The regulation of natural competence for DNA uptake and gene transfer in Salmonella and related bacteria

目的：拟议的计划将提高我们对许多细菌如何、何时以及为什么使用一种称为“自然能力”的过程来消耗细胞外DNA的理解。虽然广泛存在，但自然能力对细菌生态和基因组进化的贡献仍然知之甚少，也没有得到充分的量化。我们试图利用经过充分研究的物种来填补我们对DNA吸收、基因转移和DNA新陈代谢的理解上的这些巨大空白，这些物种在自然能力的研究中迄今被忽视了。背景：自然能力是一个专门的过程，涉及DNA在细菌细胞被膜上的主动结合和转位。一旦进入体内，DNA就可以与宿主基因组重新结合，通过“自然转化”实现基因的水平转移。水平基因转移对细菌基因组进化和生态位扩展具有广泛而强烈的影响。大肠杆菌、沙门氏菌及其近亲是一组适应能力强的细菌，经常在不同的环境之间转换。这个家族的成员通过水平基因转移获得致病性和抗菌素抗性基因而快速进化，但尚不知道通过自然能力和转化进行基因转移的频率和时间。DNA摄取提供了有价值的营养，而自然能力已被证明支持大肠杆菌在营养有限的环境中生长，这表明能力具有从基因转移到营养获取的多种生态作用和后果。我们的目标是在大肠杆菌和沙门氏菌以及相关细菌中鉴定和表征将能力基因调控机制与环境和生理信号联系起来的分子网络。随着我们发展自然和人工刺激能力的能力，我们将量化DNA吸收如何有助于不同细菌环境中的基因转移和营养获取。科学方法：这项NSERC发现计划提出了研究肠杆菌科的三个综合目标。首先，我们将确定如何调节自然能力对环境和生理信号的反应。其次，我们将量化自然能力对水平基因转移和基因组进化的贡献。第三，我们将量化自然能力如何有助于细菌在纯物种和混合物种群落中获得营养。意义：我们的探索计划准备阐明沙门氏菌、大肠杆菌和相关细菌中一个古老而神秘的过程。自然能力在漫长的进化时间和不同的利基环境中是保守的，表明对细菌生存的基本但未被表征的贡献。拟议的发现计划将建立在我们最近的成就基础上，以推进对自然能力和基因转移的研究。

OBJECTIVE: The proposed program will improve our understanding of how, when, and why many bacteria consume extracellular DNA using a process called "natural competence". Although widespread, the contributions of natural competence to bacterial ecology and genome evolution remain poorly understood and poorly quantified. We seek to fill these large gaps in our understanding of DNA uptake, gene transfer, and DNA metabolism using well-studied species that have so far been overlooked in studies of natural competence. BACKGROUND: Natural competence is a specialized and dedicated process involving active binding and translocation of DNA across the bacterial cell envelope. Once inside, DNA can recombine with the host genome, resulting in horizontal gene transfer through "natural transformation". Horizontal gene transfer has broad and strong influences on genome evolution and niche expansion in bacteria. Escherichia coli, Salmonella, and their relatives are a group of adaptable bacteria that regularly transition between diverse environments. Members of this family evolve quickly through the acquisition of pathogenicity and antimicrobial resistance genes by horizontal gene transfer, but there is no knowledge of how often or when gene transfer through natural competence and transformation. DNA uptake provides valuable nutrients, and natural competence has been shown to support E. coli growth in nutrient limited environments, suggesting that competence has multiple ecological roles and consequences, from gene transfer to nutrient acquisition. Our goal is to identify and characterize the molecular networks that link competence gene regulatory mechanisms to environmental and physiological signals in E. coli and Salmonella, and related bacteria. As we develop the abilities to naturally and artificially stimulate competence, we will quantify how DNA uptake contributes to gene transfer and nutrient acquisition in different bacterial environments. SCIENTIFIC APPROACH: This NSERC Discovery proposal addresses three integrated goals for studying Enterobacteriaceae. First, we will determine how natural competence is regulated in response to environmental and physiological signals. Second, we will quantify how natural competence contributes to horizontal gene transfer and genome evolution. And third, we will quantify how natural competence contributes to nutrient acquisition by bacteria in pure and mixed-species communities. SIGNIFICANCE: Our Discovery program is poised to elucidate an ancient yet cryptic process in Salmonella, E. coli, and related bacteria. Natural competence is conserved over long evolutionary times and in diverse niches, indicating fundamental yet uncharacterized contributions to bacterial survival. The proposed Discovery program will build from our recent achievements to advance the study of natural competence and gene transfer.