Single-strain mobilome sequencing quantifies bacterial genetic response to stress, including activity of IS elements, prophages, RNAs, and REPINs

Microbial genomes are continuously being rearranged by mobile genetic elements (MGEs), leading to genetic configurations that may confer novel phenotypic traits such as antibiotic resistance, degradation of novel compounds, or other metabolic features. Standard genomic sequencing provides a snapshot of a genome in one configuration, but this static image does not give insight into the dynamics of genomic evolution and whether MGEs are actively changing a given genome. We applied single-strain mobilome sequencing to Escherichia coli K-12 substrain MG1655 under various stress conditions: UV, SDS, nalidixic acid, tetracycline, cetrimide, and copper. Under these conditions, we quantified the activity of a range of genetic elements, including extrachromosomal circular DNA (eccDNA) from IS elements, RNA genes, the UV-inducible e14 prophage, and intergenic repetitive sites (REP). Of the investigated stressors, copper and SDS are among the largest inducers of eccDNA formation from groups of IS elements, while elevated levels of hypothetical RNA/DNA heteroduplexes of ribosomal and transfer RNAs, and Rhs-nuclease proteins are induced under stress various stressors, especially copper and SDS. This approach holds promise for quantifying the genetic response to environmental stress and implications for genome plasticity. The observed mobilization of IS elements upon copper and other stressors helps to explain co-selection of heavy metals with antibiotic resistance genes and MGEs.