Génomique fonctionnelle des protéines de division cellulaire et du peptidoglycane : développement de nouveaux agents antibactériens

Tableau d'honneur de la Faculté des études supérieures et postdoctorales, 2006-2007Cette thèse de doctorat présente la problématique de résistance aux antibiotiques parmi les pathogènes bactériens en émergence et en réémergence à travers le monde. En effet, le développement et la propagation des mécanismes de résistance compromet l’efficacité des traitements antibactériens disponibles et met en danger la vie des patients infectés. Cette thèse se concentre sur l’identification de nouvelles cibles antibactériennes et sur le développement de nouvelles classes d’agents antibactériens en utilisant le pathogène opportuniste Pseudomonas aeruginosa en tan que modèle d’étude. Le premier chapitre aborde l’exploitation des protéines de division cellulaire FtsZ et FtsA en tant que cibles antibactériennes. Suite à une revue de la littérature détaillée, deux articles scientifiques décrivent la synthèse et la sélection d’inhibiteurs contre FtsZ et FtsA. Ces inhibiteurs représentent des candidats prometteurs en vue du développement d’une nouvelle classe d’agents antibactériens. Le deuxième chapitre du corps de la thèse porte sur l’utilisation des amides ligases MurC, MurD, MurE et MurF essentielles à la biosynthèse de la paroi bactérienne en tant que cibles antibactériennes. Suite à une revue de la littérature sur la biologie de ces enzymes, trois articles scientifiques relatent la sélection d’inhibiteurs peptidiques par présentation phagique contre les enzymes MurD, MurE et MurF. Le mode d’action innovateur de ces inhibiteurs permet d’envisager le développement de nouveaux agents antibactériens par peptidomimétisme. Le dernier chapitre expose le pouvoir antibactérien des endolysines de bactériophages. Une revue de la littérature résume le mode d’action et la biologie des endolysines en tant qu’agents antibactériens efficaces ciblant l’intégrité de la paroi bactérienne. Par la suite, un article décrit la capacité de l’endolysine du phage ΦKZ à hydrolyser la paroi bactérienne des bactéries à Gram-négatif et à outrepasser les membranes bactériennes. Ainsi, cette enzyme possède un potentiel antibactérien fort intéressant. En conclusion, cette thèse fournit plusieurs pistes attrayantes afin de développer de nouvelles stratégies antibactériennes pour contrer la problématique de résistance aux antibiotiques.This thesis first presents the critical outcome of antibiotic resistance among emerging and re-emerging bacterial pathogens worldwide. The incessant increase and spread of antibiotic resistance mechanisms compromise the efficiency of available antibacterial therapies and increase the impact of bacterial infections on human mortality and morbidity. This thesis focuses efforts to identify new antibacterial targets in order to develop novel classes of antibacterial agents using the opportunistic pathogen Pseudomonas aeruginosa as a research model. The first chapter of this thesis reports the exploitation of the cell division proteins FtsZ and FtsA as antibacterial targets. A detailed scientific review is presented along with two articles reporting the synthesis and selection of inhibitors against FtsZ and FtsA. These inhibitors represent potent candidates to develop new classes of antibacterial agents targeting the bacterial cell division process. The second chapter describes the use of the essential bacterial cell wall biosynthesis enzymes MurC, MurD, MurE and MurF as antibacterial targets. A scientific review first summarises the biology of these amide ligase enzymes and three scientific articles report the selection of peptide inhibitors against MurD, MurE and MurF by phage display. The novel mode of action of these inhibitors against the unexploited Mur enzymes can be the basis for future development of antibacterial agents targeting the cell wall biosynthesis pathway by peptidomimetism. The last chapter exposes the antibacterial potential of the phage-encoded endolysin enzymes. A review describes the mode of action and the biology of endolysins as efficient antibacterial agents targeting the integrity of the bacterial cell wall layer. Finally, an article presents the peptidoglycan hydrolytic activity of the P. aeruginosa phage ΦKZ gp144 lytic transglycosylase. This endolysin is able to pass through the bacterial membranes and thus represents a strong candidate for developing new antibacterial therapies against Gram-negative bacteria. In conclusion, this thesis provides various attractive ways to develop new antibacterial strategies and face the problem of antibiotic resistance

