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Wang Z, Wei P. Shifting the paradigm in RNA virus detection: integrating nucleic acid testing and immunoassays through single-molecule digital ELISA. Front Immunol 2024; 14:1331981. [PMID: 38235132 PMCID: PMC10791976 DOI: 10.3389/fimmu.2023.1331981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024] Open
Abstract
In this review article, we explore the characteristics of RNA viruses and their potential threats to humanity. We also provide a brief overview of the primary contemporary techniques used for the early detection of such viruses. After thoroughly analyzing the strengths and limitations of these methods, we highlight the importance of integrating nucleic acid testing with immunological assays in RNA virus detection. Although notable methodological differences between nucleic acid testing and immune assays pose challenges, the emerging single-molecule immunoassay-digital ELISA may be applied to technically integrate these techniques. We emphasize that the greatest value of digital ELISA is its extensive compatibility, which creates numerous opportunities for real-time, large-scale testing of RNA viruses. Furthermore, we describe the possible developmental trends of digital ELISA in various aspects, such as reaction carriers, identification elements, signal amplification, and data reading, thus revealing the remarkable potential of single-molecule digital ELISA in future RNA virus detection.
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Affiliation(s)
| | - Pei Wei
- Department of Immunology, Zunyi Medical University, Zhuhai, China
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2
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Tokutomi N, Nakai K, Sugano S. Extreme value theory as a framework for understanding mutation frequency distribution in cancer genomes. PLoS One 2021; 16:e0243595. [PMID: 34424899 PMCID: PMC8382180 DOI: 10.1371/journal.pone.0243595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 08/10/2021] [Indexed: 12/31/2022] Open
Abstract
Currently, the population dynamics of preclonal cancer cells before clonal expansion of tumors has not been sufficiently addressed thus far. By focusing on preclonal cancer cell population as a Darwinian evolutionary system, we formulated and analyzed the observed mutation frequency among tumors (MFaT) as a proxy for the hypothesized sequence read frequency and beneficial fitness effect of a cancer driver mutation. Analogous to intestinal crypts, we assumed that sample donor patients are separate culture tanks where proliferating cells follow certain population dynamics described by extreme value theory (EVT). To validate this, we analyzed three large-scale cancer genome datasets, each harboring > 10000 tumor samples and in total involving > 177898 observed mutation sites. We clarified the necessary premises for the application of EVT in the strong selection and weak mutation (SSWM) regime in relation to cancer genome sequences at scale. We also confirmed that the stochastic distribution of MFaT is likely of the Fréchet type, which challenges the well-known Gumbel hypothesis of beneficial fitness effects. Based on statistical data analysis, we demonstrated the potential of EVT as a population genetics framework to understand and explain the stochastic behavior of driver-mutation frequency in cancer genomes as well as its applicability in real cancer genome sequence data.
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Affiliation(s)
- Natsuki Tokutomi
- Department of Computational Biology and Medical Science, Graduate School of Frontier Science, University of Tokyo, Kashiwa, Chiba, Japan
- * E-mail:
| | - Kenta Nakai
- Department of Computational Biology and Medical Science, Graduate School of Frontier Science, University of Tokyo, Kashiwa, Chiba, Japan
- Human Genome Center, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan
| | - Sumio Sugano
- Medical Research Institute, Tokyo Medical and Dental University, Bunkyou-ku, Tokyo, Japan
- Future Medicine Education and Research Organization, Chiba University, Chiba, Chiba, Japan
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3
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Singhal S, Turner PE. Effects of historical co-infection on host shift abilities of exploitative and competitive viruses. Evolution 2021; 75:1878-1888. [PMID: 33969482 DOI: 10.1111/evo.14263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 04/03/2021] [Accepted: 04/16/2021] [Indexed: 12/29/2022]
Abstract
Rapid evolution contributes to frequent emergence of RNA viral pathogens on novel hosts. However, accurately predicting which viral genotypes will emerge has been elusive. Prior work with lytic RNA bacteriophage ɸ6 (family Cystoviridae) suggested that evolution under low multiplicity of infection (MOI; proportion of viruses to susceptible cells) selected for greater host exploitation, while evolution under high MOI selected for better intracellular competition against co-infecting viruses. We predicted that phage genotypes that had experienced 300 generations of low MOI ecological history would be relatively advantaged in initial growth on two novel hosts. We inferred viral growth through changes in host population density, specifically by analyzing five attributes of growth curves of infected bacteria. Despite equivalent growth of evolved viruses on the original host, low MOI evolved clones were generally advantaged relative to high MOI clones in exploiting novel hosts. However, the specific attributes of growth curves that supported their advantage differed by host, indicating interactions between both viral and host genotype. Although there will be host specificity in viral growth, we suggest based on infectivity differences of viruses from high versus low MOI histories that prior MOI selection can later affect emergence potential.
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Affiliation(s)
- Sonia Singhal
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, 06520, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, 48824, USA.,Current affiliation: Department of Biological Sciences, San José Sate University, San José, California, 95192, USA
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, 06520, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, 48824, USA.,Graduate Program in Microbiology, Yale School of Medicine, New Haven, Connecticut, 06520, USA
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4
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de Leeuw M, Baron M, Ben David O, Kushmaro A. Molecular Insights into Bacteriophage Evolution toward Its Host. Viruses 2020; 12:E1132. [PMID: 33036277 PMCID: PMC7599783 DOI: 10.3390/v12101132] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 09/24/2020] [Accepted: 09/29/2020] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages (phages), viruses that infect bacteria, are considered to be highly host-specific. To add to the knowledge about the evolution and development of bacteriophage speciation toward its host, we conducted a 21-day experiment with the broad host-range bacteriophage Aquamicrobium phage P14. We incubated the phage, which was previously isolated and enriched with the Alphaproteobacteria Aquamicrobium H14, with the Betaproteobacteria Alcaligenaceae H5. During the experiment, we observed an increase in the phage's predation efficacy towards Alcaligenaceae H5. Furthermore, genome analysis and the comparison of the bacteriophage's whole genome indicated that rather than being scattered evenly along the genome, mutations occur in specific regions. In total, 67% of the mutations with a frequency higher than 30% were located in genes that encode tail proteins, which are essential for host recognition and attachment. As control, we incubated the phage with the Alphaproteobacteria Aquamicrobium H8. In both experiments, most of the mutations appeared in the gene encoding the tail fiber protein. However, mutations in the gene encoding the tail tubular protein B were only observed when the phage was incubated with Alcaligenaceae H5. This highlights the phage's tail as a key player in its adaptation to different hosts. We conclude that mutations in the phage's genome were mainly located in tail-related regions. Further investigation is needed to fully characterize the adaptation mechanisms of the Aquamicrobium phage P14.
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Affiliation(s)
- Marina de Leeuw
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Be’er Sheva 8410501, Israel; (M.d.L.); (M.B.); (O.B.D.)
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Maayan Baron
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Be’er Sheva 8410501, Israel; (M.d.L.); (M.B.); (O.B.D.)
| | - Oshrit Ben David
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Be’er Sheva 8410501, Israel; (M.d.L.); (M.B.); (O.B.D.)
| | - Ariel Kushmaro
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Be’er Sheva 8410501, Israel; (M.d.L.); (M.B.); (O.B.D.)
- The Ilse Katz Center for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, Be’er Sheva 8410501, Israel
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5
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Visher E, Boots M. The problem of mediocre generalists: population genetics and eco-evolutionary perspectives on host breadth evolution in pathogens. Proc Biol Sci 2020; 287:20201230. [PMID: 32811306 PMCID: PMC7482275 DOI: 10.1098/rspb.2020.1230] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 07/22/2020] [Indexed: 01/29/2023] Open
Abstract
Many of our theories for the generation and maintenance of diversity in nature depend on the existence of specialist biotic interactions which, in host-pathogen systems, also shape cross-species disease emergence. As such, niche breadth evolution, especially in host-parasite systems, remains a central focus in ecology and evolution. The predominant explanation for the existence of specialization in the literature is that niche breadth is constrained by trade-offs, such that a generalist is less fit on any particular environment than a given specialist. This trade-off theory has been used to predict niche breadth (co)evolution in both population genetics and eco-evolutionary models, with the different modelling methods providing separate, complementary insights. However, trade-offs may be far from universal, so population genetics theory has also proposed alternate mechanisms for costly generalism, including mutation accumulation. However, these mechanisms have yet to be integrated into eco-evolutionary models in order to understand how the mechanism of costly generalism alters the biological and ecological circumstances predicted to maintain specialism. In this review, we outline how population genetics and eco-evolutionary models based on trade-offs have provided insights for parasite niche breadth evolution and argue that the population genetics-derived mutation accumulation theory needs to be better integrated into eco-evolutionary theory.
