Correlation between mutation rate and genome size in riboviruses: mutation rate of bacteriophage Qβ

Abstract

Genome sizes and mutation rates covary across all domains of life. In unicellular organisms and DNA viruses, they show an inverse relationship known as Drake's rule. However, it is still unclear whether a similar relationship exists between genome sizes and mutation rates in RNA genomes. Coronaviruses, the RNA viruses with the largest genomes (∼30 kb), encode a proofreading 3' exonuclease that allows them to increase replication fidelity. However, it is unknown whether, conversely, the RNA viruses with the smallest genomes tend to show particularly high mutation rates. To test this, we measured the mutation rate of bacteriophage Qβ, a 4.2-kb levivirus. Amber reversion-based Luria-Delbrück fluctuation tests combined with mutant sequencing gave an estimate of 1.4 × 10(-4) substitutions per nucleotide per round of copying, the highest mutation rate reported for any virus using this method. This estimate was confirmed using a direct plaque sequencing approach and after reanalysis of previously published estimates for this phage. Comparison with other riboviruses (all RNA viruses except retroviruses) provided statistical support for a negative correlation between mutation rates and genome sizes. We suggest that the mutation rates of RNA viruses might be optimized for maximal adaptability and that the value of this optimum may in turn depend inversely on genome size.

Figure 1

(A) Mutation rate (s/n/c) vs. genome size in riboviruses. From left to right, data points correspond to bacteriophage Qβ (this study), tobacco mosaic virus, human rhinovirus 14, poliovirus 1, tobacco etch virus, hepatitis C virus, vesicular stomatitis virus, bacteriophage φ6, influenza A virus, influenza B virus, and murine hepatitis coronavirus (reviewed in Sanjuán et al. 2010). The dashed least-squares regression line has slope –2.06 ± 0.79. (B) Mutation rates (s/n/r) from Luria–Delbrück tests vs. genome size in riboviruses. From left to right, data points correspond to bacteriophage Qβ (this study), poliovirus 1, turnip mosaic virus, vesicular stomatitis virus, bacteriophage φ6, influenza A virus, and measles virus (reviewed in Sanjuán et al. 2010). For turnip mosaic virus, it was estimated that the rate of appearance of mutants escaping an artificial microRNA was 5.55 × 10⁻⁵ s/r (de La Iglesia et al. 2012). Assuming that escape was conferred by every single substitution in the 21-nucleotide micro RNA target, and assuming that ∼40% of such substitutions are lethal to the virus as in other plant viruses (Carrasco et al. 2007), $T_{\text{s}}$ = 21 × 3 × 0.4 = 25.2 and the per-nucleotide mutation rate is µ = 5.55 × 10⁻⁵ × 3 / 25.2 = 6.6 × 10⁻⁶ s/n/r. The dashed least-squares regression line is shown and has slope –1.79 ± 1.23.