Understanding the Functional Effects of Genetic Variation in the Promoters of Bacterial Pathogens

A recently published paper by the Bayliss lab described the allelic variation in Neisseria meningitidis for the intergenic region upstream of a gene coding a vaccine antigen. This antigen fHbp is a component of Bexsero (4C-MenB), a new recombinant vaccine for preventing meningitis and septicaemia by serogroup B strains of N. meningitidis. Analysis of ~1,000 genomes determined that nine sequences of this region were found in ~90% of N. meningitidis isolates. Experimental quantification of gene expression combined with mathematical treatments allowed association of specific variant nucleotides and genetic elements with difference in gene expression.
By employing a combination of bioinformatic analyses of genome sequences, mathematical treatments of datasets and experimental tests of predictions this project aims to produce a global analysis of gene expression in three bacterial pathogens - Neisseria meningitidis, Neisseria gonorrhoeae and Campylobaster jejuni. The project will aim to determine the extent of genetic variation in the intergenic regions for multiple genes with a range of functions. Genetic variation will be assessed by bioinformatic analyses and correlated with experimentally determined gene expression levels (determined by RNA-Seq and/or qPCR). Mathematical testing will be utilised to determine the specific sequences controlling expression with confirmation by site-directed mutagenesis of key nucleotides. Further work may involve mechanistic testing of the trans-acting factors (e.g. RNA polymerase binding) or extrapolation to other promoters and species through bioinformatic and mathematical testing.