Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
Nat Chem Biol. 2018 Sep;14(9):887-894. doi: 10.1038/s41589-018-0114-4. Epub 2018 Aug 17.
The ykkC family of bacterial riboswitches combines several widespread classes that have similar secondary structures and consensus motifs but control different genes in response to different cellular metabolites. Here we report the crystal structures of two distinct ykkC riboswitches specifically bound to their cognate ligand ppGpp, a second messenger involved in stress response, or PRPP, a precursor in purine biosynthesis. Both RNAs adopt similar structures and contain a conserved core previously observed in the guanidine-specific ykkC riboswitch. However, ppGpp and PRPP riboswitches uniquely employ an additional helical element that joins the ends of the ligand-sensing domains and creates a tunnel for direct and Mg-mediated binding of ligands. Mutational and footprinting experiments highlight the importance of conserved nucleotides forming the tunnel and long-distance contacts for ligand binding and genetic response. Our work provides new insights into the specificity of riboswitches and gives a unique opportunity for future studies of RNA evolution.
细菌的 ykkC 型核糖体开关家族结合了几个广泛存在的类别，这些类别具有相似的二级结构和共识基序，但能响应不同的细胞代谢物来控制不同的基因。在这里，我们报告了两种不同的 ykkC 核糖体开关的晶体结构，它们分别与它们的同源配体 ppGpp（一种参与应激反应的第二信使）或 PRPP（嘌呤生物合成的前体）特异性结合。这两种 RNA 采用了相似的结构，并且包含了先前在胍特异性 ykkC 核糖体开关中观察到的保守核心。然而，ppGpp 和 PRPP 核糖体开关独特地利用了一个额外的螺旋元件，该元件连接了配体感应结构域的末端，并为配体的直接和 Mg 介导的结合创建了一个隧道。突变和足迹实验强调了形成隧道的保守核苷酸以及长距离接触对于配体结合和遗传反应的重要性。我们的工作为核糖体开关的特异性提供了新的见解，并为未来的 RNA 进化研究提供了独特的机会。
