To Knot or Not to Knot: Multiple Conformations of the SARS-CoV-2 Frameshifting RNA Element
To Knot or Not to Knot: Multiple Conformations of the SARS-CoV-2 Frameshifting RNA Element
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DOI：
10.1021/jacs.1c03003
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发表时间：
2021-07-20
影响因子：
15
通讯作者：
Laederach, Alain
中科院分区：
文献类型：
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作者：
Schlick, Tamar;Zhu, Qiyao;Laederach, Alain
SARS-CoV-2移码RNA元件（FSE）是针对Covid-19的治疗干预的极好靶点。这个小的基因元件采用一种移位机制，在编码病毒多聚蛋白的开放阅读框架1a和1b之间的翻译过程中暂停和回溯核糖体。对这一过程的任何干扰都会对病毒的复制和繁殖产生深远的影响。精确定位FSE所适应的结构以及框架转换中涉及的相关结构转换一直是一个挑战。使用我们的基于图论的建模工具来表示RNA二级结构，“RAG”（RNA-As-Graphs）和化学结构探测实验，我们表明，长期以来被认为是主导结构的3-茎H型假结（3_6对偶图）具有可行的替代方案，HL型3-茎假结（3_3）用于更长的构建体。此外，未打结的3向连接RNA（3_5）作为次要构象出现。这三种构象共享茎1和3，而不同的茎2可能参与构象转换，并可能在翻译过程中与核糖体相关。对于全长基因组，茎环基序（2_2）可能与这些形式竞争。这些结构和机制的见解推进了我们对SARS-CoV-2移码过程和伴随的病毒生命周期的理解，并指出了三种治疗干预的途径。
The SARS-CoV-2 frameshifting RNA element (FSE) is an excellent target for therapeutic intervention against Covid-19. This small gene element employs a shifting mechanism to pause and backtrack the ribosome during translation between Open Reading Frames 1a and 1b, which code for viral polyproteins. Any interference with this process has a profound effect on viral replication and propagation. Pinpointing the structures adapted by the FSE and associated structural transformations involved in frameshifting has been a challenge. Using our graph-theory-based modeling tools for representing RNA secondary structures, "RAG" (RNA-As-Graphs), and chemical structure probing experiments, we show that the 3-stem H-type pseudoknot (3_6 dual graph), long assumed to be the dominant structure, has a viable alternative, an HL-type 3-stem pseudoknot (3_3) for longer constructs. In addition, an unknotted 3-way junction RNA (3_5) emerges as a minor conformation. These three conformations share Stems 1 and 3, while the different Stem 2 may be involved in a conformational switch and possibly associations with the ribosome during translation. For full-length genomes, a stem-loop motif (2_2) may compete with these forms. These structural and mechanistic insights advance our understanding of the SARS-CoV-2 frameshifting process and concomitant virus life cycle, and point to three avenues of therapeutic intervention.