The peptidoglycan layer of Vitreoscilla stercoraria, ATCC 15218, was isolated from intact cells after treatment with sodium lauryl sulfate (SLS) and digestion with Pronase. Amino acid and amino sugar content was analyzed and 67% of the total present was made up of glutamic acid, alanine, diaminopimelic acid (DAP), and glucosamine in a molar ratio of 1:1.7:1:0.7. Electron microscopy of the final peptidoglycan product showed a thin, delicately folded sacculus which exhibited a morphology different from that of the intact vegetative cells. Within these sacculi occurred electron-dense structures which were assayed and found to be poly- 3-hydroxybutyrate (PHB) granules. The final yield of peptidoglycan was 2.9% of the dry weight of the intact vegetative cell.

The survival of all organisms depends on their ability to perform certain enzymatic activities and the ability to construct certain structures. In prokaryotes, enzymes are required for the final reactions of peptidoglycan (PG) synthesis, the structural element of the bacterial cell wall. These proteins, known as penicillin-binding proteins (PBPs), are identified through the presence of conserved motifs within their functional domains. The Class A high-molecular weight PBPs are bifunctional, performing the penicillin-sensitive transpeptidase activity and the glycosyl transferase (GT) activity required for the polymerization of the glycan strands. The Class A PBPs in Bacillus subtilis are PBP1, PBP4, PBP2c, and PBP2d (YwheE) and they are encoded by ponA, pbpD, pbpF, and pbpG (ywhE), respectively. These proteins appear to be somewhat functionally redundant because removal of one or more does not cause any noticeable change in phenotype. However, the loss of PBP1 has previously been demonstrated in B. subtilis to cause a decreased growth rate and changes in morphology of vegetative cells, both of which are increased upon the additional loss of PBP4. Furthermore, the loss of sporulation-expressed Class A PBPs, PBP2c and 2d, causes a 10,000-fold decrease in the production of heat resistant spores. This double mutant is shown to have changes in the structural parameters of cortex PG that appear minor when compared to other strains, but are coupled with a large defect on the deposition of cortex PG, apparently from the synthesis of an abnormal germ cell wall. The Class A PBPs are believed to be the only proteins capable of performing the GT activity and it is therefore believed that cell viability requires the presence of at least one functional Class A PBP. This requirement has been demonstrated in other organisms, but a B. subtilis strain lacking all Class A PBPs is viable. The phenotypical changes seen in the PBP1 mutant are exacerbated in this strain. The GT activity remaining in this strain is sensitive to the antibiotic moenomycin in vitro whereas it appears resistant in vivo. Identification of the protein(s) performing this novel GT activity will rely on the demonstration of the GT activity in vitro. / Ph. D.

The Gram-negative bacterium Photorhabdus luminescens is a pathogen of insects. It is able to secrete a variety of toxins and effectors against its host in order to escape its immune defences. The model insect Manduca sexta is able to mount a variety of humoral and cellular responses against pathogen attack. Ultimately these prove ineffective against P. luminescens. The pre-treatment of M. sexta with Escherichia coli provides protection against the pathogenesis of P. luminescens. Here, I use RNA interference and Fluorescence-assisted cell sorting techniques to investigate interactions between pathogen and host to further elucidate the roles of various host factors in mounting the immune response. I also investigate the nutrient requirements of the bacteria for pathogenesis. I show data that peptidoglycan recognition protein (PGRP) is essential for the up-regulation of antimicrobial peptides, an important immune defence. I also show that P. luminescens has a requirement for two types of iron during pathogenesis of M. sexta. And lastly I show that P. luminescens is able to avoid phagocytosis, another important immune defence.

No description available.

The fruit fly Drosophila melanogaster is an excellent model organism to study the innate immune response, because insects and mammals share conserved features regarding the recognition and destruction of microorganisms and Drosophila is easily accessible to genetic manipulation. In my present study, I identified a new family of pattern recognition molecules for bacterial peptidoglycan in Drosophila, the Peptidoglycan Recognition Proteins (PGRP). This family of proteins is widespread in the animal kingdom, for instance there are 4 PGRP genes in humans with unknown function. So far, all tested PGRPs (from insects and mammals) have been shown to bind peptidoglycan. In Drosophila, we found and characterized 13 PGRP genes, which fall into two classes: Short PGRPs and Long PGRPs. To the short group belong PGRP-SA, SB1, SB2, SC1A, SC1B, SC2, and SD with short transcripts and predicted extracellular proteins. The long members are PGRP-LA, LB, LC, LD, LE, and LF with long transcripts and predicted intracellular and membrane spanning proteins. Transcripts from the 13 different PGRP genes are present in immune competent organs, and the majority are inducible by infection. The transcriptional regulation of the inducible PGRP genes occurs either via the imd/Relish or in some cases Toll/Dif pathway. My RNAi experiments in mbn-2 cells revealed that the peptidoglycan recognition protein PGRP-LC is a major activator of the imd/Relish pathway. In PGRP-LC deficient mbn-2 cells, Relish signalling is almost entirely blocked. However, the complex PGRP-LC gene generates three alternative splice forms, each of them carrying one of three possible PGRP domains, LCx, LCy, and LCa. I found that in the tissue culture system PGRP-LCa plays a specific role in the recognition of Gram-negative bacteria, while PGRP-LCx is crucial for the recognition of Gram-positive and Gram-negative bacteria, and peptidoglycan. Targeted mutagenesis of the PGRP-LCa isoform in vivo shows that the situation is more complicated than in the cell culture experiments. In conclusion, PGRPs constitute a highly diversified family of proteins, including key players of the innate immune response.

