Aptamer-Enabled Modification of Bacteriophage Host Range

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Project Summary The term “superbug” conjures up in public consciousness the imagery of nasty bacteria recalcitrant to antibiotic treatments, a public health threat further heightened by the dwindling supply of new antibiotics in the development pipeline. Imprudent use of broad-spectrum antibiotics is also harmful to the beneficial microbiota. With the renewed urgency, the US National Institutes of Health listed phage therapy as one of seven prongs in its plan to combat antibiotic resistance. Bacteriophages (phages) are viruses that only infect and kill bacteria. Phage therapy is the targeted application of phages as bactericidal agent to treat bacterial infections. However, to better respond to emerging and evolving bacterial pathogens, all therapeutic and prophylactic phage products will require periodic updates, which will inevitably incur further cost in product maintenance. The unpatentability of “product of nature” further reduces incentives for commercial entities to participate in the research and development (R&D) to realize the full potential of phage therapy. Here we propose an innovative approach to bypass the required updates that can plague the conventional whole-phage products, and at the same time provide an incentive for R&D with an intellectual property that is easily securable and defendable. Our proposal is made possible by recent studies, revealing intricate steps involved in host recognition by a phage and how the signal of recognition is able to trigger the preprogrammed conformational changes in the phage tail that eventually leads to the delivery of phage DNA genome into the infected bacterial cell, thus killing it. We take advantages of the extensively studied classics, T4 and T7, and their host, Escherichia coli, as the model system to test the hypothesis that an artificially tethered phage can be triggered to deliver its DNA genome into a non-host cell. In this scheme, phage tethering is achieved by chemically stable RNA aptamers that specifically bind to the phage tail fiber, the receptor-binding protein of the phage, and those that bind to the surface macromolecules of E. coli. By coupling together these two types of aptamers, we can bring a phage to close physical proximity of the cell surface, a pre-requisite for a successful infection. Based on the hypothesis, the Brownian motion, experienced by an attached phage, will trigger the preprogrammed deployment of the proteins involved in phage tail such that the DNA genome can be delivered. We will use the well-established molecular breeding process, called SELEX, to generate the required aptamers. Our proposed study represents a unique solution to the problems—especially the scalability and the patentability—encountered by using phage as a therapeutic and prophylactic agent against bacterial infection. If the result is encouraging from this proof-of-concept study, we believe we will be able to open an entirely new and impactful revenue of research.