1
|
Laguna-Castro M, Rodríguez-Moreno A, Lázaro E. Evolutionary Adaptation of an RNA Bacteriophage to Repeated Freezing and Thawing Cycles. Int J Mol Sci 2024; 25:4863. [PMID: 38732084 PMCID: PMC11084849 DOI: 10.3390/ijms25094863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Bacteriophage fitness is determined by factors influencing both their replication within bacteria and their ability to maintain infectivity between infections. The latter becomes particularly crucial under adverse environmental conditions or when host density is low. In such scenarios, the damage experienced by viral particles could lead to the loss of infectivity, which might be mitigated if the virus undergoes evolutionary optimization through replication. In this study, we conducted an evolution experiment involving bacteriophage Qβ, wherein it underwent 30 serial transfers, each involving a cycle of freezing and thawing followed by replication of the surviving viruses. Our findings show that Qβ was capable of enhancing its resistance to this selective pressure through various adaptive pathways that did not impair the virus replicative capacity. Notably, these adaptations predominantly involved mutations located within genes encoding capsid proteins. The adapted populations exhibited higher resistance levels than individual viruses isolated from them, and the latter surpassed those observed in single mutants generated via site-directed mutagenesis. This suggests potential interactions among mutants and mutations. In conclusion, our study highlights the significant role of extracellular selective pressures in driving the evolution of phages, influencing both the genetic composition of their populations and their phenotypic properties.
Collapse
Affiliation(s)
| | | | - Ester Lázaro
- Centro de Astrobiología (CAB), CSIC-INTA, Carretera de Ajalvir Km 4, 28850 Torrejón de Ardoz, Madrid, Spain; (M.L.-C.); (A.R.-M.)
| |
Collapse
|
2
|
Chen TH, Tsai MJ, Chang CS, Xu L, Fu YS, Weng CF. The exploration of phytocompounds theoretically combats SARS-CoV-2 pandemic against virus entry, viral replication and immune evasion. J Infect Public Health 2023; 16:42-54. [PMID: 36470006 PMCID: PMC9675089 DOI: 10.1016/j.jiph.2022.11.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The novel coronavirus disease-2019 (COVID-19) that emerged in China, is an extremely contagious and pathogenic viral infection caused by the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) that has sparked a global pandemic. The few and limited availability of approved therapeutic agents or vaccines is of great concern. Urgently, Remdesivir, Nirmatrelvir, Molnupiravir, and some phytochemicals including polyphenol, flavonoid, alkaloid, and triterpenoid are applied to develop as repurposing drugs against the SARS-CoV-2 invasion. METHODS This study was conducted to perform molecular docking and absorption, distribution, metabolism, excretion and toxicity (ADMET) analysis of the potential phytocompounds and repurposing drugs against three targets of SARS-CoV-2 proteins (RNA dependent RNA polymerase, RdRp, Endoribonclease, S-protein of ACE2-RBD). RESULTS The docking data illustrated Arachidonic acid, Rutin, Quercetin, and Curcumin were highly bound with coronavirus polyprotein replicase and Ebolavirus envelope protein. Furthermore, anti- Ebolavirus molecule Remedesivir, anti-HIV molecule Chloroquine, and Darunavir were repurposed with coronavirus polyprotein replicase as well as Ebolavirus envelope protein. The strongest binding interaction of each targets are Rutin with RdRp, Endoribonclease with Amentoflavone, and ACE2-RBD with Epigallocatechin gallate. CONCLUSIONS Taken altogether, these results shed a light on that phytocompounds have a therapeutic potential for the treatment of anti-SARS-CoV-2 may base on multi-target effects or cocktail formulation for blocking viral infection through invasion/activation, transcription/reproduction, and posttranslational cleavage to battle COVID-19 pandemic.
