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

Bailey, Christopher Michael (2010). A Bioinformatics Analysis of Bacterial Type-III Secretion System Genes and Proteins. University of Birmingham. Ph.D.

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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.

Type of Work:

Thesis (Doctorates > Ph.D.)

Award Type:

Doctorates > Ph.D.

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