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Xue M, Sofer L, Simon V, Arvy N, Diop M, Lion R, Beucher G, Bordat A, Tilsner J, Gallois J, German‐Retana S. AtHVA22a, a plant-specific homologue of Reep/DP1/Yop1 family proteins is involved in turnip mosaic virus propagation. MOLECULAR PLANT PATHOLOGY 2024; 25:e13466. [PMID: 38767756 PMCID: PMC11104427 DOI: 10.1111/mpp.13466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 04/08/2024] [Accepted: 04/14/2024] [Indexed: 05/22/2024]
Abstract
The movement of potyviruses, the largest genus of single-stranded, positive-sense RNA viruses responsible for serious diseases in crops, is very complex. As potyviruses developed strategies to hijack the host secretory pathway and plasmodesmata (PD) for their transport, the goal of this study was to identify membrane and/or PD-proteins that interact with the 6K2 protein, a potyviral protein involved in replication and cell-to-cell movement of turnip mosaic virus (TuMV). Using split-ubiquitin membrane yeast two-hybrid assays, we screened an Arabidopsis cDNA library for interactors of TuMV6K2. We isolated AtHVA22a (Hordeum vulgare abscisic acid responsive gene 22), which belongs to a multigenic family of transmembrane proteins, homologous to Receptor expression-enhancing protein (Reep)/Deleted in polyposis (DP1)/Yop1 family proteins in animal and yeast. HVA22/DP1/Yop1 family genes are widely distributed in eukaryotes, but the role of HVA22 proteins in plants is still not well known, although proteomics analysis of PD fractions purified from Arabidopsis suspension cells showed that AtHVA22a is highly enriched in a PD proteome. We confirmed the interaction between TuMV6K2 and AtHVA22a in yeast, as well as in planta by using bimolecular fluorescence complementation and showed that TuMV6K2/AtHVA22a interaction occurs at the level of the viral replication compartment during TuMV infection. Finally, we showed that the propagation of TuMV is increased when AtHVA22a is overexpressed in planta but slowed down upon mutagenesis of AtHVA22a by CRISPR-Cas9. Altogether, our results indicate that AtHVA22a plays an agonistic effect on TuMV propagation and that the C-terminal tail of the protein is important in this process.
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Affiliation(s)
- Mingshuo Xue
- Univ. Bordeaux UMR 1332, Biologie du Fruit et Pathologie, INRAe, Equipe de VirologieVillenave d'Ornon CedexFrance
| | - Luc Sofer
- Univ. Bordeaux UMR 1332, Biologie du Fruit et Pathologie, INRAe, Equipe de VirologieVillenave d'Ornon CedexFrance
| | - Vincent Simon
- Univ. Bordeaux UMR 1332, Biologie du Fruit et Pathologie, INRAe, Equipe de VirologieVillenave d'Ornon CedexFrance
| | - Nathalie Arvy
- Univ. Bordeaux UMR 1332, Biologie du Fruit et Pathologie, INRAe, Equipe de VirologieVillenave d'Ornon CedexFrance
| | - Mamoudou Diop
- UR 1052, INRAe, GAFL Domaine St MauriceMontfavet CedexFrance
| | - Roxane Lion
- Univ. Bordeaux UMR 1332, Biologie du Fruit et Pathologie, INRAe, Equipe de VirologieVillenave d'Ornon CedexFrance
| | - Guillaume Beucher
- Univ. Bordeaux UMR 1332, Biologie du Fruit et Pathologie, INRAe, Equipe de VirologieVillenave d'Ornon CedexFrance
| | - Amandine Bordat
- Univ. Bordeaux UMR 1332, Biologie du Fruit et Pathologie, INRAe, Equipe de VirologieVillenave d'Ornon CedexFrance
| | - Jens Tilsner
- Cell and Molecular SciencesJames Hutton InstituteDundeeUK
- Biomedical Sciences Research ComplexUniversity of St AndrewsSt AndrewsUK
| | | | - Sylvie German‐Retana
- Univ. Bordeaux UMR 1332, Biologie du Fruit et Pathologie, INRAe, Equipe de VirologieVillenave d'Ornon CedexFrance
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2
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Bonnamy M, Brousse A, Pirolles E, Michalakis Y, Blanc S. The genome formula of a multipartite virus is regulated both at the individual segment and the segment group levels. PLoS Pathog 2024; 20:e1011973. [PMID: 38271470 PMCID: PMC10846721 DOI: 10.1371/journal.ppat.1011973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 02/06/2024] [Accepted: 01/14/2024] [Indexed: 01/27/2024] Open
Abstract
Differential accumulation of the distinct genome segments is a common feature of viruses with segmented genomes. The reproducible and specific pattern of genome segment accumulation within the host is referred to as the "genome formula". There is speculation and some experimental support for a functional role of the genome formula by modulating gene expression through copy number variations. However, the mechanisms of genome formula regulation have not yet been identified. In this study, we investigated whether the genome formula of the octopartite nanovirus faba bean necrotic stunt virus (FBNSV) is regulated by processes acting at the individual segment vs. viral population levels. We used a leaf infiltration system to show that the two most accumulated genome segments of the FBNSV possess a greater intrinsic accumulation capacity in Vicia faba tissues than the other segments. Nevertheless, processes acting at the individual segment level are insufficient to generate the genome formula, suggesting the involvement of additional mechanisms acting at the supra-segment level. Indeed, the absence of segments with important functions during systemic infection strongly modifies the relative frequency of the others, indicating that the genome formula is a property of the segment group. Together, these results demonstrate that the FBNSV genome formula is shaped by a complex process acting at both the individual segment and the segment group levels.
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Affiliation(s)
- Mélia Bonnamy
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- MIVEGEC, CNRS, IRD, Univ Montpellier, Montpellier, France
| | - Andy Brousse
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- MIVEGEC, CNRS, IRD, Univ Montpellier, Montpellier, France
| | - Elodie Pirolles
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | - Stéphane Blanc
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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3
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Dall'Ara M, Guo Y, Poli D, Gilmer D, Ratti C. Analysis of the relative frequencies of the multipartite BNYVV genomic RNAs in different plants and tissues. J Gen Virol 2024; 105. [PMID: 38197877 DOI: 10.1099/jgv.0.001950] [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] [Indexed: 01/11/2024] Open
Abstract
Multipartite virus genomes are composed of two or more segments, each packaged into an independent viral particle. A potential advantage of multipartitism is the regulation of gene expression through changes in the segment copy number. Soil-borne beet necrotic yellow vein virus (BNYVV) is a typical example of multipartism, given its high number of genomic positive-sense RNAs (up to five). Here we analyse the relative frequencies of the four genomic RNAs of BNYVV type B during infection of different host plants (Chenopodium quinoa, Beta macrocarpa and Spinacia oleracea) and organs (leaves and roots). By successfully validating a two-step reverse-transcriptase digital droplet PCR protocol, we show that RNA1 and -2 genomic segments always replicate at low and comparable relative frequencies. In contrast, RNA3 and -4 accumulate with variable relative frequencies, resulting in distinct RNA1 : RNA2 : RNA3 : RNA4 ratios, depending on the infected host species and organ.
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Affiliation(s)
- M Dall'Ara
- DISTAL-Plant pathology, University of Bologna, Viale G. Fanin, 40, 40127 Bologna, Italy
| | - Y Guo
- DISTAL-Plant pathology, University of Bologna, Viale G. Fanin, 40, 40127 Bologna, Italy
| | - D Poli
- DISTAL-Plant pathology, University of Bologna, Viale G. Fanin, 40, 40127 Bologna, Italy
| | - D Gilmer
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, France
| | - C Ratti
- DISTAL-Plant pathology, University of Bologna, Viale G. Fanin, 40, 40127 Bologna, Italy
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Ren R, Zheng L, Han J, Perdoncini Carvalho C, Miyashita S, Zhang D, Qu F. Intracellular bottlenecking permits no more than three tomato yellow leaf curl virus genomes to initiate replication in a single cell. PLoS Pathog 2023; 19:e1011365. [PMID: 37126519 PMCID: PMC10174518 DOI: 10.1371/journal.ppat.1011365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 05/11/2023] [Accepted: 04/17/2023] [Indexed: 05/02/2023] Open
Abstract
Viruses are constantly subject to natural selection to enrich beneficial mutations and weed out deleterious ones. However, it remains unresolved as to how the phenotypic gains or losses brought about by these mutations cause the viral genomes carrying the very mutations to become more or less numerous. Previous investigations by us and others suggest that viruses with plus strand (+) RNA genomes may compel such selection by bottlenecking the replicating genome copies in each cell to low single digits. Nevertheless, it is unclear if similarly stringent reproductive bottlenecks also occur in cells invaded by DNA viruses. Here we investigated whether tomato yellow leaf curl virus (TYLCV), a small virus with a single-stranded DNA genome, underwent population bottlenecking in cells of its host plants. We engineered a TYLCV genome to produce two replicons that express green fluorescent protein and mCherry, respectively, in a replication-dependent manner. We found that among the cells entered by both replicons, less than 65% replicated both, whereas at least 35% replicated either of them alone. Further probability computation concluded that replication in an average cell was unlikely to have been initiated with more than three replicon genome copies. Furthermore, sequential inoculations unveiled strong mutual exclusions of these two replicons at the intracellular level. In conclusion, the intracellular population of the small DNA virus TYLCV is actively bottlenecked, and such bottlenecking may be a virus-encoded, evolutionarily conserved trait that assures timely selection of new mutations emerging through error-prone replication.