Développement accéléré de nouveaux inhibiteurs contre les protéines de division cellulaire FtsZ et FtsA de Pseudomonas aeruginosa

L’impact des infections bactériennes couplé à l’émergence des mécanismes de résistance aux antibiotiques suscite un besoin urgent de nouvelles classes d’agents antibactériens. D’ailleurs, la résistance du pathogène opportuniste P. aeruginosa diminue l’efficacité de traitement et met en danger la vie des personnes infectées. Dans le but d’identifier de nouveaux antimicrobiens, nous exploitons la machinerie de division cellulaire bactérienne en tant que cible. Ainsi, les protéines de division cellulaire FtsZ et FtsA de P. aeruginosa ont été utilisées afin d’identifier des inhibiteurs protéiques spécifiques à l’aide de la technique de présentation phagique. Nous avons identifié des peptides détenant une affinité pour les enzymes FtsZ et FtsA puis nous avons caractérisé 3 peptides inhibiteurs de l’activité GTPase de FtsZ. Le peptidomimétisme devrait permettre le développement d’une nouvelle classe d’agents antimicrobiens à partir de ces peptides.The impact of bacterial infections and emergence of antibiotic resistance led to a serious need to develop new class of antibacterials. The acute resistance of the opportunistic pathogen Pseudomonas aeruginosa lowers the treatment efficiency of infected cystic fibrosis patients and immuno-compromised individuals. In the perspective of finding new antimicrobial agents, we are using the bacterial cell division machinery of as a new target. Thus, P. aeruginosa cell division proteins FtsZ and FtsA have been used to identify inhibitory peptides with the phage-display technique. We identified FtsZ and FtsA tight binding peptides and we characterized three inhibitory peptides of FtsZ GTPase activity. Peptidomimetism will allow the development of new antimicrobial agents with these leader peptides

Phage display-derived inhibitor of the essential cell wall biosynthesis enzyme MurF

Background To develop antibacterial agents having novel modes of action against bacterial cell wall biosynthesis, we targeted the essential MurF enzyme of the antibiotic resistant pathogen Pseudomonas aeruginosa. MurF catalyzes the formation of a peptide bond between D-Alanyl-D-Alanine (D-Ala-D-Ala) and the cell wall precursor uridine 5'-diphosphoryl N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-diaminopimelic acid (UDP-MurNAc-Ala-Glu-meso-A2pm) with the concomitant hydrolysis of ATP to ADP and inorganic phosphate, yielding UDP-N-acetylmuramyl-pentapeptide. As MurF acts on a dipeptide, we exploited a phage display approach to identify peptide ligands having high binding affinities for the enzyme. Results Screening of a phage display 12-mer library using purified P. aeruginosa MurF yielded to the identification of the MurFp1 peptide. The MurF substrate UDP-MurNAc-Ala-Glumeso-A2pm was synthesized and used to develop a sensitive spectrophotometric assay to quantify MurF kinetics and inhibition. MurFp1 acted as a weak, time-dependent inhibitor of MurF activity but was a potent inhibitor when MurF was pre-incubated with UDP-MurNAc-Ala-Glu-meso-A2pm or ATP. In contrast, adding the substrate D-Ala-D-Ala during the pre-incubation nullified the inhibition. The IC50 value of MurFp1 was evaluated at 250 μM, and the Ki was established at 420 μM with respect to the mixed type of inhibition against D-Ala-D-Ala. Conclusion MurFp1 exerts its inhibitory action by interfering with the utilization of D-Ala-D-Ala by the MurF amide ligase enzyme. We propose that MurFp1 exploits UDP-MurNAc-Ala-Glu-meso-A2pm-induced structural changes for better interaction with the enzyme. We present the first peptide inhibitor of MurF, an enzyme that should be exploited as a target for antimicrobial drug development

A Genome-Wide Screen for Bacterial Envelope Biogenesis Mutants Identifies a Novel Factor Involved in Cell Wall Precursor Metabolism

