1. Biochemistry and Chemical Biology
  2. Computational and Systems Biology
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Profiling the E. coli membrane interactome captured in peptidisc libraries

  1. Michael Luke Carlson
  2. R Greg Stacey
  3. John William Young
  4. Irvinder Singh Wason
  5. Zhiyu Zhao
  6. David G Rattray
  7. Nichollas Scott
  8. Craig H Kerr
  9. Mohan Babu
  10. Leonard J Foster
  11. Franck Van Hoa Duong  Is a corresponding author
  1. University of British Columbia, Canada
  2. University of Regina, Canada
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Cite this article as: eLife 2019;8:e46615 doi: 10.7554/eLife.46615

Abstract

Protein-correlation-profiling (PCP), in combination with quantitative proteomics, has emerged as a high-throughput method for the rapid identification of dynamic protein complexes in native conditions. While PCP has been successfully applied to soluble proteomes, characterization of the membrane interactome has lagged, partly due to the necessary use of detergents to maintain protein solubility. Here, we apply the peptidisc, a 'one-size fits all' membrane mimetic, for the capture of the Escherichia coli cell envelope proteome and its high-resolution fractionation in the absence of detergent. Analysis of the SILAC-labeled peptidisc library via PCP allows generation of over 4900 possible binary interactions out of >700,000 random associations. Using well-characterized membrane protein systems such as the SecY translocon, the Bam complex and the MetNI transporter, we demonstrate that our dataset is a useful resource for identifying transient and surprisingly novel protein interactions, some of them with profound biological implications, and many of them largely undetected by standard detergent-based purification. The peptidisc workflow applied to the proteomic field is a promising novel approach to characterize membrane protein interactions under native expression conditions and without genetic manipulation.

Data availability

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

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Author details

  1. Michael Luke Carlson

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3807-6516

  2. R Greg Stacey

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4496-8131

  3. John William Young

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3541-509X

  4. Irvinder Singh Wason

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
    Competing interests
    No competing interests declared.

  5. Zhiyu Zhao

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
    Competing interests
    No competing interests declared.

  6. David G Rattray

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
    Competing interests
    No competing interests declared.

  7. Nichollas Scott

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2556-8316

  8. Craig H Kerr

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
    Competing interests
    No competing interests declared.

  9. Mohan Babu

    Department of Biochemistry, University of Regina, Regina, Canada
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4118-6406

  10. Leonard J Foster

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8551-4817

  11. Franck Van Hoa Duong

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
    For correspondence
    fduong@mail.ubc.ca
    Competing interests
    Franck Van Hoa Duong, has a website which sells the peptide used in this study.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7328-6124

Funding

Canadian Institutes of Health Research

  • Franck Van Hoa Duong

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

Reviewing Editor

  1. Nir Ben-Tal, Tel Aviv University, Israel

Publication history

  1. Received: March 7, 2019
  2. Accepted: July 30, 2019
  3. Accepted Manuscript published: July 31, 2019 (version 1)
  4. Version of Record published: August 16, 2019 (version 2)

Copyright

© 2019, Carlson 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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