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.
Highlights
ATCC1402816 revealed a number of transcripts showing high relative abundance and strong σS-dependency in stationary phase, including the σS-dependent small RNAs (sRNAs) STnc1110, SdsR, STnc1330, IsrI, and SraL16 (Supplementary Fig. S1)
Open reading frames (ORFs) showing good potential ribosome binding sites were predicted in the sequences of IsrI26, and of STnc1110 and STnc1330 which originally were considered non-coding[27] (Fig. 1a and Supplementary Fig. S2)
Typhimurium proteome, including a broad spectrum of Salmonella proteins needed for various biological processes, and proteins that have not been functionally characterized
Summary
Typhimurium) is a facultative intracellular bacterial pathogen capable of colonizing a wide range of hosts, including humans and many animal species This serotype is ubiquitous in the environment, and its capacity to adapt to many environmental conditions depends on its ability to integrate various environmental signals to coordinate gene expression appropriately. The expression of dozens of proteins correlated with transcriptomic data, only a small fraction of the proteome was assessed in those studies, and the σS-dependent proteome was largely underestimated. Complementary assays, unravelled the large impact of σS on the Salmonella proteome in stationary phase, and validated translation and σS regulation of more than twenty sRNAs. As expected, the majority of genes up-regulated by σS at the protein level were up-regulated at the transcript level[16]. The complexity of the σS regulatory network and its impact on cell physiology, revealed by this study, points to a key role of σS, at the transcriptional and post-transcriptional levels, in maintaining the delicate balance between cellular resistance during quiescence and re-growth potential, under diverse environmental conditions
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