Molecular Basis for mRNA Decay in Bacteria

细菌中 mRNA 衰变的分子基础

• 批准号: 9893215
• 负责人: Alexander Serganov
• 金额: $ 5.74万
• 依托单位: NEW YORK UNIVERSITY SCHOOL OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-09-21 至 2020-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9893215
• 关键词: Address; Adopted; Affect; Affinity; Bacteria; Binding; Biochemical; Bioinformatics; Biological Assay; Biological Process; Biology; Catalysis; Cell physiology; Cells; Crystallization; DNA Repair; Data; Dinucleoside Polyphosphates; Diphosphates; Enzymes; Escherichia coli; Excision; Foundations; Future; Gene Expression; Gene Expression Regulation; Genetic; Host Defense; In Vitro; Invaded; Mammalian Cell; Mediating; Messenger RNA; Metabolic; Metabolism; Methodology; Methods; Modeling; Molecular; Mutagenesis; Organism; Pathway interactions; Personal Satisfaction; Physiological; Positioning Attribute; Protein Biosynthesis; Proteins; RNA; RNA Binding; RNA Degradation; RNA triphosphatase; Reaction; Regulation; Research Proposals; Resistance; Role; Signal Transduction; Specificity; Stress; Structure; Substrate Specificity; System; Testing; Time; Transcript; Translating; Virulence; X-Ray Crystallography; base; cellular targeting; crosslink; decapping enzyme; design; diadenosine tetraphosphate; environmental change; enzyme activity; experimental study; genome-wide; in vitro activity; in vivo; inhibitor/antagonist; inorganic phosphate; insight; mRNA Decay; mRNA Transcript Degradation; mRNA decapping; member; novel; nudix hydrolase; pathogenic bacteria; protective effect; response; transcriptome sequencing; tripolyphosphate

Summary A central problem in biology is to understand how cells optimize biological processes in response to changing environmental conditions. mRNA decay mechanisms contribute to coordination of activities by limiting the number of times each mRNA can be translated into protein molecules. Recent studies have identified a novel 5'-end-dependent mRNA decay pathway in bacteria triggered by the initial conversion of the triphosphorylated 5' end of primary transcripts to a monophosphate by the Nudix hydrolase RppH. A triphosphate on the 5'-end of bacterial mRNA has a protective effect analogous to that of the cap structure of eukaryotic mRNAs; therefore, pyrophosphate removal by RppH parallels the action of eukaryotic decapping enzymes. Despite its vital importance, 5'-end-dependent mRNA decay is among the least understood mechanisms of gene regulation. This proposal details a set of specific aims that address specificity, catalytic mechanism, and the role of RppH and RppH-associated factors in regulating gene expression in bacteria. The proposal integrates X-ray crystallography, genetics, biochemical methods, focused genome-wide RNA sequencing and bioinformatics. Specific Aim 1 is devoted to the determination of the catalytic mechanism of RppH and understanding the substrate specificity of RppH. This Aim will address molecular principles of RNA `decapping' based on the crystal structures of Escherichia coli RppH bound to model RNAs and structure-guided mutagenesis. Specific Aim 2 will validate a new model for the 5'-end-dependent mRNA decay. This Aim will identify and characterize new factors involved in the pathway and their impact on gene expression landscape. Specific Aim 3 will identify cellular mRNA targets of RppH on a genome-wide scale under various environmental conditions. This Aim will reveal the molecular features of RNAs that are important for RppH recognition and uncover the contribution of RppH to the control of gene expression in bacteria. The results of these studies will provide a comprehensive picture of the critical steps in the 5'-end-dependent pathway for bacterial mRNA decay and thereby address a fundamental gap in our understanding of the regulatory networks controlled by RNA degradation.

摘要 生物学中的一个中心问题是了解细胞如何优化生物过程以应对变化 环境条件。信使核糖核酸衰变机制有助于协调活动，通过限制 每个信使核糖核酸被翻译成蛋白质分子的次数。最近的研究发现了一部小说 三磷酸化的初始转化在细菌中触发的5‘端依赖的mRNA衰变途径 由Nudex水解酶RppH将初级转录本5‘端终止为单磷酸。5‘端的三磷酸 细菌信使核糖核酸的保护作用类似于真核生物信使核糖核酸的帽子结构； 因此，RppH去除焦磷酸盐的作用与真核生物解脱解酶的作用类似。尽管它的 重要的是，5‘端依赖的mRNA衰退是最不了解的基因机制之一 监管。这项建议详细说明了一系列具体目标，这些目标涉及特殊性、催化机制和 RppH及其相关因子在细菌基因表达调控中的作用该提案整合了 X射线结晶学、遗传学、生化方法、全基因组RNA测序和 生物信息学。具体目标1致力于确定RppH和RppH的催化机理 了解RppH的底物特异性。这一目标将解决RNA‘解链’的分子原理。 基于大肠杆菌RppH与模型RNA结合和结构导向的晶体结构 诱变。特殊目的2将验证一个新的5‘端依赖的mRNA衰变模型。这一目标将 识别和表征参与该途径的新因素及其对基因表达格局的影响。 特异性目标3将在全基因组范围内识别RppH的细胞mRNA靶点 环境条件。这一目标将揭示对RppH重要的RNA的分子特征 认识并揭示RppH在细菌基因表达控制中的贡献。结果是 这些研究将提供5‘末端依赖途径中的关键步骤的综合图景 细菌的信使核糖核酸腐烂，从而解决了我们对调控网络理解上的一个根本鸿沟 受RNA降解控制。