimbaud L, Dallot S, Delaunay A, Borron S, Soubeyrand S, Thébaud G, Jacquot E. Assessing the Mismatch Between Incubation and Latent Periods for Vector-Borne Diseases: The Case of Sharka. PHYTOPATHOLOGY 2015; 105:1408-16. [PMID: 26512749 DOI: 10.1094/phyto-01-15-0014-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The relative durations of the incubation period (the time between inoculation and symptom expression) and of the latent period (the time between inoculation and infectiousness of the host) are poorly documented for plant diseases. However, the extent of asynchrony between the ends of these two periods (i.e., their mismatch) can be a key determinant of the epidemic dynamics for many diseases and consequently it is of primary interest in the design of disease management strategies. In order to assess this mismatch, an experimental approach was developed and applied using sharka, a severe disease caused by Plum pox virus (PPV, genus Potyvirus, family Potyviridae) affecting trees belonging to the genus Prunus. Leaves of infected young peach trees were used individually as viral sources in aphid-mediated transmission tests carried out at different time points postinoculation in order to bracket symptom onset. By fitting a nonlinear logistic model to the obtained transmission rates, we demonstrated that the first symptoms appear on leaves 1 day before they rapidly become infectious. In addition, among symptomatic leaves, symptom intensity and transmission rate are positively correlated. These results strengthen the conclusion that, under our experimental conditions, incubation and latent periods of PPV infection are almost synchronous.
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Affiliation(s)
- Loup Rimbaud
- First author: Montpellier SupAgro, UMR 385 BGPI (Biology and Genetics of Plant-Pathogen Interactions), Cirad TA A-54/K, 34398 Montpellier Cedex 5, France; second, third, fourth, sixth, and seventh authors: INRA, UMR 385 BGPI, Cirad TA A-54/K, 34398 Montpellier Cedex 5, France; and fifth author: INRA, UR 546 Biostatistics and Spatial Processes, 84914 Avignon Cedex 9, France
| | - Sylvie Dallot
- First author: Montpellier SupAgro, UMR 385 BGPI (Biology and Genetics of Plant-Pathogen Interactions), Cirad TA A-54/K, 34398 Montpellier Cedex 5, France; second, third, fourth, sixth, and seventh authors: INRA, UMR 385 BGPI, Cirad TA A-54/K, 34398 Montpellier Cedex 5, France; and fifth author: INRA, UR 546 Biostatistics and Spatial Processes, 84914 Avignon Cedex 9, France
| | - Agnès Delaunay
- First author: Montpellier SupAgro, UMR 385 BGPI (Biology and Genetics of Plant-Pathogen Interactions), Cirad TA A-54/K, 34398 Montpellier Cedex 5, France; second, third, fourth, sixth, and seventh authors: INRA, UMR 385 BGPI, Cirad TA A-54/K, 34398 Montpellier Cedex 5, France; and fifth author: INRA, UR 546 Biostatistics and Spatial Processes, 84914 Avignon Cedex 9, France
| | - Sonia Borron
- First author: Montpellier SupAgro, UMR 385 BGPI (Biology and Genetics of Plant-Pathogen Interactions), Cirad TA A-54/K, 34398 Montpellier Cedex 5, France; second, third, fourth, sixth, and seventh authors: INRA, UMR 385 BGPI, Cirad TA A-54/K, 34398 Montpellier Cedex 5, France; and fifth author: INRA, UR 546 Biostatistics and Spatial Processes, 84914 Avignon Cedex 9, France
| | - Samuel Soubeyrand
- First author: Montpellier SupAgro, UMR 385 BGPI (Biology and Genetics of Plant-Pathogen Interactions), Cirad TA A-54/K, 34398 Montpellier Cedex 5, France; second, third, fourth, sixth, and seventh authors: INRA, UMR 385 BGPI, Cirad TA A-54/K, 34398 Montpellier Cedex 5, France; and fifth author: INRA, UR 546 Biostatistics and Spatial Processes, 84914 Avignon Cedex 9, France
| | - Gaël Thébaud
- First author: Montpellier SupAgro, UMR 385 BGPI (Biology and Genetics of Plant-Pathogen Interactions), Cirad TA A-54/K, 34398 Montpellier Cedex 5, France; second, third, fourth, sixth, and seventh authors: INRA, UMR 385 BGPI, Cirad TA A-54/K, 34398 Montpellier Cedex 5, France; and fifth author: INRA, UR 546 Biostatistics and Spatial Processes, 84914 Avignon Cedex 9, France
