1
|
O’Brien NLV, Holland B, Engelstädter J, Ortiz-Barrientos D. The distribution of fitness effects during adaptive walks using a simple genetic network. PLoS Genet 2024; 20:e1011289. [PMID: 38787919 PMCID: PMC11156440 DOI: 10.1371/journal.pgen.1011289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 06/06/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024] Open
Abstract
The tempo and mode of adaptation depends on the availability of beneficial alleles. Genetic interactions arising from gene networks can restrict this availability. However, the extent to which networks affect adaptation remains largely unknown. Current models of evolution consider additive genotype-phenotype relationships while often ignoring the contribution of gene interactions to phenotypic variance. In this study, we model a quantitative trait as the product of a simple gene regulatory network, the negative autoregulation motif. Using forward-time genetic simulations, we measure adaptive walks towards a phenotypic optimum in both additive and network models. A key expectation from adaptive walk theory is that the distribution of fitness effects of new beneficial mutations is exponential. We found that both models instead harbored distributions with fewer large-effect beneficial alleles than expected. The network model also had a complex and bimodal distribution of fitness effects among all mutations, with a considerable density at deleterious selection coefficients. This behavior is reminiscent of the cost of complexity, where correlations among traits constrain adaptation. Our results suggest that the interactions emerging from genetic networks can generate complex and multimodal distributions of fitness effects.
Collapse
Affiliation(s)
- Nicholas L. V. O’Brien
- School of the Environment, The University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, Australia
| | - Barbara Holland
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Jan Engelstädter
- School of the Environment, The University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, Australia
| | - Daniel Ortiz-Barrientos
- School of the Environment, The University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, Australia
| |
Collapse
|
2
|
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
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Abstract
RNA viruses, such as hepatitis C virus (HCV), influenza virus, and SARS-CoV-2, are notorious for their ability to evolve rapidly under selection in novel environments. It is known that the high mutation rate of RNA viruses can generate huge genetic diversity to facilitate viral adaptation. However, less attention has been paid to the underlying fitness landscape that represents the selection forces on viral genomes, especially under different selection conditions. Here, we systematically quantified the distribution of fitness effects of about 1,600 single amino acid substitutions in the drug-targeted region of NS5A protein of HCV. We found that the majority of nonsynonymous substitutions incur large fitness costs, suggesting that NS5A protein is highly optimized. The replication fitness of viruses is correlated with the pattern of sequence conservation in nature, and viral evolution is constrained by the need to maintain protein stability. We characterized the adaptive potential of HCV by subjecting the mutant viruses to selection by the antiviral drug daclatasvir at multiple concentrations. Both the relative fitness values and the number of beneficial mutations were found to increase with the increasing concentrations of daclatasvir. The changes in the spectrum of beneficial mutations in NS5A protein can be explained by a pharmacodynamics model describing viral fitness as a function of drug concentration. Overall, our results show that the distribution of fitness effects of mutations is modulated by both the constraints on the biophysical properties of proteins (i.e., selection pressure for protein stability) and the level of environmental stress (i.e., selection pressure for drug resistance). IMPORTANCE Many viruses adapt rapidly to novel selection pressures, such as antiviral drugs. Understanding how pathogens evolve under drug selection is critical for the success of antiviral therapy against human pathogens. By combining deep sequencing with selection experiments in cell culture, we have quantified the distribution of fitness effects of mutations in hepatitis C virus (HCV) NS5A protein. Our results indicate that the majority of single amino acid substitutions in NS5A protein incur large fitness costs. Simulation of protein stability suggests viral evolution is constrained by the need to maintain protein stability. By subjecting the mutant viruses to selection under an antiviral drug, we find that the adaptive potential of viral proteins in a novel environment is modulated by the level of environmental stress, which can be explained by a pharmacodynamics model. Our comprehensive characterization of the fitness landscapes of NS5A can potentially guide the design of effective strategies to limit viral evolution.
