Rapid Evolution of PARP Genes Suggests a Broad Role for ADP-Ribosylation in Host-Virus Conflicts

Post-translational protein modifications such as phosphorylation and ubiquitinylation are common molecular targets of conflict between viruses and their hosts. However, the role of other post-translational modifications, such as ADP-ribosylation, in host-virus interactions is less well characterized. ADP-ribosylation is carried out by proteins encoded by the PARP (also called ARTD) gene family. The majority of the 17 human PARP genes are poorly characterized. However, one PARP protein, PARP13/ZAP, has broad antiviral activity and has evolved under positive (diversifying) selection in primates. Such evolution is typical of domains that are locked in antagonistic ‘arms races’ with viral factors. To identify additional PARP genes that may be involved in host-virus interactions, we performed evolutionary analyses on all primate PARP genes to search for signatures of rapid evolution. Contrary to expectations that most PARP genes are involved in ‘housekeeping’ functions, we found that nearly one-third of PARP genes are evolving under strong recurrent positive selection. We identified a >300 amino acid disordered region of PARP4, a component of cytoplasmic vault structures, to be rapidly evolving in several mammalian lineages, suggesting this region serves as an important host-pathogen specificity interface. We also found positive selection of PARP9, 14 and 15, the only three human genes that contain both PARP domains and macrodomains. Macrodomains uniquely recognize, and in some cases can reverse, protein mono-ADP-ribosylation, and we observed strong signatures of recurrent positive selection throughout the macro-PARP macrodomains. Furthermore, PARP14 and PARP15 have undergone repeated rounds of gene birth and loss during vertebrate evolution, consistent with recurrent gene innovation. Together with previous studies that implicated several PARPs in immunity, as well as those that demonstrated a role for virally encoded macrodomains in host immune evasion, our evolutionary analyses suggest that addition, recognition and removal of ADP-ribosylation is a critical, underappreciated currency in host-virus conflicts.磷酸化（phosphorylation）、泛素化（ubiquitinylation）等翻译后蛋白质修饰（post-translational protein modifications）是病毒与其宿主之间冲突的常见分子靶点。然而，ADP-核糖基化（ADP-ribosylation）等其他翻译后修饰在宿主-病毒互作中的作用尚未得到充分阐释。ADP-核糖基化由PARP（也称为ARTD）基因家族编码的蛋白质所催化。人类17个PARP基因中的大多数功能尚未明确。其中，PARP13/ZAP这一PARP蛋白具有广谱抗病毒活性，且在灵长类动物中经历了正向（多样化）选择。这种进化模式与那些与病毒因子处于拮抗“军备竞赛”的结构域所典型呈现的特征一致。为了识别可能参与宿主-病毒互作的其他PARP基因，我们对所有灵长类PARP基因开展进化分析，以寻找快速进化的信号。与“多数PARP基因参与持家功能”的预期相反，我们发现近三分之一的PARP基因在持续强烈的正向选择下进化。我们鉴定出PARP4中一段超过300个氨基酸的无序区域——该区域是细胞质穹窿体结构的组成部分，在多个哺乳动物谱系中呈现快速进化特征，提示该区域是决定宿主-病原体特异性相互作用的关键界面。我们还发现PARP9、14和15这三个人类基因是唯一同时包含PARP结构域与宏结构域（macrodomains）的基因，且它们受到正向选择。宏结构域可特异性识别蛋白质单ADP-核糖基化，在部分情况下还可逆转该修饰；我们在宏-PARP宏结构域中观察到持续强烈的正向选择信号。此外，在脊椎动物进化过程中，PARP14与PARP15经历了多轮基因诞生与丢失事件，这与基因反复创新的特征一致。结合此前多项研究——包括证实PARP家族成员参与免疫过程，以及证明病毒编码的宏结构域参与宿主免疫逃逸的研究，我们的进化分析表明，ADP-核糖基化的添加、识别与移除是宿主-病毒冲突中一种关键且未被充分重视的核心交互介质。