Collapse
Affiliation(s)
- Ting-Hsu Chen
- Functional Physiology Section, Department of Basic Medical Science, Xiamen Medical College, Xiamen 361023, Fujian, China
| | - May-Jywan Tsai
- Department of Neurosurgery, Neurological Institute, Neurological Institute, Taipei 11217, Taiwan
| | - Chun-Sheng Chang
- Department of biotechnology and food technology, Southern Taiwan University of Science and Technology, Yungkang City 701, Taiwan
| | - Linxi Xu
- Functional Physiology Section, Department of Basic Medical Science, Xiamen Medical College, Xiamen 361023, Fujian, China
| | - Yaw-Syan Fu
- Functional Physiology Section, Department of Basic Medical Science, Xiamen Medical College, Xiamen 361023, Fujian, China,Institute of Respiratory Disease, Department of Basic Medical Science, Xiamen Medical College, Xiamen 361023, Fujian, China,Corresponding author
| | - Ching-Feng Weng
- Functional Physiology Section, Department of Basic Medical Science, Xiamen Medical College, Xiamen 361023, Fujian, China,Institute of Respiratory Disease, Department of Basic Medical Science, Xiamen Medical College, Xiamen 361023, Fujian, China,Corresponding author
| |
Collapse
|
3
|
Abstract
Viruses are the most abundant biological entities on Earth, and yet, they have not received enough consideration in astrobiology. Viruses are also extraordinarily diverse, which is evident in the types of relationships they establish with their host, their strategies to store and replicate their genetic information and the enormous diversity of genes they contain. A viral population, especially if it corresponds to a virus with an RNA genome, can contain an array of sequence variants that greatly exceeds what is present in most cell populations. The fact that viruses always need cellular resources to multiply means that they establish very close interactions with cells. Although in the short term these relationships may appear to be negative for life, it is evident that they can be beneficial in the long term. Viruses are one of the most powerful selective pressures that exist, accelerating the evolution of defense mechanisms in the cellular world. They can also exchange genetic material with the host during the infection process, providing organisms with capacities that favor the colonization of new ecological niches or confer an advantage over competitors, just to cite a few examples. In addition, viruses have a relevant participation in the biogeochemical cycles of our planet, contributing to the recycling of the matter necessary for the maintenance of life. Therefore, although viruses have traditionally been excluded from the tree of life, the structure of this tree is largely the result of the interactions that have been established throughout the intertwined history of the cellular and the viral worlds. We do not know how other possible biospheres outside our planet could be, but it is clear that viruses play an essential role in the terrestrial one. Therefore, they must be taken into account both to improve our understanding of life that we know, and to understand other possible lives that might exist in the cosmos.
Collapse
Affiliation(s)
- Ignacio de la Higuera
- Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, OR, United States
| | - Ester Lázaro
- Centro de Astrobiología (CAB), CSIC-INTA, Torrejón de Ardoz, Spain
| |
Collapse
|
4
|
Segredo-Otero E, Sanjuán R. Cooperative Virus-Virus Interactions: An Evolutionary Perspective. BIODESIGN RESEARCH 2022; 2022:9819272. [PMID: 37850129 PMCID: PMC10521650 DOI: 10.34133/2022/9819272] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/21/2022] [Indexed: 10/19/2023] Open
Abstract
Despite extensive evidence of virus-virus interactions, not much is known about their biological significance. Importantly, virus-virus interactions could have evolved as a form of cooperation or simply be a by-product of other processes. Here, we review and discuss different types of virus-virus interactions from the point of view of social evolution, which provides a well-established framework for interpreting the fitness costs and benefits of such traits. We also classify interactions according to their mechanisms of action and speculate on their evolutionary implications. As in any other biological system, the evolutionary stability of viral cooperation critically requires cheaters to be excluded from cooperative interactions. We discuss how cheater viruses exploit cooperative traits and how viral populations are able to counteract this maladaptive process.
