The small RNA ErsA of Pseudomonas aeruginosa, transcribed from the same genomic context of the well-known Escherichia coli Spot 42, has been characterized. We show that, different from Spot 42, ErsA is under the transcriptional control of the envelope stress response, which is known to impact the pathogenesis of P. aeruginosa through the activity of the alternative sigma factor σ(22) . The transcriptional responsiveness of ErsA RNA also spans infection-relevant cues that P. aeruginosa can experience in mammalian hosts, such as limited iron availability, temperature shifts from environmental to body temperature and reduced oxygen conditions. Another difference between Spot 42 and ErsA is that ErsA does not seem to be involved in the regulation of carbon source catabolism. Instead, our results suggest that ErsA is linked to anabolic functions for the synthesis of exoproducts from sugar precursors. We show that ErsA directly operates in the negative post-transcriptional regulation of the algC gene that encodes the virulence-associated enzyme AlgC, which provides sugar precursors for the synthesis of several P. aeruginosa polysaccharides. Like ErsA, the activation of algC expression is also dependent on σ(22) . Altogether, our results suggest that ErsA and σ(22) combine in an incoherent feed-forward loop to fine-tune AlgC enzyme expression.

The small RNA ReaL of the opportunistic pathogen Pseudomonas aeruginosa has been characterized. Our results indicate that ReaL contributes to P. aeruginosa virulence. In the Galleria mellonella infection model, reaL gene deletion resulted in decreased virulence, while ReaL overexpression resulted in a hyper-virulent phenotype. We also demonstrate that ReaL is embedded in the P. aeruginosa quorum sensing (QS) with the role of linking las to pqs systems. We show that ReaL is negatively regulated by the las regulator LasR and impacts positively the synthesis of the pqs quinolone signal PQS by a positive post-transcriptional effect on the pqsC gene. Perturbations of ReaL levels affect pyocyanin synthesis, biofilm formation and swarming motility, processes that are known to be influenced by PQS synthesis. In addition to being regulated by LasR, ReaL is also responding to infection relevant cues that P. aeruginosa can experience in mammalian hosts such as temperature and oxygen availability. Furthermore, ReaL shows a growth phase-dependent pattern of expression, being up-regulated in stationary phase, due to the activity of the alternative σ factor RpoS. Together, these regulations of ReaL expression are expected to contribute to the fine co-modulation of PQS synthesis and, ultimately, virulence.

Collagen-based skin-like scaffolds (CBSS) are promising alternatives to skin grafts to repair wounds and injuries. In this work, we propose that the common marine invertebrate sea urchin represents a promising and eco-friendly source of native collagen to develop innovative CBSS for skin injury treatment. Sea urchin food waste after gonad removal was here used to extract fibrillar glycosaminoglycan (GAG)-rich collagen to produce bilayer (2D + 3D) CBSS. Microstructure, mechanical stability, permeability to water and proteins, ability to exclude bacteria and act as scaffolding for fibroblasts were evaluated. Our data show that the thin and dense 2D collagen membrane strongly reduces water evaporation (less than 5% of water passes through the membrane after 7 days) and protein diffusion (less than 2% of BSA passes after 7 days), and acts as a barrier against bacterial infiltration (more than 99% of the different tested bacterial species is retained by the 2D collagen membrane up to 48 h), thus functionally mimicking the epidermal layer. The thick sponge-like 3D collagen scaffold, structurally and functionally resembling the dermal layer, is mechanically stable in wet conditions, biocompatible in vitro (seeded fibroblasts are viable and proliferate), and efficiently acts as a scaffold for fibroblast infiltration. Thus, thanks to their chemical and biological properties, CBSS derived from sea urchins might represent a promising, eco-friendly, and economically sustainable biomaterial for tissue regenerative medicine.