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Affiliation(s)
- Ruifan Ren
- Longping Branch, College of Biology, Hunan University, Changsha, China
- Department of Plant Pathology, The Ohio State University, Wooster, Ohio, United States of America
- Hunan Plant Protection Institute, Changsha, China
| | - Limin Zheng
- Department of Plant Pathology, The Ohio State University, Wooster, Ohio, United States of America
| | - Junping Han
- Department of Plant Pathology, The Ohio State University, Wooster, Ohio, United States of America
| | | | - Shuhei Miyashita
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Deyong Zhang
- Longping Branch, College of Biology, Hunan University, Changsha, China
- Hunan Plant Protection Institute, Changsha, China
| | - Feng Qu
- Department of Plant Pathology, The Ohio State University, Wooster, Ohio, United States of America
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Saeki K, Sasaki A. Cell-to-cell transmission promotes the emergence of double-drug resistance. Virus Evol 2023; 9:vead017. [PMID: 37744652 PMCID: PMC10517696 DOI: 10.1093/ve/vead017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 01/13/2023] [Accepted: 03/08/2023] [Indexed: 09/26/2023] Open
Abstract
The use of multiple antivirals in a single patient increases the risk of emergence of multidrug-resistant viruses, posing a public health challenge and limiting management options. Cell-to-cell viral transmission allows a pair of viruses that are each resistant to a single drug to persist for a prolonged period of passages although neither can survive alone under double-drug treatment. This pair should then persist until they accumulate a second mutation to generate resistance to both drugs. Accordingly, we here propose a hypothesis that viruses have a much higher probability of developing double-drug resistance when they are transmitted via a cell-to-cell mode than when they are transmitted via a cell-free mode through released virions. By using a stochastic model describing the changes in the frequencies of viral genotypes over successive infections, we analytically demonstrate that the emergence probability of double resistance is approximately the square of the number of viral genomes that establish infection times greater in cell-to-cell transmission than in cell-free transmission. Our study suggests the importance of inhibiting cell-to-cell transmission during multidrug treatment.
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Affiliation(s)
- Koichi Saeki
- Department of Computational Biology and Medical Sciences, Graduate School for Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0885, Japan
| | - Akira Sasaki
- Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies, SOKENDAI, Hayama, Kanagawa 240-0193, Japan
- Evolution and Ecology Program, International Institute for Applied Systems Analysis, Laxenburg A-2361, Austria
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6
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Plant Virus Adaptation to New Hosts: A Multi-scale Approach. Curr Top Microbiol Immunol 2023; 439:167-196. [PMID: 36592246 DOI: 10.1007/978-3-031-15640-3_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Viruses are studied at each level of biological complexity: from within-cells to ecosystems. The same basic evolutionary forces and principles operate at each level: mutation and recombination, selection, genetic drift, migration, and adaptive trade-offs. Great efforts have been put into understanding each level in great detail, hoping to predict the dynamics of viral population, prevent virus emergence, and manage their spread and virulence. Unfortunately, we are still far from this. To achieve these ambitious goals, we advocate for an integrative perspective of virus evolution. Focusing in plant viruses, we illustrate the pervasiveness of the above-mentioned principles. Beginning at the within-cell level, we describe replication modes, infection bottlenecks, and cellular contagion rates. Next, we move up to the colonization of distal tissues, discussing the fundamental role of random events. Then, we jump beyond the individual host and discuss the link between transmission mode and virulence. Finally, at the community level, we discuss properties of virus-plant infection networks. To close this review we propose the multilayer network theory, in which elements at different layers are connected and submit to their own dynamics that feed across layers, resulting in new emerging properties, as a way to integrate information from the different levels.
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Determinants of Virus Variation, Evolution, and Host Adaptation. Pathogens 2022; 11:pathogens11091039. [PMID: 36145471 PMCID: PMC9501407 DOI: 10.3390/pathogens11091039] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/06/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
Abstract
Virus evolution is the change in the genetic structure of a viral population over time and results in the emergence of new viral variants, strains, and species with novel biological properties, including adaptation to new hosts. There are host, vector, environmental, and viral factors that contribute to virus evolution. To achieve or fine tune compatibility and successfully establish infection, viruses adapt to a particular host species or to a group of species. However, some viruses are better able to adapt to diverse hosts, vectors, and environments. Viruses generate genetic diversity through mutation, reassortment, and recombination. Plant viruses are exposed to genetic drift and selection pressures by host and vector factors, and random variants or those with a competitive advantage are fixed in the population and mediate the emergence of new viral strains or species with novel biological properties. This process creates a footprint in the virus genome evident as the preferential accumulation of substitutions, insertions, or deletions in areas of the genome that function as determinants of host adaptation. Here, with respect to plant viruses, we review the current understanding of the sources of variation, the effect of selection, and its role in virus evolution and host adaptation.
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Kadoya SS, Urayama SI, Nunoura T, Hirai M, Takaki Y, Kitajima M, Nakagomi T, Nakagomi O, Okabe S, Nishimura O, Sano D. The Intrapopulation Genetic Diversity of RNA Virus May Influence the Sensitivity of Chlorine Disinfection. Front Microbiol 2022; 13:839513. [PMID: 35668760 PMCID: PMC9163991 DOI: 10.3389/fmicb.2022.839513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
RNA virus populations are not clonal; rather, they comprise a mutant swarm in which sequences are slightly different from the master sequence. Genetic diversity within a population (intrapopulation genetic diversity) is critical for RNA viruses to survive under environmental stresses. Disinfection has become an important practice in the control of pathogenic viruses; however, the impact of intrapopulation genetic diversity on the sensitivity of disinfection, defined as -log10 (postdisinfected infectious titer/predisinfected titer), has not been elucidated. In this study, we serially passaged populations of rhesus rotavirus. We demonstrated that populations with reduced chlorine sensitivity emerged at random and independently of chlorine exposure. Sequencing analysis revealed that compared with sensitive populations, less-sensitive ones had higher non-synonymous genetic diversity of the outer capsid protein gene, suggesting that changes in the amino acid sequences of the outer capsid protein were the main factors influencing chlorine sensitivity. No common mutations were found among less-sensitive populations, indicating that rather than specific mutations, the diversity of the outer capsid protein itself was associated with the disinfection sensitivity and that the disinfection sensitivity changed stochastically. Simulation results suggest that the disinfection sensitivity of a genetically diverse population is destabilized if cooperative viral clusters including multiple sequences are formed. These results advocate that any prevention measures leading to low intrapopulation genetic diversity are important to prevent the spread and evolution of pathogenic RNA viruses in society.
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Affiliation(s)
- Syun-suke Kadoya
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
- Department of Urban Engineering, The University of Tokyo, Tokyo, Japan
| | - Syun-ichi Urayama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Miho Hirai
- Super-Cutting-Edge Grand and Advanced Research Program, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Yoshihiro Takaki
- Super-Cutting-Edge Grand and Advanced Research Program, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Japan
| | - Toyoko Nakagomi
- Department of Molecular Microbiology and Immunology, Nagasaki University, Nagasaki, Japan
| | - Osamu Nakagomi
- Department of Molecular Microbiology and Immunology, Nagasaki University, Nagasaki, Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Japan
| | - Osamu Nishimura
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
- Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Sendai, Japan
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Fang X, Qiao J, Zang Y, Gao Q, Xu W, Gao D, Yang Y, Xie L, Wang Y, Wang X. Developing reverse genetics systems of northern cereal mosaic virus to reveal superinfection exclusion of two cytorhabdoviruses in barley plants. MOLECULAR PLANT PATHOLOGY 2022; 23:749-756. [PMID: 35124878 PMCID: PMC8995060 DOI: 10.1111/mpp.13188] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 06/11/2023]
Abstract
Recently, reverse genetics systems of plant negative-stranded RNA (NSR) viruses have been developed to study virus-host interactions. Nonetheless, genetic rescue of plant NSR viruses in both insect vectors and monocot plants is very limited. Northern cereal mosaic virus (NCMV), a plant cytorhabdovirus, causes severe diseases in cereal plants through transmission by the small brown planthopper (SBPH, Laodelphax striatellus) in a propagative manner. In this study, we first developed a minireplicon system of NCMV in Nicotiana benthamiana plants, and then recovered a recombinant NCMV virus (rNCMV-RFP), with a red fluorescent protein (RFP) insertion, in SBPHs and barley plants. We further used rNCMV-RFP and green fluorescent protein (GFP)-tagged barley yellow striate mosaic virus (rBYSMV-GFP), a closely related cytorhabdovirus, to study superinfection exclusion, a widely observed phenomenon in dicot plants rarely studied in monocot plants. Interestingly, cellular superinfection exclusion of rBYSMV-GFP and rNCMV-RFP was observed in barley leaves. Our results demonstrate that two insect-transmitted cytorhabdoviruses are enemies rather than friends at the cellular level during coinfections in plants.
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Affiliation(s)
- Xiao‐Dong Fang
- State Key Laboratory of Agro‐BiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Ji‐Hui Qiao
- State Key Laboratory of Agro‐BiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Ying Zang
- State Key Laboratory of Agro‐BiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Qiang Gao
- State Key Laboratory of Agro‐BiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
- College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Wen‐Ya Xu
- State Key Laboratory of Agro‐BiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Dong‐Min Gao
- State Key Laboratory of Agro‐BiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Yi‐Zhou Yang
- State Key Laboratory of Agro‐BiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Liang Xie
- State Key Laboratory of Agro‐BiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Ying Wang
- College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Xian‐Bing Wang
- State Key Laboratory of Agro‐BiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
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Short 5' Untranslated Region Enables Optimal Translation of Plant Virus Tricistronic RNA via Leaky Scanning. J Virol 2022; 96:e0214421. [PMID: 35262378 DOI: 10.1128/jvi.02144-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Regardless of the general model of translation in eukaryotic cells, a number of studies suggested that many mRNAs encode multiple proteins. Leaky scanning, which supplies ribosomes to downstream open reading frames (ORFs) by readthrough of upstream ORFs, has great potential to translate polycistronic mRNAs. However, the mRNA elements controlling leaky scanning and their biological relevance have rarely been elucidated, with exceptions such as the Kozak sequence. Here, we have analyzed the strategy of a plant RNA virus to translate three movement proteins from a single RNA molecule through leaky scanning. The in planta and in vitro results indicate thatthe significantly shorter 5' untranslated region (UTR) of the most upstream ORF promotes leaky scanning, potentially fine-tuning the translation efficiency of the three proteins in a single RNA molecule to optimize viral propagation. Our results suggest that the remarkably short length of the leader sequence, like the Kozak sequence, is a translational regulatory element with a biologically important role, as previous studies have shown biochemically. IMPORTANCE Potexvirus, a group of plant viruses, infect a variety of crops, including cultivated crops. It has been thought that the three transition proteins that are essential for the cell-to-cell transfer of potexviruses are translated from two subgenomic RNAs, sgRNA1 and sgRNA2. However, sgRNA2 has not been clearly detected. In this study, we have shown that sgRNA1, but not sgRNA2, is the major translation template for the three movement proteins. In addition, we determined the transcription start site of sgRNA1 in flexiviruses and found that the efficiency of leaky scanning caused by the short 5' UTR of sgRNA1, a widely conserved feature, regulates the translation of the three movement proteins. When we tested the infection of viruses with mutations introduced into the length of the 5' UTR, we found that the movement efficiency of the virus was affected. Our results provide important additional information on the protein translation strategy of flexiviruses, including Potexvirus, and provide a basis for research on their control as well as the need to reevaluate the short 5' UTR as a translational regulatory element with an important role in vivo.
