Phage Foundry: A High-Throughput Platform for Rapid Design and Development of Countermeasures to Combat Emerging Drug-Resistant Pathogens

Bacteriophages (viruses of bacteria) are being explored as diagnostic and therapeutic tools. Bacteriophages that display a broad host range, i.e. those that infect different bacterial strains and even different bacterial species, are of particular interest as they hold a promise of replacing conventional broad spectrum antibiotics. We have discovered that bacteriophage phi92 can infect several clinically important strains of Escherichia coli including those carrying polysialic acid and colanic acid capsules, several strains of Salmonella, and even one strain of Pseudomonas aeruginosa. The mechanisms by which phi92 recognizes the surfaces of these bacteria and attaches to their outer membrane is not understood.

The project aims to define determine the structure of polyvalent bacteriophage phi92 and define the proteins it uses to recognize the surface of different bacterial species. A hybrid approach will be used. The structure of the phi92 virus particle will be determined using cryogenic electron microscopy (cryo-EM) while the structure of phi92 surface receptor ­binding proteins will be determined by X-ray crystallography. The ultimate objective is to provide the Phage Foundry team lead by Vivek K. Mutalik at LBNL with a tunable platform for the design of broad host range bacteriophages.

The project will employ a comprehensive approach to derive the structure of the phi92 virus particle and its host cell-binding proteins in atomic detail. The approach will involve virus growth and purification; protein cloning, expression and crystallization; and determination of the atomic structure by cryo-EM and X-ray crystallography.