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Affiliation(s)
- Elisa Visher
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Mike Boots
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- College of Life and Environmental Sciences, University of Exeter, Cornwall Campus, Ringgold Standard Institution, Penryn, Cornwall, UK
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6
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Variation Profile of the Orthotospovirus Genome. Pathogens 2020; 9:pathogens9070521. [PMID: 32610472 PMCID: PMC7400459 DOI: 10.3390/pathogens9070521] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 06/26/2020] [Accepted: 06/26/2020] [Indexed: 12/13/2022] Open
Abstract
Orthotospoviruses are plant-infecting members of the family Tospoviridae (order Bunyavirales), have a broad host range and are vectored by polyphagous thrips in a circulative-propagative manner. Because diverse hosts and vectors impose heterogeneous selection constraints on viral genomes, the evolutionary arms races between hosts and their pathogens might be manifested as selection for rapid changes in key genes. These observations suggest that orthotospoviruses contain key genetic components that rapidly mutate to mediate host adaptation and vector transmission. Using complete genome sequences, we profiled genomic variation in orthotospoviruses. Results show that the three genomic segments contain hypervariable areas at homologous locations across species. Remarkably, the highest nucleotide variation mapped to the intergenic region of RNA segments S and M, which fold into a hairpin. Secondary structure analyses showed that the hairpin is a dynamic structure with multiple functional shapes formed by stems and loops, contains sites under positive selection and covariable sites. Accumulation and tolerance of mutations in the intergenic region is a general feature of orthotospoviruses and might mediate adaptation to host plants and insect vectors.
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7
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Mougari S, Chelkha N, Sahmi-Bounsiar D, Di Pinto F, Colson P, Abrahao J, La Scola B. A virophage cross-species infection through mutant selection represses giant virus propagation, promoting host cell survival. Commun Biol 2020; 3:248. [PMID: 32439847 PMCID: PMC7242381 DOI: 10.1038/s42003-020-0970-9] [Citation(s) in RCA: 8] [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: 10/01/2019] [Accepted: 04/15/2020] [Indexed: 01/03/2023] Open
Abstract
Virus adaptation to new hosts is a major cause of infectious disease emergence. This mechanism has been intensively studied in the context of zoonotic virus spillover, due to its impact on global health. However, it remains unclear for virophages, parasites of giant viruses and potential regulators of microbial communities. Here, we present, for the first time to our knowledge, evidence of cross-species infection of a virophage. We demonstrated that challenging the native population of Guarani virophage with two previously unidentified giant viruses, previously nonpermissive to this virophage, allows the selection of a mutant genotype able to infect these giant viruses. We were able to characterize the potential genetic determinant (deletion) carried by the virophage with the expanded-host range. Our study also highlights the relevant biological impact of this host adaptation by demonstrating that coinfection with the mixture containing the mutant virophage abolishes giant virus production and rescues the host cell population from lysis.
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Affiliation(s)
- Said Mougari
- Unité MEPHI, Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), 19-21 boulevard Jean Moulin, 13005, Marseille, France.
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.
| | - Nisrine Chelkha
- Unité MEPHI, Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), 19-21 boulevard Jean Moulin, 13005, Marseille, France
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Dehia Sahmi-Bounsiar
- Unité MEPHI, Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), 19-21 boulevard Jean Moulin, 13005, Marseille, France
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Fabrizio Di Pinto
- Unité MEPHI, Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), 19-21 boulevard Jean Moulin, 13005, Marseille, France
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Philippe Colson
- Unité MEPHI, Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), 19-21 boulevard Jean Moulin, 13005, Marseille, France
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Jonatas Abrahao
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil, postal code 31270-901.
| | - Bernard La Scola
- Unité MEPHI, Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), 19-21 boulevard Jean Moulin, 13005, Marseille, France.
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.
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8
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Bono LM, Draghi JA, Turner PE. Evolvability Costs of Niche Expansion. Trends Genet 2019; 36:14-23. [PMID: 31699305 DOI: 10.1016/j.tig.2019.10.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 08/22/2019] [Accepted: 10/07/2019] [Indexed: 01/31/2023]
Abstract
What prevents generalists from displacing specialists, despite obvious competitive advantages of utilizing a broad niche? The classic genetic explanation is antagonistic pleiotropy: genes underlying the generalism produce 'jacks-of-all-trades' that are masters of none. However, experiments challenge this assumption that mutations enabling niche expansion must reduce fitness in other environments. Theory suggests an alternative cost of generalism: decreased evolvability, or the reduced capacity to adapt. Generalists using multiple environments experience relaxed selection in any one environment, producing greater relative lag load. Additionally, mutations fixed by generalist lineages early during their evolution that avoid or compensate for antagonistic pleiotropy may limit access to certain future evolutionary trajectories. Hypothesized evolvability costs of generalism warrant further exploration, and we suggest outstanding questions meriting attention.
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Affiliation(s)
- Lisa M Bono
- Department of Ecology, Evolution, and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Jeremy A Draghi
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA; Department of Biology, Brooklyn College, City University of New York, Brooklyn, NY 11210, USA; Program in Ecology, Evolutionary Biology and Behavior, Graduate Center, City University of New York, New York, NY 10016, USA
| | - Paul E Turner
- Microbiology Program, Yale School of Medicine, New Haven, CT 06510, USA; Yale University, Department of Ecology and Evolutionary Biology, New Haven, CT 06511, USA.
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9
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Large Phenotypic and Genetic Diversity of Prophages Induced from the Fish Pathogen Vibrio anguillarum. Viruses 2019; 11:v11110983. [PMID: 31653117 PMCID: PMC6893619 DOI: 10.3390/v11110983] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 10/15/2019] [Indexed: 01/07/2023] Open
Abstract
Vibrio anguillarum is a marine pathogenic bacterium that causes vibriosis in fish and shellfish. Although prophage-like sequences have been predicted in V. anguillarum strains, many are not characterized, and it is not known if they retain the functional capacity to form infectious particles that can infect and lysogenize other bacterial hosts. In this study, the genome sequences of 28 V. anguillarum strains revealed 55 different prophage-related elements. Chemical and spontaneous induction allowed a collection of 42 phage isolates, which were classified in seven different groups according to a multiplex PCR assay. One shared prophage sequence, p41 (group III), was present in 17 V. anguillarum strains, suggesting that this specific element is very dynamically exchanged among V. anguillarum populations. Interestingly, the host range of genetically identical phages was highly dependent on the strains used for proliferation, indicating that phenotypic properties of phages were partly regulated by the host. Finally, experimental evidence displayed that the induced phage ɸVa_90-11-287_p41 was able to lysogenize V. anguillarum strain Ba35, and subsequently spontaneously become released from the lysogenized cells, demonstrating an efficient transfer of the phage among V. anguillarum strains. Altogether, the results showed large genetic and functional diversity and broad distribution of prophages in V. anguillarum, and demonstrated the potential of prophages as drivers of evolution in V. anguillarum strains.
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10
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Pinheiro LAM, Pereira C, Frazão C, Balcão VM, Almeida A. Efficiency of Phage φ6 for Biocontrol of Pseudomonas syringae pv. syringae: An in Vitro Preliminary Study. Microorganisms 2019; 7:E286. [PMID: 31450735 PMCID: PMC6780397 DOI: 10.3390/microorganisms7090286] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 07/31/2019] [Accepted: 08/21/2019] [Indexed: 12/14/2022] Open
Abstract
Pseudomonas syringae is a plant-associated bacterial species that has been divided into more than 60 pathovars, with the Pseudomonas syringae pv. syringae being the main causative agent of diseases in a wide variety of fruit trees. The most common treatments for biocontrol of P. syringae pv. syringae infections has involved copper derivatives and/or antibiotics. However, these treatments should be avoided due to their high toxicity to the environment and promotion of bacterial resistance. Therefore, it is essential to search for new approaches for controlling P. syringae pv. syringae. Phage therapy can be a useful alternative tool to the conventional treatments to control P. syringae pv. syringae infections in plants. In the present study, the efficacy of bacteriophage (or phage) φ6 (a commercially available phage) was evaluated in the control of P. syringae pv. syringae. As the plants are exposed to the natural variability of physical and chemical parameters, the influence of pH, temperature, solar radiation and UV-B irradiation on phage φ6 viability was also evaluated in order to develop an effective phage therapy protocol. The host range analysis revealed that the phage, besides its host (P. syringae pv. syringae), also infects the Pseudomonas syringae pv. actinidiae CRA-FRU 12.54 and P. syringae pv. actinidiae CRA-FRU 14.10 strains, not infecting strains from the other tested species. Both multiplicities of infection (MOIs) tested, 1 and 100, were effective to inactivate the bacterium, but the MOI 1 (maximum reduction of 3.9 log CFU/mL) was more effective than MOI 100 (maximum reduction of 2.6 log CFU/mL). The viability of phage φ6 was mostly affected by exposure to UV-B irradiation (decrease of 7.3 log PFU/mL after 8 h), exposure to solar radiation (maximum reduction of 2.1 PFU/mL after 6 h), and high temperatures (decrease of 8.5 PFU/mL after 6 days at 37 °C, but a decrease of only 2.0 log PFU/mL after 67 days at 15 °C and 25 °C). The host range, high bacterial control and low rates of development of phage-resistant bacterial clones (1.20 × 10-3) suggest that this phage can be used to control P. syringae pv. syringae infections in plants, but also to control infections by P. syringae pv. actinidiae, the causal agent of bacterial canker of kiwifruit. Although the stability of phage φ6 was affected by UV-B and solar radiation, this can be overcome by the application of phage suspensions at the end of the day or at night.