Collapse
|
5
|
Weng ML, Ågren J, Imbert E, Nottebrock H, Rutter MT, Fenster CB. Fitness effects of mutation in natural populations of Arabidopsis thaliana reveal a complex influence of local adaptation. Evolution 2020; 75:330-348. [PMID: 33340094 DOI: 10.1111/evo.14152] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 08/21/2020] [Accepted: 09/13/2020] [Indexed: 12/22/2022]
Abstract
Little is empirically known about the contribution of mutations to fitness in natural environments. However, Fisher's Geometric Model (FGM) provides a conceptual foundation to consider the influence of the environment on mutational effects. To quantify mutational properties in the field, we established eight sets of MA lines (7-10 generations) derived from eight founders collected from natural populations of Arabidopsis thaliana from French and Swedish sites, representing the range margins of the species in Europe. We reciprocally planted the MA lines and their founders at French and Swedish sites, allowing us to test predictions of FGM under naturally occurring environmental conditions. The performance of the MA lines relative to each other and to their respective founders confirmed some and contradicted other predictions of the FGM: the contribution of mutation to fitness variance increased when the genotype was in an environment where its fitness was low, that is, in the away environment, but mutations were more likely to be beneficial when the genotype was in its home environment. Consequently, environmental context plays a large role in the contribution of mutations to the evolutionary process and local adaptation does not guarantee that a genotype is at or close to its optimum.
Collapse
Affiliation(s)
- Mao-Lun Weng
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, USA.,Current address: Department of Biology, Westfield State University, Westfield, Massachusettes, USA
| | - Jon Ågren
- Plant Ecology and Evolution, Department of Ecology and Genetics, EBC, Uppsala University, Uppsala, Sweden
| | - Eric Imbert
- Institut des Sciences de la Évolution, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France
| | - Henning Nottebrock
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, USA.,Current address: Plant Ecology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Universitätsstrasse 30, Bayreuth, Germany
| | - Matthew T Rutter
- Department of Biology, College of Charleston, South Carolina, USA
| | - Charles B Fenster
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, USA.,Oak Lake Field Station, South Dakota State University, Brookings, South Dakota, USA
| |
Collapse
|
6
|
Singhal S, Gomez SM, Burch CL. Recombination drives the evolution of mutational robustness. ACTA ACUST UNITED AC 2019; 13:142-149. [PMID: 31572829 DOI: 10.1016/j.coisb.2018.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Recombination can impose fitness costs as beneficial parental combinations of alleles are broken apart, a phenomenon known as recombination load. Computational models suggest that populations may evolve a reduced recombination load by reducing either the likelihood of recombination events (bring interacting loci in physical proximity) or the strength of interactions between loci (make loci more independent of one another). We review evidence for each of these possibilities and their consequences for the genotype-fitness relationship. In particular, we expect that reducing interaction strengths between loci will lead to genomes that are also robust to mutational perturbations, but reducing recombination rates alone will not. We note that both mechanisms most likely played a role in the evolution of extant populations, and that both can result in the frequently-observed pattern of physical linkage between interacting loci.
Collapse
Affiliation(s)
- Sonia Singhal
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shawn M Gomez
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514.,Joint Department of Biomedical Engineering at University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, USA
| | - Christina L Burch
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
7
|
Dolan PT, Whitfield ZJ, Andino R. Mechanisms and Concepts in RNA Virus Population Dynamics and Evolution. Annu Rev Virol 2018; 5:69-92. [PMID: 30048219 DOI: 10.1146/annurev-virology-101416-041718] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA viruses are unique in their evolutionary capacity, exhibiting high mutation rates and frequent recombination. They rapidly adapt to environmental changes, such as shifts in immune pressure or pharmacological challenge. The evolution of RNA viruses has been brought into new focus with the recent developments of genetic and experimental tools to explore and manipulate the evolutionary dynamics of viral populations. These studies have uncovered new mechanisms that enable viruses to overcome evolutionary challenges in the environment and have emphasized the intimate relationship of viral populations with evolution. Here, we review some of the emerging viral and host mechanisms that underlie the evolution of RNA viruses. We also discuss new studies that demonstrate that the relationship between evolutionary dynamics and virus biology spans many spatial and temporal scales, affecting transmission dynamics within and between hosts as well as pathogenesis.