| | - Emmanuel Jacquot
- First author: Montpellier SupAgro, UMR 385 BGPI (Biology and Genetics of Plant-Pathogen Interactions), Cirad TA A-54/K, 34398 Montpellier Cedex 5, France; second, third, fourth, sixth, and seventh authors: INRA, UMR 385 BGPI, Cirad TA A-54/K, 34398 Montpellier Cedex 5, France; and fifth author: INRA, UR 546 Biostatistics and Spatial Processes, 84914 Avignon Cedex 9, France
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Random Plant Viral Variants Attain Temporal Advantages During Systemic Infections and in Turn Resist other Variants of the Same Virus. Sci Rep 2015; 5:15346. [PMID: 26481091 PMCID: PMC4612314 DOI: 10.1038/srep15346] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 09/22/2015] [Indexed: 01/19/2023] Open
Abstract
Infection of plants with viruses containing multiple variants frequently leads to dominance by a few random variants in the systemically infected leaves (SLs), for which a plausible explanation is lacking. We show here that SL dominance by a given viral variant is adequately explained by its fortuitous lead in systemic spread, coupled with its resistance to superinfection by other variants. We analyzed the fate of a multi-variant turnip crinkle virus (TCV) population in Arabidopsis and N. benthamiana plants. Both wild-type and RNA silencing-defective plants displayed a similar pattern of random dominance by a few variant genotypes, thus discounting a prominent role for RNA silencing. When introduced to plants sequentially as two subpopulations, a twelve-hour head-start was sufficient for the first set to dominate. Finally, SLs of TCV-infected plants became highly resistant to secondary invasions of another TCV variant. We propose that random distribution of variant foci on inoculated leaves allows different variants to lead systemic movement in different plants. The leading variants then colonize large areas of SLs, and resist the superinfection of lagging variants in the same areas. In conclusion, superinfection resistance is the primary driver of random enrichment of viral variants in systemically infected plants.
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9
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Cuevas JM, Willemsen A, Hillung J, Zwart MP, Elena SF. Temporal dynamics of intrahost molecular evolution for a plant RNA virus. Mol Biol Evol 2015; 32:1132-47. [PMID: 25660377 DOI: 10.1093/molbev/msv028] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Populations of plant RNA viruses are highly polymorphic in infected plants, which may allow rapid within-host evolution. To understand tobacco etch potyvirus (TEV) evolution, longitudinal samples from experimentally evolved populations in the natural host tobacco and from the alternative host pepper were phenotypically characterized and genetically analyzed. Temporal and compartmental variabilities of TEV populations were quantified using high throughput Illumina sequencing and population genetic approaches. Of the two viral phenotypic traits measured, virulence increased in the novel host but decreased in the original one, and viral load decreased in both hosts, though to a lesser extent in the novel one. Dynamics of population genetic diversity were also markedly different among hosts. Population heterozygosity increased in the ancestral host, with a dominance of synonymous mutations fixed, whereas it did not change or even decreased in the new host, with an excess of nonsynonymous mutations. All together, these observations suggest that directional selection is the dominant evolutionary force in TEV populations evolving in a novel host whereas either diversifying selection or random genetic drift may play a fundamental role in the natural host. To better understand these evolutionary dynamics, we developed a computer simulation model that incorporates the effects of mutation, selection, and drift. Upon parameterization with empirical data from previous studies, model predictions matched the observed patterns, thus reinforcing our idea that the empirical patterns of mutation accumulation represent adaptive evolution.
