Tailoring Escherichia coli Chemotactic Sensing towards Cadmium by Computational Redesign of Ribose-Binding Protein

Periplasmic binding proteins such as ribose-binding proteins (RBPs) are involved in the bacterial chemotaxis two-component system. RBP selectively identifies and interacts with ribose to induce a conformational change that leads to chemotaxis. Here, we report the development of an engineered Escherichia coli (E. coli) strain expressing a redesigned RBP that can effectively sense cadmium ions and regulate chemotactic movement of cells toward a cadmium ion gradient. RBP was computationally redesigned to bind cadmium ions and produce the conformational change required for chemoreceptor binding. The successful design, CdRBP1, binds to cadmium ions with a dissociation constant of 268 nM. When CdRBP1 was expressed in the periplasmic space of E. coli, the bacteria became live cadmium ion hunters with high selectivity over other divalent metal ions. This work presents an example of making cadmium ions, which are toxic for most organisms, as an attractant to regulate cells movement. Our approach also demonstrates that RBP can be precisely designed to develop metal-detecting living systems for potential applications in synthetic biology and environmental studies. IMPORTANCE Cadmium pollution is one of the major environmental problems due to excessive release and accumulation. New technologies that can auto-detect cadmium ions with good biocompatibility are in urgent need. In this study, we engineered the bacterial chemotaxis system to positively sense cadmium ions by redesigning ribose-binding protein (RBP) to tightly bind cadmium ion and produce the right conformational change for receptor binding and signaling. Our engineered E. coli cells can auto-detect and chase cadmium ions with divalent metal ion selectivity. Many attempts have been carried out to redesign RBP at the ribose binding site with little success. Instead of the ribose binding site, we introduced the cadmium binding site in the opening of the ribose binding pocket by a specially developed computational algorithm. Our design strategy can be applied to engineer live bacteria with autonomous detection and remediation abilities for metal ions or other chemicals in the future.