Molecular determinants of survival in non-growing bacteria

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This project will begin to answer the fundamental question of how bacteria survive long-term starvation. A great deal is known about the mechanics of how bacteria grow and multiply. By contrast, little is known about how bacteria survive long periods of nutrient starvation. This is a considerable knowledge gap given that natural environments tend to be nutrient-poor. As a consequence bacteria are forced to persist in a state of non-growth or very slow growth. How do bacteria survive long-term starvation? What is the genetic and physiological basis for this? When cells do die ? what are the most common causes of death? The proposed research will focus on a bacterium named Rhodopseudomonas palustris that has been identified as a good model for these studies. This bacterium stays alive for periods of weeks in a laboratory setting in a starved non-growing state. A comprehensive program of mutagenesis and high throughput DNA sequencing technology will define genes that contribute to starvation survival. These genes will be validated and their role in starvation survival defined in an iterative process of mutagenesis, laboratory studies and gene expression studies. Broader impacts. The project will establish a user group in functional genomics of microbes. A group of eighteen investigators at the University of Washington who focus on microbial biology will form the core of this user group. The group will develop novel experimental and computational tools for data analysis that will be freely available to the scientific community. This will also serve as a focal point to train graduate students and undergraduates to apply global systems biology approaches to bacteria. The user group will seek to engage faculty and students from smaller schools in the area, including University of Puget Sound, Seattle Pacific University, Seattle University, Evergreen College, Bellevue Community College, and the Seattle Community Colleges. This project will also support a female postdoctoral fellow who will be trained to integrate data from bacterial genetics, physiology and computational analyses to answer questions about how cells function at the whole cell level. Finally, this research will lead to a better understanding of the role of non-growing microbes, which dominate in nature, and drive the global carbon and nitrogen cycles. It will also promote more efficient use of non-growing microbes as cell factories for production of value added products like biofuels.