The interactions between the 54 -containing RNA polymerase ( 54 -RNAP) and the region of the Pseudomonas putida Pu promoter spanning from the enhancer to the binding site for the integration host factor (IHF) were analyzed both by DNase I and hydroxyl radical footprinting. A short Pu region centered at position ؊104 was found to be involved in the interaction with 54 -RNAP, both in the absence and in the presence of IHF protein. Deletion or scrambling of the ؊104 region strongly reduced promoter affinity in vitro and promoter activity in vivo, respectively. The reduction in promoter affinity coincided with the loss of IHF-mediated recruitment of the 54 -RNAP in vitro. The experiments with oriented-␣ 54 -RNAP derivatives containing bound chemical nuclease revealed interchangeable positioning of only one of the two ␣ subunit carboxylterminal domains (␣CTDs) both at the ؊104 region and in the surroundings of position ؊78. The addition of IHF resulted in perfect position symmetry of the two ␣CTDs. These results indicate that, in the absence of IHF, the 54 -RNAP asymmetrically uses only one ␣CTD subunit to establish productive contacts with upstream sequences of the Pu promoter. In the presence of IHFinduced curvature, the closer proximity of the upstream DNA to the body of the 54 -RNAP can allow the other ␣CTD to be engaged in and thus favor closed complex formation.Bacterial promoters are modular DNA regions able to establish productive interactions both with subunits of RNA polymerase holoenzyme (RNAP 1 ; subunit composition: ␣ 2 ␤␤Ј ) and regulatory proteins (1-4). The core promoter elements are signature tags for factor selectivity (4). The major sigma factor 70 generally directs RNAP to interact with the core DNA elements Ϫ10 and Ϫ35 (hexamers with consensus 5Ј-TATAAT-3Ј and 5Ј-TTGACA-3Ј, respectively) (5). The core promoter elements can be both overlapped and flanked by protein-bound DNA sites involved in the fine modulation of promoter activity (2, 4). In the last decade, a considerable amount of attention has been given to a A ϩ T-rich promoter sequence, the UP element, located upstream of the core promoter region and consisting of two distinct subsites, each of which, by itself, can be bound by the carboxyl-terminal domain of the RNAP ␣ subunit (␣CTD) (3, 6 -10). ␣CTD recognizes and interacts with the backbone structure in the minor groove of the UP element. The A ϩ T-rich sequence of the UP element are needed to provide the optimum width of minor groove for interaction with ␣CTD (7, 11). Several lines of evidence showed that the role of the UP elements is to stimulate transcription in an activator protein-independent manner and to a different extent (from 1.5 to ϳ90-fold) depending on the similarity with the consensus UP element sequence (3, 9). It is currently believed that the transcription stimulation by an UP element has to be traced mainly to the cooperation of the sigma factor and the ␣ subunit in RNAP binding to the promoter (1, 12). Thus, the presence of an UP element in a promoter plays the major ...

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Adherent-invasive Escherichia coli (AIEC) strains are overrepresented in the dysbiotic microbiota of Crohn’s disease (CD) patients, and contribute to the onset of the chronic inflammation typical of the disease. However, the effects of anti-inflammatory drugs used for CD treatment on AIEC virulence have not yet been investigated. In this report, we show that exposure of AIEC LF82 strain to amino-6-mercaptopurine (6-MP) riboside, one of the most widely used anti-inflammatory drugs in CD, impairs its ability to adhere to, and consequently to invade, human epithelial cells. Notably, phagocytosis of LF82 treated with 6-MP by human macrophages is also reduced, suggesting that 6-MP affects AIEC cell surface determinants involved both in interaction with epithelial cells and in uptake by macrophages. Since a main target of 6-MP in bacterial cells is the inhibition of the important signal molecule c-di-GMP, we also tested whether perturbations in cAMP, another major signaling pathway in E. coli, might have similar effects on interactions with human cells. To this aim, we grew LF82 in the presence of glucose, which leads to inhibition of cAMP synthesis. Growth in glucose-supplemented medium resulted in a reduction in AIEC adhesion to epithelial cells and uptake by macrophages. Consistent with these results, both 6-MP and glucose can affect expression of cell adhesion-related genes, such as the csg genes, encoding thin aggregative fimbriae (curli). In addition, glucose strongly inhibits expression of the fim operon, encoding type 1 pili, a known AIEC determinant for adhesion to human cells. To further investigate whether 6-MP can indeed inhibit c-di-GMP signaling in AIEC, we performed biofilm and motility assays and determination of extracellular polysaccharides. 6-MP clearly affected biofilm formation and cellulose production, but also, unexpectedly, reduced cell motility, itself an important virulence factor for AIEC. Our results provide strong evidence that 6-MP can affect AIEC-host cell interaction by acting on the bacterial cell, thus strengthening the hypothesis that mercaptopurines might promote CD remission also by affecting gut microbiota composition and/or physiology, and suggesting that novel drugs targeting bacterial virulence and signaling might be effective in preventing chronic inflammation in CD.

