Poster Presentation BacPath 13: Molecular Analysis of Bacterial Pathogens Conference 2015

Mapping the methylome: Distribution of methyltransferase target sites in the uropathogen Escherichia coli EC958 (#182)

Melinda M. Ashcroft 1 2 , Brian M. Forde 1 2 , Minh-Duy Phan 1 2 , Jayde A. Gawthorne 1 2 , Kate Peters 1 2 , Kok-Gan Chan 3 , Tiek Min Chong 3 , Wai-Fong Yin 3 , Mathew Upton 4 , Mark A. Schembri 1 2 , Scott A. Beatson 1 2
  1. School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
  2. Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, QLD, Australia
  3. Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
  4. School of Biomedical and Healthcare Science, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth, UK

Epigenetic systems are important in bacteria, where DNA methylation is the most common epigenetic modification and is involved in genome defense, DNA replication, gene expression and virulence. Additionally, epigenetic systems are often associated with mobile genetic elements (MGEs), which form the accessory genome and are important in pathogenicity and evolution. Recently, we have defined the complete methylome of Escherichia coli strain EC958, a highly virulent uropathogen of the ST131 lineage, using Pacific Biosciences Single Molecule Real Time sequencing. Our analysis identified 11 methyltransferases (MTases), including 2 Type I and 1 Type IIG that have not been described previously. Using this data, we have analysed the MTase target site distribution within the genome of EC958 and examined the gene content of hyper- and hypo-methylated regions, with a focus on genes known to be regulated by methylation, including autotransporters and chaperone usher fimbriae. Bioinformatic analyses indicate that the distribution of MTase target sites significantly differs between the core and accessory genome of EC958. Specifically, a higher density of MTase target sites within MGEs were found to be associated with a Restriction Modification system comprising of two Type IIS MTases, which were previously defined as essential for EC958 growth1. In contrast, the MTase target sites associated with Dam are under-represented in the majority of MGEs compared to the core-genome. For Dam target sites, this difference in distribution is partially accounted for by large methylation-free regions (>= 1000 bp) that are associated with MGEs, which is suggestive of evolutionary pressure and selection against Dam methylation in MGEs. This is the first study to analyse the distribution of methylation across the genome of a uropathogen of the ST131 lineage and will help us elucidate the role of methylation in the regulation of uropathogenicity. 

  1. Phan, M.D., Peters, K.M., Sarkar, S., Lukowski, S.W., Allsopp, L.P. et al. (2013) PLoS Genet. 9, e1003834