Collapse
Affiliation(s)
- Ernesto Segredo-Otero
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, C/ Catedrático Agustín Escardino 9, 46980 Paterna, València, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, C/ Catedrático Agustín Escardino 9, 46980 Paterna, València, Spain
| |
Collapse
|
5
|
Xavier CAD, Godinho MT, Mar TB, Ferro CG, Sande OFL, Silva JC, Ramos-Sobrinho R, Nascimento RN, Assunção I, Lima GSA, Lima ATM, Murilo Zerbini F. Evolutionary dynamics of bipartite begomoviruses revealed by complete genome analysis. Mol Ecol 2021; 30:3747-3767. [PMID: 34021651 DOI: 10.1111/mec.15997] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/07/2021] [Accepted: 05/14/2021] [Indexed: 12/17/2022]
Abstract
Several key evolutionary events marked the evolution of geminiviruses, culminating with the emergence of divided (bipartite) genomes represented by viruses classified in the genus Begomovirus. This genus represents the most abundant group of multipartite viruses, contributing significantly to the observed abundance of multipartite species in the virosphere. Although aspects related to virus-host interactions and evolutionary dynamics have been extensively studied, the bipartite nature of these viruses has been little explored in evolutionary studies. Here, we performed a parallel evolutionary analysis of the DNA-A and DNA-B segments of New World begomoviruses. A total of 239 full-length DNA-B sequences obtained in this study, combined with 292 DNA-A and 76 DNA-B sequences retrieved from GenBank, were analysed. The results indicate that the DNA-A and DNA-B respond differentially to evolutionary processes, with the DNA-B being more permissive to variation and more prone to recombination than the DNA-A. Although a clear geographic segregation was observed for both segments, differences in the genetic structure between DNA-A and DNA-B were also observed, with cognate segments belonging to distinct genetic clusters. DNA-B coding regions evolve under the same selection pressures than DNA-A coding regions. Together, our results indicate an interplay between reassortment and recombination acting at different levels across distinct subpopulations and segments.
Collapse
Affiliation(s)
- César A D Xavier
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Márcio T Godinho
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Talita B Mar
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Camila G Ferro
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Osvaldo F L Sande
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - José C Silva
- Dep. de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Roberto Ramos-Sobrinho
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Renato N Nascimento
- Centro de Ciências Agrárias/Fitossanidade, Universidade Federal de Alagoas, Rio Largo, Alagoas, Brazil
| | - Iraildes Assunção
- Centro de Ciências Agrárias/Fitossanidade, Universidade Federal de Alagoas, Rio Largo, Alagoas, Brazil
| | - Gaus S A Lima
- Centro de Ciências Agrárias/Fitossanidade, Universidade Federal de Alagoas, Rio Largo, Alagoas, Brazil
| | - Alison T M Lima
- Instituto de Ciências Agrárias, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - F Murilo Zerbini
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| |
Collapse
|
6
|
Farooq T, Umar M, She X, Tang Y, He Z. Molecular phylogenetics and evolutionary analysis of a highly recombinant begomovirus, Cotton leaf curl Multan virus, and associated satellites. Virus Evol 2021; 7:veab054. [PMID: 34532058 PMCID: PMC8438885 DOI: 10.1093/ve/veab054] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/24/2021] [Accepted: 06/04/2021] [Indexed: 11/12/2022] Open
Abstract
Cotton leaf curl Multan virus (CLCuMuV) and its associated satellites are a major part of the cotton leaf curl disease (CLCuD) caused by the begomovirus species complex. Despite the implementation of potential disease management strategies, the incessant resurgence of resistance-breaking variants of CLCuMuV imposes a continuous threat to cotton production. Here, we present a focused effort to map the geographical prevalence, genomic diversity, and molecular evolutionary endpoints that enhance disease complexity by facilitating the successful adaptation of CLCuMuV populations to the diversified ecosystems. Our results demonstrate that CLCuMuV populations are predominantly distributed in China, while the majority of alphasatellites and betasatellites exist in Pakistan. We demonstrate that together with frequent recombination, an uneven genetic variation mainly drives CLCuMuV and its satellite's virulence and evolvability. However, the pattern and distribution of recombination breakpoints greatly vary among viral and satellite sequences. The CLCuMuV, Cotton leaf curl Multan alphasatellite, and Cotton leaf curl Multan betasatellite populations arising from distinct regions exhibit high mutation rates. Although evolutionarily linked, these populations are independently evolving under strong purifying selection. These findings will facilitate to comprehensively understand the standing genetic variability and evolutionary patterns existing among CLCuMuV populations across major cotton-producing regions of the world.
