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Butkovic A, Ellis TJ, Gonzalez R, Jaegle B, Nordborg M, Elena SF. Genetic basis of Arabidopsis thaliana responses to infection by naïve and adapted isolates of turnip mosaic virus. eLife 2024; 12:RP89749. [PMID: 38240739 PMCID: PMC10945600 DOI: 10.7554/elife.89749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024] Open
Abstract
Plant viruses account for enormous agricultural losses worldwide, and the most effective way to combat them is to identify genetic material conferring plant resistance to these pathogens. Aiming to identify genetic associations with responses to infection, we screened a large panel of Arabidopsis thaliana natural inbred lines for four disease-related traits caused by infection by A. thaliana-naïve and -adapted isolates of the natural pathogen turnip mosaic virus (TuMV). We detected a strong, replicable association in a 1.5 Mb region on chromosome 2 with a 10-fold increase in relative risk of systemic necrosis. The region contains several plausible causal genes as well as abundant structural variation, including an insertion of a Copia transposon into a Toll/interleukin receptor (TIR-NBS-LRR) coding for a gene involved in defense, that could be either a driver or a consequence of the disease-resistance locus. When inoculated with TuMV, loss-of-function mutant plants of this gene exhibited different symptoms than wild-type plants. The direction and severity of symptom differences depended on the adaptation history of the virus. This increase in symptom severity was specific for infections with the adapted isolate. Necrosis-associated alleles are found worldwide, and their distribution is consistent with a trade-off between resistance during viral outbreaks and a cost of resistance otherwise, leading to negative frequency-dependent selection.
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Affiliation(s)
- Anamarija Butkovic
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Parc Científic UVValènciaSpain
| | - Thomas James Ellis
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter, Doktor-Bohr-GasseViennaAustria
| | - Ruben Gonzalez
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Parc Científic UVValènciaSpain
| | - Benjamin Jaegle
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter, Doktor-Bohr-GasseViennaAustria
| | - Magnus Nordborg
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter, Doktor-Bohr-GasseViennaAustria
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Parc Científic UVValènciaSpain
- The Santa Fe InstituteSanta FeUnited States
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Lezcano OM, Fuhrmann L, Ramakrishnan G, Beerenwinkel N, Huynen MA, van Rij RP. Parallel evolution and enhanced virulence upon in vivo passage of an RNA virus in Drosophila melanogaster. Virus Evol 2023; 9:vead074. [PMID: 38162315 PMCID: PMC10757409 DOI: 10.1093/ve/vead074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/30/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024] Open
Abstract
Virus evolution is strongly affected by antagonistic co-evolution of virus and host. Host immunity positively selects for viruses that evade the immune response, which in turn may drive counter-adaptations in host immune genes. We investigated how host immune pressure shapes virus populations, using the fruit fly Drosophila melanogaster and its natural pathogen Drosophila C virus (DCV), as a model. We performed an experimental evolution study in which DCV was serially passaged for ten generations in three fly genotypes differing in their antiviral RNAi response: wild-type flies and flies in which the endonuclease gene Dicer-2 was either overexpressed or inactivated. All evolved virus populations replicated more efficiently in vivo and were more virulent than the parental stock. The number of polymorphisms increased in all three host genotypes with passage number, which was most pronounced in Dicer-2 knockout flies. Mutational analysis showed strong parallel evolution, as mutations accumulated in a specific region of the VP3 capsid protein in every lineage in a host genotype-independent manner. The parental tyrosine at position ninety-five of VP3 was substituted with either one of five different amino acids in fourteen out of fifteen lineages. However, no consistent amino acid changes were observed in the viral RNAi suppressor gene 1A, nor elsewhere in the genome in any of the host backgrounds. Our study indicates that the RNAi response restricts the sequence space that can be explored by viral populations. Moreover, our study illustrates how evolution towards higher virulence can be a highly reproducible, yet unpredictable process.