Mycobacterium tuberculosis est responsable de 8,7 millions de nouveaux cas de tuberculose et de 1,4 millions de décès en 2011. L’émergence de souches résistantes aux deux antituberculeux majeurs, isoniazide et rifampicine, (MDR) et aux antibiotiques de seconde ligne (XDR), ainsi que la difficulté d’éradiquer les formes « dormantes » du bacille nécessitent la recherche de nouveaux antibiotiques. Les β-lactamines n’ont jamais été utilisées en thérapeutique car M. tuberculosis produit une β-lactamase à large spectre, BlaC. Cependant, l’association d’une β-lactamine appartenant à la classe des carbapénèmes, le méropénème, et d’un inhibiteur de β-lactamase, l’acide clavulanique, est active sur M. tuberculosis incluant des souches XDR. Notre objectif a été de caractériser les cibles des carbapénèmes qui sont atypiques chez M. tuberculosis, parce que le peptidoglycane de cette bactérie contient majoritairement (80%) des ponts interpeptidiques formés par une classe particulière de transpeptidases, les L,D-transpeptidases. Nous avons comparé les cinq L,D-transpeptidases de M. tuberculosis au niveau de leur activité in vitro dans la formation des ponts interpeptidiques du peptidoglycane et dans la réaction d’inactivation par les carbapénèmes. Nous avons ainsi pu montrer que les cinq L,D-transpeptidases sont fonctionnelles in vitro. LdtMt1, LdtMt2, LdtMt4 et LdtMt5 sont capables de former des ponts interpeptidiques du peptidoglycane reliant l’acide aminé en position 3 d’un substrat tétrapeptidique donneur à l’acide aminé en position 3 d’un substrat tétrapeptidique accepteur. Ces mêmes enzymes peuvent également utiliser la D-méthionine comme accepteur dans une réaction d’échange de la D-Ala4 du substrat tétrapeptidique. LdtMt1, LdtMt2, LdtMt3 et LdtMt4 forment un complexe covalent avec les carbapénèmes. La réaction d’inactivation des L,D-transpeptidases par les carbapénèmes se déroulent en deux étapes. Dans un premier temps, un intermédiaire covalent réversible est formé (constante catalytique k1) puis la deuxième étape aboutit à la formation de l’acylenzyme (constante catalytique k2). La détermination des constantes catalytiques d’inactivation k1 et k2 a révélé d’importantes différences entre les carbapénèmes. Excepté pour LdtMt1, l’imipénème inactive plus rapidement les L,D-transpeptidases que les autres carbapénèmes suggérant que des modifications de la chaine latérale pourraient être envisagées pour optimiser l’activité « anti-mycobactérienne » de cette classe de β-lactamines. Nous avons en parallèle initié l’étude de la régulation des L,D-transpeptidases dans différentes conditions de culture ce qui permettra à terme d’identifier les L,D-transpeptidases essentielles pour la croissance et la persistance de M. tuberculosis. Ce travail pourrait déboucher sur l’identification de cibles essentielles permettant l’éradication des formes dormantes de M. tuberculosis qui sont très difficile à traiter. / Mycobacterium tuberculosis is responsible for 8.7 million of new cases of tuberculosis (TB) and 1.4 million of deaths in 2011. The emergence of strains resistant to the two first-line anti-TB drugs, isoniazid and rifampicin, (MDR), to second line-drugs (XDR) and the difficult to kill dormant forms of the bacilli require the discovery of new anti-TB antibiotics. β-lactams are usually not considered for tuberculosis treatment since M. tuberculosis produces a broad-spectrum β-lactamase, BlaC. However, the combination of β-lactam belonging to the carbapenem class, meropenem, with β-lactamase inhibitor, clavulanate, is notably active on XDR strains. Our aim was to characterize the carbapenem targets, atypical in M. tuberculosis, since peptidoglycan of this bacteria contains a majority (80%) of cross-links formed by a special transpeptidase family, the L,D-transpeptidases. We have compared the five L,D-transpeptidases of M. tuberculosis for their in vitro activities with respect to peptidoglycan dimers formation and for inactivation reaction by carbapenems. Thus, we have showed that the five L,D-transpeptidases were functional in vitro. LdtMt1, LdtMt2, LdtMt4 et LdtMt5 were able to form peptidoglycan cross-links binding the third amino acid of a donor tetrapeptide substrate with the third amino acid of an acceptor tetrapeptide substrate. These enzymes were also able to use D-methionine as an acceptor in exchange reaction of D-Ala4 of the donor tetrapeptide substrate. LdtMt1, LdtMt2, LdtMt3 et LdtMt4 formed a covalent adduct with carbapenems. The inactivation reaction of L,D-transpeptidases by carbapenems proceed through two steps. In first, a reversible covalent adduct is formed (catalytic constant k1), followed by a second step leading to acylenzyme formation (catalytic constant k2). The determination of kinetic constants of inactivation k1 et k2 revealed important differences between carbapenems. Except for LdtMt1, Imipenem inactivates L,D-transpeptidases more rapidly than other carbapenems indicating that modification of the carbapenem side chain could be used to optimize their anti-mycobacterial activity. In parallel, we have started the study of the L,D-transpeptidases regulation in various culture conditions will allow identifying the L,D-transpeptidases essential for growth and persistence of M. tuberculosis. This work might lead to identification of essential targets allowing eradication of M. tuberculosis dormant forms, which are difficult to treat with conventional anti-TB drugs.

