Global transcriptome analysis reveals Salmonella Typhimurium employs nitrate metabolism to combat bile stress

Salmonella Typhimurium is an enteric pathogen that is highly tolerant to bile. Next-generation mRNA sequencing was performed to analyse the stress and adaptive responses of S. Typhimurium to bile. We identified the cellular pathways affected during bile stress in wild type (WT) and a mutant lacking cspE (?cspE), which plays an essential role in protection from bile stress. We observed transcriptional upregulation of several genes involved in nitrate metabolism, in response to bile stress. These genes were also differentially expressed between the bile-resilient WT and the bile-sensitive ?cspE strain. To understand the role of nitrate metabolism in bile stress response, we generated a strain lacking fnr (?fnr), which is the global regulator of nitrate metabolism in S. Typhimurium. fnr was highly induced in the bile treated WT strain but not in the ?cspE strain. Notably, the ?fnr strain was susceptible to bile-mediated killing. Our studies revealed a new role for fnr in mediating the bile stress response. Importantly, overexpression of fnr lowered reactive oxygen species and significantly enhanced the survival of the bile-sensitive ?cspE strain. We also observed that S. Typhimurium pre-treated with nitrate displayed better growth in the presence of bile. Together, these results demonstrate that nitrate-dependent anaerobic metabolism promotes adaptation of S. Typhimurium to bile. Overall design: RNA-sequencing was performed to understand the differences between S. Typhimurium 14028s wild type (WT) strain, which is bile resilient and bile sensitive ?cspE strain (cspE gene knockout). The gene expression profile was obtained for control and bile treated WT and ?cspE strains (in three biological replicates) at 90 minutes post bile treatment.