DNA methylation epigenetically regulates gene expression inBurkholderia cenocepacia

Abstract

AbstractRespiratory tract infections by the opportunistic pathogenBurkholderia cenocepaciaoften lead to severe lung damage in cystic fibrosis (CF) patients. New insights in how to tackle these infections might emerge from the field of epigenetics, as DNA methylation has shown to be an important regulator of gene expression. The present study focused on two DNA methyltransferases (MTases) inB. cenocepaciastrains J2315 and K56-2, and their role in regulating gene expression.In silicopredicted DNA MTase genes BCAL3494 and BCAM0992 were deleted in both strains, and the phenotypes of the resulting deletion mutants were studied: deletion mutant ΔBCAL3494 showed changes in biofilm structure and cell aggregation, ΔBCAM0992 was less motile.B. cenocepaciawild type cultures treated with sinefungin, a known DNA MTase inhibitor, exhibited the same phenotype as DNA MTase deletion mutants. Single-Molecule Real-Time sequencing was used to characterize the methylome ofB. cenocepacia, including methylation at the origin of replication, and motifs CACAG and GTWWAC were identified as targets of BCAL3494 and BCAM0992, respectively. All genes with methylated motifs in their putative promoter region were identified and qPCR experiments showed an upregulation of several genes, including biofilm and motility related genes, in MTase deletion mutants with unmethylated motifs, explaining the observed phenotypes in these mutants. In summary, our data confirm that DNA methylation plays an important role in regulating the expression ofB. cenocepaciagenes involved in biofilm formation and motility.ImportanceCF patients diagnosed withB. cenocepaciainfections often experience rapid deterioration of lung function, known ascepacia syndrome. B. cenocepaciahas a large multi-replicon genome and a lot remains to be learned about regulation of gene expression in this organism. From studies in other (model) organisms, it is known that epigenetic changes through DNA methylation play an important role in this regulation. The identification ofB. cenocepaciagenes of which the expression is regulated by DNA methylation and identification of the regulatory systems involved in this methylation are likely to lead to new insights in how to tackleB. cenocepaciainfections in CF patients.