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Next-generation proteomics for quantitative Jumbophage-bacteria interaction mapping

Author

Listed:
  • Andrea Fossati

    (J. David Gladstone Institutes
    University of California San Francisco
    University of California San Francisco)

  • Deepto Mozumdar

    (University of California San Francisco)

  • Claire Kokontis

    (University of California San Francisco)

  • Melissa Mèndez-Moran

    (University of California San Francisco)

  • Eliza Nieweglowska

    (University of California San Francisco)

  • Adrian Pelin

    (J. David Gladstone Institutes
    University of California San Francisco
    University of California San Francisco)

  • Yuping Li

    (University of California San Francisco)

  • Baron Guo

    (University of California San Francisco)

  • Nevan J. Krogan

    (J. David Gladstone Institutes
    University of California San Francisco
    University of California San Francisco)

  • David A. Agard

    (University of California San Francisco)

  • Joseph Bondy-Denomy

    (University of California San Francisco)

  • Danielle L. Swaney

    (J. David Gladstone Institutes
    University of California San Francisco
    University of California San Francisco)

Abstract

Host-pathogen interactions are pivotal in regulating establishment, progression, and outcome of an infection. While affinity-purification mass spectrometry has become instrumental in characterizing such interactions, it suffers from limitations in scalability and biological authenticity. Here we present the use of co-fractionation mass spectrometry for high throughput analysis of host-pathogen interactions from native viral infections of two jumbophages (ϕKZ and ϕPA3) in Pseudomonas aeruginosa. This approach enabled the detection of > 6000 unique host-pathogen interactions for each phage, encompassing > 50% of their respective proteomes. This deep coverage provided evidence for interactions between KZ-like phage proteins and the host ribosome, and revealed protein complexes for previously undescribed phage ORFs, including a ϕPA3 complex showing strong structural and sequence similarity to ϕKZ non-virion RNA polymerase. Interactome-wide comparison across phages showed similar perturbed protein interactions suggesting fundamentally conserved mechanisms of phage predation within the KZ-like phage family. To enable accessibility to this data, we developed PhageMAP, an online resource for network query, visualization, and interaction prediction ( https://phagemap.ucsf.edu/ ). We anticipate this study will lay the foundation for the application of co-fractionation mass spectrometry for the scalable profiling of host-pathogen interactomes and protein complex dynamics upon infection.

Suggested Citation

  • Andrea Fossati & Deepto Mozumdar & Claire Kokontis & Melissa Mèndez-Moran & Eliza Nieweglowska & Adrian Pelin & Yuping Li & Baron Guo & Nevan J. Krogan & David A. Agard & Joseph Bondy-Denomy & Daniell, 2023. "Next-generation proteomics for quantitative Jumbophage-bacteria interaction mapping," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-40724-w
    DOI: 10.1038/s41467-023-40724-w
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    References listed on IDEAS

    as
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