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11
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Abebe DA, van Bentum S, Suzuki M, Ando S, Takahashi H, Miyashita S. Plant death caused by inefficient induction of antiviral R-gene-mediated resistance may function as a suicidal population resistance mechanism. Commun Biol 2021; 4:947. [PMID: 34373580 PMCID: PMC8352862 DOI: 10.1038/s42003-021-02482-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 07/23/2021] [Indexed: 11/15/2022] Open
Abstract
Land plant genomes carry tens to hundreds of Resistance (R) genes to combat pathogens. The induction of antiviral R-gene-mediated resistance often results in a hypersensitive response (HR), which is characterized by virus containment in the initially infected tissues and programmed cell death (PCD) of the infected cells. Alternatively, systemic HR (SHR) is sometimes observed in certain R gene-virus combinations, such that the virus systemically infects the plant and PCD induction follows the spread of infection, resulting in systemic plant death. SHR has been suggested to be the result of inefficient resistance induction; however, no quantitative comparison has been performed to support this hypothesis. In this study, we report that the average number of viral genomes that establish cell infection decreased by 28.7% and 12.7% upon HR induction by wild-type cucumber mosaic virus and SHR induction by a single-amino acid variant, respectively. These results suggest that a small decrease in the level of resistance induction can change an HR to an SHR. Although SHR appears to be a failure of resistance at the individual level, our simulations imply that suicidal individual death in SHR may function as an antiviral mechanism at the population level, by protecting neighboring uninfected kin plants.
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Affiliation(s)
- Derib A Abebe
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Sietske van Bentum
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Machi Suzuki
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Sugihiro Ando
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Hideki Takahashi
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Shuhei Miyashita
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.
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12
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In-Tree Behavior of Diverse Viruses Harbored in the Chestnut Blight Fungus, Cryphonectria parasitica. J Virol 2021; 95:JVI.01962-20. [PMID: 33361433 DOI: 10.1128/jvi.01962-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/17/2020] [Indexed: 12/20/2022] Open
Abstract
The ascomycete Cryphonectria parasitica causes destructive chestnut blight. Biological control of the fungus by virus infection (hypovirulence) has been shown to be an effective control strategy against chestnut blight in Europe. To provide biocontrol effects, viruses must be able to induce hypovirulence and spread efficiently in chestnut trees. Field studies using living trees to date have focused on a selected family of viruses called hypoviruses, especially prototypic hypovirus CHV1, but there are now known to be many other viruses that infect C. parasitica Here, we tested seven different viruses for their hypovirulence induction, biocontrol potential, and transmission properties between two vegetatively compatible but molecularly distinguishable fungal strains in trees. The test included cytosolically and mitochondrially replicating viruses with positive-sense single-stranded RNA or double-stranded RNA genomes. The seven viruses showed different in planta behaviors and were classified into four groups. Group I, including CHV1, had great biocontrol potential and could protect trees by efficiently spreading and converting virulent to hypovirulent cankers in the trees. Group II could induce high levels of hypovirulence but showed much smaller biocontrol potential, likely because of inefficient virus transmission. Group III showed poor performance in hypovirulence induction and biocontrol, while efficiently being transmitted in the infected trees. Group IV could induce hypovirulence and spread efficiently but showed poor biocontrol potential. Nuclear and mitochondrial genotyping of fungal isolates obtained from the treated cankers confirmed virus transmission between the two fungal strains in most isolates. These results are discussed in view of dynamic interactions in the tripartite pathosystem.IMPORTANCE The ascomycete Cryphonectria parasitica causes destructive chestnut blight, which is controllable by hypovirulence-conferring viruses infecting the fungus. The tripartite chestnut/C. parasitica/virus pathosystem involves the dynamic interactions of their genetic elements, i.e., virus transmission and lateral transfer of nuclear and mitochondrial genomes between fungal strains via anastomosis occurring in trees. Here, we tested diverse RNA viruses for their hypovirulence induction, biocontrol potential, and transmission properties between two vegetatively compatible but molecularly distinguishable fungal strains in live chestnut trees. The tested viruses, which are different in genome type (single-stranded or double-stranded RNA) and organization, replication site (cytosol or mitochondria), virus form (encapsidated or capsidless) and/or symptomatology, have been unexplored in the aforementioned aspects under controlled conditions. This study showed intriguing different in-tree behaviors of the seven viruses and suggested that to exert significant biocontrol effects, viruses must be able to induce hypovirulence and spread efficiently in the fungus infecting the chestnut trees.
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Qu F, Zheng L, Zhang S, Sun R, Slot J, Miyashita S. Bottleneck, Isolate, Amplify, Select (BIAS) as a mechanistic framework for intracellular population dynamics of positive-sense RNA viruses. Virus Evol 2020; 6:veaa086. [PMID: 33343926 PMCID: PMC7733609 DOI: 10.1093/ve/veaa086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Many positive-sense RNA viruses, especially those infecting plants, are known to experience stringent, stochastic population bottlenecks inside the cells they invade, but exactly how and why these populations become bottlenecked are unclear. A model proposed ten years ago advocates that such bottlenecks are evolutionarily favored because they cause the isolation of individual viral variants in separate cells. Such isolation in turn allows the viral variants to manifest the phenotypic differences they encode. Recently published observations lend mechanistic support to this model and prompt us to refine the model with novel molecular details. The refined model, designated Bottleneck, Isolate, Amplify, Select (BIAS), postulates that these viruses impose population bottlenecks on themselves by encoding bottleneck-enforcing proteins (BNEPs) that function in a concentration-dependent manner. In cells simultaneously invaded by numerous virions of the same virus, BNEPs reach the bottleneck-ready concentration sufficiently early to arrest nearly all internalized viral genomes. As a result, very few (as few as one) viral genomes stochastically escape to initiate reproduction. Repetition of this process in successively infected cells isolates viral genomes with different mutations in separate cells. This isolation prevents mutant viruses encoding defective viral proteins from hitchhiking on sister genome-encoded products, leading to the swift purging of such mutants. Importantly, genome isolation also ensures viral genomes harboring beneficial mutations accrue the cognate benefit exclusively to themselves, leading to the fixation of such beneficial mutations. Further interrogation of the BIAS hypothesis promises to deepen our understanding of virus evolution and inspire new solutions to virus disease mitigation.
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Affiliation(s)
- Feng Qu
- Department of Plant Pathology and.,Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA
| | - Limin Zheng
- Department of Plant Pathology and.,Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA
| | - Shaoyan Zhang
- Department of Plant Pathology and.,Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA
| | - Rong Sun
- Department of Plant Pathology and.,Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA
| | | | - Shuhei Miyashita
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-aoba, Aoba-ku, Sendai 980-0845, Japan
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14
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Jensen JD, Stikeleather RA, Kowalik TF, Lynch M. Imposed mutational meltdown as an antiviral strategy. Evolution 2020; 74:2549-2559. [PMID: 33047822 PMCID: PMC7993354 DOI: 10.1111/evo.14107] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/30/2020] [Accepted: 10/10/2020] [Indexed: 12/25/2022]
Abstract
Following widespread infections of the most recent coronavirus known to infect humans, SARS‐CoV‐2, attention has turned to potential therapeutic options. With no drug or vaccine yet approved, one focal point of research is to evaluate the potential value of repurposing existing antiviral treatments, with the logical strategy being to identify at least a short‐term intervention to prevent within‐patient progression, while long‐term vaccine strategies unfold. Here, we offer an evolutionary/population‐genetic perspective on one approach that may overwhelm the capacity for pathogen defense (i.e., adaptation) – induced mutational meltdown – providing an overview of key concepts, review of previous theoretical and experimental work of relevance, and guidance for future research. Applied with appropriate care, including target specificity, induced mutational meltdown may provide a general, rapidly implemented approach for the within‐patient eradication of a wide range of pathogens or other undesirable microorganisms.
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Affiliation(s)
- Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, Arizona, 85281.,Center for Evolution & Medicine, Arizona State University, Tempe, Arizona, 85281
| | - Ryan A Stikeleather
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, 85281
| | - Timothy F Kowalik
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, 01655
| | - Michael Lynch
- School of Life Sciences, Arizona State University, Tempe, Arizona, 85281.,Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, 85281
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15
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Zwart MP, Elena SF. Modeling multipartite virus evolution: the genome formula facilitates rapid adaptation to heterogeneous environments †. Virus Evol 2020; 6:veaa022. [PMID: 32405432 PMCID: PMC7206449 DOI: 10.1093/ve/veaa022] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Multipartite viruses have two or more genome segments, and package different segments into different particle types. Although multipartition is thought to have a cost for virus transmission, its benefits are not clear. Recent experimental work has shown that the equilibrium frequency of viral genome segments, the setpoint genome formula (SGF), can be unbalanced and host-species dependent. These observations have reinvigorated the hypothesis that changes in genome-segment frequencies can lead to changes in virus-gene expression that might be adaptive. Here we explore this hypothesis by developing models of bipartite virus infection, leading to a threefold contribution. First, we show that the SGF depends on the cellular multiplicity of infection (MOI), when the requirements for infection clash with optimizing the SGF for virus-particle yield per cell. Second, we find that convergence on the SGF is very rapid, often occurring within a few cellular rounds of infection. Low and intermediate MOIs lead to faster convergence on the SGF. For low MOIs, this effect occurs because of the requirements for infection, whereas for intermediate MOIs this effect is also due to the high levels of variation generated in the genome formula (GF). Third, we explored the conditions under which a bipartite virus could outcompete a monopartite one. As the heterogeneity between environments and specificity of gene-expression requirements for each environment increased, the bipartite virus was more likely to outcompete the monopartite virus. Under some conditions, changes in the GF helped to exclude the monopartite competitor, highlighting the versatility of the GF. Our results show the inextricable relationship between MOI and the SGF, and suggest that under some conditions, the cost of multipartition can be outweighed by its benefits for the rapid tuning of viral gene expression.