Collapse
Affiliation(s)
- Tahir Farooq
- Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China
| | - Muhammad Umar
- Tasmanian Institute of Agriculture, New Town Research Laboratories, University of Tasmania, 13 St. Johns Avenue, New Town, TAS 7008, Australia
| | - Xiaoman She
- Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China
| | - Yafei Tang
- Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China
| | - Zifu He
- Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China
| |
Collapse
|
7
|
Zanardo LG, Trindade TA, Mar TB, Barbosa TMC, Milanesi DF, Alves MS, Lima RRPN, Zerbini FM, Janssen A, Mizubuti ESG, Elliot SL, Carvalho CM. Experimental evolution of cowpea mild mottle virus reveals recombination-driven reduction in virulence accompanied by increases in diversity and viral fitness. Virus Res 2021; 303:198389. [PMID: 33716182 DOI: 10.1016/j.virusres.2021.198389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 12/22/2022]
Abstract
Major themes in pathogen evolution are emergence, evolution of virulence, host adaptation and the processes that underlie them. RNA viruses are of particular interest due to their rapid evolution. The in vivo molecular evolution of an RNA plant virus was demonstrated here using a necrotic isolate of cowpea mild mottle virus (CPMMV) and a susceptible soybean genotype submitted to serial inoculations. We show that the virus lost the capacity to cause necrosis after six passages through the host plant. When a severe bottleneck was imposed, virulence reduction occurred in the second passage. The change to milder symptoms had fitness benefits for the virus (higher RNA accumulation) and for its vector, the whitefly Bemisia tabaci. Genetic polymorphisms were highest in ORF1 (viral replicase) and were independent of the symptom pattern. Recombination was a major contributor to this diversity - even with the strong genetic bottleneck, recombination events and hot spots were detected within ORF1. Virulence reduction was associated with different sites in ORF1 associated to recombination events in both experiments. Overall, the results demonstrate that the reduction in virulence was a consequence of the emergence of new variants, driven by recombination. Besides providing details of the evolutionary mechanisms behind a reduction in virulence and its effect under viral and vector fitness, we propose that this recombination-driven switch in virulence allows the pathogen to rapidly adapt to a new host and, potentially, switch back.
Collapse
Affiliation(s)
- Larissa G Zanardo
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Tiago A Trindade
- Departamento de Entomologia, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Talita B Mar
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Tarsiane M C Barbosa
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Diogo F Milanesi
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Murilo S Alves
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | - Roberta R P N Lima
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - F Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Arne Janssen
- Departamento de Entomologia, Universidade Federal de Viçosa, Viçosa, MG, Brazil; IBED, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Eduardo S G Mizubuti
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Simon L Elliot
- Departamento de Entomologia, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Claudine M Carvalho
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
| |
Collapse
|
8
|
Ryabov EV, Christmon K, Heerman MC, Posada-Florez F, Harrison RL, Chen Y, Evans JD. Development of a Honey Bee RNA Virus Vector Based on the Genome of a Deformed Wing Virus. Viruses 2020; 12:E374. [PMID: 32231059 PMCID: PMC7232236 DOI: 10.3390/v12040374] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/24/2020] [Accepted: 03/26/2020] [Indexed: 12/22/2022] Open
Abstract
We developed a honey bee RNA-virus vector based on the genome of a picorna-like Deformed wing virus (DWV), the main viral pathogen of the honey bee (Apis mellifera). To test the potential of DWV to be utilized as a vector, the 717 nt sequence coding for the enhanced green fluorescent protein (eGFP), flanked by the peptides targeted by viral protease, was inserted into an infectious cDNA clone of DWV in-frame between the leader protein and the virus structural protein VP2 genes. The in vitro RNA transcripts from egfp-tagged DWV cDNA clones were infectious when injected into honey bee pupae. Stable DWV particles containing genomic RNA of the recovered DWV with egfp inserts were produced, as evidenced by cesium chloride density gradient centrifugation. These particles were infectious to honey bee pupae when injected intra-abdominally. Fluorescent microscopy showed GFP expression in the infected cells and Western blot analysis demonstrated accumulation of free eGFP rather than its fusions with DWV leader protein (LP) and/or viral protein (VP) 2. Analysis of the progeny egfp-tagged DWV showed gradual accumulation of genome deletions for egfp, providing estimates for the rate of loss of a non-essential gene an insect RNA virus genome during natural infection.
