Proteome remodelling by the stress sigma factor RpoS/σS in Salmonella: identification of small proteins and evidence for post-transcriptional regulation

The RpoS/σ S sigma subunit of RNA polymerase is the master regulator of the general stress response in many Gram-negative bacteria. Extensive studies have been conducted on σ S -regulated gene expression at the transcriptional level. In contrast, very limited information regarding the impact of σ S on global protein production is available. In this study, we used a mass spectrometry-based proteomics approach to explore the wide σ S -dependent proteome of the human pathogen Salmonella enterica serovar Typhimurium. Our present goals were twofold: (1) to survey the protein changes associated with the Δ rpoS mutation and (2) to assess the coding capacity of σ S -dependent small RNAs. Our proteomics data, and complementary assays, unravelled the large impact of σ S on the Salmonella proteome, and validated expression and σ S regulation of twenty uncharacterized small proteins of 27 to 96 amino acids. Furthermore, a large number of genes regulated at the protein level only were identified, suggesting that post-transcriptional regulation is an important component of the σ S response. Novel aspects of σ S in the control of important catabolic pathways such as myo-inositol, L-fucose, propanediol, and ethanolamine were illuminated by this work, providing new insights into the physiological remodelling involved in bacterial adaptation to a non-actively growing state.