1
|
Mahillon M, Brodard J, Dubuis N, Gugerli P, Blouin AG, Schumpp O. Mixed infection of ITPase-encoding potyvirid and secovirid in Mercurialis perennis: evidences for a convergent euphorbia-specific viral counterstrike. Virol J 2024; 21:6. [PMID: 38178191 PMCID: PMC10768138 DOI: 10.1186/s12985-023-02257-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/04/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND In cellular organisms, inosine triphosphate pyrophosphatases (ITPases) prevent the incorporation of mutagenic deaminated purines into nucleic acids. These enzymes have also been detected in the genomes of several plant RNA viruses infecting two euphorbia species. In particular, two ipomoviruses produce replicase-associated ITPases to cope with high concentration of non-canonical nucleotides found in cassava tissues. METHOD Using high-throughput RNA sequencing on the wild euphorbia species Mercurialis perennis, two new members of the families Potyviridae and Secoviridae were identified. Both viruses encode for a putative ITPase, and were found in mixed infection with a new partitivirid. Following biological and genomic characterization of these viruses, the origin and function of the phytoviral ITPases were investigated. RESULTS While the potyvirid was shown to be pathogenic, the secovirid and partitivirid could not be transmitted. The secovirid was found belonging to a proposed new Comovirinae genus tentatively named "Mercomovirus", which also accommodates other viruses identified through transcriptome mining, and for which an asymptomatic pollen-associated lifestyle is suspected. Homology and phylogenetic analyses inferred that the ITPases encoded by the potyvirid and secovirid were likely acquired through independent horizontal gene transfer events, forming lineages distinct from the enzymes found in cassava ipomoviruses. Possible origins from cellular organisms are discussed for these proteins. In parallel, the endogenous ITPase of M. perennis was predicted to encode for a C-terminal nuclear localization signal, which appears to be conserved among the ITPases of euphorbias but absent in other plant families. This subcellular localization is in line with the idea that nucleic acids remain protected in the nucleus, while deaminated nucleotides accumulate in the cytoplasm where they act as antiviral molecules. CONCLUSION Three new RNA viruses infecting M. perennis are described, two of which encoding for ITPases. These enzymes have distinct origins, and are likely required by viruses to circumvent high level of cytoplasmic non-canonical nucleotides. This putative plant defense mechanism has emerged early in the evolution of euphorbias, and seems to specifically target certain groups of RNA viruses infecting perennial hosts.
Collapse
Affiliation(s)
- Mathieu Mahillon
- Research Group Virology, Bacteriology and Phytoplasmology, Plant Protection Department, Agroscope, Nyon, Switzerland
| | - Justine Brodard
- Research Group Virology, Bacteriology and Phytoplasmology, Plant Protection Department, Agroscope, Nyon, Switzerland
| | - Nathalie Dubuis
- Research Group Virology, Bacteriology and Phytoplasmology, Plant Protection Department, Agroscope, Nyon, Switzerland
| | - Paul Gugerli
- Research Group Virology, Bacteriology and Phytoplasmology, Plant Protection Department, Agroscope, Nyon, Switzerland
| | - Arnaud G Blouin
- Research Group Virology, Bacteriology and Phytoplasmology, Plant Protection Department, Agroscope, Nyon, Switzerland
| | - Olivier Schumpp
- Research Group Virology, Bacteriology and Phytoplasmology, Plant Protection Department, Agroscope, Nyon, Switzerland.
| |
Collapse
|
2
|
Kormelink R, Verchot J, Tao X, Desbiez C. The Bunyavirales: The Plant-Infecting Counterparts. Viruses 2021; 13:842. [PMID: 34066457 PMCID: PMC8148189 DOI: 10.3390/v13050842] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 12/18/2022] Open
Abstract
Negative-strand (-) RNA viruses (NSVs) comprise a large and diverse group of viruses that are generally divided in those with non-segmented and those with segmented genomes. Whereas most NSVs infect animals and humans, the smaller group of the plant-infecting counterparts is expanding, with many causing devastating diseases worldwide, affecting a large number of major bulk and high-value food crops. In 2018, the taxonomy of segmented NSVs faced a major reorganization with the establishment of the order Bunyavirales. This article overviews the major plant viruses that are part of the order, i.e., orthospoviruses (Tospoviridae), tenuiviruses (Phenuiviridae), and emaraviruses (Fimoviridae), and provides updates on the more recent ongoing research. Features shared with the animal-infecting counterparts are mentioned, however, special attention is given to their adaptation to plant hosts and vector transmission, including intra/intercellular trafficking and viral counter defense to antiviral RNAi.
