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Leskinen K, Pajunen MI, Vilanova MVGR, Kiljunen S, Nelson A, Smith D, Skurnik M. YerA41, a Yersinia ruckeri Bacteriophage: Determination of a Non-Sequencable DNA Bacteriophage Genome via RNA-Sequencing. Viruses 2020; 12:v12060620. [PMID: 32517038 PMCID: PMC7354516 DOI: 10.3390/v12060620] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/25/2020] [Accepted: 06/04/2020] [Indexed: 12/19/2022] Open
Abstract
YerA41 is a Myoviridae bacteriophage that was originally isolated due its ability to infect Yersinia ruckeri bacteria, the causative agent of enteric redmouth disease of salmonid fish. Several attempts to determine its genomic DNA sequence using traditional and next generation sequencing technologies failed, indicating that the phage genome is modified in such a way that it is an unsuitable template for PCR amplification and for conventional sequencing. To determine the YerA41 genome sequence, we performed RNA-sequencing from phage-infected Y. ruckeri cells at different time points post-infection. The host-genome specific reads were subtracted and de novo assembly was performed on the remaining unaligned reads. This resulted in nine phage-specific scaffolds with a total length of 143 kb that shared only low level and scattered identity to known sequences deposited in DNA databases. Annotation of the sequences revealed 201 predicted genes, most of which found no homologs in the databases. Proteome studies identified altogether 63 phage particle-associated proteins. The RNA-sequencing data were used to characterize the transcriptional control of YerA41 and to investigate its impact on the bacterial gene expression. Overall, our results indicate that RNA-sequencing can be successfully used to obtain the genomic sequence of non-sequencable phages, providing simultaneous information about the phage-host interactions during the process of infection.
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Affiliation(s)
- Katarzyna Leskinen
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00014 UH Helsinki, Finland; (K.L.); (M.I.P.); (M.V.G.-R.V.); (S.K.)
| | - Maria I. Pajunen
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00014 UH Helsinki, Finland; (K.L.); (M.I.P.); (M.V.G.-R.V.); (S.K.)
| | - Miguel Vincente Gomez-Raya Vilanova
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00014 UH Helsinki, Finland; (K.L.); (M.I.P.); (M.V.G.-R.V.); (S.K.)
| | - Saija Kiljunen
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00014 UH Helsinki, Finland; (K.L.); (M.I.P.); (M.V.G.-R.V.); (S.K.)
| | - Andrew Nelson
- Applied Sciences, University of Northumbria, Newcastle upon Tyne NE1 8ST, UK; (A.N.); (D.S.)
| | - Darren Smith
- Applied Sciences, University of Northumbria, Newcastle upon Tyne NE1 8ST, UK; (A.N.); (D.S.)
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00014 UH Helsinki, Finland; (K.L.); (M.I.P.); (M.V.G.-R.V.); (S.K.)
- Division of Clinical Microbiology, Helsinki University Hospital, HUSLAB, 00290 Helsinki, Finland
- Correspondence: ; Tel.: +358-2941-26464
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Welch TJ. Characterization of a novel Yersinia ruckeri serotype O1-specific bacteriophage with virulence-neutralizing activity. J Fish Dis 2020; 43:285-293. [PMID: 31828808 DOI: 10.1111/jfd.13124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/12/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
A lytic bacteriophage (φNC10) specific to serotype O1 Yersinia ruckeri has been identified and evaluated as a model to assess the potential use of bacteriophages and their products for disease control in aquaculture. Electron microscopy of purified φNC10 revealed a virion particle with a small (70 nm) polyhedral head and short tail. φNC10 infected only serotype O1 strains of Y. ruckeri and failed to bind a defined Y. ruckeri mutant strain lacking O1 lipopolysaccharides (O1-LPS), suggesting that φNC10 uses O1-LPS as its receptor. In addition, spontaneous φNC10-resistant mutants of Y. ruckeri exhibited defects in O1-LPS production and were sensitive to rainbow trout serum. Purified φNC10 displayed a polysaccharide depolymerase activity capable of degrading Y. ruckeri O1-LPS and thereby sensitizing Y. ruckeri to the bactericidal effects of rainbow trout serum. The φNC10-associated polysaccharide depolymerase activity also reduced the ability of Y. ruckeri cells to cause mortality following intraperitoneal injection into rainbow trout. These data demonstrate a potential utility of φNC10 and its associated polysaccharide depolymerase activity for Y. ruckeri disease prevention.
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Affiliation(s)
- Timothy J Welch
- Agricultural Research Service/U.S. Department of Agriculture, National Center for Cool and Cold Water Aquaculture, Kearneysville, West Virginia
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