Global Analysis of SalmonellaAlternative Sigma Factor E on Protein Translation

The alternative sigma factor E (σE) is critical for response to extracytoplasmic stress in Salmonella. Extensive studies have been conducted on σE-regulated gene expression, particularly at the transcriptional level. Increasing evidence suggests however that σEmay 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 σEin Salmonella. Samples were analyzed from wild-type and isogenic rpoEmutant Salmonellacultivated 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 σEcombining all three conditions. In different growth conditions, σEaffected the expression of a broad spectrum of Salmonellaproteins 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 σEand found that post-transcriptional regulation was responsible for a majority of changes observed in the σE-regulated proteome. Further, comparison of transcriptomic and proteomic data from hfqmutant of Salmonellademonstrated that σE-mediated post-transcriptional regulation was partially dependent on the RNA-binding protein Hfq.