Time-resolved transcriptomic mapping reveals conserved stress programs and metabolic rewiring in Escherichia coli under antimicrobial photodynamic and blue light exposure

Abstract Antimicrobial photodynamic inactivation (aPDI) and antimicrobial blue light (aBL) are emerging, resistance-agnostic strategies for controlling bacterial pathogens, yet their systems-level impact on prokaryotic physiology remains incompletely understood. Here, we used time-resolved global transcriptomics to define how Escherichia coli reprograms gene expression in response to diverse photodynamic stresses. E. coli K-12 BW25113 was exposed to five phototreatments differing in photosensitizer chemistry and light wavelength, including rose bengal, TMPyP, new methylene blue, aBL alone, and aBL combined with 5-aminolevulinic acid, and transcriptional responses were profiled after short (30 min) and prolonged (7–8 h) exposure. Short-term phototreatments triggered rapid and extensive transcriptional remodeling, affecting up to ∼58% of the genes and dominated by conserved stress programs including oxidative defense, sulfur metabolism, and a broad downshift in biosynthesis and energy generation. In contrast, prolonged exposure elicited more restrained but highly treatment-specific adaptive responses, characterized by suppression of core energy metabolism, including oxidative phosphorylation and the tricarboxylic acid cycle, coupled with activation of alternative catabolic pathways. Together, these findings reveal a common acute stress architecture across photodynamic modalities followed by divergent long-term adaptive trajectories, providing a systems-level framework for understanding bacterial responses to light-based antimicrobials and informing the rational optimization of photodynamic therapies. Abstract Figure