Small non-coding RNAs (sRNAs) are post-transcriptional regulators of gene expression that have been recognized as key contributors to bacterial virulence and pathogenic mechanisms. In this study, we characterized the sRNA PesA of the opportunistic human pathogen Pseudomonas aeruginosa. We show that PesA, which is transcribed within the pathogenicity island PAPI-1 of P. aeruginosa strain PA14, contributes to P. aeruginosa PA14 virulence. In fact, pesA gene deletion resulted in a less pathogenic strain, showing higher survival of cystic fibrosis human bronchial epithelial cells after infection. Moreover, we show that PesA influences positively the expression of pyocin S3 whose genetic locus comprises two structural genes, pyoS3A and pyoS3I, encoding the killing S3A and the immunity S3I proteins, respectively. Interestingly, the deletion of pesA gene results in increased sensitivity to UV irradiation and to the fluoroquinolone antibiotic ciprofloxacin. The degree of UV sensitivity displayed by the PA14 strain lacking PesA is comparable to that of a strain deleted for pyoS3A-I. These results suggest an involvement of pyocin S3 in DNA damage repair and a regulatory role of PesA on this function.

BackgroundAntibiotics in current use target a surprisingly small number of cellular functions: cell wall, DNA, RNA, and protein biosynthesis. Targeting of novel essential pathways is expected to play an important role in the discovery of new antibacterial agents against bacterial pathogens, such as Pseudomonas aeruginosa, that are difficult to control because of their ability to develop resistance, often multiple, to all current classes of clinical antibiotics.ResultsWe aimed to identify novel essential genes in P. aeruginosa by shotgun antisense screening. This technique was developed in Staphylococcus aureus and, following a period of limited success in Gram-negative bacteria, has recently been used effectively in Escherichia coli. To also target low expressed essential genes, we included some variant steps that were expected to overcome the non-stringent regulation of the promoter carried by the expression vector used for the shotgun antisense libraries. Our antisense screenings identified 33 growth-impairing single-locus genomic inserts that allowed us to generate a list of 28 “essential-for-growth” genes: five were “classical” essential genes involved in DNA replication, transcription, translation, and cell division; seven were already reported as essential in other bacteria; and 16 were “novel” essential genes with no homologs reported to have an essential role in other bacterial species. Interestingly, the essential genes in our panel were suggested to take part in a broader range of cellular functions than those currently targeted by extant antibiotics, namely protein secretion, biosynthesis of cofactors, prosthetic groups and carriers, energy metabolism, central intermediary metabolism, transport of small molecules, translation, post-translational modification, non-ribosomal peptide synthesis, lipopolysaccharide synthesis/modification, and transcription regulation. This study also identified 43 growth-impairing inserts carrying multiple loci targeting 105 genes, of which 25 have homologs reported as essential in other bacteria. Finally, four multigenic growth-impairing inserts belonged to operons that have never been reported to play an essential role.ConclusionsFor the first time in P. aeruginosa, we applied regulated antisense RNA expression and showed the feasibility of this technology for the identification of novel essential genes.