Department of Theoretical Physics, Jožef Stefan Institute, Ljubljana, Slovenia; Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia.
Department of Theoretical Physics, Jožef Stefan Institute, Ljubljana, Slovenia.
Biophys J. 2024 Oct 1;123(19):3397-3407. doi: 10.1016/j.bpj.2024.08.004. Epub 2024 Aug 8.
Many functions of ribonucleic acid (RNA) rely on its ability to assume specific sequence-structure motifs. Packaging signals found in certain RNA viruses are one such prominent example of functional RNA motifs. These signals are short hairpin loops that interact with coat proteins and drive viral self-assembly. As they are found in different positions along the much longer genomic RNA, the formation of their correct structure occurs as a part of a larger context. Any changes to this context can consequently lead to changes in the structure of the motifs themselves. In fact, previous studies have shown that structure and function of RNA motifs can be highly context sensitive to the flanking sequence surrounding them. However, in what ways different flanking sequences influence the structure of an RNA motif they surround has yet to be studied in detail. We focus on a hairpin-rich region of the RNA genome of bacteriophage MS2-a well-studied RNA virus with a wide potential for use in biotechnology-and systematically examine context-dependent structural stability of 14 previously identified hairpin motifs, which include putative and confirmed packaging signals. Combining secondary and tertiary RNA structure prediction of the hairpin motifs placed in different contexts, ranging from the native genomic sequence to random RNA sequences and unstructured poly-U sequences, we determine different measures of motif structural stability. In this way, we show that while some motif structures can be stable in any context, others require specific context provided by the genome. Our results demonstrate the importance of context in RNA structure formation and how changes in the flanking sequence of an RNA motif sometimes lead to drastic changes in its structure. Structural stability of a motif in different contexts could provide additional insights into its functionality as well as assist in determining whether it remains functional when intentionally placed in other contexts.
许多 RNA（核糖核酸）的功能都依赖于其形成特定序列结构基序的能力。某些 RNA 病毒中的包装信号就是功能 RNA 基序的一个突出例子。这些信号是短发夹环，与外壳蛋白相互作用并驱动病毒自我组装。由于它们存在于基因组 RNA 更长的不同位置，因此正确结构的形成是更大上下文的一部分。这种上下文的任何变化都会导致基序本身结构的变化。事实上，先前的研究表明，RNA 基序的结构和功能对其周围的侧翼序列高度敏感。然而，不同侧翼序列如何影响它们所包围的 RNA 基序的结构，尚未得到详细研究。我们专注于噬菌体 MS2 的 RNA 基因组中的一个富含发夹的区域——一种研究广泛的 RNA 病毒，具有广泛的生物技术应用潜力——并系统地检查了 14 个先前确定的发夹基序的结构稳定性，这些基序包括推测的和已确认的包装信号。我们将发夹基序的二级和三级 RNA 结构预测结合起来，这些基序被放置在不同的环境中，从原始基因组序列到随机 RNA 序列和无结构的聚 U 序列，我们确定了基序结构稳定性的不同衡量标准。通过这种方式，我们表明虽然一些基序结构在任何环境中都可以稳定，但其他结构则需要基因组提供的特定环境。我们的研究结果表明了上下文在 RNA 结构形成中的重要性，以及 RNA 基序侧翼序列的变化如何导致其结构的剧烈变化。在不同环境中基序的结构稳定性可以为其功能提供更多的见解，并有助于确定当它被有意放置在其他环境中时是否仍然具有功能。
