Broad-spectrum CRISPR-Cas13a enables efficient phage genome editing

Scientists from the Innovative Genomics Institute at UC Berkeley, North Carolina State University and Lawrence Berkeley National Lab use RNA-targeting CRISPR systems to drive genome editing across phage diversity.

Bacterial viruses (bacteriophages or phages) are estimated to be among the most diverse and abundant biological entities on earth. As bacterial predators, phages are their host bacteria are locked in a coevolutionary arms race, driving the evolution of phage defense-systems such as CRISPR-Cas and ways to undermine these systems encoded by phages. Because many of the genome editing tools are derived from this arms race, tools for phage genome-editing have limited efficacy. Scientists’ ability to perform genetics in, nonetheless engineer, phages remains inherently limited.

By investigating a rare and unconventional CRISPR-Cas system (Cas13a), researchers from the Innovative Genomics Institute at University of California Berkeley in collaboration with North Carolina State University and Lawrence Berkeley National Lab found phage-encoded defense  against Cas13a targeting to be incredibly rare across E. coli phage diversity. By using this broad vulnerability to Cas13a, they were able to establish a robust phage genome-editing practice across phage diversity. Critically, they demonstrated the capacity to perform precise and diverse edits ranging from single codons up to multi-gene deletions.

As a result of this study, researchers are now capable of genome-editing in diverse phages. Use of these findings and tools allows us to easily perform genetics in phages, allowing us to better understand phage-host interactions and discover phage-encoded biotechnological tools. Additionally this study greatly facilitates phage engineering for phage therapy and microbiome engineering.