Institute of Bioorganic Chemistry Polish Academy of Sciences, Zygmunta Noskowskiego 12/14, 61-704 Poznań, Poland.
Viruses. 2020 Oct 30;12(11):1232. doi: 10.3390/v12111232.
Here we present a set of new structural elements formed within the open reading frame of the virus, which are highly probable, evolutionarily conserved and may interact with host proteins. This work focused on the coding regions of the CVB3 genome (particularly the V4-, V1-, 2C-, and 3D-coding regions), which, with the exception of the -acting replication element (CRE), have not yet been subjected to experimental analysis of their structures. The SHAPE technique, chemical modification with DMS and RNA cleavage with Pb, were performed in order to characterize the RNA structure. The experimental results were used to improve the computer prediction of the structural models, whereas a phylogenetic analysis was performed to check universality of the newly identified structural elements for twenty CVB3 genomes and 11 other enteroviruses. Some of the RNA motifs turned out to be conserved among different enteroviruses. We also observed that the 3'-terminal region of the genome tends to dimerize in a magnesium concentration-dependent manner. RNA affinity chromatography was used to confirm RNA-protein interactions hypothesized by database searches, leading to the discovery of several interactions, which may be important for virus propagation.
在这里，我们提出了一组在病毒开放阅读框内形成的新结构元件，这些元件高度可能是进化保守的，并且可能与宿主蛋白相互作用。这项工作集中在 CVB3 基因组的编码区（特别是 V4-、V1-、2C-和 3D-编码区），除了 - 作用复制元件（CRE）之外，这些结构尚未经过实验分析。我们使用 SHAPE 技术、DMS 化学修饰和 Pb 切割 RNA 来对 RNA 结构进行了表征。实验结果用于改进结构模型的计算机预测，而系统发育分析则用于检查二十种 CVB3 基因组和十一种其他肠道病毒中新鉴定的结构元件的普遍性。一些 RNA 基序在不同的肠道病毒中是保守的。我们还观察到，基因组的 3'-末端区域倾向于在镁浓度依赖性的方式下二聚化。RNA 亲和层析用于验证数据库搜索假设的 RNA-蛋白相互作用，导致发现了几个可能对病毒传播很重要的相互作用。