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Affiliation(s)
- Larindja A M Pinheiro
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Carla Pereira
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| | - Carolina Frazão
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Victor M Balcão
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
- PhageLab-Laboratory of Biofilms and Bacteriophages, University of Sorocaba, 18023-000 Sorocaba, São Paulo, Brazil
| | - Adelaide Almeida
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
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11
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Bergman J, Eyre-Walker A. Does Adaptive Protein Evolution Proceed by Large or Small Steps at the Amino Acid Level? Mol Biol Evol 2019; 36:990-998. [PMID: 30903659 DOI: 10.1093/molbev/msz033] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A long-standing question in evolutionary biology is the relative contribution of large and small effect mutations to the adaptive process. We have investigated this question in proteins by estimating the rate of adaptive evolution between all pairs of amino acids separated by one mutational step using a McDonald-Kreitman type approach and genome-wide data from several Drosophila species. We find that the rate of adaptive evolution is highest among amino acids that are more similar. This is partly due to the fact that the proportion of mutations that are adaptive is higher among more similar amino acids. We also find that the rate of neutral evolution between amino acids is higher among more similar amino acids. Overall our results suggest that both the adaptive and nonadaptive evolution of proteins are dominated by substitutions between similar amino acids.
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Affiliation(s)
- Juraj Bergman
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria.,Vienna Graduate School of Population Genetics, Wien, Austria
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
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12
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Habusha M, Tzipilevich E, Fiyaksel O, Ben‐Yehuda S. A mutant bacteriophage evolved to infect resistant bacteria gained a broader host range. Mol Microbiol 2019; 111:1463-1475. [DOI: 10.1111/mmi.14231] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2019] [Indexed: 02/04/2023]
Affiliation(s)
- Michal Habusha
- Department of Microbiology and Molecular Genetics Institute for Medical Research Israel‐Canada (IMRIC), The Hebrew University‐Hadassah Medical School, The Hebrew University of Jerusalem Jerusalem Israel
| | - Elhanan Tzipilevich
- Department of Microbiology and Molecular Genetics Institute for Medical Research Israel‐Canada (IMRIC), The Hebrew University‐Hadassah Medical School, The Hebrew University of Jerusalem Jerusalem Israel
| | - Osher Fiyaksel
- Department of Microbiology and Molecular Genetics Institute for Medical Research Israel‐Canada (IMRIC), The Hebrew University‐Hadassah Medical School, The Hebrew University of Jerusalem Jerusalem Israel
| | - Sigal Ben‐Yehuda
- Department of Microbiology and Molecular Genetics Institute for Medical Research Israel‐Canada (IMRIC), The Hebrew University‐Hadassah Medical School, The Hebrew University of Jerusalem Jerusalem Israel
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13
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Existing Host Range Mutations Constrain Further Emergence of RNA Viruses. J Virol 2019; 93:JVI.01385-18. [PMID: 30463962 DOI: 10.1128/jvi.01385-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/06/2018] [Indexed: 02/07/2023] Open
Abstract
RNA viruses are capable of rapid host shifting, typically due to a point mutation that confers expanded host range. As additional point mutations are necessary for further expansions, epistasis among host range mutations can potentially affect the mutational neighborhood and frequency of niche expansion. We mapped the mutational neighborhood of host range expansion using three genotypes of the double-stranded RNA (dsRNA) bacteriophage φ6 (wild type and two isogenic host range mutants) on the novel host Pseudomonas syringae pv. atrofaciens. Both Sanger sequencing of 50 P. syringae pv. atrofaciens mutant clones for each genotype and population Illumina sequencing revealed the same high-frequency mutations allowing infection of P. syringae pv. atrofaciens. Wild-type φ6 had at least nine different ways of mutating to enter the novel host, eight of which are in p3 (host attachment protein gene), and 13/50 clones had unchanged p3 genes. However, the two isogenic mutants had dramatically restricted neighborhoods: only one or two mutations, all in p3. Deep sequencing revealed that wild-type clones without mutations in p3 likely had changes in p12 (morphogenic protein), a region that was not polymorphic for the two isogenic host range mutants. Sanger sequencing confirmed that 10/13 of the wild-type φ6 clones had nonsynonymous mutations in p12, and 2 others had point mutations in p9 and p5. None of these genes had previously been associated with host range expansion in φ6. We demonstrate, for the first time, epistatic constraint in an RNA virus due to host range mutations themselves, which has implications for models of serial host range expansion.IMPORTANCE RNA viruses mutate rapidly and frequently expand their host ranges to infect novel hosts, leading to serial host shifts. Using an RNA bacteriophage model system (Pseudomonas phage φ6), we studied the impact of preexisting host range mutations on another host range expansion. Results from both clonal Sanger and Illumina sequencing show that extant host range mutations dramatically narrow the neighborhood of potential host range mutations compared to that of wild-type φ6. This research suggests that serial host-shifting viruses may follow a small number of molecular paths to enter additional novel hosts. We also identified new genes involved in φ6 host range expansion, expanding our knowledge of this important model system in experimental evolution.
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14
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Maxwell CS. Hypothesis: a Plastically Produced Phenotype Predicts Host Specialization and Can Precede Subsequent Mutations in Bacteriophage. mBio 2018; 9:e00765-18. [PMID: 30425142 PMCID: PMC6234872 DOI: 10.1128/mbio.00765-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 10/04/2018] [Indexed: 01/24/2023] Open
Abstract
The role of phenotypic plasticity in the evolution of new traits is controversial due to a lack of direct evidence. Phage host range becomes plastic in the presence of restriction-modification (R-M) systems in their hosts. I modeled the evolution of phage host range in the presence of R-M systems. The model makes two main predictions. The first prediction is that the offspring of the first phage to gain a new methylation pattern by infecting a new host make up a disproportionate fraction of the subsequent specialist population, indicating that the plastically produced phenotype is highly predictive of evolutionary outcome. The second prediction is that the first phage to gain this pattern is not always genetically distinct from other phages in the population. Taken together, these results suggest that plasticity could play a causal role on par with mutation during the evolution of phage host range. This uniquely tractable system could enable the first direct test of "plasticity first" evolution.
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Affiliation(s)
- Colin S Maxwell
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
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15
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Schönherz AA, Forsberg R, Guldbrandtsen B, Buitenhuis AJ, Einer-Jensen K. Introduction of Viral Hemorrhagic Septicemia Virus into Freshwater Cultured Rainbow Trout Is Followed by Bursts of Adaptive Evolution. J Virol 2018; 92:e00436-18. [PMID: 29643236 PMCID: PMC5974487 DOI: 10.1128/jvi.00436-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 03/20/2018] [Indexed: 12/25/2022] Open
Abstract
Viral hemorrhagic septicemia virus (VHSV), a rhabdovirus infecting teleost fish, has repeatedly crossed the boundary from marine fish species to freshwater cultured rainbow trout. These naturally replicated cross-species transmission events permit the study of general and repeatable evolutionary events occurring in connection with viral emergence in a novel host species. The purpose of the present study was to investigate the adaptive molecular evolution of the VHSV glycoprotein, one of the key virus proteins involved in viral emergence, following emergence from marine species into freshwater cultured rainbow trout. A comprehensive phylogenetic reconstruction of the complete coding region of the VHSV glycoprotein was conducted, and adaptive molecular evolution was investigated using a maximum likelihood approach to compare different codon substitution models allowing for heterogeneous substitution rate ratios among amino acid sites. Evidence of positive selection was detected at six amino acid sites of the VHSV glycoprotein, within the signal peptide, the confirmation-dependent major neutralizing epitope, and the intracellular tail. Evidence of positive selection was found exclusively in rainbow trout-adapted virus isolates, and amino acid combinations found at the six sites under positive selection pressure differentiated rainbow trout- from non-rainbow trout-adapted isolates. Furthermore, four adaptive sites revealed signs of recurring identical changes across phylogenetic groups of rainbow trout-adapted isolates, suggesting that repeated VHSV emergence in freshwater cultured rainbow trout was established through convergent routes of evolution that are associated with immune escape.IMPORTANCE This study is the first to demonstrate that VHSV emergence from marine species into freshwater cultured rainbow trout has been accompanied by bursts of adaptive evolution in the VHSV glycoprotein. Furthermore, repeated detection of the same adaptive amino acid sites across phylogenetic groups of rainbow trout-adapted isolates indicates that adaptation to rainbow trout was established through parallel evolution. In addition, signals of convergent evolution toward the maintenance of genetic variation were detected in the conformation-dependent neutralizing epitope or in close proximity to disulfide bonds involved in the structural conformation of the neutralizing epitope, indicating adaptation to immune response-related genetic variation across freshwater cultured rainbow trout.
