Acinetobacter baumannii ATCC 17978 Epigenomics
Individual deletions of three genes encoding orphan DNA methyltransferases resulted in the occurrence of growth defect only in the dam mutant of A. baumannii strain ATCC 17978. Our single-molecule real-time sequencing-based methylome analysis revealed multiple Dam-mediated DNA methylation sites and proposed a potent census target motif (TTTRAATTYAAA). Loss of Dam led to modulation of genome-wide gene expression, and several Dam-target sites including the promoter region of the trmD operon (rpsP, rimM, trmD, and rplS) were identified through our methylome and transcriptome analyses. Dam methylation also appeared to control the expression of many genes linked to membrane functions (lolAB, lpxO) , replication (dnaA), and protein synthesis (trmD operon) in the strain ATCC 17978. Interestingly, cellular resistance against several antibiotics and ethidium bromide through functions of efflux pumps diminished in the absence of the dam gene, and the complementation of dam gene restored the wildtype phenotypes. Other tested phenotypic traits such as outer membrane vesicle production, biofilm formation, and virulence were also affected in the dam mutant. Collectively, our data indicated that epigenetic regulation through Dam-mediated DNA methylation of novel target sites mostly in the regulatory regions could contribute significantly to changes in multiple phenotypic traits in A. baumannii ATCC 17978.