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1.
Int J Mol Sci ; 25(9)2024 Apr 29.
Artigo em Inglês | MEDLINE | ID: mdl-38732084

RESUMO

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 Qß, 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 Qß 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.


Assuntos
Congelamento , Mutação , Fagos RNA/genética , Fagos RNA/fisiologia , Adaptação Fisiológica/genética , Evolução Molecular , Replicação Viral/genética , Proteínas do Capsídeo/genética
2.
Int J Mol Sci ; 23(16)2022 Aug 09.
Artigo em Inglês | MEDLINE | ID: mdl-36012143

RESUMO

A critical issue to understanding how populations adapt to new selective pressures is the relative contribution of the initial standing genetic diversity versus that generated de novo. RNA viruses are an excellent model to study this question, as they form highly heterogeneous populations whose genetic diversity can be modulated by factors such as the number of generations, the size of population bottlenecks, or exposure to new environment conditions. In this work, we propagated at nonoptimal temperature (43 °C) two bacteriophage Qß populations differing in their degree of heterogeneity. Deep sequencing analysis showed that, prior to the temperature change, the most heterogeneous population contained some low-frequency mutations that had previously been detected in the consensus sequences of other Qß populations adapted to 43 °C. Evolved populations with origin in this ancestor reached similar growth rates, but the adaptive pathways depended on the frequency of these standing mutations and the transmission bottleneck size. In contrast, the growth rate achieved by populations with origin in the less heterogeneous ancestor did depend on the transmission bottleneck size. The conclusion is that viral diversification in a particular environment may lead to the emergence of mutants capable of accelerating adaptation when the environment changes.


Assuntos
Bacteriófagos , Vírus de RNA , Aclimatação , Adaptação Fisiológica/genética , Bacteriófagos/genética , Variação Genética , Mutação , Vírus de RNA/genética
3.
Int J Mol Sci ; 22(13)2021 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-34202838

RESUMO

Evolution of RNA bacteriophages of the family Leviviridae is governed by the high error rates of their RNA-dependent RNA polymerases. This fact, together with their large population sizes, leads to the generation of highly heterogeneous populations that adapt rapidly to most changes in the environment. Throughout adaptation, the different mutants that make up a viral population compete with each other in a non-trivial process in which their selective values change over time due to the generation of new mutations. In this work we have characterised the intra-population dynamics of a well-studied levivirus, Qß, when it is propagated at a higher-than-optimal temperature. Our results show that adapting populations experienced rapid changes that involved the ascent of particular genotypes and the loss of some beneficial mutations of early generation. Artificially reconstructed populations, containing a fraction of the diversity present in actual populations, fixed mutations more rapidly, illustrating how population bottlenecks may guide the adaptive pathways. The conclusion is that, when the availability of beneficial mutations under a particular selective condition is elevated, the final outcome of adaptation depends more on the occasional occurrence of population bottlenecks and how mutations combine in genomes than on the selective value of particular mutations.


Assuntos
Adaptação Biológica , Fagos RNA/fisiologia , Temperatura , Evolução Biológica , Evolução Molecular , Regulação Viral da Expressão Gênica , Genoma Viral , Genômica/métodos , Mutação , RNA Viral/genética , Seleção Genética
4.
Curr Top Microbiol Immunol ; 392: 201-17, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-26271604

RESUMO

Viral populations are formed by complex ensembles of genomes with broad phenotypic diversity. The adaptive strategies deployed by these ensembles are multiple and often cannot be predicted a priori. Our understanding of viral dynamics is mostly based on two kinds of empirical approaches: one directed towards characterizing molecular changes underlying fitness changes and another focused on population-level responses. Simultaneously, theoretical efforts are directed towards developing a formal picture of viral evolution by means of more realistic fitness landscapes and reliable population dynamics models. New technologies, chiefly the use of next-generation sequencing and related tools, are opening avenues connecting the molecular and the population levels. In the near future, we hope to be witnesses of an integration of these still decoupled approaches, leading into more accurate and realistic quasispecies models able to capture robust generalities and endowed with a satisfactory predictive power.


