The adenine-sensing riboswitch from the Gram-negative bacterium Vibrio vulnificus is an RNA-based gene regulatory element that acts in response to both its cognate low-molecular weight ligand and temperature. The combined sensitivity to environmental temperature and ligand concentration is maintained by an equilibrium of three distinct conformations involving two ligand-free states and one ligand-bound state. The key structural element that undergoes refolding in the ligand-free states comprises a 35-nucleotide temperature response module. Here, we present the structural characterization of this temperature response module. We employ high-resolution NMR spectroscopy and photocaged RNAs as molecular probes to decipher the kinetic and thermodynamic framework of the secondary structure transition in the apo state of the riboswitch. We propose a model for the transition state adopted during the thermal refolding of the temperature response module that connects two mutually exclusive long-lived and stable conformational states. This transition state is characterized by a comparatively low free activation enthalpy. A pseudoknot conformation in the transition state, as commonly seen in RNA refolding, is therefore unlikely. More likely, the transition state of the adenine-sensing riboswitch temperature response module features a linear conformation.

中文翻译：

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通过线性过渡状态重新折叠可实现平移核糖开关的快速温度适应

革兰氏阴性细菌弧菌弧菌的腺嘌呤敏感核糖开关是基于RNA的基因调控元件，可同时响应其同源的低分子量配体和温度。对环境温度和配体浓度的综合敏感性通过涉及两个无配体状态和一个配体结合状态的三个不同构象的平衡来维持。在无配体状态下重新折叠的关键结构元件包括35个核苷酸的温度响应模块。在这里，我们介绍该温度响应模块的结构特征。我们采用高分辨率的核磁共振波谱和光笼RNA作为分子探针来解密核糖开关的载脂蛋白状态二级结构转变的动力学和热力学框架。我们提出了一个温度响应模块在热折叠过程中采用的过渡状态模型，该模型将两个互斥的长寿命和稳定构象状态连接起来。该过渡态的特征在于相对较低的游离活化焓。因此，如在RNA重折叠中常见的那样，过渡状态下的假结构象不太可能。腺嘌呤感应核糖开关温度响应模块的过渡状态更可能具有线性构象。