References of "Joris, Bernard"
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See detailPrediction of membrane protein structures and TM interactions Rosetta and molecular dynamic studies
Crowet, Jean-Marc ULg; Dony, Nicolas ULg; Joris, Bernard ULg et al

Poster (2013, February 26)

The structures of membrane domains of the Divisome proteins and BlaR are not known and there is no homolog proteins of known structure to build homolgy models. Although the structure prediction of ... [more ▼]

The structures of membrane domains of the Divisome proteins and BlaR are not known and there is no homolog proteins of known structure to build homolgy models. Although the structure prediction of membrane proteins seems easier than for globular proteins, their ab initio prediction remains a difficult task. Only few methods have been used and validated on experimental pdb structures. By using the MARTINI or Bond coarse grain representation, the multimerization of transmembrane helices has been carried out by molecular dynamics, and the structure of several membrane proteins has been predicted by a tool of the Rosetta package. These methods are used here to predict the structure of the membrane embedded part of the politopic proteins from the divisome (FtsW, FtsK, FtsX and MraY) and BlaR. In a following part the MARTINI force field can be used to predict the TM helices interactions between the Divisome protein members. [less ▲]

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See detailSAHBEN, an accessible surface-based elastic network to insert a protein in a complex lipid membrane
Dony, Nicolas ULg; Crowet, Jean-Marc ULg; Joris, Bernard ULg et al

Poster (2013, February 26)

Study of membrane proteins have become one of the most challenging fields in biology. Solving their structure is one important step toward the understanding of their physiological activity but despite the ... [more ▼]

Study of membrane proteins have become one of the most challenging fields in biology. Solving their structure is one important step toward the understanding of their physiological activity but despite the recent advances in membrane protein crystallization, it represents less than 1 % of the entries in the Protein Data Bank. Therefore, calculation methods to study membrane proteins are helpful to complement experimental studies and fill the gap between the information obtained from the sequence and/or structure, the experimental results and the biological activity. Molecular Dynamics (MD) is a method of choice for membrane simulations and the rising of coarse-grained forcefields has opened the way to longer simulations with reduced calculations times. However, these approaches have two main drawbacks, the preparation of the membrane system and the preservation of the 3D protein structure, which is not trivial in CG approach. To circumvent these problems, we propose to use a modified version of the Gromacs tool genbox to easily insert lipids and a network based on hydrogen bonds and accessible surface to maintain the protein 3D structure. This protocol is available through a website (gcgs.gembloux.ulg.ac.be). [less ▲]

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See detailCharacterization of amylolysin, a novel lantibiotic from Bacillus amyloliquefaciens GA1
Arguelles Arias, Anthony ULg; Ongena, Marc ULg; Devreese, Bart et al

in PLoS ONE (2013), 8(12),

Background: Lantibiotics are heat-stable peptides characterized by the presence of thioether amino acid lanthionine and methyllanthionine. They are capable to inhibit the growth of Gram-positive bacteria ... [more ▼]

