Bacterial Regulon Evolution: Distinct Responses and Roles for the Identical OmpR Proteins of Salmonella Typhimurium and Escherichia coli in the Acid Stress Response

Abstract

The evolution of new gene networks is a primary source of genetic innovation that allows bacteria to explore and exploit new niches, including pathogenic interactions with host organisms. For example, the archetypal DNA binding protein, OmpR, is identical between Salmonella Typhimurium serovar Typhimurium and Escherichia coli, but regulatory specialization has resulted in different environmental triggers of OmpR expression and largely divergent OmpR regulons. Specifically, ompR mRNA and OmpR protein levels are elevated by acid pH in S. Typhimurium but not in E. coli. This differential expression pattern is due to differences in the promoter regions of the ompR genes and the E. coli ompR orthologue can be made acid-inducible by introduction of the appropriate sequences from S. Typhimurium. The OmpR regulon in S. Typhimurium overlaps that of E. coli at only 15 genes and includes many horizontally acquired genes (including virulence genes) that E. coli does not have. We found that OmpR binds to its genomic targets in higher abundance when the DNA is relaxed, something that occurs in S. Typhimurium as a result of acid stress and which is a requirement for optimal expression of its virulence genes. The genomic targets of OmpR do not share a strong nucleotide sequence consensus: we propose that the ability of OmpR to recruit additional genes to its regulon arises from its modest requirements for specificity in its DNA targets with its preference for relaxed DNA allowing it to cooperate with DNA-topology-based allostery to modulate transcription in response to acid stress.

DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression

“…Experimental data demonstrating a response at the level of DNA supercoiling to variations in pH (Bang et al 2002;Karem and Foster 1993;Quinn et al 2014), temperature (Goldstein and Drlica 1984), osmotic pressure (Alice and Sanchez-Rivas 1997; Bordes et al 2003;Cheung et al 2003;Higgins et al 1988;Meury and Kohiyama 1992;O'Byrne et al 1992;Sheehan et al 1992), oxygen supply (Bebbington and Williams 2001;Cameron et al 2011Cameron et al , 2013Cortassa and Aon 1993;Dixon et al 1988;Dorman et al 1988;Malkhosyan et al 1991;Yamamoto and Droffner 1985), oxidative stress (Weinstein-Fischer et al 2000), nutrition (Balke and Gralla 1987), growth phase (Bordes et al 2003;Conter et al 1997), intracellular growth (Ó Cróinín et al 2006) and much more have been reported. A rapidly growing cell has different gene expression requirements to one that is in stationary phase and one that is undergoing a growth phase transition has yet another set of needs.…”

“…Because they rely on DNA structure rather than the presence of a specific base sequence, indirect readout mechanisms of DNA binding offer a powerful means to drive the evolution of gene regulation (Xu et al 2014). Proteins like OmpR, with low requirements for specific base sequences in their binding sites but which are sensitive to the superhelicity of the binding site DNA, are well placed to recruit new genes to their regulons (Quinn et al 2014), including genes that arrive in the bacterial cell via horizontal gene transfer (Cordeiro et al 2011). …”

“…Comprehensive information about the average superhelical density of DNA in different bacterial species is not available and the information that is in the literature has come from studies of just a few model organisms. However, it is clear that supercoiling set points can differ even between closely related examples, such as E. coli and Salmonella Typhimurium (Cameron et al 2011;Champion and Higgins 2007;Quinn et al 2014). Despite this, groups of genes that respond to changes in DNA supercoiling in one species may still do so in another; for example, the supercoiling-dependent promoter coupling that affects leuABCD expression in Salmonella Typhimurium is conserved in E. coli .…”

“…DNA relaxation is an important event in controlling the expression of genes that adjust Salmonella physiology to its host (Cameron and Dorman 2012;Ó Cróinín et al 2006;Quinn et al 2014). This bacterium is a facultative intracellular pathogen that can survive in the normally lethal environment of the macrophage in mammalian hosts.…”

“…It does this by expressing clusters of horizontally acquired genes coding for an elaborate protein secretion machine and effector proteins that, once exported, modify the vacuole to render it harmless to the bacterium (Fass and Groisman 2009). This gene cluster is located within the SPI2 pathogenicity island and the transcription promoters in SPI2 become more active when the DNA template relaxes (Cameron and Dorman 2012;Quinn et al 2014). In part, this is because the relaxed DNA conformation makes the promoters into better binding targets for the OmpR transcription factor, with its winged helix-turn-helix DNAbinding motif (Cameron and Dorman 2012).…”