Journal
NATURE GENETICS
Volume 48, Issue 5, Pages 581-+Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/ng.3530
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Funding
- Defense Threat Reduction Agency [HDTRA1-15-1-0051]
- US National Institutes of Health [1U54GM114838-01]
- Mayo Clinic Center for Individualized Medicine
- Donors Cure Foundation
- Howard Hughes Medical Institute
- Banting Postdoctoral Fellowship from the Canadian Institutes of Health and Research
- Wyss Institute for Biologically Inspired Engineering, Harvard University
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Antibiotic resistance is an increasingly serious public health threat(1). Understanding pathways allowing bacteria to survive antibiotic stress may unveil new therapeutic targets(2-8). We explore the role of the bacterial epigenome in antibiotic stress survival using classical genetic tools and single-molecule real-time sequencing to characterize genomic methylation kinetics. We find that Escherichia coli survival under antibiotic pressure is severely compromised without adenine methylation at GATC sites. Although the adenine methylome remains stable during drug stress, without GATC methylation, methyl-dependent mismatch repair (MMR) is deleterious and, fueled by the drug-induced error-prone polymerase Pol IV, overwhelms cells with toxic DNA breaks. In multiple E. coli strains, including pathogenic and drug-resistant clinical isolates, DNA adenine methyltransferase deficiency potentiates antibiotics from the beta-lactam and quinolone classes. This work indicates that the GATC methylome provides structural support for bacterial survival during antibiotic stress and suggests targeting bacterial DNA methylation as a viable approach to enhancing antibiotic activity.
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