The interaction between a bacteriophage and its host is mediated by the phage's receptor binding protein (RBP). Despite its fundamental role in governing phage activity and host range, molecular rules of RBP function remain a mystery. Here, we systematically dissect the functional role of every residue in the tip domain of T7 phage RBP (1660 variants) by developing a high-throughput, locus-specific, phage engineering method. This rich dataset allowed us to cross compare functional profiles across hosts to precisely identify regions of functional importance, many which were previously unknown. Substitution patterns showed host-specific differences in position and physicochemical properties of mutations, revealing molecular adaptation to individual hosts. We discovered gain-of-function variants against resistant hosts and host-constricting variants that eliminated certain hosts. To demonstrate therapeutic utility, we engineered highly active T7 variants against urinary tract pathogen. Our approach presents a generalized framework for characterizing sequence-function relationships in many phage-bacterial systems.
Source code has been deposited on github here: https://github.com/raman-lab/oracle.Raw NGS data is publicly available through our institutional repository UW Box here:https://uwmadison.box.com/s/7fa1mk7hcznf9unhzubzey9h1un8wrbv.Other data generated or analyzed during this study are included in the manuscript and supporting files. Source data files have been provided for Figures 1, 2, 3, 4 and 6.
- Srivatsan Raman
- Srivatsan Raman
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
- Peter Turnbaugh, University of California, San Francisco, United States
© 2021, Huss et al.
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