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.

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.

Metrics

  • 1,787
    views
  • 283
    downloads
  • 4
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  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

Further reading

    1. Computational and Systems Biology
    2. Genetics and Genomics
    Fangluo Chen, Dylan C Sarver ... G William Wong
    Research Article

    Obesity is a major risk factor for type 2 diabetes, dyslipidemia, cardiovascular disease, and hypertension. Intriguingly, there is a subset of metabolically healthy obese (MHO) individuals who are seemingly able to maintain a healthy metabolic profile free of metabolic syndrome. The molecular underpinnings of MHO, however, are not well understood. Here, we report that CTRP10/C1QL2-deficient mice represent a unique female model of MHO. CTRP10 modulates weight gain in a striking and sexually dimorphic manner. Female, but not male, mice lacking CTRP10 develop obesity with age on a low-fat diet while maintaining an otherwise healthy metabolic profile. When fed an obesogenic diet, female Ctrp10 knockout (KO) mice show rapid weight gain. Despite pronounced obesity, Ctrp10 KO female mice do not develop steatosis, dyslipidemia, glucose intolerance, insulin resistance, oxidative stress, or low-grade inflammation. Obesity is largely uncoupled from metabolic dysregulation in female KO mice. Multi-tissue transcriptomic analyses highlighted gene expression changes and pathways associated with insulin-sensitive obesity. Transcriptional correlation of the differentially expressed gene (DEG) orthologs in humans also shows sex differences in gene connectivity within and across metabolic tissues, underscoring the conserved sex-dependent function of CTRP10. Collectively, our findings suggest that CTRP10 negatively regulates body weight in females, and that loss of CTRP10 results in benign obesity with largely preserved insulin sensitivity and metabolic health. This female MHO mouse model is valuable for understanding sex-biased mechanisms that uncouple obesity from metabolic dysfunction.

    1. Computational and Systems Biology
    Huiyong Cheng, Dawson Miller ... Qiuying Chen
    Research Article

    Mass spectrometry imaging (MSI) is a powerful technology used to define the spatial distribution and relative abundance of metabolites across tissue cryosections. While software packages exist for pixel-by-pixel individual metabolite and limited target pairs of ratio imaging, the research community lacks an easy computing and application tool that images any metabolite abundance ratio pairs. Importantly, recognition of correlated metabolite pairs may contribute to the discovery of unanticipated molecules in shared metabolic pathways. Here, we describe the development and implementation of an untargeted R package workflow for pixel-by-pixel ratio imaging of all metabolites detected in an MSI experiment. Considering untargeted MSI studies of murine brain and embryogenesis, we demonstrate that ratio imaging minimizes systematic data variation introduced by sample handling, markedly enhances spatial image contrast, and reveals previously unrecognized metabotype-distinct tissue regions. Furthermore, ratio imaging facilitates identification of novel regional biomarkers and provides anatomical information regarding spatial distribution of metabolite-linked biochemical pathways. The algorithm described herein is applicable to any MSI dataset containing spatial information for metabolites, peptides or proteins, offering a potent hypothesis generation tool to enhance knowledge obtained from current spatial metabolite profiling technologies.