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The Bacillus phage SPβ and its relatives: A temperate phage model system reveals new strains, species, prophage integration loci, conserved proteins and lysogeny management components

Katharina Kohm, Valentina A. Floccari, Veronika T. Lutz, Birthe Nordmann, Carolin Mittelstädt, Anja Poehlein, Anna Dragoš, Fabian M. Commichau, View ORCID ProfileRobert Hertel
doi: https://doi.org/10.1101/2021.11.22.469490
Katharina Kohm
1FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968 Senftenberg, Germany
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Valentina A. Floccari
2Biotechnical Faculty, University of Ljubljana, Ljubljana, 1000, Slovenia
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Veronika T. Lutz
3Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, 1870, Denmark
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Birthe Nordmann
4Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University, Göttingen, 37077, Germany
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Carolin Mittelstädt
1FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968 Senftenberg, Germany
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Anja Poehlein
4Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University, Göttingen, 37077, Germany
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Anna Dragoš
2Biotechnical Faculty, University of Ljubljana, Ljubljana, 1000, Slovenia
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Fabian M. Commichau
1FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968 Senftenberg, Germany
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Robert Hertel
1FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968 Senftenberg, Germany
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  • ORCID record for Robert Hertel
  • For correspondence: Robert.Hertel@b-tu.de
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Abstract

The Bacillus phage SPβ has been known for about 50 years, but only a few strains are avalible. We isolated four new wild type strains of the SPbeta species. Phage vB_BsuS-Goe14 introduces its prophage into the spoVK locus, previously not observed to be used by SPβ-like phages. We could also reveal the SPβ-like phage genome replication strategy, the genome packaging mode, and the phage genome opening point. We extracted 55 SPβ-like prophages from public Bacillus genomes, thereby discovering three more integration loci and one additional type of integrase. The identified prophages resembled four new species clusters and three species orphans in the genus Spbetavirus. The determined core proteome of all SPβ-like prophages consists of 38 proteins. The integration cassette proved to be not conserved even though present in all strains. It consists of distinct integrases. Analysis of SPβ transcriptomes revealed three conserved genes, yopQ, yopR, and yokI, to be transcribed from a dormant prophage. While yopQ and yokI could be deleted from the prophage without activating the prophage, damaging of yopR led to a clear-plaque phenotype. Under the applied laboratory conditions, the yokI mutant showed an elevated virion release implying the YokI protein being a component of the arbitrium system.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted November 22, 2021.
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The Bacillus phage SPβ and its relatives: A temperate phage model system reveals new strains, species, prophage integration loci, conserved proteins and lysogeny management components
Katharina Kohm, Valentina A. Floccari, Veronika T. Lutz, Birthe Nordmann, Carolin Mittelstädt, Anja Poehlein, Anna Dragoš, Fabian M. Commichau, Robert Hertel
bioRxiv 2021.11.22.469490; doi: https://doi.org/10.1101/2021.11.22.469490
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The Bacillus phage SPβ and its relatives: A temperate phage model system reveals new strains, species, prophage integration loci, conserved proteins and lysogeny management components
Katharina Kohm, Valentina A. Floccari, Veronika T. Lutz, Birthe Nordmann, Carolin Mittelstädt, Anja Poehlein, Anna Dragoš, Fabian M. Commichau, Robert Hertel
bioRxiv 2021.11.22.469490; doi: https://doi.org/10.1101/2021.11.22.469490

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