Structure and Mechanism of SAM-responsive Riboswitches

SAM响应核糖开关的结构和机制

• 批准号: 8036043
• 负责人: Robert T Batey
• 金额: $ 28.55万
• 依托单位: UNIVERSITY OF COLORADO
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-05-01 至 2012-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8036043
• 关键词: 5' Untranslated Regions; Acids; Address; Affinity; Anhydrides; Anti-Bacterial Agents; Architecture; Bacillus (bacterium); Bacillus anthracis; Bacteria; Binding; Biochemical; Biological; Calorimetry; Charge; Chemicals; Chromosomes; Communication; Complement; Complex; Decision Making; Discrimination; Drug Design; Elements; Event; Flavin Mononucleotide; Foundations; Functional RNA; Gene Expression; Gene Expression Regulation; Genes; Genetic Transcription; Goals; Gram-Positive Bacteria; Health; Ions; Knowledge; Lead; Ligand Binding; Ligands; Location; Magnesium; Maintenance; Maps; Messenger RNA; Metabolic Pathway; Metabolism; Metals; Methionine; Modification; Mycobacterium tuberculosis; Nucleotides; Pathway interactions; Play; Process; Proteins; Pseudomonas aeruginosa; Purines; RNA; RNA Sequences; Regulation; Research; Resolution; Ribonucleoproteins; Ribose; Role; S-Adenosylhomocysteine; S-Adenosylmethionine; Secondary to; Series; Signal Transduction; Site-Directed Mutagenesis; Solvents; Specificity; Staphylococcus aureus; Structure; Sulfides; Sulfur; Sulfur Metabolism Pathway; Surveys; Techniques; Temperature; Therapeutic; Thiamin Metabolism Pathway; Titrations; Transcription Process; Translations; Work; X Inactivation; X-Ray Crystallography; antimicrobial; aptamer; base; cis acting element; flexibility; hydroxyl group; improved; methyl group; methylisoamylnitrosamine; mutant; pathogenic bacteria; plant fungi; programs; purine; response; small molecule; sugar; therapeutic target; transmission process; uptake; 5' Untranslated Regions; Acids; Address; Affinity; Anhydrides; Anti-Bacterial Agents; Architecture; Bacillus (bacterium); Bacillus anthracis; Bacteria; Binding; Biochemical; Biological; Calorimetry; Charge; Chemicals; Chromosomes; Communication; Complement; Complex; Decision Making; Discrimination; Drug Design; Elements; Event; Flavin Mononucleotide; Foundations; Functional RNA; Gene Expression; Gene Expression Regulation; Genes; Genetic Transcription; Goals; Gram-Positive Bacteria; Health; Ions; Knowledge; Lead; Ligand Binding; Ligands; Location; Magnesium; Maintenance; Maps; Messenger RNA; Metabolic Pathway; Metabolism; Metals; Methionine; Modification; Mycobacterium tuberculosis; Nucleotides; Pathway interactions; Play; Process; Proteins; Pseudomonas aeruginosa; Purines; RNA; RNA Sequences; Regulation; Research; Resolution; Ribonucleoproteins; Ribose; Role; S-Adenosylhomocysteine; S-Adenosylmethionine; Secondary to; Series; Signal Transduction; Site-Directed Mutagenesis; Solvents; Specificity; Staphylococcus aureus; Structure; Sulfides; Sulfur; Sulfur Metabolism Pathway; Surveys; Techniques; Temperature; Therapeutic; Thiamin Metabolism Pathway; Titrations; Transcription Process; Translations; Work; X Inactivation; X-Ray Crystallography; antimicrobial; aptamer; base; cis acting element; flexibility; hydroxyl group; improved; methyl group; methylisoamylnitrosamine; mutant; pathogenic bacteria; plant fungi; programs; purine; response; small molecule; sugar; therapeutic target; transmission process; uptake

