Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA.
RNA BioScience Initiative, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA.
RNA. 2021 Jan;27(1):54-65. doi: 10.1261/rna.077065.120. Epub 2020 Oct 1.
During infection by a flavivirus (FV), cells accumulate noncoding subgenomic flavivirus RNAs (sfRNAs) that interfere with several antiviral pathways. These sfRNAs are formed by structured RNA elements in the 3' untranslated region (UTR) of the viral genomic RNA, which block the progression of host cell exoribonucleases that have targeted the viral RNA. Previous work on these exoribonuclease-resistant RNAs (xrRNAs) from mosquito-borne FVs revealed a specific three-dimensional fold with a unique topology in which a ring-like structure protectively encircles the 5' end of the xrRNA. Conserved nucleotides make specific tertiary interactions that support this fold. Examination of more divergent FVs reveals differences in their 3' UTR sequences, raising the question of whether they contain xrRNAs and if so, how they fold. To answer this, we demonstrated the presence of an authentic xrRNA in the 3' UTR of the Tamana bat virus (TABV) and solved its structure by X-ray crystallography. The structure reveals conserved features from previously characterized xrRNAs, but in the TABV version these features are created through a novel set of tertiary interactions not previously seen in xrRNAs. This includes two important A-C interactions, four distinct backbone kinks, several ordered Mg ions, and a C-G-C base triple. The discovery that the same overall architecture can be achieved by very different sequences and interactions in distantly related flaviviruses provides insight into the diversity of this type of RNA and will inform searches for undiscovered xrRNAs in viruses and beyond.
在黄病毒（FV）感染过程中，细胞会积累非编码亚基因组黄病毒 RNA（sfRNA），这些 RNA 会干扰几种抗病毒途径。这些 sfRNA 是由病毒基因组 RNA 的 3'非翻译区（UTR）中的结构 RNA 元件形成的，这些元件阻止了靶向病毒 RNA 的宿主细胞外切核酸酶的进展。先前对来自蚊媒 FV 的这些抗外切核酸酶 RNA（xrRNA）的研究揭示了一种具有独特拓扑结构的特定三维折叠结构，其中环状结构保护性地环绕 xrRNA 的 5'端。保守核苷酸形成特定的三级相互作用，支持这种折叠。对更具差异性的 FV 的检查显示出其 3'UTR 序列的差异，这引发了一个问题，即它们是否包含 xrRNA，如果包含，它们是如何折叠的。为了解决这个问题，我们证明了 Tamana 蝙蝠病毒（TABV）的 3'UTR 中存在真正的 xrRNA，并通过 X 射线晶体学解决了其结构。该结构揭示了先前表征的 xrRNA 中的保守特征，但在 TABV 版本中，这些特征是通过一组以前在 xrRNA 中未见过的新型三级相互作用产生的。这包括两个重要的 A-C 相互作用、四个不同的骨架弯曲、几个有序的 Mg 离子和一个 C-G-C 碱基三链。发现结构非常不同的序列和相互作用在远缘黄病毒中可以实现相同的总体结构，这为这种 RNA 的多样性提供了深入的了解，并将为在病毒内外寻找未被发现的 xrRNA 提供信息。
