HilD induces expression of a novel Salmonella Typhimurium invasion factor, YobH, through a regulatory cascade involving SprB

Pan-Genome Analysis of Transcriptional Regulation in Six Salmonella enterica Serovar Typhimurium Strains Reveals Their Different Regulatory Structures

Establishing transcriptional regulatory networks (TRNs) in bacteria has been limited to well-characterized model strains. Using machine learning methods, we established the transcriptional regulatory networks of six Salmonella enterica serovar Typhimurium strains from their transcriptomes. By decomposing a compendia of RNA sequencing (RNA-seq) data with independent component analysis, we obtained 400 independently modulated sets of genes, called iModulons. We (i) performed pan-genome analysis of the phylogroup structure of S. Typhimurium and analyzed the iModulons against this background, (ii) revealed different genetic signatures in pathogenicity islands that explained phenotypes, (iii) discovered three transport iModulons linked to antibiotic resistance, (iv) described concerted responses to cationic antimicrobial peptides, and (v) uncovered new regulons. Thus, by combining pan-genome and transcriptomic analytics, we revealed variations in TRNs across six strains of serovar Typhimurium. IMPORTANCE Salmonella enterica serovar Typhimurium is a pathogen involved in human nontyphoidal infections. Treating S. Typhimurium infections is difficult due to the species's dynamic adaptation to its environment, which is dictated by a complex transcriptional regulatory network (TRN) that is different across strains. In this study, we describe the use of independent component analysis to characterize the differential TRNs across the S. Typhimurium pan-genome using a compendium of high-quality RNA-seq data. This approach provided unprecedented insights into the differences between regulation of key cellular functions and pathogenicity in the different strains. The study provides an impetus to initiate a large-scale effort to reveal the TRN differences between the major phylogroups of the pathogenic bacteria, which could fundamentally impact personalizing treatments of bacterial pathogens.

Two Additional Connections between the Transcriptional Programs Controlling Invasion and Intracellular Replication of Salmonella: HilD-SprB Positively Regulates phoP and slyA

Salmonella virulence relies on the ability of this bacterium to invade the intestinal epithelium and to replicate inside macrophages, which are functions mainly encoded in Salmonella pathogenicity islands 1 and 2 (SPI-1 and SPI-2), respectively. Complex regulatory programs control the expression of SPI-1 and SPI-2 and functionally related genes, involving the integration of ancestral regulators and regulators that Salmonella has acquired during its evolution. Interestingly, some previous studies have revealed cross talk between the regulatory programs for SPI-1 and SPI-2. Here, we report two additional connections between the regulatory programs controlling the expression of genes for invasion and intracellular replication. Our results show that the acquired regulators HilD and SprB, both encoded in SPI-1, induce, in a cascade fashion, the expression of PhoP and SlyA, two ancestral regulators that activate the expression of SPI-2 and other genes required for intracellular replication. We provide evidence supporting that the regulation of phoP and slyA by HilD-SprB was adapted during the divergence of Salmonella from its closer species, Escherichia coli, with the acquisition of SPI-1 and thus the gain of HilD and SprB, as well as through cis-regulatory evolution of phoP and slyA. Therefore, our study further expands the knowledge about the intricate regulatory network controlling the expression of virulence genes in Salmonella. IMPORTANCE Bacteria have developed diverse regulatory mechanisms to control genetic expression, in the case of pathogenic bacteria, to induce the expression of virulence genes in particular niches during host infection. In Salmonella, an intricate regulatory network has been determined, which controls the spatiotemporal expression of the SPI-1 and SPI-2 gene clusters that mediate the invasion to and the replication inside host cells, respectively. In this study, we report two additional pathways of cross talk between the transcriptional programs for SPI-1 and SPI-2. Additionally, our results support that these additional regulatory pathways were adapted during the divergence of Salmonella from its closer species, Escherichia coli. This study further expands the knowledge about the mechanisms determining the Salmonella virulence.