Collapse
Affiliation(s)
- Patrick T Dolan
- Department of Biology, Stanford University, Stanford, California 94305, USA.,Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA;
| | - Zachary J Whitfield
- Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA;
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA;
| |
Collapse
|
8
|
Cervera H, Ambrós S, Bernet GP, Rodrigo G, Elena SF. Viral Fitness Correlates with the Magnitude and Direction of the Perturbation Induced in the Host's Transcriptome: The Tobacco Etch Potyvirus-Tobacco Case Study. Mol Biol Evol 2018; 35:1599-1615. [PMID: 29562354 PMCID: PMC5995217 DOI: 10.1093/molbev/msy038] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Determining the fitness of viral genotypes has become a standard practice in virology as it is essential to evaluate their evolutionary potential. Darwinian fitness, defined as the advantage of a given genotype with respect to a reference one, is a complex property that captures, in a single figure, differences in performance at every stage of viral infection. To what extent does viral fitness result from specific molecular interactions with host factors and regulatory networks during infection? Can we identify host genes in functional classes whose expression depends on viral fitness? Here, we compared the transcriptomes of tobacco plants infected with seven genotypes of tobacco etch potyvirus that differ in fitness. We found that the larger the fitness differences among genotypes, the more dissimilar the transcriptomic profiles are. Consistently, two different mutations, one in the viral RNA polymerase and another in the viral suppressor of RNA silencing, resulted in significantly similar gene expression profiles. Moreover, we identified host genes whose expression showed a significant correlation, positive or negative, with the virus' fitness. Differentially expressed genes which were positively correlated with viral fitness activate hormone- and RNA silencing-mediated pathways of plant defense. In contrast, those that were negatively correlated with fitness affect metabolism, reducing growth, and development. Overall, these results reveal the high information content of viral fitness and suggest its potential use to predict differences in genomic profiles of infected hosts.
Collapse
Affiliation(s)
- Héctor Cervera
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnia de València, Campus UPV CPI 8E, València, Spain
| | - Silvia Ambrós
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnia de València, Campus UPV CPI 8E, València, Spain
| | - Guillermo P Bernet
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnia de València, Campus UPV CPI 8E, València, Spain
| | - Guillermo Rodrigo
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnia de València, Campus UPV CPI 8E, València, Spain
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, Parc Científic UV, Catedrático Agustín Escardino 9, Paterna, València, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnia de València, Campus UPV CPI 8E, València, Spain
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, Parc Científic UV, Catedrático Agustín Escardino 9, Paterna, València, Spain
- The Santa Fe Institute, Santa Fe, NM
| |
Collapse
|
9
|
Rutter MT, Wieckowski YM, Murren CJ, Strand AE. Fitness effects of mutation: testing genetic redundancy in Arabidopsis thaliana. J Evol Biol 2017; 30:1124-1135. [PMID: 28387971 DOI: 10.1111/jeb.13081] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 03/09/2017] [Indexed: 01/05/2023]
Abstract
Screens of organisms with disruptive mutations in a single gene often fail to detect phenotypic consequences for the majority of mutants. One explanation for this phenomenon is that the presence of paralogous loci provides genetic redundancy. However, it is also possible that the assayed traits are affected by few loci, that effects could be subtle or that phenotypic effects are restricted to certain environments. We assayed a set of T-DNA insertion mutant lines of Arabidopsis thaliana to determine the frequency with which mutation affected fitness-related phenotypes. We found that between 8% and 42% of the assayed lines had altered fitness from the wild type. Furthermore, many of these lines exhibited fitness greater than the wild type. In a second experiment, we grew a subset of the lines in multiple environments and found whether a T-DNA insert increased or decreased fitness traits depended on the assay environment. Overall, our evidence contradicts the hypothesis that genetic redundancy is a common phenomenon in A. thaliana for fitness traits. Evidence for redundancy from prior screens of knockout mutants may often be an artefact of the design of the phenotypic assays which have focused on less complex phenotypes than fitness and have used single environments. Finally, our study adds to evidence that beneficial mutations may represent a significant component of the mutational spectrum of A. thaliana.