Assuntos
Evolução Molecular , Vírus/genética , Variação Genética , Sequenciamento de Nucleotídeos em Larga Escala , Modelos Genéticos , Taxa de Mutação , Fenômenos Fisiológicos Virais , Vírus/classificação
5.
J Virol ; 88(18): 10480-7, 2014 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-24965463

RESUMO

UNLABELLED: The high genetic heterogeneity and great adaptability of RNA viruses are ultimately caused by the low replication fidelity of their polymerases. However, single amino acid substitutions that modify replication fidelity can evolve in response to mutagenic treatments with nucleoside analogues. Here, we investigated how two independent mutants of the bacteriophage Qß replicase (Thr210Ala and Tyr410His) reduce sensitivity to the nucleoside analogue 5-azacytidine (AZC). Despite being located outside the catalytic site, both mutants reduced the mutation frequency in the presence of the drug. However, they did not modify the type of AZC-induced substitutions, which was mediated mainly by ambiguous base pairing of the analogue with purines. Furthermore, the Thr210Ala and Tyr410His substitutions had little or no effect on replication fidelity in untreated viruses. Also, both substitutions were costly in the absence of AZC or when the action of the drug was suppressed by adding an excess of natural pyrimidines (uridine or cytosine). Overall, the phenotypic properties of these two mutants were highly convergent, despite the mutations being located in different domains of the Qß replicase. This suggests that treatment with a given nucleoside analogue tends to select for a unique functional response in the viral replicase. IMPORTANCE: In the last years, artificial increase of the replication error rate has been proposed as an antiviral therapy. In this study, we investigated the mechanisms by which two substitutions in the Qß replicase confer partial resistance to the mutagenic nucleoside analogue AZC. As opposed to previous work with animal viruses, where different mutations selected sequentially conferred nucleoside analogue resistance through different mechanisms, our results suggest that there are few or no alternative AZC resistance phenotypes in Qß. Also, despite resistance mutations being highly costly in the absence of the drug, there was no sequential fixation of secondary mutations. Bacteriophage Qß is the virus with the highest reported mutation rate, which should make it particularly sensitive to nucleoside analogue treatments, probably favoring resistance mutations even if they incur high costs. The results are also relevant for understanding the possible pathways by which fidelity of the replication machinery can be modified.


Assuntos
Allolevivirus/enzimologia , Azacitidina/farmacologia , Mutagênicos/farmacologia , Q beta Replicase/química , Proteínas Virais/química , Allolevivirus/química , Allolevivirus/efeitos dos fármacos , Allolevivirus/genética , Allolevivirus/fisiologia , Substituição de Aminoácidos , Domínio Catalítico/efeitos dos fármacos , Estrutura Terciária de Proteína , Q beta Replicase/genética , Q beta Replicase/metabolismo , Proteínas Virais/genética , Proteínas Virais/metabolismo , Replicação Viral/efeitos dos fármacos
6.
BMC Evol Biol ; 13: 11, 2013 Jan 16.
Artigo em Inglês | MEDLINE | ID: mdl-23323937

RESUMO

BACKGROUND: When beneficial mutations present in different genomes spread simultaneously in an asexual population, their fixation can be delayed due to competition among them. This interference among mutations is mainly determined by the rate of beneficial mutations, which in turn depends on the population size, the total error rate, and the degree of adaptation of the population. RNA viruses, with their large population sizes and high error rates, are good candidates to present a great extent of interference. To test this hypothesis, in the current study we have investigated whether competition among beneficial mutations was responsible for the prolonged presence of polymorphisms in the mutant spectrum of an RNA virus, the bacteriophage Qß, evolved during a large number of generations in the presence of the mutagenic nucleoside analogue 5-azacytidine. RESULTS: The analysis of the mutant spectra of bacteriophage Qß populations evolved at artificially increased error rate shows a large number of polymorphic mutations, some of them with demonstrated selective value. Polymorphisms distributed into several evolutionary lines that can compete among them, making it difficult the emergence of a defined consensus sequence. The presence of accompanying deleterious mutations, the high degree of recurrence of the polymorphic mutations, and the occurrence of epistatic interactions generate a highly complex interference dynamics. CONCLUSIONS: Interference among beneficial mutations in bacteriophage Qß evolved at increased error rate permits the coexistence of multiple adaptive pathways that can provide selective advantages by different molecular mechanisms. In this way, interference can be seen as a positive factor that allows the exploration of the different local maxima that exist in rugged fitness landscapes.