Collapse
Affiliation(s)
- Richard Kormelink
- Laboratory of Virology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jeanmarie Verchot
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA;
| | - Xiaorong Tao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China;
| | | |
Collapse
|
3
|
Roques L, Desbiez C, Berthier K, Soubeyrand S, Walker E, Klein EK, Garnier J, Moury B, Papaïx J. Emerging strains of watermelon mosaic virus in Southeastern France: model-based estimation of the dates and places of introduction. Sci Rep 2021; 11:7058. [PMID: 33782446 PMCID: PMC8007712 DOI: 10.1038/s41598-021-86314-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 02/16/2021] [Indexed: 11/09/2022] Open
Abstract
Where and when alien organisms are successfully introduced are central questions to elucidate biotic and abiotic conditions favorable to the introduction, establishment and spread of invasive species. We propose a modelling framework to analyze multiple introductions by several invasive genotypes or genetic variants, in competition with a resident population, when observations provide knowledge on the relative proportions of each variant at some dates and places. This framework is based on a mechanistic-statistical model coupling a reaction–diffusion model with a probabilistic observation model. We apply it to a spatio-temporal dataset reporting the relative proportions of five genetic variants of watermelon mosaic virus (WMV, genus Potyvirus, family Potyviridae) in infections of commercial cucurbit fields. Despite the parsimonious nature of the model, it succeeds in fitting the data well and provides an estimation of the dates and places of successful introduction of each emerging variant as well as a reconstruction of the dynamics of each variant since its introduction.
Collapse
Affiliation(s)
- L Roques
- INRAE, BioSP, 84914, Avignon, France.
| | - C Desbiez
- INRAE, Pathologie Végétale, 84140, Montfavet, France
| | - K Berthier
- INRAE, Pathologie Végétale, 84140, Montfavet, France
| | | | - E Walker
- INRAE, BioSP, 84914, Avignon, France
| | - E K Klein
- INRAE, BioSP, 84914, Avignon, France
| | - J Garnier
- Laboratoire de Mathématiques (LAMA), CNRS and Université de Savoie-Mont Blanc, Chambéry, France
| | - B Moury
- INRAE, Pathologie Végétale, 84140, Montfavet, France
| | - J Papaïx
- INRAE, BioSP, 84914, Avignon, France
| |
Collapse
|
4
|
Petrzik K. Evolutionary forces at work in partitiviruses. Virus Genes 2019; 55:563-573. [PMID: 31230256 DOI: 10.1007/s11262-019-01680-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023]
Abstract
The family Partitiviridae consists of dsRNA viruses with genome separated into two segments and encoding replicase and capsid protein only. We examined the nucleotide diversity expressed as the ratio dN/dS of nonsynonymous and synonymous substitutions, which has been calculated for 12 representative viruses of all five genera of partitiviruses. We can state that strong purifying selection works on both the RdRp and CP genes and propose that putative positive selection occurs also on the RdRp genes in two viruses. Among the 95 evaluated viruses, wherein both segments had been sequenced, 8 viruses in betapartitiviruses and 9 in alphapartitiviruses were identified as reassortment candidates because they differ extremely in their CP identity even as they are related in terms of RdRp. Furthermore, there are indications that reassortants are present among isolates of different viruses.