Background: Lantibiotics are heat-stable peptides characterized by the presence of thioether amino acid lanthionine and methyllanthionine. They are capable to inhibit the growth of Gram-positive bacteria, including Listeria monocytogenes, Staphylococcus aureus or Bacillus cereus, the causative agents of food-borne diseases or nosocomial infections. Lantibiotic biosynthetic machinery is encoded by gene cluster composed by a structural gene that codes for a pre-lantibiotic peptide and other genes involved in pre-lantibiotic modifications, regulation, export and immunity. Methodology/Findings: Bacillus amyloliquefaciens GA1 was found to produce an antimicrobial peptide, named amylolysin, active on an array of Gram-positive bacteria, including methicillin resistant S. aureus. Genome characterization led to the identification of a putative lantibiotic gene cluster that comprises a structural gene (amlA) and genes involved in modification (amlM), transport (amlT), regulation (amlKR) and immunity (amlFE). Disruption of amlA led to loss of biological activity, confirming thus that the identified gene cluster is related to amylolysin synthesis. MALDI-TOF and LC-MS analysis on purified amylolysin demonstrated that this latter corresponds to a novel lantibiotic not described to date. The ability of amylolysin to interact in vitro with the lipid II, the carrier of peptidoglycan monomers across the cytoplasmic membrane and the presence of a unique modification gene suggest that the identified peptide belongs to the group B lantibiotic. Amylolysin immunity seems to be driven by only two AmlF and AmlE proteins, which is uncommon within the Bacillus genus. Conclusion/Significance: Apart from mersacidin produced by Bacillus amyloliquefaciens strains Y2 and HIL Y-85,544728, reports on the synthesis of type B-lantibiotic in this species are scarce. This study reports on a genetic and structural characterization of another representative of the type B lantibiotic in B. amyloliquefaciens. Copyright: © 2013 Arguelles Arias et al. [less ▲]

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See detailSevoflurane inhibits equine myeloperoxidase release and activity in vitro.
MINGUET, Grégory ULg; de la Rebière de Pouyade, Geoffroy ULg; Franck, Thierry ULg et al

in Veterinary Anaesthesia & Analgesia (2013), 40

Objective To investigate the effects of the volatile anaesthetic sevoflurane on the release of total and active myeloperoxidase (MPO) by non-stimulated and stimulated polymorphonuclear neutrophils (PMNs ... [more ▼]

Objective To investigate the effects of the volatile anaesthetic sevoflurane on the release of total and active myeloperoxidase (MPO) by non-stimulated and stimulated polymorphonuclear neutrophils (PMNs) in whole blood from healthy horses. Study design In vitro experimental study. Animals Adult healthy horses. Methods Samples of whole venous blood were collected and incubated in air or in air plus 2.3% or 4.6% sevoflurane for 1 hour. PMNs were stimulated with N-formyl-methionyl-leucyl-phenylalanine (fMLP), with a combination of cytochalasin B (CB) and fMLP or with phorbol myristate acetate (PMA). Total and active MPO contents released by PMNs in blood were measured by enzyme-linked immunosorbent assay (ELISA) and specific immunological extraction followed by enzymatic detection (SIEFED) respectively. Additional experiments were performed to assess the effect of sevoflurane on the peroxidase and chlorination cycles of purified equine MPO using Amplex Red and 3'-(p-aminophenyl) fluorescein as fluorogenic substrates respectively. Results As compared with air alone, 1 hour exposure of whole blood to 4.6% sevoflurane in air significantly inhibited the release of total and active MPO by unstimulated and both fMLP- and CB + fMLP-stimulated PMNs but not by PMA-stimulated PMNs. Although 2.3% sevoflurane had no effect on total MPO release by unstimulated and stimulated PMNs, it significantly reduced the release of active MPO by unstimulated and fMLP-stimulated PMNs. Additionally, sevoflurane reversibly inhibited the activity of MPO, especially the peroxidase cycle of the enzyme. Conclusions and clinical relevance Although our experimental study was not designed to assess the effects of sevoflurane in vivo, this inhibition of MPO release and activity may have relevance for anaesthetized horses and deserves further studies to examine the clinical importance of these findings. [less ▲]

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See detailSynthesis and biological evaluation of potential threonine synthase inhibitors: Rhizocticin A and Plumbemycin A.
Gahungu, Mathias; Arguelles-Arias, Anthony; Fickers, Patrick et al

in Bioorganic & Medicinal Chemistry (2013), 21(17), 4958-67

Rhizocticins and Plumbemycins are natural phosphonate antibiotics produced by the bacterial strains Bacillus subtilis ATCC 6633 and Streptomyces plumbeus, respectively. Up to now, these potential ... [more ▼]