Assuntos
Adaptação Fisiológica/genética , Bacteriófagos/genética , Evolução Molecular , Mutação , Azacitidina/farmacologia , Bacteriófagos/efeitos dos fármacos , Escherichia coli/virologia , Aptidão Genética , Genoma Viral , Polimorfismo Genético , Vírus de RNA/efeitos dos fármacos , Vírus de RNA/genética , RNA Viral/genética , Análise de Sequência de RNA
7.
Front Microbiol ; 14: 1197085, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37303783

RESUMO

Introduction: Host density is one of the main factors affecting the infective capacity of viruses. When host density is low, it is more difficult for the virus to find a susceptible cell, which increases its probability of being damaged by the physicochemical agents of the environment. Nevertheless, viruses can adapt to variations in host density through different strategies that depend on the particular characteristics of the life cycle of each virus. In a previous work, using the bacteriophage Qß as an experimental model, we found that when bacterial density was lower than optimal the virus increased its capacity to penetrate into the bacteria through a mutation in the minor capsid protein (A1) that is not described to interact with the cell receptor. Results: Here we show that the adaptive pathway followed by Qß in the face of similar variations in host density depends on environmental temperature. When the value for this parameter is lower than optimal (30°C), the mutation selected is the same as at the optimal temperature (37°C). However, when temperature increases to 43°C, the mutation selected is located in a different protein (A2), which is involved both in the interaction with the cell receptor and in the process of viral progeny release. The new mutation increases the entry of the phage into the bacteria at the three temperatures assayed. However, it also considerably increases the latent period at 30 and 37°C, which is probably the reason why it is not selected at these temperatures. Conclusion: The conclusion is that the adaptive strategies followed by bacteriophage Qß, and probably other viruses, in the face of variations in host density depend not only on their advantages at this selective pressure, but also on the fitness costs that particular mutations may present in function of the rest of environmental parameters that influence viral replication and stability.

8.
Int J Surg Case Rep ; 106: 108245, 2023 May.
Artigo em Inglês | MEDLINE | ID: mdl-37126924

RESUMO

INTRODUCTION AND IMPORTANCE: Penile fracture is uncommon entity that rarely involves all the three erectile bodies (the two corpora carvenosa and corpus spongiosum). The diagnosis is clinical as most cases presents with typical signs and symptoms. CASE PRESENTATION: We present a case of young man who sustained penile fracture involving the two corpora cavernosum and corpus spongiosum with associated urethral injury that was successfully repaired primarily. CLINICAL DISCUSSION: In this case apart from MRI confirming the diagnosis it showed the injury to involve all the three corpora bodies as well as the urethral. Although MRI is reserved for controversial cases, when available, apart from just confirming the diagnosis, it can help in showing the extent of the injury and assist surgeon in management. Primary repair of the erectile bodies as well as the urethral gives excellent outcome. CONCLUSION: This case reminds surgeons the possibility of having such extensive injury with promising outcome if properly managed.

9.
Front Microbiol ; 13: 1032918, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36386652

RESUMO

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.