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Affiliation(s)
- José M Cuevas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain
| | - Anouk Willemsen
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain
| | - Julia Hillung
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain
| | - Mark P Zwart
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain The Santa Fe Institute, Santa Fe, NM
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10
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Zwart MP, Elena SF. Testing the independent action hypothesis of plant pathogen mode of action: a simple and powerful new approach. PHYTOPATHOLOGY 2015; 105:18-25. [PMID: 25098495 DOI: 10.1094/phyto-04-14-0111-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The independent action hypothesis is a simple model of pathogen infection that can make many useful predictions on infection kinetics and, therefore, a number of different tests of independent action have been developed. However, some of these analyses are rather sophisticated, limiting their appeal to experimentalists, and it is also unclear how well the different tests perform. Here, we developed and evaluated a simple and robust new test of independent action. Our new test is based on using a constant inoculum dose of one pathogen variant, varying the dose of a second variant, and then quantifying the infection response for the first variant. We simulated infection data in which we introduced deviations from independent action, experimental variation, or both. Simulations showed that our new procedure has many advantages over the existing tests of independent action, especially if only systemic-infection data are available. We also performed experimental tests of our new procedure using two marked Tobacco etch virus (TEV) variants. We found minor deviations from the independent action model, which were not detected by previous tests using existing methods, exemplifying the utility of this approach. We discuss the implications for TEV infection kinetics and consider how to reconcile different dose-dependent effects.
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11
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Dunham JP, Simmons HE, Holmes EC, Stephenson AG. Analysis of viral (zucchini yellow mosaic virus) genetic diversity during systemic movement through a Cucurbita pepo vine. Virus Res 2014; 191:172-179. [PMID: 25107623 PMCID: PMC4176823 DOI: 10.1016/j.virusres.2014.07.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/23/2014] [Accepted: 07/26/2014] [Indexed: 01/04/2023]
Abstract
Determining the extent and structure of intra-host genetic diversity and the magnitude and impact of population bottlenecks is central to understanding the mechanisms of viral evolution. To determine the nature of viral evolution following systemic movement through a plant, we performed deep sequencing of 23 leaves that grew sequentially along a single Cucurbita pepo vine that was infected with zucchini yellow mosaic virus (ZYMV), and on a leaf that grew in on a side branch. Strikingly, of 112 genetic (i.e. sub-consensus) variants observed in the data set as a whole, only 22 were found in multiple leaves. Similarly, only three of the 13 variants present in the inoculating population were found in the subsequent leaves on the vine. Hence, it appears that systemic movement is characterized by sequential population bottlenecks, although not sufficient to reduce the population to a single virion as multiple variants were consistently transmitted between leaves. In addition, the number of variants within a leaf increases as a function of distance from the inoculated (source) leaf, suggesting that the circulating sap may serve as a continual source of virus. Notably, multiple mutational variants were observed in the cylindrical inclusion (CI) protein (known to be involved in both cell-to-cell and systemic movement of the virus) that were present in multiple (19/24) leaf samples. These mutations resulted in a conformational change, suggesting that they might confer a selective advantage in systemic movement within the vine. Overall, these data reveal that bottlenecks occur during systemic movement, that variants circulate in the phloem sap throughout the infection process, and that important conformational changes in CI protein may arise during individual infections.
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Affiliation(s)
- J P Dunham
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90033, USA
| | - H E Simmons
- Seed Science Center, Iowa State University, Ames, IA 50011, USA
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - E C Holmes
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Marie Bashir Institute for Emerging Diseases & Biosecurity, Charles Perkins Centre, School of Biological Sciences and Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - A G Stephenson
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
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12
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Rodrigo G, Zwart MP, Elena SF. Onset of virus systemic infection in plants is determined by speed of cell-to-cell movement and number of primary infection foci. J R Soc Interface 2014; 11:20140555. [PMID: 24966241 PMCID: PMC4233706 DOI: 10.1098/rsif.2014.0555] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 06/04/2014] [Indexed: 11/12/2022] Open
Abstract
The cornerstone of today's plant virology consists of deciphering the molecular and mechanistic basis of host-pathogen interactions. Among these interactions, the onset of systemic infection is a fundamental variable in studying both within- and between-host infection dynamics, with implications in epidemiology. Here, we developed a mechanistic model using probabilistic and spatio-temporal concepts to explain dynamic signatures of virus systemic infection. The model dealt with the inherent characteristic of plant viruses to use two different and sequential stages for their within-host propagation: cell-to-cell movement from the initial infected cell and systemic spread by reaching the vascular system. We identified the speed of cell-to-cell movement and the number of primary infection foci in the inoculated leaf as the key factors governing this dynamic process. Our results allowed us to quantitatively understand the timing of the onset of systemic infection, describing this global process as a consequence of local spread of viral populations. Finally, we considered the significance of our predictions for the evolution of plant RNA viruses.
