Systematic and scalable genome-wide essentiality mapping to identify nonessential genes in phages

Piya, Denish; Nolan, Nicholas; Moore, Madeline L.; Ramirez Hernandez, Luis A.; Cress, Brady F.; Young, Ry; Arkin, Adam P.; Mutalik, Vivek K.

doi:10.1371/journal.pbio.3002416

Title: Systematic and scalable genome-wide essentiality mapping to identify nonessential genes in phages

Journal Article · 04 December 2023 · PLoS Biology (Online)

DOI: https://doi.org/10.1371/journal.pbio.3002416 · OSTI ID:2228385

Piya, Denish ^[1]; Nolan, Nicholas ^[1]; Moore, Madeline L. ^[2]; Ramirez Hernandez, Luis A. ^[2]; Cress, Brady F. ^[1]; Young, Ry ^[3];

^[4];

^[4]

Univ. of California, Berkeley, CA (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Texas A & M Univ., College Station, TX (United States)
Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Phages are one of the key ecological drivers of microbial community dynamics, function, and evolution. Despite their importance in bacterial ecology and evolutionary processes, phage genes are poorly characterized, hampering their usage in a variety of biotechnological applications. Methods to characterize such genes, even those critical to the phage life cycle, are labor intensive and are generally phage specific. Here, we develop a systematic gene essentiality mapping method scalable to new phage–host combinations that facilitate the identification of nonessential genes. As a proof of concept, we use an arrayed genome-wide CRISPR interference (CRISPRi) assay to map gene essentiality landscape in the canonical coliphages λ and P1. Results from a single panel of CRISPRi probes largely recapitulate the essential gene roster determined from decades of genetic analysis for lambda and provide new insights into essential and nonessential loci in P1. We present evidence of how CRISPRi polarity can lead to false positive gene essentiality assignments and recommend caution towards interpreting CRISPRi data on gene essentiality when applied to less studied phages. Finally, we show that we can engineer phages by inserting DNA barcodes into newly identified inessential regions, which will empower processes of identification, quantification, and tracking of phages in diverse applications.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institute of General Medical Sciences (NIGMS); USDOE

Grant/Contract Number:: AC02-05CH11231; R35GM136396; National Virtual Biotechnology Laboratory at LBNL

OSTI ID:: 2228385

Alternate ID(s):: OSTI ID: 2228323

Journal Information:: PLoS Biology (Online), Vol. 21, Issue 12; ISSN 1545-7885

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
Bacteriophages
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Viral genomics
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Title: Systematic and scalable genome-wide essentiality mapping to identify nonessential genes in phages

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