No description available.

<p>Bacterial outer membrane vesicles (OMVs) are spherical buds of the outer membrane (OM) containing periplasmic lumenal components. OMVs have been demonstrated to play a critical part in the transmission of virulence factors, immunologically active compounds, and bacterial survival, however vesiculation also appears to be a ubiquitous physiological process for Gram-negative bacteria. Despite their characterized biological roles, especially for pathogens, very little is known about their importance for the originating organism as well as regulation and mechanism of production. Only when we have established their biogenesis can we fully uncover their roles in pathogenesis and bacterial physiology. The overall goal of this research was to characterize bacterial mutants which display altered vesiculation phenotypes using genetic and biochemical techniques, and thereby begin to elucidate the mechanism of vesicle production and regulation. One part of this work elucidated a synthetic genetic growth defect for a strain with reduced OMV production (&#916;nlpA, inner membrane lipoprotein with a minor role in methionine transport) and envelope stress (&#916;degP, dual function periplasmic chaperone/ protease responsible for managing proteinaceous waste). This research showed that the growth defect of &#916;nlpA&#916;degP correlated with reduced OMV production with respect to the hyprevesiculator &#916;degP and the accumulation of protein in the periplasm and DegP substrates in the lumen of OMVs. We further demonstrated that OMVs do not solely act as a stress response pathway to rid the periplasm of otherwise damaging misfolded protein but also of accumulated peptidoglycan (PG) fragments and lipopolysaccharide (LPS), elucidating OMVs as a general stress response pathway critical for bacterial well-being. The second part of this work, focused on the role of PG structure, turnover and covalent crosslinks to the OM in vesiculation. We established a direct link between PG degradation and vesiculation: Mutations in the OM lipoprotein nlpI had been previously established as a very strong hypervesiculation phenotype. In the literature NlpI had been associated with another OM lipoprotein, Spr that was recently identified as a PG hydrolase. The data presented here suggest that NlpI acts as a negative regulator of Spr and that the &#916;nlpI hypervesiculation phenotype is a result of rampantly degraded PG by Spr. Additionally, we found that changes in PG structure and turnover correlate with altered vesiculation levels, as well as non-canonical D-amino acids, which are secreted by numerous bacteria on the onset of stationary phase, being a natural factor to increase OMV production. Furthermore, we discovered an inverse relationship between the concentration of Lpp-mediated, covalent crosslinks and the level of OMV production under conditions of modulated PG metabolism and structure. In contrast, situations that lead to periplasmic accumulation (protein, PG fragments, and LPS) and consequent hypervesiculation the overall OM-PG crosslink concentration appears to be unchanged. Form this work, we conclude that multiple pathways lead to OMV production: Lpp concentration-dependent and bulk driven, Lpp concentration-independent.</p> / Dissertation

Šiame darbe tirtas gramteigiamųjų ir gramneigiamųjų bakterijų atsakas į natyvaus ir katalitiškai neaktyvaus lizocimo bei jo 9 aminorūgščių katijoninio peptido sukeltus ląstelės apvalkalo pažeidimus. Panaudojant potenciometrinius metodus, buvo nustatyta, kad šie junginiai sukelia viduląstelinio K+ ištekėjimą iš L. lactis, B. subtilis ir P. aeruginosa ląstelių ir dalinę jų citoplazminės membranos depoliarizaciją, tačiau natyvus, kaitintas lizocimas ir 9a peptidas skirtingai veikia L. lactis apvalkalėlio laidumą. Peptidas bei kaitintas lizocimas sukelia staigesnį K+ jonų ištekėjimą ir membranos įtampos sumažėjimą nei natyvus lizocimas. Peptido sukeliamas K+ jonų ištekėjimas yra grįžtamas. Taip pat buvo įvertintas įvairių mutantinių L. lactis padermių jautrumas lizocimui. Pastebėta, kad kuo padermė atsparesnė lizocimui, tuo vėliau prasideda K+ jonų ištekėjimas iš šios padermės ląstelių. Pasitelkus DNR mikrogardelių metodą, buvo tiriamas lizocimo bei peptido poveikis L. lactis MG1363 bei &#916;oppA ląstelių genų raiškos pokyčiams. Nustatyta, jog peptidu ir lizocimu veiktose ląstelėse iššaukiama dvikomponentės valdymo sistemos CesSR raiška ir sukeliamas nuo SpxB priklausomas ląstelių atsparumas lizocimui. Gauti rezultatai rodo, jog lizocimas ir 9a peptidas sukelia kiek skirtingus L. lactis transkriptomo pokyčius: lizocimas savitai skatina nuo N-deacetilazės priklausomo atsparumo mechanizmo įsijungimą, taip pat skiriasi OpuA sistemą koduojančių genų raiška. / We used potenciometric measurments to investigate the response of Gram-positive and Gram-negative bacteria to cell envelope stress, caused by native and heat-inactivated lysozyme and lysozyme-derived 9 amino acid peptide. It was found that these antimicrobial compounds induce leakage of K+ outside the cells of L. lactis, B. subtilis and P. aeruginosa and cause partial depolarization of bacterial cytoplasmic membrane. We observed different response of L. lactis cells to these compounds – peptide and heat-inactivated lysozyme cause more rapid efflux of K+ ions than native lysozyme. Peptide has a reversible effect on K+ leakage. Sensitivity of different mutant strains of L. lactis to lysozyme was studied. It was shown that more resistant the strain is, the later the leakage of K+ ions is induced by lysozyme. To investigate the genome-wide response of L. lactis MG1363 and &#916;oppA strains to lysozyme and 9 a.a. peptide, changes of gene expression after challenging cells with these antimicrobial compounds were analysed using DNA microarrays. It was estimated, that lysozyme and lysozyme-derived 9a.a. peptide induce CesSR system and SpxB-mediated response. It was also shown that L. lactis response to 9a.a. peptide and lysozyme differs. Lysozyme specifically induces PgdA-mediated resistance mechanism. Changes of expression of OpuA system in lysozyme and peptide treated cells are also different.

