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Harris EB, Ewool KKK, Bowden LC, Fierro J, Johnson D, Meinzer M, Tayler S, Grose JH. Genomic and Proteomic Analysis of Six Vi01-like Phages Reveals Wide Host Range and Multiple Tail Spike Proteins. Viruses 2024; 16:289. [PMID: 38400064 PMCID: PMC10892097 DOI: 10.3390/v16020289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Enterobacteriaceae is a large family of Gram-negative bacteria composed of many pathogens, including Salmonella and Shigella. Here, we characterize six bacteriophages that infect Enterobacteriaceae, which were isolated from wastewater plants in the Wasatch front (Utah, United States). These phages are highly similar to the Kuttervirus vB_SenM_Vi01 (Vi01), which was isolated using wastewater from Kiel, Germany. The phages vary little in genome size and are between 157 kb and 164 kb, which is consistent with the sizes of other phages in the Vi01-like phage family. These six phages were characterized through genomic and proteomic comparison, mass spectrometry, and both laboratory and clinical host range studies. While their proteomes are largely unstudied, mass spectrometry analysis confirmed the production of five hypothetical proteins, several of which unveiled a potential operon that suggests a ferritin-mediated entry system on the Vi01-like phage family tail. However, no dependence on this pathway was observed for the single host tested herein. While unable to infect every genus of Enterobacteriaceae tested, these phages are extraordinarily broad ranged, with several demonstrating the ability to infect Salmonella enterica and Citrobacter freundii strains with generally high efficiency, as well as several clinical Salmonella enterica isolates, most likely due to their multiple tail fibers.
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Affiliation(s)
| | | | | | | | | | | | | | - Julianne H. Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84604, USA; (E.B.H.); (K.K.K.E.)
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Yang Y, Dufault-Thompson K, Yan W, Cai T, Xie L, Jiang X. Large-scale genomic survey with deep learning-based method reveals strain-level phage specificity determinants. Gigascience 2024; 13:giae017. [PMID: 38649301 PMCID: PMC11034027 DOI: 10.1093/gigascience/giae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 01/23/2024] [Accepted: 03/24/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Phage therapy, reemerging as a promising approach to counter antimicrobial-resistant infections, relies on a comprehensive understanding of the specificity of individual phages. Yet the significant diversity within phage populations presents a considerable challenge. Currently, there is a notable lack of tools designed for large-scale characterization of phage receptor-binding proteins, which are crucial in determining the phage host range. RESULTS In this study, we present SpikeHunter, a deep learning method based on the ESM-2 protein language model. With SpikeHunter, we identified 231,965 diverse phage-encoded tailspike proteins, a crucial determinant of phage specificity that targets bacterial polysaccharide receptors, across 787,566 bacterial genomes from 5 virulent, antibiotic-resistant pathogens. Notably, 86.60% (143,200) of these proteins exhibited strong associations with specific bacterial polysaccharides. We discovered that phages with identical tailspike proteins can infect different bacterial species with similar polysaccharide receptors, underscoring the pivotal role of tailspike proteins in determining host range. The specificity is mainly attributed to the protein's C-terminal domain, which strictly correlates with host specificity during domain swapping in tailspike proteins. Importantly, our dataset-driven predictions of phage-host specificity closely match the phage-host pairs observed in real-world phage therapy cases we studied. CONCLUSIONS Our research provides a rich resource, including both the method and a database derived from a large-scale genomics survey. This substantially enhances understanding of phage specificity determinants at the strain level and offers a valuable framework for guiding phage selection in therapeutic applications.