10.
BMC Evol Biol ; 10: 46, 2010 Feb 17.
Artigo em Inglês | MEDLINE | ID: mdl-20163698

RESUMO

BACKGROUND: The secondary structure of folded RNA sequences is a good model to map phenotype onto genotype, as represented by the RNA sequence. Computational studies of the evolution of ensembles of RNA molecules towards target secondary structures yield valuable clues to the mechanisms behind adaptation of complex populations. The relationship between the space of sequences and structures, the organization of RNA ensembles at mutation-selection equilibrium, the time of adaptation as a function of the population parameters, the presence of collective effects in quasispecies, or the optimal mutation rates to promote adaptation all are issues that can be explored within this framework. RESULTS: We investigate the effect of microscopic mutations on the phenotype of RNA molecules during their in silico evolution and adaptation. We calculate the distribution of the effects of mutations on fitness, the relative fractions of beneficial and deleterious mutations and the corresponding selection coefficients for populations evolving under different mutation rates. Three different situations are explored: the mutation-selection equilibrium (optimized population) in three different fitness landscapes, the dynamics during adaptation towards a goal structure (adapting population), and the behavior under periodic population bottlenecks (perturbed population). CONCLUSIONS: The ratio between the number of beneficial and deleterious mutations experienced by a population of RNA sequences increases with the value of the mutation rate mu at which evolution proceeds. In contrast, the selective value of mutations remains almost constant, independent of mu, indicating that adaptation occurs through an increase in the amount of beneficial mutations, with little variations in the average effect they have on fitness. Statistical analyses of the distribution of fitness effects reveal that small effects, either beneficial or deleterious, are well described by a Pareto distribution. These results are robust under changes in the fitness landscape, remarkably when, in addition to selecting a target secondary structure, specific subsequences or low-energy folds are required. A population perturbed by bottlenecks behaves similarly to an adapting population, struggling to return to the optimized state. Whether it can survive in the long run or whether it goes extinct depends critically on the length of the time interval between bottlenecks.


Assuntos
Evolução Molecular , RNA/genética , Aptidão Genética , Mutação , Conformação de Ácido Nucleico , Fenótipo , RNA/química , Seleção Genética
11.
Case Rep Surg ; 2020: 6694990, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33457036

RESUMO

Breach in diaphragmatic musculature permits abdominal viscera to herniate into the thoracic cavity. Time of presentation and associated injuries determines the surgical approach in management. This case report sets to highlight the challenges in clinical diagnosis, radiological interpretation, and surgical management approaches of posttraumatic diaphragmatic hernia. We report a case of a 43 years old male who was diagnosed with traumatic diaphragmatic hernia 6 months post blunt thoracoabdominal trauma due to motor traffic accident. He was initially diagnosed with haemothorax, drained with an underwater thoracostomy tube, and discharged. He continued to experience on and off chest pain worsening postfeeding, difficulty in breathing and abdominal pain for the next six months until his eventual diaphragmatic hernia diagnosis. He was scheduled for an elective thoracotomy. A left posterolateral thoracic over the 7th intercostal space incision was used. Intraoperatively, the stomach, left lobe of liver, part of transverse colon, small bowel, and omentum had herniated into the thoracic cavity adhering into thoracic viscera and wall. Adhesiolysis was done, and abdominal organs reduced into abdominal cavity. Rent was closed by interrupted Prolene sutures reinforced with a mesh. In patients with delayed presentation of diaphragmatic hernia post blunt thoracoabdominal injury without associated intra-abdominal visceral injury, we recommend the thoracic diaphragmatic repair approach as long-standing herniated bowels might adhere with thoracic cavity walls or viscera. In such cases, adhesiolysis and rent repair is easier through thoracotomy.

12.
J Theor Biol ; 261(1): 148-55, 2009 Nov 07.
Artigo em Inglês | MEDLINE | ID: mdl-19664640

RESUMO

Theoretical studies of quasispecies usually focus on two properties of those populations at the mutation-selection equilibrium, namely asymptotic growth rate and population diversity. It has been postulated that, as a consequence of the high error rate of quasispecies replication, an increase of neutrality facilitates population optimization by reducing the amount of mutations with a deleterious effect on fitness. In this study we analyse how the optimization of equilibrium properties is affected when a quasispecies evolves in an environment perturbed through frequent bottleneck events. By means of a simple model we demonstrate that high neutrality may be detrimental when the population has to overcome repeated reductions in the population size, and that the property to be optimized in this situation is the time required to regenerate the quasispecies, i.e. its adaptability. In the scenario described, neutrality and adaptability cannot be simultaneously optimized. When fitness is equated with long-term survivability, high neutrality is the appropriate strategy in constant environments, while populations evolving in fluctuating environments are fitter when their neutrality is low, such that they can respond faster to perturbations. Our results might be relevant to better comprehend how a minority virus could displace the circulating quasispecies, a fact observed in natural infections and essential in viral evolution.


