Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER-R)-Raebareli, Lucknow 226002, India
Department of Chemistry, New York University, New York, New York 10003, USA.
RNA. 2024 Oct 16;30(11):1437-1450. doi: 10.1261/rna.080035.124.
The SARS-CoV-2 frameshifting element (FSE) has been intensely studied and explored as a therapeutic target for coronavirus diseases, including COVID-19. Besides the intriguing virology, this small RNA is known to adopt many length-dependent conformations, as verified by multiple experimental and computational approaches. However, the role these alternative conformations play in the frameshifting mechanism and how to quantify this structural abundance has been an ongoing challenge. Here, we show by DMS and dual-luciferase functional assays that previously predicted FSE mutants (using the RAG graph theory approach) suppress structural transitions and abolish frameshifting. Furthermore, correlated mutation analysis of DMS data by three programs (DREEM, DRACO, and DANCE-MaP) reveals important differences in their estimation of specific RNA conformations, suggesting caution in the interpretation of such complex conformational landscapes. Overall, the abolished frameshifting in three different mutants confirms that all alternative conformations play a role in the pathways of ribosomal transition.
SARS-CoV-2 框架移位元件（FSE）已被深入研究和探索，作为包括 COVID-19 在内的冠状病毒疾病的治疗靶点。除了引人入胜的病毒学之外，这种小 RNA 已知会采用许多依赖长度的构象，这已通过多种实验和计算方法得到证实。然而，这些替代构象在框架移位机制中所扮演的角色，以及如何量化这种结构丰度，一直是一个持续的挑战。在这里，我们通过 DMS 和双荧光素酶功能测定表明，以前使用 RAG 图论方法预测的 FSE 突变体抑制结构转变并消除框架移位。此外，通过三个程序（DREEM、DRACO 和 DANCE-MaP）对 DMS 数据进行相关突变分析，揭示了它们对特定 RNA 构象估计的重要差异，这表明在解释这种复杂的构象景观时应谨慎。总体而言，三种不同突变体中框架移位的消除证实了所有替代构象都在核糖体转变途径中发挥作用。