Collapse
Affiliation(s)
- M T Rutter
- Department of Biology, College of Charleston, Charleston, SC, USA
| | - Y M Wieckowski
- Department of Biology, College of Charleston, Charleston, SC, USA
| | - C J Murren
- Department of Biology, College of Charleston, Charleston, SC, USA
| | - A E Strand
- Department of Biology, College of Charleston, Charleston, SC, USA
| |
Collapse
|
10
|
Minicka J, Elena SF, Borodynko-Filas N, Rubiś B, Hasiów-Jaroszewska B. Strain-dependent mutational effects for Pepino mosaic virus in a natural host. BMC Evol Biol 2017; 17:67. [PMID: 28264646 PMCID: PMC5339997 DOI: 10.1186/s12862-017-0920-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 02/20/2017] [Indexed: 11/10/2022] Open
Abstract
Background Pepino mosaic virus (PepMV) is an emerging plant pathogen that infects tomatoes worldwide. Understanding the factors that influence its evolutionary success is essential for developing new control strategies that may be more robust against the evolution of new viral strains. One of these evolutionary factors is the distribution of mutational fitness effect (DMFE), that is, the fraction of mutations that are lethal, deleterious, neutral, and beneficial on a given viral strain and host species. The goal of this study was to characterize the DMFE of introduced nonsynonymous mutations on a mild isolate of PepMV from the Chilean 2 strain (PepMV-P22). Additionally, we also explored whether the fitness effect of a given mutation depends on the gene where it appears or on epistatic interactions with the genetic background. To address this latter possibility, a subset of mutations were also introduced in a mild isolate of the European strain (PepMV-P11) and the fitness of the resulting clones measured. Results A collection of 25 PepMV clones each containing a single nucleotide nonsynonymous substitution was created by site-directed mutagenesis and the fitness of each mutant was determined. PepMV-P22 genome showed a high degree of robustness against point mutations, with 80% of mutations being either neutral or even beneficial and only 20% being deleterious or lethal. We found that the effect of mutations strongly depended on the gene in which they were introduced. Mutations with the largest average beneficial effects were those affecting the RdRp gene, in contrast to mutations affecting TGB1 and CP genes, for which the average effects were deleterious. Moreover, significant epistatic interactions were observed between nonsynonymous mutations and the genetic background, meaning that the effect of a given nucleotide substitution on a particular genomic context cannot be predicted by knowing its effect in a different one. Conclusions Our results indicated that PepMV genome has a surprisingly high robustness against mutations. We also found that fitness consequences of a given mutation differ between the two strains analyzed. This discovery suggests that the strength of selection, and thus the rates of evolution, vary among PepMV strains.
Collapse
Affiliation(s)
- Julia Minicka
- Department of Virology and Bacteriology, Institute of Plant Protection-National Research Institute, Poznan, Poland
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain.,Instituto de Biología Integrativa y de Sistemas, Consejo Superior de Investigaciones Científicas-Universitat de València, València, Spain.,The Santa Fe Institute, Santa Fe, New Mexico, USA
| | - Natasza Borodynko-Filas
- Department of Virology and Bacteriology, Institute of Plant Protection-National Research Institute, Poznan, Poland
| | - Błażej Rubiś
- Department of Clinical Chemistry and Molecular Diagnostics, Poznan University of Medical Sciences, Poznan, Poland
| | - Beata Hasiów-Jaroszewska
- Department of Virology and Bacteriology, Institute of Plant Protection-National Research Institute, Poznan, Poland.
| |
Collapse
|
11
|
Redondo RAF, de Vladar HP, Włodarski T, Bollback JP. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. J R Soc Interface 2017; 14:20160139. [PMID: 28053111 PMCID: PMC5310724 DOI: 10.1098/rsif.2016.0139] [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: 05/06/2016] [Accepted: 11/29/2016] [Indexed: 01/01/2023] Open
Abstract
Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ϕX174 phage family by first reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima.
