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.
Highlights
Bacterial viruses, or bacteriophages, are obligate parasites that infect specific bacterial strains
Using E. coli K-12 strain and 14 diverse double-stranded DNA phages, we show that our screens successfully identify known receptors and other host factors important in infection pathways, and they yield additional novel loci that contribute to phage resistance
We demonstrate how these methods can rapidly identify phage receptors and both novel and previously described non-phage-receptor-related host factors involved in resistance across a wide panel of double-stranded DNA (dsDNA) phage types
Summary
Bacteriophages (phages), are obligate parasites that infect specific bacterial strains. There have been few attempts to use genetic approaches for studying genome-wide host factors essential in phage infection These loss-of-function (LOF) genetic screens broadly use bacterial saturation mutagenesis [49,54,58,59,60,61] or an arrayed library of single-gene deletion strains for studying phage-host interactions [50,51,53,62,63]. These studies have generally involved laborious experiments on relatively few phages and their hosts, and scaling the approach to characterize hundreds of phages is challenging
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