Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan, Department of Life Science, National Taiwan University, Taipei 10617, Taiwan and Genome and Systems Biology Degree Program, National Taiwan University, Taipei 10617, Taiwan.
Nucleic Acids Res. 2014 Apr;42(7):4505-15. doi: 10.1093/nar/gkt1396. Epub 2014 Jan 22.
Folding messenger RNA into specific structures is a common regulatory mechanism involved in translation. In Escherichia coli, the operator of the rpsO gene transcript folds into a pseudoknot or double-hairpin conformation. S15, the gene product, binds only to the pseudoknot, thereby repressing its own synthesis when it is present in excess in the cell. The two RNA conformations have been proposed to exist in equilibrium. However, it remained unclear how structural changes can be achieved between these two topologically distinct conformations. We used optical tweezers to study the structural dynamics and rearrangements of the rpsO operator RNA at the single-molecule level. We discovered that the two RNA structures can be interchanged spontaneously and the pseudoknot can exist in conformations that exhibit various levels of stability. Conversion from the double hairpin to a pseudoknot through potential hairpin-hairpin interactions favoured the high-stability conformation. By contrast, mutations that blocked the formation of a hairpin typically resulted in alternative low-stability pseudoknots. These results demonstrate that specific tertiary interactions of RNA can be established and modulated based on the interactions and rearrangements between secondary structural components. Our findings provide new insight into the RNA folding pathway that leads to a regulatory conformation for target protein binding.
将信使 RNA 折叠成特定的结构是一种常见的翻译调控机制。在大肠杆菌中，rpsO 基因转录本的操纵子折叠成假结或双发夹构象。S15 是该基因的产物，仅与假结结合，从而在细胞中过量存在时抑制自身的合成。这两种 RNA 构象被认为处于平衡状态。然而，目前尚不清楚如何在这两种拓扑结构不同的构象之间实现结构变化。我们使用光学镊子在单分子水平上研究了 rpsO 操纵子 RNA 的结构动力学和重排。我们发现这两种 RNA 结构可以自发地相互转换，并且假结可以存在各种稳定性水平的构象。通过潜在的发夹-发夹相互作用从双链发夹转化为假结有利于高稳定性构象。相比之下，阻止发夹形成的突变通常会导致替代的低稳定性假结。这些结果表明，特定的 RNA 三级相互作用可以基于二级结构组件之间的相互作用和重排来建立和调节。我们的发现为导致靶蛋白结合的调节构象的 RNA 折叠途径提供了新的见解。
