Antibiotic Resistance and Epigenetics: More to It than Meets the Eye

Abstract

The discovery of antibiotics in the last century is considered one of the most important achievements in the history of medicine. Antibiotic usage has significantly reduced morbidity and mortality associated with bacterial infections. However, inappropriate use of antibiotics has led to emergence of antibiotic resistance at an alarming rate. Antibiotic resistance is regarded as a major health care challenge of this century. Despite extensive research, well-documented biochemical mechanisms and genetic changes fail to fully explain mechanisms underlying antibiotic resistance. Several recent reports suggest a key role for epigenetics in the development of antibiotic resistance in bacteria. The intrinsic heterogeneity as well as transient nature of epigenetic inheritance provides a plausible backdrop for high-paced emergence of drug resistance in bacteria. The methylation of adenines and cytosines can influence mutation rates in bacterial genomes, thus modulating antibiotic susceptibility. In this review, we discuss a plethora of recently discovered epigenetic mechanisms and their emerging roles in antibiotic resistance. We also highlight specific epigenetic mechanisms that merit further investigation for their role in antibiotic resistance.

Keywords: adaptive resistance; antibiotic resistance; antibiotics; bacterial epigenetics; methylation.

FIG 1

An outline of the genetic basis of antibiotic resistance. Bacteria can acquire resistance to antibiotics by spontaneous mutations in the target genes or their regulators. Interchange of mobile genetic elements among bacteria (horizontal gene transfer [HGT]) also contributes to the dissemination of antibiotic resistance genes. In addition to acquisition of genetic modifications, bacteria can also survive antibiotic stress by modulating their gene expression. Well-known mediators of gene expression changes in response to antibiotic stress include two-component systems, insertion sequence (IS) elements, and posttranscriptional attenuation of gene expression.

FIG 2

Overview of bacterial epigenetics. (a) There are two broad classes of bacterial DNA modifications: methylation of adenines and cytosines and phosphorothioation of the DNA backbone, where a nonbridging oxygen gets replaced by sulfur. Bacterial DNA methylation is mediated by enzymes belonging to the restriction-modification (R-M) systems or orphan methyltransferases. Phosphorothioation is facilitated by the gene products of a DNA degradation (DND) system, dndABCDE. (b) Two classes of epigenetic modifications of bacterial mRNA have been discovered: methylation of adenine at N⁶ and NAD capping at the 5′ end.

FIG 3

Epigenetic basis of adaptive resistance. (a) When bacteria are exposed to subinhibitory concentrations of an antibiotic, they acquire adaptive resistance and are able to survive in increasing concentrations of the antibiotic. (b) When the antibiotic is withdrawn, the bacteria that have acquired adaptive resistance revert to the susceptible phenotype (48). (c) The instability of the resistance phenotype can be explained by the dynamic nature of epigenetic inheritance that governs gene expression. In the presence of the antibiotic, the epigenetic landscape of the resistant bacteria is passed on to subsequent generations, whereas in the absence of the antibiotic, the epigenetic tags are lost. Epigenetic changes thus modulate gene expression patterns, allowing the bacteria to switch between susceptible and resistant phenotypes.

FIG 4

Bacterial persistence can contribute to development of resistance-conferring mutations. Persister cells represent a small proportion of the bacterial population that are growth arrested or slow growing. Persister cells are neither defective nor have specific genetic changes; they are present in bacterial populations as a seed bank to survive rapidly changing environments. When the bacterial population is subjected to antibiotic therapy, typical bacterial cells rapidly decline in numbers, but the persister cells are able to survive in the presence of antibiotics. Persister cells can even be induced by environmental stresses or other factors. Epigenetic inheritance has been predicted to be a key player contributing to phenotypic drug tolerance in persister cells. Persister cells can lead to adaptive evolution of drug-resistant mutants due to the low rate of growth and mutations induced by stress conditions.

FIG 5

Contrasting roles of Dam- and Dcm-mediated methylation in antibiotic stress. Global methylation profiling identified increased adenine methylation and reduced cytosine methylation in antibiotic-resistant bacteria compared to levels in bacteria susceptible to antibiotics. (a) Dam-mediated adenine methylation facilitates DNA repair, reducing deleterious mutations in the bacterial genome and enhancing bacterial survival under antibiotic stress (55). (b) On the other hand, cytosine methylation has been linked to reduced expression of resistance-conferring genes such as sugE (a multidrug efflux pump) and rpoS (a sigma factor which modulates sugE expression), leading to poor survival under antibiotic stress. Robust rpoS expression from the Δdcm strain can enhance transcription of the sugE gene, representing a second layer of control or downstream effects linked to epigenetic control of gene expression in bacteria. In other words, sugE transcript levels are controlled by epigenetic mechanisms at two levels, as follows. (i) The presence of methylated cytosines in the sugE promoter or gene body is associated with reduced levels of sugE transcripts. (ii) The extent of inhibition of sugE transcription is further augmented by the lack of rpoS (a transcription factor) expression (91).

FIG 6

The epigenetic landscape influences bacterial genetics. Spontaneous deamination of cytosine yields uracil that is recognized by the DNA repair machinery, which corrects it back to cytosine. However, in case of methylated cytosines, deamination yields thymines which are not recognized as aberrant nucleotides in DNA, making an irreparable lesion; during subsequent DNA replication the thymine base pairs with adenine, and the lesion becomes permanent or fixed (left box). Methyl-dependent mismatch repair mechanisms correct mutations in the complementary strand during replication; this mode of repair is dependent on the presence of GATC sites with methylated adenines on the parental strand in the vicinity of the lesion on the complementary (nascent) strand. In the absence of methylated adenine in the parent strand, the mutation in the complementary (nascent) strand is not repaired (right box).

FIG 7

Uncharted epigenetic mechanisms and their putative role in antibiotic resistance. Some epigenetic mechanisms are putatively associated with antibiotic resistance but remain poorly documented or partially understood. When methyltransferase-encoding phages infect bacteria, the phage DNA encoding methyltransferases (Mtases) can get integrated into the bacterial genome and influence the methylomes of the daughter cells. The link between altered methylomes and antibiotic resistance has been proposed by several groups, but direct evidence for this hypothesis is still lacking (left box). Epigenetic regulation of expression of genes that are not directly associated with antibiotic resistance has been predicted to contribute to the resistant phenotype, but the underlying mechanisms are poorly understood (right box).