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Affiliation(s)
- Yiyan Yang
- National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | | | - Wei Yan
- National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Tian Cai
- Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, NY 10016, USA
| | - Lei Xie
- Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, NY 10016, USA
- Department of Computer Science, Hunter College, The City University of New York, New York, NY 10065, USA
| | - Xiaofang Jiang
- National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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Gil J, Paulson J, Zahn H, Brown M, Nguyen MM, Erickson S. Development of a Replication-Deficient Bacteriophage Reporter Lacking an Essential Baseplate Wedge Subunit. Viruses 2023; 16:8. [PMID: 38275943 PMCID: PMC10821221 DOI: 10.3390/v16010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
Engineered bacteriophages (phages) can be effective diagnostic reporters for detecting a variety of bacterial pathogens. Although a promising biotechnology, the large-scale use of these reporters may result in the unintentional release of genetically modified viruses. In order to limit the potential environmental impact, the ability of these phages to propagate outside the laboratory was targeted. The phage SEA1 has been previously engineered to facilitate food safety as an accurate and sensitive reporter for Salmonella contamination. In this study, homologous recombination was used to replace the expression of an essential baseplate wedge subunit (gp141) in SEA1 with a luciferase, NanoLuc®. This reporter, referred to as SEA1Δgp141.NL, demonstrated a loss of plaque formation and a failure to increase in titer following infection of Salmonella. SEA1Δgp141.NL was thus incapable of producing infectious progeny in the absence of gp141. In contrast, production of high titer stocks was possible when gp141 was artificially supplied in trans during infection. As a reporter, SEA1Δgp141.NL facilitated rapid, sensitive, and robust detection of Salmonella despite an inability to replicate. These results suggest that replication-deficient reporter phages are an effective method to obtain improved containment without sacrificing significant performance or the ease of production associated with many phage-based diagnostic methods.
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Affiliation(s)
- Jose Gil
- Laboratory Corporation of America Holdings, Los Angeles, CA 90062, USA;
| | - John Paulson
- Laboratory Corporation of America Holdings, New Brighton, MN 55112, USA; (J.P.); (H.Z.); (M.M.N.)
| | - Henriett Zahn
- Laboratory Corporation of America Holdings, New Brighton, MN 55112, USA; (J.P.); (H.Z.); (M.M.N.)
| | - Matthew Brown
- Laboratory Corporation of America Holdings, Burlington, NC 27215, USA;
| | - Minh M. Nguyen
- Laboratory Corporation of America Holdings, New Brighton, MN 55112, USA; (J.P.); (H.Z.); (M.M.N.)
| | - Stephen Erickson
- Laboratory Corporation of America Holdings, New Brighton, MN 55112, USA; (J.P.); (H.Z.); (M.M.N.)
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Pas C, Latka A, Fieseler L, Briers Y. Phage tailspike modularity and horizontal gene transfer reveals specificity towards E. coli O-antigen serogroups. Virol J 2023; 20:174. [PMID: 37550759 PMCID: PMC10408124 DOI: 10.1186/s12985-023-02138-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/23/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND The interaction between bacteriophages and their hosts is intricate and highly specific. Receptor-binding proteins (RBPs) of phages such as tail fibers and tailspikes initiate the infection process. These RBPs bind to diverse outer membrane structures, including the O-antigen, which is a serogroup-specific sugar-based component of the outer lipopolysaccharide layer of Gram-negative bacteria. Among the most virulent Escherichia coli strains is the Shiga toxin-producing E. coli (STEC) pathotype dominated by a subset of O-antigen serogroups. METHODS Extensive phylogenetic and structural analyses were used to identify and validate specificity correlations between phage RBP subtypes and STEC O-antigen serogroups, relying on the principle of horizontal gene transfer as main driver for RBP evolution. RESULTS We identified O-antigen specific RBP subtypes for seven out of nine most prevalent STEC serogroups (O26, O45, O103, O104, O111, O145 and O157) and seven additional E. coli serogroups (O2, O8, O16, O18, 4s/O22, O77 and O78). Eight phage genera (Gamaleya-, Justusliebig-, Kaguna-, Kayfuna-, Kutter-, Lederberg-, Nouzilly- and Uetakeviruses) emerged for their high proportion of serogroup-specific RBPs. Additionally, we reveal sequence motifs in the RBP region, potentially serving as recombination hotspots between lytic phages. CONCLUSION The results contribute to a better understanding of mosaicism of phage RBPs, but also demonstrate a method to identify and validate new RBP subtypes for current and future emerging serogroups.
