Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, A-6020 Innsbruck, Austria.
Proc Natl Acad Sci U S A. 2013 Aug 27;110(35):E3256-64. doi: 10.1073/pnas.1304585110. Epub 2013 Aug 12.
Structural and dynamic features of RNA folding landscapes represent critical aspects of RNA function in the cell and are particularly central to riboswitch-mediated control of gene expression. Here, using single-molecule fluorescence energy transfer imaging, we explore the folding dynamics of the preQ1 class II riboswitch, an upstream mRNA element that regulates downstream encoded modification enzymes of queuosine biosynthesis. For reasons that are not presently understood, the classical pseudoknot fold of this system harbors an extra stem-loop structure within its 3'-terminal region immediately upstream of the Shine-Dalgarno sequence that contributes to formation of the ligand-bound state. By imaging ligand-dependent preQ1 riboswitch folding from multiple structural perspectives, we reveal that the extra stem-loop strongly influences pseudoknot dynamics in a manner that decreases its propensity to spontaneously fold and increases its responsiveness to ligand binding. We conclude that the extra stem-loop sensitizes this RNA to broaden the dynamic range of the ON/OFF regulatory switch.
RNA 折叠景观的结构和动态特征代表了 RNA 在细胞中功能的关键方面，特别是对核酶介导的基因表达调控至关重要。在这里，我们使用单分子荧光能量转移成像技术，研究了 preQ1 类 II 核酶的折叠动力学，这是一种上游 mRNA 元件，可调节 queuosine 生物合成的下游编码修饰酶。由于目前尚不清楚的原因，该系统的经典假结折叠在其 3' 末端区域紧邻 Shine-Dalgarno 序列处具有额外的茎环结构，有助于配体结合状态的形成。通过从多个结构角度成像配体依赖性 preQ1 核酶折叠，我们揭示了额外的茎环结构以降低其自发折叠倾向并增加其对配体结合响应的方式强烈影响假结动力学。我们得出结论，额外的茎环结构使这种 RNA 更加敏感，从而拓宽了 ON/OFF 调节开关的动态范围。