Collapse
Affiliation(s)
| | - Harold P de Vladar
- IST Austria, Am Campus 1, 3400 Klosterneuburg, Austria
- Center for the Conceptual Foundations of Science, Parmenides Foundation, 82049 Pullach, Germany
| | - Tomasz Włodarski
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | | |
Collapse
|
12
|
Roles AJ, Rutter MT, Dworkin I, Fenster CB, Conner JK. Field measurements of genotype by environment interaction for fitness caused by spontaneous mutations in Arabidopsis thaliana. Evolution 2016; 70:1039-50. [PMID: 27061194 DOI: 10.1111/evo.12913] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 03/24/2016] [Indexed: 12/24/2022]
Abstract
As the ultimate source of genetic diversity, spontaneous mutation is critical to the evolutionary process. The fitness effects of spontaneous mutations are almost always studied under controlled laboratory conditions rather than under the evolutionarily relevant conditions of the field. Of particular interest is the conditionality of new mutations-that is, is a new mutation harmful regardless of the environment in which it is found? In other words, what is the extent of genotype-environment interaction for spontaneous mutations? We studied the fitness effects of 25 generations of accumulated spontaneous mutations in Arabidopsis thaliana in two geographically widely separated field environments, in Michigan and Virginia. At both sites, mean total fitness of mutation accumulation lines exceeded that of the ancestors, contrary to the expected decrease in the mean due to new mutations but in accord with prior work on these MA lines. We observed genotype-environment interactions in the fitness effects of new mutations, such that the effects of mutations in Michigan were a poor predictor of their effects in Virginia and vice versa. In particular, mutational variance for fitness was much larger in Virginia compared to Michigan. This strong genotype-environment interaction would increase the amount of genetic variation maintained by mutation-selection balance.
Collapse
Affiliation(s)
- Angela J Roles
- Biology Department, Oberlin College, Oberlin, Ohio, 44074. .,Kellogg Biological Station, Michigan State University, East Lansing, Michigan, 48824. .,Department of Integrative Biology, Michigan State University, East Lansing, Michigan, 48824.
| | - Matthew T Rutter
- Department of Biology, College of Charleston, Charleston, South Carolina, 29401.,Department of Biology, University of Maryland, College Park, Maryland, 20742
| | - Ian Dworkin
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan, 48824.,Department of Biology, McMaster University, Hamilton, Ontario, L8S 4L8, Canada
| | - Charles B Fenster
- Department of Biology, University of Maryland, College Park, Maryland, 20742
| | - Jeffrey K Conner
- Kellogg Biological Station, Michigan State University, East Lansing, Michigan, 48824.,Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824
| |
Collapse
|
13
|
Stearns FW, Fenster CB. Fisher's geometric model predicts the effects of random mutations when tested in the wild. Evolution 2016; 70:495-501. [PMID: 26768168 DOI: 10.1111/evo.12858] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 12/21/2015] [Accepted: 12/23/2015] [Indexed: 01/30/2023]
Abstract
Fisher's geometric model of adaptation (FGM) has been the conceptual foundation for studies investigating the genetic basis of adaptation since the onset of the neo Darwinian synthesis. FGM describes adaptation as the movement of a genotype toward a fitness optimum due to beneficial mutations. To date, one prediction of FGM, the probability of improvement is related to the distance from the optimum, has only been tested in microorganisms under laboratory conditions. There is reason to believe that results might differ under natural conditions where more mutations likely affect fitness, and where environmental variance may obscure the expected pattern. We chemically induced mutations into a set of 19 Arabidopsis thaliana accessions from across the native range of A. thaliana and planted them alongside the premutated founder lines in two habitats in the mid-Atlantic region of the United States under field conditions. We show that FGM is able to predict the outcome of a set of random induced mutations on fitness in a set of A. thaliana accessions grown in the wild: mutations are more likely to be beneficial in relatively less fit genotypes. This finding suggests that FGM is an accurate approximation of the process of adaptation under more realistic ecological conditions.
Collapse
Affiliation(s)
- Frank W Stearns
- Department of Biology, University of Maryland College Park, Maryland, 20742. .,Current Address: Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, 21218.
