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

Abstract

The RpoS/σS 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 σS-regulated gene expression at the transcriptional level. In contrast, very limited information regarding the impact of σS on global protein production is available. In this study, we used a mass spectrometry-based proteomics approach to explore the wide σS-dependent proteome of the human pathogen Salmonella enterica serovar Typhimurium. Our present goals were twofold: (1) to survey the protein changes associated with the ΔrpoS mutation and (2) to assess the coding capacity of σS-dependent small RNAs. Our proteomics data, and complementary assays, unravelled the large impact of σS on the Salmonella proteome, and validated expression and σS 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 σS response. Novel aspects of σS 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.

Loving the poison: the methylcitrate cycle and bacterial pathogenesis

“…However, and since rpoS disruption did not improve E. coli K12 growth on propionate, prp regulation appears to be different in E. coli and S. enterica. This may be related to the finding that in contrast to the situation in S. enterica, the prp operon of E. coli is interrupted by repetitive elements [30]. Dual antagonistic control of prp expression at both the RNA and protein levels may be a mechanism that allows S. enterica s S to Fig.…”

“…maintain finely balanced Prp expression, with greater responsiveness to changing environmental conditions [30].…”

CotL, a new morphogenetic spore coat protein of Clostridium difficile

“…The column temperature was set to 60°C. The data were acquired as previously described (Lago et al ., ).…”

“…For each sample, 1 μg of peptides was injected onto a 50-cm homemade C18 column (1.9 μm particles, 100 Å pore size, ReproSil-Pur Basic C18, Dr. Maisch GmbH) and separated with a multi-step gradient from 2% to 45% ACN in 105 min at a flow rate of 250 nl/min over 132 min. The column temperature was set to 60 C. The data were acquired as previously described (Lago et al, 2017).…”

“…The MS/MS spectra were searched against an internal C. difficile database containing 3957 proteins, and the contaminant file included in MaxQuant. The database search parameters were fixed as described (Lago et al, 2017). For the quantification, skip normalization option was used.…”