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Affiliation(s)
- Guillermo Rodrigo
- Institute of Systems and Synthetic Biology, CNRS-Université d'Évry Val d'Essonne-Genopole, Évry 91030, France Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de Valencia, Valencia 46022, Spain
| | - Mark P Zwart
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de Valencia, Valencia 46022, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de Valencia, Valencia 46022, Spain The Santa Fe Institute, Santa Fe, NM 87501, USA
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13
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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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14
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Tromas N, Zwart MP, Lafforgue G, Elena SF. Within-host spatiotemporal dynamics of plant virus infection at the cellular level. PLoS Genet 2014; 10:e1004186. [PMID: 24586207 PMCID: PMC3937225 DOI: 10.1371/journal.pgen.1004186] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 01/06/2014] [Indexed: 11/27/2022] Open
Abstract
A multicellular organism is not a monolayer of cells in a flask; it is a complex, spatially structured environment, offering both challenges and opportunities for viruses to thrive. Whereas virus infection dynamics at the host and within-cell levels have been documented, the intermediate between-cell level remains poorly understood. Here, we used flow cytometry to measure the infection status of thousands of individual cells in virus-infected plants. This approach allowed us to determine accurately the number of cells infected by two virus variants in the same host, over space and time as the virus colonizes the host. We found a low overall frequency of cellular infection (<0.3), and few cells were coinfected by both virus variants (<0.1). We then estimated the cellular contagion rate (R), the number of secondary infections per infected cell per day. R ranged from 2.43 to values not significantly different from zero, and generally decreased over time. Estimates of the cellular multiplicity of infection (MOI), the number of virions infecting a cell, were low (<1.5). Variance of virus-genotype frequencies increased strongly from leaf to cell levels, in agreement with a low MOI. Finally, there were leaf-dependent differences in the ease with which a leaf could be colonized, and the number of virions effectively colonizing a leaf. The modeling of infection patterns suggests that the aggregation of virus-infected cells plays a key role in limiting spread; matching the observation that cell-to-cell movement of plant viruses can result in patches of infection. Our results show that virus expansion at the between-cell level is restricted, probably due to the host environment and virus infection itself.
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Affiliation(s)
- Nicolas Tromas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València, Spain
| | - Mark P. Zwart
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València, Spain
| | - Guillaume Lafforgue
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València, Spain
| | - Santiago F. Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València, Spain
- The Santa Fe Institute, Santa Fe, New Mexico, United States of America
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15
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Zwart MP, Willemsen A, Daròs JA, Elena SF. Experimental evolution of pseudogenization and gene loss in a plant RNA virus. Mol Biol Evol 2014; 31:121-34. [PMID: 24109604 PMCID: PMC3879446 DOI: 10.1093/molbev/mst175] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Viruses have evolved highly streamlined genomes and a variety of mechanisms to compress them, suggesting that genome size is under strong selection. Horizontal gene transfer has, on the other hand, played an important role in virus evolution. However, evolution cannot integrate initially nonfunctional sequences into the viral genome if they are rapidly purged by selection. Here we report on the experimental evolution of pseudogenization in virus genomes using a plant RNA virus expressing a heterologous gene. When long 9-week passages were performed, the added gene was lost in all lineages, whereas viruses with large genomic deletions were fixed in only two out of ten 3-week lineages and none in 1-week lineages. Illumina next-generation sequencing revealed considerable convergent evolution in the 9- and 3-week lineages with genomic deletions. Genome size was correlated to within-host competitive fitness, although there was no correlation with virus accumulation or virulence. Within-host competitive fitness of the 3-week virus lineages without genomic deletions was higher than for the 1-week lineages. Our results show that the strength of selection for a reduced genome size and the rate of pseudogenization depend on demographic conditions. Moreover, for the 3-week passage condition, we observed increases in within-host fitness, whereas selection was not strong enough to quickly remove the nonfunctional heterologous gene. These results suggest a demographically determined "sweet spot" might exist, where heterologous insertions are not immediately lost while evolution can act to integrate them into the viral genome.
