Staphylococcus aureus Prophage-Encoded Protein Causes Abortive Infection and Provides Population Immunity against Kayviruses

Abstract

Both temperate and obligately lytic phages have crucial roles in the biology of staphylococci. While superinfection exclusion among closely related temperate phages is a well-characterized phenomenon, the interactions between temperate and lytic phages in staphylococci are not understood. Here, we present a resistance mechanism toward lytic phages of the genus Kayvirus, mediated by the membrane-anchored protein designated PdpSau encoded by Staphylococcus aureus prophages, mostly of the Sa2 integrase type. The prophage accessory gene pdpSau is strongly linked to the lytic genes for holin and ami2-type amidase and typically replaces genes for the toxin Panton-Valentine leukocidin (PVL). The predicted PdpSau protein structure shows the presence of a membrane-binding a-helix in its N-terminal part and a cytoplasmic positively charged C terminus. We demonstrated that the mechanism of action of PdpSau does not prevent the infecting kayvirus from adsorbing onto the host cell and delivering its genome into the cell, but phage DNA replication is halted. Changes in the cell membrane polarity and permeability were observed from 10 min after the infection, which led to prophage-activated cell death. Furthermore, we describe a mechanism of overcoming this resistance in a host-range Kayvirus mutant, which was selected on an S. aureus strain harboring prophage 53 encoding PdpSau, and in which a chimeric gene product emerged via adaptive laboratory evolution. This first case of staphylococcal interfamily phage-phage competition is analogous to some other abortive infection defense systems and to systems based on membrane-destructive proteins. IMPORTANCE Prophages play an important role in virulence, pathogenesis, and host preference, as well as in horizontal gene transfer in staphylococci. In contrast, broad-host-range lytic staphylococcal kayviruses lyse most S. aureus strains, and scientists worldwide have come to believe that the use of such phages will be successful for treating and preventing bacterial diseases. The effectiveness of phage therapy is complicated by bacterial resistance, whose mechanisms related to therapeutic staphylococcal phages are not understood in detail. In this work, we describe a resistance mechanism targeting kayviruses that is encoded by a prophage. We conclude that the defense mechanism belongs to a broader group of abortive infections, which is characterized by suicidal behavior of infected cells that are unable to produce phage progeny, thus ensuring the survival of the host population. Since the majority of staphylococcal strains are lysogenic, our findings are relevant for the advancement of phage therapy.

Metadata

Item Type:	Article
Authors/Creators:	Kuntová, Lucie Mašlanová, Ivana Oborilová, Radka Šimecková, Hana Finstrlová, Adéla Bárdy, Pavol https://orcid.org/0000-0002-1223-2584 Šiborová, Marta Troianovska, Liudmyla Botka, Tibor Gintar, Petr Šedo, Ondrej Farka, Zdenek Doškar, Jirí Pantůcek, Roman
Copyright, Publisher and Additional Information:	Funding Information: This work was supported by a National Institute of Virology and Bacteriology project (Program EXCELES, ID project no. LX22NPO5103) funded by the European Union - Next Generation EU, a grant (18-13064S) from the Czech Science Foundation to R.P., grants (NU22-05-00042 and NU21J-05-00035) from the Ministry of Health of the Czech Republic to I.M. and T.B., respectively, a project from the Grant Agency of Masaryk University (MUNI/A/ 1325/2021) to J.D., and Wellcome Trust grant 224067/Z/21/Z to P.B. Funding Information: This work was supported by a National Institute of Virology and Bacteriology project (Program EXCELES, ID project no. LX22NPO5103) funded by the European Union - Next Generation EU, a grant (18-13064S) from the Czech Science Foundation to R.P., grants (NU22-05-00042 and NU21J-05-00035) from the Ministry of Health of the Czech Republic to I.M. and T.B., respectively, a project from the Grant Agency of Masaryk University (MUNI/A/ 1325/2021) to J.D., and Wellcome Trust grant 224067/Z/21/Z to P.B. We gratefully acknowledge the CIISB, Instruct-CZ Centre of Instruct-ERIC EU consortium, and the NCMG research infrastructure funded by the Ministry of Education, Youth and Sports of the Czech Republic (LM2018127) and European Regional Development Fund-Project “UP CIISB” (no. CZ.02.1.01/0.0/0.0/18_046/0015974) for their financial support of the measurements at the Proteomics, Nanobiotechnology, and Cryo-electron Microscopy and Tomography Core Facilities of CEITEC MU. The computational resources were supplied by the project e-INFRA CZ funded by the Ministry of Education, Youth and Sports of the Czech Republic (LM2018140). We thank P. Formanová (Faculty of Science, Masaryk University) for valuable help with the pilot experiments. We thank C. Wolz (Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen) for providing the delysogenized S. aureus USA300c strain. Funding Information: We gratefully acknowledge the CIISB, Instruct-CZ Centre of Instruct-ERIC EU consortium, and the NCMG research infrastructure funded by the Ministry of Education, Youth and Sports of the Czech Republic (LM2018127) and European Regional Development Fund-Project “UP CIISB” (no. CZ.02.1.01/0.0/0.0/18_046/0015974) for their financial support of the measurements at the Proteomics, Nanobiotechnology, and Cryo-electron Microscopy and Tomography Core Facilities of CEITEC MU. The computational resources were supplied by the project e-INFRA CZ funded by the Ministry of Education, Youth and Sports of the Czech Republic (LM2018140). Publisher Copyright: Copyright © 2023 Kuntová et al.
Keywords:	abortive infection,bacteriophage evolution,bacteriophage therapy,bacteriophages,cell death,Kayvirus,lysogeny,phage resistance,phage therapy,Staphylococcus aureus
Dates:	Published: 25 April 2023 Accepted: 19 January 2023
Institution:	The University of York
Academic Units:	The University of York > Faculty of Sciences (York) > Chemistry (York)
Depositing User:	Pure (York)
Date Deposited:	08 Aug 2023 07:50
Last Modified:	31 Oct 2024 01:06
Published Version:	https://doi.org/10.1128/mbio.02490-22
Status:	Published
Refereed:	Yes
Identification Number:	10.1128/mbio.02490-22
Related URLs:	http://www.scopus.com/inward/record.url?...
Open Archives Initiative ID (OAI ID):	oai:eprints.whiterose.ac.uk:202255

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Staphylococcus aureus Prophage-Encoded Protein Causes Abortive Infection and Provides Population Immunity against Kayviruses

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