Comparison ofYersinia enterocoliticaDNA methylation at ambient and host temperatures

Abstract

10Pathogenic bacteria recognize environmental cues to vary gene expression for host adaptation. 11Moving from ambient to host temperature, Yersinia enterocolitica responds by immediately 12repressing flagella synthesis and inducing the virulence plasmid (pYV)-encoded type III secretion 13 system. In contrast, shifting from host to ambient temperature requires 2.5 generations to restore 14 motility suggesting a link to the cell cycle. We hypothesized that differential DNA methylation 15 contributes to temperature-regulated gene expression. We tested this hypothesis by comparing 16 single-molecule real-time (SMRT) sequencing of Y. enterocolitica DNA from cells growing 17 exponentially at 22°C and 37°C. The inter-pulse duration ratio rather than the traditional QV scoring 18 was the kinetic metric to compare DNA from cells grown at each temperature. All 565 YenI 19 restriction sites were fully methylated at both temperatures. Among the 27,118 DNA adenine 20 methylase (Dam) sites, 42 had differential methylation patterns while 17 remained unmethylated 21 regardless of temperature. A subset of the differentially methylated Dam sites localized to promoter 22 regions of predicted regulatory genes including LysR-type and PadR-like transcriptional regulators, 23 and a cyclic-di-GMP phosphodiesterase. The unmethylated Dam sites localized with a bias to the 24 replication terminus, suggesting they were protected from Dam methylase. No cytosine methylation 25 was detected at Dcm sites. 26 27 28 DATA SUMMARY 29 30 All methylation/base modification data are available at figshare at 31 https://dx.doi.org/10.6084/m9.figshare.3493247 and 32 https://dx.doi.org/10.6084/m9.figshare.3493310. 33 34 35 IMPACT STATEMENT 36 37 Organisms sense and respond to their environment, in part, by epigenetic variation mediated by 38 DNA methylation. Pathogenic bacteria vary gene expression to allow survival and activate virulence 39 systems in response to host temperature. Yersinia enterocolitica, a facultative intracellular 40 pathogen, respond by immediately repressing flagella synthesis and inducing the virulence plasmid-41 encoded type III secretion system. In this work, we examined the locations of DNA methylation 42 throughout the Y. enterocolitica genome. While most methylation target sites were fully methylated, 43 we identified sites with disparate temperature-dependent methylation. Several of these sites were 44 within promoter regions of predicted regulatory genes. Differences in DNA methylation in promoter 45 sequences are often responsible for variations in transcription. Identification of these differences in 46 methylation provide likely candidates for regulators responsible for temperature-dependent 47 phenotypes. 48 49 50