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

The RpoS/sigma(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 sigma(S)-regulated gene expression at the transcriptional level. In contrast, very limited information regarding the impact of sigma(S) on global protein production is available. In this study, we used a mass spectrometry-based proteomics approach to explore the wide sigma(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 Delta rpoS mutation and (2) to assess the coding capacity of sigma(S)-dependent small RNAs. Our proteomics data, and complementary assays, unravelled the large impact of sigma(S) on the Salmonella proteome, and validated expression and sS 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 sigma(S) response. Novel aspects of sigma(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.