Selection for thermostability can lead to the emergence of mutational robustness in an RNA virus

Evolutionary Adaptation of an RNA Bacteriophage to Repeated Freezing and Thawing Cycles

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.

Evolution of thermal performance curves: A meta-analysis of selection experiments

Temperatures are increasing due to global changes, putting biodiversity at risk. Organisms are faced with a limited set of options to cope with this situation: adapt, disperse or die. We here focus on the first possibility, more specifically, on evolutionary adaptations to temperature. Ectotherms are usually characterized by a hump-shaped relationship between fitness and temperature, a non-linear reaction norm that is referred to as thermal performance curve (TPC). To understand and predict impacts of global change, we need to know whether and how such TPCs evolve. Therefore, we performed a systematic literature search and a statistical meta-analysis focusing on experimental evolution and artificial selection studies. This focus allows us to directly quantify relative fitness responses to temperature selection by calculating fitness differences between TPCs from ancestral and derived populations after thermal selection. Out of 7561 publications screened, we found 47 studies corresponding to our search criteria representing taxa across the tree of life, from bacteria, to plants and vertebrates. We show that, independently of species identity, the studies we found report a positive response to temperature selection. Considering entire TPC shapes, adaptation to higher temperatures traded off with fitness at lower temperatures, leading to niche shifts. Effects were generally stronger in unicellular organisms. By contrast, we do not find statistical support for the often discussed "Hotter is better" hypothesis. While our meta-analysis provides evidence for adaptive potential of TPCs across organisms, it also highlights that more experimental work is needed, especially for under-represented taxa, such as plants and non-model systems.

A Trait-Based Approach to Predicting Viral Host-Range Evolvability

Predicting the evolution of virus host range has proven to be extremely difficult, in part because of the sheer diversity of viruses, each with unique biology and ecological interactions. We have not solved this problem, but to make the problem more tractable, we narrowed our focus to three traits intrinsic to all viruses that may play a role in host-range evolvability: mutation rate, recombination rate, and phenotypic heterogeneity. Although each trait should increase evolvability, they cannot do so unbounded because fitness trade-offs limit the ability of all three traits to maximize evolvability. By examining these constraints, we can begin to identify groups of viruses with suites of traits that make them especially concerning, as well as ecological and environmental conditions that might push evolution toward accelerating host-range expansion.

Why are viral genomes so fragile? The bottleneck hypothesis

If they undergo new mutations at each replication cycle, why are RNA viral genomes so fragile, with most mutations being either strongly deleterious or lethal? Here we provide theoretical and numerical evidence for the hypothesis that genetic fragility is partly an evolutionary response to the multiple population bottlenecks experienced by viral populations at various stages of their life cycles. Modelling within-host viral populations as multi-type branching processes, we show that mutational fragility lowers the rate at which Muller’s ratchet clicks and increases the survival probability through multiple bottlenecks. In the context of a susceptible-exposed-infectious-recovered epidemiological model, we find that the attack rate of fragile viral strains can exceed that of more robust strains, particularly at low infectivities and high mutation rates. Our findings highlight the importance of demographic events such as transmission bottlenecks in shaping the genetic architecture of viral pathogens.

Given that most mutations are deleterious, high mutation rates carry a significant evolutionary cost. To reduce this burden, an obvious evolutionary solution would be to reduce the fitness cost of mutations by becoming more robust; this solution is indeed selected in populations of constantly large size. Here, we show that when populations regularly experience bottlenecks, as viruses do upon transmission to a new host, a less obvious solution becomes more viable: namely, to increase the fitness cost of mutations so that unfit mutants are less likely to fix at each passage. This could explain why viruses—especially RNA viruses—do in fact have very fragile genomes.

Phage engineering and the evolutionary arms race

Phages are versatile agents for delivering a variety of cargo, including nanomaterials, nucleic acids, and small molecules. A potentially important application is treatment of antibiotic-resistant infections. All of these applications require molecular engineering of the phages, including chemical modification and genetic engineering. Phages are remarkably amenable to such engineering. We review some examples, including for controlled phage therapy. We suggest that the ability of phages to support extensive engineering may have evolutionary origins in the billions-year-old 'arms race' between bacteria and phages, which selects for sequences and structures that are robust in the face of rapid evolutionary change. This leads to high tolerance of both naturally evolved mutations and synthetic molecular engineering.

