An investigation of Burkholderia cepacia complex methylomes via SMRT sequencing and mutant analysis

While nucleotide sequences determine an organism’s proteins, methylation of the nucleotides themselves can confer additional properties. In bacteria, differences in methylation can be used to identify incoming DNA, for example from bacteriophages. Restriction enzymes detect the methylation status at specific sequence motifs, and cleave improperly methylated, foreign DNA. Furthermore, methylation of key genetic regions can influence gene expression and hence phenotype. In this study, we determined the methylated motifs of three strains from the closely-related Burkholderia cepacia complex of opportunistic pathogens. Three of these motifs were novel, while two are methylated throughout this group of bacteria and beyond and had already been assigned putative causative genes. To investigate the contribution of the enzymes that methylate and cut DNA, we deleted the genes encoding them from a representative strain. We found that these genes are important for traits including motility, biofilm formation, cell shape and production of iron acquisition elements. The mutant strain showed marked defects in replicon partitioning and was more efficient at acquiring foreign DNA, illustrating the importance of methylation in maintaining genome integrity. Interestingly, we found that one methylase, part of an integrated bacteriophage genome, was essential for maintaining the phage in a dormant state. Burkholderia cepacia complex epigenetics