Assuntos
Adaptação Fisiológica/fisiologia , Modelos Genéticos , Mutação , Vírus/genética , Animais , Variação Genética , Fenótipo , Densidade Demográfica , Dinâmica Populacional , Seleção Genética , Vírus/crescimento & desenvolvimento
13.
Pathogens ; 8(2)2019 Jun 18.
Artigo em Inglês | MEDLINE | ID: mdl-31216651

RESUMO

The rate of change in selective pressures is one of the main factors that determines the likelihood that populations can adapt to stress conditions. Generally, the reduction in the population size that accompanies abrupt environmental changes makes it difficult to generate and select adaptive mutations. However, in systems with high genetic diversity, as happens in RNA viruses, mutations with beneficial effects under new conditions can already be present in the population, facilitating adaptation. In this work, we have propagated an RNA bacteriophage (Qß) at temperatures higher than the optimum, following different patterns of change. We have determined the fitness values and the consensus sequences of all lineages throughout the evolutionary process in order to establish correspondences between fitness variations and adaptive pathways. Our results show that populations subjected to a sudden temperature change gain fitness and fix mutations faster than those subjected to gradual changes, differing also in the particular selected mutations. The life-history of populations prior to the environmental change has great importance in the dynamics of adaptation. The conclusion is that in the bacteriophage Qß, the standing genetic diversity together with the rate of temperature change determine both the rapidity of adaptation and the followed evolutionary pathways.

14.
Virus Evol ; 4(1): vex043, 2018 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-29340211

RESUMO

Virus fitness is a complex parameter that results from the interaction of virus-specific characters (e.g. intracellular growth rate, adsorption rate, virion extracellular stability, and tolerance to mutations) with others that depend on the underlying fitness landscape and the internal structure of the whole population. Individual mutants usually have lower fitness values than the complex population from which they come from. When they are propagated and allowed to attain large population sizes for a sufficiently long time, they approach mutation-selection equilibrium with the concomitant fitness gains. The optimization process follows dynamics that vary among viruses, likely due to differences in any of the parameters that determine fitness values. As a consequence, when different mutants spread together, the number of generations experienced by each of them prior to co-propagation may determine its particular fate. In this work we attempt a clarification of the effect of different levels of population diversity in the outcome of competition dynamics. To this end, we analyze the behavior of two mutants of the RNA bacteriophage Qß that co-propagate with the wild-type virus. When both competitor viruses are clonal, the mutants rapidly outcompete the wild type. However, the outcome in competitions performed with partially optimized virus populations depends on the distance of the competitors to their clonal origin. We also implement a theoretical population dynamics model that describes the evolution of a heterogeneous population of individuals, each characterized by a fitness value, subjected to subsequent cycles of replication and mutation. The experimental results are explained in the framework of our theoretical model under two non-excluding, likely complementary assumptions: (1) The relative advantage of both competitors changes as populations approach mutation-selection equilibrium, as a consequence of differences in their growth rates and (2) one of the competitors is more robust to mutations than the other. The main conclusion is that the nearness of an RNA virus population to mutation-selection equilibrium is a key factor determining the fate of particular mutants arising during replication.

