UC San Diego

The ferric uptake regulator, Fur, is a highly conserved global transcriptional regulator in gram-negative bacteria that maintains iron homeostasis through its binding of Fe2+. Proper management of iron ensures that pivotal processes such as DNA repair, aerobic respiration, and cell proliferation can occur fluidly without threat of iron-mediated ROS production and accumulation. Though Fur’s targets, regulon, regulatory methods, and effects on phenotypes have been extensively studied in many model E. coli strains, its range of action in non-model systems remains unexplored. Studying Fur in the latter scenario might provide data that is paramount towards expanding our knowledge of microbial iron metabolism. In this study, we combine genome-scale data from high-throughput sequencing (ChIP-exo) with strand-specific massively parallel complementary DNA sequencing (RNA-seq) to uncover the Fur regulon of two clinical E. coli strains isolated from bacteremia patients, No. 131 and No. 158. Furthermore, we assess the effect of Fur on bacterial growth and antibiotic resistance by knocking out Fur and comparing fur mutants to their wild-type counterparts. We find that the Fur regulon of the two strains shares major conserved regions that overlap with the closely related uropathogenic (UPEC) E. coli strain, CFT073, and the distantly related E. coli K-12 strain, MG1655. This is not without outliers, nonetheless – the unique genes that do surface in each clinical strain’s respective regulons provide us with a distinct perspective by which to explore Fur’s regulatory modes and regulatory scope. We also find that an absence of Fur does hinder growth of the two strains and changes the scope of their antibiotic resistances albeit in distinct fashions.