Pervasive transcription in bacterial genomes

描述(由申请人提供) 摘要：我们以大肠杆菌为模式生物，研究细菌的基因调控机制。基因表达的调控是细菌发病机制的一个关键方面，我们的大部分了解都来自于对大肠杆菌的研究。绝大多数关于基因表达的工作都集中在蛋白质调控上，但最近在真核生物中的研究发现了数千个非编码RNA(NcRNAs)，其中许多具有调节功能。我们最近在大肠杆菌中发现了1000多个新的转录本，它们起源于蛋白质编码基因，在两条DNA链上。我们有强有力的证据表明，许多这些基因内RNA(IRNAs)具有调节功能。IRNAs普遍转录的发现从根本上改变了对细菌转录本的既定观点。这项建议的目标是确定普遍存在的iRNA转录是否是细菌中一种重要的、广泛的调控机制，类似于真核生物中的microRNAs。为了实现这一目标，我们将使用多学科方法来(I)全面鉴定iRNAs，(Ii)确定关键的选定iRNA实例的调控机制，(Iii)确定iRNAs对致病性大肠杆菌毒力的影响。由于我在细菌遗传学和基因组学方面的专业知识和培训，以及我愿意挑战细菌基因调控领域的长期范式，我们为开展这一项目做好了理想的准备。沃兹沃斯中心为这些研究提供了一个出色的环境，因为它对细菌和基因调控进行了出色的研究，并拥有强大的核心设施网络。这项工作将改变我们对细菌基因表达的理解，并对细菌生理学和致病机理的研究具有重要意义。 与公共卫生相关：RNA最近被认为是基因表达的关键调节因子。我们已经在模式细菌大肠杆菌中发现了1,000多个新的RNA。我们将确定这些RNA对基因表达的影响。

DESCRIPTION (Provided by the applicant) Abstract: We use Escherichia coli as a model organism to define the mechanisms of gene regulation in bacteria. Regulation of gene expression is a critical aspect of bacterial pathogenesis, and much of our understanding has come from studies of E. coli. The vast majority of work on gene expression has focused on protein regulators, but recent studies in eukaryotes have identified thousands of non-coding RNAs (ncRNAs), many of which have regulatory functions. We have recently identified over 1,000 novel transcripts in E. coli that initiate within protein-coding genes, on both DNA strands. We have strong evidence that many of these intragenic RNAs (iRNAs) have a regulatory function. Discovery of pervasive transcription of iRNAs fundamentally changes the established view of bacterial transcriptomes. The goal of this proposal is to determine whether pervasive iRNA transcription is an important, widespread, regulatory mechanism in bacteria, analogous to microRNAs in eukaryotes. To achieve this goal we will use a multidisciplinary approach to (i) comprehensively identify iRNAs, (ii) determine the mechanisms of regulation for key selected iRNA examples, (iii) determine the impact of gene regulation by iRNAs on virulence in a pathogenic strain of E. coli. We are ideally prepared to undertake this project due to my expertise and training in bacterial genetics and genomics, and my willingness to challenge long-standing paradigms in the field of bacterial gene regulation. The Wadsworth Center provides an outstanding environment for these studies because of its excellent research into bacteria and gene regulation, and a strong network of core facilities. The work proposed here will transform our understanding of bacterial gene expression and has major implications for the study of bacterial physiology and pathogenesis. Public Health Relevance: RNA has recently been recognized as a key regulator of gene expression. We have identified over 1,000 novel RNAs in the model bacterium, Escherichia coli. We will determine the impact of these RNAs on gene expression.