Collapse
Affiliation(s)
- Karel Petrzik
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice, Czech Republic.
| |
Collapse
|
5
|
Hameed A, Shan-E-Ali Zaidi S, Sattar MN, Iqbal Z, Tahir MN. CRISPR technology to combat plant RNA viruses: A theoretical model for Potato virus Y (PVY) resistance. Microb Pathog 2019; 133:103551. [PMID: 31125685 DOI: 10.1016/j.micpath.2019.103551] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 05/17/2019] [Indexed: 12/26/2022]
Abstract
RNA viruses are the most diverse phytopathogens which cause severe epidemics in important agricultural crops and threaten the global food security. Being obligatory intracellular pathogens, these viruses have developed fine-tuned evading mechanisms and are non-responsive to most of the prophylactic treatments. Additionally, their sprint ability to overcome host defense demands a broad-spectrum and durable mechanism of resistance. In context of CRISPR-Cas discoveries, some variants of Cas effectors have been characterized as programmable RNA-guided RNases in the microbial genomes and could be reprogramed in mammalian and plant cells with guided RNase activity. Recently, the RNA variants of CRISPR-Cas systems have been successfully employed in plants to engineer resistance against RNA viruses. Some variants of CRISPR-Cas9 have been tamed either for directly targeting plant RNA viruses' genome or through targeting the host genes/factors assisting in viral proliferation. The new frontiers in CRISPR-Cas discoveries, and more importantly shifting towards RNA targeting will pyramid the opportunities in plant virus research. The current review highlights the probable implications of CRISPR-Cas system to confer the pathogen-derived or host-mediated resistance against phytopathogenic RNA viruses. Furthermore, a multiplexed CRISPR-Cas13a methodology is proposed here to combat Potato virus Y (PVY); a globally diverse phytopathogen infecting multiple crops.
Collapse
Affiliation(s)
- Amir Hameed
- Akhuwat Faisalabad Institute of Research Science and Technology, Faisalabad, Pakistan; Department of Bioinformatics & Biotechnology, Government College University, Allama Iqbal Road, Faisalabad, Pakistan.
| | | | - Muhammad Naeem Sattar
- Department of Biotechnology, College of Agriculture and Food Science, King Faisal University, Box 400, Al-Ahsa, 3192, Saudi Arabia
| | - Zafar Iqbal
- Department of Plant Pathology, University of Florida, Gainesville, 32611, FL, USA
| | | |
Collapse
|
6
|
Chisholm PJ, Busch JW, Crowder DW. Effects of life history and ecology on virus evolutionary potential. Virus Res 2019; 265:1-9. [PMID: 30831177 DOI: 10.1016/j.virusres.2019.02.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 11/28/2022]
Abstract
The life history traits of viruses pose many consequences for viral population structure. In turn, population structure may influence the evolutionary trajectory of a virus. Here we review factors that affect the evolutionary potential of viruses, including rates of mutation and recombination, bottlenecks, selection pressure, and ecological factors such as the requirement for hosts and vectors. Mutation, while supplying a pool of raw genetic material, also results in the generation of numerous unfit mutants. The infection of multiple host species may expand a virus' ecological niche, although it may come at a cost to genetic diversity. Vector-borne viruses often experience a diminished frequency of positive selection and exhibit little diversity, and resistance against vector-borne viruses may thus be more durable than against non-vectored viruses. Evidence indicates that adaptation to a vector is more evolutionarily difficult than adaptation to a host. Overall, a better understanding of how various factors influence viral dynamics in both plant and animal pathosystems will lead to more effective anti-viral treatments and countermeasures.
Collapse
Affiliation(s)
- Paul J Chisholm
- Department of Entomology, Washington State University, 166 FSHN Building, Pullman, WA, 99164, USA.
| | - Jeremiah W Busch
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA, 99164, USA.
| | - David W Crowder
- Department of Entomology, Washington State University, 166 FSHN Building, Pullman, WA, 99164, USA.
| |
Collapse
|
7
|
Lucía-Sanz A, Aguirre J, Manrubia S. Theoretical approaches to disclosing the emergence and adaptive advantages of multipartite viruses. Curr Opin Virol 2018; 33:89-95. [PMID: 30121469 DOI: 10.1016/j.coviro.2018.07.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/19/2018] [Accepted: 07/31/2018] [Indexed: 01/02/2023]
Abstract
Multipartite viruses have a segmented genome encapsidated in different viral particles that, in principle, propagate independently. Current empirical knowledge on the molecular, ecological and evolutionary features underlying the very existence of multipartitism is fragmented and puzzling. Although it is generally assumed that multipartitism is viable only when propagation occurs at high multiplicity of infection, evidence indicates that severe population bottlenecks are common. Mathematical models aimed at describing the dynamics of multipartite viruses typically assign an advantage to the multipartite form to compensate for the cost of high multiplicity of infection. Since progress in the theoretical understanding of the evolutionary ecology of multipartitism is strongly conditioned by empirical advances, both aspects are jointly revised in this contribution.