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Affiliation(s)
- Anna A Schönherz
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Albert J Buitenhuis
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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16
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Immune loss as a driver of coexistence during host-phage coevolution. ISME JOURNAL 2018; 12:585-597. [PMID: 29328063 PMCID: PMC5776473 DOI: 10.1038/ismej.2017.194] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 09/18/2017] [Accepted: 10/09/2017] [Indexed: 12/26/2022]
Abstract
Bacteria and their viral pathogens face constant pressure for augmented immune and
infective capabilities, respectively. Under this reciprocally imposed selective regime, we
expect to see a runaway evolutionary arms race, ultimately leading to the extinction of
one species. Despite this prediction, in many systems host and pathogen coexist with
minimal coevolution even when well-mixed. Previous work explained this puzzling phenomenon
by invoking fitness tradeoffs, which can diminish an arms race dynamic. Here we propose
that the regular loss of immunity by the bacterial host can also produce host-phage
coexistence. We pair a general model of immunity with an experimental and theoretical case
study of the CRISPR-Cas immune system to contrast the behavior of tradeoff and loss
mechanisms in well-mixed systems. We find that, while both mechanisms can produce stable
coexistence, only immune loss does so robustly within realistic parameter ranges.
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17
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Mäntynen S, Sundberg LR, Poranen MM. Recognition of six additional cystoviruses: Pseudomonas virus phi6 is no longer the sole species of the family Cystoviridae. Arch Virol 2017; 163:1117-1124. [PMID: 29260329 DOI: 10.1007/s00705-017-3679-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/10/2017] [Indexed: 12/27/2022]
Abstract
Cystoviridae is a family of bacterial viruses (bacteriophages) with a tri-segmented dsRNA genome. It includes a single genus Cystovirus, which has presently only one recognised virus species, Pseudomonas virus phi6. However, a large number of additional dsRNA phages have been isolated from various environmental samples, indicating that such viruses are more widespread and abundant than previously recognised. Six of the additional dsRNA phage isolates (Pseudomonas phages phi8, phi12, phi13, phi2954, phiNN and phiYY) have been fully sequenced. They all infect Pseudomonas species, primarily plant pathogenic Pseudomonas syringae strains. Due to the notable genetic and structural similarities with Pseudomonas phage phi6, we propose that these viruses should be included into the Cystovirus genus (and consequently into the Cystoviridae family). Here, we present an updated taxonomy of the family Cystoviridae and give a short overview of the properties of the type member phi6 as well as the putative new members of the family.
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Affiliation(s)
- Sari Mäntynen
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, P.O. Box 35, 40014, Jyväskylä, Finland.
| | - Lotta-Riina Sundberg
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, P.O. Box 35, 40014, Jyväskylä, Finland
| | - Minna M Poranen
- Department of Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland
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18
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Chanpanitkitchote P, Chen Y, Evans JD, Li W, Li J, Hamilton M, Chantawannakul P. Acute bee paralysis virus occurs in the Asian honey bee Apis cerana and parasitic mite Tropilaelaps mercedesae. J Invertebr Pathol 2017; 151:131-136. [PMID: 29158015 DOI: 10.1016/j.jip.2017.11.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 11/08/2017] [Accepted: 11/15/2017] [Indexed: 10/18/2022]
Abstract
Viruses, and especially RNA viruses, constantly change and adapt to new host species and vectors, posing a potential threat of new and reemerging infectious diseases. Honey bee Acute bee paralysis virus (ABPV) and Deformed wing virus (DWV) are two of the most common honey bee viruses found in European honey bees Apis mellifera and have been implicated in worldwide Varroa-associated bee colony losses. Previous studies have shown that DWV has jumped hosts several times in history causing infection in multiple host species. In the present study, we show that DWV infection could be detected in the Asian honey bee, A. cerana, and the parasitic mite Tropilaelaps mercedesae, confirming previous findings that DWV is a multi-host pathogen and supporting the notion that the high prevalence of DWV in honey bee host populations could be attributed to the high adaptability of this virus. Furthermore, our study provides the first evidence that ABPV occurs in both A. cerana and T. mercedesae in northern Thailand. The geographical proximity of host species likely played an important role in the initial exposure and the subsequent cross-species transmission of these viruses. Phylogenetic analyses suggest that ABPV might have moved from T. mercedesae to A. mellifera and to A. cerana while DWV might have moved in the opposite direction from A. cerana to A. mellifera and T. mercedesae. This result may reflect the differences in virus life history and virus-host interactions, warranting further investigation of virus transmission, epidemiology, and impacts of virus infections in the new hosts. The results from this study indicate that viral populations will continue to evolve and likely continue to expand host range, increasing the need for effective surveillance and control of virus infections in honey bee populations.
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Affiliation(s)
- Pichaya Chanpanitkitchote
- Bee Protection Laboratory, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Yanping Chen
- USDA-ARS Beltsville Bee Research Laboratory, Beltsville, MD 20705, USA
| | - Jay D Evans
- USDA-ARS Beltsville Bee Research Laboratory, Beltsville, MD 20705, USA
| | - Wenfeng Li
- USDA-ARS Beltsville Bee Research Laboratory, Beltsville, MD 20705, USA
| | - Jianghong Li
- USDA-ARS Beltsville Bee Research Laboratory, Beltsville, MD 20705, USA; College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Michele Hamilton
- USDA-ARS Beltsville Bee Research Laboratory, Beltsville, MD 20705, USA
| | - Panuwan Chantawannakul
- Bee Protection Laboratory, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; Environmental Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.
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19
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Bono LM, Gensel CL, Pfennig DW, Burch CL. Evolutionary rescue and the coexistence of generalist and specialist competitors: an experimental test. Proc Biol Sci 2017; 282:20151932. [PMID: 26702041 DOI: 10.1098/rspb.2015.1932] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Competition for resources is thought to play a critical role in both the origins and maintenance of biodiversity. Although numerous laboratory evolution experiments have confirmed that competition can be a key driver of adaptive diversification, few have demonstrated its role in the maintenance of the resulting diversity. We investigate the conditions that favour the origin and maintenance of alternative generalist and specialist resource-use phenotypes within the same population. Previously, we confirmed that competition for hosts among φ6 bacteriophage in a mixed novel (non-permissive) and ancestral (permissive) host microcosm triggered the evolution of a generalist phenotype capable of infecting both hosts. However, because the newly evolved generalists tended to competitively exclude the ancestral specialists, coexistence between the two phenotypes was rare. Here, we show that reducing the relative abundance of the novel host slowed the increase in frequency of the generalist phenotype, allowing sufficient time for the specialist to further adapt to the ancestral host. This adaptation resulted in 'evolutionary rescue' of the specialists, preventing their competitive exclusion by the generalists. Thus, our results suggest that competition promotes both the origin and maintenance of biodiversity when it is strong enough to favour a novel resource-use phenotype, but weak enough to allow adaptation of both the novel and ancestral phenotypes to their respective niches.
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Affiliation(s)
- Lisa M Bono
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520-8106, USA
| | - Catharine L Gensel
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - David W Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Christina L Burch
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
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20
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Bono LM, Smith LB, Pfennig DW, Burch CL. The emergence of performance trade‐offs during local adaptation: insights from experimental evolution. Mol Ecol 2017; 26:1720-1733. [DOI: 10.1111/mec.13979] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 12/15/2016] [Accepted: 12/19/2016] [Indexed: 01/05/2023]
Affiliation(s)
- Lisa M. Bono
- Department of Biology University of North Carolina at Chapel Hill CB# 3280 Chapel Hill NC 27599 USA
| | - Leno B. Smith
- Department of Biology University of North Carolina at Chapel Hill CB# 3280 Chapel Hill NC 27599 USA
| | - David W. Pfennig
- Department of Biology University of North Carolina at Chapel Hill CB# 3280 Chapel Hill NC 27599 USA
| | - Christina L. Burch
- Department of Biology University of North Carolina at Chapel Hill CB# 3280 Chapel Hill NC 27599 USA
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21
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Dennehy JJ. Evolutionary ecology of virus emergence. Ann N Y Acad Sci 2016; 1389:124-146. [PMID: 28036113 PMCID: PMC7167663 DOI: 10.1111/nyas.13304] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/24/2016] [Accepted: 11/09/2016] [Indexed: 12/22/2022]
Abstract
The cross-species transmission of viruses into new host populations, termed virus emergence, is a significant issue in public health, agriculture, wildlife management, and related fields. Virus emergence requires overlap between host populations, alterations in virus genetics to permit infection of new hosts, and adaptation to novel hosts such that between-host transmission is sustainable, all of which are the purview of the fields of ecology and evolution. A firm understanding of the ecology of viruses and how they evolve is required for understanding how and why viruses emerge. In this paper, I address the evolutionary mechanisms of virus emergence and how they relate to virus ecology. I argue that, while virus acquisition of the ability to infect new hosts is not difficult, limited evolutionary trajectories to sustained virus between-host transmission and the combined effects of mutational meltdown, bottlenecking, demographic stochasticity, density dependence, and genetic erosion in ecological sinks limit most emergence events to dead-end spillover infections. Despite the relative rarity of pandemic emerging viruses, the potential of viruses to search evolutionary space and find means to spread epidemically and the consequences of pandemic viruses that do emerge necessitate sustained attention to virus research, surveillance, prophylaxis, and treatment.
