A New Phage-engineering Platform Allows High-throughput Assembly of Hybrid Viral Genomes in Yeast

Bacteriophages target bacteria with high specificity, a feature that has been exploited for biotechnology and therapeutics. That same exquisite specificity has, however, also been limiting — identifying or engineering phages with new specificities is often a prohibitively time consuming and laborious process. Scientists at MIT have now developed a yeast-based phage-engineering platform that overcomes these hurdles.

Traditionally new phages are isolated from nature. This poses a challenge because phage diversity is great, making new phages difficult to manipulate, manufacture, and shepherd through regulatory processes. An alternative approach is to alter the specificity of known phages, a difficult undertaking as phage genomes are too large to manipulate easily in vitro and exist in bacteria for too short of a time to manipulate effectively in vivo. This has led scientists to resort to altering individual phage genes in bacterial cloning vectors using classical biology. Upon infection phages are then engineered through recombination with the bacterial plasmid. Not only is this a slow and tedious process it also limits which phage genes can be altered, as many are toxic to bacteria.

To circumvent these challenges Ando et al took advantage of gap repair cloning in Saccharomyces cerevisiae. Each gene of the phage of interest is PCR amplified such that a region of homology with adjacent fragments is maintained. The entire viral genome is reassembled and ligated into a yeast artificial chromosome (YAC) fragment via gap repair upon transformation into yeast. Phages assembled in this manner could infect and lyse their host bacteria. Host range could be tuned by generating hybrid viruses using PCR amplicons from different phages. By creating a method to quickly and efficiently assembly viral genomes, Ando et al have created a tool that can accelerate the study of phage biology and carries great hope for future treatments of infectious disease.

Source: Ando H et al. (2015). Engineering Modular Viral Scaffolds for Targeted Bacterial Population Editing. Cell Systems 1, 187–196.