Tunable Protein Degradation for Control of Synthetic and Endogenous Bacterial Systems

Tunable control of protein degradation in bacteria would provide a powerful research tool to develop synthetic gene circuits and probe natural cellular systems. Here we use components of the Mesoplasma florum tmRNA system to create a targeted degradation system in E. coli that provides control of both the initial steady-state level and the inducible degradation rate of the targeted protein. We demonstrate the system’s use in synthetic circuit development and in exogenous control of core bacterial processes including peptidoglycan biosynthesis, cell division and chemotactic motility. We transfer the system to Lactococcus lactis to establish its broad functionality in bacteria, and we create a 238-member library of tagged essential proteins in E. coli that can serve as both a research tool to study essential gene function and an applied system for antibiotic discovery. The synthetic degradation system is modular, requiring a small peptide tag and a single protease gene, does not require disruption of host systems, and can be transferred to other bacteria with minimal modification.