Propionibacterium acnes and its phages Lood, Rolf 2011 Link to publication Citation for published version (APA): Lood, R. (2011). Propionibacterium acnes and its phages. Department of Clinical Sciences, Lund University. 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LUND UNIVERSITY PO Box 117 221 00 Lund +46 46-222 00 00 Propionibacterium acnes and its phages Rolf Lood Department of Clinical Sciences, Lund Division of Infection Medicine Faculty of Medicine Lund University, Sweden Doctoral dissertation With due permission from the Medical Faculty at Lund University this doctoral thesis is to be publicly defended on the 7th of October 2011, at 9.00 in Segerfalksalen, Biomedical Center, Sölvegatan 17, Lund. Faculty opponent Dr. Holger Brüggemann Department of Molecular Biology Max Planck Institute for Infection Biology Berlin, Germany Propionibacterium acnes and its phages Rolf Lood Department of Clinical Sciences, Lund Division of Infection Medicine Faculty of Medicine Lund University, Sweden Lund 2011 Rolf Lood Department of Clinical Sciences, Lund Division of Infection Medicine Faculty of Medicine Lund University Biomedical Center, B14 221 84 Lund Sweden E-mail: [email protected] Mobile phone: +46 739 032 117 Phone: +46 46 222 98 73 Fax: +46 46 157 756 Cover image: The lysis of Propionibacterium acnes infected with bacteriophages, and the subsequent release of the bacteriophages, as visualized using scanning electron microscopy. Maria Baumgarten and Dr. Matthias Mörgelin are acknowledged for the negative staining and electron microscopy, respectively. Printed by E-huset tryckeri, Lund, Sweden © Rolf Lood, 2011 © John Wiley and Sons, 2008 ISSN 1652-8220 ISBN 978-91-86871-43-7 Lund University, Faculty of Medicine Doctoral Dissertation Series 2011:94 To Mom and Dad The first to present his case seems right, till another comes forward and questions him -Proverbs 18:17 Table of Contents 1 Introduction 10 1.1 List of papers . 10 1.2 Abbreviations . 12 1.3 Acknowledgements . 14 1.4 Populärvetenskaplig sammanfattning . 17 2 Summary 21 The Bad Guys 22 3 Propionibacterium acnes 23 3.1 Nomenclature . 23 3.2 Genetics of the Propionibacteriaceae family ................. 24 3.3 Different types of P. acnes .......................... 24 3.4 Plasmids in Propionibacteria ......................... 25 3.5 Transformation systems in Propionibacteria ................. 26 3.6 Morphological characteristics . 26 3.7 Growth characteristics . 27 3.8 Antibiotic resistance . 28 3.9 Virulence of P. acnes ............................. 29 3.10 Acne . 29 3.11 Prostate cancer . 30 3.12 Prosthesis removal - biofilm formation . 30 3.13 Characterized proteins from P. acnes ..................... 32 4 Virulence factors 34 4.1 Introduction . 34 4.2 Virulence factors . 34 4.3 Triplets in virulence factors . 35 4.3.1 Biofilms . 35 4.3.2 Sialidases . 38 4.3.3 Protection from reactive oxygen species . 40 4.4 How to study virulence factors in P. acnes .................. 42 8 The Good Guys 44 5 Bacteriophages 45 5.1 Introduction . 45 5.2 Classification . 45 5.2.1 Introduction . 45 5.2.2 Classification . 45 5.2.3 Identification of phages . 46 5.3 Life cycle . 48 5.3.1 Introduction . 48 5.3.2 Attachment . 48 5.3.3 DNA injection . 50 5.3.4 Life cycle decision . 50 5.3.5 Integration . 52 5.3.6 Phage release . 52 5.4 Phage mediated virulence . 53 5.5 Phages in the industry . 56 5.5.1 Industrial problems with phages . 56 5.5.2 Phage display . 56 5.6 Phage therapy . 56 5.6.1 Phage therapy using whole phages . 56 5.6.2 Phage therapy using phage endolysins . 59 6 References 61 9 1 Introduction 1.1 List of papers Articles included in this thesis 1. Lood, R∗., Garbe, J∗., and Collin, M. Development of a genetic toolbox for studies of Propionibacterium acnes. Manuscript in preparation. 2. Holmberg, A., Lood, R., Mörgelin, M., Söderquist, B., Holst, E., Collin, M., Chris- tensson, B., and Rasmussen, M. 2009. Biofilm formation by Propionibacterium ac- nes is a characteristic of invasive isolates. Clinical Microbiology & Infection 15(8):787- 95. 3. Lood, R., Olin, AI, Collin, M., and Allhorn, M. Commensal skin bacteria increase the viability of human cells by protecting them from harmful reactive oxygen species. Submitted. 4. Lood, R., Mörgelin, M., Holmberg, A., Rasmussen, M., and Collin, M. 2008. In- ducible Siphoviruses in superficial and deep tissue isolates of Propionibacterium ac- nes. BMC Microbiology 8:139. 5. Lood, R., and Collin, M. 2011. Characterization and genome sequencing of two Pro- pionibacterium acnes phages displaying pseudolysogeny. BMC Genomics 12:198. Paper 2 has been reprinted with the permission from John Wiley & Sons. Paper 4 and 5 have been reprinted under the Creative Commons license. 