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Affiliation(s)
- Mark P. Zwart
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València, Spain
| | - Anouk Willemsen
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València, Spain
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València, Spain
| | - Santiago F. Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València, Spain
- The Santa Fe Institute
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16
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Hillung J, Elena SF, Cuevas JM. Intra-specific variability and biological relevance of P3N-PIPO protein length in potyviruses. BMC Evol Biol 2013; 13:249. [PMID: 24225158 PMCID: PMC3840659 DOI: 10.1186/1471-2148-13-249] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 11/06/2013] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Pipo was recently described as a new ORF encoded within the genome of the Potyviridae family members (PNAS 105:5897-5902, 2008). It is embedded within the P3 cistron and is translated in the +2 reading frame relative to the potyviral long ORF as the P3N-PIPO fusion protein. In this work, we first collected pipo nucleotide sequences available for different isolates of 48 Potyvirus species. Second, to determine the biological implications of variation in pipo length, we measured infectivity, viral accumulation, cell-to-cell and systemic movements for two Turnip mosaic virus (TuMV) variants with pipo alleles of different length in three different susceptible host species, and tested for differences between the two variants. RESULTS In addition to inter-specific variation, there was high variation in the length of the PIPO protein among isolates within species (ranging from 1 to 89 amino acids). Furthermore, selection analyses on the P3 cistron did not account for the existence of stop codons in the pipo ORF, but showed that positive selection was significant in the overlapping region for Potato virus Y (PVY) and TuMV. In some cases, variability in length was associated with host species, geographic provenance and/or other strain features. We found significant empirical differences among the phenotypes associated with TuMV pipo alleles, though the magnitude and sign of the effects were host-dependent. CONCLUSIONS The combination of computational molecular evolution analyses and experiments stemming from these analyses provide clues about the selective pressures acting upon the different-length pipo alleles and show that variation in length may be maintained by host-driven selection.
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Affiliation(s)
- Julia Hillung
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València 46022, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València 46022, Spain
- The Santa Fe Institute, 87501, Santa Fe, NM, USA
| | - José M Cuevas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València 46022, Spain
- Present address: Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València 46980, Spain
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17
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Sánchez-Navarro JA, Zwart MP, Elena SF. Effects of the number of genome segments on primary and systemic infections with a multipartite plant RNA virus. J Virol 2013; 87:10805-15. [PMID: 23903837 PMCID: PMC3807391 DOI: 10.1128/jvi.01402-13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 07/24/2013] [Indexed: 01/06/2023] Open
Abstract
Multipartite plant viruses were discovered because of discrepancies between the observed dose response and predictions of the independent-action hypothesis (IAH) model. Theory suggests that the number of genome segments predicts the shape of the dose-response curve, but a rigorous test of this hypothesis has not been reported. Here, Alfalfa mosaic virus (AMV), a tripartite Alfamovirus, and transgenic Nicotianatabacum plants expressing no (wild type), one (P2), or two (P12) viral genome segments were used to test whether the number of genome segments necessary for infection predicts the dose response. The dose-response curve of wild-type plants was steep and congruent with the predicted kinetics of a multipartite virus, confirming previous results. Moreover, for P12 plants, the data support the IAH model, showing that the expression of virus genome segments by the host plant can modulate the infection kinetics of a tripartite virus to those of a monopartite virus. However, the different types of virus particles occurred at different frequencies, with a ratio of 116:45:1 (RNA1 to RNA2 to RNA3), which will affect infection kinetics and required analysis with a more comprehensive infection model. This analysis showed that each type of virus particle has a different probability of invading the host plant, at both the primary- and systemic-infection levels. While the number of genome segments affects the dose response, taking into consideration differences in the infection kinetics of the three types of AMV particles results in a better understanding of the infection process.