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Affiliation(s)
- Mark P Zwart
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Postbus 50, 6700 AB, Wageningen, The Netherlands
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Parc Cientific UV, Catedrático Agustín Escardino 9, Paterna, Valéncia 46980, Spain.,The Santa Fe Institute, Santa Fe, 1399 Hyde Park Road, NM 87501, USA
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16
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Rousseau E, Bonneault M, Fabre F, Moury B, Mailleret L, Grognard F. Virus epidemics, plant-controlled population bottlenecks and the durability of plant resistance. Philos Trans R Soc Lond B Biol Sci 2020; 374:20180263. [PMID: 31056046 DOI: 10.1098/rstb.2018.0263] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Plant qualitative resistances to viruses are natural exhaustible resources that can be impaired by the emergence of resistance-breaking (RB) virus variants. Mathematical modelling can help determine optimal strategies for resistance durability by a rational deployment of resistance in agroecosystems. Here, we propose an innovative approach, built up from our previous empirical studies, based on plant cultivars combining qualitative resistance with quantitative resistance narrowing population bottlenecks exerted on viruses during host-to-host transmission and/or within-host infection. Narrow bottlenecks are expected to slow down virus adaptation to plant qualitative resistance. To study the effect of bottleneck size on yield, we developed a stochastic epidemic model with mixtures of susceptible and resistant plants, relying on continuous-time Markov chain processes. Overall, narrow bottlenecks are beneficial when the fitness cost of RB virus variants in susceptible plants is intermediate. In such cases, they could provide up to 95 additional percentage points of yield compared with deploying a qualitative resistance alone. As we have shown in previous works that virus population bottlenecks are at least partly heritable plant traits, our results suggest that breeding and deploying plant varieties exposing virus populations to narrowed bottlenecks will increase yield and delay the emergence of RB variants. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'. This issue is linked with the subsequent theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'.
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Affiliation(s)
- Elsa Rousseau
- 1 Université Côte d'Azur, Inria, INRA, CNRS, Sorbonne Université, Biocore team , Sophia Antipolis , France.,2 Université Côte d'Azur, INRA, CNRS, ISA , France.,3 Pathologie Végétale, INRA , F-84140 Montfavet , France
| | - Mélanie Bonneault
- 1 Université Côte d'Azur, Inria, INRA, CNRS, Sorbonne Université, Biocore team , Sophia Antipolis , France
| | - Frédéric Fabre
- 4 UMR 1065 SAVE, INRA , Bordeaux Sciences Agro, F-33882, Villenave d'Ornon , France
| | - Benoît Moury
- 3 Pathologie Végétale, INRA , F-84140 Montfavet , France
| | - Ludovic Mailleret
- 1 Université Côte d'Azur, Inria, INRA, CNRS, Sorbonne Université, Biocore team , Sophia Antipolis , France.,2 Université Côte d'Azur, INRA, CNRS, ISA , France
| | - Frédéric Grognard
- 1 Université Côte d'Azur, Inria, INRA, CNRS, Sorbonne Université, Biocore team , Sophia Antipolis , France
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17
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Guo Q, Zhang S, Sun R, Yao X, Zhang XF, Tatineni S, Meulia T, Qu F. Superinfection Exclusion by p28 of Turnip Crinkle Virus Is Separable from Its Replication Function. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:364-375. [PMID: 31880982 DOI: 10.1094/mpmi-09-19-0258-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We recently reported that the p28 auxiliary replication protein encoded by turnip crinkle virus (TCV) is also responsible for eliciting superinfection exclusion (SIE) against superinfecting TCV. However, it remains unresolved whether the replication function of p28 could be separated from its ability to elicit SIE. Here, we report the identification of two single amino acid mutations that decouple these two functions. Using an Agrobacterium infiltration-based delivery system, we transiently expressed a series of p28 deletion and point mutants, and tested their ability to elicit SIE against a cointroduced TCV replicon. We found that substituting alanine (A) for valine (V) and phenylalanine (F) at p28 positions 181 and 182, respectively, modestly compromised SIE in transiently expressed p28 derivatives. Upon incorporation into TCV replicons, V181A and F182A decoupled TCV replication and SIE diametrically. Although V181A impaired SIE without detectably compromising replication, F182A abolished TCV replication but had no effect on SIE once the replication of the defective replicon was restored through complementation. Both mutations diminished accumulation of p28 protein, suggesting that p28 must reach a concentration threshold in order to elicit a strong SIE. Importantly, the severe reduction of F182A protein levels correlated with a dramatic loss in the number of intracellular p28 foci formed by p28-p28 interactions. Together, these findings not only decouple the replication and SIE functions of p28 but also unveil a concentration dependence for p28 coalescence and SIE elicitation. These data further highlight the role of p28 multimerization in driving the exclusion of secondary TCV infections.
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Affiliation(s)
- Qin Guo
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, U.S.A
| | - Shaoyan Zhang
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, U.S.A
| | - Rong Sun
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, U.S.A
| | - Xiaolong Yao
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, U.S.A
| | - Xiao-Feng Zhang
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, U.S.A
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Satyanarayana Tatineni
- United States Department of Agriculture-Agricultural Research Service and Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583, U.S.A
| | - Tea Meulia
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, U.S.A
- Molecular and Cellular Imaging Center, Ohio Agricultural Research and Development Center, The Ohio State University
| | - Feng Qu
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, U.S.A
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18
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Tuo D, Zhou P, Zhao G, Yan P, Tan D, Li X, Shen W. A Double Mutation in the Conserved Motifs of the Helper Component Protease of Papaya Leaf Distortion Mosaic Virus for the Generation of a Cross-Protective Attenuated Strain. PHYTOPATHOLOGY 2020; 110:187-193. [PMID: 31516080 DOI: 10.1094/phyto-09-19-0328-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Potyviral helper component protease (HC-Pro), as a major determinant of symptom expression in susceptible plants, is a likely target candidate in the production of attenuated strains for cross-protection. In this study, single or double mutations of Lys (K) to Glu (E) in the Lys-Ile-Thr-Cys motif and Arg (R) to Ile (I) in the Phe-Arg-Asn-Lys motif of the HC-Pro from the severe papaya leaf distortion mosaic virus strain DF (PLDMV-DF) reduced symptom expression and virus accumulation in infected papaya (Carica papaya) plants. The papaya plants infected with the attenuated double mutant of PLDMV-EI presented as symptomless. PLDMV-EI provided effective protection against PLDMV-DF infection in three papaya cultivars and had no effect on plant growth and development. Our result showed that PLDMV-EI is a promising mild strain for the practical use of cross-protection in the field.
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Affiliation(s)
- Decai Tuo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Key Laboratory of Tropical Microbe Resources, Haikou 571101, China
| | - Peng Zhou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Key Laboratory of Tropical Microbe Resources, Haikou 571101, China
| | - Guangyuan Zhao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Pu Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Key Laboratory of Tropical Microbe Resources, Haikou 571101, China
| | - Dong Tan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xiaoying Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Key Laboratory of Tropical Microbe Resources, Haikou 571101, China
| | - Wentao Shen
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Key Laboratory of Tropical Microbe Resources, Haikou 571101, China
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19
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The Matrix Protein of a Plant Rhabdovirus Mediates Superinfection Exclusion by Inhibiting Viral Transcription. J Virol 2019; 93:JVI.00680-19. [PMID: 31341043 DOI: 10.1128/jvi.00680-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/16/2019] [Indexed: 11/20/2022] Open
Abstract
Superinfection exclusion (SIE) or cross-protection phenomena have been documented for plant viruses for nearly a century and are widespread among taxonomically diverse viruses, but little information is available about SIE of plant negative-strand RNA viruses. Here, we demonstrate that SIE by sonchus yellow net nucleorhabdovirus virus (SYNV) is mediated by the viral matrix (M) protein, a multifunctional protein involved in transcription regulation, virion assembly, and virus budding. We show that fluorescent protein-tagged SYNV variants display mutual exclusion/cross-protection in Nicotiana benthamiana plants. Transient expression of the SYNV M protein, but not other viral proteins, interfered with SYNV local infections. In addition, SYNV M deletion mutants failed to exclude superinfection by wild-type SYNV. An SYNV minireplicon reporter gene expression assay showed that the M protein inhibited viral transcription. However, M protein mutants with weakened nuclear localization signals (NLS) and deficient nuclear interactions with the SYNV nucleocapsid protein were unable to suppress transcription. Moreover, SYNV with M NLS mutations exhibited compromised SIE against wild-type SYNV. From these data, we propose that M protein accumulating in nuclei with primary SYNV infections either coils or prevents uncoiling of nucleocapsids released by the superinfecting SYNV virions and suppresses transcription of superinfecting genomes, thereby preventing superinfection. Our model suggests that the rhabdovirus M protein regulates the transition from replication to virion assembly and renders the infected cells nonpermissive for secondary infections.IMPORTANCE Superinfection exclusion (SIE) is a widespread phenomenon in which an established virus infection prevents reinfection by closely related viruses. Understanding the mechanisms governing SIE will not only advance our basic knowledge of virus infection cycles but may also lead to improved design of antiviral measures. Despite the significance of SIE, our knowledge about viral SIE determinants and their modes of actions remain limited. In this study, we show that sonchus yellow net virus (SYNV) SIE is mediated by the viral matrix (M) protein. During primary infections, accumulation of M protein in infected nuclei results in coiling of genomic nucleocapsids and suppression of viral transcription. Consequently, nucleocapsids released by potential superinfectors are sequestered and are unable to initiate new infections. Our data suggest that SYNV SIE is caused by M protein-mediated transition from replication to virion assembly and that this process prevents secondary infections.