| | - Charles B Fenster
- Department of Biology, University of Maryland College Park, Maryland, 20742
| |
Collapse
|
14
|
Bernet GP, Elena SF. Distribution of mutational fitness effects and of epistasis in the 5' untranslated region of a plant RNA virus. BMC Evol Biol 2015; 15:274. [PMID: 26643527 PMCID: PMC4672503 DOI: 10.1186/s12862-015-0555-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/02/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding the causes and consequences of phenotypic variability is a central topic of evolutionary biology. Mutations within non-coding cis-regulatory regions are thought to be of major effect since they affect the expression of downstream genes. To address the evolutionary potential of mutations affecting such regions in RNA viruses, we explored the fitness properties of mutations affecting the 5'-untranslated region (UTR) of a prototypical member of the picorna-like superfamily, Tobacco etch virus (TEV). This 5' UTR acts as an internal ribosomal entry site (IRES) and is essential for expression of all viral genes. RESULTS We determined in vitro the folding of 5' UTR using the selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) technique. Then, we created a collection of single-nucleotide substitutions on this region and evaluated the statistical properties of their fitness effects in vivo. We found that, compared to random mutations affecting coding sequences, mutations at the 5' UTR were of weaker effect. We also created double mutants by combining pairs of these single mutations and found variation in the magnitude and sign of epistatic interactions, with an enrichment of cases of positive epistasis. A correlation exists between the magnitude of fitness effects and the size of the perturbation made in the RNA folding structure, suggesting that the larger the departure from the predicted fold, the more negative impact in viral fitness. CONCLUSIONS Evidence that mutational fitness effects on the short 5' UTR regulatory sequence of TEV are weaker than those affecting its coding sequences have been found. Epistasis among pairs of mutations on the 5' UTR ranged between the extreme cases of synthetic lethal and compensatory. A plausible hypothesis to explain all these observations is that the interaction between the 5' UTR and the host translational machinery was shaped by natural selection to be robust to mutations, thus ensuring the homeostatic expression of viral genes even at high mutation rates.
Collapse
Affiliation(s)
- Guillermo P Bernet
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022, València, Spain.
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022, València, Spain.
- The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA.
| |
Collapse
|
15
|
Martin G, Lenormand T. The fitness effect of mutations across environments: Fisher's geometrical model with multiple optima. Evolution 2015; 69:1433-1447. [DOI: 10.1111/evo.12671] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 04/07/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Guillaume Martin
- Institut des Sciences de l'Evolution de Montpellier, UMR CNRS-UM II 5554; Université Montpellier II; 34 095 Montpellier cedex 5 France
| | - Thomas Lenormand
- UMR 5175 CEFE; CNRS - Université Montpellier - Université P. Valéry, EPHE; 1919 route de Mende 34293 Montpellier Cedex 5 France
| |
Collapse
|
16
|
Aguirre J, Manrubia S. Tipping points and early warning signals in the genomic composition of populations induced by environmental changes. Sci Rep 2015; 5:9664. [PMID: 25962603 PMCID: PMC4428070 DOI: 10.1038/srep09664] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 03/12/2015] [Indexed: 01/04/2023] Open
Abstract
We live in an ever changing biosphere that faces continuous and often stressing environmental challenges. From this perspective, much effort is currently devoted to understanding how natural populations succeed or fail in adapting to evolving conditions. In a different context, many complex dynamical systems experience critical transitions where their dynamical behaviour or internal structure changes suddenly. Here we connect both approaches and show that in rough and correlated fitness landscapes, population dynamics shows flickering under small stochastic environmental changes, alerting of the existence of tipping points. Our analytical and numerical results demonstrate that transitions at the genomic level preceded by early-warning signals are a generic phenomenon in constant and slowly driven landscapes affected by even slight stochasticity. As these genomic shifts are approached, the time to reach mutation-selection equilibrium dramatically increases, leading to the appearance of hysteresis in the composition of the population. Eventually, environmental changes significantly faster than the typical adaptation time may result in population extinction. Our work points out several indicators that are at reach with current technologies to anticipate these sudden and largely unavoidable transitions.