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Affiliation(s)
- Jesús A. Sánchez-Navarro
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València, Spain
| | - Mark P. Zwart
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València, Spain
| | - Santiago F. Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València, Spain
- The Santa Fe Institute, Santa Fe, New Mexico, USA
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18
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Majer E, Daròs JA, Zwart MP. Stability and fitness impact of the visually discernible Rosea1 marker in the Tobacco etch virus genome. Viruses 2013; 5:2153-68. [PMID: 24022073 PMCID: PMC3798895 DOI: 10.3390/v5092153] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 08/26/2013] [Accepted: 08/29/2013] [Indexed: 11/24/2022] Open
Abstract
Antirrhinum majus Rosea1 (Ros1) is an MYB-related transcription factor that induces anthocyanin biosynthesis in plant tissues, and has been shown to be suitable for visual tracking of virus infection in plants. However, activation of anthocyanin biosynthesis has far reaching effects on plant physiology and could consequently have negative effects on viral replication. Therefore, viruses carrying the Ros1 marker might have a low fitness and consequently rapidly lose the marker. To compare the stability of the Ros1 marker, we generated Tobacco etch virus (TEV) based constructs containing either Ros1 or the enhanced green fluorescent protein (eGFP) between the NIb and CP cistrons (TEV-Ros1 and TEV-eGFP, respectively). We measured the within-host competitive fitness of both viruses by direct competitions with a common competitor during infection of Nicotiana tabacum. The fitness of TEV-Ros1 was significantly lower than that of TEV-eGFP, and both recombinant viruses had a significantly lower fitness than the wild-type virus. Nevertheless, after seven weeks of infection in N. tabacum, similar levels of marker gene instability where found for both viruses. Despite lower fitness of the marked virus, Ros1 is therefore a viable alternative marker for tracking viral infection in plants.
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Affiliation(s)
| | | | - Mark P. Zwart
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Ingeniero Fausto Elio s/n, 46022 València, Spain; E-Mails: (E.M.); (J.-A.D.)
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19
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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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20
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Lafforgue G, Tromas N, Elena SF, Zwart MP. Dynamics of the establishment of systemic Potyvirus infection: independent yet cumulative action of primary infection sites. J Virol 2012; 86:12912-22. [PMID: 22993154 PMCID: PMC3497618 DOI: 10.1128/jvi.02207-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 09/11/2012] [Indexed: 11/20/2022] Open
Abstract
In the clinic, farm, or field, for many viruses there is a high prevalence of mixed-genotype infections, indicating that multiple virions have initiated infection and that there can be multiple sites of primary infection within the same host. The dynamic process by which multiple primary infection sites interact with each other and the host is poorly understood, undoubtedly due to its high complexity. In this study, we attempted to unravel the basic interactions underlying this process using a plant RNA virus, as removing the inoculated leaf can instantly and rigorously eliminate all primary infection sites. Effective population size in the inoculated leaf and time of removal of the inoculated leaf were varied in experiments, and it was found that both factors positively influenced if the plant became systemically infected and what proportion of cells in the systemic tissue were infected, as measured by flow cytometry. Fitting of probabilistic models of infection to our data demonstrated that a null model in which the action of each focus is independent of the presence of other foci was better supported than a dependent-action model. The cumulative effect of independently acting foci therefore determined when plants became infected and how many individual cells were infected. There was no evidence for interference between primary infection sites, which is surprising given the planar structure of leaves. By showing that a simple null model is supported, we experimentally confirmed--to our knowledge for the first time--the minimal components that dictate interactions of a conspecific virus population establishing systemic infection.
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Affiliation(s)
- Guillaume Lafforgue
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València, Spain
| | - Nicolas Tromas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València, Spain
| | - Santiago F. Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València, Spain
- The Santa Fe Institute, Santa Fe, New Mexico, USA
| | - Mark P. Zwart
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València, Spain
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