Temperature-dependent dynamics of DNA methylation and plasmid copy number in Yersinia pestis.

A number of mechanisms that control Yersinia pestis behavior during its complex life cycle in both mammalian hosts and arthropod vectors are known to be thermally regulated. In bacteria, the response to temperature shifts often involves epigenetic factors, particularly changes in DNA methylation. In this study, we aimed to fully characterize the methylome of eleven Y. pestis strains from different subspecies. We described its temperature-dependent features by comparing cultures grown at 22 °C (typical flea environment) and 37 °C (mammalian host temperature). Only two methylation motifs were detected: GATC with 6 mA modifications and CCWGG with 4mC modifications. GATC sites were almost fully methylated across the genome, except regions encoding the Type II secretion system and O‑antigen biosynthesis cluster, and four loci in the pMT1 plasmid. CCWGG sites were reproducibly less methylated at 37 °C than at 22 °C. This cytosine under‑methylation was more pronounced in strains from the ancient 0.PE4 lineage than in the highly pathogenic 0.ANT5 and 2.MED1 strains. Six genes showed reproducible differential methylation in CCWGG sites, including the virulence factor gene yopD and the plasmid gene parA, which is involved in plasmid replication and segregation. Subsequently, we observed a significant increase in the copy number of all Y. pestis plasmids in samples grown at 37 °C compared to those at 22 °C.