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Affiliation(s)
- John J Dennehy
- Biology Department, Queens College of the City University of New York, Queens, New York and The Graduate Center of the City University of New York, New York, New York
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22
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Characterization of the first double-stranded RNA bacteriophage infecting Pseudomonas aeruginosa. Sci Rep 2016; 6:38795. [PMID: 27934909 PMCID: PMC5146939 DOI: 10.1038/srep38795] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/14/2016] [Indexed: 11/29/2022] Open
Abstract
Bacteriophages (phages) are widely distributed in the biosphere and play a key role in modulating microbial ecology in the soil, ocean, and humans. Although the role of DNA bacteriophages is well described, the biology of RNA bacteriophages is poorly understood. More than 1900 phage genomes are currently deposited in NCBI, but only 6 dsRNA bacteriophages and 12 ssRNA bacteriophages genome sequences are reported. The 6 dsRNA bacteriophages were isolated from legume samples or lakes with Pseudomonas syringae as the host. Here, we report the first Pseudomonas aeruginosa phage phiYY with a three-segmented dsRNA genome. phiYY was isolated from hospital sewage in China with the clinical P. aeruginosa strain, PAO38, as a host. Moreover, the dsRNA phage phiYY has a broad host range, which infects 99 out of 233 clinical P. aeruginosa strains isolated from four provinces in China. This work presented a detailed characterization of the dsRNA bacteriophage infecting P. aeruginosa.
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23
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Hillung J, Cuevas JM, Elena SF. Evaluating the within-host fitness effects of mutations fixed during virus adaptation to different ecotypes of a new host. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0292. [PMID: 26150658 DOI: 10.1098/rstb.2014.0292] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The existence of genetic variation for resistance in host populations is assumed to be essential to the spread of an emerging virus. Models predict that the rate of spread slows down with the increasing frequency and higher diversity of resistance alleles in the host population. We have been using the experimental pathosystem Arabidopsis thaliana-tobacco etch potyvirus (TEV) to explore the interplay between genetic variation in host's susceptibility and virus diversity. We have recently shown that TEV populations evolving in A. thaliana ecotypes that differ in susceptibility to infection gained within-host fitness, virulence and infectivity in a manner compatible with a gene-for-gene model of host-parasite interactions: hard-to-infect ecotypes were infected by generalist viruses, whereas easy-to-infect ecotypes were infected by every virus. We characterized the genomes of the evolved viruses and found cases of host-driven convergent mutations. To gain further insights in the mechanistic basis of this gene-for-gene model, we have generated all viral mutations individually as well as in specific combinations and tested their within-host fitness effects across ecotypes. Most of these mutations were deleterious or neutral in their local ecotype and only a very reduced number had a host-specific beneficial effect. We conclude that most of the mutations fixed during the evolution experiment were so by drift or by selective sweeps along with the selected driver mutation. In addition, we evaluated the ruggedness of the underlying adaptive fitness landscape and found that mutational effects were mostly multiplicative, with few cases of significant epistasis.
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Affiliation(s)
- Julia Hillung
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València 46022, Spain
| | - José M Cuevas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València 46022, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València 46022, Spain The Santa Fe Institute, Santa Fe, NM 87501, USA
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24
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Simpson DJ, Sacher JC, Szymanski CM. Development of an Assay for the Identification of Receptor Binding Proteins from Bacteriophages. Viruses 2016; 8:v8010017. [PMID: 26761028 PMCID: PMC4728577 DOI: 10.3390/v8010017] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 12/11/2015] [Accepted: 12/18/2015] [Indexed: 12/13/2022] Open
Abstract
Recently, a large number of new technologies have been developed that exploit the unique properties of bacteriophage receptor binding proteins (RBPs). These include their use in diagnostic applications that selectively capture bacteria and as therapeutics that reduce bacterial colonization in vivo. RBPs exhibit comparable, and in many cases superior, stability, receptor specificity, and affinity to other carbohydrate binding proteins such as antibodies or lectins. In order to further exploit the use of RBPs, we have developed an assay for discovering RBPs using phage genome expression libraries and protein screens to identify binding partners that recognize the host bacterium. When phage P22 was screened using this assay, Gp9 was the only RBP discovered, confirming previous predictions that this is the sole RBP encoded by this phage. We then examined the Escherichia coli O157:H7 typing phage 1 in our assay and identified a previously undescribed RBP. This general approach has the potential to assist in the identification of RBPs from other bacteriophages.
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Affiliation(s)
- David J Simpson
- Alberta Glycomics Centre and Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Jessica C Sacher
- Alberta Glycomics Centre and Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Christine M Szymanski
- Alberta Glycomics Centre and Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
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25
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Abstract
A pattern in which nucleotide transitions are favored several fold over transversions is common in molecular evolution. When this pattern occurs among amino acid replacements, explanations often invoke an effect of selection, on the grounds that transitions are more conservative in their effects on proteins. However, the underlying hypothesis of conservative transitions has never been tested directly. Here we assess support for this hypothesis using direct evidence: the fitness effects of mutations in actual proteins measured via individual or paired growth experiments. We assembled data from 8 published studies, ranging in size from 24 to 757 single-nucleotide mutations that change an amino acid. Every study has the statistical power to reveal significant effects of amino acid exchangeability, and most studies have the power to discern a binary conservative-vs-radical distinction. However, only one study suggests that transitions are significantly more conservative than transversions. In the combined set of 1,239 replacements (544 transitions, 695 transversions), the chance that a transition is more conservative than a transversion is 53 % (95 % confidence interval 50 to 56) compared with the null expectation of 50 %. We show that this effect is not large compared with that of most biochemical factors, and is not large enough to explain the several-fold bias observed in evolution. In short, the available data have the power to verify the “conservative transitions” hypothesis if true, but suggest instead that selection on proteins plays at best a minor role in the observed bias.
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Affiliation(s)
- Arlin Stoltzfus
- Institute for Bioscience and Biotechnology Research, Rockville, MD Genome-scale Measurements Group, National Institute of Standards and Technology, Gaithersburg, MD
| | - Ryan W Norris
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University
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26
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Mäntynen S, Laanto E, Kohvakka A, Poranen MM, Bamford JKH, Ravantti JJ. New enveloped dsRNA phage from freshwater habitat. J Gen Virol 2015; 96:1180-1189. [PMID: 25614591 DOI: 10.1099/vir.0.000063] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/15/2015] [Indexed: 12/27/2022] Open
Abstract
Cystoviridae is a family of bacteriophages with a tri-segmented dsRNA genome enclosed in a tri-layered virion structure. Here, we present a new putative member of the Cystoviridae family, bacteriophage ϕNN. ϕNN was isolated from a Finnish lake in contrast to the previously identified cystoviruses, which originate from various legume samples collected in the USA. The nucleotide sequence of the virus reveals a strong genetic similarity (~80 % for the L-segments, ~55 % for the M-segments and ~84 % for the S-segments) to Pseudomonas phage ϕ6, the type member of the virus family. However, the relationship between ϕNN and other cystoviruses is more distant. In general, proteins located in the internal parts of the virion were more conserved than those exposed on the virion surface, a phenomenon previously reported among eukaryotic dsRNA viruses. Structural models of several putative ϕNN proteins propose that cystoviral structures are highly conserved.
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Affiliation(s)
- Sari Mäntynen
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Elina Laanto
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Annika Kohvakka
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Minna M Poranen
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Jaana K H Bamford
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Janne J Ravantti
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Department of Biosciences, University of Helsinki, Helsinki, Finland.,Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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27
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Rosenblum EB, Parent CE, Brandt EE. The Molecular Basis of Phenotypic Convergence. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2014. [DOI: 10.1146/annurev-ecolsys-120213-091851] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Erica Bree Rosenblum
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720; ,
| | - Christine E. Parent
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720; ,
- Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844;
| | - Erin E. Brandt
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720; ,
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28
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Ford BE, Sun B, Carpino J, Chapler ES, Ching J, Choi Y, Jhun K, Kim JD, Lallos GG, Morgenstern R, Singh S, Theja S, Dennehy JJ. Frequency and fitness consequences of bacteriophage φ6 host range mutations. PLoS One 2014; 9:e113078. [PMID: 25409341 PMCID: PMC4237377 DOI: 10.1371/journal.pone.0113078] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 10/15/2014] [Indexed: 11/19/2022] Open
Abstract
Viruses readily mutate and gain the ability to infect novel hosts, but few data are available regarding the number of possible host range-expanding mutations allowing infection of any given novel host, and the fitness consequences of these mutations on original and novel hosts. To gain insight into the process of host range expansion, we isolated and sequenced 69 independent mutants of the dsRNA bacteriophage Φ6 able to infect the novel host, Pseudomonas pseudoalcaligenes. In total, we found at least 17 unique suites of mutations among these 69 mutants. We assayed fitness for 13 of 17 mutant genotypes on P. pseudoalcaligenes and the standard laboratory host, P. phaseolicola. Mutants exhibited significantly lower fitnesses on P. pseudoalcaligenes compared to P. phaseolicola. Furthermore, 12 of the 13 assayed mutants showed reduced fitness on P. phaseolicola compared to wildtype Φ6, confirming the prevalence of antagonistic pleiotropy during host range expansion. Further experiments revealed that the mechanistic basis of these fitness differences was likely variation in host attachment ability. In addition, using computational protein modeling, we show that host-range expanding mutations occurred in hotspots on the surface of the phage's host attachment protein opposite a putative hydrophobic anchoring domain.
