Synthetic Regulatory Small RNAs for Genome-Wide Metabolic Engineering

Optimized modulation of metabolic fluxes through the control of gene expression is one of the key challenges in metabolic engineering. Here, we developed rational design principles for synthetic regulatory small RNAs (sRNAs) for adjustable expression control. We then expanded our method to create a system utilizing synthetic sRNAs as a portable and conditional chromosomal gene controller, and engineered Escherichia coli to produce tyrosine and cadaverine as a model. An engineered E. coli strain (tyrR csrA repressed S17-1 strain) capable of producing 21.9 g/L of tyrosine was developed by combinatorial knockdown experiments on various candidate genes in 14 different strains using respective synthetic sRNAs. As another example, this strategy was applied to an already metabolically engineered strain producing cadaverine by applying a library of 130 synthetic sRNAs. Repression of murE allowed 55% increase in cadaverine production. The feasibility of using synthetic sRNAs to modulate gene expression holds great promise in next-generation metabolic engineering and synthetic biology applications. [This work was supported by the Technology Development Program to Solve Climate Changes on Systems Metabolic Engineering for Biorefineries from the Ministry of Science, ICT and Future Planning (MSIP) through the National Research Foundation (NRF) of Korea (NRF-2012-C1AAA001-2012M1A2A2026556).]