Previous research discovered the existence of sedimentation-resistant mutants of E. coli. Genomic studies revealed that these mutants resisted sedimentation due to independent modifications to genes that influenced the Rcs signal transduction pathway, causing increased secretion of an exopolysaccharide capsule comprised primarily of colanic acid. The Rcs system is responsible for detecting envelope stressors; consequently, ampicillin and osmotic stress were used to perturb the cellular envelope and study the response of the mutants compared to wild-type cells. It was found that the overproduction of colanic acid in the mutants confers some resistance to envelope stress; however, the mutants still behaved similarly to wild-type cells. The doubling times of the strains grown in sodium chloride solutions were calculated. A wavelength scan from 400 nm to 800 nm was performed on strains grown in different salt concentrations to determine if there were significant differences in light scattering between the wild-type and mutant cells. Further analysis was performed that, along with the doubling time data, suggested that wild-type cells may have turned on genes for capsule production in response to being grown in high salt concentrations. Additional research could be conducted to test this hypothesis, perhaps through the quantification of colanic acid through a methyl pentose assay for wild-type cultures grown with high salt concentrations. The idea that wild-type cells could digest colanic acid as a carbon source when lacking resources was also investigated with different preparations of colanic acid. One preparation of colanic acid showed promising results, which could indicate that bacteria are able to digest their capsule in a novel method to produce energy when starved. Again, additional investigation should be conducted to confirm these results. Other future experiments could study the metabolome of these mutants to determine if they have increased quantities of alarmones related to biofilm formation.