15.
Sci Rep ; 8(1): 8080, 2018 05 24.
Artigo em Inglês | MEDLINE | ID: mdl-29795535

RESUMO

Bacteriophages are the most numerous biological entities on Earth. They are on the basis of most ecosystems, regulating the diversity and abundance of bacterial populations and contributing to the nutrient and energy cycles. Bacteriophages have two well differentiated phases in their life cycle, one extracellular, in which they behave as inert particles, and other one inside their hosts, where they replicate to give rise to a progeny. In both phases they are exposed to environmental conditions that often act as selective pressures that limit both their survival in the environment and their ability to replicate, two fitness traits that frequently cannot be optimised simultaneously. In this study we have analysed the evolutionary ability of an RNA bacteriophage, the bacteriophage Qß, when it is confronted with a temperature increase that affects both the extracellular and the intracellular media. Our results show that Qß can optimise its survivability when exposed to short-term high temperature extracellular heat shocks, as well as its replicative ability at higher-than-optimal temperature. Mutations responsible for simultaneous adaptation were the same as those selected when adaptation to each condition proceeded separately, showing the absence of important trade-offs between survival and reproduction in this virus.


Assuntos
Adaptação Fisiológica/genética , Evolução Molecular , Interações Hospedeiro-Patógeno , Fagos RNA/fisiologia , Temperatura , Aclimatação/genética , Ecossistema , Escherichia coli/virologia , Aptidão Genética , Resposta ao Choque Térmico/genética , Temperatura Alta , Fenótipo , Fagos RNA/genética , Seleção Genética
16.
Virology ; 497: 163-170, 2016 10.
Artigo em Inglês | MEDLINE | ID: mdl-27471955

RESUMO

RNA viruses replicate with very high error rates, which makes them more sensitive to additional increases in this parameter. This fact has inspired an antiviral strategy named lethal mutagenesis, which is based on the artificial increase of the error rate above a threshold incompatible with virus infectivity. A relevant issue concerning lethal mutagenesis is whether incomplete treatments might enhance the adaptive possibilities of viruses. We have addressed this question by subjecting an RNA virus, the bacteriophage Qß, to different transmission regimes in the presence or the absence of sublethal concentrations of the mutagenic nucleoside analogue 5-azacytidine (AZC). Populations obtained were subsequently exposed to a non-optimal temperature and analyzed to determine their consensus sequences. Our results show that previously mutagenized populations rapidly fixed a specific set of mutations upon propagation at the new temperature, suggesting that the expansion of the mutant spectrum caused by AZC has an influence on later evolutionary behavior.


Assuntos
Adaptação Biológica , Allolevivirus/fisiologia , Temperatura Alta , Mutagênese , Mutação , Alelos , Substituição de Aminoácidos , Evolução Molecular , Polimorfismo Genético , Replicação Viral
17.
Gene ; 347(2): 273-82, 2005 Mar 14.
Artigo em Inglês | MEDLINE | ID: mdl-15777632

RESUMO

Population bottlenecks are stochastic events that strongly condition the structure and evolution of natural populations. Their effects are readily observable in highly heterogeneous populations, such as RNA viruses, since bottlenecks cause a fast accumulation of mutations. Considering that most mutations are deleterious, it was predicted that the frequent application of bottlenecks would yield a population unable to replicate. However, in vitro as well as in vivo systems evolving through bottlenecks present a remarkable resistance to extinction. This observation reveals the robustness of RNA viruses and points to the existence of internal mechanisms which must confer a high degree of adaptability to fast mutating populations. In this contribution, we review experimental observations regarding the survival of RNA viruses, both in laboratory experiments and in natural populations. By means of a simple theoretical model of evolution which incorporates strong reductions of the population size, we explore the relationship between the number of replication rounds that a single founder particle undergoes before the next bottleneck is applied, and the mutation rate in a particular environment. Our numerical results reveal that the mutation rate has evolved in a concerted way with the degree of optimization achieved by the population originated from the founder particle. We hypothesize that this mechanism generates a mutation-selection equilibrium in natural populations that maximizes adaptability while maintaining their structure.