Antibiotic resistance and siderophores production by clinical Escherichia coli strains

The phenomenon of antibiotic resistance has dramatically increased in the last few decades, especially in enterobacterial pathogens. Different strains of Escherichia coli have been reported to produce a variety of structurally different siderophores. In the present study, 32 E. coli strains were collected from different clinical settings in Cairo, Egypt and subjected to the antibiotic susceptibility test by using 19 antibiotics belonging to 7 classes of chemical groups. The results indicated that 31 strains could be considered as extensively drug-resistant and only one strain as pan drug-resistant. Siderophores production by all the tested E. coli strains was determined qualitatively and quantitatively. Two E. coli strains coded 21 and 49 were found to be the most potent siderophores producers, with 79.9 and 46.62%, respectively. Bacterial colonies with cured plasmids derived from strain 49 showed susceptibility to all the tested antibiotics. Furthermore, E. coli DH5α cells transformed with the plasmid isolated from E. coli strain 21 or E. coli strain 49 were found to be susceptible to ansamycins, quinolones, and sulfonamide groups of antibiotics. In contrast, both plasmid-cured and plasmid-transformed strains did not produce siderophores, indicating that the genes responsible for siderophores production were located on plasmids and regulated by genes located on the chromosome. On the basis of the obtained results, it could be concluded that there is a positive correlation between antibiotic resistance, especially to quinolones and sulfonamide groups, and siderophores production by E. coli strains used in this study.

Regulatory Evolution of the phoH Ancestral Gene in Salmonella enterica Serovar Typhimurium

One important event for the divergence of Salmonella from Escherichia coli was the acquisition by horizontal transfer of the Salmonella pathogenicity island 1 (SPI-1), containing genes required for the invasion of host cells by Salmonella. HilD is an AraC-like transcriptional regulator in SPI-1 that induces the expression of the SPI-1 and many other acquired virulence genes located in other genomic regions of Salmonella. Additionally, HilD has been shown to positively control the expression of some ancestral genes (also present in E. coli and other bacteria), including phoH. In this study, we determined that both the gain of HilD and cis-regulatory evolution led to the integration of the phoH gene into the HilD regulon. Our results indicate that a HilD-binding sequence was generated in the regulatory region of the S. enterica serovar Typhimurium phoH gene, which mediates the activation of promoter 1 of this gene under SPI-1-inducing conditions. Furthermore, we found that repression by H-NS, a histone-like protein, was also adapted on the S. Typhimurium phoH gene and that HilD activates the expression of this gene in part by antagonizing H-NS. Additionally, our results revealed that the expression of the S. Typhmurium phoH gene is also activated in response to low phosphate but independently of the PhoB/R two-component system, known to regulate the E. coli phoH gene in response to low phosphate. Thus, our results indicate that cis-regulatory evolution has played a role in the expansion of the HilD regulon and illustrate the phenomenon of differential regulation of ortholog genes. IMPORTANCE Two mechanisms mediating differentiation of bacteria are well known: acquisition of genes by horizontal transfer events and mutations in coding DNA sequences. In this study, we found that the phoH ancestral gene is differentially regulated between Salmonella Typhimurium and Escherichia coli, two closely related bacterial species. Our results indicate that this differential regulation was generated by mutations in the regulatory sequence of the S. Typhimurium phoH gene and by the acquisition by S. Typhimurium of foreign DNA encoding the transcriptional regulator HilD. Thus, our results, together with those from an increasing number of studies, indicate that cis-regulatory evolution can lead to the rewiring and reprogramming of transcriptional regulation, which also plays an important role in the divergence of bacteria through time.

