Mapping the functional landscape of the receptor binding domain of T7 bacteriophage by deep mutational scanning

  1. Phil Huss
  2. Anthony Meger
  3. Megan Leander
  4. Kyle K Nishikawa
  5. Srivatsan Raman  Is a corresponding author
  1. University of Wisconsin-Madison, United States

Abstract

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.

Data availability

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.

Article and author information

Author details

  1. Phil Huss

    Biochemistry, Microbiology, University of Wisconsin-Madison, Madison, United States
    Competing interests
    Phil Huss, P.H and S.R have filed a provisional patent application on this technology (patent application number WIS0055US)..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4064-9333
  2. Anthony Meger

    Biochemistry, University of Wisconsin-Madison, Madison, United States
    Competing interests
    No competing interests declared.
  3. Megan Leander

    Biochemistry, University of Wisconsin-Madison, Madison, United States
    Competing interests
    No competing interests declared.
  4. Kyle K Nishikawa

    Biochemistry, University of Wisconsin-Madison, Madison, United States
    Competing interests
    No competing interests declared.
  5. Srivatsan Raman

    Biochemistry, University of Wisconsin-Madison, Madison, United States
    For correspondence
    sraman4@wisc.edu
    Competing interests
    Srivatsan Raman, P.H and S.R have filed a provisional patent application on this technology (patent application number WIS0055US). S.R is on the scientific advisory board of MAP/PATH LLC..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2461-1589

Funding

U.S. Department of Agriculture

  • Srivatsan Raman

Bill and Melinda Gates Foundation

  • Srivatsan Raman

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Peter Turnbaugh, University of California, San Francisco, United States

Version history

  1. Received: October 7, 2020
  2. Accepted: March 4, 2021
  3. Accepted Manuscript published: March 9, 2021 (version 1)
  4. Version of Record published: April 13, 2021 (version 2)

Copyright

© 2021, Huss et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Phil Huss
  2. Anthony Meger
  3. Megan Leander
  4. Kyle K Nishikawa
  5. Srivatsan Raman
(2021)
Mapping the functional landscape of the receptor binding domain of T7 bacteriophage by deep mutational scanning
eLife 10:e63775.
https://doi.org/10.7554/eLife.63775

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https://doi.org/10.7554/eLife.63775

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