Genomewide Patterns of Substitution in Adaptively Evolving Populations of the RNA Bacteriophage MS2

Betancourt, Andrea J.

doi:10.1534/genetics.107.085837

Cited by 56 publications

(55 citation statements)

References 45 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A qualitative pattern that arises from this assumption is that the size of fitness effects will decrease as fitness increases along a walk. This pattern has been observed previously in experimental evolution (Holder and Bull 2001;Silander et al 2007;Betancourt 2009). Our data show the same pattern, although in greater detail for only the first two steps: second-steps have both smaller absolute fitness effects (Figure 3) and smaller selection coefficients than first-steps (Figure 4).…”

Section: Discussionsupporting

confidence: 91%

Mutational Effects and Population Dynamics During Viral Adaptation Challenge Current Models

Joyce²,

2011

View full text Add to dashboard Cite

Adaptation in haploid organisms has been extensively modeled but little tested. Using a microvirid bacteriophage (ID11), we conducted serial passage adaptations at two bottleneck sizes (10 4 and 10 6 ), followed by fitness assays and whole-genome sequencing of 631 individual isolates. Extensive genetic variation was observed including 22 beneficial, several nearly neutral, and several deleterious mutations. In the three large bottleneck lines, up to eight different haplotypes were observed in samples of 23 genomes from the final time point. The small bottleneck lines were less diverse. The small bottleneck lines appeared to operate near the transition between isolated selective sweeps and conditions of complex dynamics (e.g., clonal interference). The large bottleneck lines exhibited extensive interference and less stochasticity, with multiple beneficial mutations establishing on a variety of backgrounds. Several leapfrog events occurred. The distribution of first-step adaptive mutations differed significantly from the distribution of second-steps, and a surprisingly large number of second-step beneficial mutations were observed on a highly fit first-step background. Furthermore, few first-step mutations appeared as second-steps and second-steps had substantially smaller selection coefficients. Collectively, the results indicate that the fitness landscape falls between the extremes of smooth and fully uncorrelated, violating the assumptions of many current mutational landscape models.

show abstract

Section: Discussionsupporting

confidence: 91%

Mutational Effects and Population Dynamics During Viral Adaptation Challenge Current Models

Joyce²,

2011

View full text Add to dashboard Cite

show abstract

“…The interactions in the Q␤ genome structure described above, especially the interaction between the S site and M site, may contribute to the epistasis observed here. In adaptation to the cold temperature of ssRNA bacteriophage MS2, it was reported that sign epistasis was not observed (53,54). In the present study, sign epistasis may have been observed due to the genetic background of 5mut, which may be adaptive in terms of RNA secondary or higher-order structure as described above.…”

Section: Figsupporting

confidence: 51%

Contribution of Silent Mutations to Thermal Adaptation of RNA Bacteriophage Qβ

Kashiwagi

Sugawara

Tsushima

et al. 2014

J Virol

View full text Add to dashboard Cite

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 Q␤ 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 Q␤ 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. IMPORTANCERecent 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 Q␤ based on experimental evolution during which Q␤ showed adaptation to growth at an inhibitory temperature. Intriguingly, four synonymous mutations and one mutation in the untranslated region that spread widely in the Q␤ 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.

show abstract

“…Such studies have indicated that (i) frequent base substitutions lead to adaptations to changing environmental conditions (20), (ii) deletions as well as duplications occurring by random recombination are readily introduced into the ssRNA of leviviruses in response to various deliberate changes to the genome sequence and structure (161,192), and (iii) genomic defects can be repaired by illegitimate as well as less frequent homologous recombination occurring as a result of transesterification and template switching, respectively (47,196).…”

Section: Leviviridaementioning

confidence: 99%

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

Krupovìč

Prangishvili

Hendrix

et al. 2011

Microbiol Mol Biol Rev

216

176

View full text Add to dashboard Cite

SUMMARY Prokaryotes, bacteria and archaea, are the most abundant cellular organisms among those sharing the planet Earth with human beings (among others). However, numerous ecological studies have revealed that it is actually prokaryotic viruses that predominate on our planet and outnumber their hosts by at least an order of magnitude. An understanding of how this viral domain is organized and what are the mechanisms governing its evolution is therefore of great interest and importance. The vast majority of characterized prokaryotic viruses belong to the order Caudovirales, double-stranded DNA (dsDNA) bacteriophages with tails. Consequently, these viruses have been studied (and reviewed) extensively from both genomic and functional perspectives. However, albeit numerous, tailed phages represent only a minor fraction of the prokaryotic virus diversity. Therefore, the knowledge which has been generated for this viral system does not offer a comprehensive view of the prokaryotic virosphere. In this review, we discuss all families of bacterial and archaeal viruses that contain more than one characterized member and for which evolutionary conclusions can be attempted by use of comparative genomic analysis. We focus on the molecular mechanisms of their genome evolution as well as on the relationships between different viral groups and plasmids. It becomes clear that evolutionary mechanisms shaping the genomes of prokaryotic viruses vary between different families and depend on the type of the nucleic acid, characteristics of the virion structure, as well as the mode of the life cycle. We also point out that horizontal gene transfer is not equally prevalent in different virus families and is not uniformly unrestricted for diverse viral functions.

show abstract

Genomewide Patterns of Substitution in Adaptively Evolving Populations of the RNA Bacteriophage MS2

Cited by 56 publications

References 45 publications

Mutational Effects and Population Dynamics During Viral Adaptation Challenge Current Models

Mutational Effects and Population Dynamics During Viral Adaptation Challenge Current Models

Contribution of Silent Mutations to Thermal Adaptation of RNA Bacteriophage Qβ

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

Contact Info

Product

Resources

About