Collapse
Affiliation(s)
- Eugene V. Ryabov
- USDA, Agricultural Research Service, Bee Research Lab, Beltsville, MD 20705, USA; (K.C.); (M.C.H.); (F.P.-F.); (Y.C.); (J.D.E.)
| | - Krisztina Christmon
- USDA, Agricultural Research Service, Bee Research Lab, Beltsville, MD 20705, USA; (K.C.); (M.C.H.); (F.P.-F.); (Y.C.); (J.D.E.)
- Department of Entomology, University of Maryland, College Park, MD 20742, USA
| | - Matthew C. Heerman
- USDA, Agricultural Research Service, Bee Research Lab, Beltsville, MD 20705, USA; (K.C.); (M.C.H.); (F.P.-F.); (Y.C.); (J.D.E.)
| | - Francisco Posada-Florez
- USDA, Agricultural Research Service, Bee Research Lab, Beltsville, MD 20705, USA; (K.C.); (M.C.H.); (F.P.-F.); (Y.C.); (J.D.E.)
| | - Robert L. Harrison
- USDA, Agricultural Research Service, Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, MD 20705, USA;
| | - Yanping Chen
- USDA, Agricultural Research Service, Bee Research Lab, Beltsville, MD 20705, USA; (K.C.); (M.C.H.); (F.P.-F.); (Y.C.); (J.D.E.)
| | - Jay D. Evans
- USDA, Agricultural Research Service, Bee Research Lab, Beltsville, MD 20705, USA; (K.C.); (M.C.H.); (F.P.-F.); (Y.C.); (J.D.E.)
| |
Collapse
|
9
|
Zhao L, Duffy S. Gauging genetic diversity of generalists: A test of genetic and ecological generalism with RNA virus experimental evolution. Virus Evol 2019; 5:vez019. [PMID: 31275611 PMCID: PMC6599687 DOI: 10.1093/ve/vez019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Generalist viruses, those with a comparatively larger host range, are considered more likely to emerge on new hosts. The potential to emerge in new hosts has been linked to viral genetic diversity, a measure of evolvability. However, there is no consensus on whether infecting a larger number of hosts leads to higher genetic diversity, or whether diversity is better maintained in a homogeneous environment, similar to the lifestyle of a specialist virus. Using experimental evolution with the RNA bacteriophage phi6, we directly tested whether genetic generalism (carrying an expanded host range mutation) or environmental generalism (growing on heterogeneous hosts) leads to viral populations with more genetic variation. Sixteen evolved viral lineages were deep sequenced to provide genetic evidence for population diversity. When evolved on a single host, specialist and generalist genotypes both maintained the same level of diversity (measured by the number of single nucleotide polymorphisms (SNPs) above 1%, P = 0.81). However, the generalist genotype evolved on a single host had higher SNP levels than generalist lineages under two heterogeneous host passaging schemes (P = 0.001, P < 0.001). RNA viruses’ response to selection in alternating hosts reduces standing genetic diversity compared to those evolving in a single host to which the virus is already well-adapted.
Collapse
Affiliation(s)
- Lele Zhao
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, 14 College Farm Road, New Brunswick, NJ, USA
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, 14 College Farm Road, New Brunswick, NJ, USA
| |
Collapse
|
10
|
Fortuna MA, Zaman L, Wagner A, Bascompte J. Non-adaptive origins of evolutionary innovations increase network complexity in interacting digital organisms. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0431. [PMID: 29061902 DOI: 10.1098/rstb.2016.0431] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2017] [Indexed: 12/27/2022] Open
Abstract
The origin of evolutionary innovations is a central problem in evolutionary biology. To what extent such innovations have adaptive or non-adaptive origins is hard to assess in real organisms. This limitation, however, can be overcome using digital organisms, i.e. self-replicating computer programs that mutate, evolve and coevolve within a user-defined computational environment. Here, we quantify the role of the non-adaptive origins of host resistance traits in determining the evolution of ecological interactions among host and parasite digital organisms. We find that host resistance traits arising spontaneously as exaptations increase the complexity of antagonistic host-parasite networks. Specifically, they lead to higher host phenotypic diversification, a larger number of ecological interactions and higher heterogeneity in interaction strengths. Given the potential of network architecture to affect network dynamics, such exaptations may increase the persistence of entire communities. Our in silico approach, therefore, may complement current theoretical advances aimed at disentangling the ecological and evolutionary mechanisms shaping species interaction networks.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'.
