TY - JOUR T1 - Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems JF - bioRxiv DO - 10.1101/2020.01.31.928689 SP - 2020.01.31.928689 AU - Timothy C. Yu AU - Winnie L. Liu AU - Marcia Brinck AU - Jessica E. Davis AU - Jeremy Shek AU - Grace Bower AU - Tal Einav AU - Kimberly D. Insigne AU - Rob Phillips AU - Sriram Kosuri AU - Guillaume Urtecho Y1 - 2020/01/01 UR - http://biorxiv.org/content/early/2020/02/02/2020.01.31.928689.abstract N2 - A crucial step towards engineering biological systems is the ability to precisely tune the genetic response to environmental stimuli. In the case of Escherichia coli inducible promoters, our incomplete understanding of the relationship between sequence composition and gene expression hinders our ability to predictably control transcriptional responses. Here, we profile the expression dynamics of 8,269 rationally designed IPTG-inducible promoters that collectively explore the individual and combinatorial effects of RNA polymerase and LacI repressor binding site strengths. Using these data, we fit a statistical mechanics model that accurately models gene expression and reveals properties of theoretically optimal inducible promoters. Furthermore, we characterize three novel promoter architectures and show that repositioning binding sites within promoters influences the types of combinatorial effects observed between promoter elements. In total, this approach enables us to deconstruct relationships between inducible promoter elements and discover practical insights for engineering inducible promoters with desirable characteristics. ER -