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Fossati A, Mozumdar D, Kokontis C, Mèndez-Moran M, Nieweglowska E, Pelin A, Li Y, Guo B, Krogan NJ, Agard DA, Bondy-Denomy J, Swaney DL. Next-generation proteomics for quantitative Jumbophage-bacteria interaction mapping. Nat Commun 2023; 14:5156. [PMID: 37620325 PMCID: PMC10449902 DOI: 10.1038/s41467-023-40724-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023] Open
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.
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Affiliation(s)
- Andrea Fossati
- J. David Gladstone Institutes, San Francisco, 94158, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, 94158, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Deepto Mozumdar
- Department of Immunology and Microbiology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Claire Kokontis
- Department of Immunology and Microbiology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Melissa Mèndez-Moran
- Department of Biochemistry, University of California San Francisco, San Francisco, 94143, CA, USA
| | - Eliza Nieweglowska
- Department of Biochemistry, University of California San Francisco, San Francisco, 94143, CA, USA
| | - Adrian Pelin
- J. David Gladstone Institutes, San Francisco, 94158, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, 94158, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Yuping Li
- Department of Immunology and Microbiology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Baron Guo
- Department of Immunology and Microbiology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Nevan J Krogan
- J. David Gladstone Institutes, San Francisco, 94158, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, 94158, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - David A Agard
- Department of Biochemistry, University of California San Francisco, San Francisco, 94143, CA, USA
| | - Joseph Bondy-Denomy
- Department of Immunology and Microbiology, University of California San Francisco, San Francisco, 94158, CA, USA.
| | - Danielle L Swaney
- J. David Gladstone Institutes, San Francisco, 94158, CA, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, 94158, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, 94158, CA, USA.
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Fossati A, Mozumdar D, Kokontis C, Mèndez-Moran M, Nieweglowska E, Pelin A, Li Y, Guo B, Krogan NJ, Agard DA, Bondy-Denomy J, Swaney DL. Next-generation interaction proteomics for quantitative Jumbophage-bacteria interaction mapping. bioRxiv 2023:2023.01.13.523954. [PMID: 36711836 PMCID: PMC9882154 DOI: 10.1101/2023.01.13.523954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Host-pathogen interactions (HPIs) are pivotal in regulating establishment, progression, and outcome of an infection. Affinity-purification mass spectrometry has become instrumental for the characterization of HPIs, however the targeted nature of exogenously expressing individual viral proteins has limited its utility to the analysis of relatively small pathogens. Here we present the use of co-fractionation mass spectrometry (SEC-MS) for the high-throughput analysis of HPIs from native viral infections of two jumbophages ( ϕ KZ and ϕ PA3) in Pseudomonas aeruginosa . This enabled the detection > 6000 unique host-pathogen and > 200 pathogen-pathogen interactions for each phage, encompassing > 50% of the phage proteome. Interactome-wide comparison across phages showed similar perturbed protein interactions suggesting fundamentally conserved mechanisms of phage predation within the KZ-like phage family. Prediction of novel ORFs revealed a ϕ PA3 complex showing strong structural and sequence similarity to ϕ KZ nvRNAp, suggesting ϕ PA3 also possesses two RNA polymerases acting at different stages of the infection cycle. We further expanded our understanding on the molecular organization of the virion packaged and injected proteome by identifying 23 novel virion components and 5 novel injected proteins, as well as providing the first evidence for interactions between KZ-like phage proteins and the host ribosome. 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 hostpathogen interactomes and protein complex dynamics upon infection.
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Nieweglowska ES, Brilot AF, Méndez-Moran M, Kokontis C, Baek M, Li J, Cheng Y, Baker D, Bondy-Denomy J, Agard DA. The ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice. Nat Commun 2023; 14:927. [PMID: 36807264 PMCID: PMC9938867 DOI: 10.1038/s41467-023-36526-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 02/03/2023] [Indexed: 02/20/2023] Open
Abstract
To protect themselves from host attack, numerous jumbo bacteriophages establish a phage nucleus-a micron-scale, proteinaceous structure encompassing the replicating phage DNA. Bacteriophage and host proteins associated with replication and transcription are concentrated inside the phage nucleus while other phage and host proteins are excluded, including CRISPR-Cas and restriction endonuclease host defense systems. Here, we show that nucleus fragments isolated from ϕPA3 infected Pseudomonas aeruginosa form a 2-dimensional lattice, having p2 or p4 symmetry. We further demonstrate that recombinantly purified primary Phage Nuclear Enclosure (PhuN) protein spontaneously assembles into similar 2D sheets with p2 and p4 symmetry. We resolve the dominant p2 symmetric state to 3.9 Å by cryo-EM. Our structure reveals a two-domain core, organized into quasi-symmetric tetramers. Flexible loops and termini mediate adaptable inter-tetramer contacts that drive subunit assembly into a lattice and enable the adoption of different symmetric states. While the interfaces between subunits are mostly well packed, two are open, forming channels that likely have functional implications for the transport of proteins, mRNA, and small molecules.
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Affiliation(s)
- Eliza S Nieweglowska
- Department of Biochemistry, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Axel F Brilot
- Department of Biochemistry, University of California San Francisco, San Francisco, CA, 94143, USA
- Sauer Structural Biology Laboratory, Center for Biomedical Research Support, University of Texas at Austin, Austin, TX, USA
| | - Melissa Méndez-Moran
- Department of Biochemistry, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Claire Kokontis
- Department of Microbiology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Minkyung Baek
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Junrui Li
- Howard Hughes Medical Institute, University of California, San Francisco, CA, 94143, USA
| | - Yifan Cheng
- Department of Biochemistry, University of California San Francisco, San Francisco, CA, 94143, USA
- Howard Hughes Medical Institute, University of California, San Francisco, CA, 94143, USA
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - David A Agard
- Department of Biochemistry, University of California San Francisco, San Francisco, CA, 94143, USA.
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