Distribution of Spontaneous Mutants and Inferences about the Replication Mode of the RNA Bacteriophage φ6

Chao, Lin; Rang, Camilla U.; Wong, Linda

doi:10.1128/jvi.76.7.3276-3281.2002

Cited by 83 publications

(102 citation statements)

References 30 publications

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“…Although the exact value of the mutation rate is important for several evolutionary theories, accurate estimates are available only for a handful of organisms. RNA viruses show mutation rates that are orders of magnitude higher than those of their DNA-based hosts and in the range of 0.03-2 per genome and replication round (Drake et al 1998;Drake and Holland 1999;Chao et al 2002). This difference results from the lack of proofreading activity of the virusencoded RNA-dependent RNA polymerases (Steinhauer et al 1992).…”

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confidence: 95%

The Rate and Spectrum of Spontaneous Mutations in a Plant RNA Virus

Tromas

Elena

2010

Genetics

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Knowing mutation rates and the molecular spectrum of spontaneous mutations is important to understanding how the genetic composition of viral populations evolves. Previous studies have shown that the rate of spontaneous mutations for RNA viruses widely varies between 0.01 and 2 mutations per genome and generation, with plant RNA viruses always occupying the lower side of this range. However, this peculiarity of plant RNA viruses is based on a very limited number of studies. Here we analyze the spontaneous mutational spectrum and the mutation rate of Tobacco etch potyvirus, a model system of positive sense RNA viruses. Our experimental setup minimizes the action of purifying selection on the mutational spectrum, thus giving a picture of what types of mutations are produced by the viral replicase. As expected for a neutral target, we found that transitions and nonsynonymous (including a few stop codons and small deletions) mutations were the most abundant type. This spectrum was notably different from the one previously described for another plant virus. We have estimated that the spontaneous mutation rate for this virus was in the range 10 À6 À10À5 mutations per site and generation. Our estimates are in the same biological ballpark that previous values reported for plant RNA viruses. This finding gives further support to the idea that plant RNA viruses may have lower mutation rates than their animal counterparts.T HE rate of spontaneous mutation is a key parameter to understanding the genetic structure of populations over time. Mutation represents the primary source of genetic variation on which natural selection and genetic drift operate. Although the exact value of the mutation rate is important for several evolutionary theories, accurate estimates are available only for a handful of organisms. RNA viruses show mutation rates that are orders of magnitude higher than those of their DNA-based hosts and in the range of 0

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confidence: 95%

The Rate and Spectrum of Spontaneous Mutations in a Plant RNA Virus

Tromas

Elena

2010

Genetics

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“…However, when this data point is removed ters in φ6. Chao et al (2002) measured the mutation rate in φ6 by determining the reversion rate of an amber from our data set, the regression of s on log W remains significant (discussed above). Since there is less varimutation.…”

Section: Estimating Environmental Effects On Genotypes Of Var-mentioning

confidence: 99%

Epistasis and Its Relationship to Canalization in the RNA Virus φ6

2004

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Although deleterious mutations are believed to play a critical role in evolution, assessing their realized effect has been difficult. A key parameter governing the effect of deleterious mutations is the nature of epistasis, the interaction between the mutations. RNA viruses should provide one of the best systems for investigating the nature of epistasis because the high mutation rate allows a thorough investigation of mutational effects and interactions. Nonetheless, previous investigations of RNA viruses by S. Crotty and co-workers and by S. F. Elena have been unable to detect a significant effect of epistasis. Here we provide evidence that positive epistasis is characteristic of deleterious mutations in the RNA bacteriophage φ6. We estimated the effects of deleterious mutations by performing mutation-accumulation experiments on five viral genotypes of decreasing fitness. We inferred positive epistasis because viral genotypes with low fitness were found to be less sensitive to deleterious mutations. We further examined environmental sensitivity in these genotypes and found that low-fitness genotypes were also less sensitive to environmental perturbations. Our results suggest that even random mutations impact the degree of canalization, the buffering of a phenotype against genetic and environmental perturbations. In addition, our results suggest that genetic and environmental canalization have the same developmental basis and finally that an understanding of the nature of epistasis may first require an understanding of the nature of canalization. W HEN mutations occur together, their realized efa genome with other mutations more rapidly than a mutation in a genome without additional mutations. fects depend on the epistasis, or interaction, between them. In the absence of epistasis, mutations act However, despite the importance of these acknowledged roles for epistasis, quantitative measurements of independently and are expected to have a multiplicative effect on fitness (additive on a log scale). When epistasis epistasis are still not numerous and the few existing measurements have often been challenged (Chao 1988; is present, it can be of two forms: negative if the fitness of organisms bearing two mutations is lower than ex- (Wagner and Krall 1993). In infectivity and number of mutations in polioviruses and most cases, the impact of epistasis stems from the fact found evidence for positive epistasis (their Figure 4). that natural selection is more or less effective in changHowever, in both studies the statistical power of the ing the frequency of advantageous or deleterious mutadata was limited. Although Elena's result did not find tions depending on the form of epistasis. Thus, negative a significant deviation from log-linearity, an epistatic epistasis decreases the load of deleterious mutations effect up to a magnitude of 70.5% of the effect of individbecause selection eliminates a mutation that occurs in ual mutations could have been missed by the power of his analysis. Our own reanalysis of Crotty ...