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Affiliation(s)
- Brian E. Ford
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
- The Graduate Center of the City University of New York, New York, New York, United States of America
| | - Bruce Sun
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
| | - James Carpino
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
| | - Elizabeth S. Chapler
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
| | - Jane Ching
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
| | - Yoon Choi
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
| | - Kevin Jhun
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
| | - Jung D. Kim
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
| | - Gregory G. Lallos
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
| | - Rachelle Morgenstern
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
| | - Shalini Singh
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
| | - Sai Theja
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
| | - John J. Dennehy
- Biology Department, Queens College of the City University of New York, New York, New York, United States of America
- * E-mail:
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Bedhomme S, Hillung J, Elena SF. Emerging viruses: why they are not jacks of all trades? Curr Opin Virol 2014; 10:1-6. [PMID: 25467278 DOI: 10.1016/j.coviro.2014.10.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 10/27/2014] [Accepted: 10/28/2014] [Indexed: 12/21/2022]
Abstract
In order to limit the impact of the recent pandemics ignited by viral host jumps, it is necessary to better understand the ecological and evolutionary factors influencing the early steps of emergence and the interactions between them. Antagonistic pleiotropy, that is, the negative fitness effect in the primary host of mutations allowing the infection of and the multiplication in a new host, has long been thought to be the main limitation to the evolution of generalist viruses and thus to emergence. However, the accumulation of experimental examples contradicting the hypothesis of antagonistic pleiotropy has highlighted the importance of other factors such as the epistasis between mutations increasing the adaptation to a new host. Epistasis is pervasive in viruses, affects the shape of the adaptive landscape and consequently the accessibility of evolutionary pathways. Finally, recent studies have gone steps further in the complexity of viral fitness determinism and stressed the potential importance of the epistatic pleiotropy and of the impact of host living conditions.
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Affiliation(s)
- Stéphanie Bedhomme
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, 46022 Valencia, Spain.
| | - Julia Hillung
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, 46022 Valencia, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, 46022 Valencia, Spain; The Santa Fe Institute, Santa Fe, NM 87501, USA
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30
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Abstract
Emerging viral diseases are often the product of a host shift, where a pathogen jumps from its original host into a novel species. Phylogenetic studies show that host shifts are a frequent event in the evolution of most pathogens, but why pathogens successfully jump between some host species but not others is only just becoming clear. The susceptibility of potential new hosts can vary enormously, with close relatives of the natural host typically being the most susceptible. Often, pathogens must adapt to successfully infect a novel host, for example by evolving to use different cell surface receptors, to escape the immune response, or to ensure they are transmitted by the new host. In viruses there are often limited molecular solutions to achieve this, and the same sequence changes are often seen each time a virus infects a particular host. These changes may come at a cost to other aspects of the pathogen's fitness, and this may sometimes prevent host shifts from occurring. Here we examine how these evolutionary factors affect patterns of host shifts and disease emergence.
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Affiliation(s)
- Ben Longdon
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
| | | | - Colin A. Russell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - John J. Welch
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Francis M. Jiggins
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
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31
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Joseph SB, Peck KM, Burch CL. Dominance effects of deleterious and beneficial mutations in a single gene of the RNA virus ϕ6. PLoS One 2014; 9:e97717. [PMID: 24945910 PMCID: PMC4063744 DOI: 10.1371/journal.pone.0097717] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 04/22/2014] [Indexed: 11/23/2022] Open
Abstract
Most of our knowledge of dominance stems from studies of deleterious mutations. From these studies we know that most deleterious mutations are recessive, and that this recessivity arises from a hyperbolic relationship between protein function (i.e., protein concentration or activity) and fitness. Here we investigate whether this knowledge can be used to make predictions about the dominance of beneficial and deleterious mutations in a single gene. We employed a model system--the bacteriophage φ6--that allowed us to generate a collection of mutations in haploid conditions so that it was not biased toward either dominant beneficial or recessive deleterious mutations. Screening for the ability to infect a bacterial host that does not permit infection by the wildtype φ6, we generated a collection of mutations in P3, a gene involved in attachment to the host and in phage particle assembly. The resulting collection contained mutations with both deleterious and beneficial effects on fitness. The deleterious mutations in our collection had additive effects on fitness and the beneficial mutations were recessive. Neither of these observations were predicted from previous studies of dominance. This pattern is not consistent with the hyperbolic (diminishing returns) relationship between protein function and fitness that is characteristic of enzymatic genes, but could have resulted from a curve of increasing returns.
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Affiliation(s)
- Sarah B. Joseph
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Kayla M. Peck
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Christina L. Burch
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
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32
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Martiny JBH, Riemann L, Marston MF, Middelboe M. Antagonistic coevolution of marine planktonic viruses and their hosts. ANNUAL REVIEW OF MARINE SCIENCE 2014; 6:393-414. [PMID: 23987913 DOI: 10.1146/annurev-marine-010213-135108] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The potential for antagonistic coevolution between marine viruses and their (primarily bacterial) hosts is well documented, but our understanding of the consequences of this rapid evolution is in its infancy. Acquisition of resistance against co-occurring viruses and the subsequent evolution of virus host range in response have implications for bacterial mortality rates as well as for community composition and diversity. Drawing on examples from a range of environments, we consider the potential dynamics, underlying genetic mechanisms and fitness costs, and ecological impacts of virus-host coevolution in marine waters. Given that much of our knowledge is derived from laboratory experiments, we also discuss potential challenges and approaches in scaling up to diverse, complex networks of virus-host interactions. Finally, we note that a variety of novel approaches for characterizing virus-host interactions offer new hope for a mechanistic understanding of antagonistic coevolution in marine plankton.
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Affiliation(s)
- Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697;
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33
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Keen EC. Tradeoffs in bacteriophage life histories. BACTERIOPHAGE 2014; 4:e28365. [PMID: 24616839 PMCID: PMC3942329 DOI: 10.4161/bact.28365] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 02/24/2014] [Accepted: 02/26/2014] [Indexed: 11/19/2022]
Abstract
Viruses are the most abundant biological entities on the planet, yet most classical principles of evolutionary biology and ecology were not developed with viruses in mind. Here, the concept of biological tradeoffs, a fundamental tenet of life history theory, is examined in the context of bacteriophage biology. Specifically, several important parameters of phage life histories-replication, persistence, host range, and adsorption-are evaluated for tradeoffs. Available data indicate that replication rate is strongly negatively correlated with both persistence and host range, suggesting that the well-documented tradeoff in macroorganisms between offspring production and offspring quality also applies to phages. The biological tradeoffs that appear to characterize viruses' life histories have potential importance for viral evolution, ecology, and pathogenesis.
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Affiliation(s)
- Eric C Keen
- Department of Biology; University of Miami; Coral Gables, FL USA
- Laboratory of Molecular Biology; Center for Cancer Research; National Cancer Institute; National Institutes of Health; Bethesda, MD USA
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34
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Sieber M, Robb M, Forde SE, Gudelj I. Dispersal network structure and infection mechanism shape diversity in a coevolutionary bacteria-phage system. ISME JOURNAL 2013; 8:504-514. [PMID: 24088626 DOI: 10.1038/ismej.2013.169] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 08/17/2013] [Indexed: 11/09/2022]
Abstract
Resource availability, dispersal and infection genetics all have the potential to fundamentally alter the coevolutionary dynamics of bacteria-bacteriophage interactions. However, it remains unclear how these factors synergise to shape diversity within bacterial populations. We used a combination of laboratory experiments and mathematical modeling to test how the structure of a dispersal network affects host phenotypic diversity in a coevolving bacteria-phage system in communities of differential resource input. Unidirectional dispersal of bacteria and phage from high to low resources consistently increased host diversity compared with a no dispersal regime. Bidirectional dispersal, on the other hand, led to a marked decrease in host diversity. Our mathematical model predicted these opposing outcomes when we incorporated modified gene-for-gene infection genetics. To further test how host diversity depended on the genetic underpinnings of the bacteria-phage interaction, we expanded our mathematical model to include different infection mechanisms. We found that the direction of dispersal had very little impact on bacterial diversity when the bacteria-phage interaction was mediated by matching alleles, gene-for-gene or related infection mechanisms. Our experimental and theoretical results demonstrate that the effects of dispersal on diversity in coevolving host-parasite systems depend on an intricate interplay of the structure of the underlying dispersal network and the specifics of the host-parasite interaction.