Collapse
Affiliation(s)
- Adriana Lucía-Sanz
- Spanish National Centre for Biotechnology (CSIC), Madrid, Spain; Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
| | - Jacobo Aguirre
- Spanish National Centre for Biotechnology (CSIC), Madrid, Spain; Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
| | - Susanna Manrubia
- Spanish National Centre for Biotechnology (CSIC), Madrid, Spain; Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain.
| |
Collapse
|
8
|
Jeger MJ, Madden LV, van den Bosch F. Plant Virus Epidemiology: Applications and Prospects for Mathematical Modeling and Analysis to Improve Understanding and Disease Control. PLANT DISEASE 2018; 102:837-854. [PMID: 30673389 DOI: 10.1094/pdis-04-17-0612-fe] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In recent years, mathematical modeling has increasingly been used to complement experimental and observational studies of biological phenomena across different levels of organization. In this article, we consider the contribution of mathematical models developed using a wide range of techniques and uses to the study of plant virus disease epidemics. Our emphasis is on the extent to which models have contributed to answering biological questions and indeed raised questions related to the epidemiology and ecology of plant viruses and the diseases caused. In some cases, models have led to direct applications in disease control, but arguably their impact is better judged through their influence in guiding research direction and improving understanding across the characteristic spatiotemporal scales of plant virus epidemics. We restrict this article to plant virus diseases for reasons of length and to maintain focus even though we recognize that modeling has played a major and perhaps greater part in the epidemiology of other plant pathogen taxa, including vector-borne bacteria and phytoplasmas.
Collapse
Affiliation(s)
- M J Jeger
- Centre for Environmental Policy, Imperial College London, Silwood Park, Ascot SL5 7PY, United Kingdom
| | - L V Madden
- Department of Plant Pathology, Ohio State University, Wooster, OH 44691
| | - F van den Bosch
- Computational and Systems Biology, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom
| |
Collapse
|
9
|
Lucía-Sanz A, Manrubia S. Multipartite viruses: adaptive trick or evolutionary treat? NPJ Syst Biol Appl 2017; 3:34. [PMID: 29263796 PMCID: PMC5680193 DOI: 10.1038/s41540-017-0035-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 09/25/2017] [Accepted: 10/04/2017] [Indexed: 12/18/2022] Open
Abstract
Multipartitism counts amongst the weirdest lifestyles found in the virosphere. Multipartite viruses have genomes segmented in pieces enclosed in different capsids that are independently transmitted. Since all segments have to meet in the host for complementation and completion of the viral cycle, multipartite viruses are bound to fight the loss of genomic information. While this is an obvious disadvantage of this strategy, no consensus on its actual advantages has been reached. In this review we present an exhaustive summary of all multipartite viruses described to date. Based on evidence, we discuss possible mechanistic and evolutionary origins of different groups, as well as their mutual relationships. We argue that the ubiquitous interactions of viruses with other unrelated viruses and with subviral elements might be regarded as a plausible first step towards multipartitism. In agreement with the view of the Virosphere as a deeply entangled network of gene sharing, we contend that the power of multipartitism relies on its dynamical and opportunistic nature, because it enables immediate adaptive responses to environmental changes. As such, perhaps the reasons for its success should be shought in multipartitism itself as an adaptive mechanism, to which its evolutionarily short-lived products (that is, the extant ensemble of multipartite viral species) are subordinated. We close by discussing how our understanding of multipartitism would improve by using concepts and tools from systems biology. The faithful transmission of the genome of an organism is a fundamental step to preserve information essential for survivability. However, multipartite viruses thrive with segmented genomes that propagate in independent viral particles. Though this adaptive strategy appears as counterintuitive and suboptimal, multipartitism is common in the viral world and has very likely arisen several times. Here we review the distribution and abundance of multipartite viruses and discuss possible evolutionary pathways for their emergence. Though no clear advantage of multipartitism has been identified, we suggest that the high prevalence of this strategy relies on its dynamic and opportunistic nature, and that it can only be understood in an ecological context. A systems biology perspective could help understanding some of the open questions regarding this weird lifestyle, while multipartitism could in turn inspire design principles based on the simultaneous exploration of an exploding number of transient collaborative associations.