10 Articles not included in this thesis 1. Karlsson, C., Mörgelin, M., Collin, M., Lood, R., Andersson, ML., Schmidtchen, A., Björck, L., and Frick, IM. 2009. SufA - a bacterial enzyme that cleaves fibrinogen and blocks fibrin network formation. Microbiology 155:238-248. 11 1.2 Abbreviations AHL - acyl homoserine lactone B. acnes - Bacillus acnes C. acnes - Corynebacterium acnes C. parvum - Corynebacterium parvum CAMP - Christie, Atkins, and Munch-Petersen cfu - colony forming units CXCL8 - Interleukin 8 (IL-8) DNA - deoxyribonucleic acid DNAse - deoxyribonuclease dsDNA - double stranded deoxyribonucleic acid dsRNA - double stranded ribonucleic acid E. coli - Escherichia coli GFP - green fluorescent protein ICTV - International committee on taxonomy of viruses IgA - immunoglobulin A IL-8 - interleukin 8 kb - kilo bases kDa - kilo Dalton LPS - lipopolysaccharide MAC - membrane attack complex Mb - mega bases NCBI - National Center for Biotechnology Information ORF - open reading frame P. acidifaciens - Propionibacterium acidifaciens P. acidipropionici - Propionibacterium acidipropionici P. acnes - Propionibacterium acnes P. australiense - Propionibacterium australiense P. avidum - Propionibacterium avidum P. cyclohexanicum - Propionibacterium cyclohexanicum P. freudenreichii - Propionibacterium freudenreichii P. granulosum - Propionibacterium granulosum 12 P. humerusii - Propionibacterium humerusii P. jensenii - Propionibacterium jensenii P. lymphophilum - Propionibacterium lymphophilum P. microaerophilum - Propionibacterium microaerophilum P. propionicus - Propionibacterium propionicus P. thoenii - Propionibacterium thoenii PCR - polymerase chain reaction pfu - plaque forming units RDE - receptor destroying enzyme ROS - reactive oxygen species rRNA - ribosomal ribonucleic acid RT-PCR - reverse transcriptase polymerase chain reaction SDS-PAGE - sodium dodecyl sulfate polyacrylamide gel electrophoresis SOD - superoxide dismutase ssDNA - single stranded deoxyribonucleic acid ssRNA - single stranded ribonucleic acid TNF-α - tumor necrosis factor alpha 13 1.3 Acknowledgements My supervisor Mattias Thanks for everything! Your supporting leadership, your enthusiasm and for many many interesting discussions where you always have let me come up with my own ideas. I can not imagine any better supervisor for me than you. Also thanks for friendship, not only in the lab but also outside the lab. I have really enjoyed working with you these years. Your ways of supervising and performing science will always serve as an example to me. My co-supervisors Inga-Maria Thanks for always being a support and for introducing me to the world of science. Also thanks for believing in me when I still was an undergraduate student, even though there was a small accident with the centrifuge, and the pH-meter, and...! I have much to thank you for. Matthias Thanks for all ”friendly” comments in the corridors, and for being more than helpful with electron microscopy. I hope you enjoyed looking for phages as much as I did! The thesis would not have had any good figures if it had not been for your help! The Collin-group Maria My room-partner. Thanks for your never ending enthusiasm and happiness, it has helped me a lot! And for lots of discussions – it can not always have been easy to share the office with me! Ulla For having a really good sense of humor and not being afraid of telling me how things should be done... And also for teaching me the importance of starting early in the morning – I think I won most of the days? Julia 14 Thanks for skillfully making some of my more crazy ideas working, and also for letting me know what ideas I probably should not think any more on. I have really enjoyed our collaboration! Furthermore, a huge thanks for teaching me some basics in LaTex, I had lots of fun! Who is going to press the electroporation button when I am leaving? Marta Thanks for taking lots of uncomfortable phone calls for me, reminding me of booking a place to defend my thesis in, and being a great support with the thesis. And of course with all things concerning the party afterwards! I’m looking forward to read your book! Sara Thanks for letting me help you in the beginning, making me feel smart. Unfortunately, that did not last long... Also thanks for all encouraging comments and helpful advices! Jonathan For showing me that recombinant proteins can be expressed at the first time, I do not envy you at all... Also thanks for being a great friend in the lab, and for the moment at the sunrise..