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20
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González R, Wu B, Li X, Martínez F, Elena SF. Mutagenesis Scanning Uncovers Evolutionary Constraints on Tobacco Etch Potyvirus Membrane-Associated 6K2 Protein. Genome Biol Evol 2019; 11:1207-1222. [PMID: 30918938 PMCID: PMC6482416 DOI: 10.1093/gbe/evz069] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2019] [Indexed: 12/30/2022] Open
Abstract
RNA virus high mutation rate is a double-edged sword. At the one side, most mutations jeopardize proteins functions; at the other side, mutations are needed to fuel adaptation. The relevant question then is the ratio between beneficial and deleterious mutations. To evaluate this ratio, we created a mutant library of the 6K2 gene of tobacco etch potyvirus that contains every possible single-nucleotide substitution. 6K2 protein anchors the virus replication complex to the network of endoplasmic reticulum membranes. The library was inoculated into the natural host Nicotiana tabacum, allowing competition among all these mutants and selection of those that are potentially viable. We identified 11 nonsynonymous mutations that remain in the viral population at measurable frequencies and evaluated their fitness. Some had fitness values higher than the wild-type and some were deleterious. The effect of these mutations in the structure, transmembrane properties, and function of 6K2 was evaluated in silico. In parallel, the effect of these mutations in infectivity, virus accumulation, symptoms development, and subcellular localization was evaluated in the natural host. The α-helix H1 in the N-terminal part of 6K2 turned out to be under purifying selection, while most observed mutations affect the link between transmembrane α-helices H2 and H3, fusing them into a longer helix and increasing its rigidity. In general, these changes are associated with higher within-host fitness and development of milder or no symptoms. This finding suggests that in nature selection upon 6K2 may result from a tradeoff between within-host accumulation and severity of symptoms.
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Affiliation(s)
- Rubén González
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, València, Spain
| | - Beilei Wu
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, València, Spain.,Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianghua Li
- Systems Biology Program, Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology, PRBB, Barcelona, Spain
| | - Fernando Martínez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, València, Spain
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, València, Spain.,The Santa Fe Institute, Santa Fe, New Mexico
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21
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Abstract
Viruses are widely used as vectors for heterologous gene expression in cultured cells or natural hosts, and therefore a large number of viruses with exogenous sequences inserted into their genomes have been engineered. Many of these engineered viruses are viable and express heterologous proteins at high levels, but the inserted sequences often prove to be unstable over time and are rapidly lost, limiting heterologous protein expression. Although virologists are aware that inserted sequences can be unstable, processes leading to insert instability are rarely considered from an evolutionary perspective. Here, we review experimental work on the stability of inserted sequences over a broad range of viruses, and we present some theoretical considerations concerning insert stability. Different virus genome organizations strongly impact insert stability, and factors such as the position of insertion can have a strong effect. In addition, we argue that insert stability not only depends on the characteristics of a particular genome, but that it will also depend on the host environment and the demography of a virus population. The interplay between all factors affecting stability is complex, which makes it challenging to develop a general model to predict the stability of genomic insertions. We highlight key questions and future directions, finding that insert stability is a surprisingly complex problem and that there is need for mechanism-based, predictive models. Combining theoretical models with experimental tests for stability under varying conditions can lead to improved engineering of viral modified genomes, which is a valuable tool for understanding genome evolution as well as for biotechnological applications, such as gene therapy.
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Affiliation(s)
- Anouk Willemsen
- Laboratory MIVEGEC (UMR CNRS IRD University of Montpellier), Centre National de la Recherche Scientifique (CNRS), 911 Avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France
| | - Mark P Zwart
- Netherlands Institute of Ecology (NIOO-KNAW), Postbus 50, 6700 AB, Wageningen, The Netherlands
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22
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Abstract
Many organisms disperse in groups, yet this process is understudied in viruses. Recent work, however, has uncovered different types of collective infectious units, all of which lead to the joint delivery of multiple viral genome copies to target cells, favoring co-infections. Collective spread of viruses can occur through widely different mechanisms, including virion aggregation driven by specific extracellular components, cloaking inside lipid vesicles, encasement in protein matrices, or binding to cell surfaces. Cell-to-cell viral spread, which allows the transmission of individual virions in a confined environment, is yet another mode of clustered virus dissemination. Nevertheless, the selective advantages of dispersing in groups remain poorly understood in most cases. Collective dispersal might have emerged as a means of sharing efficacious viral transmission vehicles. Alternatively, increasing the cellular multiplicity of infection may confer certain short-term benefits to viruses, such as overwhelming antiviral responses, avoiding early stochastic loss of viral components required for initiating infection, or complementing genetic defects present in different viral genomes. However, increasing infection multiplicity may also entail long-term costs, such as mutation accumulation and the evolution of defective particles or other types of cheater viruses. These costs and benefits, in turn, should depend on the genetic relatedness among collective infectious unit members. Establishing the genetic basis of collective viral dispersal and performing controlled experiments to pinpoint fitness effects at different spatial and temporal scales should help us clarify the implications of these spread modes for viral fitness, pathogenicity, and evolution.
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Affiliation(s)
- Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, C/Catedrático Agustín Escardino 9, Paterna, València, Spain
| | - María-Isabel Thoulouze
- Institut Pasteur, Structural Virology Unit, Biofilm & Viral Transmission Group, Paris, France
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23
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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.
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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.
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Li X, Hataya T. Construction and characterization of an infectious cDNA clone of potato virus S developed from selected populations that survived genetic bottlenecks. Virol J 2019; 16:18. [PMID: 30728059 PMCID: PMC6364481 DOI: 10.1186/s12985-019-1124-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 01/23/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Infectious cDNA clones are a powerful tool for studies on RNA viruses using reverse genetics. Potato virus S (PVS) is a carlavirus with a worldwide distribution. Although the complete genome sequences of many PVS isolates have been reported, the construction of an infectious cDNA clone of PVS is yet to be reported. The aim of this study is the development and molecular characterization of an infectious cDNA clone of PVS. METHODS A full-length cDNA clone pPVS-H-FL-AB was constructed by connecting eight cDNA clones of PVS isolate H95. Capped RNA transcripts from pPVS-H-FL-AB and a modified clone pPVS-H-FL-H, containing the consensus genome sequence of PVS-H95, proved to be non-infectious. Therefore, a full-length cDNA clone pPVS-H-FL-β was reconstructed from PVS-H00, isolated from PVS-H95 populations by repeating a single local lesion isolation in Chenopodium quinoa three times; PVS-H00 appeared to be a selected variant that survived genetic bottlenecks. The sequence of cDNA clone pPVS-H-FL-β was determined as the genome sequence of PVS-H00 and compared with the consensus sequence of PVS-H95 genome. RESULTS All Nicotiana occidentalis plants inoculated with ≥0.2 μg capped RNA transcripts from pPVS-H-FL-β developed symptoms on upper leaves, as observed with PVS-H00 inoculation. Similar levels of viral genomic and subgenomic RNAs and coat protein were detected in systemically infected leaves. Sequence comparison of PVS-H95 and PVS-H00 revealed 370 nucleotide polymorphisms (4.4% of the entire genome sequence), causing 91 amino acid substitutions in six open reading frames (ORFs). The infectivity of chimeric RNAs derived from recombinants between the two cDNA clones revealed that the lack of infectivity of pPVS-H-FL-H transcripts was due to ORF1, which encodes replicase and harbors 80 amino acid substitutions compared with pPVS-H-FL-β. Approximately 71.3% amino acid substitutions in replicase were located within the variable region of unknown function between the putative methyltransferase and ovarian tumor-like protease domains. CONCLUSIONS This is the first report of the development of an infectious cDNA clone of PVS. Our analyses suggest that PVS population within a plant exists as quasispecies and the replicase sequence diversity of PVS obstruct the construction of a full-length infectious cDNA clone.
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Affiliation(s)
- Xin Li
- Laboratory of Pathogen-Plant Interactions, Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Tatsuji Hataya
- Laboratory of Pathogen-Plant Interactions, Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
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25
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Affiliation(s)
| | - Stéphane Blanc
- BGPI, INRA, CIRAD, Montpellier SupAgro, Univ Montpellier, Montpellier, France.
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Population bottlenecks in multicomponent viruses: first forays into the uncharted territory of genome-formula drift. Curr Opin Virol 2018; 33:184-190. [DOI: 10.1016/j.coviro.2018.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/28/2018] [Accepted: 09/07/2018] [Indexed: 11/23/2022]
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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.
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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.
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Zhang XF, Zhang S, Guo Q, Sun R, Wei T, Qu F. A New Mechanistic Model for Viral Cross Protection and Superinfection Exclusion. FRONTIERS IN PLANT SCIENCE 2018; 9:40. [PMID: 29422912 PMCID: PMC5788904 DOI: 10.3389/fpls.2018.00040] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/09/2018] [Indexed: 05/05/2023]
Abstract
Plants pre-infected with a mild variant of a virus frequently become protected against more severe variants of the same virus through the cross protection phenomenon first discovered in 1929. Despite its widespread use in managing important plant virus diseases, the mechanism of cross protection remains poorly understood. Recent investigations in our labs, by analyzing the whole-plant dynamics of a turnip crinkle virus (TCV) population, coupled with cell biological interrogation of individual TCV variants, revealed possible novel mechanisms for cross protection and the closely related process of superinfection exclusion (SIE). Our new mechanistic model postulates that, for RNA viruses like TCV, SIE manifests a viral function that denies progeny viruses the chance of re-replicating their genomes in the cells of their "parents," and it collaterally targets highly homologous superinfecting viruses that are indistinguishable from progeny viruses. We further propose that SIE may be evolutionarily selected to maintain an optimal error frequency in progeny genomes. Although primarily based on observations made with TCV, this new model could be broadly applicable to other viruses as it provides a molecular basis for maintaining virus genome fidelity in the face of the error-prone nature of virus replication process.
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Affiliation(s)
- Xiao-Feng Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Feng Qu, Xiao-Feng Zhang,
| | - Shaoyan Zhang
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, Ohio State University, Wooster, OH, United States
| | - Qin Guo
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, Ohio State University, Wooster, OH, United States
| | - Rong Sun
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, Ohio State University, Wooster, OH, United States
| | - Taiyun Wei
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Feng Qu
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, Ohio State University, Wooster, OH, United States
- *Correspondence: Feng Qu, Xiao-Feng Zhang,
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29
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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.
