Defining hierarchical protein interaction networks from spectral analysis of bacterial proteomes

  1. Mark A Zaydman  Is a corresponding author
  2. Alexander A Little
  3. Fidel Haro
  4. Valeryia Aksianiuk
  5. William J Buchser
  6. Aaron DiAntonio
  7. Jeffrey I Gordon
  8. Jeffrey Milbrandt
  9. Arjun S Raman  Is a corresponding author
  1. Washington University in St. Louis, United States
  2. University of Chicago, United States

Abstract

Cellular behaviors emerge from layers of molecular interactions: proteins interact to form complexes, pathways, and phenotypes. We show that hierarchical networks of protein interactions can be defined from the statistical pattern of proteome variation measured across thousands of diverse bacteria and that these networks reflect the emergence of complex bacterial phenotypes. Our results are validated through gene-set enrichment analysis and comparison to existing experimentally-derived databases. We demonstrate the biological utility of our approach by creating a model of motility in Pseudomonas aeruginosa and using it to identify a protein that affects pilus-mediated motility. Our method, SCALES (Spectral Correlation Analysis of Layered Evolutionary Signals), may be useful for interrogating genotype-phenotype relationships in bacteria.

Data availability

All data relevant to this manuscript can be downloaded, in Table format, at www.github.com/arjunsraman/Zaydman_et_al. All tables are available for download in .zip format. All code used for analyses contained within the manuscript can also be found within the same github repository; please refer to Readme.m and Supplemental_Code_9_23_2020.m for relevant Matlab scripts and to reproduce results.

Article and author information

Author details

  1. Mark A Zaydman

    Department of Pathology, Washington University in St. Louis, St Louis, United States
    For correspondence
    zaydmanm@wustl.edu
    Competing interests
    The authors declare that no competing interests exist.
  2. Alexander A Little

    Duchossois Family Institute, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Fidel Haro

    Duchossois Family Institute, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Valeryia Aksianiuk

    Duchossois Family Institute, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. William J Buchser

    Department of Genetics, Washington University in St. Louis, St Louis, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Aaron DiAntonio

    Department of Developmental Biology, Washington University in St. Louis, St Louis, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7262-0968
  7. Jeffrey I Gordon

    Department of Pathology, Washington University in St. Louis, St Louis, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8304-3548
  8. Jeffrey Milbrandt

    Department of Genetics, Washington University in St. Louis, St Louis, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Arjun S Raman

    Duchossois Family Institute, University of Chicago, Chicago, United States
    For correspondence
    araman@bsd.uchicago.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0070-1953

Funding

No external funding was received for this work.

Reviewing Editor

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

Version history

  1. Received: September 21, 2021
  2. Preprint posted: September 28, 2021 (view preprint)
  3. Accepted: August 17, 2022
  4. Accepted Manuscript published: August 17, 2022 (version 1)
  5. Version of Record published: August 30, 2022 (version 2)

Copyright

© 2022, Zaydman 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. Mark A Zaydman
  2. Alexander A Little
  3. Fidel Haro
  4. Valeryia Aksianiuk
  5. William J Buchser
  6. Aaron DiAntonio
  7. Jeffrey I Gordon
  8. Jeffrey Milbrandt
  9. Arjun S Raman
(2022)
Defining hierarchical protein interaction networks from spectral analysis of bacterial proteomes
eLife 11:e74104.
https://doi.org/10.7554/eLife.74104

Share this article

https://doi.org/10.7554/eLife.74104

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