L'enveloppe cellulaire bactérienne joue plus qu'un rôle de barrière d'échange. Elle est au coeur des processus cellulaires essentiels comme la morphogenèse et la division. Cette structure abrite environ un quart des protéines codées par le génome. Le but de mon travail a été de mieux comprendre le rôle de deux protéines membranaires dans la construction et la dynamique de l'enveloppe chez Bacillus subtilis. GluP est une protéase intramembranaire rhomboïde. Ces protéases clivent des segments transmembranaires dans la membrane afin de moduler l'activité de diverses protéines. Elles participent à de nombreux processus cellulaires chez les eucaryotes. Cependant, les fonctions biologiques des rhomboïdes procaryotes sont pour l'heure presque totalement inconnues. Nos résultats suggèrent que GluP participe au contrôle qualité des protéines membranaires à la manière des pseudo-rhomboïdes associées au système ERAD eucaryote. Elle forme un complexe avec FtsH, une protéase majeure du contrôle qualité des protéines. Ce complexe est impliqué dans la dégradation d'un substrat de rhomboïde. Le rôle de GluP serait de permettre la dislocation du segment transmembranaire et faciliter la prise en charge du substrat par FtsH. Le second projet auquel j'ai participé a consisté à comprendre le rôle de la protéine CmmB dans la morphogenèse. Son absence conduit à une morphologie cellulaire élargie. CmmB semble faire partie de la machinerie de synthèse du peptidoglycane au cours de l'élongation de la paroi. Elle serait nécessaire au bon fonctionnement d'une ou de plusieurs penicillin-binding proteins (PBPs). En particulier, nous proposons que CmmB est un cofacteur de la transpeptidase PBP2a. / The bacterial cell envelope is an obligatory barrier. It is a fundamental component in essential cellular processes such as morphogenesis and cell division. It hosts about a quarter of the proteins encoded in the genome. My work was aimed at understanding the function of two membrane proteins in the building and the dynamics of the cell envelope in the model bacterium Bacillus subtilis.GluP is a rhomboid intramembrane protease. Usually, rhomboids cleave transmembrane segments within the membrane to modulate protein functions. In eukaryotes, they participate in many cellular processes and their dysfunction lead to several pathologies. However, prokaryotic rhomboid functions remain almost totally unknown. Our results suggest that GluP is involved in bacterial membrane protein quality control, in a process akin to pseudo-rhomboid dependent endoplasmic reticulum associated protein degradation in eukaryotes. GluP forms a complex with FtsH, a major protease in protein quality control. That complex is not involved in the cleavage of a membrane substrate but in its degradation. We propose that GluP is required for the dislocation of the transmembrane segment, thus facilitating full-length substrate degradation by FtsH in the cytoplasm. My thesis second objective was to understand the role of the CmmB protein in morphogenesis. The absence of CmmB leads to slightly enlarged cells. CmmB seems to belong to the peptidoglycan synthesis machinery for cell-wall elongation. Our data support the idea that it is required for the proper activity of one or several penicillin-binding proteins (PBPs). In particular, we propose that CmmB is a cofactor of the PBP2a transpeptidase.

