Probing the Function and Evolution of the Bacterial Envelope Architecture

描述（由申请人提供）：基于基因组学的模式生物资源最近推动了各种功能基因组学方法的发展，这些方法都旨在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。一些最强大的全球方法是基于扩大生物学中长期存在的概念，即上位性/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，为它们找到定量读数，并设计出全局评估数据和最大化提取信息的方法。加州大学旧金山分校在上述过程中发挥了关键作用，完善了酿酒葡萄球菌的遗传互作技术，并为这些方法可以提取的生物学添加了新的维度。高度协作和互动的研究精神是学校的特色，其最先进的机器人设备和互补设施的优化管道使UCSF成为将这些技术扩展到其他生物的独特场所。自从我以著名的EMBO奖学金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种方法，并应用它们来推断其生物学的机制见解。我们最近发表的关于大肠杆菌的技术在两篇评论文章中都有介绍，我们目前的工作是对整个大肠杆菌基因组进行系统的化学遗传分析，并为其包膜室绘制全面的遗传相互作用图，这几乎已经完成，并包含了许多新生物学的见解。在这里，我首次提出在模型病原微生物鼠伤寒沙门氏菌中开发和实施等效技术。拥有大肠杆菌和鼠伤寒沙门氏菌的可比数据将使我能够对原核生物进行开创性的全面跨物种研究，并监测简单而密切相关的单细胞生物如何调整其网络以适应不同的生活方式并满足多种环境的需求。随着关键革兰氏阳性菌的工具和数据的出现，这项工作将得到扩展。在我的本科和研究生学习期间，作为生物化学家和分子微生物学家，我对解决各种领域的机制假设驱动问题变得自信。在过去的两年里，我在系统生物学方面也获得了重要的技能，但要担任领导角色并能够推动这一领域的发展，我需要在生物信息学/生物统计学和发病机理方面进行额外的培训。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)一个世界领先的科学家团队，他们在这个项目的所有可能方面都拥有尖端的专业知识，作为我的顾问委员会，c)两位鼓舞人心的导师，他们一直在我的系统生物学努力中帮助我；他们的经验和指导将促进拟议工作的进展，并帮助我提高我作为小组领导的个人技能。从提议的工作中产生的过多的机械推断将作为我自己实验室的出发点。我设想我的独立研究者的职业生涯是在系统生物学和假设驱动的机制研究的界面，连接两者，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节，信号转导，转录级联反应，药物同化/副作用和组合使用，以及进化适应。

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.