The cell envelope of Gram-negative bacteria is a formidable barrier that is difficult for antimicrobial drugs to penetrate. Thus, the list of treatments effective against these organisms is small and with the rise of new resistance mechanisms is shrinking rapidly. New therapies to treat Gram-negative bacterial infections are therefore sorely needed. This goal will be greatly aided by a detailed mechanistic understanding of envelope assembly. Although excellent progress in the identification of essential envelope biogenesis systems has been made in recent years, many aspects of the process remain to be elucidated. We therefore developed a simple, quantitative, and high-throughput assay for mutants with envelope biogenesis defects and used it to screen an ordered single-gene deletion library of Escherichia coli. The screen was robust and correctly identified numerous mutants known to be involved in envelope assembly. Importantly, the screen also implicated 102 genes of unknown function as encoding factors that likely impact envelope biogenesis. As a proof of principle, one of these factors, ElyC (YcbC), was characterized further and shown to play a critical role in the metabolism of the essential lipid carrier used for the biogenesis of cell wall and other bacterial surface polysaccharides. Further analysis of the function of ElyC and other hits identified in our screen is likely to uncover a wealth of new information about the biogenesis of the Gram-negative envelope and the vulnerabilities in the system suitable for drug targeting. Moreover, the screening assay described here should be readily adaptable to other organisms to study the biogenesis of different envelope architectures

Hydroxyl radical overproduction in the envelope : an achilles' heel in peptidoglycan synthesis

While many mechanisms governing bacterial envelope homeostasis have been identified, others remain poorly understood. To decipher these processes, we previously developed an assay in the Gram-negative model Escherichia coli to identify genes involved in maintenance of envelope integrity. One such gene was ElyC, which was shown to be required for envelope integrity and peptidoglycan synthesis at room temperature. ElyC is predicted to be an integral inner membrane protein with a highly conserved domain of unknown function (DUF218). In this study, and stemming from a further characterization of the role of ElyC in maintaining cell envelope integrity, we serendipitously discovered an unappreciated form of oxidative stress in the bacterial envelope. We found that cells lacking ElyC overproduce hydroxyl radicals (HO ) in their envelope compartment and that HO overproduction is directly or indirectly responsible for the peptidoglycan synthesis arrest, cell envelope integrity defects, and cell lysis of the Δ mutant. Consistent with these observations, we show that the Δ mutant defect is suppressed during anaerobiosis. HO is known to cause DNA damage but to our knowledge has not been shown to interfere with peptidoglycan synthesis. Thus, our work implicates oxidative stress as an important stressor in the bacterial cell envelope and opens the door to future studies deciphering the mechanisms that render peptidoglycan synthesis sensitive to oxidative stress. Oxidative stress is caused by the production and excessive accumulation of oxygen reactive species. In bacterial cells, oxidative stress mediated by hydroxyl radicals is typically associated with DNA damage in the cytoplasm. Here, we reveal the existence of a pathway for oxidative stress in the envelope of Gram-negative bacteria. Stemming from the characterization of a poorly characterized gene, we found that HO overproduction specifically in the envelope compartment causes inhibition of peptidoglycan synthesis and eventually bacterial cell lysis

The Chaperone Activities of DsbG and Spy Restore Peptidoglycan Biosynthesis in the Mutant by Preventing Envelope Protein Aggregation.

Peptidoglycan (PG) is the main structural component of bacterial envelopes. It protects bacterial cells against variations in osmotic pressure and cell lysis. The newly discovered factor ElyC has been shown to be important for peptidoglycan biosynthesis at low temperatures. PG production in Δ mutant cells is totally blocked after a few hours of growth at 21°C, triggering cell lysis. In this study, we took a candidate approach to identify genetic suppressors of the Δ mutant cell lysis phenotype. We identified the periplasmic proteins DsbG and Spy as multicopy suppressors and showed that their overproduction restores PG biosynthesis in the Δ mutant. Interestingly, we found that DsbG acts by a novel mechanism, which is independent of its known reductase activity and substrates. DsbG, like Spy, acts as a chaperone to reduce the amounts of protein aggregates in the envelopes of Δ cells. In fact, we found that the amount of protein aggregates was greater in the Δ mutant than in the wild type. Taken together, our results show a protein-folding defect in the envelope compartments of Δ cells that blocks PG production, and they reveal a new physiological activity of DsbG. Peptidoglycan biosynthesis is a dynamic and well-controlled pathway. The molecular assembly of PG and the regulatory pathways ensuring its maintenance are still not well understood. Here we studied the newly discovered factor ElyC, which is important for PG biosynthesis at low temperatures. We revealed an important protein-folding defect in the Δ mutant and showed that overproduction of the periplasmic chaperone DsbG or Spy was sufficient to correct the protein-folding defect and restore PG biosynthesis. These results show that the PG defect in the absence of ElyC is caused, at least in part, by a protein-folding problem in the cell envelope. Furthermore, we showed, for the first time, that the periplasmic protein DsbG has chaperone activity

