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Castiglioni VG, Olmo-Uceda MJ, Martín S, Félix MA, González R, Elena SF. Experimental evolution of an RNA virus in Caenorhabditis elegans. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105623. [PMID: 38901623 DOI: 10.1016/j.meegid.2024.105623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/02/2024] [Accepted: 06/17/2024] [Indexed: 06/22/2024]
Abstract
The discovery of Orsay virus (OrV), the first virus infecting wild populations of Caenorhabditis elegans, has boosted studies of viral immunity pathways in this nematode. Considering the many advantages that C. elegans offers for fundamental research in host-pathogen interactions, this pathosystem has high potential to become a model system for experimental virus evolution studies. However, the evolutionary constraints - i.e, the balance between genetic variation, selection, drift and historical contingency- operating in this pathosystem have barely been explored. Here we describe for the first time an evolution experiment of two different OrV strains in C. elegans. Comparison of the two ancestral strains showed differences in infectivity and sequence, and highlighted the importance of consistently normalize viral inocula for meaningful comparisons among strains. After 10 serial passages of evolution, we report slight changes in infectivity and non-synonymous mutations fixed in the evolved viral populations. In addition, we observed numerous minor variants emerging in the viral population. These minor variants were not randomly distributed along the genome but concentrated in polymorphic genomic regions. Overall, our work established the grounds for future experimental virus evolution studies using Caenorhabditis nematodes.
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Affiliation(s)
- Victoria G Castiglioni
- Instituto de Biología Integrativa de Sistemas (CSIC-Universitat de València), Paterna, 46980 València, Spain
| | - María J Olmo-Uceda
- Instituto de Biología Integrativa de Sistemas (CSIC-Universitat de València), Paterna, 46980 València, Spain
| | - Susana Martín
- Instituto de Biología Integrativa de Sistemas (CSIC-Universitat de València), Paterna, 46980 València, Spain
| | - Marie-Anne Félix
- Institut de Biologie de l'École Normale Supérieure, CNRS, INSERM, 75005 Paris, France
| | - Rubén González
- Instituto de Biología Integrativa de Sistemas (CSIC-Universitat de València), Paterna, 46980 València, Spain; Institut de Biologie de l'École Normale Supérieure, CNRS, INSERM, 75005 Paris, France.
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (CSIC-Universitat de València), Paterna, 46980 València, Spain; Santa Fe Institute, Sant Fe, NM 87501, USA.
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Nigg JC, Castelló-Sanjuán M, Blanc H, Frangeul L, Mongelli V, Godron X, Bardin AJ, Saleh MC. Viral infection disrupts intestinal homeostasis via Sting-dependent NF-κB signaling in Drosophila. Curr Biol 2024:S0960-9822(24)00607-9. [PMID: 38823381 DOI: 10.1016/j.cub.2024.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/11/2024] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
Abstract
Host-microbe interactions influence intestinal stem cell (ISC) activity to modulate epithelial turnover and composition. Here, we investigated the functional impacts of viral infection on intestinal homeostasis and the mechanisms by which viral infection alters ISC activity. We report that Drosophila A virus (DAV) infection disrupts intestinal homeostasis in Drosophila by inducing sustained ISC proliferation, resulting in intestinal dysplasia, loss of gut barrier function, and reduced lifespan. We found that additional viruses common in laboratory-reared Drosophila also promote ISC proliferation. The mechanism of DAV-induced ISC proliferation involves progenitor-autonomous epidermal growth factor receptor (EGFR) signaling, c-Jun N-terminal kinase (JNK) activity in enterocytes, and requires Sting-dependent nuclear factor κB (NF-κB) (Relish) activity. We further demonstrate that activating Sting-Relish signaling is sufficient to induce ISC proliferation, promote intestinal dysplasia, and reduce lifespan in the absence of infection. Our results reveal that viral infection can significantly disrupt intestinal physiology, highlight a novel role for Sting-Relish signaling, and support a role for viral infection in aging.
