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: 9897557
• 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 2023-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9897557
• 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; Structure; Testing; Translation Initiation; Translations; base; experimental study; frontier; gene product; genome-wide; inducible gene expression; inhibitor/antagonist; insight; operation; protein S precursor; 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并不完全 理解和使用抗生素可以在洞察翻译的未知方面发挥关键作用。 我们的实验室一直走在抗生素研究的前沿，并对抗生素的功能作用进行了研究 核糖体RNA(RRNA)。我们已经阐明了一些分子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，我们提出了语境的新概念--以及 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 诱导型抗生素的几种耐药机制及其表达调控原理 抗性基因。在我们研究抗生素的同时，我们在核糖体领域取得了进展。 基于16S-23S杂交构建了第一个具有不可分离亚基的核糖体的工程 RRNA，为基础研究和生物工程开辟了新的实验场所。 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 将这些领域推进到主要是新的领域。我们未来的研究将主要朝着三个方向进行：1) 我们将致力于将细菌核糖体抑制物的上下文特异性概念推广到 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在新生的多肽出口隧道的化合物 真核核糖体和干扰蛋白质子集的产生。2)我们的抗生素强化的核糖体 剖析实验导致了一个意外且令人兴奋的发现，即在一个数字内部启动内部翻译 细菌基因。我们将分析内启动的生理意义，测试内启动的产生 “替代”基因产物，研究来自两个不同起始密码子和 探索这一现象的进化外显性。3)核糖体被认为起源于 蛋白质前核糖核酸世界。然而，之前所有证明无蛋白rRNA能力的尝试 催化多肽键的形成一直没有成功。我们将利用核糖体之间的协同作用 工程和抗生素研究，以产生催化活性的rRNA核心。总而言之，建议的 研究方向应显著促进抗生素作为药物和治疗工具的使用 探索核糖体在蛋白质合成和翻译调控中的功能。我们将利用这些知识 抗生素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。