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“…The ability of viral RNAs to assume multiple conformations combined with evidence that newly synthesized plus strands may assume forms that suppress transcription (43) supports the "stamping model" hypothesis for viral replication. This model, based on the distribution of mutants arising from single bursts in the RNA bacteriophage 6, suggests that most progeny plus strands are derived from minus strands synthesized from the original entering plus-strand genome (6). This increasingly complex image of RNA virus replication is requiring a reevaluation of conclusions reached using reductionist, cell-free approaches, where RNA elements are isolated from other cisacting sequences with which they may normally communicate or form functional domains.…”

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confidence: 99%

Structural Domains within the 3′ Untranslated Region of Turnip Crinkle Virus

McCormack

Yuan

Yingling

et al. 2008

J Virol

159

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The genomes of positive-strand RNA viruses undergo conformational shifts that complicate efforts to equate structures with function. We have initiated a detailed analysis of secondary and tertiary elements within the 3 end of Turnip crinkle virus (TCV) that are required for viral accumulation in vivo. MPGAfold, a massively parallel genetic algorithm, suggested the presence of five hairpins (H4a, H4b, and previously identified hairpins H4, H5, and Pr) and one H-type pseudoknot (⌿ 3 ) within the 3-terminal 194 nucleotides (nt). In vivo compensatory mutagenesis analyses confirmed the existence of H4a, H4b, ⌿ 3 and a second pseudoknot (⌿ 2 ) previously identified in a TCV satellite RNA. In-line structure probing of the 194-nt fragment supported the coexistence of H4, H4a, H4b, ⌿ 3 and a pseudoknot that connects H5 and the 3 end (⌿ 1 ). Stepwise replacements of TCV elements with the comparable elements from Cardamine chlorotic fleck virus indicated that the complete 142-nt 3 end, and subsets containing ⌿ 3 , H4a, and H4b or ⌿ 3 , H4a, H4b, H5, and ⌿ 2 , form functional domains for virus accumulation in vivo. A new 3-D molecular modeling protocol (RNA2D3D) predicted that H4a, H4b, H5, ⌿ 3 , and ⌿ 2 are capable of simultaneous existence and bears some resemblance to a tRNA. The related Japanese iris necrotic ring virus does not have comparable domains. These results provide a framework for determining how interconnected elements participate in processes that require 3 untranslated region sequences such as translation and replication.Replication of plus-strand RNA viruses initially requires translation of the genomic RNA to produce the virus-encoded, RNA-dependent RNA polymerase (RdRp) and any auxiliary viral proteins necessary for transcription. In a process that is poorly defined but likely dictated by viral and/or cellular factors, translation is terminated and the genomic RNA becomes available for reiterative synthesis of complementary strands, a process that requires membrane association (1, 2, 26). For some viruses, subsequent viral plus-strand synthesis occurs in virus-specific membrane invaginations known as spherules, which contain a limited number of minus-sense genomes and whose formation is induced by specific viral proteins (1,15,26). Although the process of producing viral progeny has been extensively studied using many different viral systems, it remains poorly understood. For example, fundamental questions, such as the role that conformational shifts in RNA structure play in switching the template from translation to replication, the proteins required to enact such events, and if cis-acting core promoters, enhancers, and repressors are organized into functional, interacting modules, remain virtually unanswered.Recent reports that portions of RNA viral genomes undergo conformational shifts to execute different functions (10, 13, 21, 28) complicate efforts to assign biological roles to groups of cis-acting elements that may not structurally coexist. The ability of viral RNAs to assume multiple conformation...

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Distribution of Spontaneous Mutants and Inferences about the Replication Mode of the RNA Bacteriophage φ6

Cited by 83 publications

References 30 publications

The Rate and Spectrum of Spontaneous Mutations in a Plant RNA Virus

The Rate and Spectrum of Spontaneous Mutations in a Plant RNA Virus

Epistasis and Its Relationship to Canalization in the RNA Virus φ6

Structural Domains within the 3′ Untranslated Region of Turnip Crinkle Virus

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