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Affiliation(s)
- Jared C Nigg
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
| | - Mauro Castelló-Sanjuán
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
| | - Hervé Blanc
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
| | - Lionel Frangeul
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
| | - Vanesa Mongelli
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
| | - Xavier Godron
- DNA Script SAS, 67 Avenue de Fontainebleau, 94270 Le Kremlin-Bicêtre, France
| | - Allison J Bardin
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Maria-Carla Saleh
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France.
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Hoang KL, Read TD, King KC. Incomplete immunity in a natural animal-microbiota interaction selects for higher pathogen virulence. Curr Biol 2024; 34:1357-1363.e3. [PMID: 38430909 PMCID: PMC10962313 DOI: 10.1016/j.cub.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/18/2023] [Accepted: 02/07/2024] [Indexed: 03/05/2024]
Abstract
Incomplete immunity in recovered hosts is predicted to favor more virulent pathogens upon re-infection in the population.1 The microbiota colonizing animals can generate a similarly long-lasting, partial immune response, allowing for infection but dampened disease severity.2 We tracked the evolutionary trajectories of a widespread pathogen (Pseudomonas aeruginosa), experimentally passaged through populations of nematodes immune-primed by a natural microbiota member (P. berkeleyensis). This bacterium can induce genes regulated by a mitogen-activated protein kinase (MAPK) signaling pathway effective at conferring protection against pathogen-induced death despite infection.3 Across host populations, this incomplete immunity selected for pathogens more than twice as likely to kill as those evolved in non-primed (i.e., naive) or immune-compromised (mutants with a knockout of the MAPK ortholog) control populations. Despite the higher virulence, pathogen molecular evolution in immune-primed hosts was slow and constrained. In comparison, evolving pathogens in immune-compromised hosts were characterized by substantial genomic differentiation and attenuated virulence. These findings directly attribute the incomplete host immunity induced from microbiota as a significant force shaping the virulence and evolutionary dynamics of novel infectious diseases.
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Affiliation(s)
- Kim L Hoang
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK; Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA 30322, USA.
| | - Timothy D Read
- Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA 30322, USA
| | - Kayla C King
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK; Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada; Department of Microbiology & Immunology, University of British Columbia, 1365 - 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.
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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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Maringer K. Re-evaluating the mosquito RNAi pathway's influence on arbovirus transmission. Trends Parasitol 2023; 39:898-899. [PMID: 37758630 DOI: 10.1016/j.pt.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
With new RNA interference (RNAi) pathway-deficient mosquitoes, Merkling et al. invite a shift in our view of this pathway's role in regulating arthropod-borne virus (arbovirus) transmission. While loss of RNAi function enhanced early viral replication, little impact on transmission was observed, inviting renewed exploration of molecular barriers to arbovirus transmission.
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Affiliation(s)
- Kevin Maringer
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK.
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Origins and diversification of animal innate immune responses against viral infections. Nat Ecol Evol 2023; 7:182-193. [PMID: 36635343 DOI: 10.1038/s41559-022-01951-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/11/2022] [Indexed: 01/14/2023]
Abstract
Immune systems are of pivotal importance to any living organism on Earth, as they protect the organism against deleterious effects of viral infections. Though the current knowledge about these systems is still biased towards the immune response in vertebrates, some studies have focused on the identification and characterization of components of invertebrate antiviral immune systems. Two classic model organisms, the insect Drosophila melanogaster and the nematode Caenorhabditis elegans, were instrumental in the discovery of several important components of the innate immune system, such as the Toll-like receptors and the RNA interference pathway. However, these two model organisms provide only a limited view of the evolutionary history of the immune system, as they both are ecdysozoan protostomes. Recent functional studies in non-classic models such as unicellular holozoans (for example, choanoflagellates), lophotrochozoans (for example, oysters) and cnidarians (for example, sea anemones) have added crucial information for understanding the evolution of antiviral systems, as they revealed unexpected ancestral complexity. This Review aims to summarize this information and present the ancestral nature of the antiviral immune response in animals. We also discuss lineage-specific adaptations and future perspectives for the comparative study of the innate immune system that are essential for understanding its evolution.