DESCRIPTION (provided by applicant): Non-coding RNA is known to play crucial roles at almost every level of the maintenance and transmission of biological information. These RNAs and their assemblies into ribonucleoproteins (RNPs) perform diverse tasks such as maintaining the ends of chromosomes, X-chromosome inactivation, processing and modification of pre-RNAs, and the targeting of proteins to specific cellular locations. My research program focuses on understanding the relationship between non-coding RNA structure and function. In this proposal, we aim to study a class of non-coding RNAs called riboswitches, cis-acting elements found in the 5'-untranslated region (5'-UTR) of bacterial mRNAs that regulate gene expression via their ability to directly bind small molecule metabolites. These riboregulatory elements control a variety of basic metabolic pathways in a number of pathogenic bacteria, including B. anthracis, S. aureus and M. tuberculosis; in Bacillus species, over 2% of all genes are controlled in this fashion. Sulfur metabolism is one of the most important aspects of cellular metabolism controlled by riboswitches, which is effected through direct interaction of S-adenosylmethionine (SAM) with four distinct subclasses of SAM-responsive RNAs. To develop a detailed structural and biochemical understanding of these SAM-responsive riboswitches, we have solved the structure of two separate subclasses using X-ray crystallography. Building from this work, we propose to use a combination of X-ray crystallography, binding studies and chemical probing to address: (1) what is the structural basis for SAM recognition, (2) how does RNA effectively discriminate between SAM and the product form S- adenosylhomocysteine (SAH), (3) what are the conformational changes in the RNA that accompany ligand binding, and (4) how are these conformational changes used to effect gene regulation. The results of these proposed studies will serve to broaden our knowledge of RNA-based gene regulation as well as provide an atomic-level understanding of an RNA that is a promising antimicrobial therapeutic target. PUBLIC HEALTH RELEVANCE: Riboswitches are a form of RNA-based gene regulation that is widely utilized in bacteria, including a number of medically important pathogenic bacteria such as B. anthracis, M. tuberculosis, P. aeruginosa and S. aureus. Our work seeks to develop an atomic-level understanding of how these RNAs regulate sulfur metabolism through their ability to directly bind S-adenosylmethionine. These studies serve to develop these RNAs as potential targets of antibacterial therapeutics via structure-based drug design.

描述（由申请人提供）：已知非编码RNA几乎在维护和传播生物学信息的各个层面上扮演关键角色。这些RNA及其组合物成核糖核蛋白（RNP）执行了各种任务，例如维持染色体的末端，X染色体灭活，加工和修饰Pre-RNAS以及将蛋白质的靶向靶向特定的细胞位置。我的研究计划着重于理解非编码RNA结构与功能之间的关系。在该提案中，我们旨在研究一类称为核糖开关的非编码RNA，即在5'-非翻译区（5'-UTR）中发现的细菌mRNA中的顺式作用元件，这些元件通过其通过直接结合小分子代谢物的能力来调节基因表达。这些核糖调节元素控制着许多致病细菌的各种基本代谢途径，包括炭疽芽孢杆菌，金黄色葡萄球菌和结核分枝杆菌；在芽孢杆菌物种中，以这种方式控制了所有基因的2％以上。硫代谢是由核糖开关控制的细胞代谢的最重要方面之一，这是通过与S-腺苷甲硫代氨酸（SAM）与四个不同的SAM响应性RNA的四个不同亚类的直接相互作用来实现的。为了对这些SAM响应性核能开关发展详细的结构和生化理解，我们使用X射线晶体学解决了两个单独的子类的结构。通过这项工作的构建，我们建议将X射线晶体学，结合研究和化学探测的结合进行解决：（1）SAM识别的结构基础是什么，（2）RNA如何有效区分SAM和产物形成S-腺苷基体系半径为s-腺苷（SAH）（SAH）（SAH）的结构变化，（3）与rna的结构变化，（3）是什么相结合的效果，（3）基因调节。这些拟议的研究的结果将有助于扩大我们对基于RNA的基因调节的了解，并提供对RNA的原子水平的理解，这是一个有希望的抗菌治疗靶标。 公共卫生相关性：核糖开关是一种基于RNA的基因调节的一种形式，在细菌中广泛使用，包括许多医学上重要的病原菌，例如炭疽芽孢杆菌，结核分枝杆菌，绿os鸟和金黄色葡萄球菌。我们的工作旨在通过它们直接结合S-腺苷甲氨酸的能力来对这些RNA如何调节硫代谢的方式发展原子水平的理解。这些研究通过基于结构的药物设计将这些RNA作为抗菌治疗剂的潜在靶标。