Les polluants atmosphériques de type oxydes d’azote (NOx), principalement constitués du NO, NO2 et leurs dérivés, représentent une énorme menace d’un point de vue environnemental et sanitaire. Leurs propriétés chimiques sont largement exploitées à l’échelle du vivant pour leur rôle dans divers processus de signalisation (systèmes nerveux et cardiovasculaire) ou l’élimination de pathogènes (système immunitaire). Néanmoins, des dérégulations dans la production cellulaire ou l’apport exogène de ces composés est à l’origine de nombreuses pathologies humaines (e.g. pulmonaires), généralement attribuées à la pollution. Toutefois, un grand nombre de microorganismes aéroportés sont continuellement exposés à ces composés délétères, intimement connectés aux espèces réactives de l’oxygène (ROS). Ainsi l’hypothèse de l’ensemble de ce travail a porté sur l’impact du NO2, NOx majoritairement retrouvés dans l’atmosphère, sur une souche aéroportée de P. fluorescens, espèce désormais associée aux voies aériennes et potentiellement pathogène. A l’issue d’une exposition à 45 ppm de NO2, la survie de P. fluorescens MFAF76a est significativement impactée suggérant un effet bactériostatique, conforté par l’impact observé sur le métabolisme énergétique. De plus, le NO2 induit un stress d’enveloppe via la perte d’un glycérophospholipide (UGP) et le remaniement de divers composants membranaires (LPS, peptidoglycane, acides gras). La pompe à efflux MexEF-OprN semblent participer à la stabilisation de la membrane et pourraient être également impliquée dans l’efflux des oxydes d’azotes, mécanismes confortés par l’étude d’un mutant MFAF76a-oprN. La porine majoritaire OprF semble également contribuer à la stabilisation de la membrane externe, néanmoins son implication reste à confirmer. De plus, une interconnexion entre ROS et NOx dans la signalisation (OxyR, IscR), et les mécanismes de détoxification, a été observée. La flavohémoprotéine Hmp semble être un élément crucial dans la détoxification des NOx chez P. fluorescens comme l’illustre un mutant MFAF76a-hmp. Les similitudes importantes entre les effets connus du NO et ceux observés lors d’une exposition au NO2 suggèrent une conversion non enzymatique du NO2, une fois pénétré dans la cellule, en NO. Désormais, une étude plus approfondie est nécessaire afin de décrypter (i) les mécanismes impliqués dans la régulation de la pompe à efflux RND MexEF-OprN et de la flavohémoprotéine Hmp, (ii) d’autres acteurs intervenant dans la réponse au stress d’enveloppe et la détoxification ainsi que (iii) le devenir de NO2 dans la cellule. / Nitrogen oxides (NOx) atmospheric pollutants, mainly constituted of NO, NO2 and derived compounds, are a big threat to the environment and health. Their chemical properties are largely exploited at the cellular scale for their role in diverse physiological processes such as signalisation (nervous and cardiovascular systems) or in pathogens eradication (immunity system).However, dysregulation in production pathways or exogenous input of these compounds lead to several pathologies (e.g. respiratory diseases), usually attributed to atmospheric pollution. However, a wide range of airborne microorganisms are constantly exposed to these deleterious compounds, intimately connected to reactive oxygen species (ROS). Thus, the hypothesis of this work deals with the impact of NO2, the main atmospheric NOx, on an airborne P. fluorescens, a strain usually neglected but yet associated with human airways, and potentially pathogenic. Following an exposure to 45 ppm of NO2, the survival of P. fluorescens MFAF76a is severely impaired, suggesting a bacteriostatic effect, as comforted by NO2 impact on energetic metabolism. Moreover, an exposure to NO2 induces an envelope stress through the loss of an Unknown Glycerophospholipid (UGP) and the reorganisation of membrane constituents (LPS, peptidoglycan, fatty acids). The efflux pump MexEF-OprN is involved in membrane stabilization and could also efflux NOx, as highlighted by a MFAF76a-oprN mutant. The major porin OprF could also contribute in external membrane stabilisation, however its implication is still under investigation. Moreover, ROS and NOx are interconnected as illustrated by their shared signalisation (OxyR, IscR) and detoxification pathways. The flavohemoprotein Hmp is a crucial element in the detoxification of NOx in P. fluorescens as illustrated in an MFAF76a-hmp mutant. The similarities between the known effects of NO and those observed in the case of an exposure to NO2, suggest a non-enzymatic conversion of NO2, following cell penetration, into NO. Henceforth, deeper studies are required to decode (i) the mechanisms involved in the regulation of the RND efflux pump MexEF-OprN and the flavohemoprotein Hmp, (ii) other relevant actor implicated in the envelope stress response and in detoxification pathways as well as (iii) the fate of NO2 within the cell.

