A Bioinformatics Analysis of Bacterial Type-III Secretion System Genes and Proteins

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http://eprints.org/relation/isVolatileVersionOf http://etheses.bham.ac.uk/id/document/3238 http://eprints.org/relation/ispreviewThumbnailVersionOf http://etheses.bham.ac.uk/id/document/3238 http://eprints.org/relation/isVersionOf http://etheses.bham.ac.uk/id/document/3238 archive 4031 disk0/00/00/13/00 2011-01-24 13:28:38 2019-01-23 09:53:53 2011-07-19 16:32:49 thesis show 0 Bailey Christopher Michael Pallen Mark J. University of Birmingham A Bioinformatics Analysis of Bacterial Type-III Secretion System Genes and Proteins unpub RB 10col_mede 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with in vitro assays) for identification of many novel effectors in E. coli. 2010-12 2010-11 graduation eng This unpublished thesis/dissertation is copyright of the author and/or third parties.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. public 246 University of Birmingham School of Immunity and Infection d_ph na 2010-12 graduation