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Genetic and Functional Studies of the Mip Protein of Legionella

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t1.ì. Genetic and Functional Studies of the Mip Protein of Legionella Rodney Mark Ratcliff, BSc (Hons)' MASM Infectious Diseases Laboratories Institute of Medical and Veterinary Science and Department of Microbiology and Immunology UniversitY of Adelaide. Adelaide, South Australia A thesis submitted to the University of Adelaide for the degree of I)octor of Philosophy 15'h March 2000 amended 14th June 2000 Colonies of several Legionella strains on charcoal yeast extract agar (CYE) after 4 days incubation at 37"C in air. Various magnifications show typical ground-glass opalescent appearance. Some pure strains exhibit pleomorphic growth or colour. The top two photographs demonstrate typical red (LH) and blue-white (RH) fluorescence exhibited by some species when illuminated by a Woods (IJV) Lamp. * t Table of Contents .1 Chapter One: Introduction .1 Background .............'. .2 Morphology and TaxonomY J Legionellosis ............. 5 Mode of transmission "..'....'. 7 Environmental habitat 8 Interactions between Legionella and phagocytic hosts 9 Attachment 11 Engulfment and internalisation.'.. 13 Intracellular processing 13 Intracellular replication of legionellae .. " "' " "' 15 Host cell death and bacterial release 18 Virulence (the Genetic factors involved with intracellular multiplication and host cell killing .20 icm/dot system) Legiolysin .25 Msp (Znn* metaloprotease) ...'..... .25 .28 Lipopolysaccharide .29 The association of flagella with disease.. .30 Type IV fimbriae.... .31 Major outer membrane proteins....'.......'. JJ Heat shock proteins'.'. .34 Macrophage infectivity potentiator (Mip) protein Virulenceiraits of Legionella species other than L. pneumophila..........' .39 phylogeny .41 Chapter One (continued): Introduction to bacterial classification and .41 Identificati on of Legionella...'.,..'.. .46 Phylogeny .52 Methods of phylogenetic analysis' .53 Parsimony methods.'.. .55 Distance methods UPGMA cluster analYsis.'.'.... 56 ............56 Neighbour-j oining method'.'...' ............57 Maximum likelihood methods . ............58 Rooting trees ........'..'.... ............58 Reliability of a tree.'...'. ............60 Ecological diversitY..''.. ..',...,..,'64 Aims and objectives .'..".. ,'.'...',.'.7| Chapter Two: Materials and methods."..'. ............71 Growth media.............'. ............72 Chemicals and reagents......'.....".. Antibody.. 73 73 Enzymes..... ...........73 Synthesis of synthetic oligonucleotides .... "' .,,......'.74 Culture and maintenance of bacterial strains ...........74 Genetic transfer methods'.'. ...........7 4 Transformation.......... ...........75 Electroporation...'...... ...........76 Screening of transformants ........'.' ,.,........76 DNA extraction Protocols 1 Chromosomal DNA extraction methods' Method 1 ............... Method 2 (raPid) Method 3 (heat lYsis) Plasmid DNA extraction methods Method 1 (large scale) 8 Method 2 (small scale). "..'.. PEG precipitation Purifi cation Analysis and manipulation of DNA......""' DNA quantitatton......... "..'. Restriction endonuclease digestion of DNA""' Analytical and preparative separation of restriction fragments Dephosphorylation of DNA using alkaline phosphatase """""""' In vitro cloning...... Plasmid nested deletions Labelling of DNA fragments with Digoxigenin-dUTP "' Southern blot analysis ....'........'. Colony hybridisation probing method Hybridisation and development ...'.. " " " " 4 DNA sequencing and analysis ."..'.'... " "' Polymerase chain reaction Protein Analysis Whole cell method SDS polyacrylamide gel electrophoresis (PAGE) " Western blot analYsls .'. "...'. Colony transfer and immuno-blotting. Phylogenetic analysis of sequence data ' Analysis of the Legionella genus...'."' Analysis of the anisa-worsleiensis clade """"' Chapter ih..., Functional implications of the inter-species gene variation .,............. Introduction 9l Method and sequencing strategy'...'.'..... " " "' 93 Sequencing strategy for other species..""" 94 Results 94 The open reading frame..... 96 Flanking sequences 97 Discussion 105 Chapter Four: Phylogeny of the genus Legíonella 105 Introduction .....,....,.... 105 Phylogenetic anatysis :. :.. :' :' :. :.'. :..' : : :.' :.' : " " "' 106 Results Maximum parsimonY analYsis Distance analysis....' Congruence among distance and MP trees Non-congruence among distance and MP trees 110 Discussion (anisø- chapter Five: Further phylogenetic analysis or. Legíonel/ø species within the 123 worsleíensis) clade Introduction........'.. ".. Sequence strategY..'