Adaptation of turnip mosaic potyvirus to a specific niche reduces its genetic and environmental robustness

Robustness is the preservation of the phenotype in the face of genetic and environmental perturbations. It has been argued that robustness must be an essential fitness component of RNA viruses owed to their small and compacted genomes, high mutation rates and living in ever-changing environmental conditions. Given that genetic robustness might hamper possible beneficial mutations, it has been suggested that genetic robustness can only evolve as a side-effect of the evolution of robustness mechanisms specific to cope with environmental perturbations, a theory known as plastogenetic congruence. However, empirical evidences from different viral systems are contradictory. To test how adaptation to a particular environment affects both environmental and genetic robustness, we have used two strains of turnip mosaic potyvirus (TuMV) that differ in their degree of adaptation to Arabidopsis thaliana at a permissive temperature. We show that the highly adapted strain is strongly sensitive to the effect of random mutations and to changes in temperature conditions. In contrast, the non-adapted strain shows more robustness against both the accumulation of random mutations and drastic changes in temperature conditions. Together, these results are consistent with the predictions of the plastogenetic congruence theory, suggesting that genetic and environmental robustnesses may be two sides of the same coin for TuMV.

Evolutionary adaptation of an RNA bacteriophage to the simultaneous increase in the within-host and extracellular temperatures

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 Qβ, when it is confronted with a temperature increase that affects both the extracellular and the intracellular media. Our results show that Qβ 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.

Differences in adaptive dynamics determine the success of virus variants that propagate together

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 Qβ 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.

Impact of increased mutagenesis on adaptation to high temperature in bacteriophage Qβ

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 Qβ, 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.

Antigenic diversification is correlated with increased thermostability in a mammalian virus

The theory of plastogenetic congruence posits that ultimately, the pressure to maintain function in the face of biomolecular destabilization produces robustness. As temperature goes up so does destabilization. Thus, genetic robustness, defined as phenotypic constancy despite mutation, should correlate with survival during thermal challenge. We tested this hypothesis using vesicular stomatitis virus (VSV). We produced two sets of evolved strains after selection for higher thermostability by either preincubation at 37°C or by incubation at 40°C during infection. These VSV populations became more thermostable and also more fit in the absence of thermal selection, demonstrating an absence of tradeoffs. Eleven out of 12 evolved populations had a fixed, nonsynonymous substitution in the nucleocapsid (N) open reading frame. There was a partial correlation between thermostability and mutational robustness that was observed when the former was measured at 42°C, but not at 37°C. These results are consistent with our earlier work and suggest that the relationship between robustness and thermostability is complex. Surprisingly, many of the thermostable strains also showed increased resistance to monoclonal antibody and polyclonal sera, including sera from natural hosts. These data suggest that evolved thermostability may lead to antigenic diversification and an increased ability to escape immune surveillance in febrile hosts, and potentially to an improved robustness. These relationships have important implications not only in terms of viral pathogenesis, but also for the development of vaccine vectors and oncolytic agents.

Back to the future: bacteriophages as promising therapeutic tools

Bacteriophages (phages), natural predators of bacteria, are becoming increasingly attractive in medical and pharmaceutical applications. After their discovery almost a century ago, they have been particularly instrumental in the comprehension of basic molecular biology and genetics processes. The more recent emergence of multi-drug-resistant bacteria requires novel therapeutic strategies, and phages are being (re)considered as promising potential antibacterial tools. Furthermore, phages are also used for other purposes, e.g. vaccine production, gene/drug carriers, bacterial detection and typing. These new alternative approaches using phages are of major interest and have allowed unexpected developments, from the decipherment of fundamental biological processes to potential clinical applications.

Evolution on neutral networks accelerates the ticking rate of the molecular clock

Large sets of genotypes give rise to the same phenotype, because phenotypic expression is highly redundant. Accordingly, a population can accept mutations without altering its phenotype, as long as the genotype mutates into another one on the same set. By linking every pair of genotypes that are mutually accessible through mutation, genotypes organize themselves into neutral networks (NNs). These networks are known to be heterogeneous and assortative, and these properties affect the evolutionary dynamics of the population. By studying the dynamics of populations on NNs with arbitrary topology, we analyse the effect of assortativity, of NN (phenotype) fitness and of network size. We find that the probability that the population leaves the network is smaller the longer the time spent on it. This progressive 'phenotypic entrapment' entails a systematic increase in the overdispersion of the process with time and an acceleration in the fixation rate of neutral mutations. We also quantify the variation of these effects with the size of the phenotype and with its fitness relative to that of neighbouring alternatives.

