Exploiting antibiotics to understand the ribosome and translation

核糖体在蛋白质合成中起着关键作用，是抗生素的主要靶标之一。 抑制细菌细胞的生长。核糖体功能的几个关键方面尚不完全 抗生素可以在深入了解翻译的未知方面方面发挥关键作用。 我们的实验室一直处于抗生素研究和功能作用研究的前沿 核糖体 RNA (rRNA)。我们已经阐明了许多结合模式和作用机制 主要类别的抗生素。根据我们的研究结果，我们提出了上下文和上下文的新概念 几种蛋白质合成抑制剂的蛋白质特异性作用。我们还公布了 几种耐药机制并揭示了诱导型抗生素表达调控的原理 抗性基因。在我们研究抗生素的同时，我们也推进了核糖体领域的发展 工程构建了第一个基于 16S-23S 杂合体且具有不可分离亚基的核糖体 rRNA，为基础研究和生物工程开辟新的实验场所。 基于我们在抗生素、基因调控和核糖体工程方面的专业知识，我们现在将 将这些领域推进到新的领域。我们未来的研究将朝着三个主要方向进行：1） 我们将致力于推进细菌核糖体抑制剂的背景特异性概念 适用于真核核糖体。通过使用核糖体工程、结构分析和 通过全基因组测试，我们将鉴定能够与新生肽出口通道结合的化合物 真核核糖体并干扰蛋白质子集的产生。 2) 我们的抗生素强化核糖体 分析实验得出了一个意想不到的、令人兴奋的发现，即在许多细胞内存在内部翻译起始。 细菌基因。我们将分析内部启动的生理意义，测试内部启动的产生 “替代”基因产物，研究两个不同起始密码子的基因表达调节 探索这种现象的进化渗透率。 3) 核糖体被认为起源于 前蛋白RNA世界。然而，之前所有的尝试都证明了无蛋白 rRNA 能够 催化肽键形成尚未成功。我们将利用核糖体之间的协同作用 工程和抗生素研究以产生催化活性 rRNA 核心。总而言之，拟议的 研究方向应显着推进抗生素作为药物和工具的使用 探索核糖体在蛋白质合成和翻译调控中的功能。我们将利用以下知识 抗生素的作用扩大了我们对基因组可塑性和基因编码的理解，并阐明了关键的 核糖体起源和进化的问题。

The ribosome plays the key role in protein synthesis and is one of the main targets for antibiotics that inhibit the growth of bacterial cells. Several key aspects of the functions of the ribosome are not fully understood and antibiotics could play a critical role in gaining insights into unknown facets of translation. Our laboratory has been on the forefront of antibiotics research and studies of the functional role of ribosomal RNA (rRNA). We have elucidated the binding modes and mechanisms of action of a number of major classes of antibiotics. On the basis of our findings we have proposed the new concept of context- and protein-specific action of several types of protein synthesis inhibitors. We have also unveiled the operations of several resistance mechanisms and revealed the principles of regulation of expression of inducible antibiotic resistance genes. In parallel with our studies of antibiotics, we have advanced the field of ribosome engineering having constructed the first ribosome with inseparable subunits based on a hybrid of 16S-23S rRNA, opening new experimental venues for basic research and bioengineering. Building upon our expertise in antibiotics, gene regulation and ribosome engineering, we will now advance these areas to principally new frontiers. Our future research will proceed in three main directions: 1) We will dedicate our effort to advancing the concept of context-specificity of bacterial ribosomal inhibitors to become applicable to the eukaryotic ribosome. By using ribosome engineering, structural analysis and genome-wide tests, we will identify compounds capable of binding in the nascent peptide exit tunnel of the eukaryotic ribosome and interfering with production of a subset of proteins. 2) Our antibiotic-enforced ribosome profiling experiments led to an unexpected and exciting finding of internal translation initiation inside a number of bacterial genes. We will analyze the physiological significance of internal initiation, test the production of the `alternative' gene products, study the regulation of expression of the genes from two different start codons and explore the evolutionary penetrance of this phenomenon. 3) The ribosome is believed to have originated in the pre-protein RNA World. However, all the previous attempts to demonstrate the ability of protein-free rRNA to catalyze peptide bond formation have been unsuccessful. We will use the synergy between ribosome engineering and antibiotic studies to generate catalytically active rRNA core. Altogether, the proposed directions of research should significantly advance the use of antibiotics as medicines and as tools for exploring ribosome functions in protein synthesis and translation regulation. We will use the knowledge of antibiotic action to expand our understanding of genome plasticity and gene coding and illuminate the critical questions of the ribosome origin and evolution.