Global Analysis of Salmonella Alternative 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 σE 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 σE 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 σE combining all three conditions. In different
growth conditions, σE 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 σE and
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 hfq mutant of Salmonella demonstrated
that σE-mediated post-transcriptional regulation
was partially dependent on the RNA-binding protein Hfq.