Effective temperature of mutations

Biological macromolecules experience two seemingly very different types of noise acting on different time scales: (i) point mutations corresponding to changes in molecular sequence and (ii) thermal fluctuations. Examining the secondary structures of a large number of microRNA precursor sequences and model lattice proteins, we show that the effects of single point mutations are statistically indistinguishable from those of an increase in temperature by a few tens of kelvins. The existence of such an effective mutational temperature establishes a quantitative connection between robustness to genetic (mutational) and environmental (thermal) perturbations.

Payoffs, not tradeoffs, in the adaptation of a virus to ostensibly conflicting selective pressures

The genetic architecture of many phenotypic traits is such that genes often contribute to multiple traits, and mutations in these genes can therefore affect multiple phenotypes. These pleiotropic interactions often manifest as tradeoffs between traits where improvement in one property entails a cost in another. The life cycles of many pathogens include periods of growth within a host punctuated with transmission events, such as passage through a digestive tract or a passive stage of exposure in the environment. Populations exposed to such fluctuating selective pressures are expected to acquire mutations showing tradeoffs between reproduction within and survival outside of a host. We selected for individual mutations under fluctuating selective pressures for a ssDNA microvirid bacteriophage by alternating selection for increased growth rate with selection on biophysical properties of the phage capsid in high-temperature or low-pH conditions. Surprisingly, none of the seven unique mutations identified showed a pleiotropic cost; they all improved both growth rate and pH or temperature stability, suggesting that single mutations even in a simple genetic system can simultaneously improve two distinct traits. Selection on growth rate alone revealed tradeoffs, but some mutations still benefited both traits. Tradeoffs were therefore prevalent when selection acted on a single trait, but payoffs resulted when multiple traits were selected for simultaneously. We employed a molecular-dynamics simulation method to determine the mechanisms underlying beneficial effects for three heat-shock mutations. All three mutations significantly enhanced the affinities of protein-protein interfacial bindings, thereby improving capsid stability. The ancestral residues at the mutation sites did not contribute to protein-protein interfacial binding, indicating that these sites acquired a new function. Computational models, such as those used here, may be used in future work not only as predictive tools for mutational effects on protein stability but, ultimately, for evolution.

Contribution of silent mutations to thermal adaptation of RNA bacteriophage Qβ

Changes in protein function and other biological properties, such as RNA structure, are crucial for adaptation of organisms to novel or inhibitory environments. To investigate how mutations that do not alter amino acid sequence may be positively selected, we performed a thermal adaptation experiment using the single-stranded RNA bacteriophage Qβ in which the culture temperature was increased from 37.2°C to 41.2°C and finally to an inhibitory temperature of 43.6°C in a stepwise manner in three independent lines. Whole-genome analysis revealed 31 mutations, including 14 mutations that did not result in amino acid sequence alterations, in this thermal adaptation. Eight of the 31 mutations were observed in all three lines. Reconstruction and fitness analyses of Qβ strains containing only mutations observed in all three lines indicated that five mutations that did not result in amino acid sequence changes but increased the amplification ratio appeared in the course of adaptation to growth at 41.2°C. Moreover, these mutations provided a suitable genetic background for subsequent mutations, altering the fitness contribution from deleterious to beneficial. These results clearly showed that mutations that do not alter the amino acid sequence play important roles in adaptation of this single-stranded RNA virus to elevated temperature.

IMPORTANCE

Recent studies using whole-genome analysis technology suggested the importance of mutations that do not alter the amino acid sequence for adaptation of organisms to novel environmental conditions. It is necessary to investigate how these mutations may be positively selected and to determine to what degree such mutations that do not alter amino acid sequences contribute to adaptive evolution. Here, we report the roles of these silent mutations in thermal adaptation of RNA bacteriophage Qβ based on experimental evolution during which Qβ showed adaptation to growth at an inhibitory temperature. Intriguingly, four synonymous mutations and one mutation in the untranslated region that spread widely in the Qβ population during the adaptation process at moderately high temperature provided a suitable genetic background to alter the fitness contribution of subsequent mutations from deleterious to beneficial at a higher temperature.

RNA virus evolution at variable error rate

ABSTRACT: 

RNA viruses replicate their genomes with very high error rates, which leads to the generation of a large genetic diversity that makes them highly adaptable to most environmental pressures, including antiviral drugs and immune responses. However, since most mutations are deleterious, an excess of errors can be very negative for RNA viruses, entailing that error rates must be finely regulated. Currently, the manipulation of the error rate is emerging as a promising antiviral therapy that could minimize the problem of virus adaptation to classical treatments. This review provides a detailed analysis of the different outcomes that can result from the variation of the error rate in RNA viruses, on the basis of the more relevant findings obtained in experimental studies.

