Probing the Function and Evolution of the Bacterial Envelope Architecture

描述（由申请人提供）：用于模式生物体的基于基因组学的资源最近促进了各种功能基因组学方法的发展，这些方法的目的都是加速我们理解基因功能和绘制细胞通路/蛋白质复合物的能力。一些最强大的全球性方法是基于扩大生物学中长期存在的概念，iidoepistasis/遗传相互作用-一个基因的功能如何依赖于第二个基因的功能，以及化学遗传相互作用-一个基因的功能如何影响细胞对化学应激的反应，找到它们的定量读数，并设计出全面评估数据和最大化所提取信息的方法。UCSF在这一过程中发挥了关键作用，完善了S.并为可从这些方法中提取的生物学增加了新的维度。作为学校特点的高度协作和互动的研究精神，以及其最先进的机器人设备和辅助设施的优化管道，使加州大学旧金山分校成为将这些技术推广到其他生物体的独特场所。自从我以一个享有盛誉的EMBO奖学金的身份来到加州大学旧金山分校以来，我一直致力于为原核生物开发这样的方法，并将其应用于推断有关其生物学的机制见解。我们最近为E.我们目前的工作是对整个大肠杆菌进行系统的化学遗传图谱分析。大肠杆菌基因组和其包膜区室的全面遗传相互作用图谱的研究已经接近完成，并包含了许多关于新生物学的见解。在此，我建议首次在模式致病微生物S.鼠伤寒。结果表明，两种方法的数据具有可比性。coli和革兰氏阳性菌S.鼠伤寒将使我能够在原核生物中进行一项开创性的全面的跨物种研究，并监测简单而密切相关的单细胞生物如何调整它们的网络，以适应不同的生活方式，并满足多样化环境的需要。随着关键革兰氏阳性微生物的工具和数据的可用性，这项工作将得到扩展。在本科和研究生阶段，我接受了生物化学家和分子微生物学家的培训，对解决各种领域中关于机制的假设驱动问题充满信心。在过去的两年里，我还获得了系统生物学方面的重要技能，但要担任领导角色并能够推动该领域向前发展，我需要在生物信息学/生物统计学和发病机制方面接受额外的培训。为此，我组织了一个严格的职业发展计划，其中包括：a）一系列有针对性的课程; B）一个由世界领先的科学家组成的团队，他们在该项目的所有可能方面都拥有最前沿的专业知识，作为我的顾问委员会; c）两位鼓舞人心的导师，他们沿着在帮助我进行系统生物学研究;他们的经验和指导将有助于拟议工作的进展，并帮助我提高作为小组领导的个人技能。从拟议工作中产生的大量机械论推论将作为我自己实验室的起点。我设想我的独立研究员职业是在系统生物学和假说驱动的机制研究的界面，桥接两者，以提高我们对各种关键生物学方面的知识，如膜组装、细胞生长和分裂的调控、信号转导、转录级联、药物同化/副作用和组合使用，以及进化适应。 公共卫生关系：细菌是自然界中最简单同时也是最多样的生物体之一。在这里，我们建议建立第一个全面的功能网络组织的一个隔间的图片，构成细菌的界面，以环境。我们的努力将集中在两个密切相关的生物，S。鼠伤寒杆菌是西方国家食源性疾病的头号病因，而一种无害的“驯化”E.大肠杆菌菌株。这两种生物体之间的比较将阐明细菌进化和发病机制的重要方面，这些信息可用于了解新药的作用模式和改进细菌性疾病的治疗。

DESCRIPTION (provided by applicant): Genomics-based resources for model organisms have recently fuelled the development of various functional genomics approaches that all aim to accelerate our ability to understand gene function and map cellular pathways/protein complexes. Some of the most powerful global approaches are based on scaling up long- standing concepts in biology, i.e. epistasis/genetic interactions - how the function of one gene depends on the function of a second gene, and chemical genetic interactions - how the function of one gene affects cellular responses to chemical stress, finding a quantitative readout for them and devising ways to globally assess the data and maximize the extracted information. UCSF has played a pivotal role in the above process, perfecting the genetic interaction technology for S. cerevisiae and adding a new dimension to the biology that can be extracted from these methods. The highly collaborative and interactive research spirit that characterizes the school, and its optimized pipeline of state-of-the-art robotic equipment and complementary facilities make UCSF a unique place for extending these technologies to other organisms. Since I arrived at UCSF on a prestigious EMBO fellowship, I have led an effort to develop such methodologies for prokaryotes and apply them to infer mechanistic insights on their biology. The technology we recently published for E. coli was featured in two comment articles, and our current work on generating a systematic chemical genetic profiling of the entire E. coli genome and a comprehensive genetic interaction map for its envelope compartment is almost completed and contains numerous insights on new biology. Here, I propose to develop and implement equivalent technology for the first time in a model pathogenic micoorganism, S. typhimurium. Having comparable data in both E. coli and S. typhimurium will allow me to perform a seminal comprehensive cross-species study in prokaryotes and monitor how simple and closely related unicellular organisms adjust their networks to adapt to different lifestyles and meet the needs of versatile environments. This effort will be extended as tools and data for key gram-positive organisms become available. Being trained as a biochemist and molecular microbiologist in my undergraduate and graduate studies, I have become confident in tackling hypothesis-driven questions on mechanism in a variety of fields. I also have acquired important skills in systems biology in the past two years, but to assume a leadership role and be able to drive this field forward, I need additional training in bioinformatics/biostatistics and pathogenesis. For this I have organized a rigorous career development plan that includes: a) a selection of targeted coursework, b) a team of world-leading scientists with cutting-edge expertise on all possible aspects of this project as my advisory board and c) two inspiring mentors who have been helping me all along in my systems biology endeavors; their experience and guidance will both facilitate the progress of the proposed work and help me improve my personal skills as a group leader. A plethora of mechanistic inferences stemming out of the proposed work will serve as a jumping-off point for my own lab. I envision my independent investigator career being in the interface of systems biology and hypothesis-driven mechanistic research, bridging the two to improve our knowledge on various key-biological aspects such as membrane assembly, regulation of cell growth and division, signal transduction, transcriptional cascades, drug assimilation/side- effects and combinatorial use, and evolutionary adaptation. PUBLIC HEALTH RELEVANCE: Bacteria are among the simplest and at the same time most diverse organisms in nature. Here, we propose to build the first comprehensive picture of the functional network organization of a compartment that constitutes the bacterium's interface to the environment. Our efforts will be concentrated on two closely related organisms, S. typhimurium, the number one cause of food-borne illnesses in western countries, and a harmless "domesticated" E. coli strain. Comparisons between the two organisms will illuminate important aspects of bacterial evolution and pathogenesis, and the information can be used to understand the mode of action of novel drugs and improve therapy for bacterial disease.