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Prakash A, Monteith KM, Vale PF. Mechanisms of damage prevention, signalling and repair impact disease tolerance. Proc Biol Sci 2022; 289:20220837. [PMID: 35975433 PMCID: PMC9382215 DOI: 10.1098/rspb.2022.0837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The insect gut is frequently exposed to pathogenic threats and must not only clear these potential infections, but also tolerate relatively high microbe loads. In contrast to the mechanisms that eliminate pathogens, we currently know less about the mechanisms of disease tolerance. We investigated how well-described mechanisms that prevent, signal, control or repair damage during infection contribute to the phenotype of disease tolerance. We established enteric infections with the bacterial pathogen Pseudomonas entomophila in transgenic lines of Drosophila melanogaster fruit flies affecting dcy (a major component of the peritrophic matrix), upd3 (a cytokine-like molecule), irc (a negative regulator of reactive oxygen species) and egfr1 (epithelial growth factor receptor). Flies lacking dcy experienced the highest mortality, while loss of function of either irc or upd3 reduced tolerance in both sexes. The disruption of egfr1 resulted in a severe loss in tolerance in male flies but had no substantial effect on the ability of female flies to tolerate P. entomophila infection, despite carrying greater microbe loads than males. Together, our findings provide evidence for the role of damage limitation mechanisms in disease tolerance and highlight how sexual dimorphism in these mechanisms could generate sex differences in infection outcomes.
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Affiliation(s)
- Arun Prakash
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Katy M. Monteith
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Pedro F. Vale
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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Navarro R, Ambrós S, Butković A, Carrasco JL, González R, Martínez F, Wu B, Elena SF. Defects in Plant Immunity Modulate the Rates and Patterns of RNA Virus Evolution. Virus Evol 2022; 8:veac059. [PMID: 35821716 PMCID: PMC9272744 DOI: 10.1093/ve/veac059] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 06/10/2022] [Accepted: 06/18/2022] [Indexed: 11/13/2022] Open
Abstract
It is assumed that host genetic variability for susceptibility to infection conditions virus evolution. Differences in host susceptibility can drive a virus to diversify into strains that track different defense alleles (e.g. antigenic diversity) or to infect only the most susceptible genotypes. Here, we have studied how variability in host defenses determines the evolutionary fate of a plant RNA virus. We performed evolution experiments with Turnip mosaic potyvirus in Arabidopsis thaliana mutants that had disruptions in infection-response signaling pathways or in genes whose products are essential for potyvirus infection. Plant genotypes were classified into five phenogroups according to their response to infection. We found that evolution proceeded faster in more restrictive hosts than in more permissive ones. Most of the phenotypic differences shown by the ancestral virus across host genotypes were removed after evolution, suggesting the combined action of selection and chance. When all evolved viral lineages were tested in all plant genotypes used in the experiments, we found compelling evidences that the most restrictive plant genotypes selected for more generalist viruses, while more permissive genotypes selected for more specialist viruses. Sequencing the genomes of the evolved viral lineages, we found that selection targeted the multifunctional genome-linked protein VPg in most host genotypes. Overall, this work illustrates how different host defenses modulate the rates and extent of virus evolution.
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Affiliation(s)
- Rebeca Navarro
- Instituto de Biología Integrativa de Sistemas (CSIC - Universitat de València) , Paterna, 46182 València, Spain
| | - Silvia Ambrós
- Instituto de Biología Integrativa de Sistemas (CSIC - Universitat de València) , Paterna, 46182 València, Spain
| | - Anamarija Butković
- Instituto de Biología Integrativa de Sistemas (CSIC - Universitat de València) , Paterna, 46182 València, Spain
| | - José L Carrasco
- 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
| | - Fernando Martínez
- Instituto de Biología Integrativa de Sistemas (CSIC - Universitat de València) , Paterna, 46182 València, Spain
| | - Beilei Wu
- 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 NM87501, USA
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