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Affiliation(s)
| | - Matthew Robb
- Department of Mathematics, Imperial College London, London, UK
| | - Samantha E Forde
- Ecology and Evolutionary Biology Department, University of California, Santa Cruz, CA, USA.
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35
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Hall JPJ, Harrison E, Brockhurst MA. Viral host-adaptation: insights from evolution experiments with phages. Curr Opin Virol 2013; 3:572-7. [PMID: 23890845 DOI: 10.1016/j.coviro.2013.07.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 06/27/2013] [Accepted: 07/01/2013] [Indexed: 11/26/2022]
Abstract
Phages, viral parasites of bacteria, share fundamental features of pathogenic animal and plant viruses and represent a highly tractable empirical model system to understand viral evolution and in particular viral host-adaptation. Phage adaptation to a particular host genotype often results in improved fitness by way of parallel evolution whereby independent lineages hit upon identical adaptive solutions. By contrast, phage adaptation to an evolving host population leads to the evolution of increasing host-range over time and correlated phenotypic and genetic divergence between populations. Phage host-range expansion frequently occurs by a process of stepwise evolution of multiple mutations, and host-shifts are often constrained by mutational availability, pleiotropic costs or ecological conditions.
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Affiliation(s)
- James P J Hall
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
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36
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Dennehy JJ, Duffy S, O'Keefe KJ, Edwards SV, Turner PE. Frequent Coinfection Reduces RNA Virus Population Genetic Diversity. J Hered 2013; 104:704-12. [DOI: 10.1093/jhered/est038] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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37
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Weitz JS, Poisot T, Meyer JR, Flores CO, Valverde S, Sullivan MB, Hochberg ME. Phage-bacteria infection networks. Trends Microbiol 2012; 21:82-91. [PMID: 23245704 DOI: 10.1016/j.tim.2012.11.003] [Citation(s) in RCA: 193] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 11/07/2012] [Accepted: 11/09/2012] [Indexed: 01/21/2023]
Abstract
Phage and their bacterial hosts are the most abundant and genetically diverse group of organisms on the planet. Given their dominance, it is no wonder that many recent studies have found that phage-bacteria interactions strongly influence global biogeochemical cycles, incidence of human diseases, productivity of industrial microbial commodities, and patterns of microbial genome diversity. Unfortunately, given the extreme diversity and complexity of microbial communities, traditional analyses fail to characterize interaction patterns and underlying processes. Here, we review emerging systems approaches that combine empirical data with rigorous theoretical analysis to study phage-bacterial interactions as networks rather than as coupled interactions in isolation.
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Affiliation(s)
- Joshua S Weitz
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA.
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38
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Poullain V, Nuismer SL. Infection Genetics and the Likelihood of Host Shifts in Coevolving Host-Parasite Interactions. Am Nat 2012; 180:618-28. [DOI: 10.1086/667889] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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39
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Remold S. Understanding specialism when the Jack of all trades can be the master of all. Proc Biol Sci 2012; 279:4861-9. [PMID: 23097515 DOI: 10.1098/rspb.2012.1990] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Specialism is widespread in nature, generating and maintaining diversity, but recent work has demonstrated that generalists can be equally fit as specialists in some shared environments. This no-cost generalism challenges the maxim that 'the jack of all trades is the master of none', and requires evolutionary genetic mechanisms explaining the existence of specialism and no-cost generalism, and the persistence of specialism in the face of selection for generalism. Examining three well-described mechanisms with respect to epistasis and pleiotropy indicates that sign (or antagonistic) pleiotropy without epistasis cannot explain no-cost generalism and that magnitude pleiotropy without epistasis (including directional selection and mutation accumulation) cannot explain the persistence of specialism. However, pleiotropy with epistasis can explain all. Furthermore, epistatic pleiotropy may allow past habitat use to influence future use of novel environments, thereby affecting disease emergence and populations' responses to habitat change.
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Affiliation(s)
- Susanna Remold
- Department of Biology, University of Louisville, Louisville, KY 40292, USA.
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40
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Bono LM, Gensel CL, Pfennig DW, Burch CL. Competition and the origins of novelty: experimental evolution of niche-width expansion in a virus. Biol Lett 2012; 9:20120616. [PMID: 23075527 DOI: 10.1098/rsbl.2012.0616] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Competition for resources has long been viewed as a key agent of divergent selection. Theory holds that populations facing severe intraspecific competition will tend to use a wider range of resources, possibly even using entirely novel resources that are less in demand. Yet, there have been few experimental tests of these ideas. Using the bacterial virus (bacteriophage) 6 as a model system, we examined whether competition for host resources promotes the evolution of novel resource use. In the laboratory, 6 exhibits a narrow host range but readily produces mutants capable of infecting novel bacterial hosts. Here, we show that when 6 populations were subjected to intense intraspecific competition for their standard laboratory host, they rapidly evolved new generalist morphs that infect novel hosts. Our results therefore suggest that competition for host resources may drive the evolution of host range expansion in viruses. More generally, our findings demonstrate that intraspecific resource competition can indeed promote the evolution of novel resource-use phenotypes.
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Affiliation(s)
- Lisa M Bono
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
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41
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Characterization of novel phages isolated in coagulase-negative staphylococci reveals evolutionary relationships with Staphylococcus aureus phages. J Bacteriol 2012; 194:5829-39. [PMID: 22923589 DOI: 10.1128/jb.01085-12] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Despite increasing interest in coagulase-negative staphylococci (CoNS), little information is available about their bacteriophages. We isolated and sequenced three novel temperate Siphoviridae phages (StB12, StB27, and StB20) from the CoNS Staphylococcus hominis and S. capitis species. The genome sizes are around 40 kb, and open reading frames (ORFs) are arranged in functional modules encoding lysogeny, DNA metabolism, morphology, and cell lysis. Bioinformatics analysis allowed us to assign a potential function to half of the predicted proteins. Structural elements were further identified by proteomic analysis of phage particles, and DNA-packaging mechanisms were determined. Interestingly, the three phages show identical integration sites within their host genomes. In addition to this experimental characterization, we propose a novel classification based on the analysis of 85 phage and prophage genomes, including 15 originating from CoNS. Our analysis established 9 distinct clusters and revealed close relationships between S. aureus and CoNS phages. Genes involved in DNA metabolism and lysis and potentially in phage-host interaction appear to be widespread, while structural genes tend to be cluster specific. Our findings support the notion of a possible reciprocal exchange of genes between phages originating from S. aureus and CoNS, which may be of crucial importance for pathogenesis in staphylococci.
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42
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Turner PE, McBride RC, Duffy S, Montville R, Wang LS, Yang YW, Lee SJ, Kim J. Evolutionary genomics of host-use in bifurcating demes of RNA virus phi-6. BMC Evol Biol 2012; 12:153. [PMID: 22913547 PMCID: PMC3495861 DOI: 10.1186/1471-2148-12-153] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 08/16/2012] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Viruses are exceedingly diverse in their evolved strategies to manipulate hosts for viral replication. However, despite these differences, most virus populations will occasionally experience two commonly-encountered challenges: growth in variable host environments, and growth under fluctuating population sizes. We used the segmented RNA bacteriophage ϕ6 as a model for studying the evolutionary genomics of virus adaptation in the face of host switches and parametrically varying population sizes. To do so, we created a bifurcating deme structure that reflected lineage splitting in natural populations, allowing us to test whether phylogenetic algorithms could accurately resolve this 'known phylogeny'. The resulting tree yielded 32 clones at the tips and internal nodes; these strains were fully sequenced and measured for phenotypic changes in selected traits (fitness on original and novel hosts). RESULTS We observed that RNA segment size was negatively correlated with the extent of molecular change in the imposed treatments; molecular substitutions tended to cluster on the Small and Medium RNA chromosomes of the virus, and not on the Large segment. Our study yielded a very large molecular and phenotypic dataset, fostering possible inferences on genotype-phenotype associations. Using further experimental evolution, we confirmed an inference on the unanticipated role of an allelic switch in a viral assembly protein, which governed viral performance across host environments. CONCLUSIONS Our study demonstrated that varying complexities can be simultaneously incorporated into experimental evolution, to examine the combined effects of population size, and adaptation in novel environments. The imposed bifurcating structure revealed that some methods for phylogenetic reconstruction failed to resolve the true phylogeny, owing to a paucity of molecular substitutions separating the RNA viruses that evolved in our study.