Rhizocticins and Plumbemycins are natural phosphonate antibiotics produced by the bacterial strains Bacillus subtilis ATCC 6633 and Streptomyces plumbeus, respectively. Up to now, these potential threonine synthase inhibitors have only been synthesized under enzymatic catalysis. Here we report the chemical stereoselective synthesis of the non-proteinogenic (S,Z)-2-amino-5-phosphonopent-3-enoic acid [(S,Z)-APPA] and its use for the synthesis of Rhizocticin A and Plumbemycin A. In this work, (S,Z)-APPA was synthesized via the Still-Gennari olefination starting from Garner's aldehyde. The Michaelis-Arbuzov reaction was used to form the phosphorus-carbon bond. Oligopeptides were prepared using liquid phase peptide synthesis (LPPS) and were tested against selected bacteria and fungi. [less ▲]

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See detail2-nitrobenzyl esters of penam and cephem derivatives as inhibitors of penicillin-binding proteins
Brulé, Cédric; Grugier, Jérôme; Brans, Alain ULg et al

in Asian Journal of Organic Chemistry (2013), 2

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See detailThe MicroH2 project:an association of four laboratories to improve theknowledge on biohydrogen production precesses
Beckers, Laurent ULg; Calusinska, Magdalena ULg; Hamilton, Christopher ULg et al

Poster (2012, June 04)

This poster presents a collaborative research project (MicroH2) held at the University of Liège (Belgium) since 2007 (www.microh2.ulg.ac.be) and involving four different research groups. The project aims ... [more ▼]

This poster presents a collaborative research project (MicroH2) held at the University of Liège (Belgium) since 2007 (www.microh2.ulg.ac.be) and involving four different research groups. The project aims to develop a center of excellence in the fields of photo- and dark- biohydrogen production. Our studies contribute to improve the knowledge of the processes involved in the microbiological production of hydrogen, from a fundamental and practical point of view. Some results are highlighted here. The research concerning photofermentation focuses on the interactions between respiration, photosynthesis and H2-producing pathways in algal microorganisms, by using mitochondrial mutants and genetically modified strains with modified ability for hydrogen production [1-2]. To study the metabolism of the hydrogen production by anaerobic bacteria, pure cultures and defined consortia are used and their production of biogas and soluble metabolites is measured. Moreover, we have developed and optimized molecular tools, like quantitative RT-PCR and FISH, to monitor the variations of bacterial populations in novel bioreactors for hydrogen production [3-4]. We have also mined the complete genomes of Clostridium spp. for putative hydrogenase genes and found a large diversity of them [5]. [less ▲]

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See detailSynthesis and evaluation of boronic acids as inhibitors of Penicillin Binding Proteins of classes A, B and C
Zervosen, Astrid ULg; Sauvage, Eric ULg; Bouillez, André ULg et al

Poster (2012, April 18)

The widespread use of beta-lactam antibiotics has lead to the worldwide appearance of drug-resistant strains. Bacteria have developed resistance to beta-lactams by three main mechanisms: the production of ... [more ▼]