Les bactéries sont exposées aux perturbations externes causées par les changements environnementaux ou la présence d’agents antibactériens nocifs. L’enveloppe bactérienne forme une barrière entre le milieu externe et l’intérieur de la cellule et se trouve donc potentiellement exposée aux dommages causées par les perturbations et forme la première ligne de défense pour les bactéries. Pour survivre à ces conditions, les bactéries ont développé des systèmes à deux composantes (TCS) qui détectent et permettent la réponse à ces stress.Bien qu’ils soient associés à la protéine périplasmique ZraP, ZraSR constitue un de ces TCS. La présence de cette protéine accessoire associé au système ZraSR montre une homologie avec le système CpxPAR qui capte un grand nombre de stress d’enveloppe. Le système Zra est activé en présence de zinc et cause l’expression de zraP, zraS et zraR. Les protéines ZraP et ZraR ont été étudiées mais aucun travail n’a encore impliqué l’étude de la protéine membranaire ZraS et son mécanisme d’activation. En effet, l’étude des senseurs de TCS s’est beaucoup focalisée sur la compréhension de la partie cytoplasmique mais très peu sur le domaine périplasmique. Dans le cas du système Zra, il y a encore des interrogations sur l’activation ainsi que la régulation de ce système. Lors de ma thèse j’ai concentré mes recherches sur le domaine périplasmique de ZraS. Nous avons d’abord voulu comprendre comment le zinc active le système Zra mais aussi par quel moyen la protéine ZraP influe sur cette activation par le zinc. Pour cela, la caractérisation biochimique du domaine périplasmique de ZraS a été effectué et l’effet du zinc sur ce domaine a été observé. De ce fait, nous avons aussi tenté de déterminer quels sont les résidus de ce domaine qui permettent la liaison du zinc. Par une approche in vivo et in vitro, nous avons voulu comprendre le rôle régulateur de ZraP sur le système Zra. Ce travail s’inscrit dans l’objectif de mieux comprendre les différents mécanismes d’activation des différents ESR. / Bacteria are exposed to external perturbations due to environmental changes or to the presence of noxious agents. Because the bacterial cell envelope forms the barrier between the inside and the outside of the cell it is highly susceptible to be damaged by these perturbations but it is also the first line of defense. To survive gram-negative bacteria have developed two component systems (TCS) that detect and respond to these envelope stresses.ZraSR is one of these TCS, although it is atypical because associated with ZraP, a periplasmic protein. The presence of an accessory protein associated with ZraSR system shows that it is functionally homologous to the CpxPAR system, a sensor of a variety of envelope stress signals. In presence of zinc, Zra system is activated and allows the expression of zraP, zraS and zraR. The periplasmic protein ZraP and the response regulator ZraR have been studied but the activation of the membrane histidine kinase by zinc has not been studied yet. Indeed, studying of TCS sensors was focused on the understanding of the cytoplasmic domain and less on the periplasmic part.During my thesis, I tried to concentrate my study on the periplasmic domain of ZraS. We first tried to understand how the zinc is activating the Zra system but also how ZraP is regulating this activation. For that purpose, we characterized ZraS periplasmic domain and analyzed the effect of zinc binding on it. Hence, we also tried to identify all of ZraS residues that are coordinating the zinc. By combining in vitro and in vivo assays, we tried to determine ZraP role in the regulation of Zra system. This study could help for the understanding of the mechanisms important for the activation of bacterial stress response systems.

No description available.

Maintaining cell envelope integrity is of vital importance for all microorganisms. Not surprisingly, evolution has shaped conserved protein protection networks that connect stress perception, transmembrane signal transduction, and mediation of cellular responses upon cell envelope stress. The phage shock protein (Psp) stress response is one such conserved protection network. Most knowledge about the Psp response derives from studies in the Gram-negative model bacterium Escherichia coli, where the Psp system consists of several well-defined protein components. Homologous systems were identified in representatives of the Proteobacteria, Actinobacteria, and Firmicutes. However, the Psp system distribution in the microbial world remains largely unknown. By carrying out a large-scale, unbiased comparative genomics analysis, we found components of the Psp system in many bacterial and archaeal phyla and describe that the predicted Psp systems deviate dramatically from the known prototypes. The core proteins PspA and PspC have been integrated into various (often phylum-specifically) conserved protein networks during evolution. Based on protein domain-based and gene neighborhood analyses of pspA and pspC homologs, we built a natural classification system for Psp networks in bacteria and archaea. We validate our approach by performing a comprehensive in vivo protein interaction study of Psp domains identified in the Gram-positive model organism Bacillus subtilis and found a strong interconnected protein network. Our study highlights the diversity of Psp domain organizations and potentially diverse functions across the plethora of the microbial landscape, thus laying the ground for studies beyond known Psp functions in underrepresented organisms.

Over the course of the last decades, the continuous exposure of bacteria to antibiotics—at least in parts due to misprescription, misuse, and misdosing—has led to the widespread development of antimicrobial resistances. This development poses a threat to the available medication in losing their effectiveness in treating bacterial infections. On the drug development side, only minor advances have been made to bring forward novel therapeutics. In addition to increasing the efforts and approaches of tapping the natural sources of new antibiotics, synthetic approaches to developing novel antimicrobials are being pursued. In this study, BDTL049 was rationally designed using knowledge based on the properties of natural antibiotics. BDTL049 is a carbosilane dendritic system with bow-tie type topology, which has antimicrobial activity at concentrations comparable to clinically established natural antibiotics. In this report, we describe its mechanism of action on the Gram-positive model organism Bacillus subtilis. Exposure to BDTL049 resulted in a complex transcriptional response, which pointed toward disturbance of the cell envelope homeostasis accompanied by disruption of other central cellular processes of bacterial metabolism as the primary targets of BDTL049 treatment. By applying a combination of whole-cell biosensors, molecular staining, and voltage sensitive dyes, we demonstrate that the mode of action of BDTL049 comprises membrane depolarization concomitant with pore formation. As a result, this new molecule kills Gram-positive bacteria within minutes. Since BDTL049 attacks bacterial cells at different targets simultaneously, this might decrease the chances for the development of bacterial resistances, thereby making it a promising candidate for a future antimicrobial agent.