Minicka Julia, Elena Santiago F, Borodynko-Filas Natasza, Rubiś Błażej, Hasiów-Jaroszewska Beata
Department of Virology and Bacteriology, Institute of Plant Protection-National Research Institute, Poznan, Poland.
Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain.
BMC Evol Biol. 2017 Mar 6;17(1):67. doi: 10.1186/s12862-017-0920-4.
Pepino mosaic virus (PepMV) is an emerging plant pathogen that infects tomatoes worldwide. Understanding the factors that influence its evolutionary success is essential for developing new control strategies that may be more robust against the evolution of new viral strains. One of these evolutionary factors is the distribution of mutational fitness effect (DMFE), that is, the fraction of mutations that are lethal, deleterious, neutral, and beneficial on a given viral strain and host species. The goal of this study was to characterize the DMFE of introduced nonsynonymous mutations on a mild isolate of PepMV from the Chilean 2 strain (PepMV-P22). Additionally, we also explored whether the fitness effect of a given mutation depends on the gene where it appears or on epistatic interactions with the genetic background. To address this latter possibility, a subset of mutations were also introduced in a mild isolate of the European strain (PepMV-P11) and the fitness of the resulting clones measured.
A collection of 25 PepMV clones each containing a single nucleotide nonsynonymous substitution was created by site-directed mutagenesis and the fitness of each mutant was determined. PepMV-P22 genome showed a high degree of robustness against point mutations, with 80% of mutations being either neutral or even beneficial and only 20% being deleterious or lethal. We found that the effect of mutations strongly depended on the gene in which they were introduced. Mutations with the largest average beneficial effects were those affecting the RdRp gene, in contrast to mutations affecting TGB1 and CP genes, for which the average effects were deleterious. Moreover, significant epistatic interactions were observed between nonsynonymous mutations and the genetic background, meaning that the effect of a given nucleotide substitution on a particular genomic context cannot be predicted by knowing its effect in a different one.
Our results indicated that PepMV genome has a surprisingly high robustness against mutations. We also found that fitness consequences of a given mutation differ between the two strains analyzed. This discovery suggests that the strength of selection, and thus the rates of evolution, vary among PepMV strains.
番木瓜花叶病毒（PepMV）是一种新出现的植物病原体，在全球范围内感染番茄。了解影响其进化成功的因素对于制定可能对新病毒株进化更具抗性的新控制策略至关重要。这些进化因素之一是突变适应性效应分布（DMFE），即给定病毒株和宿主物种上致死、有害、中性和有益突变的比例。本研究的目的是表征智利2号株系（PepMV-P22）的温和分离株中引入的非同义突变的DMFE。此外，我们还探讨了给定突变的适应性效应是否取决于其出现的基因或与遗传背景的上位性相互作用。为了解决后一种可能性，还在欧洲株系（PepMV-P11）的温和分离株中引入了一部分突变，并测量了所得克隆的适应性。
通过定点诱变创建了一组25个PepMV克隆，每个克隆包含一个单核苷酸非同义替换，并确定了每个突变体的适应性。PepMV-P22基因组对点突变表现出高度的稳健性，80%的突变是中性的甚至是有益的，只有20%是有害的或致死的。我们发现突变的影响强烈取决于它们所引入的基因。平均有益效应最大的突变是那些影响RdRp基因的突变，而影响TGB1和CP基因的突变平均效应是有害的。此外，在非同义突变和遗传背景之间观察到显著的上位性相互作用，这意味着给定核苷酸替换在特定基因组背景下的效应不能通过了解其在不同背景下的效应来预测。
我们的结果表明，PepMV基因组对突变具有惊人的高稳健性。我们还发现，给定突变的适应性后果在分析的两个株系之间有所不同。这一发现表明，选择强度以及进化速率在PepMV株系之间有所变化。
