McDougal Matthew B, Boys Ian N, De Maria Anthony M, Nakahara Emi, Schoggins John W
Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
bioRxiv. 2025 Jul 1:2024.05.13.593954. doi: 10.1101/2024.05.13.593954.
Mammalian mRNAs possess an N7-methylguanosine (m7G) cap and 2'O methylation of the initiating nucleotide at their 5' end, whereas certain viral RNAs lack these characteristic features. The human antiviral restriction factor IFIT1 recognizes and binds to specific viral RNAs that lack the 5' features of host mRNAs, resulting in targeted suppression of viral RNA translation. This interaction imposes significant host-driven evolutionary pressures on viruses, and many viruses have evolved mechanisms to evade the antiviral action of human IFIT1. However, little is known about the virus-driven pressures that may have shaped the antiviral activity of IFIT1 genes across mammals. Here, we take an evolution-guided approach to show that the IFIT1 gene is rapidly evolving in multiple mammalian clades, with positive selection acting upon several residues in distinct regions of the protein. In functional assays with 39 IFIT1s spanning diverse mammals, we demonstrate that IFIT1 exhibits a range of antiviral phenotypes, with many orthologs lacking antiviral activity against viruses that are strongly suppressed by other IFIT1s. We further show that IFIT1s from human and a bat, the black flying fox, inhibit Venezuelan equine encephalitis virus (VEEV) and strongly bind to Cap0 RNAs. Unexpectedly, chimpanzee IFIT1, which differs from human IFIT1 by only 8 amino acids, does not inhibit VEEV infection and exhibits minimal Cap0 RNA-binding. In mutagenesis studies, we determine that amino acids 364 and 366, the latter of which is rapidly evolving, are sufficient to confer the differential anti-VEEV activity between human and chimpanzee IFIT1. These data suggest that virus-host genetic conflicts have influenced the antiviral specificity of IFIT1 across diverse mammalian orders.
哺乳动物的信使核糖核酸（mRNA）在其5'端具有N7-甲基鸟苷（m7G）帽以及起始核苷酸的2'O甲基化，而某些病毒RNA缺乏这些特征。人类抗病毒限制因子IFIT1识别并结合缺乏宿主mRNA 5'特征的特定病毒RNA，从而靶向抑制病毒RNA翻译。这种相互作用给病毒带来了巨大的宿主驱动的进化压力，许多病毒已经进化出逃避人类IFIT1抗病毒作用的机制。然而，对于可能塑造IFIT1基因在整个哺乳动物中的抗病毒活性的病毒驱动压力知之甚少。在这里，我们采用进化引导的方法来表明IFIT1基因在多个哺乳动物进化枝中快速进化，正选择作用于该蛋白质不同区域的几个残基。在对来自不同哺乳动物的39种IFIT1进行的功能测定中，我们证明IFIT1表现出一系列抗病毒表型，许多直系同源物对其他IFIT1强烈抑制的病毒缺乏抗病毒活性。我们进一步表明，来自人类和蝙蝠（黑狐蝠）的IFIT1抑制委内瑞拉马脑炎病毒（VEEV）并与Cap0 RNA强烈结合。出乎意料的是，与人类IFIT1仅相差8个氨基酸的黑猩猩IFIT1不抑制VEEV感染，并且与Cap0 RNA的结合最少。在诱变研究中，我们确定氨基酸364和366（后者正在快速进化）足以赋予人类和黑猩猩IFIT1之间不同的抗VEEV活性。这些数据表明，病毒-宿主基因冲突影响了不同哺乳动物目中IFIT1的抗病毒特异性。
