Structure and Function of S-adenosyl-L-methionine Riboswitches

描述（由申请人提供）：核糖开关是识别特定小分子的调控rna，通常是关键代谢物，并在转录或翻译水平上“开关”下游基因表达的开启或关闭。这些短顺式作用RNA元件的发现极大地改变了我们对遗传调控机制的理解。核糖体开关在革兰氏阳性细菌中尤其普遍，例如作为模式生物的枯草芽孢杆菌，但也被发现控制重要病原体的必需基因，如炭疽芽孢杆菌、葡萄球菌、肠球菌、链球菌、李斯特菌、梭状芽孢杆菌和分枝杆菌。这一特点和其他特点吸引了越来越多的关注核糖体开关介导的调节。三种不同类型的s -腺苷蛋氨酸（SAM）核蛋白开关是自然界中最常见的核蛋白开关。这些rna代表了三个独立的进化解决方案，以实现特定的SAM识别。我们最近测定了粪肠杆菌SMK盒和枯草芽孢杆菌S盒两类SAM核糖开关的晶体结构。这些结构揭示了SAM是如何被特异性识别的，但并没有提供足够的证据来支持在以前的遗传和生化研究中观察到的SAM依赖的大构象变化。为了充分了解它们的结构-功能关系和构象动力学，我们建议：(1)了解SMK盒核开关中的配体识别机制。(2)表征无配体的SMK构象并寻找真核生物的核开关。(3)开展化学探测实验，揭示配体诱导的SMK RNA构象动力学

DESCRIPTION (provided by applicant): Riboswitches are regulatory RNAs that recognize specific small molecules, usually key metabolites, and "switch" downstream gene expression on or off at either the transcriptional or translational level. The discovery of these short cis-acting RNA elements has drastically changed our understanding of genetic regulatory mechanisms. Riboswitches are especially prevalent in Gram-positive bacteria, exemplified by Bacillus subtilis as a model organism, but are also found to control essential genes in important pathogens such as Bacillus anthracis, Staphylococcus, Enterococcus, Streptococcus, Listeria, Clostridium, and Mycobacterium. This and other characteristics have attracted increasing attention to riboswitch-mediated regulation. The three distinct classes of S-adenosyl methionine (SAM) riboswitches are the most commonly found riboswitch classes in nature. These RNAs represent three independent evolution solutions to achieve specific SAM recognition. We recently determined the crystal structures of SAM riboswitches from two classes, the E. faecalis SMK box and the B. subtilis S box. These structures shed light into the how SAM is specifically recognized, but did not provide enough evidence to support the large SAM-dependent conformational changes observed in the previous genetic and biochemical studies. To fully understand their structure-functional relationship and conformational dynamics, we propose to: (1) Understand the ligand recognition mechanism in the SMK box riboswitch. (2) Characterize the ligand-free SMK conformation and search for eukaryotic riboswitches. (3) Carry out chemical probing experiments to reveal ligand-induced conformational dynamics in the SMK RNA