Collapse
Affiliation(s)
- Miguel A Fortuna
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
| | - Luis Zaman
- Department of Biology, University of Washington, Seattle, WA 98195-1800, USA.,Center for the Study of Complex Systems, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,The Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Jordi Bascompte
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
| |
Collapse
|
11
|
Berliner AJ, Mochizuki T, Stedman KM. Astrovirology: Viruses at Large in the Universe. ASTROBIOLOGY 2018; 18:207-223. [PMID: 29319335 DOI: 10.1089/ast.2017.1649] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Viruses are the most abundant biological entities on modern Earth. They are highly diverse both in structure and genomic sequence, play critical roles in evolution, strongly influence terran biogeochemistry, and are believed to have played important roles in the origin and evolution of life. However, there is yet very little focus on viruses in astrobiology. Viruses arguably have coexisted with cellular life-forms since the earliest stages of life, may have been directly involved therein, and have profoundly influenced cellular evolution. Viruses are the only entities on modern Earth to use either RNA or DNA in both single- and double-stranded forms for their genetic material and thus may provide a model for the putative RNA-protein world. With this review, we hope to inspire integration of virus research into astrobiology and also point out pressing unanswered questions in astrovirology, particularly regarding the detection of virus biosignatures and whether viruses could be spread extraterrestrially. We present basic virology principles, an inclusive definition of viruses, review current virology research pertinent to astrobiology, and propose ideas for future astrovirology research foci. Key Words: Astrobiology-Virology-Biosignatures-Origin of life-Roadmap. Astrobiology 18, 207-223.
Collapse
Affiliation(s)
| | | | - Kenneth M Stedman
- 3 Center for Life in Extreme Environments and Biology Department, Portland State University , Oregon, USA
| |
Collapse
|
12
|
Solé R. The major synthetic evolutionary transitions. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2016.0175. [PMID: 27431528 DOI: 10.1098/rstb.2016.0175] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2016] [Indexed: 12/16/2022] Open
Abstract
Evolution is marked by well-defined events involving profound innovations that are known as 'major evolutionary transitions'. They involve the integration of autonomous elements into a new, higher-level organization whereby the former isolated units interact in novel ways, losing their original autonomy. All major transitions, which include the origin of life, cells, multicellular systems, societies or language (among other examples), took place millions of years ago. Are these transitions unique, rare events? Have they instead universal traits that make them almost inevitable when the right pieces are in place? Are there general laws of evolutionary innovation? In order to approach this problem under a novel perspective, we argue that a parallel class of evolutionary transitions can be explored involving the use of artificial evolutionary experiments where alternative paths to innovation can be explored. These 'synthetic' transitions include, for example, the artificial evolution of multicellular systems or the emergence of language in evolved communicating robots. These alternative scenarios could help us to understand the underlying laws that predate the rise of major innovations and the possibility for general laws of evolved complexity. Several key examples and theoretical approaches are summarized and future challenges are outlined.This article is part of the themed issue 'The major synthetic evolutionary transitions'.
Collapse
Affiliation(s)
- Ricard Solé
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain Institut de Biologia Evolutiva, CSIC-UPF, Pg Maritim de la Barceloneta 37, 08003 Barcelona, Spain Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| |
Collapse
|
13
|
Abstract
Multicomponent viruses are common in plants and fungi. In this issue of Cell Host & Microbe, Ladner et al. (2016) describe a multicomponent virus from animals. This supports an emerging view that invertebrates harbor a remarkable viral diversity and highlights how little of the virosphere has been explored.
Collapse
Affiliation(s)
- Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, the University of Sydney, Sydney NSW 2006, Australia.
| |
Collapse
|