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

Abstract

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

Diversity of Plant Virus Populations: A Valuable Tool for Epidemiological Studies

“…In both cases, measurements were performed in similar experimental conditions of minimum purifying selection against deleterious mutants because the wild-type function was provided by complementation. Also in both cases, values obtained were similar and fell near the lower threshold of estimates reported for animal RNA viruses and bacteriophages, suggesting that plant RNA viruses show, indeed, lower mutation rates than animal RNA viruses [7]. In contrast, these works reported quite different spectra of mutations for the two plant viruses: preponderance (two-thirds) of insertions and deletions and a significant fraction (one-third) of multiple mutants for TMV, whereas most of TEV mutants were single-nucleotide substitutions, with the fraction of transitions being twice that of transversions.…”

“…Its calculation is often more complex than that of mutation frequency, which estimates the proportion of mutations remaining in a population after the action of selection, for instance, a fraction of mutations are deleterious and has been eliminated by purifying selection. Rates of spontaneous mutation of RNA viruses have been estimated to be several orders of magnitude higher that those of DNA viruses [5,7] and this difference has been attributed to the lack of proofreading activity of virus encoded RNA-dependent RNA polymerases. For plant RNA viruses, direct estimates of spontaneous mutation rates have been obtained for only two viruses, Tobacco mosaic virus (TMV) and Tobacco etch virus (TEV) [7,8].…”

“…Rates of spontaneous mutation of RNA viruses have been estimated to be several orders of magnitude higher that those of DNA viruses [5,7] and this difference has been attributed to the lack of proofreading activity of virus encoded RNA-dependent RNA polymerases. For plant RNA viruses, direct estimates of spontaneous mutation rates have been obtained for only two viruses, Tobacco mosaic virus (TMV) and Tobacco etch virus (TEV) [7,8]. In both cases, measurements were performed in similar experimental conditions of minimum purifying selection against deleterious mutants because the wild-type function was provided by complementation.…”

“…In contrast, these works reported quite different spectra of mutations for the two plant viruses: preponderance (two-thirds) of insertions and deletions and a significant fraction (one-third) of multiple mutants for TMV, whereas most of TEV mutants were single-nucleotide substitutions, with the fraction of transitions being twice that of transversions. These differences could be explained by a different behavior of the respective replicases or by differences in the experimental approach [7]. Lower mutation rates in plant than in animal RNA viruses could partially explain their generally lower rates of molecular evolution and the high genetic stability of plant RNA virus populations [2].…”

“…Lower mutation rates in plant than in animal RNA viruses could partially explain their generally lower rates of molecular evolution and the high genetic stability of plant RNA virus populations [2]. These differences in mutation rates could derive from different selective pressures acting in the mutational strategy of RNA viruses in the two types of hosts, although the role of natural selection on the evolution of mutation still needs to be demonstrated [7]. An alternative hypothesis set out that mutation rates in RNA viruses are not adaptive but are required to replace their chemically unstable genomes [5].…”