Genetic Systems Bioengineering for Escherichia coli

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Synthetic genetic systems displaying interesting behaviors will be designed, constructed, and characterized, and used as model systems for the elucidation of the system design principles responsible for the interesting behaviors. This work will advance our understanding of gene control mechanisms and system design principles, and is also likely to advance our understanding of regulatory factors from several natural systems. In addition, our work will provide highly-engineered and well characterized modules that will be suitable for the construction of sophisticated synthetic genetic networks. In the first Specific Aim, we propose the characterization of our synthetic genetic clock for E. coli. This clock provides for synchronous but damped oscillations of activator and represser expression in large cell populations, which can be used to bring about the periodic expression of reporter genes. The proposed approaches directly test various aspects of the system design and should reveal the design features responsible for oscillatory behavior and controlling period and amplitude of the output, as well as lead to the development of a better clock. These studies will advance our understanding of fundamental aspects of gene regulation in bacteria, and will reveal design principles involved in the production of oscillations of gene expression in biological systems. Other proposed experiments will explore the relationship of the genetic clock to the host cells that contain it, with an eye towards isolating the clock from normal cellular physiological processes and improving system performance. In the second Specific Aim improved methods for studying oscillating systems are proposed. These include strategies for the development and analysis of improved models for clock function, as well as the development of instruments and methods for conducting experiments with the synthetic genetic clock. In the third Specific Aim, we propose the development of additional sophisticated genetic clocks. Some of these genetic clocks are based on designs that have been extensively modeled by other labs, but have not been constructed and tested. In addition we propose designs for novel genetic clocks that test the role of various system design principles in the production of biological oscillations.