Collapse
Affiliation(s)
- Jacobo Aguirre
- Centro de Astrobiología (INTA-CSIC), ctra. de Ajalvir km 4, 28850 Torrejón de Ardoz, Madrid, Spain.,Centro Nacional de Biotecnología, CSIC, c/Darwin 3, 28049 Madrid, Spain.,Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
| | - Susanna Manrubia
- Centro de Astrobiología (INTA-CSIC), ctra. de Ajalvir km 4, 28850 Torrejón de Ardoz, Madrid, Spain.,Centro Nacional de Biotecnología, CSIC, c/Darwin 3, 28049 Madrid, Spain.,Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
| |
Collapse
|
17
|
A new Microviridae phage isolated from a failed biotechnological process driven by Escherichia coli. Appl Environ Microbiol 2014; 80:6992-7000. [PMID: 25192988 DOI: 10.1128/aem.01365-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteriophages are present in every environment that supports bacterial growth, including man made ecological niches. Virulent phages may even slow or, in more severe cases, interrupt bioprocesses driven by bacteria. Escherichia coli is one of the most widely used bacteria for large-scale bioprocesses; however, literature describing phage-host interactions in this industrial context is sparse. Here, we describe phage MED1 isolated from a failed industrial process. Phage MED1 (Microviridae family, with a single-stranded DNA [ssDNA] genome) is highly similar to the archetypal phage phiX174, sharing >95% identity between their genomic sequences. Whole-genome phylogenetic analysis of 52 microvirus genomes from public databases revealed three genotypes (alpha3, G4, and phiX174). Phage MED1 belongs to the phiX174 group. We analyzed the distribution of single nucleotide variants in MED1 and 18 other phiX174-like genomes and found that there are more missense mutations in genes G, B, and E than in the other genes of these genomes. Gene G encodes the spike protein, involved in host attachment. The evolution of this protein likely results from the selective pressure on phages to rapidly adapt to the molecular diversity found at the surface of their hosts.
Collapse
|
18
|
Stern A, Bianco S, Yeh MT, Wright C, Butcher K, Tang C, Nielsen R, Andino R. Costs and benefits of mutational robustness in RNA viruses. Cell Rep 2014; 8:1026-36. [PMID: 25127138 DOI: 10.1016/j.celrep.2014.07.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 05/18/2014] [Accepted: 07/11/2014] [Indexed: 12/19/2022] Open
Abstract
The accumulation of mutations in RNA viruses is thought to facilitate rapid adaptation to changes in the environment. However, most mutations have deleterious effects on fitness, especially for viruses. Thus, tolerance to mutations should determine the nature and extent of genetic diversity that can be maintained in the population. Here, we combine population genetics theory, computer simulation, and experimental evolution to examine the advantages and disadvantages of tolerance to mutations, also known as mutational robustness. We find that mutational robustness increases neutral diversity and, as expected, can facilitate adaptation to a new environment. Surprisingly, under certain conditions, robustness may also be an impediment for viral adaptation, if a highly diverse population contains a large proportion of previously neutral mutations that are deleterious in the new environment. These findings may inform therapeutic strategies that cause extinction of otherwise robust viral populations.
Collapse
Affiliation(s)
- Adi Stern
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Simone Bianco
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; IBM Research-Almaden, Industrial and Applied Genomics, 650 Harry Road, San Jose, CA 95120-6099, USA
| | - Ming Te Yeh
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Caroline Wright
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kristin Butcher
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Chao Tang
- Center for Quantitative Biology, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
19
|
SENSITIVITY OF THE DISTRIBUTION OF MUTATIONAL FITNESS EFFECTS TO ENVIRONMENT, GENETIC BACKGROUND, AND ADAPTEDNESS: A CASE STUDY WITHDROSOPHILA. Evolution 2013; 68:840-53. [DOI: 10.1111/evo.12309] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 10/22/2013] [Indexed: 12/22/2022]
|
20
|
Hietpas RT, Bank C, Jensen JD, Bolon DNA. Shifting fitness landscapes in response to altered environments. Evolution 2013; 67:3512-22. [PMID: 24299404 PMCID: PMC3855258 DOI: 10.1111/evo.12207] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/25/2013] [Indexed: 12/14/2022]
Abstract
The role of adaptation in molecular evolution has been contentious for decades. Here, we shed light on the adaptive potential in Saccharomyces cerevisiae by presenting systematic fitness measurements for all possible point mutations in a region of Hsp90 under four environmental conditions. Under elevated salinity, we observe numerous beneficial mutations with growth advantages up to 7% relative to the wild type. All of these beneficial mutations were observed to be associated with high costs of adaptation. We thus demonstrate that an essential protein can harbor adaptive potential upon an environmental challenge, and report a remarkable fit of the data to a version of Fisher's geometric model that focuses on the fitness trade-offs between mutations in different environments.