.' Results mspA sequence analYsis Maximum parsimony (MP) analysis" " " " " "' 11 Maximum likelihood (ML) and distance analysis Congruence and non-congruence among MP, ML and NJ trees "' Discussion chapter six: A røþ sequence-based classification scheme Introduction Summary of methodology and sequence strategy""' Results....., Discussion chapter seven : Ecological diversity o1 Legionel/ø strains Introduction......... Sequence strategY Results mip data......... mspA data...'.. Discussion ........ Chapter Eight: SummarY discussion Functional analYsis...'. Phylogeny Further analysis of the anisa - worsleiens¿s clade"""' Classification scheme Ecological diversitY.'. Bibliography ..........'.. Appendices.............'..- Àppendix 1: Distance matrices used in Chapter Four' Appendix 2: Distance matrices used in Chapter Five ' Appendix 3: Copies of published papers Appendix 4: Alignment files used in chapters Four and Five ltl Table of Abbreviations this thesis The following abbreviations and gene designations have been used throughout ATP adeno sine- 5' -triPhosPhate C-terminal carboxyl-terminal of a protein sequence CYE Charcoal Yeast Extract Agar dot defective in organelle trafficking dNTP deoxy-nucleotide tri-PhosPhate EDTA etþlenediaminetetra acetic acid ER endoplasmic reticulum FKBP FK506 binding Protein GTP guanosine- 5' -trþho sPhate of invariant sites, GTR+I+G leneral time revèrsible method, I is the proportion and G is the y-shaPe Parameter icm intracellular multiPlication IPTG isopropyl-cr-D-thio galactopyranoside kDa kilodalton Kb kilobase LLAPS Le gi onell a-like amo ebic p atho gens LPS lipopolysaccharide MEE multilocus eîzyme electrophoesis mip orMip macrophage infectivity potentiator gene or protein ML maximum liklihood method MOMP major outer membrane Protein MP maximum parsimonY method mspA major secretory protein gene (also termed proA) Msp major secretory Protein MW molecular weight MLST multilocus sequence tYPing NBT nitroblue tetrazolium chloride NJ neighbour j oining method N-terminal amino-terminal of a protein sequence nt nucleotide OMP outer membrane Protein O/NI over night ORF open reading frame PAGE polyacrylamide gel electrophoresis PCR polymerase chain reaction PLF phagosome-lysosome fusion PPIase peptidyl-pr olyl cis /tr ans isomerase PFGE pulsed-field gel electrophoresis metho d QP Quartet puzzling RBS ribosomal binding site RFLP restriction fragment-length polymorphism rpoB RNA polymerase B-subunit gene co serogroup SDS sodium dodecYl sulPhate TAE Tris-Acetate-EDTA TE Tris-EDTA TEMED N,N,N,N, -tetrametþletþlenedi amine TBS Tris buffered saline Tris Tris(fhydroxymetþl] aminomethane) 1V TTBS Tween 20 / Tris buffered saline UPGMA unweighted pair group method with arithmetic averages vlv volume per volume w/v weight per volume galactopyrano side X-gal 5 -bromo -4-chloro-3 -indolyl-o-D- x-P 5-bromo-4-chloro-3-indolyl-phosphate toluidine salt V Declaration I declare that the work described herein contains no material that has been previously submitted for the award of any degree or diploma in any university and to the best of my knowledge and belief contains no material previously published or written by anothe, p.ttott, except where due reference is made in the text. I give consent to this copy of my thesis, when deposited in the University Llbrary,being available for loan and photocopying' Date: I I* J ,-'n'r r looo Signature: v1 Acknowledgements I would like to acknowledge the support of the following people. Paul .:. Drs. Jan Lanser and Michael Heuzenroeder, IMVS, Adelaide, and Professor and support' Manning, University of Adelaide, for their supervision, encouragement V/ithouitheir support, it just would not have happened' for n Ms. Robyn Doyle, and Ms. Rina Dalcin, IMVS, Adelaide, for technical help and the mysteries of being such a pláasure to work with. Robyn especially inducted me into her own molecular biology, as she has with many others, before and since' Often to tasks detriment, Robylwas always generous with her time and reagents, making difficult so much easier. for the supply of the Australian Legionella strains * Ms. Norma Sangster,-*itf, IMVS, Adelaide, and assistan.. the maintenance and storage of the remaining strains' Norma's its integrity' safeguard of the collection was a significant source of confidence in Museum, Adelaide, , Dr. Stephen Donnellan, Evolutionary Biology Unit, South Australian thought v/as a for assistance with the phylogenetic analyses. His lucid skill with critical constant challenge to my muddle-headed equivalent' I now * Richard Lumb, IMVS, Adelaide, for assistance in the preparation of the manuscript' and t's are know that inhnitives are not to be split, and am confident that all i's are dotted, crossed. proud to now * The following persons for the supply or Legionella stains and DNA' I am count many of these colleagues among my füends: . Dr. Timothy Harrison, Public Health Laboratory Services, Collindale, London, England. Also Dr. Norman Fry from the same laboratory for collaborative assistance.
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