Clostridium difficile est une bactérie anaérobie sporulante responsable de 15 à 25% des diarrhées post-antibiotiques. Les N-déacétylases sont largement distribuées parmi les bactéries à Gram positif et elles sont impliquées dans différentes fonctions de surface. L'analyse du génome de C. difficile montre que 13 gènes codent pour des N-déacétylases potentielles, et nous avons caractérisé l’ensemble de ces N-déacétylases.Le peptidoglycane de la cellule végétative de C. difficile est N-déacétylé sur 93% des glucosamines, et cette modification participe à la résistance de la bactérie au lysozyme, un composant majeur de l’immunité innée. Nous avons identifié les N-déacétylases PgdA, PgdB et PdaV responsables de cette N-déacétylation, et nous avons évalué leur impact au sein de la virulence de C. difficile. Nous avons également défini le rôle de deux N-déacétylases NagA dans le recyclage du peptidoglycane.Le peptidoglycane de la spore, ou cortex, a été analysé lors de ce travail et sa structure chez C. difficile est atypique par rapport au cortex décrit pour d’autres espèces bactériennes. Nous avons défini les N-déacétylases responsables de la N-déacétylation de la glucosamine du cortex. Nous avons également caractérisé les deux N-déacétylases PdaA1 et PdaA2 responsables de la synthèse des δ-lactames, une modification spécifique du cortex, ainsi que leur influence dans la virulence de C. difficile. Dans ce cadre, nous avons montré que les δ-lactames ont un rôle physiologique plus large pour C. difficile que chez Bacillus subtilis. De plus, nous avons identifié deux N-déacétylases potentiellement impliquées dans la synthèse de ce cortex.À travers ces résultats, ce travail apporte de nouvelles connaissances dans le rôle des N-déacétylases bactériennes. / Clostridium difficile is an anaerobic and spore-forming bacteria responsible for 15 to 25% of post-antibiotic diarrhea. N-deacetylases are largely distributed among Gram positive bacteria and are involved in many surface processes. C. difficile genome analysis showed that 13 genes potentially encode N-deacetylases. In this work, we have characterized all of these enzymes.The vegetative cell peptidoglycan of C. difficile is deacetylated on 93% its glucosamine, and this modification is involved in the resistance of C. difficile against lysozyme, a major component of the innate immunity. We identified the N-deacetylases PgdA, PgdB and PdaV responsible for this N-deacetylation, and we assessed their impact on C. difficile virulence. The role of two N-deacetylases involved in peptidoglycan recycling has also been assessed.The spore peptidoglycan, known as the cortex, has also been characterized during this work, and its structure is atypical in C. difficile compared to other bacterial species. We showed that N-deacetylation of the glucosamine is present in the cortex peptidoglycan, and we identified the N-deacetylases responsible for this modification. Additionally, we characterized the N-deacetylases PdaA1 and PdaA2 responsible for the synthesis of muramic-δ-lactams, a cortex specific modification, as well as their impact on C. difficile virulence. In his context, we determined that muramic-δ-lactams have a broader role in C. difficile compared to their role in Bacillus subtilis. Moreover, two N-deacetylases involved in cortex synthesis have been identified.This work adds a contribution in the knowledge of the roles of bacterial N-deacetylases.

No description available.

Several lipopeptidyl nucleoside antibiotics that inhibit bacterial translocase I (MraY) involved in peptidoglycan cell wall biosynthesis contain an aminoribosyl moiety, an unusual sugar appendage in natural products. A-90289 and muraminomicin are the two representative antibiotics that belong to this family. Bioinformatic analysis of the biosynthetic A-90289 gene clusters revealed that five enzymes are likely involved in the assembly and attachment of the aminoribosyl unit. These enzymes of A-90289 are functionally assigned by in vitro characterization. The results reveal a unique ribosylation pathway that highlighted by uridine-5′-monophosphate as the source of the sugar, a phosphorylase strategy to generate a sugar-1-phosphate, and a primary amine-requiring nucleotidylyltransferase that generates the NDP-sugar donor. Muraminomicin, which has a structure similar to A-90289, holds the distinction in that both ribose units are 2-deoxy sugars. The biosynthetic gene cluster of muraminomicin has been identified, cloned and sequenced, and bioinformatic analysis revealed a minimum of 24 open reading frames putatively involved in the biosynthesis, resistance, and regulation of muraminomicin. Similar to the A-90289 pathway, fives enzymes are still likely involved in the assembly of the 2,5-dideoxy-5-aminoribose saccharide unit, and two are now functionally assigned and characterized: Mra20, a 5′-amino-2′,5′-dideoxyuridine phosphorylase and Mra23, a UTP:5-amino-2,5-dideoxy-α-D-ribose-1-phosphate uridylyltransferase. The cumulative results are consistent with the incorporation of the ribosyl appendage of muraminomicin via the archetypical sugar biosynthetic pathway that parallels A-90289 biosynthesis