Smith-Peter Erich, Lamontagne Anne-Marie, Lafontaine Daniel A
a Department of Biology ; Faculty of Science, RNA Group, Université de Sherbrooke , Sherbrooke ; Quebec , Canada.
RNA Biol. 2015;12(12):1372-82. doi: 10.1080/15476286.2015.1094603.
Riboswitches regulate gene expression by rearranging their structure upon metabolite binding. The lysine-sensing lysC riboswitch is a rare example of an RNA aptamer organized around a 5-way helical junction in which ligand binding is performed exclusively through nucleotides located at the junction core. We have probed whether the nucleotides involved in ligand binding play any role in the global folding of the riboswitch. As predicted, our findings indicate that ligand-binding residues are critical for the lysine-dependent gene regulation mechanism. We also find that these residues are not important for the establishment of key magnesium-dependent tertiary interactions, suggesting that folding and ligand recognition are uncoupled in this riboswitch for the formation of specific interactions. However, FRET assays show that lysine binding results in an additional conformational change, indicating that lysine binding may also participate in a specific folding transition. Thus, in contrast to helical junctions being primary determinants in ribozymes and rRNA folding, we speculate that the helical junction of the lysine-sensing lysC riboswitch is not employed as structural a scaffold to direct global folding, but rather has a different role in establishing RNA-ligand interactions required for riboswitch regulation. Our work suggests that helical junctions may adopt different functions such as the coordination of global architecture or the formation of specific ligand binding site.
核糖开关通过在代谢物结合时重新排列其结构来调节基因表达。赖氨酸感应型lysC核糖开关是围绕一个5向螺旋连接点组织的RNA适体的罕见例子，其中配体结合仅通过位于连接点核心的核苷酸进行。我们探究了参与配体结合的核苷酸在核糖开关的整体折叠中是否起任何作用。正如所预测的，我们的研究结果表明，配体结合残基对于赖氨酸依赖性基因调控机制至关重要。我们还发现这些残基对于建立关键的镁依赖性三级相互作用并不重要，这表明在这个核糖开关中，折叠和配体识别在形成特定相互作用时是解偶联的。然而，荧光共振能量转移（FRET）分析表明，赖氨酸结合会导致额外的构象变化，这表明赖氨酸结合也可能参与特定的折叠转变。因此，与螺旋连接点是核酶和rRNA折叠的主要决定因素不同，我们推测赖氨酸感应型lysC核糖开关的螺旋连接点并非作为指导整体折叠的结构支架，而是在建立核糖开关调控所需的RNA-配体相互作用中具有不同的作用。我们的工作表明，螺旋连接点可能具有不同的功能，如整体结构的协调或特定配体结合位点的形成。