Assuntos
Genética Populacional , Modelos Genéticos , Mutação , Vírus de RNA/fisiologia , Sequência de Bases , Efeito Fundador , Genoma Viral , Matemática , Dados de Sequência Molecular , Densidade Demográfica , Replicação Viral
18.
J Mol Biol ; 315(4): 647-61, 2002 Jan 25.
Artigo em Inglês | MEDLINE | ID: mdl-11812137

RESUMO

Plaque-to-plaque transfers of RNA viruses lead to accumulation of mutations and fitness decrease. To test whether continuing plaque-to-plaque transfers would lead to viral extinction, we have subjected several low fitness foot-and-mouth disease virus (FMDV) clones to up to 130 successive plaque transfers, and have analyzed the evolution of plaque titers and genomic nucleotide sequences. No case of viral extinction could be documented. Some low fitness clones that posses an internal poly(A) tract evaded extinction by modifying the length or base composition of the poly(A) tract. The comparison of entire genomic sequences of FMDV clones at increasing plaque transfer number revealed that mutations accumulated at a uniform rate, and that they were distributed unevenly along the genome. Clusters of mutations were identified at different genomic sites in two plaque transfer lineages. Mutation clustering appears to occur stochastically and could not be related to fixation of compensatory mutations. The results document resistance of viral clones to extinction, and suggest that mutation clustering may be a mechanism of genetic diversification of low fitness virus.


Assuntos
Evolução Biológica , Vírus da Febre Aftosa/genética , Vírus da Febre Aftosa/fisiologia , Variação Genética/genética , Mutação/genética , Replicação Viral , Animais , Composição de Bases , Linhagem Celular , Mapeamento Cromossômico , Clonagem Molecular , Cricetinae , Evolução Molecular , Frequência do Gene , Genoma Viral , Poli A/genética , RNA Viral/análise , RNA Viral/genética , Análise de Sequência de RNA , Inoculações Seriadas , Processos Estocásticos , Ensaio de Placa Viral
19.
Virus Res ; 107(2): 129-39, 2005 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-15649559

RESUMO

The extinction of foot-and-mouth disease virus (FMDV) is strongly influenced by mutation rates, types of mutations, relative viral fitness and virus population regimens during infection. Here we review experimental results and theoretical models that describe a contrast between the effective extinction of FMDV subjected to increased mutagenesis, and the remarkable resistance to extinction of the same and related FMDV clones subjected to serial bottleneck events. The results suggest procedures to master key parameters to develop effective antiviral strategies based on virus entry into error catastrophe.


Assuntos
Vírus da Febre Aftosa/genética , Mutagênicos/farmacologia , Mutação , Animais , Azacitidina/farmacologia , Evolução Biológica , Fluoruracila/farmacologia , Vírus da Febre Aftosa/efeitos dos fármacos , Vírus da Febre Aftosa/patogenicidade , Vírus da Febre Aftosa/fisiologia
20.
PLoS One ; 9(6): e100940, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24963780

RESUMO

The frequency of change in the selective pressures is one of the main factors driving evolution. It is generally accepted that constant environments select specialist organisms whereas changing environments favour generalists. The particular outcome achieved in either case also depends on the relative strength of the selective pressures and on the fitness costs of mutations across environments. RNA viruses are characterized by their high genetic diversity, which provides fast adaptation to environmental changes and helps them evade most antiviral treatments. Therefore, the study of the adaptive possibilities of RNA viruses is highly relevant for both basic and applied research. In this study we have evolved an RNA virus, the bacteriophage Qß, under three different temperatures that either were kept constant or alternated periodically. The populations obtained were analyzed at the phenotypic and the genotypic level to characterize the evolutionary process followed by the virus in each case and the amount of convergent genetic changes attained. Finally, we also investigated the influence of the pre-existent genetic diversity on adaptation to high temperature. The main conclusions that arise from our results are: i) under periodically changing temperature conditions, evolution of bacteriophage Qß is driven by the most stringent selective pressure, ii) there is a high degree of evolutionary convergence between replicated populations and also among populations evolved at different temperatures, iii) there are mutations specific of a particular condition, and iv) adaptation to high temperatures in populations differing in their pre-existent genetic diversity takes place through the selection of a common set of mutations.


Assuntos
Adaptação Fisiológica/genética , Allolevivirus/genética , Evolução Biológica , Mutação/genética , Seleção Genética/genética , Meio Ambiente , Evolução Molecular , Aptidão Genética , Variação Genética , Humanos , RNA Viral/genética , Temperatura , Proteínas Virais/genética
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