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Affiliation(s)
- Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Robert C McBride
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Current address: Sapphire Energy, Inc., 3115 Merryfield Row, San Diego, CA 92121, USA
| | - Siobain Duffy
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Current address: Department of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Rebecca Montville
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Li-San Wang
- Department of Pathology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yul W Yang
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Current address: Stanford School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
| | - Sun Jin Lee
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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43
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Ching J, Musheyev SA, Chowdhury D, Kim JA, Choi Y, Dennehy JJ. MIGRATION ENHANCES ADAPTATION IN BACTERIOPHAGE POPULATIONS EVOLVING IN ECOLOGICAL SINKS. Evolution 2012; 67:10-7. [DOI: 10.1111/j.1558-5646.2012.01742.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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44
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Wojtowicz AJ, Miller CR, Joyce P. Estimating the number of one-step beneficial mutations. Stat Appl Genet Mol Biol 2012; 11:/j/sagmb.2012.11.issue-4/1544-6115.1788/1544-6115.1788.xml. [PMID: 22850060 DOI: 10.1515/1544-6115.1788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Mutations that confer a selective advantage to an organism are the raw material upon which natural selection acts. The number of such mutations that are available is a central quantity of interest for understanding the tempo and trajectory of adaptive evolution. While this quantity is typically unknown, it can be estimated with varying levels of accuracy based on data obtained experimentally. We propose a method for estimating the number of beneficial mutations that accounts for the evolutionary forces that generate the data. Our model-based parametric approach is compared to an adjusted nonparametric abundance-based coverage estimator. We show that, in general, our estimator performs better. When the number of mutations is small, however, the performances of the two estimators are similar.
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45
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ARBIV A, KHOKHLOVA IS, OVADIA O, NOVOPLANSKY A, KRASNOV BR. Use it or lose it: reproductive implications of ecological specialization in a haematophagous ectoparasite. J Evol Biol 2012; 25:1140-8. [DOI: 10.1111/j.1420-9101.2012.02499.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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46
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Nguyen AH, Molineux IJ, Springman R, Bull JJ. Multiple genetic pathways to similar fitness limits during viral adaptation to a new host. Evolution 2012; 66:363-74. [PMID: 22276534 PMCID: PMC3377685 DOI: 10.1111/j.1558-5646.2011.01433.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The gain in fitness during adaptation depends on the supply of beneficial mutations. Despite a good theoretical understanding of how evolution proceeds for a defined set of mutations, there is little understanding of constraints on net fitness-whether fitness will reach a limit despite ongoing selection and mutation, and if there is a limit, what determines it. Here, the dsDNA bacteriophage SP6, a virus of Salmonella, was adapted to Escherichia coli K-12. From an isolate capable of modest growth on E. coli, four lines were adapted for rapid growth by protocols differing in use of mutagen, propagation method, and duration, but using the same media, temperature, and a continual excess of the novel host. Nucleotide changes underlying those adaptations differed greatly in number and identity, but the four lines achieved similar absolute fitness at the end, an increase of more than 4000-fold phage descendants per hour. Thus, the fitness landscape allows multiple genetic paths to the same approximate fitness limit. The existence and causes of fitness limits have ramifications to genome engineering, vaccine design, and "lethal mutagenesis" treatments to cure viral infections.
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Affiliation(s)
- Andre H Nguyen
- Section of Integrative Biology, The University of Texas at Austin Austin, Texas 78712, USA
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47
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Meyer JR, Dobias DT, Weitz JS, Barrick JE, Quick RT, Lenski RE. Repeatability and contingency in the evolution of a key innovation in phage lambda. Science 2012; 335:428-32. [PMID: 22282803 PMCID: PMC3306806 DOI: 10.1126/science.1214449] [Citation(s) in RCA: 307] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The processes responsible for the evolution of key innovations, whereby lineages acquire qualitatively new functions that expand their ecological opportunities, remain poorly understood. We examined how a virus, bacteriophage λ, evolved to infect its host, Escherichia coli, through a novel pathway. Natural selection promoted the fixation of mutations in the virus's host-recognition protein, J, that improved fitness on the original receptor, LamB, and set the stage for other mutations that allowed infection through a new receptor, OmpF. These viral mutations arose after the host evolved reduced expression of LamB, whereas certain other host mutations prevented the phage from evolving the new function. This study shows the complex interplay between genomic processes and ecological conditions that favor the emergence of evolutionary innovations.
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Affiliation(s)
- Justin R Meyer
- Department of Zoology, Michigan State University, East Lansing, MI 48824, USA.
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48
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Novella IS, Presloid JB, Smith SD, Wilke CO. Specific and nonspecific host adaptation during arboviral experimental evolution. J Mol Microbiol Biotechnol 2012; 21:71-81. [PMID: 22248544 PMCID: PMC3697271 DOI: 10.1159/000332752] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
During the past decade or so, there has been a substantial body of work to dissect arboviral evolution and to develop models of adaptation during host switching. Regardless of what species serve as host or vectors, and of the geographic distribution and the mechanisms of replication, arboviruses tend to have slow evolutionary rates in nature. The hypothesis that this is the result of replication in the disparate environments provided by host and vector did not receive solid experimental support in any of the many viral species tested. Instead, it seems that from the virus's point of view, either the two environments are sufficiently similar or one of the environments so dominates viral evolution that there is tolerance for suboptimal adaptation to the other environment. Replication in alternating environments has an unexpected cost in that there is decreased genetic variance that translates into a compromised adaptability for bypassed environments. Arboviruses under strong and continuous positive selection may have unusual patterns of genomic changes, with few or no mutations accumulated in the consensus sequence or with dN/dS values typically consistent with random drift in DNA-based organisms.
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Affiliation(s)
- Isabel S Novella
- Department of Medical Microbiology and Immunology, College of Medicine, University of Toledo Health Science Campus, Toledo, Ohio, USA.
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49
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Lalić J, Cuevas JM, Elena SF. Effect of host species on the distribution of mutational fitness effects for an RNA virus. PLoS Genet 2011; 7:e1002378. [PMID: 22125497 PMCID: PMC3219607 DOI: 10.1371/journal.pgen.1002378] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 09/22/2011] [Indexed: 12/15/2022] Open
Abstract
Knowledge about the distribution of mutational fitness effects (DMFE) is essential for many evolutionary models. In recent years, the properties of the DMFE have been carefully described for some microorganisms. In most cases, however, this information has been obtained only for a single environment, and very few studies have explored the effect that environmental variation may have on the DMFE. Environmental effects are particularly relevant for the evolution of multi-host parasites and thus for the emergence of new pathogens. Here we characterize the DMFE for a collection of twenty single-nucleotide substitution mutants of Tobacco etch potyvirus (TEV) across a set of eight host environments. Five of these host species were naturally infected by TEV, all belonging to family Solanaceae, whereas the other three were partially susceptible hosts belonging to three other plant families. First, we found a significant virus genotype-by-host species interaction, which was sustained by differences in genetic variance for fitness and the pleiotropic effect of mutations among hosts. Second, we found that the DMFEs were markedly different between Solanaceae and non-Solanaceae hosts. Exposure of TEV genotypes to non-Solanaceae hosts led to a large reduction of mean viral fitness, while the variance remained constant and skewness increased towards the right tail. Within the Solanaceae hosts, the distribution contained an excess of deleterious mutations, whereas for the non-Solanaceae the fraction of beneficial mutations was significantly larger. All together, this result suggests that TEV may easily broaden its host range and improve fitness in new hosts, and that knowledge about the DMFE in the natural host does not allow for making predictions about its properties in an alternative host.
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Affiliation(s)
- Jasna Lalić
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas–Universidad Politécnica de Valencia, València, Spain
| | - José M. Cuevas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas–Universidad Politécnica de Valencia, València, Spain
| | - Santiago F. Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas–Universidad Politécnica de Valencia, València, Spain
- The Santa Fe Institute, Santa Fe, New Mexico, United States of America
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Acosta-Leal R, Duffy S, Xiong Z, Hammond RW, Elena SF. Advances in plant virus evolution: translating evolutionary insights into better disease management. PHYTOPATHOLOGY 2011; 101:1136-48. [PMID: 21554186 DOI: 10.1094/phyto-01-11-0017] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Recent studies in plant virus evolution are revealing that genetic structure and behavior of virus and viroid populations can explain important pathogenic properties of these agents, such as host resistance breakdown, disease severity, and host shifting, among others. Genetic variation is essential for the survival of organisms. The exploration of how these subcellular parasites generate and maintain a certain frequency of mutations at the intra- and inter-host levels is revealing novel molecular virus-plant interactions. They emphasize the role of host environment in the dynamic genetic composition of virus populations. Functional genomics has identified host factors that are transcriptionally altered after virus infections. The analyses of these data by means of systems biology approaches are uncovering critical plant genes specifically targeted by viruses during host adaptation. Also, a next-generation resequencing approach of a whole virus genome is opening new avenues to study virus recombination and the relationships between intra-host virus composition and pathogenesis. Altogether, the analyzed data indicate that systematic disruption of some specific parameters of evolving virus populations could lead to more efficient ways of disease prevention, eradication, or tolerable virus-plant coexistence.
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