Tunable low-rate genomic recombination with Cre-lox in Escherichia coli: a versatile tool for dynamical phenotypic state transitions and environmental sensing

Ecological and environmental research would benefit from the ability to induce in vivo genomic alterations at low, tunable rates, enabling dynamic cell transitions into different phenotypic or physiological states. Proteins like site-specific recombinases enable targeted DNA modifications such as excisions, inversions, and integrations. Their specificity and efficiency are offset by leaky expression and challenges in engineering a broad dynamic range of activity. Here, we developed a tightly regulated, titratable Cre recombinase-lox system that is tailored to achieve low recombination rates in Escherichia coli. This system exploits chemically inducible promoters and post-translational regulation to reduce Cre activity. As a proof-of-concept demonstration of the broad applicability of this design, we developed a whole-cell, recombination-based arsenic biosensor with detection sensitivity comparable to traditional wet chemical methods. Our biosensor allows decoupling exposure from measurement, potentially enabling its deployment and assays in anaerobic environments. This work provides a tool enabling targeted genetic recombination events at experimentally tunable rates that has potential applications in ecological, environmental and cell physiology research.