Collapse
Affiliation(s)
- Adriana Lucía-Sanz
- Grupo Interdisciplinar de Sistemas Complejos (GISC), National Centre for Biotechnology (CSIC), c/Darwin 3, 28049 Madrid, Spain
| | - Susanna Manrubia
- Grupo Interdisciplinar de Sistemas Complejos (GISC), National Centre for Biotechnology (CSIC), c/Darwin 3, 28049 Madrid, Spain
| |
Collapse
|
10
|
Moury B, Fabre F, Hébrard E, Froissart R. Determinants of host species range in plant viruses. J Gen Virol 2017; 98:862-873. [PMID: 28475036 DOI: 10.1099/jgv.0.000742] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Prediction of pathogen emergence is an important field of research, both in human health and in agronomy. Most studies of pathogen emergence have focused on the ecological or anthropic factors involved rather than on the role of intrinsic pathogen properties. The capacity of pathogens to infect a large set of host species, i.e. to possess a large host range breadth (HRB), is tightly linked to their emergence propensity. Using an extensive plant virus database, we found that four traits related to virus genome or transmission properties were strongly and robustly linked to virus HRB. Broader host ranges were observed for viruses with single-stranded genomes, those with three genome segments and nematode-transmitted viruses. Also, two contrasted groups of seed-transmitted viruses were evidenced. Those with a single-stranded genome had larger HRB than non-seed-transmitted viruses, whereas those with a double-stranded genome (almost exclusively RNA) had an extremely small HRB. From the plant side, the family taxonomic rank appeared as a critical threshold for virus host range, with a highly significant increase in barriers to infection between plant families. Accordingly, the plant-virus infectivity matrix shows a dual structure pattern: a modular pattern mainly due to viruses specialized to infect plants of a given family and a nested pattern due to generalist viruses. These results contribute to a better prediction of virus host jumps and emergence risks.
Collapse
Affiliation(s)
- Benoît Moury
- Pathologie Végétale, INRA, 84140 Montfavet, France
| | - Frédéric Fabre
- UMR 1065, Santé et Agroécologie du Vignoble, INRA, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, F-33883 Villenave d'Ornon, France
| | - Eugénie Hébrard
- UMR186, IRD-Cirad-UM, Laboratory 'Interactions Plantes Microorganismes Environnement', Montpellier, France
| | - Rémy Froissart
- UMR5290, CNRS-IRD-UM1-UM2, Laboratory 'Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle', Montpellier, France.,UMR385, INRA-Cirad-SupAgro, Laboratory 'Biologie des Interactions Plantes-Parasites', Campus International de Baillarguet, F-34398 Montpellier, France
| |
Collapse
|
11
|
Obbard DJ, Dudas G. The genetics of host-virus coevolution in invertebrates. Curr Opin Virol 2014; 8:73-8. [PMID: 25063907 PMCID: PMC4199324 DOI: 10.1016/j.coviro.2014.07.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 06/30/2014] [Accepted: 07/03/2014] [Indexed: 11/19/2022]
Abstract
Although viral infection and antiviral defence are ubiquitous, genetic data are currently unavailable from the vast majority of animal phyla-potentially biasing our overall perspective of the coevolutionary process. Rapid adaptive evolution is seen in some insect antiviral genes, consistent with invertebrate-virus 'arms-race' coevolution, but equivalent signatures of selection are hard to detect in viruses. We find that, despite the large differences in vertebrate, invertebrate, and plant immune responses, comparison of viral evolution fails to identify any difference among these hosts in the impact of positive selection. The best evidence for invertebrate-virus coevolution is currently provided by large-effect polymorphisms for host resistance and/or viral evasion, as these often appear to have arisen and spread recently, and can be favoured by virus-mediated selection.
