BME PhD Dissertation Defense - Caroline Blassick

Title: "CHARACTERIZING HETEROGENEITY IN ESCHERICHIA COLI GENE EXPRESSION AND ITS CONSEQUENCES FOR ANTIMICROBIAL TOLERANCE"

Advisory Committee: John Ngo, PhD – BU BME (Chair) Mary Dunlop, PhD – BU BME (Advisor) Mo Khalil, PhD – BU BME Joseph W. Larkin, PhD – BU Biology and Physics Trevor Siggers, PhD – BU Biology

Abstract: Escherichia coli have evolved pathways to enable survival under a wide range of environmental stressors, including low pH, osmotic stress, and the presence of antimicrobial drugs. While these stress responses as a whole are carefully tuned for activation by specific environmental signals, heterogeneity in stress response gene expression is also commonly found in E. coli, even in isogeneic populations growing under steady state conditions and in the absence of external stressors. We investigate the origins of this heterogeneity for a range of stress response genes and find it stems from periods of pulsatile expression that are often correlated with periods of slower growth. We find that both slow growth and the expression of a number of these genes are each independently correlated with the ability of cells to tolerate the antibiotic ciprofloxacin. We then move from observation to control by applying an optogenetic feedback platform to precisely control the amounts of a tetracycline efflux pump and examine the consequences for cell survival, finding a trade-off between growth rate in the absence of tetracycline and the survival rate when exposed to the antibiotic. Finally, we apply this optogenetic platform to the native E. coli transcription factor PhoP, which coordinates the cell response to low Mg2+ conditions and exposure to cationic antimicrobial peptides. We find differences in the response pattern of E. coli to given levels of PhoP stimulation, both among different genes in the regulon and individual cells in the population, and that these differences may be linked to survival of the clinically relevant antimicrobial peptide Polymyxin B. Overall, we find that heterogeneity in gene expression is pervasive in E. coli, and this heterogeneity has important consequences in enabling tolerance to a range of antimicrobial agents.