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Gram Negative Bacteria Have Evolved a Series of Secretion Systems Which A Bioinformatics Analysis of Bacterial Type-III Secretion System Genes and Proteins By Christopher Michael Bailey A thesis submitted to The University of Birmingham for the degree of DOCTOR OF PHILOSOPHY Division of Immunity and Infection The School of Medicine The University of Birmingham November 2010 University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. Abstract Type-III secretion systems (T3SSs) are responsible for the biosynthesis of flagella, and the interaction of many animal and plant pathogens with eukaryotic cells. T3SSs consist of multiple proteins which assemble to form an apparatus capable of exporting proteins through both membranes of Gram-negative bacteria in one step. Proteins conserved amongst T3SSS can be used for analysis of these systems using computational homology searching. By using tools including BLAST and HMMER in conjunction phylogenetic analysis this thesis examines the range of T3SSs, both in terms of the proteins they contain, and also the bacteria which contain them. In silico analysis of several of the conserved components of T3SSs shows similarities between them and other secretion systems, as well as components of ATPases. Use of conserved components allows for identification of T3SS loci in diverse bacteria, in order to assess in the different proteins used by different T3SSs, and to see where, in evolutionary space, these differences arose. Analysis of homology data also allows for comprehensive re-annotation of T3SS loci within Desulfovibrio, Lawsonia and Hahella, and subsequent comparison of these T3SSs with related Yersinial T3SSs, and also (in conjunction with in vitro assays) for identification of many novel effectors in E. coli. Authors Contributions All the work presented here is the authors own with the exception of portions of Chapter 2 and Chapter 3. Within Chapter 2 initial survey work leading to the work on the relationship between b-subunit proteins of ATPases and SctL/FliH components was undertaken by Professor Mark Pallen, before being taken on by the Author. Within Chapter 3, the work presented was part of a collaborative effort between three separate lab groups: The Pallen group at the University of Birmingham, The Frankel group at Imperial College, London and the Hayashi group at Osaka University, Japan. Initial bioinformatics survey work was performed by Scott Beatson, all secretome, Flag and CyeA assays were performed by Toru Tobe, Hisaaki Taniguchi and Hiroyuki Abe at Osaka University. -lactamase assays were prepared by the Author, Scott Beatson, Amanda Fivian, Rasha Younis and Sophie Matthews. The -lactamase assay itself was performed under the supervision of Olivier Marches. Out of the complete set of all -lactamase assays the author worked with half of the effector candidates from the stage of production of amplified DNA for effector candidates to production of source and destination gateway plasmids. Of this 50%, the author also and undertook the assay from start to finish for half (i.e. 25% of the all the effector candidates). Dedication To my parents Dorrien and Michael Acknowledgements The division of immunity and infection for funding my work. Prof Mark Pallen for his supervision, ideas, and support. Prof Charles Penn and Dr. Roy Chaudhuri for their stimulating insight. Dr Lori Snyder, Dr Scott Beatson and Dr Nick Loman for proof- reading, and last but not least, Dr. Dov Stekel for his mathematical knowledge, support and advice. Table of Contents Chapter 1 - Introduction ................................................................................................. 1 1.1. Molecular Evolution ............................................................................................... 1 1.1.1. Gene Gain, Gene Loss and Gene Mutation ..................................................... 2 1.1.2. Vertical Gene Transfer..................................................................................... 3 1.1.3. Horizontal Gene Transfer................................................................................. 4 1.1.3.1. Plasmids .................................................................................................... 6 1.1.3.2. Bacteriophage............................................................................................ 6 1.1.4. Homology, Orthology and Parology ................................................................ 8 1.1.5. Detection of evolutionarily related sequences in silico ................................... 9 1.1.5.1. Simple sequence alignment algorithms .................................................. 10 1.1.5.2. Scoring alignments.................................................................................. 14 1.1.5.3. Heuristic methods for searching large datasets: BLAST ........................ 16 1.1.5.4. Detecting distant homology .................................................................... 19 1.1.5.4.1. Alignment based methods: PSI-BLAST .............................................. 20 1.1.5.4.2. Markov model based methods: HMMER ............................................ 21 1.1.6. Sequence similarity as a predictor of structure and function ......................... 24 1.1.6.1. Divergence between sequence, structure and function ........................... 25 1.1.6.2. Conserved sequence, un-conserved structure ......................................... 26 1.1.6.3. Conserved sequence and structure, un-conserved function .................... 27 1.1.6.4. Conserved sequence, unknown function................................................. 27 1.1.6.5. Un-conserved sequence, conserved structure ......................................... 28 1.1.6.6. Un-conserved sequence and structure, conserved function .................... 30 1.1.6.7. Implications for assignments based on sequence similarity alone.......... 31 1.1.7. Phylogenetics and phylogenomics ................................................................. 32 1.1.7.1. Methods for classifying proteins and larger units into trees ................... 33 1.2. Protein Secretion by Bacteria................................................................................ 34 1.2.1. Secretion across the inner membrane............................................................. 35 1.2.2. Secretion across the outer membrane............................................................. 37 1.2.2.1. Type I Secretion ...................................................................................... 37 1.2.2.2. Type II secretion ..................................................................................... 39 1.2.2.3. Type IV secretion.................................................................................... 42 1.2.2.4. Type V secretion ..................................................................................... 43 1.2.2.5. Type III secretion .................................................................................... 45 1.3. Type III Secretion Systems ................................................................................... 46 1.3.1. The bacterial Flagellum and Non-Flagellar secretion systems ...................... 46 1.3.2. The construction of type-III secretion systems .............................................. 47 1.3.2.1. Cytoplasmic and Inner Membrane Proteins............................................ 47 1.3.2.2. Periplasmic and outer membrane proteins .............................................. 51 1.3.3. Directing secretion: T3S needle and translocon ............................................ 53 1.3.3.1. The needle and associated proteins ......................................................... 53 1.3.3.2. The translocon - proteins that put the tip on the needle .......................... 56 1.3.4. Control of apparatus and effectors: Regulators and chaperones.................... 57 1.3.5. Communicating with the host: effector proteins............................................ 60 i 1.4. Viewing Type-III Secretion in an Evolutionary Context...................................... 61 1.5. Sequence – Structure – Function Relationships in Type-III secretion proteins.... 62 1.6. Aims ...................................................................................................................... 63 Chapter 2 - Specific T3ss components......................................................................... 66 2.1. Introduction ........................................................................................................... 66 2.1.1. NF-T3SS components shared with other systems ......................................... 66 2.1.2. The machinery of ATP synthesis and utilisation ........................................... 67 2.1.3. Aims ............................................................................................................... 69 2.2. Methods................................................................................................................. 70 2.2.1. BLAST and PSI-BLAST ..............................................................................
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