Quantifying the Evolutionary Constraints and Potential of Hepatitis C Virus NS5A Protein.
Quantifying the Evolutionary Constraints and Potential of Hepatitis C Virus NS5A Protein.
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DOI：
10.1128/msystems.01111-20
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发表时间：
2021-04-13
期刊：
影响因子：
6.4
通讯作者：
Sun R
中科院分区：
文献类型：
--
作者：
Dai L;Du Y;Qi H;Huber CD;Chen D;Zhang TH;Wu NC;Wang E;Lloyd-Smith JO;Sun R
RNA 病毒，例如丙型肝炎病毒 (HCV)、流感病毒和 SARS-CoV-2，因其在新环境中的选择下快速进化的能力而臭名昭著。众所周知，RNA病毒的高突变率可以产生巨大的遗传多样性，以促进病毒的适应。然而，人们对代表病毒基因组选择力的潜在适应度景观的关注较少，特别是在不同的选择条件下。在这里，我们系统地量化了 HCV NS5A 蛋白药物靶向区域中约 1,600 个单个氨基酸取代的适应度效应分布。我们发现大多数非同义替换都会产生巨大的适应成本，这表明 NS5A 蛋白是高度优化的。病毒的复制适应性与自然界中序列保守的模式相关，并且病毒的进化受到维持蛋白质稳定性的需要的限制。我们通过使用多个浓度的抗病毒药物达卡他韦对突变病毒进行选择来表征 HCV 的适应潜力。发现相对适合度值和有益突变的数量随着达卡他韦浓度的增加而增加。 NS5A 蛋白有益突变谱的变化可以通过药效学模型来解释，该模型将病毒适应性描述为药物浓度的函数。总的来说，我们的结果表明，突变的适应度效应的分布受到蛋白质生物物理特性的限制（即蛋白质稳定性的选择压力）和环境压力水平（即耐药性的选择压力）的调节。重要性 许多病毒会迅速适应新的选择压力，例如抗病毒药物。了解病原体在药物选择下如何进化对于针对人类病原体的抗病毒治疗的成功至关重要。通过将深度测序与细胞培养中的选择实验相结合，我们量化了丙型肝炎病毒 (HCV) NS5A 蛋白突变的适应度效应分布。我们的结果表明，NS5A 蛋白中的大多数单一氨基酸取代都会产生巨大的适应性成本。蛋白质稳定性的模拟表明病毒进化受到维持蛋白质稳定性的需要的限制。通过在抗病毒药物下对突变病毒进行选择，我们发现病毒蛋白在新环境中的适应潜力受到环境应激水平的调节，这可以通过药效学模型来解释。我们对 NS5A 适应度景观的全面表征可以潜在地指导限制病毒进化的有效策略的设计。
RNA viruses, such as hepatitis C virus (HCV), influenza virus, and SARS-CoV-2, are notorious for their ability to evolve rapidly under selection in novel environments. It is known that the high mutation rate of RNA viruses can generate huge genetic diversity to facilitate viral adaptation. However, less attention has been paid to the underlying fitness landscape that represents the selection forces on viral genomes, especially under different selection conditions. Here, we systematically quantified the distribution of fitness effects of about 1,600 single amino acid substitutions in the drug-targeted region of NS5A protein of HCV. We found that the majority of nonsynonymous substitutions incur large fitness costs, suggesting that NS5A protein is highly optimized. The replication fitness of viruses is correlated with the pattern of sequence conservation in nature, and viral evolution is constrained by the need to maintain protein stability. We characterized the adaptive potential of HCV by subjecting the mutant viruses to selection by the antiviral drug daclatasvir at multiple concentrations. Both the relative fitness values and the number of beneficial mutations were found to increase with the increasing concentrations of daclatasvir. The changes in the spectrum of beneficial mutations in NS5A protein can be explained by a pharmacodynamics model describing viral fitness as a function of drug concentration. Overall, our results show that the distribution of fitness effects of mutations is modulated by both the constraints on the biophysical properties of proteins (i.e., selection pressure for protein stability) and the level of environmental stress (i.e., selection pressure for drug resistance). IMPORTANCE Many viruses adapt rapidly to novel selection pressures, such as antiviral drugs. Understanding how pathogens evolve under drug selection is critical for the success of antiviral therapy against human pathogens. By combining deep sequencing with selection experiments in cell culture, we have quantified the distribution of fitness effects of mutations in hepatitis C virus (HCV) NS5A protein. Our results indicate that the majority of single amino acid substitutions in NS5A protein incur large fitness costs. Simulation of protein stability suggests viral evolution is constrained by the need to maintain protein stability. By subjecting the mutant viruses to selection under an antiviral drug, we find that the adaptive potential of viral proteins in a novel environment is modulated by the level of environmental stress, which can be explained by a pharmacodynamics model. Our comprehensive characterization of the fitness landscapes of NS5A can potentially guide the design of effective strategies to limit viral evolution.
影响因子：
4.3
作者：
Ke R;Loverdo C;Qi H;Sun R;Lloyd-Smith JO
通讯作者：
Lloyd-Smith JO