Comparison of Yersinia enterocolitica DNA methylation at ambient and host temperatures

ABSTRACT Pathogenic bacteria recognize environmental cues to vary gene expression for host adaptation. Moving from ambient to host temperature, Yersinia enterocolitica responds by immediately repressing flagella synthesis and inducing the virulence plasmid (pYV)-encoded type III secretion system. In contrast, shifting from host to ambient temperature requires 2.5 generations to restore motility suggesting a link to the cell cycle. We hypothesized that differential DNA methylation contributes to temperature-regulated gene expression. We tested this hypothesis by comparing single-molecule real-time (SMRT) sequencing of Y. enterocolitica DNA from cells growing exponentially at 22°C and 37°C. The inter-pulse duration ratio rather than the traditional QV scoring was the kinetic metric to compare DNA from cells grown at each temperature. All 565 YenI restriction sites were fully methylated at both temperatures. Among the 27,118 DNA adenine methylase (Dam) sites, 42 had differential methylation patterns while 17 remained unmethylated regardless of temperature. A subset of the differentially methylated Dam sites localized to promoter regions of predicted regulatory genes including LysR-type and PadR-like transcriptional regulators, and a cyclic-di-GMP phosphodiesterase. The unmethylated Dam sites localized with a bias to the replication terminus, suggesting they were protected from Dam methylase. No cytosine methylation was detected at Dcm sites. DATA SUMMARY All methylation/base modification data are available at figshare at https://dx.doi.org/10.6084/m9.figshare.3493247 and https://dx.doi.org/10.6084/m9.figshare.3493310 . IMPACT STATEMENT Organisms sense and respond to their environment, in part, by epigenetic variation mediated by DNA methylation. Pathogenic bacteria vary gene expression to allow survival and activate virulence systems in response to host temperature. Yersinia enterocolitica, a facultative intracellular pathogen, respond by immediately repressing flagella synthesis and inducing the virulence plasmid-encoded type III secretion system. In this work, we examined the locations of DNA methylation throughout the Y. enterocolitica genome. While most methylation target sites were fully methylated, we identified sites with disparate temperature-dependent methylation. Several of these sites were within promoter regions of predicted regulatory genes. Differences in DNA methylation in promoter sequences are often responsible for variations in transcription. Identification of these differences in methylation provide likely candidates for regulators responsible for temperature-dependent phenotypes.