6th International Conference on Microbiome Engineering

Genome-Wide Characterization of Diverse Bacteriophages Enabled By RNA-Binding Crispri

Authors

Benjamin A. Adler, UC Berkeley?UCSF Graduate Program in Bioengineering
Muntathar Al-Shimary, University of California, Berkeley
Jaymin Patel, University of California, Berkeley
Joseph Schoeniger, Sandia National Laboratories
David Savage, UC Berkeley
Jennifer A. Doudna, University of California Berkeley
Emily Armbruster, University of California, San Diego
Joseph Pogliano, University of California, San Diego
David Colognori, University of California, Berkeley
Emeric Charles, University of California, Berkeley
Kate V Miller, University of California, Berkeley
Marena Trinidad, University of California, Berkeley
Ron Boger, University of California, Berkeley
Jason Nomburg, University of California, Berkeley
Sebastien Beurnier, University of California, Berkeley
Rodolphe Barrangou, North Carolina State University
Vivek K. Mutalik, Lawrence Berkeley National Lab
Arushi Lahiri, University of California, Berkeley
Bacteriophages play a pivotal role in shaping human health and environmental ecosystems through interactions with bacteria in complex microbial communities. Phages also represent one of the largest reservoirs of unexplored gene content in the biosphere. Even for well-studied model phages, rapid and efficient experimental approaches to identify and investigate their essential genes remain elusive. Here we uncover and exploit the conserved vulnerability of the phage transcriptome to facilitate genome-wide protein expression knockdown via programmable RNA-binding protein dRfxCas13d (CRISPRi-ART) across diverse phages and their host. Establishing the first broad-spectrum phage functional genomics platform, we predict over 90 essential genes across four phage genomes, a third of which have no known function. These results highlight hidden infection strategies encoded in the most abundant biological entities on earth and provide a facile platform to study them. We anticipate that CRISPRi-ART will guide phage engineering strategies for phage therapy and microbiome editing applications.