Collapse
Affiliation(s)
- Ryan T. Hietpas
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Claudia Bank
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB)
| | - Jeffrey D. Jensen
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB)
| | - Daniel N. A. Bolon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| |
Collapse
|
21
|
Yuan Y, Gao M, Peng Q, Wu D, Liu P, Wu Y. Genomic analysis of a phage and prophage from a Bacillus thuringiensis strain. J Gen Virol 2013; 95:751-761. [PMID: 24285088 DOI: 10.1099/vir.0.058735-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteriophages have been found to be the most abundant and also potentially most diverse biological entities on Earth. In the present study, Bacillus phages were isolated rapidly and shown to have a high degree of diversity. The genomes of a newly isolated phage, phiCM3, and a prophage, proCM3, from the Bacillus thuringiensis strain YM-03 were sequenced and characterized. Comparative genome analysis showed that the phiCM3 genome is highly similar to the genomes of eight other Bacillus phages and seven of these phages were classified as the Wβ group of phages. Analysis of the differential evolution of the genes in the Wβ-group phages indicated that the genes encoding the antirepressor and tail fibre protein were more highly conserved than those encoding the major capsid protein, DNA replication protein, and RNA polymerase σ factor, which might have diverged to acquire mechanisms suitable for survival in different microbial hosts. Genome analysis of proCM3 revealed that proCM3 might be a defective phage because of mutations in the minor structural protein, and it was not inducible by mitomycin C treatment. The proCM3 genome was similar to those of two lytic Bacillus phages in sequence, but had a different genomic structure, composed of three regions in a different order. These data suggest that the three phages might have had a common ancestor and that genome rearrangement might have occurred during evolution. The findings of this study enrich our current knowledge of Bacillus phage diversity and evolution, especially for the Wβ-group and TP21-L-like phages, and may help the development of practical applications of Bacillus phages.
Collapse
Affiliation(s)
- Yihui Yuan
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Meiying Gao
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Qin Peng
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Dandan Wu
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Pengming Liu
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Yan Wu
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| |
Collapse
|
22
|
Abstract
Despite the accumulation of substantial quantities of information about epistatic interactions among both deleterious and beneficial mutations in a wide array of experimental systems, neither consistent patterns nor causal explanations for these interactions have yet emerged. Furthermore, the effects of mutations depend on the environment in which they are characterized, implying that the environment may also influence epistatic interactions. Recent work with beneficial mutations for the single-stranded DNA bacteriophage ID11 demonstrated that interactions between pairs of mutations could be understood by means of a simple model that assumes that mutations have additive phenotypic effects and that epistasis arises through a nonlinear phenotype-fitness map with a single intermediate optimum. To determine whether such a model could also explain changes in epistatic patterns associated with changes in environment, we measured epistatic interactions for these same mutations under conditions for which we expected to find the wild-type ID11 at different distances from its phenotypic optimum by assaying fitnesses at three different temperatures: 33°, 37°, and 41°. Epistasis was present and negative under all conditions, but became more pronounced as temperature increased. We found that the additive-phenotypes model explained these patterns as changes in the parameters of the phenotype-fitness map, but that a model that additionally allows the phenotypes to vary across temperatures performed significantly better. Our results show that ostensibly complex patterns of fitness effects and epistasis across environments can be explained by assuming a simple structure for the genotype-phenotype relationship.
Collapse
|
23
|
Vale PF. Killing them softly: managing pathogen polymorphism and virulence in spatially variable environments. Trends Parasitol 2013; 29:417-22. [PMID: 23928098 PMCID: PMC3764335 DOI: 10.1016/j.pt.2013.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Revised: 07/04/2013] [Accepted: 07/05/2013] [Indexed: 11/30/2022]
Abstract
Understanding why pathogen populations are genetically variable is vital because genetic variation fuels evolution, which often hampers disease control efforts. Here I argue that classical models of evolution in spatially variable environments - specifically, models of hard and soft selection - provide a useful framework to understand the maintenance of pathogen polymorphism and the evolution of virulence. First, the similarities between models of hard and soft selection and pathogen life cycles are described, highlighting how the type and timing of pathogen control measures impose density regulation that may affect both the level of pathogen polymorphism and virulence. The article concludes with an outline of potential lines of future theoretical and experimental work.
Collapse
Affiliation(s)
- Pedro F Vale
- Centre for Immunity, Infection, and Evolution and Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, West Mains Road, Edinburgh EH9 3JT, UK.
| |
Collapse
|