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Backman T, Latorre SM, Symeonidi E, Muszyński A, Bleak E, Eads L, Martinez-Koury PI, Som S, Hawks A, Gloss AD, Belnap DM, Manuel AM, Deutschbauer AM, Bergelson J, Azadi P, Burbano HA, Karasov TL. A phage tail-like bacteriocin suppresses competitors in metapopulations of pathogenic bacteria. Science 2024; 384:eado0713. [PMID: 38870284 DOI: 10.1126/science.ado0713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/24/2024] [Indexed: 06/15/2024]
Abstract
Bacteria can repurpose their own bacteriophage viruses (phage) to kill competing bacteria. Phage-derived elements are frequently strain specific in their killing activity, although there is limited evidence that this specificity drives bacterial population dynamics. Here, we identified intact phage and their derived elements in a metapopulation of wild plant-associated Pseudomonas genomes. We discovered that the most abundant viral cluster encodes a phage remnant resembling a phage tail called a tailocin, which bacteria have co-opted to kill bacterial competitors. Each pathogenic Pseudomonas strain carries one of a few distinct tailocin variants that target the variable polysaccharides in the outer membrane of co-occurring pathogenic Pseudomonas strains. Analysis of herbarium samples from the past 170 years revealed that the same tailocin and bacterial receptor variants have persisted in Pseudomonas populations. These results suggest that tailocin genetic diversity can be mined to develop targeted "tailocin cocktails" for microbial control.
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Affiliation(s)
- Talia Backman
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Sergio M Latorre
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
| | - Efthymia Symeonidi
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Artur Muszyński
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Ella Bleak
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Lauren Eads
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Sarita Som
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Aubrey Hawks
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Andrew D Gloss
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - David M Belnap
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Allison M Manuel
- Mass Spectrometry and Proteomics Core, The University of Utah, Salt Lake City, UT 84112, USA
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Joy Bergelson
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Hernán A Burbano
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
| | - Talia L Karasov
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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Backman T, Latorre SM, Symeonidi E, Muszyński A, Bleak E, Eads L, Martinez-Koury PI, Som S, Hawks A, Gloss AD, Belnap DM, Manuel AM, Deutschbauer AM, Bergelson J, Azadi P, Burbano HA, Karasov TL. A weaponized phage suppresses competitors in historical and modern metapopulations of pathogenic bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.17.536465. [PMID: 38352526 PMCID: PMC10862724 DOI: 10.1101/2023.04.17.536465] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Bacteriophages, the viruses of bacteria, are proposed to drive bacterial population dynamics, yet direct evidence of their impact on natural populations is limited. Here we identified viral sequences in a metapopulation of wild plant-associated Pseudomonas spp. genomes. We discovered that the most abundant viral cluster does not encode an intact phage but instead encodes a tailocin - a phage-derived element that bacteria use to kill competitors for interbacterial warfare. Each pathogenic Pseudomonas sp. strain carries one of a few distinct tailocin variants, which target variable polysaccharides in the outer membrane of co-occurring pathogenic strains. Analysis of historic herbarium samples from the last 170 years revealed that the same tailocin and receptor variants have persisted in the Pseudomonas populations for at least two centuries, suggesting the continued use of a defined set of tailocin haplotypes and receptors. These results indicate that tailocin genetic diversity can be mined to develop targeted "tailocin cocktails" for microbial control. One-Sentence Summary Bacterial pathogens in a host-associated metapopulation use a repurposed prophage to kill their competitors.
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