{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:20:01Z","timestamp":1792790401006,"version":"4.5.0"},"posted":{"date-parts":[[2026,9,18]]},"group-title":"Microbiology","reference-count":119,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T00:00:00Z","timestamp":1789689600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"United States Department of Energy","award":["Biopreparedness Research Virtual Environment (BRaVE) Phage Foundry at Lawrence Berkeley National Laboratory is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Biological & Environmental Research under contract number DE-AC02-05CH11231"],"award-info":[{"award-number":["Biopreparedness Research Virtual Environment (BRaVE) Phage Foundry at Lawrence Berkeley National Laboratory is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Biological & Environmental Research under contract number DE-AC02-05CH11231"]}],"id":[{"id":"https:\/\/ror.org\/01znn6x10","id-type":"ROR","asserted-by":"crossref"}]},{"name":"United States Department of Energy","award":["U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231"],"award-info":[{"award-number":["U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231"]}],"id":[{"id":"https:\/\/ror.org\/01znn6x10","id-type":"ROR","asserted-by":"crossref"}]},{"name":"United States Department of Energy","award":["Complex Carbohydrate Research Center was supported in part by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Chemical Sciences, Geosciences and Biosciences Division, under award DE-SC0015662"],"award-info":[{"award-number":["Complex Carbohydrate Research Center was supported in part by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Chemical Sciences, Geosciences and Biosciences Division, under award DE-SC0015662"]}],"id":[{"id":"https:\/\/ror.org\/01znn6x10","id-type":"ROR","asserted-by":"crossref"}]},{"name":"United States Department of Energy","award":["NIH R01GM141659"],"award-info":[{"award-number":["NIH R01GM141659"]}],"id":[{"id":"https:\/\/ror.org\/01znn6x10","id-type":"ROR","asserted-by":"crossref"}]},{"name":"United States Department of Energy","award":["NIH R24GM137782"],"award-info":[{"award-number":["NIH R24GM137782"]}],"id":[{"id":"https:\/\/ror.org\/01znn6x10","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Single stranded RNA (ssRNA) and single stranded DNA (ssDNA) bacteriophages represent a key component of the global virome, yet the host genetic networks supporting their infection cycles remain poorly understood. Here, we present a comprehensive, genome-wide mapping of the genetic landscape regulating infection cycles for F pilus-dependent ssRNA and ssDNA phages in\n                  <jats:italic>Escherichia coli<\/jats:italic>\n                  .\n                <\/jats:p>\n                <jats:p>\n                  Genetic screens across ssRNA phages spanning all four genogroups of the\n                  <jats:italic>Leviviricetes<\/jats:italic>\n                  revealed a highly conserved network of host dependencies, with the notable exception of the F plasmid gene\n                  <jats:italic>traD<\/jats:italic>\n                  . While primary structural receptor components and\n                  <jats:italic>dsbA<\/jats:italic>\n                  mediated disulfide bond formation are universally required across all lineages to ensure F pilus integrity,\n                  <jats:italic>traD<\/jats:italic>\n                  exhibits a strict genogroup-specific requirement during entry, showing variable essentiality across different viral groups despite sharing an identical primary receptor. Our gene dosage screens revealed that an elevated copy number of the\n                  <jats:italic>hslU<\/jats:italic>\n                  protease or the RNA chaperone\n                  <jats:italic>stpA<\/jats:italic>\n                  restricts infection, identifying clear genetic barriers that can perturb the viral life cycle.\n                <\/jats:p>\n                <jats:p>Parallel assays with filamentous ssDNA phages produced host factor profiles consistent with published literature, while revealing additional variations in host dependency. These screens confirmed that ssDNA phages strictly rely on the host TolQRA complex for entry downstream of pilus engagement. The assays tracked prominent negative fitness signatures across homeostatic clusters, highlighting how the physiological burden of continuous, non-lytic virion extrusion strains the host envelope.<\/jats:p>\n                <jats:p>\n                  Finally, this comparative approach traced the selectivity of our isolation host (\n                  <jats:italic>E. coli<\/jats:italic>\n                  HSF) to a horizontally acquired capsule architecture from\n                  <jats:italic>Klebsiella<\/jats:italic>\n                  . This surface shield excludes a large panel of double stranded DNA phages isolated on diverse\n                  <jats:italic>E. coli<\/jats:italic>\n                  strains, while allowing virions from ssDNA and ssRNA phages to engage the extended F pilus and bypass the barrier via native pilus retraction. Together, this work provides a systematic, class-wide map of single stranded phage-host interactions, bridging classical genetics with modern viral discovery while establishing a robust host platform to access uncultured viral diversity and a functional blueprint to design next generation diagnostics, protein antibiotics, and biocontrol tools to halt horizontal gene transfer.\n                <\/jats:p>","DOI":"10.64898\/2026.09.17.752499","type":"posted-content","created":{"date-parts":[[2026,9,19]],"date-time":"2026-09-19T02:25:12Z","timestamp":1789784712000},"source":"Crossref","is-referenced-by-count":0,"title":["Genome-wide characterization of host factors involved in single-stranded RNA and DNA phage infection pathways"],"prefix":"10.64898","author":[{"given":"Isabella","family":"Murray","sequence":"first","affiliation":[{"name":"Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA"},{"name":"Molecular and Cell Biology Department, 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