Collapse
Affiliation(s)
- Darren J Obbard
- Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, Edinburgh, UK; Centre for Infection Immunity and Evolution, University of Edinburgh, Kings Buildings, Edinburgh, UK.
| | - Gytis Dudas
- Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, Edinburgh, UK
| |
Collapse
|
12
|
de Oliveira CF, Long EY, Finke DL. A negative effect of a pathogen on its vector? A plant pathogen increases the vulnerability of its vector to attack by natural enemies. Oecologia 2013; 174:1169-77. [DOI: 10.1007/s00442-013-2854-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 11/27/2013] [Indexed: 11/25/2022]
|
13
|
Medina-Hernández D, Rivera-Bustamante RF, Tenllado F, Holguín-Peña RJ. Effects and effectiveness of two RNAi constructs for resistance to Pepper golden mosaic virus in Nicotiana benthamiana plants. Viruses 2013; 5:2931-45. [PMID: 24287597 PMCID: PMC3967154 DOI: 10.3390/v5122931] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 11/14/2013] [Accepted: 11/20/2013] [Indexed: 01/11/2023] Open
Abstract
ToChLPV and PepGMV are Begomoviruses that have adapted to a wide host range and are able to cause major diseases in agronomic crops. We analyzed the efficacy of induced resistance to PepGMV in Nicotiana benthamiana plants with two constructs: one construct with homologous sequences derived from PepGMV, and the other construct with heterologous sequences derived from ToChLPV. Plants protected with the heterologous construct showed an efficacy to decrease the severity of symptoms of 45%, while plants protected with the homologous construct showed an efficacy of 80%. Plants protected with the heterologous construct showed a reduction of incidence of 42.86%, while the reduction of incidence in plants protected with the homologous construct was 57.15%. The efficacy to decrease viral load was 95.6% in plants protected with the heterologous construct, and 99.56% in plants protected with the homologous construct. We found, in both constructs, up-regulated key components of the RNAi pathway. This demonstrates that the efficacy of the constructs was due to the activation of the gene silencing mechanism, and is reflected in the decrease of viral genome copies, as well as in recovery phenotype. We present evidence that both constructs are functional and can efficiently induce transient resistance against PepGMV infections. This observation guarantees a further exploration as a strategy to control complex Begomovirus diseases in the field.
Collapse
Affiliation(s)
- Diana Medina-Hernández
- Laboratorio de Fitopatología, Centro de Investigaciones Biológicas del Noroeste, Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita, La Paz, Baja California Sur, 23096, Mexico; E-Mails: (R.J.H.P.); (D.M.H.)
| | - Rafael Francisco Rivera-Bustamante
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Km. 9.6 Libramiento Norte, Irapuato, Guanajuato, 36821, Mexico; E-Mail: (R.F.R.B.)
| | - Francisco Tenllado
- Departamento de Biología Medioambiental, Centro de Investigaciones Biológicas, Ramiro de Maeztu 9, Madrid, 28040, Spain; E-Mail: (F.T.)
| | - Ramón Jaime Holguín-Peña
- Laboratorio de Fitopatología, Centro de Investigaciones Biológicas del Noroeste, Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita, La Paz, Baja California Sur, 23096, Mexico; E-Mails: (R.J.H.P.); (D.M.H.)
| |
Collapse
|
14
|
Rozák J, Predajňa L, Gálová Z, Glasa M. Detection and characterisation of Plum pox virus (PPV) isolates from Eastern Slovakia revealed the presence of three main viral strains. POTRAVINARSTVO 2013. [DOI: 10.5219/315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plum pox virus (PPV), the agent responsible for Sharka disease, is the most important viral pathogen of stone fruit trees world-wide, having an endemic status in Slovakia. To increase knowledge of PPV diversity in Slovakia, a set of 11 isolates, originated from the eastern part of the country, was characterised. The isolates were chip-budded from their original Prunus hosts to the susceptible GF305 indicators, exhibiting the symptoms of variable severity. A genomic region encompassing the partial NIb and the hypervariable 5´terminal region of the CP gene was amplified from all 11 isolates in RT-PCR and directly sequenced. The phylogenetic analysis revealed the grouping of the 11 Slovak isolates into 3 distinct clusters, representing the PPV-M (2 isolates), D (7 isolates) and Rec strains (2 isolates). The strain affiliation of isolates was further confirmed by strain-specific RT-PCR, using which the presence of additional mixed infection by minor PPV variants was detected in 2 samples. The results further contribute to the understanding of PPV diversity in Slovakia and confirm the specificity and sensitivity of molecular approaches used for the virus strain determination.