The widespread use of beta-lactam antibiotics has lead to the worldwide appearance of drug-resistant strains. Bacteria have developed resistance to beta-lactams by three main mechanisms: the production of beta-lactamases that catalyze hydrolysis of beta-lactams, the production of low-affinity, drug resistant Penicillin Binding Proteins (PBPs) and the over expression of resistant PBPs. PBPs are interesting targets because they catalyse the last steps of the biosynthesis of peptidoglycan, which is unique in bacteria and has no mammalian analogs, outside the cytoplasmic membrane. Various non-ß-lactam inhibitors of PBPs have been developed with the objective of attempting to stall the development of ß-lactam resistance. Boronic acids are potent beta-lactamase inhibitors and have been shown to display some specificity for soluble transpeptidases and PBPs, but their potential as inhibitors of the latter enzymes is yet to be widely explored. Recently, a (2, 6-dimethoxybenzamido)methylboronic acid was identified as being a potent inhibitor of Actinomadura sp. R39 transpeptidase (IC50: 1.3 µM). Here, we will discuss the synthesis of a number of acylaminomethylboronic acids, analogs of (2, 6-dimethoxybenzamido)methylboronic acid, and their potential as inhibitors of PBPs. Several boronic acids of this library were able to inhibit PBPs of classes A, B and C from penicillin sensitive strains. Thus (2-nitrobenzamido)methylboronic acid was identified as a good inhibitor of class A PBP (PBP1b from S. pneumoniae, IC50 = 26 µM), class B PBP (PBP2xR6 from S. pneumoniae, IC50 = 138 µM) and class C PBP (R39 from Actinomadura sp., IC50 = 0.6 µM). Crystal structures of complexes of R39 and PBP1b with boronic acid analogs of our library have already been solved and allowed an interpretation of results. We believe that this work opens new avenues towards the development of molecules that will inhibit PBPs, and eventually display bactericidal effect, on distinct bacterial species. [less ▲]

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See detailFermentative hydrogen production from glucose and starch using pure strains and artificial co-cultures ofClostridium spp.
Masset, Julien; Calusinska, Magdalena ULg; Hamilton, Christopher et al

in Biotechnology for biofuels (2012), 5(35), 1-15

ABSTRACT: BACKGROUND: Pure bacterial strains give better yields when producing H2 than mixed, natural communities. However the main drawback with the pure cultures is the need to perform the fermentations ... [more ▼]

ABSTRACT: BACKGROUND: Pure bacterial strains give better yields when producing H2 than mixed, natural communities. However the main drawback with the pure cultures is the need to perform the fermentations under sterile conditions. Therefore, H2 production using artificial co-cultures, composed of well characterized strains, is one of the directions currently undertaken in the field of biohydrogen research. RESULTS: Four pure Clostridium cultures, including C. butyricum CWBI1009, C. pasteurianum DSM525, C. beijerinckii DSM1820 and C. felsineum DSM749, and three different co-cultures composed of (1) C. pasteurianum and C. felsineum, (2) C. butyricum and C. felsineum, (3) C. butyricum and C. pasteurianum, were grown in 20 L batch bioreactors. In the first part of the study a strategy composed of three-culture sequences was developed to determine the optimal pH for H2 production (sequence 1); and the H2-producing potential of each pure strain and co-culture, during glucose (sequence 2) and starch (sequence 3) fermentations at the optimal pH. The best H2 yields were obtained for starch fermentations, and the highest yield of 2.91 mol H2/ mol hexose was reported for C. butyricum. By contrast, the biogas production rates were higher for glucose fermentations and the highest value of 1.5 L biogas/ h was observed for the co-culture (1). In general co-cultures produced H2 at higher rates than the pure Clostridium cultures, without negatively affecting the H2 yields. Interestingly, all the Clostridium strains and co-cultures were shown to utilize lactate (present in a starch-containing medium), and C. beijerinckii was able to re-consume formate producing additional H2. In the second part of the study the co-culture (3) was used to produce H2 during 13 days of glucose fermentation in a sequencing batch reactor (SBR). In addition, the species dynamics, as monitored by qPCR (quantitative real-time PCR), showed a stable coexistence of C. pasteurianum and C. butyricum during this fermentation. CONCLUSIONS: The four pure Clostridium strains and the artificial co-cultures tested in this study were shown to efficiently produce H2 using glucose and starch as carbon sources. The artificial co-cultures produced H2 at higher rates than the pure strains, while the H2 yields were only slightly affected. [less ▲]

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See detailSynthesis of Modified Peptidoglycan Precursor Analogues for the Inhibition of Glycosyltransferase.
Dumbre, S; Derouaux, Adeline ULg; Lescrinier, E et al

in Journal of the American Chemical Society (2012)

