Global analysis of Salmonella alternative sigma factor E on protein translation.

The alternative sigma factor E (sigma(E)) is critical for response to extracytoplasmic stress in Salmonella. Extensive studies have been conducted on sigma(E)-regulated gene expression, particularly at the transcriptional level. Increasing evidence suggests however that sigma(E) may indirectly participate in post-transcriptional regulation. In this study, we conducted sample-matched global proteomic and transcriptomic analyses to determine the level of regulation mediated by sigma(E) in Salmonella. Samples were analyzed from wild-type and isogenic rpoE mutant Salmonella cultivated in three different conditions: nutrient-rich and conditions that mimic early and late intracellular infection. We found that 30% of the observed proteome was regulated by sigma(E) combining all three conditions. In different growth conditions, sigma(E) affected the expression of a broad spectrum of Salmonella proteins required for miscellaneous functions. Those involved in transport and binding, protein synthesis, and stress response were particularly highlighted. By comparing transcriptomic and proteomic data, we identified genes post-transcriptionally regulated by sigma(E) and found that post-transcriptional regulation was responsible for a majority of changes observed in the sigma(E)-regulated proteome. Further, comparison of transcriptomic and proteomic data from hfq mutant of Salmonella demonstrated that sigma(E)-mediated post-transcriptional regulation was partially dependent on the RNA-binding protein Hfq.