Colicin E1 opens its hinge to plug TolC

  1. S Jimmy Budiardjo
  2. Jacqueline J Stevens
  3. Anna L Calkins
  4. Ayotunde P Ikujuni
  5. Virangika K Wimalasena
  6. Emre Firlar
  7. David A Case
  8. Julie S Biteen
  9. Jason T Kaelber
  10. Joanna SG Slusky  Is a corresponding author
  1. University of Kansas, United States
  2. University of Michigan, United States
  3. Rutgers University, United States
  4. Rutgers, The State University of New Jersey, United States

Abstract

The double membrane architecture of Gram-negative bacteria forms a barrier that is impermeable to most extracellular threats. Bacteriocin proteins evolved to exploit the accessible, surface-exposed proteins embedded in the outer membrane to deliver cytotoxic cargo. Colicin E1 is a bacteriocin produced by, and lethal to, Escherichia coli that hijacks the outer membrane proteins TolC and BtuB to enter the cell. Here we capture the colicin E1 translocation domain inside its membrane receptor, TolC, by high-resolution cryoEM to obtain the first reported structure of a bacteriocin bound to TolC. Colicin E1 binds stably to TolC as an open hinge through the TolC pore-an architectural rearrangement from colicin E1's unbound conformation. This binding is stable in live E. coli cells as indicated by single-molecule fluorescence microscopy. Finally, colicin E1 fragments binding to TolC plug the channel, inhibiting its native efflux function as an antibiotic efflux pump and heightening susceptibility to three antibiotic classes. In addition to demonstrating that these protein fragments are useful starting points for developing novel antibiotic potentiators, this method could be expanded to other colicins to inhibit other outer membrane protein functions.

Data availability

The manuscript has been deposited in BioRXiv BIORXIV/2019/692251CryoEM maps and models have been deposited with accession codes EMD-21960, EMD-21959, PDB ID 6WXI, and PDB ID 6WXH. The following data are publically available for the two structures:6WXH TolC + colE1Structure: https://files.rcsb.org/download/6WXH.cifEM map: https://ftp.wwpdb.org/pub/emdb/structures/EMD-21959/map/emd_21959.map.gzValidation report: https://files.rcsb.org/pub/pdb/validation_reports/wx/6wxh/6wxh_full_validation.pdf6WXI TolC aloneStructure: https://files.rcsb.org/download/6WXI.cifEM map: https://ftp.wwpdb.org/pub/emdb/structures/EMD-21960/map/emd_21960.map.gzValidation report: https://files.rcsb.org/pub/pdb/validation_reports/wx/6wxi/6wxi_full_validation.pdf

The following data sets were generated

Article and author information

Author details

  1. S Jimmy Budiardjo

    Center for Computational Biology, University of Kansas, Lawrence, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2094-9179
  2. Jacqueline J Stevens

    Department of Molecular Biosciences, University of Kansas, Lawrence, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2235-0522
  3. Anna L Calkins

    Department of Chemistry, University of Michigan, Ann Arbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Ayotunde P Ikujuni

    Department of Molecular Biosciences, University of Kansas, Lawrence, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8951-3440
  5. Virangika K Wimalasena

    Department of Molecular Biosciences, University of Kansas, Lawrence, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1061-3439
  6. Emre Firlar

    Institute for Quantitative Biomedicine, Rutgers University, Piscataway, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. David A Case

    Institute for Quantitative Biomedicine, Rutgers University, Piscataway, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Julie S Biteen

    Department of Chemistry, University of Michigan, Ann Arbor, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2038-6484
  9. Jason T Kaelber

    Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9426-1030
  10. Joanna SG Slusky

    Center for Computational Biology, University of Kansas, Lawrence, United States
    For correspondence
    slusky@ku.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0842-6340

Funding

National Institute of General Medical Sciences (DP2GM128201)

  • Joanna SG Slusky

National Institute of General Medical Sciences (P20GM113117)

  • Joanna SG Slusky

National Institute of General Medical Sciences (P20GM103638)

  • Joanna SG Slusky

Gordon and Betty Moore Foundation (Moore Inventor Fellowship)

  • Joanna SG Slusky

National Institute of General Medical Sciences (P20 GM103418)

  • S Jimmy Budiardjo

National Institute of General Medical Sciences (2K12GM063651)

  • S Jimmy Budiardjo

National Institute of General Medical Sciences (R21-GM128022)

  • Julie S Biteen

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

Reviewing Editor

  1. David Drew, Stockholm University, Sweden

Publication history

  1. Preprint posted: July 4, 2019 (view preprint)
  2. Received: August 24, 2021
  3. Accepted: February 21, 2022
  4. Accepted Manuscript published: February 24, 2022 (version 1)
  5. Version of Record published: April 20, 2022 (version 2)

Copyright

© 2022, Budiardjo 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. S Jimmy Budiardjo
  2. Jacqueline J Stevens
  3. Anna L Calkins
  4. Ayotunde P Ikujuni
  5. Virangika K Wimalasena
  6. Emre Firlar
  7. David A Case
  8. Julie S Biteen
  9. Jason T Kaelber
  10. Joanna SG Slusky
(2022)
Colicin E1 opens its hinge to plug TolC
eLife 11:e73297.
https://doi.org/10.7554/eLife.73297

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