Selection of peptide inhibitors against the Pseudomonas aeruginosa MurD cell wall enzyme

The purified Pseudomonas aeruginosa cell wall biosynthesis MurD amide ligase enzyme was used to screen C-7-C and 12 mers peptides from phage display libraries using competitive biopanning approaches with the specific substrates D-glutamate and ATP. From the 60 phage-encoded peptides identified, DNA was sequenced, deduced amino acid sequences aligned and two peptides were synthesized from consensus sequences identified. The UDPN-acetylmuramyl-L-alanine MurD substrate was synthesized, purified and used to develop a spectrophotometric assay. One peptide synthesized was found to specifically inhibit ATPase activity of MurD. The IC50 value was estimated at 4 mu M for the C-7-C MurDp1 peptide. The loop conformation of MurDp1 was shown to be important for the inhibition of the UDP-N-acetylmuramyl-L-alanine:D-glutamate MurD ligase. The linear 12 mers MurD2 peptide has an IC50 value of 15 mM. A conserved amino acid motif was found between MurDp2 and the bacterial glyceraldehyde 3-phosphate dehydrogenase indicating that MurDp2 binds at a protein-protein interacting site. The approach proposed and results obtained suggest that efficient peptide inhibitors as well as protein-protein interaction domains can be identified by phage display. (c) 2006 Elsevier Inc. All rights reserved

Genetic interaction between ElyC and the ECA biogenesis pathway.

<p>A. Diagram of the ECA precursor synthesis pathway. G, GlcNAc; Mu, ManNAcA; Gt, Fuc4NAc; P-Gc, glucose-1-phosphate. B. Cells of MG1655 [WT], EM9 [Δ<i>elyC</i>], CB329 [Δ<i>elyC</i> Δ<i>wecA</i>], CB337 [Δ<i>elyC</i> Δ<i>wecB</i>], and CB265 [Δ<i>elyC</i> Δ<i>wecG</i>] were patched onto CPRG indicator agar and grown as described for <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004056#pgen-1004056-g003" target="_blank">Figure 3B</a>. C. The indicated subset of these strains was also grown in liquid LB 1% NaCl at room temperature and monitored as described for <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004056#pgen-1004056-g004" target="_blank">Figure 4A</a>. Cultures of Δ<i>elyC</i> Δ<i>wecB</i> and Δ<i>elyC</i> Δ<i>wecG</i> strains grew as well as the Δ<i>elyC</i> Δ<i>wecA</i> strain (data not shown). D. Overnight cultures of TB28 [WT] or CB152(attλCB118) [Δ<i>elyC</i> (P_ara::<i>elyC</i>)] and its Δ<i>rlmA</i>^ECA, Δ<i>wecF</i>, Δ<i>wecA</i> Δ<i>rlmA</i>^ECA, and Δ<i>wecA</i> Δ<i>wecF</i> derivatives were grown in LB supplemented with 0.2% arabinose and serially diluted following normalization for culture OD₆₀₀. Five microliters of each dilution was spotted onto LB 1% NaCl agar supplemented with 0.2% arabinose or glucose as indicated and plates were incubated at the indicated temperature.</p

Genetic interactions between <i>elyC</i> and enterobacterial common antigen biosynthesis genes revealed by high-throughput GIANT coli analysis.

<p>^a Growth score reflects the colony size of the double mutant clone in question divided by the average colony size of library clones. Scores greater than one indicate suppressive interactions and those less than one indicate negative interactions.</p