New technologies have opened a whole new world relative to non-genetic epigenetic mechanisms for gene regulation both in eukaryotes and prokaryotes. We have recently discovered a phase variable methylation system which allows apparently homogeneous populations of bacteria to generate multiple epigenetically different subpopulations (8). These systems are present in many bacterial species and have a defence role in limiting horizontal gene transfer (3) and bacteriophage infection (5) and often characterise epidemiologically successful clones since they appear to contribute to fitness (2,6). Mathematical modelling of bacterial subpopulations during experimental carriage in human volunteers by the human pathogen Streptococcus pneumoniae show that certain subpopulations of the phase variable methylation system emerge over time (1), indicating a high relevance for interaction between the bacterium and the human host. We now have exciting new data finally demonstrating the epigenetic effect of methylation on gene expression by using synthetic DNA constructs with modified promoter regions which direct reporter gene expression.
Starting from our newest observations we will build this PhD project which will be placed on the interface between cutting edge analysis of bacterial gene regulation and pathogenesis of infection with a contribution of mathematical modelling. The main aim is to nail down the molecular mechanisms driving epigenetic regulation in bacteria. Work will include cloning of synthetic promoter regions with different methylation target sites in both Streptococcus pneumoniae, Lactobacillus casei and Listeria monocytogenes. Quantification of gene expression by reporter luminescence and quantitative PCR will be part of the work. DNA supercoiling and the interactions of histones and transcriptional complexes with synthetic promoter sequences will be tested. Testing the key findings in experimental infection models (4) will aim to translate the pioneering in vitro work to concrete issues characterising treatment and prevention of infection. Findings generated by this project will not only help us to characterise and increase our knowledge of epigenetic-dependent bacterial adaptability mechanisms in environmental and host settings, but also provide new insights into how this recently discovered area of epigenetics can ultimately impact bacterial pathogenesis.
As can be seen from the publication list this work has yielded high-level first-name publications for a number of PhD students (De Ste Croix, Furi, Manso) and this project is aimed to continue in this tradition, by addressing with a unique set of tools a cutting edge question in microbial genomics.