Abstract

Changes in the spatial organization of bacterial chromosomes under stress conditions and its biological implications remain poorly understood. We mapped the structural landscape of wild-type and {Delta}dcm E. coli chromosomes under triclosan stress using Hi-C to identify triclosan-induced chromosomal interaction domains (CIDs). Two CIDs were common to the wild-type and {Delta}dcm E. coli, including a CID with a common boundary at fabI gene, which encodes the triclosan target. All mutations and structural variants under triclosan stress were observed within or in close proximity to triclosan-induced CIDs. Absence of Dcm methylation impacts both short- and long-range interactions in triclosan stress. Single-base resolution methylome maps reveal hypermethylation of adenines (in wild-type and {Delta}dcm) and cytosines (in wild-type) in the two common triclosan-induced CIDs. Furthermore, global gene expression profiling identified enrichment of highly expressed genes within the two common CIDs. Our findings suggest that stress-induced CIDs in E. coli are hotspots for genetic variations and are associated with enhanced transcriptional activity and hypermethylation of Dam/Dcm motifs.