|About the Book|
Microbes are ubiquitous in nature. They play vital roles in the carbon and nitrogen cycles of our planet and decompose complex chemicals into simple nutrients for use by other organisms. We depend on microbes for the production of food products suchMoreMicrobes are ubiquitous in nature. They play vital roles in the carbon and nitrogen cycles of our planet and decompose complex chemicals into simple nutrients for use by other organisms. We depend on microbes for the production of food products such as bread and beer as well as antibiotics and drugs. However, we have only begun to harness the diverse abilities of microbes. In the future it may be possible to use microbes as miniature surgeons, diagnosing and repairing disease from within the human body, or as programmable chemical factories, converting waste materials into fuels or other useful compounds.-Unfortunately, our ability to create designer microbes lags behind our imagination. Although we have accumulated a wealth of data on microbes, the fundamental principles that govern how cells organize their components and function in changing environments are challenging to discover. Without this information, the rational design of microbes is slow and unpredictable.-In this dissertation, I explore the fundamental principles that govern how a model microbe, Escherichia coli, harvests energy and assembles complex protein structures. I describe energy harvesting and storage using the light-driven protein proteorhodopsin, and I investigate how proteins assemble by imaging the chemotaxis network using photoactivated localization microscopy (PALM).-To understand how organisms harvest energy and convert it to useful work, we study proteorhodopsin. Proteorhodopsin is a light-driven proton pump first discovered in marine microorganisms. When expressed in E. coli, proteorhodopsin absorbs light but does not have any observable effect. We discovered that when these same cells are deprived of oxygen or treated with a respiratory poison, they become light activated: starved cells that have begun to swim slowly can be sped up with green light. We show how proteorhodopsin can be used to control the function of the flagellar motor in an energy poor environment. We also develop a quantitative model to predict how proteorhodopsin behaves in a variety of changing environmental conditions.-To understand how organisms assemble proteins into functioning complexes, we use PALM imaging. As a model system, we examined the chemotaxis network which allows bacteria to swim towards favorable stimuli in the environment. The receptors that sense stimuli are not spread throughout the membrane of E. coli- receptors are found in enormous clusters at the polar ends of the cell body. In these dense clusters, the receptors can bind each other and communicate to filter out noise and amplify weak signals. How the receptors get to these polar clusters has been a mystery. Using data from PALM images, we develop a model to understand how bacteria organize their receptors into large clusters. The model, stochastic cluster nucleation, is surprising in that is generates micron-scale periodic patterns without the need for accessory proteins to provide scaffolding or active transport. This model may be a general mechanism that cells utilize to organize small and large complexes of proteins.