Department of Computer Science, University of Victoria, Victoria, British Columbia, Canada.
Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada.
PLoS Comput Biol. 2023 Feb 28;19(2):e1010922. doi: 10.1371/journal.pcbi.1010922. eCollection 2023 Feb.
Multiple coronaviruses including MERS-CoV causing Middle East Respiratory Syndrome, SARS-CoV causing SARS, and SARS-CoV-2 causing COVID-19, use a mechanism known as -1 programmed ribosomal frameshifting (-1 PRF) to replicate. SARS-CoV-2 possesses a unique RNA pseudoknotted structure that stimulates -1 PRF. Targeting -1 PRF in SARS-CoV-2 to impair viral replication can improve patients' prognoses. Crucial to developing these therapies is understanding the structure of the SARS-CoV-2 -1 PRF pseudoknot. Our goal is to expand knowledge of -1 PRF structural conformations. Following a structural alignment approach, we identify similarities in -1 PRF pseudoknots of SARS-CoV-2, SARS-CoV, and MERS-CoV. We provide in-depth analysis of the SARS-CoV-2 and MERS-CoV -1 PRF pseudoknots, including reference and noteworthy mutated sequences. To better understand the impact of mutations, we provide insight on -1 PRF pseudoknot sequence mutations and their effect on resulting structures. We introduce Shapify, a novel algorithm that given an RNA sequence incorporates structural reactivity (SHAPE) data and partial structure information to output an RNA secondary structure prediction within a biologically sound hierarchical folding approach. Shapify enhances our understanding of SARS-CoV-2 -1 PRF pseudoknot conformations by providing energetically favourable predictions that are relevant to structure-function and may correlate with -1 PRF efficiency. Applied to the SARS-CoV-2 -1 PRF pseudoknot, Shapify unveils previously unknown paths from initial stems to pseudoknotted structures. By contextualizing our work with available experimental data, our structure predictions motivate future RNA structure-function research and can aid 3-D modeling of pseudoknots.
多种冠状病毒，包括导致中东呼吸综合征的 MERS-CoV、导致 SARS 的 SARS-CoV 和导致 COVID-19 的 SARS-CoV-2，都使用一种称为 -1 核糖体移码（-1 PRF）的机制进行复制。SARS-CoV-2 具有独特的 RNA 假结结构，可刺激 -1 PRF。靶向 SARS-CoV-2 的 -1 PRF 以损害病毒复制可以改善患者的预后。开发这些疗法的关键是了解 SARS-CoV-2 -1 PRF 假结的结构。我们的目标是扩展 -1 PRF 结构构象的知识。通过结构比对方法，我们确定了 SARS-CoV-2、SARS-CoV 和 MERS-CoV 的 -1 PRF 假结之间的相似性。我们对 SARS-CoV-2 和 MERS-CoV -1 PRF 假结进行了深入分析，包括参考序列和值得注意的突变序列。为了更好地理解突变的影响，我们提供了关于 -1 PRF 假结序列突变及其对产生结构的影响的见解。我们引入了 Shapify，这是一种新算法，它可以根据 RNA 序列，将结构反应性（SHAPE）数据和部分结构信息整合到一个生物合理的分层折叠方法中，输出 RNA 二级结构预测。Shapify 通过提供与结构功能相关且可能与 -1 PRF 效率相关的能量有利预测，增强了我们对 SARS-CoV-2 -1 PRF 假结构象的理解。应用于 SARS-CoV-2 -1 PRF 假结，Shapify 揭示了从初始茎到假结结构的先前未知路径。通过将我们的工作与可用的实验数据联系起来，我们的结构预测为未来的 RNA 结构-功能研究提供了动力，并有助于假结的 3-D 建模。