The peptidoglycan glycosyltransferases (GTs) are essential enzymes that catalyze the polymerization of glycan chains of the bacterial cell wall from lipid II and thus constitute a validated antibacterial ... [more ▼]

The peptidoglycan glycosyltransferases (GTs) are essential enzymes that catalyze the polymerization of glycan chains of the bacterial cell wall from lipid II and thus constitute a validated antibacterial target. Their enzymatic cavity is composed of a donor site for the growing glycan chain (where the inhibitor moenomycin binds) and an acceptor site for lipid II substrate. In order to find lead inhibitors able to fill this large active site, we have synthesized a series of substrate analogues of lipid I and lipid II with variations in the lipid, the pyrophosphate, and the peptide moieties and evaluated their biological effect on the GT activity of E. coli PBP1b and their antibacterial potential. We found several compounds able to inhibit the GT activity in vitro and cause growth defect in Bacillus subtilis . The more active was C16-phosphoglycerate-MurNAc-(l-Ala-d-Glu)-GlcNAc, which also showed antibacterial activity. These molecules are promising leads for the design of new antibacterial GT inhibitors. [less ▲]

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See detailExploration of the chemical space of novel naphthalene-sulfonamide and anthranilic acid-based inhibitors of penicillin-binding Proteins
Sosic, Izidor; Turk, Samo; Sinreih, Masa et al

in Acta Chimica Slovenica (2012), 59(2), 380-388

Penicillin-binding proteins are a well established, validated and still a very promising target for the design and development of new antibacterial agents. Based on our previous discovery of several ... [more ▼]

Penicillin-binding proteins are a well established, validated and still a very promising target for the design and development of new antibacterial agents. Based on our previous discovery of several noncovalent small-molecule inhibitor hits for resistant PBPs we decided to additionally explore the chemical space around these compounds. In order to clarify their structure-activity relationships for PBP inhibition two new series of compounds were synthesized, characterized and evaluated biochemically: the derivatives of anthranilic acid and naphthalene-sulfonamide derivatives. The target compounds were tested for their inhibitory activities on three different transpeptidases: PBP2a from methicillin-resistant Staphylococcus aureus (MRSA) strains, PBP5fm from Enterococcus faecium strains, and PBP1b from Streptococcus pneumoniae strains. The most promising results for both of these series of compounds were obtained against the PBP2a enzyme with the IC50 values in the micromolar range. Although these results do not represent a significant breakthrough in the field of noncovalent PBP inhibitors, they do provide useful structure-activity relationship data, and thus a more solid basis for the design of potent and noncovalent inhibitors of resistant PBPs. [less ▲]

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See detailSynthesis and evaluation of boronic acids as inhibitors of Penicillin Binding Proteins of classes A, B and C.
Zervosen, Astrid ULg; Bouillez, André ULg; Herman, Alexandre et al

in Bioorganic & Medicinal Chemistry (2012), 20(12), 3915-24

In response to the widespread use of beta-lactam antibiotics bacteria have evolved drug resistance mechanisms that include the production of resistant Penicillin Binding Proteins (PBPs). Boronic acids are ... [more ▼]

In response to the widespread use of beta-lactam antibiotics bacteria have evolved drug resistance mechanisms that include the production of resistant Penicillin Binding Proteins (PBPs). Boronic acids are potent beta-lactamase inhibitors and have been shown to display some specificity for soluble transpeptidases and PBPs, but their potential as inhibitors of the latter enzymes is yet to be widely explored. Recently, a (2,6-dimethoxybenzamido)methylboronic acid was identified as being a potent inhibitor of Actinomadura sp. R39 transpeptidase (IC(50): 1.3muM). In this work, we synthesized and studied the potential of a number of acylaminomethylboronic acids as inhibitors of PBPs from different classes. Several derivatives inhibited PBPs of classes A, B and C from penicillin sensitive strains. The (2-nitrobenzamido)methylboronic acid was identified as a good inhibitor of a class A PBP (PBP1b from Streptococcus pneumoniae, IC(50)=26muM), a class B PBP (PBP2xR6 from Streptococcus pneumoniae, IC(50)=138muM) and a class C PBP (R39 from Actinomadura sp., IC(50)=0.6muM). This work opens new avenues towards the development of molecules that inhibit PBPs, and eventually display bactericidal effects, on distinct bacterial species. [less ▲]

