{"entity": "researcher", "timestamp": "2026-11-12T14:02:48.731Z", "family": "Bondy-Denomy", "given": "Joseph", "initials": "J", "orcid": "0000-0002-4909-9481", "affiliations": ["Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA. joseph.bondy-denomy@ucsf.edu.", "Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA. joseph.bondy-denomy@ucsf.edu."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4ac66d863ed429f85fefcfc5dab6666.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4ac66d863ed429f85fefcfc5dab6666"}}, "publications": [{"entity": "publication", "iuid": "f02b2191a3854bcb8b252571823a4359", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f02b2191a3854bcb8b252571823a4359.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f02b2191a3854bcb8b252571823a4359"}}, "title": "Anti-restriction functions of injected phage proteins revealed by peeling back layers of bacterial immunity.", "authors": [{"family": "Silas", "given": "Sukrit", "initials": "S", "orcid": "0000-0003-3251-8579", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3aeebab8d28948af9403c2e16036b0ff.json"}}, {"family": "Carion", "given": "H\u00e9lo\u00efse", "initials": "H"}, {"family": "Makarova", "given": "Kira S", "initials": "KS", "orcid": "0000-0002-8174-2844", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f00f844e20e41239a8d3cb68a64bba5.json"}}, {"family": "Sanchez Godinez", "given": "David", "initials": "D"}, {"family": "Haniyur", "given": "Surabhi", "initials": "S", "orcid": "0009-0003-6914-327X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6c3c2bacd434178913a08859bef485b.json"}}, {"family": "Volino", "given": "Lucy", "initials": "L"}, {"family": "Yee", "given": "Wearn-Xin", "initials": "WX"}, {"family": "Fossati", "given": "Andrea", "initials": "A"}, {"family": "Swaney", "given": "Danielle", "initials": "D", "orcid": "0000-0001-6119-6084", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56317207941d4aaf81ab4d55de5fcba4.json"}}, {"family": "Bocek", "given": "Michael", "initials": "M"}, {"family": "Koonin", "given": "Eugene V", "initials": "EV", "orcid": "0000-0003-3943-8299", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1ab5826b43f46769b80afbc58ad4e81.json"}}, {"family": "Bondy-Denomy", "given": "Joseph", "initials": "J", "orcid": "0000-0002-4909-9481", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4ac66d863ed429f85fefcfc5dab6666.json"}}], "type": "journal article", "published": "2025-08-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "7828", "issn-l": "2041-1723"}, "abstract": "Virus-host competition drives evolution of diverse antivirus defenses, but how they co-operate in wild bacteria and how bacteriophages circumvent host immunity remains poorly understood. Here, using a functional screening platform to systematically explore the functions of phage accessory genes, we describe how cell-surface barriers can obscure the phenotypes of intracellular defenses in E. coli isolates. LPS modification emerged as a major theme, with the discovery of several small phage proteins that modify specific O-antigen structures, removing barriers to phage adsorption. Bypassing O-antigen in wild E. coli strains revealed another layer of defense: Type IV restriction endonucleases (RE) that target modified DNA of T-even phages (T2, T4, T6). We further show how injected proteins Ip2 and Ip3 of T4 inhibit distinct subtypes of these Type IV REs. Extensive variability in Type IV REs likely drives the emergence of subtype-specific inhibitors through multiple rounds of adaptation and counter-adaptation.", "doi": "10.1038/s41467-025-63056-3", "pmid": "40846711", "labels": {"Andrea Fossati": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC12373910"}, {"db": "pii", "key": "10.1038/s41467-025-63056-3"}], "notes": [], "created": "2026-11-06T08:02:55.317Z", "modified": "2026-11-06T08:02:55.598Z"}, {"entity": "publication", "iuid": "d24496ff298042db99f2c7999a565fe1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d24496ff298042db99f2c7999a565fe1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d24496ff298042db99f2c7999a565fe1"}}, "title": "Next-generation proteomics for quantitative Jumbophage-bacteria interaction mapping.", "authors": [{"family": "Fossati", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5170-4903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658637b885384441943698722fad5944.json"}}, {"family": "Mozumdar", "given": "Deepto", "initials": "D"}, {"family": "Kokontis", "given": "Claire", "initials": "C"}, {"family": "M\u00e8ndez-Moran", "given": "Melissa", "initials": "M", "orcid": "0000-0003-0817-7292", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/90d7c50c904f4c71be76e0ec228c04bc.json"}}, {"family": "Nieweglowska", "given": "Eliza", "initials": "E", "orcid": "0000-0002-9204-3002", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c23665a0824d4896a58e4d9115bbbca9.json"}}, {"family": "Pelin", "given": "Adrian", "initials": "A"}, {"family": "Li", "given": "Yuping", "initials": "Y", "orcid": "0000-0003-2057-3271", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4958e5be5fb489d93350357e471d548.json"}}, {"family": "Guo", "given": "Baron", "initials": "B"}, {"family": "Krogan", "given": "Nevan J", "initials": "NJ", "orcid": "0000-0003-4902-337X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bf20e1447b9643f599f94d983b2bd9dd.json"}}, {"family": "Agard", "given": "David A", "initials": "DA", "orcid": "0000-0003-3512-695X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/acf4cd7f71944afbbe8f579e36f6dd23.json"}}, {"family": "Bondy-Denomy", "given": "Joseph", "initials": "J", "orcid": "0000-0002-4909-9481", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4ac66d863ed429f85fefcfc5dab6666.json"}}, {"family": "Swaney", "given": "Danielle L", "initials": "DL", "orcid": "0000-0001-6119-6084", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56317207941d4aaf81ab4d55de5fcba4.json"}}], "type": "journal article", "published": "2023-08-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "5156", "issn-l": "2041-1723"}, "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 (\u03d5KZ and \u03d5PA3) 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 \u03d5PA3 complex showing strong structural and sequence similarity to \u03d5KZ 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.", "doi": "10.1038/s41467-023-40724-w", "pmid": "37620325", "labels": {"Andrea Fossati": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10449902"}, {"db": "pii", "key": "10.1038/s41467-023-40724-w"}], "notes": [], "created": "2026-11-06T08:03:13.304Z", "modified": "2026-11-06T08:03:13.672Z"}]}