Functional genomics of hypothetical genes in Gram-positive bacteria

项目摘要/摘要 大约30%的细菌基因产物是微生物“暗物质”，没有特化的 功能。开发描述共生菌和病原菌基因功能的方法 推进基础细菌学和微生物发病机制领域，推动新的抗击方法 抗生素耐药性的上升。 该提案的短期培训目标是为应聘者提供以下方面的指导和培训 计算生物学和数据科学。长期目标是建立强大的计算和 用于未确定特征的细菌基因功能分析的遗传工具。这些将适用于已建立的、 易于处理的实验系统，用于对生物膜中涉及的未表征的基因进行机械性发现 形成和多菌的相互作用。对于职业发展，应聘者将进行 全面的培训计划，有出色的导师、共同导师和咨询委员会。 目标1将使用化学遗传学来确定假想的基因功能在共生和 致病菌粪肠球菌OG1RF。在目标2中，候选人将开发化学遗传学 确定预先形成的生物膜在用生物活性化合物处理后的反应的方法 抗生素。在目标3中，这些功能基因组学方法将被扩展到研究 OG1RF和口腔病原体变形链球菌，作为确定变形链球菌杀死的候选 OG1RF和一株对万古霉素耐药的粪肠球菌，其机制未知。总而言之，这 研究将对与医学相关的细菌的基因功能进行基因组规模的描述，并定义 新因素促进生物膜形成和微生物间相互作用的机制。 明尼苏达大学为这项工作提供了理想的制度环境。如此之高 协作环境有来自不同的微生物学和计算生物学研究小组 生物医学、牙科、兽医和基础科学背景。明尼苏达大学也提供非凡的职业生涯 发展机遇，明尼苏达大学基因组学中心是一家最先进的设施， 候选人已经建立了富有成效的协作。 总之，拟议的培训和研究将成为候选人发起 将功能基因组学与体外模型系统相结合的独立研究生涯 基因在不同细菌中的功能。

Project Summary/Abstract Approximately 30% of all bacterial gene products are microbial “dark matter” and have no characterized function. Developing methods for describing gene function in commensal and pathogenic bacteria will advance the fields of fundamental bacteriology and microbial pathogenesis, driving new approaches to combat the rise of antibiotic resistance. The short-term training goal of this proposal is to provide the candidate with mentoring and training in computational biology and data science. The long-term objectives are to establish robust computational and genetic tools for functional analysis of uncharacterized bacterial genes. These will be applied to established, tractable experimental systems to make mechanistic discoveries about uncharacterized loci involved in biofilm formation and polymicrobial interactions. For career development, the candidate will undertake a comprehensive training plan with an outstanding mentor, co-mentor, and advisory committee. Aim 1 will use chemical genetics to identify hypothetical gene function in the commensal and pathogenic bacterium Enterococcus faecalis OG1RF. In Aim 2, the candidate will develop chemical genetics methodology to determine how pre-formed biofilms respond after treatment with bioactive compounds such as antibiotics. In Aim 3, these functional genomics approaches will be expanded to study interactions between OG1RF and the oral pathogen Streptococcus mutans, as the candidate determined that S. mutans kills OG1RF and a vancomycin-resistant isolate of E. faecalis through an unknown mechanism. Together, this research will generate genome-scale descriptions of gene function in medically relevant bacteria and define mechanisms by which novel factors contribute to biofilm formation and interactions between microbes. The University of Minnesota provides an ideal institutional environment for this work. This highly collaborative environment has diverse microbiology and computational biology research groups from biomedical, dental, veterinary, and basic science backgrounds. U Minnesota also offers exceptional career development opportunities, and the U Minnesota Genomics Center is a state-of-the-art facility with which the candidate has already established a productive collaboration. Together, the proposed training and research will be a platform from which the candidate will launch an independent research career combining functional genomics with in vitro model systems to study hypothetical gene function in diverse bacteria.