The Development of Legionella Pneumophila Reaches Different End Points in Amoebae, Macrophages and Ciliates
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THE DEVELOPMENT OF LEGIONELLA PNEUMOPHILA REACHES DIFFERENT END POINTS IN AMOEBAE, MACROPHAGES AND CILIATES by Hany A. M. Abdelhady Submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy at Dalhousie University Halifax, Nova Scotia December 2013 © Copyright by Hany A. M. Abdelhady, 2013 DEDICATION To the spirit of my father, who I wish was alive to share this moment with me, and to my mother, who always listened to my complaints and granted me her unlimited support over the years. ii TABLE OF CONTENTS LIST OF TABLES ......................................................................................................... viii LIST OF FIGURES .......................................................................................................... x ABSTRACT ..................................................................................................................... xii LIST OF ABBREVIATIONS USED ............................................................................ xiii ACKNOWLEDGEMENTS .......................................................................................... xvi CHAPTER 1: INTRODUCTION .................................................................................... 1 1.1. Legionella pneumophila is an environmental human pathogen ................................ 1 1.2. Legionellosis ............................................................................................................. 1 1.3. L. pneumophila, protozoa and human transmission .................................................. 4 1.4. Developmental cycle and differentiation of L. pneumophila .................................... 5 1.4.1. The central role of MIFs in the life cycle of L. pneumophila ............................. 6 1.4.2. Role of Tetrahymena ciliates in the life cycle of L. pneumophila. ..................... 9 1.5. Overview of the regulatory network of L. pneumophila differentiation ................. 10 1.5.1. Signals that trigger L. pneumophila differentiation .......................................... 10 1.5.2. LetA/LetS two-component system ................................................................... 12 1.5.3. Regulation by small non-coding RNA ............................................................. 14 1.5.4. Alternative sigma factors .................................................................................. 15 1.6. L. pneumophila intracellular trafficking and replication ......................................... 17 1.6.1. L. pneumophila internalization ......................................................................... 18 1.6.2. Inhibition of lysosome fusion with the LCV .................................................... 19 1.6.3. Recruitment of mitochondria to the LCV ......................................................... 19 1.6.4. Remodelling of the LCV into an ER-derived replicative organelle ................. 20 1.6.5. Bacterial egress from host cells ........................................................................ 20 1.7. The Dot/Icm system ................................................................................................ 21 1.8. Transcriptome analysis of L. pneumophila inside different hosts ........................... 23 1.8.1. The control of differentiation in L. pneumophila is not yet fully understood. ...................................................................................................... 24 1.8.2. Changes in the gene expression of L. pneumophila inside A. castellanii ......... 25 1.8.3. Changes in the gene expression of L. pneumophila inside human macrophages.................................................................................................... 28 iii 1.8.4. Changes in the gene expression of L. pneumophila inside Tetrahymena ciliates ............................................................................................................. 29 1.8.5. Comparison of L. pneumophila gene expression in amoebae and macrophages.................................................................................................... 30 1.9. Metabolism of L. pneumophila ............................................................................... 30 1.9.1. Amino acids ...................................................................................................... 31 1.9.2. Iron ................................................................................................................... 32 1.9.3. Carbohydrate metabolism ................................................................................. 35 1.10. Study hypotheses and objectives ........................................................................... 37 CHAPTER 2: MATERIALS AND METHODS .......................................................... 39 2.1. Bacterial strains and growth conditions .................................................................. 39 2.1.1. L. pneumophila ................................................................................................. 39 2.1.2. Escherichia coli ................................................................................................ 39 2.2. Hosts Infected with L. pneumophila ....................................................................... 41 2.2.1. Culture and infection of Acanthamoeba castellanii ......................................... 41 2.2.2. Culture of Tetrahymena tropicalis ciliates and feeding experiments ............... 42 2.2.3. Culture and infection of mammalian cell lines ................................................. 43 2.2.3.1. Human U937 and THP-1 cells .................................................................. 43 2.2.3.2. Mouse L929 cells ...................................................................................... 44 2.2.3.3. Human HeLa cells ..................................................................................... 44 2.3. Purification of L. pneumophila progenies from infected host cells ........................ 44 2.3.1. Purification of L. pneumophila progenies from infected cells ......................... 45 2.3.2. Isolation and mechanical disruption of legionellae-laden pellets ..................... 45 2.4. Characterization of L. pneumophila progenies from infected cells ........................ 46 2.4.1. Transmission electron microscopy (TEM) ....................................................... 46 2.4.2. Stress-resistance assays .................................................................................... 46 2.4.3. Intracellular growth experiments ...................................................................... 47 2.4.4. Attachment experiments ................................................................................... 48 2.4.5. Competition assays ........................................................................................... 48 2.4.6. Plaque assays .................................................................................................... 49 2.4.7. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS- PAGE) ............................................................................................................. 50 2.5. Molecular techniques .............................................................................................. 51 iv 2.5.1. Isolation of L. pneumophila genomic DNA ..................................................... 51 2.5.2. Isolation of L. pneumophila RNA .................................................................... 52 2.5.3. Polymerase chain reaction (PCR) ..................................................................... 53 2.5.4. Agarose gel electrophoresis .............................................................................. 54 2.5.5. Restriction endonuclease digestion .................................................................. 54 2.5.6. Plasmid and DNA purification ......................................................................... 54 2.5.7. DNA ligation .................................................................................................... 56 2.5.8. Preparation of electrocompetent E. coli DH5α cells ........................................ 56 2.5.9. Preparation of electrocompetent L. pneumophila cells .................................... 56 2.5.10. Bacterial transformation by electroporation ................................................... 56 2.6. Transcriptome analysis of L. pneumophila inside different hosts ........................... 57 2.6.1. Analysis of the genetic expression of L. pneumophila in different hosts ......... 57 2.6.2. Confirmation of microarray data by qRT-PCR ................................................ 58 2.6.2.1. RNA isolation and concentration calculation ........................................... 58 2.6.2.2. Deoxyribonuclease (DNase) I treatment of RNA ..................................... 59 2.6.2.3. Reverse transcription and cDNA synthesis ............................................... 59 2.6.2.4. Primer design ............................................................................................ 60 2.6.2.5. qRT-PCR reaction conditions ................................................................... 60 2.6.2.6. qRT-PCR data analysis ............................................................................. 61 2.7. Investigation of the role of lpg1669 in the differentiation of L. pneumophila ........ 61 2.7.1. Construction of an L. pneumophila JR32 ∆lpg1669 (amyA) mutant ................ 61 2.7.2. Complementation