Collapse
|
15
|
Sun BJ, Sun LY, Tugume AK, Adams MJ, Yang J, Xie LH, Chen JP. Selection pressure and founder effects constrain genetic variation in differentiated populations of soilborne bymovirus Wheat yellow mosaic virus (Potyviridae) in China. PHYTOPATHOLOGY 2013; 103:949-59. [PMID: 23550972 DOI: 10.1094/phyto-01-13-0013-r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
To study the population genetic structure and forces driving the evolution of Wheat yellow mosaic virus (WYMV), the nucleotide sequences encoding the coat protein (CP) (297 sequences) or the genome-linked virion protein (VPg) (87 sequences) were determined from wheat plants growing at 11 different locations distributed in five provinces in China. There were close phylogenetic relationships between all sequences but clustering on the phylogenetic trees was congruent with their provenance, suggesting an origin-dependent population genetic structure. There were low levels of genetic diversity, ranging from 0.00035 ± 0.00019 to 0.01536 ± 0.00043 (CP), and 0.00086 ± 0.00039 to 0.00573 ± 0.00111 (VPg), indicating genetic stability or recent emergence of WYMV in China. The results may suggest that founder effects play a role in shaping the genetic structure of WYMV. Between-population diversity was consistently higher than within-population diversity, suggesting limited gene flow between subpopulations (average FST 0.6241 for the CP and 0.7981 for the VPg). Consistent amino acid substitutions correlated with the provenance of the sequences were observed at nine positions in the CP (but none in the VPg), indicating an advanced stage in population structuring. Strong negative (purifying) selection was implicated on both the CP and VPg but positive selection on a few codons in the CP, indicating an ongoing molecular adaptation.
Collapse
Affiliation(s)
- B-J Sun
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, MoA Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | | | | | | | | | | | | |
Collapse
|
16
|
Grimová L, Winkowska L, Ryšánek P, Svoboda P, Petrzik K. Reflects the coat protein variability of apple mosaic virus host preference? Virus Genes 2013; 47:119-25. [PMID: 23740269 DOI: 10.1007/s11262-013-0925-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 05/24/2013] [Indexed: 11/27/2022]
Abstract
Apple mosaic virus (ApMV) is a widespread ssRNA virus which infects diverse species of Rosales. The phylogenetic analysis of complete capsid protein gene of the largest set of ApMV isolates discriminated two main clusters of isolates: one cluster correlates with Maloideae hosts and Trebouxia lichen algae hosts; a second with hop, Prunus, and other woody tree hosts. No correlation was found between clusters and geographic origin of virus isolates, and positive selection hypothesis in distinct hosts was not confirmed: in all virus populations, purifying selection had occurred. GGT→AAT substitution resulted in Gly→Asn change inside the zinc-finger motif in the capsid protein was revealed specific for discrimination of the clusters and we hypothesise that could influence the host preference.
Collapse
Affiliation(s)
- L Grimová
- Department of Crop Protection, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 21, Prague 6, Czech Republic
| | | | | | | | | |
Collapse
|
17
|
Song D, Cho WK, Park SH, Jo Y, Kim KH. Evolution of and horizontal gene transfer in the Endornavirus genus. PLoS One 2013; 8:e64270. [PMID: 23667703 PMCID: PMC3647011 DOI: 10.1371/journal.pone.0064270] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 04/10/2013] [Indexed: 12/20/2022] Open
Abstract
The transfer of genetic information between unrelated species is referred to as horizontal gene transfer. Previous studies have demonstrated that both retroviral and non-retroviral sequences have been integrated into eukaryotic genomes. Recently, we identified many non-retroviral sequences in plant genomes. In this study, we investigated the evolutionary origin and gene transfer of domains present in endornaviruses which are double-stranded RNA viruses. Using the available sequences for endornaviruses, we found that Bell pepper endornavirus-like sequences homologous to the glycosyltransferase 28 domain are present in plants, fungi, and bacteria. The phylogenetic analysis revealed the glycosyltransferase 28 domain of Bell pepper endornavirus may have originated from bacteria. In addition, two domains of Oryza sativa endornavirus, a glycosyltransferase sugar-binding domain and a capsular polysaccharide synthesis protein, also exhibited high similarity to those of bacteria. We found evidence that at least four independent horizontal gene transfer events for the glycosyltransferase 28 domain have occurred among plants, fungi, and bacteria. The glycosyltransferase sugar-binding domains of two proteobacteria may have been horizontally transferred to the genome of Thalassiosira pseudonana. Our study is the first to show that three glycome-related viral genes in the genus Endornavirus have been acquired from marine bacteria by horizontal gene transfer.
