病毒群体的基因型-蛋白图谱和集体适应

Ariadna Villanueva, Henry Secaira-Morocho, L. F. Seoane, E. Lázaro, S. Manrubia
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引用次数: 1

摘要

病毒种群庞大且高度异质。尽管这种异质性与进化相关,但很少采用统计方法来量化病毒保持高度基因型和/或表型多样性的程度。在这里,我们通过对适应高温的Qβ噬菌体群体进行深度测序来分析核苷酸-蛋白质序列图,从而解决了这个问题。数以万计的不同序列对应于编码病毒复制酶的两个基因片段。对两个独立种群的多样性分析一致显示,大约40%的突变引起了蛋白质氨基酸的变化,从而几乎完全探索了距离为1的(非沉默)突变体的蛋白质邻域。表型丰度经验分布的功能形式与假设核苷酸序列随机突变的分析计算一致。我们的研究结果与病毒种群保持高度多样性作为一种有效的适应机制的观点一致,并支持在生物学上有意义的基因型-表型图谱中表型丰度对数正态分布的普遍性假设,突出了分子进化中熵效应的相关性。
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Genotype-to-Protein Map and Collective Adaptation in a Viral Population
Viral populations are large and highly heterogeneous. Despite the evolutionary relevance of such heterogeneity, statistical approaches to quantifying the extent to which viruses maintain a high genotypic and/or phenotypic diversity have been rarely pursued. Here, we address this issue by analyzing a nucleotide-to-protein sequence map through deep sequencing of populations of the Qβ phage adapted to high temperatures. Tens of thousands of different sequences corresponding to two fragments of the gene coding for the viral replicase were recovered. A diversity analysis of two independent populations consistently revealed that about 40% of the mutations identified caused changes in protein amino acids, leading to an almost complete exploration of the protein neighborhood of (non-silent) mutants at a distance of one. The functional form of the empirical distribution of phenotype abundance agreed with analytical calculations that assumed random mutations in the nucleotide sequence. Our results concur with the idea that viral populations maintain a high diversity as an efficient adaptive mechanism and support the hypothesis of universality for a lognormal distribution of phenotype abundances in biologically meaningful genotype–phenotype maps, highlighting the relevance of entropic effects in molecular evolution.
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