A horizontally acquired Legionella genomic island encoding a LuxR type regulator and effector proteins displays variation in gene content and regulation

The intracellular pathogen Legionella pneumophila translocates >300 effector proteins into host cells, many of which are regulated at the transcriptional level. Here, we describe a novel L. pneumophila genomic island, which undergoes horizontal gene transfer within the Legionella genus. This island encodes two Icm/Dot effectors: LegK3 and a previously uncharacterized effector which we named CegK3, as well as a LuxR type regulator, which we named RegK3. Analysis of this island in different Legionella species revealed a conserved regulatory element located upstream to the effector-encoding genes in the island. Further analyses, including gene expression analysis, mutagenesis of the RegK3 regulatory element, controlled expression studies, and gel-mobility shift assays, all demonstrate that RegK3 directly activates the expression levels of legK3 and cegK3 effector-encoding genes. Additionally, the expression of all the components of the island is silenced by the Fis repressors. Comparison of expression profiles of these three genes among different Legionella species revealed variability in the activation levels mediated by RegK3, which were positively correlated with the Fis-mediated repression. Furthermore, LegK3 and CegK3 effectors moderately inhibit yeast growth, and importantly, they have a strong synergistic inhibitory effect on yeast growth, suggesting these two effectors are not only co-regulated but also might function together.

An incoherent feedforward loop formed by SirA/BarA, HilE and HilD is involved in controlling the growth cost of virulence factor expression by Salmonella Typhimurium

An intricate regulatory network controls the expression of Salmonella virulence genes. The transcriptional regulator HilD plays a central role in this network by controlling the expression of tens of genes mainly required for intestinal colonization. Accordingly, the expression/activity of HilD is highly regulated by multiple factors, such as the SirA/BarA two-component system and the Hcp-like protein HilE. SirA/BarA positively regulates translation of hilD mRNA through a regulatory cascade involving the small RNAs CsrB and CsrC, and the RNA-binding protein CsrA, whereas HilE inhibits HilD activity by protein-protein interaction. In this study, we show that SirA/BarA also positively regulates translation of hilE mRNA through the same mentioned regulatory cascade. Thus, our results reveal a paradoxical regulation exerted by SirA/BarA-Csr on HilD, which involves simultaneous opposite effects, direct positive control and indirect negative control through HilE. This kind of regulation is called an incoherent type-1 feedforward loop (I1-FFL), which is a motif present in certain regulatory networks and represents a complex biological problem to decipher. Interestingly, our results, together with those from a previous study, indicate that HilE, the repressor component of the I1-FFL reported here (I1-FFL_{SirA/BarA-HilE-HilD}), is required to reduce the growth cost imposed by the expression of the genes regulated by HilD. Moreover, we and others found that HilE is necessary for successful intestinal colonization by Salmonella. Thus, these findings support that I1-FFL_{SirA/BarA-HilE-HilD} cooperates to control the precise amount and activity of HilD, for an appropriate balance between the growth cost and the virulence benefit generated by the expression of the genes induced by this regulator. I1-FFL_{SirA/BarA-HilE-HilD} represents a complex regulatory I1-FFL that involves multiple regulators acting at distinct levels of gene expression, as well as showing different connections to the rest of the regulatory network governing Salmonella virulence.

To infect the intestine of a broad range of hosts, including humans, Salmonella is required to express a large number of genes encoding different cellular functions, which imposes a growth penalty. Thus, Salmonella has developed complex regulatory mechanisms that control the expression of virulence genes. Here we identified a novel and sophisticated regulatory mechanism that is involved in the fine-tuned control of the expression level and activity of the transcriptional regulator HilD, for the appropriate balance between the growth cost and the virulence benefit generated by the expression of tens of Salmonella genes. This mechanism forms an incoherent type-1 feedforward loop (I1-FFL), which involves paradoxical regulation; that is, a regulatory factor exerting simultaneous opposite control (positive and negative) on another factor. I1-FFLs are present in regulatory networks of diverse organisms, from bacteria to humans, and represent a complex biological problem to decipher. Interestingly, the I1-FFL reported here is integrated by ancestral regulators and by regulators that Salmonella has acquired during evolution. Thus, our findings reveal a novel I1-FFL of bacteria, which is involved in virulence. Moreover, our results illustrate the integration of ancestral and acquired factors into a regulatory motif, which can lead to the expansion of regulatory networks.