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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
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30
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Lequime S, Richard V, Cao-Lormeau VM, Lambrechts L. Full-genome dengue virus sequencing in mosquito saliva shows lack of convergent positive selection during transmission by Aedes aegypti. Virus Evol 2017; 3:vex031. [PMID: 29497564 PMCID: PMC5782851 DOI: 10.1093/ve/vex031] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Like other pathogens with high mutation and replication rates, within-host dengue virus
(DENV) populations evolve during infection of their main mosquito vector, Aedes
aegypti. Within-host DENV evolution during transmission provides opportunities
for adaptation and emergence of novel virus variants. Recent studies of DENV genetic
diversity failed to detect convergent evolution of adaptive mutations in mosquito tissues
such as midgut and salivary glands, suggesting that convergent positive selection is not a
major driver of within-host DENV evolution in the vector. However, it is unknown whether
this conclusion extends to the transmitted viral subpopulation because it is technically
difficult to sequence DENV genomes in mosquito saliva. Here, we achieved DENV full-genome
sequencing by pooling saliva samples collected non-sacrificially from 49 to 163 individual
Ae. aegypti mosquitoes previously infected with one of two DENV-1
genotypes. We compared the transmitted viral subpopulations found in the pooled saliva
samples collected in time series with the input viral population present in the infectious
blood meal. In all pooled saliva samples examined, the full-genome consensus sequence of
the input viral population was unchanged. Although the pooling strategy prevents analysis
of individual saliva samples, our results demonstrate the lack of strong convergent
positive selection during a single round of DENV transmission by Ae.
aegypti. This finding reinforces the idea that genetic drift and purifying
selection are the dominant evolutionary forces shaping within-host DENV genetic diversity
during transmission by mosquitoes.
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Affiliation(s)
- Sebastian Lequime
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, 28 rue du Docteur Roux, 75015 Paris, France.,Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, 25-28 rue du Docteur Roux, 75015 Paris, France.,Université Pierre et Marie Curie, Cellule Pasteur UPMC, 4 place Jussieu, 75005 Paris, France
| | - Vaea Richard
- Unit of Emerging Infectious Diseases, Institut Louis Malardé, BP 30, 98713 Papeete, Tahiti, French Polynesia
| | - Van-Mai Cao-Lormeau
- Unit of Emerging Infectious Diseases, Institut Louis Malardé, BP 30, 98713 Papeete, Tahiti, French Polynesia
| | - Louis Lambrechts
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, 28 rue du Docteur Roux, 75015 Paris, France.,Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, 25-28 rue du Docteur Roux, 75015 Paris, France
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31
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Zhang XF, Sun R, Guo Q, Zhang S, Meulia T, Halfmann R, Li D, Qu F. A self-perpetuating repressive state of a viral replication protein blocks superinfection by the same virus. PLoS Pathog 2017; 13:e1006253. [PMID: 28267773 PMCID: PMC5357057 DOI: 10.1371/journal.ppat.1006253] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/17/2017] [Accepted: 02/22/2017] [Indexed: 11/19/2022] Open
Abstract
Diverse animal and plant viruses block the re-infection of host cells by the same or highly similar viruses through superinfection exclusion (SIE), a widely observed, yet poorly understood phenomenon. Here we demonstrate that SIE of turnip crinkle virus (TCV) is exclusively determined by p28, one of the two replication proteins encoded by this virus. p28 expressed from a TCV replicon exerts strong SIE to a different TCV replicon. Transiently expressed p28, delivered simultaneously with, or ahead of, a TCV replicon, largely recapitulates this repressive activity. Interestingly, p28-mediated SIE is dramatically enhanced by C-terminally fused epitope tags or fluorescent proteins, but weakened by N-terminal modifications, and it inversely correlates with the ability of p28 to complement the replication of a p28-defective TCV replicon. Strikingly, p28 in SIE-positive cells forms large, mobile punctate inclusions that trans-aggregate a non-coalescing, SIE-defective, yet replication-competent p28 mutant. These results support a model postulating that TCV SIE is caused by the formation of multimeric p28 complexes capable of intercepting fresh p28 monomers translated from superinfector genomes, thereby abolishing superinfector replication. This model could prove to be applicable to other RNA viruses, and offer novel targets for antiviral therapy.
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Affiliation(s)
- Xiao-Feng Zhang
- Department of Plant Pathology, The Ohio State University, Wooster, Ohio, United States of America
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Rong Sun
- Department of Plant Pathology, The Ohio State University, Wooster, Ohio, United States of America
| | - Qin Guo
- Department of Plant Pathology, The Ohio State University, Wooster, Ohio, United States of America
| | - Shaoyan Zhang
- Department of Plant Pathology, The Ohio State University, Wooster, Ohio, United States of America
| | - Tea Meulia
- Department of Plant Pathology, The Ohio State University, Wooster, Ohio, United States of America
- Molecular and Cellular Imaging Center, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, United States of America
| | - Randal Halfmann
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Dawei Li
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Feng Qu
- Department of Plant Pathology, The Ohio State University, Wooster, Ohio, United States of America
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32
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Shapira L, Ralph M, Tomer E, Cohen S, Kobiler O. Histone Deacetylase Inhibitors Reduce the Number of Herpes Simplex Virus-1 Genomes Initiating Expression in Individual Cells. Front Microbiol 2016; 7:1970. [PMID: 27999572 PMCID: PMC5138200 DOI: 10.3389/fmicb.2016.01970] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 11/24/2016] [Indexed: 01/31/2023] Open
Abstract
Although many viral particles can enter a single cell, the number of viral genomes per cell that establish infection is limited. However, mechanisms underlying this restriction were not explored in depth. For herpesviruses, one of the possible mechanisms suggested is chromatinization and silencing of the incoming genomes. To test this hypothesis, we followed infection with three herpes simplex virus 1 (HSV-1) fluorescence expressing recombinants in the presence or absence of histone deacetylases inhibitors (HDACi's). Unexpectedly, a lower number of viral genomes initiated expression in the presence of these inhibitors. This phenomenon was observed using several HDACi: Trichostatin A (TSA), Suberohydroxamic Acid, Valporic Acid, and Suberoylanilide Hydroxamic Acid. We found that HDACi presence did not change the progeny outcome from the infected cells but did alter the kinetic of the gene expression from the viral genomes. Different cell types (HFF, Vero, and U2OS), which vary in their capability to activate intrinsic and innate immunity, show a cell specific basal average number of viral genomes establishing infection. Importantly, in all cell types, treatment with TSA reduced the number of viral genomes. ND10 nuclear bodies are known to interact with the incoming herpes genomes and repress viral replication. The viral immediate early protein, ICP0, is known to disassemble the ND10 bodies and to induce degradation of some of the host proteins in these domains. HDACi treated cells expressed higher levels of some of the host ND10 proteins (promyelocytic leukemia and ATRX), which may explain the lower number of viral genomes initiating expression per cell. Corroborating this hypothesis, infection with three HSV-1 recombinants carrying a deletion in the gene coding for ICP0, show a reduction in the number of genomes being expressed in U2OS cells. We suggest that alterations in the levels of host proteins involved in intrinsic antiviral defense may result in differences in the number of genomes that initiate expression.
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Affiliation(s)
- Lev Shapira
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University Tel Aviv, Israel
| | - Maya Ralph
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University Tel Aviv, Israel
| | - Enosh Tomer
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University Tel Aviv, Israel
| | - Shai Cohen
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University Tel Aviv, Israel
| | - Oren Kobiler
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University Tel Aviv, Israel
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33
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Abstract
Multipartite viruses have one of the most puzzling genetic organizations found in living organisms. These viruses have several genome segments, each containing only a part of the genetic information, and each individually encapsidated into a separate virus particle. While countless studies on molecular and cellular mechanisms of the infection cycle of multipartite viruses are available, just as for other virus types, very seldom is their lifestyle questioned at the viral system level. Moreover, the rare available “system” studies are purely theoretical, and their predictions on the putative benefit/cost balance of this peculiar genetic organization have not received experimental support. In light of ongoing progresses in general virology, we here challenge the current hypotheses explaining the evolutionary success of multipartite viruses and emphasize their shortcomings. We also discuss alternative ideas and research avenues to be explored in the future in order to solve the long-standing mystery of how viral systems composed of interdependent but physically separated information units can actually be functional.
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34
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Zwart MP, Elena SF. Matters of Size: Genetic Bottlenecks in Virus Infection and Their Potential Impact on Evolution. Annu Rev Virol 2016; 2:161-79. [PMID: 26958911 DOI: 10.1146/annurev-virology-100114-055135] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
For virus infections of multicellular hosts, narrow genetic bottlenecks during transmission and within-host spread appear to be widespread. These bottlenecks will affect the maintenance of genetic variation in a virus population and the prevalence of mixed-strain infections, thereby ultimately determining the strength with which different random forces act during evolution. Here we consider different approaches for estimating bottleneck sizes and weigh their merits. We then review quantitative estimates of bottleneck size during cellular infection, within-host spread, horizontal transmission, and finally vertical transmission. In most cases we find that bottlenecks do regularly occur, although in many cases they appear to be virion-concentration dependent. Finally, we consider the evolutionary implications of genetic bottlenecks during virus infection. Although on average strong bottlenecks will lead to declines in fitness, we consider a number of scenarios in which bottlenecks could also be advantageous for viruses.