What ecologists can tell virologists

I pictured myself as a virus…and tried to sense what it would be like. --Jonas Salk. Ecology as a science evolved from natural history, the observational study of the interactions of plants and animals with each other and their environments. As natural history matured, it became increasingly quantitative, experimental, and taxonomically broad. Focus diversified beyond the Eukarya to include the hidden world of microbial life. Microbes, particularly viruses, were shown to exist in unfathomable numbers, affecting every living organism. Slowly viruses came to be viewed in an ecological context rather than as abstract, disease-causing agents. This shift is exemplified by an increasing tendency to refer to viruses as living organisms instead of inert particles. In recent years, researchers have recognized the critical contributions of viruses to fundamental ecological processes such as biogeochemical cycling, competition, community structuring, and horizontal gene transfer. This review describes virus ecology from a virus's perspective. If we are, like Jonas Salk, to imagine ourselves as a virus, what kind of world would we experience?

Understanding specialism when the Jack of all trades can be the master of all

Specialism is widespread in nature, generating and maintaining diversity, but recent work has demonstrated that generalists can be equally fit as specialists in some shared environments. This no-cost generalism challenges the maxim that 'the jack of all trades is the master of none', and requires evolutionary genetic mechanisms explaining the existence of specialism and no-cost generalism, and the persistence of specialism in the face of selection for generalism. Examining three well-described mechanisms with respect to epistasis and pleiotropy indicates that sign (or antagonistic) pleiotropy without epistasis cannot explain no-cost generalism and that magnitude pleiotropy without epistasis (including directional selection and mutation accumulation) cannot explain the persistence of specialism. However, pleiotropy with epistasis can explain all. Furthermore, epistatic pleiotropy may allow past habitat use to influence future use of novel environments, thereby affecting disease emergence and populations' responses to habitat change.

Directional selection causes decanalization in a group I ribozyme

A canalized genotype is robust to environmental or genetic perturbations. Canalization is expected to result from stabilizing selection on a well-adapted phenotype. Decanalization, the loss of robustness, might follow periods of directional selection toward a new optimum. The evolutionary forces causing decanalization are still unknown, in part because it is difficult to determine the fitness effects of mutations in populations of organisms with complex genotypes and phenotypes. Here, we report direct experimental measurements of robustness in a system with a simple genotype and phenotype, the catalytic activity of an RNA enzyme. We find that the robustness of a population of RNA enzymes decreases during a period of directional selection in the laboratory. The decrease in robustness is primarily caused by the selective sweep of a genotype that is decanalized relative to the wild-type, both in terms of mutational robustness and environmental robustness (thermodynamic stability). Our results experimentally demonstrate that directional selection can cause decanalization on short time scales, and demonstrate co-evolution of mutational and environmental robustness.

RNA virus genetic robustness: possible causes and some consequences

In general terms, robustness is the capacity of biological systems to function in spite of genetic or environmental perturbations. The small and compacted genomes and high mutation rates of RNA viruses, as well as the ever-changing environments wherein they replicate, create the conditions for robustness to be advantageous. In this review, I will enumerate possible mechanisms by which viral populations may acquire robustness, distinguishing between mechanisms that are inherent to virus replication and population dynamics and those that result from the interaction with host factors. Then, I will move to review some evidences that RNA virus populations are robust indeed. Finally, I will comment on the implications of robustness for virus evolvability, the emergence of new viruses and the efficiency of lethal mutagenesis as an antiviral strategy.

Cell targeting with hybrid Qβ virus-like particles displaying epidermal growth factor

Structurally uniform protein nanoparticles derived from the self-assembly of viral capsid proteins are attractive platforms for the multivalent display of cell-targeting motifs for use in nanomedicine. Virus-based nanoparticles are of particular interest because the scaffold can be manipulated both genetically and chemically to simultaneously display targeting groups and carry a functional payload. Here, we displayed the human epidermal growth factor (EGF) on the exterior surface of bacteriophage Qβ as a C-terminal genetic fusion to the Qβ capsid protein. The co-assembly of wild-type Qβ and EGF-modified subunits resulted in structurally homogeneous nanoparticles displaying between 5 and 12 copies of EGF on their exterior surface. The particles were found to be amenable to bioconjugation by standard methods as well as the high-fidelity copper-catalyzed azide-alkyne cycloaddition reaction (CuAAC). Such chemical derivatization did not impair the ability of the particles to specifically interact with the EGF receptor. Additionally, the particle-displayed EGF remained biologically active promoting autophosphorylation of the EGF receptor and apoptosis of A431 cells. These results suggest that hybrid Qβ-EGF nanoparticles could be useful vehicles for targeted delivery of imaging and/or therapeutic agents.