Rieder Renate, Lang Kathrin, Graber Dagmar, Micura Ronald
Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), Leopold Franzens University, Innrain 52a, Innsbruck, Austria.
Chembiochem. 2007 May 25;8(8):896-902. doi: 10.1002/cbic.200700057.
By using a structure-based fluorescence spectroscopic approach, we have examined the folding of an adenine-responsive riboswitch that regulates translation initiation. We observed adaptive recognition of the ligand for the aptamer domain of adenosine deaminase (add) mRNA from Vibrio vulnificus, and revealed pronounced conformational changes even in the preorganized loop-loop region that is distant from the binding site. Importantly, the full-length riboswitch domain, which has a potential translational repressor stem is able to form a binary complex with adenine, and does not act as a folding trap to inhibit binding. The aptamer that is extended by the expression platform therefore remains fully responsive to its ligand; this is in contrast to the previously investigated pbuE A-riboswitch, which becomes trapped in a nonresponsive terminator fold. Consequently, the latter must employ complex response mechanisms, such as operating in kinetic-control mode or using transcriptional pausing, to provide time for the aptamer portion to fold and to bind. The different behavior of the riboswitches can be rationalized by their distinct sequence interface between the aptamer and expression platform. For the add A-riboswitch, our data suggest a thermodynamically driven response mechanism.
通过使用基于结构的荧光光谱方法，我们研究了一种调节翻译起始的腺嘌呤响应核糖开关的折叠。我们观察到来自创伤弧菌的腺苷脱氨酶（add）mRNA适配体结构域对配体的适应性识别，并揭示了即使在远离结合位点的预组织环-环区域也有明显的构象变化。重要的是，具有潜在翻译阻遏茎的全长核糖开关结构域能够与腺嘌呤形成二元复合物，并且不会作为折叠陷阱抑制结合。因此，由表达平台延伸的适配体对其配体仍保持完全响应；这与先前研究的pbuE A型核糖开关相反，后者被困在无反应的终止子折叠中。因此，后者必须采用复杂的响应机制，如在动力学控制模式下操作或使用转录暂停，为适配体部分的折叠和结合提供时间。核糖开关的不同行为可以通过它们在适配体和表达平台之间独特的序列界面来解释。对于add A型核糖开关，我们的数据表明存在一种热力学驱动的响应机制。