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Affiliation(s)
| | - Lara Fuhrmann
- Department of Biosystems Science and Engineering, ETH Zurich, Klingelbergstrasse 48, Basel 4056, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Amphipôle, Lausanne 1015, Switzerland
| | - Gayatri Ramakrishnan
- Department of Medical BioSciences, Radboud University Medical Center, P.O. Box 9101, Nijmegen 6500 HB, The Netherlands
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Klingelbergstrasse 48, Basel 4056, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Amphipôle, Lausanne 1015, Switzerland
- Department of Medical Microbiology, Radboud University Medical Center, P.O. Box 9101, Nijmegen 6500 HB, The Netherlands
| | | | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Medical Center, P.O. Box 9101, Nijmegen 6500 HB, The Netherlands
- Department of Medical BioSciences, Radboud University Medical Center, P.O. Box 9101, Nijmegen 6500 HB, The Netherlands
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Jokinen M, Sallinen S, Jones MM, Sirén J, Guilbault E, Susi H, Laine AL. The first arriving virus shapes within-host viral diversity during natural epidemics. Proc Biol Sci 2023; 290:20231486. [PMID: 37700649 PMCID: PMC10498040 DOI: 10.1098/rspb.2023.1486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 08/17/2023] [Indexed: 09/14/2023] Open
Abstract
Viral diversity has been discovered across scales from host individuals to populations. However, the drivers of viral community assembly are still largely unknown. Within-host viral communities are formed through co-infections, where the interval between the arrival times of viruses may vary. Priority effects describe the timing and order in which species arrive in an environment, and how early colonizers impact subsequent community assembly. To study the effect of the first-arriving virus on subsequent infection patterns of five focal viruses, we set up a field experiment using naïve Plantago lanceolata plants as sentinels during a seasonal virus epidemic. Using joint species distribution modelling, we find both positive and negative effects of early season viral infection on late season viral colonization patterns. The direction of the effect depends on both the host genotype and which virus colonized the host early in the season. It is well established that co-occurring viruses may change the virulence and transmission of viral infections. However, our results show that priority effects may also play an important, previously unquantified role in viral community assembly. The assessment of these temporal dynamics within a community ecological framework will improve our ability to understand and predict viral diversity in natural systems.
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Affiliation(s)
- Maija Jokinen
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, 8057 Zürich, Switzerland
| | - Suvi Sallinen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65, 00014, Finland
| | - Mirkka M. Jones
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65, 00014, Finland
- Institute of Biotechnology, HiLIFE-Helsinki Institute of Life Science, University of Helsinki, PO Box 65, 00014, Finland
| | - Jukka Sirén
- Institute of Biotechnology, HiLIFE-Helsinki Institute of Life Science, University of Helsinki, PO Box 65, 00014, Finland
| | - Emy Guilbault
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65, 00014, Finland
| | - Hanna Susi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65, 00014, Finland
| | - Anna-Liisa Laine
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, 8057 Zürich, Switzerland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65, 00014, Finland
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Melero I, González R, Elena SF. Host developmental stages shape the evolution of a plant RNA virus. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220005. [PMID: 36744567 PMCID: PMC9979778 DOI: 10.1098/rstb.2022.0005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Viruses are obligate pathogens that entirely rely on their hosts to complete their infectious cycle. The outcome of viral infections depends on the status of the host. Host developmental stage is an important but sometimes overlooked factor impacting host-virus interactions. This impact is especially relevant in a context where climate change and human activities are altering plant development. To better understand how different host developmental stages shape virus evolution, we experimentally evolved turnip mosaic virus (TuMV) on Arabidopsis thaliana at three different developmental stages: vegetative (juvenile), bolting (transition) and reproductive (mature). After infecting plants with an Arabidopsis-naive or an Arabidopsis-well-adapted TuMV isolate, we observed that hosts in later developmental stages were prone to faster and more severe infections. This observation was extended to viruses belonging to different genera. Thereafter, we experimentally evolved lineages of the naive and the well-adapted TuMV isolates in plants from each of the three developmental stages. All evolved viruses enhanced their infection traits, but this increase was more intense in viruses evolved in younger hosts. The genomic changes of the evolved viral lineages revealed mutation patterns that strongly depended on the founder viral isolate as well as on the developmental stage of the host wherein the lineages were evolved. This article is part of the theme issue 'Infectious disease ecology and evolution in a changing world'.
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Affiliation(s)
- Izan Melero
- Instituto de Biología Integrativa de Sistemas (CSIC - Universitat de València), Paterna, 46182 València, Spain
| | - Rubén González
- Instituto de Biología Integrativa de Sistemas (CSIC - Universitat de València), Paterna, 46182 València, Spain
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (CSIC - Universitat de València), Paterna, 46182 València, Spain,The Santa Fe Institute, Santa Fe 87501, NM, USA
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