The fitness effects of random mutations in single-stranded DNA and RNA bacteriophages.
The fitness effects of random mutations in single-stranded DNA and RNA bacteriophages.
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DOI：
10.1371/journal.pgen.1000742
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发表时间：
2009-11
期刊：
影响因子：
4.5
通讯作者：
Sanjuán R
中科院分区：
文献类型：
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作者：
Domingo-Calap P;Cuevas JM;Sanjuán R
由于病毒的基因组较小，可以相对较高的准确度测量病毒的突变适应性效应，这有利于全长测序和遗传操作。先前的工作表明，动物和植物RNA病毒对突变非常敏感。在这里，我们的特点突变健身效果在单链（SS）DNA和ssRNA细菌病毒。首先，我们进行了突变累积实验，其中我们对三个ssDNA（ΦX174、G4、F1）和三个ssRNA引物（Qβ、MS 2和SP）进行噬斑-噬斑转移和化学诱变。基因组测序和生长测定表明，累积突变的平均适应性效应在两组中是相似的。其次，我们使用定点突变获得了45个带有随机单核苷酸替换的ΦX174克隆和42个带有随机单核苷酸替换的Qβ克隆，并对它们进行了适合度测定。在ΦX174中，20%的这种突变是致命的，而存活的突变平均降低了13%的适应性。在Qβ中，这些数字分别为29%和10%。因此，高突变敏感性似乎是小基因组病毒的一般特性，包括那些感染动物、植物和细菌的病毒。突变适应性效应对于理解适应性下降过程以及中性进化和适应过程都很重要。因此，这些发现有助于解释ssDNA和ssRNA病毒的进化。突变的适应性效应是自然选择的原材料。已经表明，点突变通常在植物和动物RNA病毒中具有强烈的有害作用，而细胞生物体相对更稳健。在这里，我们描述了DNA病毒中随机突变的适应性效应，并将其与RNA病毒中发现的适应性效应进行了比较，使用了6种基因组大小相似的噬菌体。为了实现这一目标，我们通过化学和定点诱变引入突变，通过测序鉴定遗传变化，并使用生长速率测定量化其适应性效应。在所有情况下，突变对适应性有很强的平均影响。我们的结论是突变敏感性是一个小基因组病毒的一般属性，并讨论这些发现的进化意义。
Mutational fitness effects can be measured with relatively high accuracy in viruses due to their small genome size, which facilitates full-length sequencing and genetic manipulation. Previous work has shown that animal and plant RNA viruses are very sensitive to mutation. Here, we characterize mutational fitness effects in single-stranded (ss) DNA and ssRNA bacterial viruses. First, we performed a mutation-accumulation experiment in which we subjected three ssDNA (ΦX174, G4, F1) and three ssRNA phages (Qβ, MS2, and SP) to plaque-to-plaque transfers and chemical mutagenesis. Genome sequencing and growth assays indicated that the average fitness effect of the accumulated mutations was similar in the two groups. Second, we used site-directed mutagenesis to obtain 45 clones of ΦX174 and 42 clones of Qβ carrying random single-nucleotide substitutions and assayed them for fitness. In ΦX174, 20% of such mutations were lethal, whereas viable ones reduced fitness by 13% on average. In Qβ, these figures were 29% and 10%, respectively. It seems therefore that high mutational sensitivity is a general property of viruses with small genomes, including those infecting animals, plants, and bacteria. Mutational fitness effects are important for understanding processes of fitness decline, but also of neutral evolution and adaptation. As such, these findings can contribute to explain the evolution of ssDNA and ssRNA viruses. The fitness effects of mutations are the raw material for natural selection. It has been shown that point mutations typically have strongly deleterious effects in plant and animal RNA viruses, whereas cellular organisms are comparatively more robust. Here, we characterize the fitness effects of random mutations in DNA viruses and compare them with those found in RNA viruses, using six phage species of similar genome sizes. To achieve this goal, we introduced mutations by chemical and site-directed mutagenesis, identified the genetic changes by sequencing, and quantified their fitness effects using growth-rate assays. In all cases, mutations had a strong average impact on fitness. We conclude that mutational sensitivity is a general property of viruses with small genomes and discuss the evolutionary implications of these findings.
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