Tunable Low-Rate Genomic Recombination with Cre-lox in E. coli : A Versatile Tool for Synthetic Biology and Environmental Sensing

A variety of synthetic biology applications, from environmental sensing to bioproduction, would benefit from the ability to induce genomic alterations at low, tunable rates. Site-specific recombinases can be used to perform a variety of targeted DNA modifications such as excisions, inversions, and integrations. Their specificity and efficiency are offset by leaky expression and challenges in engineering a dynamic range of recombination rates. Here, we developed a tightly regulated, titratable Cre recombinase system that is tailored to achieve low recombination rates in Escherichia coli . As a proof-of-concept application of this design, we developed a whole-cell recombination-based arsenic biosensor, with detection sensitivity comparable to traditional wet chemical methods. Furthermore, our biosensor allows decoupling exposure from measurement, which could benefit assays in more complex, realistic settings. This system enables targeted genetic recombination events at experimentally tunable rates with application in ecological, environmental and cell physiology research, and beyond.