Structural determinants of viral RNAs resistant to exoribonucleases in the alphavirus supergroup

总结 RNA病毒基因组内的结构元件在感染过程中起着关键作用。实例是 外切核酸酶抗性RNA（xrRNA），其抵抗宿主细胞外切核糖核酸酶的降解，导致 病毒亚基因组RNA的产生。来自黄病毒的xrRNA的详细三维结构研究 和植物病毒的一个子集导致了一种机制模型，其中xrRNA使用一种酶抑制剂阻断酶消化， 环状结构支撑蛋白质表面。最近，一个新的xrRNA类被发现在 更远亲和多样化的甲病毒超组，其中包括几个重要的人类病原体。 最初在Benyviridae和其他几个病毒家族中发现，这种xrRNA与那些 以前研究过。因此，我们不知道它是如何折叠的，它如何阻断宿主核酸外切酶， 它分布广泛。这些知识上的根本差距阻碍了理解什么可以 是甲病毒超组及其他病毒中普遍存在的重要RNA元件。另外由于 在几个主要的病毒超家族中发现了xrRNA，它们可能代表了一个“分子钟”， 可以帮助我们了解病毒的进化和致病性。为此，了解xrRNA的折叠 是至关重要的在这里，我们建议解决这些关键的未知数，并使未来的研究， 追求两个目标。首先，我们将确定核酸外切酶抗性的结构基础， 来自Benyviridae的一类xrRNA。这一目标将使用先进的结构生物学方法，不仅告知 对降解抗性机制的研究，而且能够准确地搜索类似的基序 整个甲病毒超级群体其次，我们将从以下确定xrRNA折叠的分布： 病毒世界中的本尼迪克特病毒科。这一目标结合了计算和生物化学方法， 之前已经成功地表征了当时也被认为是“外来的”xrRNA。 探索这类新的xrRNA的分布范围有可能阐明病毒的生物学 不同但相关的甲病毒超组成员，扩大了我们对病毒世界中RNA结构的了解， 并推动未来对xrRNA在病毒诱导疾病中的作用的研究。

Summary Structured elements within genomes of RNA viruses have critical roles during infection. Examples are exonuclease-resistant RNAs (xrRNAs) that resist degradation by host cellular exoribonucleases, leading to the production of viral subgenomic RNAs. Detailed three-dimensional structural studies of xrRNAs from flaviviruses and a subset of plant viruses led to a mechanistic model in which xrRNAs block enzymatic digestion using a ring-like structure that braces against the protein surface. Very recently, a new xrRNA class was found in the more distantly related and diverse alphavirus supergroup, which includes several important human pathogens. Initially found in the Benyviridae and several other virus families, this xrRNA has no obvious similarity to those previously studied. Thus, we do not know how it folds, how it blocks the host exonuclease, and how widespread it is distributed. These fundamental gaps in knowledge block progress in understanding what could be a pervasive and important RNA element in the alphavirus supergroup and beyond. In addition, because xrRNAs have been found in several major superfamilies of viruses, they may represent a `molecular clock' that could help us understand virus evolution and pathogenicity. To that end, understanding the fold of the xrRNA from Benyviridae is critical. Here, we propose to address these key unknowns and enable future studies by pursuing two aims. First, we will determine the structural basis of exonuclease resistance by the new class of xrRNA from Benyviridae. This aim will use advanced structural biology methods to inform not only on the mechanism for resistance to degradation, but also enable accurate searches for similar motifs throughout the alphavirus supergroup. Second, we will determine the distribution of the xrRNA fold from Benyviridae across the viral world. This aim combines computational and biochemical approaches, which has previously led to successfully characterizing xrRNAs that were also considered `exotic' at the time. Exploring how widespread this new class of xrRNAs is has the potential to illuminate the biology of viruses of diverse but related alphavirus supergroup members, expand our knowledge of RNA structure in the viral world, and motivate futures studies into the roles of xrRNAs in virus-induced disease.