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Mechanisms of Anaerobic Nitric Oxide Detoxification by Salmonella Enterica Serovar Typhimurium

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Mechanisms of Anaerobic Nitric Oxide Detoxification by Salmonella Enterica Serovar Typhimurium Mechanisms of anaerobic nitric oxide detoxification by Salmonella enterica serovar Typhimurium Anke Arkenberg Thesis for the degree of Doctor of Philosophy School of Biological Sciences, University of East Anglia September 2013 © This copy of the thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with the author and that no quotation from the thesis, nor any information derived therefrom, may be published without the author’s prior, written consent. Acknowledgements Firstly, I would like to thank my supervisory team of Gary Rowley, David Richardson and Margaret Wexler. Their guidance and support has allowed me to finish this thesis despite starting full-time work after the third year. Also, I am grateful to my parents as without their emotional and financial support this would not have been possible. Mama und Papa, ich danke Euch von ganzem Herzen, dass Ihr soviel Vertrauen in mich gesetzt, mich die ganze Zeit voll und ganz unterstützt habt und hoffe, dass es die Investition wert war. Huge thanks go to Luke, my financé, who has supported and motivated me throughout, but especially throughout the endeavour of working full-time and continuing the thesis work in the remaining time: You have carried me through the highs and lows and helped me to stay focused! Thanks also to my friends Connie, Eileen, Hannah, Hayley, Sarah: Meeting up at the office or elsewhere, eating some home-baked goodies, going for a run around the lake, and being able to forget the long lab hours has kept me positive and sane. In addition, I owe thanks to everyone that has helped me to learn technique after technique: Gary, Karen, Lucy, Heather, Corinne, Colin and Elaine. Thanks also to the people from the Rowley lab; I have missed the atmosphere of the lab, the discussions and the laughs. Without the Pamela Salter group and the chats in the office, the waiting times in between measurements would not have been as cheerful and I would have not been able to stay as motivated. Thanks also to everyone who asked about my progress: It has helped me to evaluate appreciate my progress and has spurred me on to get finished. Special thanks to Gary and Hannah for reading and helping me to make the necessary changes to this thesis. 2 Abstract Salmonella is the cause of millions of food- and water-borne infections worldwide. Systemic infection and gastroenteritis are the main diseases and often prove fatal to immunocompromised patients. Key to Salmonella’s pathogenicity is the survival of several components of the innate immune system encountered during infection. Reactive oxygen and nitrogen species (ROS and RNS) are an integral part of this antibacterial defence of the immune system. Exposure to ROS and RNS occurs within phagocytic immune cells such as macrophages, where such generation of radicals is used to combat pathogens. NO is a radical belonging to the group of RNS that damages bacterial DNA and proteins. Detoxification of NO is essential during infection to allow Salmonella to survive and replicate within macrophages. Three enzymes are currently known to help Salmonella to detoxify NO, but their deletion, however, does not eliminate Salmonella’s survival. Therefore, it is predicted that further mechanisms for NO detoxification exist. In this study, the core NO regulon has been identified: Expression of nine genes is significantly increased during endogenous and exogenous NO exposure of S. Typhimurium. Their functions range from carbon starvation, cytochrome oxidation, iron-sulphur repair and NO reduction to putative proteins with unknown function, some of which contain domains for tellurite resistance. Single and combination deletion strains have shown that these genes are important to decrease anaerobic NO sensitivity of S. Typhimurium and for intracellular survival in murine macrophages. Furthermore, we have shown for the first time that the core NO regulon also provides protection against tellurite. Tellurite is toxic and requires detoxification when encountered. Reducing tellurite to yield the elemental tellurium results in the release of ROS, which then need to be detoxified further. Deletion strains sensitive to tellurite have also shown increased sensitivity to NO. Concurrently, tellurite resistance genes also facilitate the defence against NO. 3 Table of contents Acknowledgements .......................................................................................... 2 Abstract ............................................................................................................. 3 Table of contents .............................................................................................. 4 List of Figures ................................................................................................... 9 List of Tables ................................................................................................... 11 Abbreviations .................................................................................................. 13 1 Introduction .............................................................................................. 17 1.1 Salmonella ............................................................................................. 18 1.1.1 Nomenclature ..................................................................................... 18 1.1.2 Epidemiology of Salmonellosis ........................................................... 18 1.2 Infection biology of Salmonella ............................................................... 20 1.2.1 Route of infection ................................................................................ 20 1.2.1.1 Sources of contamination ............................................................ 20 1.2.1.2 Gastric passage and gut commensals ......................................... 22 1.2.2 Gastroenteritis .................................................................................... 23 1.2.2.1 Role of SPI-1 ............................................................................... 25 1.2.2.2 Role of SPI-2 ............................................................................... 27 1.2.3 Typhoid fever ...................................................................................... 31 1.2.4 Chronic carrier stage .......................................................................... 36 1.3 Treatment of Salmonella infections ........................................................ 37 1.4 Antibiotic resistance ............................................................................... 37 1.4.1 Vaccination ......................................................................................... 38 1.5 Immune defence: Macrophages ............................................................. 42 1.5.1 Toxicity of reactive oxygen species .................................................... 44 1.5.1.1 Enzymatic detoxification of ROS by Salmonella .......................... 45 1.5.2 Toxicity of reactive nitrogen species ................................................... 46 1.6 Detoxification of NO ............................................................................... 49 1.6.1 HmpA .................................................................................................. 54 1.6.2 NorV ................................................................................................... 56 1.6.3 NrfA .................................................................................................... 58 1.6.4 NO detoxification in other bacteria ...................................................... 59 1.7 Regulatory proteins which coordinate the NO response ........................ 60 4 1.7.1 FNR .................................................................................................... 61 1.7.2 Fur ...................................................................................................... 63 1.7.3 NorR ................................................................................................... 64 1.7.4 NsrR ................................................................................................... 66 1.8 Summary and context ............................................................................ 70 2 Materials & Methods ................................................................................ 73 2.1 Strains & culture conditions .................................................................... 74 2.1.1 Strains & plasmids .............................................................................. 74 2.1.2 Complex media ................................................................................... 74 2.1.3 Overnight cultures .............................................................................. 74 2.1.4 Minimal media .................................................................................... 74 2.2 General laboratory techniques ............................................................... 76 2.2.1 Polymerase chain reaction (PCR) ...................................................... 76 2.2.2 PCR product purification ..................................................................... 76 2.2.3 Plasmid purification............................................................................. 76 2.2.4 Gel electrophoresis ............................................................................. 78 2.3 Generation of constructs for gene knockouts ......................................... 78 2.4 De novo
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