Collapse
Affiliation(s)
- Dami Song
- Department of Agricultural Biotechnology, Plant Genomics and Breeding Institute, Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Won Kyong Cho
- Department of Agricultural Biotechnology, Plant Genomics and Breeding Institute, Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Sang-Ho Park
- Department of Agricultural Biotechnology, Plant Genomics and Breeding Institute, Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Yeonhwa Jo
- Department of Agricultural Biotechnology, Plant Genomics and Breeding Institute, Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Kook-Hyung Kim
- Department of Agricultural Biotechnology, Plant Genomics and Breeding Institute, Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| |
Collapse
|
18
|
Predajňa L, Šubr Z, Candresse T, Glasa M. Evaluation of the genetic diversity of Plum pox virus in a single plum tree. Virus Res 2012; 167:112-7. [PMID: 22521553 DOI: 10.1016/j.virusres.2012.04.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 04/02/2012] [Accepted: 04/03/2012] [Indexed: 11/26/2022]
Abstract
Genetic diversity of Plum pox virus (PPV) and its distribution within a single perennial woody host (plum, Prunus domestica) has been evaluated. A plum tree was triply infected by chip-budding with PPV-M, PPV-D and PPV-Rec isolates in 2003 and left to develop untreated under open field conditions. In September 2010 leaf and fruit samples were collected from different parts of the tree canopy. A 745-bp NIb-CP fragment of PPV genome, containing the hypervariable region encoding the CP N-terminal end was amplified by RT-PCR from each sample and directly sequenced to determine the dominant sequence. In parallel, the PCR products were cloned and a total of 105 individual clones were sequenced. Sequence analysis revealed that after 7 years of infection, only PPV-M was still detectable in the tree and that the two other isolates (PPV-Rec and PPV-D) had been displaced. Despite the fact that the analysis targeted a relatively short portion of the genome, a substantial amount of intra-isolate variability was observed for PPV-M. A total of 51 different haplotypes could be identified from the 105 individual sequences, two of which were largely dominant. However, no clear-cut structuration of the viral population by the tree architecture could be highlighted although the results obtained suggest the possibility of intra-leaf/fruit differentiation of the viral population. Comparison of the consensus sequence with the original source isolate showed no difference, suggesting within-plant stability of this original isolate under open field conditions.
Collapse
Affiliation(s)
- Lukáš Predajňa
- Institute of Virology, Department of Plant Virology, Slovak Academy of Sciences, Dúbravská cesta 9, 84505 Bratislava, Slovakia
| | | | | | | |
Collapse
|
19
|
Negative-strand RNA viruses: the plant-infecting counterparts. Virus Res 2011; 162:184-202. [PMID: 21963660 DOI: 10.1016/j.virusres.2011.09.028] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 09/15/2011] [Accepted: 09/16/2011] [Indexed: 11/21/2022]
Abstract
While a large number of negative-strand (-)RNA viruses infect animals and humans, a relative small number have plants as their primary host. Some of these have been classified within families together with animal/human infecting viruses due to similarities in particle morphology and genome organization, while others have just recently been/or are still classified in floating genera. In most cases, at least two striking differences can still be discerned between the animal/human-infecting viruses and their plant-infecting counterparts which for the latter relate to their adaptation to plants as hosts. The first one is the capacity to modify plasmodesmata to facilitate systemic spread of infectious viral entities throughout the plant host. The second one is the capacity to counteract RNA interference (RNAi, also referred to as RNA silencing), the innate antiviral defence system of plants and insects. In this review an overview will be presented on the negative-strand RNA plant viruses classified within the families Bunyaviridae, Rhabdoviridae, Ophioviridae and floating genera Tenuivirus and Varicosavirus. Genetic differences with the animal-infecting counterparts and their evolutionary descendants will be described in light of the above processes.
Collapse
|