Horizontally acquired regulatory gene activates ancestral regulatory system to promote Salmonella virulence

Horizontally acquired genes are typically regulated by ancestral regulators. This regulation enables expression of horizontally acquired genes to be coordinated with that of preexisting genes. Here, we report a singular example of the opposite regulation: a horizontally acquired gene that controls an ancestral regulator, thereby promoting bacterial virulence. We establish that the horizontally acquired regulatory gene ssrB is necessary to activate the ancestral regulatory system PhoP/PhoQ of Salmonella enterica serovar Typhimurium (S. Typhimurium) in mildly acidic pH, which S. Typhimurium experiences inside macrophages. SsrB promotes phoP transcription by binding upstream of the phoP promoter. SsrB also increases ugtL transcription by binding to the ugtL promoter region, where it overcomes gene silencing by the heat-stable nucleoid structuring protein H-NS, enhancing virulence. The largely non-pathogenic species S. bongori failed to activate PhoP/PhoQ in mildly acidic pH because it lacks both the ssrB gene and the SsrB binding site in the target promoter. Low Mg²⁺ activated PhoP/PhoQ in both S. bongori and ssrB-lacking S. Typhimurium, indicating that the SsrB requirement for PhoP/PhoQ activation is signal-dependent. By controlling the ancestral genome, horizontally acquired genes are responsible for more crucial abilities, including virulence, than currently thought.

Regulation of gene expression by protein lysine acetylation in Salmonella

Protein lysine acetylation influences many physiological functions, such as gene regulation, metabolism, and disease in eukaryotes. Although little is known about the role of lysine acetylation in bacteria, several reports have proposed its importance in various cellular processes. Here, we discussed the function of the protein lysine acetylation and the post-translational modifications (PTMs) of histone-like proteins in bacteria focusing on Salmonella pathogenicity. The protein lysine residue in Salmonella is acetylated by the Pat-mediated enzymatic pathway or by the acetyl phosphate-mediated non-enzymatic pathway. In Salmonella, the acetylation of lysine 102 and lysine 201 on PhoP inhibits its protein activity and DNA-binding, respectively. Lysine acetylation of the transcriptional regulator, HilD, also inhibits pathogenic gene expression. Moreover, it has been reported that the protein acetylation patterns significantly differ in the drug-resistant and -sensitive Salmonella strains. In addition, nucleoid-associated proteins such as histone-like nucleoid structuring protein (H-NS) are critical for the gene silencing in bacteria, and PTMs in H-NS also affect the gene expression. In this review, we suggest that protein lysine acetylation and the post-translational modifications of H-NS are important factors in understanding the regulation of gene expression responsible for pathogenicity in Salmonella.

The Salmonella Typhimurium InvF-SicA complex is necessary for the transcription of sopB in the absence of the repressor H-NS

Expression of virulence factors in non-typhoidal Salmonella enterica depends on a wide variety of general and specific transcriptional factors that act in response to multiple environmental signals. Expression of genes for cellular invasion located in the Salmonella pathogenicity island 1 (SPI-1) is tightly regulated by several transcriptional regulators arrayed in a cascade, while repression of this system is exerted mainly by H-NS. In SPI-1, H-NS represses the expression mainly by binding to the regulatory region of hilA and derepression is exercised mainly by HilD. However, the possible regulatory role of H-NS in genes downstream from HilD and HilA, such as those regulated by InvF, has not been fully explored. Here the role of H-NS on the expression of sopB, an InvF dependent gene encoded in SPI-5, was evaluated. Our data show that InvF is required for the expression of sopB even in the absence of H-NS. Furthermore, in agreement with previous results on other InvF-regulated genes, we found that the expression of sopB requires the InvF/SicA complex. Our results support that SicA is not required for DNA binding nor for increasing affinity of InvF to DNA in vitro. Moreover, by using a bacterial two-hybrid system we were able to identify interactions between SicA and InvF. Lastly, protein-protein interaction assays suggest that InvF functions as a monomer. Derived from these results we postulate that the InvF/SicA complex does not act on sopB as an anti-H-NS factor; instead, it seems to induce the expression of sopB by acting as a classical transcriptional regulator.