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

摘要 RNA病毒基因组中的结构元件在感染过程中起着关键作用。以下是例子 抗核酸外切酶RNA(XrRNAs)，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的生产。黄病毒XrRNA的详细三维结构研究 植物病毒的一个子集导致了一种机制模型，在该模型中，xrRNA通过一种 支撑在蛋白质表面的环状结构。最近，一个新的xrRNA类在 更远的亲缘关系和多样化的甲型病毒超群，其中包括几种重要的人类病原体。 最初在本尼病毒科和其他几个病毒家族中发现的这种xrRNA与那些没有明显的相似之处 以前研究过的。因此，我们不知道它如何折叠，如何阻止宿主核酸外切酶，以及如何 它是分布广泛的。这些知识上的根本差距阻碍了理解什么可以 在甲型病毒超群和更远的地方是一种普遍和重要的RNA元素。另外，因为 XrRNAs已经在几个主要的病毒超家族中被发现，它们可能代表着一个 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 来自Benyviridae的病毒是至关重要的。在这里，我们建议解决这些关键的未知因素，并通过以下方式支持未来的研究 追求两个目标。首先，我们将通过新的核酸外切酶耐药的结构基础来确定 本氏病毒科的xrRNA纲。这一目标将使用先进的结构生物学方法不仅告知 关于抵抗退化的机制，而且还能够准确地搜索相似的基序 在整个甲型病毒超群中。其次，我们将确定xrRNA折叠的分布 病毒世界中的本尼病毒科病毒。这一目标结合了计算和生物化学方法，这 之前已经成功地描述了在当时也被认为是“外来”的xrRNA。 探索这种新类别的xrRNAs有多普遍，有可能阐明 不同但相关的甲型病毒超群成员，扩大我们对病毒世界中RNA结构的知识， 并推动未来对xrRNAs在病毒诱导的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.