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Affiliation(s)
- Mark P Zwart
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politècnica de València, 46022 València, Spain; .,Institute of Theoretical Physics, University of Cologne, 50937 Cologne, Germany;
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politècnica de València, 46022 València, Spain; .,The Santa Fe Institute, Santa Fe, New Mexico 87501
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35
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Cervera H, Elena SF. Genetic variation in fitness within a clonal population of a plant RNA virus. Virus Evol 2016; 2:vew006. [PMID: 27774299 PMCID: PMC4989883 DOI: 10.1093/ve/vew006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/11/2016] [Accepted: 02/16/2016] [Indexed: 01/01/2023] Open
Abstract
A long-standing observation in evolutionary virology is that RNA virus populations are highly polymorphic, composed by a mixture of genotypes whose abundances in the population depend on complex interaction between fitness differences, mutational coupling and genetic drift. It was shown long ago, though in cell cultures, that most of these genotypes had lower fitness than the population they belong, an observation that explained why single-virion passages turned on Muller’s ratchet while very large population passages resulted in fitness increases in novel environments. Here we report the results of an experiment specifically designed to evaluate in vivo the fitness differences among the subclonal components of a clonal population of the plant RNA virus tobacco etch potyvirus (TEV). Over 100 individual biological subclones from a TEV clonal population well adapted to the natural tobacco host were obtained by infectivity assays on a local lesion host. The replicative fitness of these subclones was then evaluated during infection of tobacco relative to the fitness of large random samples taken from the starting clonal population. Fitness was evaluated at increasing number of days post-inoculation. We found that at early days, the average fitness of subclones was significantly lower than the fitness of the clonal population, thus confirming previous observations that most subclones contained deleterious mutations. However, as the number of days of viral replication increases, population size expands exponentially, more beneficial and compensatory mutations are produced, and selection becomes more effective in optimizing fitness, the differences between subclones and the population disappeared.
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Affiliation(s)
- Héctor Cervera
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain; The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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36
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Bartels M, French R, Graybosch RA, Tatineni S. Triticum mosaic virus exhibits limited population variation yet shows evidence of parallel evolution after replicated serial passage in wheat. Virology 2016; 492:92-100. [PMID: 26914507 DOI: 10.1016/j.virol.2016.02.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 02/11/2016] [Accepted: 02/12/2016] [Indexed: 10/22/2022]
Abstract
An infectious cDNA clone of Triticum mosaic virus (TriMV) (genus Poacevirus; family Potyviridae) was used to establish three independent lineages in wheat to examine intra-host population diversity levels within protein 1 (P1) and coat protein (CP) cistrons over time. Genetic variation was assessed at passages 9, 18 and 24 by single-strand conformation polymorphism, followed by nucleotide sequencing. The founding P1 region genotype was retained at high frequencies in most lineage/passage populations, while the founding CP genotype disappeared after passage 18 in two lineages. We found that rare TriMV genotypes were present only transiently and lineages followed independent evolutionary trajectories, suggesting that genetic drift dominates TriMV evolution. These results further suggest that experimental populations of TriMV exhibit lower mutant frequencies than that of Wheat streak mosaic virus (genus Tritimovirus; family Potyviridae) in wheat. Nevertheless, there was evidence for parallel evolution at a synonymous site in the TriMV CP cistron.
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Affiliation(s)
- Melissa Bartels
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Roy French
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA.
| | - Robert A Graybosch
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Satyanarayana Tatineni
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA.
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37
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Papkou A, Gokhale CS, Traulsen A, Schulenburg H. Host-parasite coevolution: why changing population size matters. ZOOLOGY 2016; 119:330-8. [PMID: 27161157 DOI: 10.1016/j.zool.2016.02.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 01/30/2016] [Accepted: 02/10/2016] [Indexed: 01/08/2023]
Abstract
Host-parasite coevolution is widely assumed to have a major influence on biological evolution, especially as these interactions impose high selective pressure on the reciprocally interacting antagonists. The exact nature of the underlying dynamics is yet under debate and may be determined by recurrent selective sweeps (i.e., arms race dynamics), negative frequency-dependent selection (i.e., Red Queen dynamics), or a combination thereof. These interactions are often associated with reciprocally induced changes in population size, which, in turn, should have a strong impact on co-adaptation processes, yet are neglected in most current work on the topic. Here, we discuss potential consequences of temporal variations in population size on host-parasite coevolution. The limited empirical data available and the current theoretical literature in this field highlight that the consideration of such interaction-dependent population size changes is likely key for the full understanding of the coevolutionary dynamics, and, thus, a more realistic view on the complex nature of species interactions.
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Affiliation(s)
- Andrei Papkou
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-University of Kiel, 24098, Kiel, Germany
| | - Chaitanya S Gokhale
- New Zealand Institute for Advanced Study, Massey University, Private Bag 102904, Auckland 0745, New Zealand
| | - Arne Traulsen
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-University of Kiel, 24098, Kiel, Germany.
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RNA Silencing May Play a Role in but Is Not the Only Determinant of the Multiplicity of Infection. J Virol 2015; 90:553-61. [PMID: 26491166 DOI: 10.1128/jvi.02345-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 10/15/2015] [Indexed: 01/01/2023] Open
Abstract
UNLABELLED The multiplicity of infection (MOI), i.e., the number of viral genomes that infect a cell, is an important parameter in virus evolution, which for each virus and environment may have an optimum value that maximizes virus fitness. Thus, the MOI might be controlled by virus functions, an underexplored hypothesis in eukaryote-infecting viruses. To analyze if the MOI is controlled by virus functions, we estimated the MOI in plants coinfected by two genetic variants of Tomato bushy stunt virus (TBSV); by TBSV and a TBSV-derived defective interfering RNA (DI-RNA); or by TBSV and a second tombusvirus, Cymbidium ringspot virus (CymRSV). The MOI was significantly larger in TBSV-CymRSV coinfections (~4.0) than in TBSV-TBSV or TBSV-DI-RNA coinfections (~1.7 to 2.2). Coinfections by CymRSV or TBSV with chimeras in which an open reading frame (ORF) of one virus species was replaced by that of the other identified a role of viral proteins in determining the MOI, which ranged from 1.6 to 3.9 depending on the coinfecting genotypes. However, no virus-encoded protein or genomic region was the sole MOI determinant. Coinfections by CymRSV and TBSV mutants in which the expression of the gene-silencing suppressor protein p19 was abolished also showed a possible role of gene silencing in MOI determination. Taken together, these results demonstrate that the MOI is a quantitative trait showing continuous variation and that as such it has a complex determination involving different virus-encoded functions. IMPORTANCE The number of viral genomes infecting a cell, or the multiplicity of infection (MOI), is an important parameter in virus evolution affecting recombination rates, selection intensity on viral genes, evolution of multipartite genomes, or hyperparasitism by satellites or defective interfering particles. For each virus and environment, the MOI may have an optimum value that maximizes virus fitness, but little is known about MOI control in eukaryote-infecting viruses. We show here that in plants coinfected by two genotypes of Tomato bushy stunt virus (TBSV), the MOI was lower than in plants coinfected by TBSV and Cymbidium ringspot virus (CymRSV). Coinfections by CymRSV or TBSV with TBSV-CymRSV chimeras showed a role of viral proteins in MOI determination. Coinfections by CymRSV and TBSV mutants not expressing the gene-silencing suppressor protein also showed a role of gene silencing in MOI determination. The results demonstrate that the MOI is a quantitative trait with a complex determination involving different viral functions.
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Blaisdell GK, Zhang S, Bratburd JR, Daane KM, Cooper ML, Almeida RPP. Interactions Within Susceptible Hosts Drive Establishment of Genetically Distinct Variants of an Insect-Borne Pathogen. JOURNAL OF ECONOMIC ENTOMOLOGY 2015; 108:1531-1539. [PMID: 26470292 DOI: 10.1093/jee/tov153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/15/2015] [Indexed: 06/05/2023]
Abstract
Coinfections are common, leading to pathogen interactions during transmission and establishment in a host. However, few studies have tested the relative strengths of pathogen interactions in vectors and hosts that determine the outcome of infection. We tested interactions between two genetically distinct variants of the mealybug-transmitted Grapevine leafroll-associated virus 3. The transmission efficiency of each variant in single variant inoculations by two vector species was determined. The effects of vector species, a coinfected source, and simultaneous inoculation from multiple hosts to one host on variant establishment were examined. Within-vector interactions could have a role in transmission from hosts containing mixed infections, but not when vectors were moved from separate singly infected source plants to a single recipient plant. The invasive Planococcus ficus (Signoret) was a more efficient vector than Pseudococcus viburni (Signoret). Transmission efficiency of the two variants did not differ in single variant inoculations. Overall infections were the same whether from singly or coinfected source plants. In mixed inoculations, establishment of one variant was reduced. Mixed inoculations from two singly infected source plants resulted in fewer mixed infections than expected by chance. Therefore, the observed outcome was determined subsequent to host inoculation rather than in the vector. The outcome may be due to resource competition between pathogens. Alternatively apparent competition may be responsible; the pathogens' differential ability to overcome host defenses and colonize the host may determine the final outcome of new infections. Detailed knowledge of interactions between pathogens during transmission and establishment could improve understanding and management of disease spread.
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Affiliation(s)
- G K Blaisdell
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720
| | - S Zhang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720
| | - J R Bratburd
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720
| | - K M Daane
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720
| | - M L Cooper
- Division of Agriculture and Natural Resources, University of California, UC Cooperative Extension, 1710 Soscol Ave., Suite 4, Napa, CA 94559
| | - R P P Almeida
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720.
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The Multiplicity of Cellular Infection Changes Depending on the Route of Cell Infection in a Plant Virus. J Virol 2015; 89:9665-75. [PMID: 26178988 DOI: 10.1128/jvi.00537-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 07/08/2015] [Indexed: 12/23/2022] Open
Abstract
UNLABELLED The multiplicity of cellular infection (MOI) is the number of virus genomes of a given virus species that infect individual cells. This parameter chiefly impacts the severity of within-host population bottlenecks as well as the intensity of genetic exchange, competition, and complementation among viral genotypes. Only a few formal estimations of the MOI currently are available, and most theoretical reports have considered this parameter as constant within the infected host. Nevertheless, the colonization of a multicellular host is a complex process during which the MOI may dramatically change in different organs and at different stages of the infection. We have used both qualitative and quantitative approaches to analyze the MOI during the colonization of turnip plants by Turnip mosaic virus. Remarkably, different MOIs were observed at two phases of the systemic infection of a leaf. The MOI was very low in primary infections from virus circulating within the vasculature, generally leading to primary foci founded by a single genome. Each lineage then moved from cell to cell at a very high MOI. Despite this elevated MOI during cell-to-cell progression, coinfection of cells by lineages originating in different primary foci is severely limited by the rapid onset of a mechanism inhibiting secondary infection. Thus, our results unveil an intriguing colonization pattern where individual viral genomes initiate distinct lineages within a leaf. Kin genomes then massively coinfect cells, but coinfection by two distinct lineages is strictly limited. IMPORTANCE The MOI is the size of the viral population colonizing cells and defines major phenomena in virus evolution, like the intensity of genetic exchange and the size of within-host population bottlenecks. However, few studies have quantified the MOI, and most consider this parameter as constant during infection. Our results reveal that the MOI can depend largely on the route of cell infection in a systemically infected leaf. The MOI is usually one genome per cell when cells are infected from virus particles moving long distances in the vasculature, whereas it is much higher during subsequent cell-to-cell movement in mesophyll. However, a fast-acting superinfection exclusion prevents cell coinfection by merging populations originating from different primary foci within a leaf. This complex colonization pattern results in a situation where within-cell interactions are occurring almost exclusively among kin and explains the common but uncharacterized phenomenon of genotype spatial segregation in infected plants.
