In situ imaging of bacterial outer membrane projections and associated protein complexes using electron cryo-tomography

  1. Mohammed Kaplan
  2. Georges Chreifi
  3. Lauren Ann Metskas
  4. Janine Liedtke
  5. Cecily R Wood
  6. Catherine M Oikonomou
  7. William J Nicolas
  8. Poorna Subramanian
  9. Lori A Zacharoff
  10. Yuhang Wang
  11. Yi-Wei Chang
  12. Morgan Beeby
  13. Megan Dobro
  14. Yongtao Zhu
  15. Mark McBride
  16. Ariane Briegel
  17. Carrie Shaffer
  18. Grant J Jensen  Is a corresponding author
  1. California Institute of Technology, United States
  2. Leiden University, United States
  3. University of Kentucky, United States
  4. University of Southern California, United States
  5. University of Pennsylvania, United States
  6. Imperial College London, United Kingdom
  7. Hampshire College, United States
  8. Minnesota State University, United States
  9. University of Wisconsin, United States
  10. Leiden University, Netherlands

Abstract

The ability to produce outer membrane projections in the form of tubular membrane extensions (MEs) and membrane vesicles (MVs) is a widespread phenomenon among diderm bacteria. Despite this, our knowledge of the ultrastructure of these extensions and their associated protein complexes remains limited. Here, we surveyed the ultrastructure and formation of MEs and MVs, and their associated protein complexes, in tens of thousands of electron cryo-tomograms of ~ 90 bacterial species that we have collected for various projects over the past 15 years (Jensen lab database), in addition to data generated in the Briegel lab. We identified outer MEs and MVs in 13 diderm bacterial species and classified several major ultrastructures: 1) tubes with a uniform diameter (with or without an internal scaffold), 2) tubes with irregular diameter, 3) tubes with a vesicular dilation at their tip, 4) pearling tubes, 5) connected chains of vesicles (with or without neck-like connectors), 6) budding vesicles and nanopods. We also identified several protein complexes associated with these MEs and MVs which were distributed either randomly or exclusively at the tip. These complexes include a secretin-like structure and a novel crown-shaped structure observed primarily in vesicles from lysed cells. In total, this work helps to characterize the diversity of bacterial membrane projections and lays the groundwork for future research in this field.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files and movies.

Article and author information

Author details

  1. Mohammed Kaplan

    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0759-0459
  2. Georges Chreifi

    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Lauren Ann Metskas

    Biological Sciences, Chemistry, California Institute of Technology, Pasadena, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8073-6960
  4. Janine Liedtke

    Leiden University, Pasadena, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2680-4130
  5. Cecily R Wood

    University of Kentucky, Kentucky, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Catherine M Oikonomou

    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2312-4746
  7. William J Nicolas

    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Poorna Subramanian

    Biological Sciences, Chemistry, California Institute of Technology, Pasadena, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Lori A Zacharoff

    University of Southern California, Los Angeles, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Yuhang Wang

    California Institute of Technology, pasadena, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3715-8349
  11. Yi-Wei Chang

    Department of Biochemistry and Biophysics, University of Pennsylvania, Pennsylvania, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2391-473X
  12. Morgan Beeby

    Department of Life Sciencesa, Imperial College London, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6413-9835
  13. Megan Dobro

    Hampshire College, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  14. Yongtao Zhu

    Department of Biological Sciences, Minnesota State University, Mankato, United States
    Competing interests
    The authors declare that no competing interests exist.
  15. Mark McBride

    University of Wisconsin, Milwaukee, United States
    Competing interests
    The authors declare that no competing interests exist.
  16. Ariane Briegel

    Leiden University, Leiden, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  17. Carrie Shaffer

    University of Kentucky, Kentucky, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7457-7422
  18. Grant J Jensen

    Biology and Bioengineering, California Institute of Technology, Pasadena, United States
    For correspondence
    jensen@caltech.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1556-4864

Funding

Foundation for the National Institutes of Health (R35 GM122588)

  • Grant J Jensen

Baxter Postdoctoral fellowship

  • Mohammed Kaplan

Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO OCENW.GROOT.2019.063)

  • Mohammed Kaplan

National Institutes of Health (P20 GM130456)

  • Carrie Shaffer

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

Reviewing Editor

  1. Bavesh D Kana, University of the Witwatersrand, South Africa

Publication history

  1. Preprint posted: July 13, 2021 (view preprint)
  2. Received: August 17, 2021
  3. Accepted: August 23, 2021
  4. Accepted Manuscript published: September 1, 2021 (version 1)
  5. Version of Record published: September 21, 2021 (version 2)

Copyright

© 2021, Kaplan 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. Mohammed Kaplan
  2. Georges Chreifi
  3. Lauren Ann Metskas
  4. Janine Liedtke
  5. Cecily R Wood
  6. Catherine M Oikonomou
  7. William J Nicolas
  8. Poorna Subramanian
  9. Lori A Zacharoff
  10. Yuhang Wang
  11. Yi-Wei Chang
  12. Morgan Beeby
  13. Megan Dobro
  14. Yongtao Zhu
  15. Mark McBride
  16. Ariane Briegel
  17. Carrie Shaffer
  18. Grant J Jensen
(2021)
In situ imaging of bacterial outer membrane projections and associated protein complexes using electron cryo-tomography
eLife 10:e73099.
https://doi.org/10.7554/eLife.73099
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