The Impact of 18 Ancestral and Horizontally-Acquired Regulatory Proteins upon the Transcriptome and sRNA Landscape of Salmonella enterica serovar Typhimurium

Abstract

We know a great deal about the genes used by the model pathogen Salmonella enterica serovar Typhimurium to cause disease, but less about global gene regulation. New tools for studying transcripts at the single nucleotide level now offer an unparalleled opportunity to understand the bacterial transcriptome, and expression of the small RNAs (sRNA) and coding genes responsible for the establishment of infection. Here, we define the transcriptomes of 18 mutants lacking virulence-related global regulatory systems that modulate the expression of the SPI1 and SPI2 Type 3 secretion systems of S. Typhimurium strain 4/74. Using infection-relevant growth conditions, we identified a total of 1257 coding genes that are controlled by one or more regulatory system, including a sub-class of genes that reflect a new level of cross-talk between SPI1 and SPI2. We directly compared the roles played by the major transcriptional regulators in the expression of sRNAs, and discovered that the RpoS (σ38) sigma factor modulates the expression of 23% of sRNAs, many more than other regulatory systems. The impact of the RNA chaperone Hfq upon the steady state levels of 280 sRNA transcripts is described, and we found 13 sRNAs that are co-regulated with SPI1 and SPI2 virulence genes. We report the first example of an sRNA, STnc1480, that is subject to silencing by H-NS and subsequent counter-silencing by PhoP and SlyA. The data for these 18 regulatory systems is now available to the bacterial research community in a user-friendly online resource, SalComRegulon.

Oxygen‐dependent regulation of SPI1 type three secretion system by small RNAs in Salmonella enterica serovar Typhimurium

“…Anaerobic activation of fnrS is mainly dependent on Fnr, but is also affected by ArcA and CRP (Durand and Storz, ). It has been reported that Fur, the ferric uptake regulator, also affects fnrS expression (Colgan et al , ). Fur is known to positively regulate HilD expression.…”

Hfq‐dependent mRNA unfolding promotes sRNA ‐based inhibition of translation

“…Their genes (Argaman et al, 2001;Wassarman et al, 2001;Vogel et al, 2003) are transcriptionally activated by the OmpR-EnvZ two-component system, e.g., under high osmolarity conditions (Guillier & Gottesman, 2006;Brosse et al, 2016). OmrA, but not OmrB, is additionally under the control of the stress sigma factor r s (rpoS; Lévi-Meyrueis et al, 2014;Peano et al, 2015;Colgan et al, 2016). Both sRNAs associate with Hfq in vitro (Holmqvist et al, 2010) and in vivo (Wassarman et al, 2001;Zhang et al, 2003;Chao et al, 2012;Tree et al, 2014;Holmqvist et al, 2016); the sRNAs are destabilized in Δhfq cells (Holmqvist et al, 2010).…”

The Hcp-like protein HilE inhibits homodimerization and DNA binding of the virulence-associated transcriptional regulator HilD in Salmonella

“…HilC and RtsA are AraC-like transcriptional regulators that bind the same DNA sequence recognized by HilD; HilC is encoded within SPI-1, whereas RtsA is encoded in another island. HilD also controls the expression of many other virulence genes located outside SPI-1, including acquired and ancestral genes, directly, or indirectly through HilA, InvF or other regulators (12,(17)(18)(19)(20)(21)(22)(23)(24)(25). In agreement with its role as a master transcriptional regulator for a high number of genes, the expression, concentration and activity of HilD is tightly controlled.…”