Xiao Wenwen, Liu Guangfeng, Chen Ting, Zhang Yunlong, Ke Ailong, Cai Rujie, Lu Changrui
College of Biological Science and Medical Engineering, Donghua University, Shanghai 201620, China.
Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.
ACS Chem Biol. 2025 May 16;20(5):1010-1019. doi: 10.1021/acschembio.4c00715. Epub 2025 Apr 19.
The riboswitch regulates and gene expression on the translation level. It contains two tandem domains regulated by Mn and pH. This study investigates the tertiary structure and conformational dynamics of the riboswitch using a combination of crystallography, small-angle X-ray scattering (SAXS), and chemical probing. Our crystal structure of the aptamer domain at 3.8 Å reveals that the riboswitch aptamer domain forms a coaxial superhelix containing three helices connected by a three-way junction (3WJ), with L1 and L3 creating a pocket-like structure that binds Mg and Mn. SHAPE probing and SAXS show that the riboswitch maintains a consistent conformation across pH conditions without Mn but exhibits significant conformational changes under alkaline conditions when Mn is present. These findings align with our proposed model, where Mn binding induces a transition from an "OFF" to an "ON" state in alkaline conditions, while the Mn remains bound to the aptamer independent of pH. This regulatory mechanism allows for more sophisticated control of gene expression, providing a finely tuned adaptive response to environmental changes.
核糖开关在翻译水平上调控基因表达。它包含两个受锰和pH值调控的串联结构域。本研究结合晶体学、小角X射线散射（SAXS）和化学探针技术，对核糖开关的三级结构和构象动力学进行了研究。我们得到的适体结构域在3.8 Å分辨率下的晶体结构表明，核糖开关适体结构域形成了一个同轴超螺旋，其中包含由一个三向连接点（3WJ）连接的三个螺旋，L1和L3形成了一个结合镁和锰的口袋状结构。SHAPE探针和SAXS结果表明，在没有锰的情况下，核糖开关在不同pH条件下保持一致的构象，但在有锰存在的碱性条件下会发生显著的构象变化。这些发现与我们提出的模型一致，即锰结合在碱性条件下诱导核糖开关从“关闭”状态转变为“开启”状态，而锰与适体的结合不依赖于pH值。这种调控机制允许对基因表达进行更复杂的控制，为对环境变化提供精细调节的适应性反应。
