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

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

Authors 

Cress, B. - Presenter
Adler, B. A., UC Berkeley?UCSF Graduate Program in Bioengineering
Al-Shimary, M., University of California, Berkeley
Patel, J., University of California, Berkeley
Schoeniger, J., Sandia National Laboratories
Savage, D., UC Berkeley
Doudna, J. A., University of California Berkeley
Armbruster, E., University of California, San Diego
Pogliano, J., University of California, San Diego
Colognori, D., University of California, Berkeley
Charles, E., University of California, Berkeley
Miller, K. V., University of California, Berkeley
Trinidad, M., University of California, Berkeley
Boger, R., University of California, Berkeley
Nomburg, J., University of California, Berkeley
Beurnier, S., University of California, Berkeley
Cui, M.
Barrangou, R., North Carolina State University
Mutalik, V. K., Lawrence Berkeley National Lab
Lahiri, A., 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.