Invasion of epithelial cells by Salmonella enterica requires expression of genes located in the pathogenicity island I (SPI-1). The expression of SPI-1 genes is very tightly regulated and activated only under specific conditions. Most studies have focused on the regulatory pathways that induce SPI-1 expression. Here, we describe a new regulatory circuit involving CRP-cAMP, a widely established metabolic regulator, in silencing of SPI-1 genes under non-permissive conditions. In CRP-cAMP-deficient strains we detected a strong upregulation of SPI-1 genes in the mid-logarithmic growth phase. Genetic analyses revealed that CRP-cAMP modulates the level of HilD, the master regulator of Salmonella invasion. This regulation occurs at the post-transcriptional level and requires the presence of a newly identified regulatory motif within the hilD 3’UTR. We further demonstrate that in Salmonella the Hfq-dependent sRNA Spot 42 is under the transcriptional repression of CRP-cAMP and, when this transcriptional repression is relieved, Spot 42 exerts a positive effect on hilD expression. In vivo and in vitro assays indicate that Spot 42 targets, through its unstructured region III, the 3’UTR of the hilD transcript. Together, our results highlight the biological relevance of the hilD 3’UTR as a hub for post-transcriptional control of Salmonella invasion gene expression. Salmonella infection is one of the major causes of foodborne illness worldwide. During infection, Salmonella expresses a set of virulence genes encoded in discrete regions of the genome. The expression of these genes is tightly regulated, being specific for different stages of the Salmonella infection process. While many regulatory mechanisms that lead to the activation of infection-related gene expression have been described, little is known about silencing mechanisms under conditions when expression is not needed and may rather represent a burden than a benefit for the bacterial fitness. Here, we report a condition-specific silencing mechanism of bacterial virulence. That is, the global transcriptional regulator CRP-cAMP represses, indirectly through a post-transcriptional mechanism, the expression of the major Salmonella virulence regulator HilD. In bacteria, post-transcriptional regulation has so far been mainly focused on 5’ untranslated regions (5’UTR). Remarkably, here we describe a molecular mechanism targeting the 3’untranslated region (3’UTR) of the mRNA of the major regulator of Salmonella virulence by a small non-coding RNA under the transcriptional control of the global regulator CRP-cAMP. Our data highlight the importance of 3’UTR in the regulation of gene expression in bacteria.

The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated process. Signaling cascades triggered by different environmental and physiological signals converge to control HilD, an AraC regulator that coordinates the expression of several virulence factors. The expression of hilD is modulated at several steps of the expression process. Here, we report that the invasion of epithelial cells by S. Typhimurium strains lacking the Gre factors, GreA and GreB, is impaired. By interacting with the RNA polymerase secondary channel, the Gre factors prevent backtracking of paused complexes to avoid arrest during transcriptional elongation. Our results indicate that the Gre factors are required for the expression of the bacterial factors needed for epithelial cell invasion by modulating expression of HilD. This regulation does not occur at transcription initiation and depends on the capacity of the Gre factors to prevent backtracking of the RNA polymerase. Remarkably, genetic analyses indicate that the 3’-untranslated region (UTR) of hilD is required for Gre-mediated regulation of hilD expression. Our data provide new insight into the complex regulation of S. Typhimurium virulence and highlight the role of the hilD 3’-UTR as a regulatory motif. Salmonella enterica serovar Typhimurium is a foodborne pathogen that causes gastroenteritis in humans. To successfully trigger infection, S. Typhimurium invades epithelial cells, a process that requires the coordinated expression of a set of genes. HilD is a pivotal regulator of S. Typhimurium pathogenicity, as it activates the expression of the genes required for invasion of intestinal epithelium. Expression and activity of HilD are tightly regulated and respond to several environmental and physiological conditions. In this report, we introduce the transcription elongation as a novel level of regulation of hilD. We describe that the Gre factors, proteins that prevent backtracking of paused RNA polymerase complexes during transcription elongation, are required for the expression of HilD and the subsequent expression of genes involved in the invasion of epithelial cells.

Different nematodes affect canines, however Acanthocheilonema reconditum was considered mostly a non-pathogenic parasite. Climate change, animal migration, and other factors transformed the dynamics of vector-borne diseases, including filariasis. Since 2016, a sudden increase in the number of dogs with microfilaremia was reported by different veterinary centers in Cali, southwest Colombia. The objective of this study was to molecularly identify the etiologic agent of this filariasis outbreak detected in this city, using PCR–RFLP and evaluating dogs’ clinical signs. From 2018–2019, canine filariasis cases were prospectively evaluated after a microscopic test, recruiting 82 cases and 43 healthy controls from 2971 samples. Acanthocheilonema reconditum (Nematoda, Onchocercidae) was identified in 61.3% of the cases (49/82) by PCR–RFLP. Sanger sequencing of the 5.8S ribosomal RNA gene and internal transcribed spacer-2 fragment was additionally performed on seven cases, confirming A. reconditum in all of them. The filariasis cases are statistically associated with male dogs who have clinical signs of anemia, low levels of hemoglobin and hematocrit (p < 0.0001), and high levels of plasma proteins (p < 0.001). This emerging canine disease constitutes an important public health concern among veterinarians and active surveillance is advised to explore its zoonotic potential.

Rdar biofilm formation of Salmonella typhimurium and Escherichia coli is a common ancient multicellular behavior relevant in cell–cell and inter-organism interactions equally, as in interaction with biotic and abiotic surfaces. With the expression of the characteristic extracellular matrix components amyloid curli fimbriae and the exopolysaccharide cellulose, the central hub for the delicate regulation of rdar morphotype expression is the orphan transcriptional regulator CsgD. Gre factors are ubiquitously interacting with RNA polymerase to selectively overcome transcriptional pausing. In this work, we found that GreA/GreB are required for expression of the csgD operon and consequently the rdar morphotype. The ability of the Gre factors to suppress transcriptional pausing and the 147 bp 5′-UTR of csgD are required for the stimulatory effect of the Gre factors on csgD expression. These novel mechanism(s) of regulation for the csgD operon might be relevant under specific stress conditions.

PpGpp is an intracellular sensor that, in response to different types of stress, coordinates the rearrangement of the gene expression pattern of bacteria to promote adaptation and survival to new environmental conditions. First described to modulate metabolic adaptive responses, ppGpp modulates the expression of genes belonging to very diverse functional categories. In Escherichia coli, ppGpp regulates the expression of cellular factors that are important during urinary tract infections. Here, we characterize the role of this alarmone in the regulation of the hlyCABD_II operon of the UPEC isolate J96, encoding the toxin α-hemolysin that induces cytotoxicity during infection of bladder epithelial cells. ppGpp is required for the expression of the α-hemolysin encoded in hlyCABD_II by stimulating its transcriptional expression. Prototrophy suppressor mutations in a ppGpp-deficient strain restore the α-hemolysin expression from this operon to wild-type levels, confirming the requirement of ppGpp for its expression. ppGpp stimulates hlyCABD_II expression independently of RpoS, RfaH, Zur, and H-NS. The expression of hlyCABD_II is promoted at 37 °C and at low osmolarity. ppGpp is required for the thermoregulation but not for the osmoregulation of the hlyCABD_II operon. Studies in both commensal and UPEC isolates demonstrate that no UPEC specific factor is strictly required for the ppGpp-mediated regulation described. Our data further support the role of ppGpp participating in the coordinated regulation of the expression of bacterial factors required during infection.