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Affiliation(s)
- Célia Pas
- Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Agnieszka Latka
- Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
- Department of Pathogen Biology and Immunology, University of Wroclaw, Przybyszewskiego 63, 51-148, Wrocław, Poland
| | - Lars Fieseler
- Centre for Food Safety and Quality Management, ZHAW School of Life Sciences and Facility Management, Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Yves Briers
- Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium.
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Yang Y, Dufault-Thompson K, Yan W, Cai T, Xie L, Jiang X. Deciphering Phage-Host Specificity Based on the Association of Phage Depolymerases and Bacterial Surface Glycan with Deep Learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.16.545366. [PMID: 37503040 PMCID: PMC10370184 DOI: 10.1101/2023.06.16.545366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Phage tailspike proteins are depolymerases that target diverse bacterial surface glycans with high specificity, determining the host-specificity of numerous phages. To address the challenge of identifying tailspike proteins due to their sequence diversity, we developed SpikeHunter, an approach based on the ESM-2 protein language model. Using SpikeHunter, we successfully identified 231,965 tailspike proteins from a dataset comprising 8,434,494 prophages found within 165,365 genomes of five common pathogens. Among these proteins, 143,035 tailspike proteins displayed strong associations with serotypes. Moreover, we observed highly similar tailspike proteins in species that share closely related serotypes. We found extensive domain swapping in all five species, with the C-terminal domain being significantly associated with host serotype highlighting its role in host range determination. Our study presents a comprehensive cross-species analysis of tailspike protein to serotype associations, providing insights applicable to phage therapy and biotechnology.
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Affiliation(s)
- Yiyan Yang
- National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Wei Yan
- National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Tian Cai
- Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, NY 10016, USA
| | - Lei Xie
- Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, NY 10016, USA
- Department of Computer Science, Hunter College, The City University of New York, New York, NY 10065, USA *
| | - Xiaofang Jiang
- National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
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Noreika A, Rutkiene R, Dumalakienė I, Vilienė R, Laurynėnas A, Povilonienė S, Skapas M, Meškys R, Kaliniene L. Insights into the Alcyoneusvirus Adsorption Complex. Int J Mol Sci 2023; 24:ijms24119320. [PMID: 37298271 DOI: 10.3390/ijms24119320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
The structures of the Caudovirales phage tails are key factors in determining the host specificity of these viruses. However, because of the enormous structural diversity, the molecular anatomy of the host recognition apparatus has been elucidated in only a number of phages. Klebsiella viruses vB_KleM_RaK2 (RaK2) and phiK64-1, which form a new genus Alcyoneusvirus according to the ICTV, have perhaps one of the most structurally sophisticated adsorption complexes of all tailed viruses described to date. Here, to gain insight into the early steps of the alcyoneusvirus infection process, the adsorption apparatus of bacteriophage RaK2 is studied in silico and in vitro. We experimentally demonstrate that ten proteins, gp098 and gp526-gp534, previously designated as putative structural/tail fiber proteins (TFPs), are present in the adsorption complex of RaK2. We show that two of these proteins, gp098 and gp531, are essential for attaching to Klebsiella pneumoniae KV-3 cells: gp531 is an active depolymerase that recognizes and degrades the capsule of this particular host, while gp098 is a secondary receptor-binding protein that requires the coordinated action of gp531. Finally, we demonstrate that RaK2 long tail fibers consist of nine TFPs, seven of which are depolymerases, and propose a model for their assembly.
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Affiliation(s)
- Algirdas Noreika
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania
| | - Rasa Rutkiene
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania
| | - Irena Dumalakienė
- Department of Immunology, State Research Institute Center for Innovative Medicine, Santariškių St. 5, LT-08410 Vilnius, Lithuania
| | - Rita Vilienė
- Department of Immunology, State Research Institute Center for Innovative Medicine, Santariškių St. 5, LT-08410 Vilnius, Lithuania
| | - Audrius Laurynėnas
- Department of Bioanalysis, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania
| | - Simona Povilonienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania
| | - Martynas Skapas
- Department of Characterisation of Materials Structure, Center for Physical Sciences and Technology, Saulėtekio Av. 3, LT-10257 Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania
| | - Laura Kaliniene
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania
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