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Miyashita S, Ishibashi K, Kishino H, Ishikawa M. Viruses roll the dice: the stochastic behavior of viral genome molecules accelerates viral adaptation at the cell and tissue levels. PLoS Biol 2015; 13:e1002094. [PMID: 25781391 PMCID: PMC4364534 DOI: 10.1371/journal.pbio.1002094] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 01/30/2015] [Indexed: 11/30/2022] Open
Abstract
Recent studies on evolutionarily distant viral groups have shown that the number of viral genomes that establish cell infection after cell-to-cell transmission is unexpectedly small (1-20 genomes). This aspect of viral infection appears to be important for the adaptation and survival of viruses. To clarify how the number of viral genomes that establish cell infection is determined, we developed a simulation model of cell infection for tomato mosaic virus (ToMV), a positive-strand RNA virus. The model showed that stochastic processes that govern the replication or degradation of individual genomes result in the infection by a small number of genomes, while a large number of infectious genomes are introduced in the cell. It also predicted two interesting characteristics regarding cell infection patterns: stochastic variation among cells in the number of viral genomes that establish infection and stochastic inequality in the accumulation of their progenies in each cell. Both characteristics were validated experimentally by inoculating tobacco cells with a library of nucleotide sequence-tagged ToMV and analyzing the viral genomes that accumulated in each cell using a high-throughput sequencer. An additional simulation model revealed that these two characteristics enhance selection during tissue infection. The cell infection model also predicted a mechanism that enhances selection at the cellular level: a small difference in the replication abilities of coinfected variants results in a large difference in individual accumulation via the multiple-round formation of the replication complex (i.e., the replication machinery). Importantly, this predicted effect was observed in vivo. The cell infection model was robust to changes in the parameter values, suggesting that other viruses could adopt similar adaptation mechanisms. Taken together, these data reveal a comprehensive picture of viral infection processes including replication, cell-to-cell transmission, and evolution, which are based on the stochastic behavior of the viral genome molecules in each cell.
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Affiliation(s)
- Shuhei Miyashita
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Kawaguchi, Japan
- Plant-Microbe Interactions Research Unit, Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Kazuhiro Ishibashi
- Plant-Microbe Interactions Research Unit, Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Hirohisa Kishino
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Masayuki Ishikawa
- Plant-Microbe Interactions Research Unit, Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba, Japan
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42
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Chujo T, Ishibashi K, Miyashita S, Ishikawa M. Functions of the 5'- and 3'-untranslated regions of tobamovirus RNA. Virus Res 2015; 206:82-9. [PMID: 25683511 DOI: 10.1016/j.virusres.2015.01.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 01/23/2015] [Accepted: 01/30/2015] [Indexed: 12/17/2022]
Abstract
The tobamovirus genome is a 5'-m(7)G-capped RNA that carries a tRNA-like structure at its 3'-terminus. The genomic RNA serves as the template for both translation and negative-strand RNA synthesis. The 5'- and 3'-untranslated regions (UTRs) of the genomic RNA contain elements that enhance translation, and the 3'-UTR also contains the elements necessary for the initiation of negative-strand RNA synthesis. Recent studies using a cell-free viral RNA translation-replication system revealed that a 70-nucleotide region containing a part of the 5'-UTR is bound cotranslationally by tobacco mosaic virus (TMV) replication proteins translated from the genomic RNA and that the binding leads the genomic RNA to RNA replication pathway. This mechanism explains the cis-preferential replication of TMV by the replication proteins. The binding also inhibits further translation to avoid a fatal ribosome-RNA polymerase collision, which might arise if translation and negative-strand synthesis occur simultaneously on a single genomic RNA molecule. Therefore, the 5'- and 3'-UTRs play multiple important roles in the life cycle of tobamovirus.
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Affiliation(s)
- Tetsuya Chujo
- Plant-Microbe Interactions Research Unit, Division of Plant Sciences, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Kazuhiro Ishibashi
- Plant-Microbe Interactions Research Unit, Division of Plant Sciences, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Shuhei Miyashita
- Plant-Microbe Interactions Research Unit, Division of Plant Sciences, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Masayuki Ishikawa
- Plant-Microbe Interactions Research Unit, Division of Plant Sciences, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan.
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43
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Affiliation(s)
- Jean-François Laliberté
- INRS–Institut Armand-Frappier, Institut National de la Recherche Scientifique, Laval, Québec H7V 1B7, Canada;
| | - Huanquan Zheng
- Department of Biology, McGill University, Montréal, Québec H3A 1B1, Canada;
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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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45
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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: 37] [Impact Index Per Article: 3.7] [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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46
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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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Fabre F, Moury B, Johansen EI, Simon V, Jacquemond M, Senoussi R. Narrow bottlenecks affect Pea seedborne mosaic virus populations during vertical seed transmission but not during leaf colonization. PLoS Pathog 2014; 10:e1003833. [PMID: 24415934 PMCID: PMC3887104 DOI: 10.1371/journal.ppat.1003833] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 10/29/2013] [Indexed: 11/19/2022] Open
Abstract
The effective size of populations (Ne) determines whether selection or genetic drift is the predominant force shaping their genetic structure and evolution. Populations having high Ne adapt faster, as selection acts more intensely, than populations having low Ne, where random effects of genetic drift dominate. Estimating Ne for various steps of plant virus life cycle has been the focus of several studies in the last decade, but no estimates are available for the vertical transmission of plant viruses, although virus seed transmission is economically significant in at least 18% of plant viruses in at least one plant species. Here we study the co-dynamics of two variants of Pea seedborne mosaic virus (PSbMV) colonizing leaves of pea plants (Pisum sativum L.) during the whole flowering period, and their subsequent transmission to plant progeny through seeds. Whereas classical estimators of Ne could be used for leaf infection at the systemic level, as virus variants were equally competitive, dedicated stochastic models were needed to estimate Ne during vertical transmission. Very little genetic drift was observed during the infection of apical leaves, with Ne values ranging from 59 to 216. In contrast, a very drastic genetic drift was observed during vertical transmission, with an average number of infectious virus particles contributing to the infection of a seedling from an infected mother plant close to one. A simple model of vertical transmission, assuming a cumulative action of virus infectious particles and a virus density threshold required for vertical transmission to occur fitted the experimental data very satisfactorily. This study reveals that vertically-transmitted viruses endure bottlenecks as narrow as those imposed by horizontal transmission. These bottlenecks are likely to slow down virus adaptation and could decrease virus fitness and virulence.
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Affiliation(s)
- Frédéric Fabre
- INRA, UR407 Pathologie Végétale, Domaine Saint Maurice, Montfavet, France
| | - Benoît Moury
- INRA, UR407 Pathologie Végétale, Domaine Saint Maurice, Montfavet, France
| | - Elisabeth Ida Johansen
- University of Copenhagen, Department of Plant and Environmental Sciences, Frederiksberg C, Denmark
| | - Vincent Simon
- INRA, UR407 Pathologie Végétale, Domaine Saint Maurice, Montfavet, France
| | | | - Rachid Senoussi
- INRA, UR546 Biostatistique et Processus Spatiaux, Domaine Saint-Paul, Site Agroparc, Avignon, France
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48
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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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49
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Simmons HE, Dunham JP, Zinn KE, Munkvold GP, Holmes EC, Stephenson AG. Zucchini yellow mosaic virus (ZYMV, Potyvirus): vertical transmission, seed infection and cryptic infections. Virus Res 2013; 176:259-64. [PMID: 23845301 PMCID: PMC3774540 DOI: 10.1016/j.virusres.2013.06.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 06/25/2013] [Accepted: 06/28/2013] [Indexed: 12/31/2022]
Abstract
The role played by seed transmission in the evolution and epidemiology of viral crop pathogens remains unclear. We determined the seed infection and vertical transmission rates of zucchini yellow mosaic virus (ZYMV), in addition to undertaking Illumina sequencing of nine vertically transmitted ZYMV populations. We previously determined the seed-to-seedling transmission rate of ZYMV in Cucurbita pepo ssp. texana (a wild gourd) to be 1.6%, and herein observed a similar rate (1.8%) in the subsequent generation. We also observed that the seed infection rate is substantially higher (21.9%) than the seed-to-seedling transmission rate, suggesting that a major population bottleneck occurs during seed germination and seedling growth. In contrast, that two thirds of the variants present in the horizontally transmitted inoculant population were also present in the vertically transmitted populations implies that the bottleneck at vertical transmission may not be particularly severe. Strikingly, all of the vertically infected plants were symptomless in contrast to those infected horizontally, suggesting that vertical infection may be cryptic. Although no known virulence determining mutations were observed in the vertically infected samples, the 5' untranslated region was highly variable, with at least 26 different major haplotypes in this region compared to the two major haplotypes observed in the horizontally transmitted population. That the regions necessary for vector transmission are retained in the vertically infected populations, combined with the cryptic nature of vertical infection, suggests that seed transmission may be a significant contributor to the spread of ZYMV.
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Affiliation(s)
- H E Simmons
- Seed Science Center, Iowa State University, Ames, IA 50011, USA.
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50
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Gene copy number is differentially regulated in a multipartite virus. Nat Commun 2013; 4:2248. [DOI: 10.1038/ncomms3248] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 07/05/2013] [Indexed: 12/14/2022] Open
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