Nucleoid compaction during antibiotic stress excludes the SOS regulator LexA

Abstract The bacterial SOS response promotes DNA repair, survival, and mutagenesis under genotoxic stress, especially during sub-lethal antibiotic exposure. This response is regulated by LexA, a transcriptional repressor controlling SOS gene expression, but how LexA coordinates this network as antibiotic stress alters nucleoid structure is unclear. Using ciprofloxacin-induced DNA damage, we investigated how increasing antibiotic stress affects the spatial relationship between LexA and the nucleoid in single E. coli cells. Through 3D single-molecule imaging and functional assays, we found that sublethal ciprofloxacin doses activated SOS, expanded nucleoids, and maintained LexA association. In contrast, higher stress caused severe DNA damage, compacted nucleoids, and LexA exclusion, yet some cells remained viable and recovered after drug removal. These results demonstrate that the SOS response involves both temporal and spatial regulation, with LexA and nucleoid organization adapting to damage severity to modulate SOS functions.