Exploiting antibiotics to understand the ribosome and translation

利用抗生素来了解核糖体和翻译

• 批准号: 10366000
• 负责人: ALEXANDER S MANKIN
• 金额: $ 36.36万
• 依托单位: UNIVERSITY OF ILLINOIS AT CHICAGO
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-04-01 至 2023-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10366000
• 关键词: Anti-Bacterial Agents; Antibiotic Resistance; Antibiotics; Area; Bacterial Genes; Basic Science; Binding; Biomedical Engineering; Cells; Clinical; Code; Engineering; Evolution; Free Ribosome; Gene Expression Regulation; Genes; Genome; Growth; Hybrids; Initiator Codon; Knowledge; Laboratories; Medicine; Organism; Penetrance; Peptides; Pharmaceutical Preparations; Physiological; Play; Production; Protein Biosynthesis; Protein Synthesis Inhibitors; Proteins; RNA; RNA, Ribosomal, 23S; Regulation; Research; Ribosomal RNA; Ribosomes; Role; Specificity; Testing; Translation Initiation; Translations; base; experimental study; frontier; gene product; genome-wide; inducible gene expression; inhibitor; insight; operation; research study; resistance gene; resistance mechanism; ribosome profiling; synergism; tool; trait

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.

核糖体在蛋白质合成中起关键作用，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不是完全 理解和抗生素可能在洞悉翻译方面的洞察力中发挥关键作用。 我们的实验室一直处于抗生素研究的最前沿，并研究了 核糖体RNA（rRNA）。我们已经阐明了许多许多人的结合模式和作用机制 抗生素的主要类别。根据我们的发现，我们提出了上下文和上下文的新概念 几种类型的蛋白质合成抑制剂的蛋白质特异性作用。我们还揭露了 几种电阻机制，揭示了诱导抗生素表达的调节原理 抗性基因。与我们的抗生素研究同时，我们已经推进了核糖体领域 工程学以基于16S-23S的混合体构建了第一个核糖体，该核糖体具有不可分割的亚基 RRNA，开设了基础研究和生物工程的新实验场所。 在我们在抗生素，基因调节和核糖体工程方面的专业知识的基础上，我们现在将 将这些区域推向主要是新的边界。我们未来的研究将以三个主要方向进行：1） 我们将致力于推进细菌核糖体抑制剂的上下文特异性概念 变得适用于真核核糖体。通过使用核糖体工程，结构分析和 全基因组测试，我们将确定能够结合新生肽出口隧道的化合物 真核生物核糖体并干扰蛋白质的子集。 2）我们的抗生素加强核糖体 分析实验导致了一个数字内部的内部翻译启动的意外而令人兴奋的发现 细菌基因。我们将分析内部启动的生理意义，测试生产 “替代”基因产物，研究来自两个不同起始密码子的基因表达的调节， 探索这种现象的进化渗透率。 3）核糖体被认为起源于 蛋白质RNA世界。但是，以前所有试图证明无蛋白质rRNA的能力 催化肽键的形成不成功。我们将使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的rRNA核心。总共提议 研究方向应大大提高使用抗生素作为药物的使用和作为工具 探索蛋白质合成和翻译调节中的核糖体功能。我们将使用知识 抗生素作用，以扩大我们对基因组可塑性和基因编码的理解并阐明关键 核糖体来源和进化的问题。