Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
Nat Commun. 2021 Nov 5;12(1):6417. doi: 10.1038/s41467-021-26616-x.
To understand how RNA dynamics is regulated and connected to its function, we investigate the folding, conformational dynamics and robustness of Xrn1 resistance of a set of flaviviral xrRNAs using SAXS, smFRET and in vitro enzymatic assays. Flaviviral xrRNAs form discrete ring-like 3D structures, in which the length of a conserved long-range pseudoknot (PK2) ranges from 2 bp to 7 bp. We find that xrRNAs' folding, conformational dynamics and Xrn1 resistance are strongly correlated and highly Mg-dependent, furthermore, the Mg-dependence is modulated by PK2 length variations. xrRNAs with long PK2 require less Mg to stabilize their folding, exhibit reduced conformational dynamics and strong Xrn1 resistance even at low Mg, and tolerate mutations at key tertiary motifs at high Mg, which generally are destructive to xrRNAs with short PK2. These results demonstrate an unusual regulatory mechanism of RNA dynamics providing insights into the functions and future biomedical applications of xrRNAs.
为了理解 RNA 动态如何受到调控以及与其功能的关联，我们利用 SAXS、smFRET 和体外酶测定法研究了一组黄病毒 xrRNAs 的折叠、构象动力学和 Xrn1 抗性。黄病毒 xrRNAs 形成离散的环状 3D 结构，其中保守的长程假结（PK2）的长度范围为 2bp 至 7bp。我们发现 xrRNAs 的折叠、构象动力学和 Xrn1 抗性具有很强的相关性，且高度依赖于 Mg，此外，PK2 长度的变化会调节 Mg 的依赖性。具有长 PK2 的 xrRNAs 需要更少的 Mg 来稳定其折叠，表现出较低的构象动力学和较强的 Xrn1 抗性，即使在低 Mg 下也是如此，并且能够在高 Mg 下耐受关键的三级基序突变，而这些突变通常对具有短 PK2 的 xrRNAs 具有破坏性。这些结果表明了一种 RNA 动力学的调节机制，为 xrRNAs 的功能和未来的生物医学应用提供了新的见解。
