High-throughput mapping of the phage resistance landscape in E. coli

PLoS Biol. 2020 Oct 13;18(10):e3000877. doi: 10.1371/journal.pbio.3000877. eCollection 2020 Oct.

Abstract

Bacteriophages (phages) are critical players in the dynamics and function of microbial communities and drive processes as diverse as global biogeochemical cycles and human health. Phages tend to be predators finely tuned to attack specific hosts, even down to the strain level, which in turn defend themselves using an array of mechanisms. However, to date, efforts to rapidly and comprehensively identify bacterial host factors important in phage infection and resistance have yet to be fully realized. Here, we globally map the host genetic determinants involved in resistance to 14 phylogenetically diverse double-stranded DNA phages using two model Escherichia coli strains (K-12 and BL21) with known sequence divergence to demonstrate strain-specific differences. Using genome-wide loss-of-function and gain-of-function genetic technologies, we are able to confirm previously described phage receptors as well as uncover a number of previously unknown host factors that confer resistance to one or more of these phages. We uncover differences in resistance factors that strongly align with the susceptibility of K-12 and BL21 to specific phage. We also identify both phage-specific mechanisms, such as the unexpected role of cyclic-di-GMP in host sensitivity to phage N4, and more generic defenses, such as the overproduction of colanic acid capsular polysaccharide that defends against a wide array of phages. Our results indicate that host responses to phages can occur via diverse cellular mechanisms. Our systematic and high-throughput genetic workflow to characterize phage-host interaction determinants can be extended to diverse bacteria to generate datasets that allow predictive models of how phage-mediated selection will shape bacterial phenotype and evolution. The results of this study and future efforts to map the phage resistance landscape will lead to new insights into the coevolution of hosts and their phage, which can ultimately be used to design better phage therapeutic treatments and tools for precision microbiome engineering.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Bacteriophages / drug effects
  • Bacteriophages / physiology*
  • Biosynthetic Pathways / drug effects
  • CRISPR-Cas Systems / genetics
  • Cyclic GMP / analogs & derivatives
  • Cyclic GMP / pharmacology
  • DNA / genetics
  • Down-Regulation / drug effects
  • Down-Regulation / genetics
  • Escherichia coli / drug effects
  • Escherichia coli / genetics
  • Escherichia coli / virology*
  • Gene Expression Regulation, Bacterial / drug effects
  • Genes, Essential
  • Genome, Bacterial
  • Mutation / genetics
  • Phenotype
  • Reproducibility of Results
  • Suppression, Genetic

Substances

  • Bacterial Proteins
  • bis(3',5')-cyclic diguanylic acid
  • DNA
  • Cyclic GMP

Associated data

  • figshare/10.6084/m9.figshare.11859216.v1
  • figshare/10.6084/m9.figshare.11413128
  • figshare/10.6084/m9.figshare.11838879.v2

Grants and funding

This project was funded by the Microbiology Program of the Innovative Genomics Institute, Berkeley (to VKM, AMD, and APA). The initial concepts for this project were funded by ENIGMA, a Scientific Focus Area Program at the Lawrence Berkeley National Laboratory, supported by the US Department of Energy, Office of Science, Office of Biological and Environmental Research under contract DE-AC02-05CH11231 (to VKM, AMD, and APA). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.