Data from: Viruses are a dominant driver of protein adaptation in mammals

Viruses interact with hundreds to thousands of proteins in mammals, yet adaptation against viruses has only been studied in a few proteins specialized in antiviral defense. Whether adaptation to viruses typically involves only specialized antiviral proteins or affects a broad array of virus-interacting proteins is unknown. Here, we analyze adaptation in ~1300 virus-interacting proteins manually curated from a set of 9900 proteins conserved in all sequenced mammalian genomes. We show that viruses (i) use the more evolutionarily constrained proteins within the cellular functions they interact with and that (ii) despite this high constraint, virus-interacting proteins account for a high proportion of all protein adaptation in humans and other mammals. Adaptation is elevated in virus-interacting proteins across all functional categories, including both immune and non-immune functions. We conservatively estimate that viruses have driven close to 30% of all adaptive amino acid changes in the part of the human proteome conserved within mammals. Our results suggest that viruses are one of the most dominant drivers of evolutionary change across mammalian and human proteomes.病毒与哺乳动物体内数百乃至数千种蛋白质存在相互作用，但目前针对病毒的适应性演化研究仅局限于少数专职抗病毒防御相关蛋白质。目前尚不明确，针对病毒的适应性演化通常仅涉及专职抗病毒蛋白质，还是会广泛影响诸多病毒互作蛋白质（virus-interacting proteins）。本研究对从所有已测序哺乳动物基因组中均保守存在的9900种蛋白质中人工筛选得到的约1300种病毒互作蛋白质展开适应性演化分析。研究结果显示：其一，病毒会靶向其相互作用的细胞功能通路中演化约束程度更高的蛋白质；其二，尽管存在这类强约束特性，病毒互作蛋白质在人类及其他哺乳动物的所有蛋白质适应性演化中占比极高。病毒互作蛋白质在所有功能类别（涵盖免疫与非免疫功能）中的适应性演化水平均显著提升。本研究保守估算表明，在哺乳动物共有的人类蛋白质组（proteome）区域内，病毒驱动了近30%的适应性氨基酸替换（adaptive amino acid changes）事件。本研究结果表明，病毒是驱动哺乳动物及人类蛋白质组演化改变的最主要因素之一。