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See detailA peptidoglycan fragment triggers beta-lactam resistance in Bacillus licheniformis.
Amoroso, Ana Maria ULg; Boudet, Julien; Berzigotti, Stephanie et al

in PLoS Pathogens (2012), 8(3), 1002571

To resist to beta-lactam antibiotics Eubacteria either constitutively synthesize a beta-lactamase or a low affinity penicillin-binding protein target, or induce its synthesis in response to the presence ... [more ▼]

To resist to beta-lactam antibiotics Eubacteria either constitutively synthesize a beta-lactamase or a low affinity penicillin-binding protein target, or induce its synthesis in response to the presence of antibiotic outside the cell. In Bacillus licheniformis and Staphylococcus aureus, a membrane-bound penicillin receptor (BlaR/MecR) detects the presence of beta-lactam and launches a cytoplasmic signal leading to the inactivation of BlaI/MecI repressor, and the synthesis of a beta-lactamase or a low affinity target. We identified a dipeptide, resulting from the peptidoglycan turnover and present in bacterial cytoplasm, which is able to directly bind to the BlaI/MecI repressor and to destabilize the BlaI/MecI-DNA complex. We propose a general model, in which the acylation of BlaR/MecR receptor and the cellular stress induced by the antibiotic, are both necessary to generate a cell wall-derived coactivator responsible for the expression of an inducible beta-lactam-resistance factor. The new model proposed confirms and emphasizes the role of peptidoglycan degradation fragments in bacterial cell regulation. [less ▲]

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See detailThe induction of beta-lactamases in Eubacteria
Joris, Bernard ULg; Dusart, Jean

in Uversky, Vladimir N.; Frère, Jean-Marie (Eds.) Beta-lactamases (2012)

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See detailMICRO-H2 – Microbiological production of hydrogen: study of microalgal and bacterial processes
Calusinska, Magdalena ULg; Joris, Bernard ULg; Wilmotte, Annick ULg et al

Poster (2011, September 07)

The project MICRO-H2 aims to study and exploit the microbial (bacterial and algal) production of hydrogen (H2). In addition to building a competence centre around the H2 production by microorganisms and ... [more ▼]

The project MICRO-H2 aims to study and exploit the microbial (bacterial and algal) production of hydrogen (H2). In addition to building a competence centre around the H2 production by microorganisms and the molecular monitoring of the processes, this project tries to address two main socio-economic issues. First, transport and many economic activities will be based on hydrogen energy in the near future. Secondly, many researches and technology developments deal with renewable resources. Therefore, a new integrated technology for a sustainable development should be promoted. Photofermentation and dark-fermentation are the most promising ways to produce biohydrogen. The main advantage of the first process is the complete conversion of substrate, if any, to hydrogen. However, present H2-production rates by microalgae remain low. Therefore, a better understanding of the microalgal hydrogen metabolism and rate improvements by genetic engineering are needed. On the other hand, dark-fermentation achieves at present far higher H2-production rates, but improvements are expected through monitoring and optimisation of bacterial diversity and activity. The objectives about bacterial H2 production were to increase knowledge, stability potentialities and investigation skills about the consortia of bacteria involved in bioreactors treating wastewater rich in carbohydrates to produce biohydrogen. The project focused mainly on the study of the potentialities of different consortia, with a focus on Clostridium strains. Concerning the microalgal production of H2, the objectives were to increase knowledge on the metabolic interactions that determine H2 evolution at the cellular level and to produce new strains with increased ability for H2 production in the two-stage process. [less ▲]

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