References of "Joris, Bernard"
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See detailNew noncovalent inhibitors of penicillin-binding proteins from penicillin-resistant bacteria.
Turk, Samo; Verlaine, Olivier ULg; Gerards, Thomas ULg et al

in PloS one (2011), 6(5), 19418

BACKGROUND: Penicillin-binding proteins (PBPs) are well known and validated targets for antibacterial therapy. The most important clinically used inhibitors of PBPs beta-lactams inhibit transpeptidase ... [more ▼]

BACKGROUND: Penicillin-binding proteins (PBPs) are well known and validated targets for antibacterial therapy. The most important clinically used inhibitors of PBPs beta-lactams inhibit transpeptidase activity of PBPs by forming a covalent penicilloyl-enzyme complex that blocks the normal transpeptidation reaction; this finally results in bacterial death. In some resistant bacteria the resistance is acquired by active-site distortion of PBPs, which lowers their acylation efficiency for beta-lactams. To address this problem we focused our attention to discovery of novel noncovalent inhibitors of PBPs. METHODOLOGY/PRINCIPAL FINDINGS: Our in-house bank of compounds was screened for inhibition of three PBPs from resistant bacteria: PBP2a from Methicillin-resistant Staphylococcus aureus (MRSA), PBP2x from Streptococcus pneumoniae strain 5204, and PBP5fm from Enterococcus faecium strain D63r. Initial hit inhibitor obtained by screening was then used as a starting point for computational similarity searching for structurally related compounds and several new noncovalent inhibitors were discovered. Two compounds had promising inhibitory activities of both PBP2a and PBP2x 5204, and good in-vitro antibacterial activities against a panel of Gram-positive bacterial strains. CONCLUSIONS: We found new noncovalent inhibitors of PBPs which represent important starting points for development of more potent inhibitors of PBPs that can target penicillin-resistant bacteria. [less ▲]

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See detailAntilisterial Activity on Poultry Meat of Amylolysin, a Bacteriocin from Bacillus amyloliquefaciens GA1
Halimi, Badre Eddine ULg; Dortu, Carine; Arguelles Arias, Anthony ULg et al

in Probiotics and Antimicrobial Proteins (2010)

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See detailThe surprising diversity of clostridial hydrogenases: a comparative genomic perspective
Calusinska, Magdalena ULg; Happe, Thomas; Joris, Bernard ULg et al

in Microbiology (2010), 156

Among the large variety of micro-organisms capable of fermentative hydrogen production, strict anaerobes such as members of the genus Clostridium are the most widely studied. They can produce hydrogen by ... [more ▼]

Among the large variety of micro-organisms capable of fermentative hydrogen production, strict anaerobes such as members of the genus Clostridium are the most widely studied. They can produce hydrogen by a reversible reduction of protons accumulated during fermentation to dihydrogen, a reaction which is catalysed by hydrogenases. Sequenced genomes provide completely new insights into the diversity of clostridial hydrogenases. Building on previous reports, we found that [FeFe] hydrogenases are not a homogeneous group of enzymes, but exist in multiple forms with different modular structures and are especially abundant in members of the genus Clostridium. This unusual diversity seems to support the central role of hydrogenases in cell metabolism. In particular, the presence of multiple putative operons encoding multisubunit [FeFe] hydrogenases highlights the fact that hydrogen metabolism is very complex in this genus. In contrast with [FeFe] hydrogenases, their [NiFe] hydrogenase counterparts, widely represented in other bacteria and archaea, are found in only a few clostridial species. Surprisingly, a heteromultimeric Ech hydrogenase, known to be an energy-converting [NiFe] hydrogenase and previously described only in methanogenic archaea and some sulfur-reducing bacteria, was found to be encoded by the genomes of four cellulolytic strains: Clostridum cellulolyticum, Clostridum papyrosolvens, Clostridum thermocellum and Clostridum phytofermentans [less ▲]

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See detailStandardized evaluation of protein stability.
Thomas, Annick ULg; Joris, Bernard ULg; Brasseur, Robert ULg

in Biochimica et Biophysica Acta (2010)

We compare Mean Force Potential values of a large series of PDB models of proteins and peptides and find that either as monomers or polymers, proteins longer than 200-250 residues have equivalent MFP ... [more ▼]

We compare Mean Force Potential values of a large series of PDB models of proteins and peptides and find that either as monomers or polymers, proteins longer than 200-250 residues have equivalent MFP values that are averaged to -65+/-3kcal/aa. This value is named the standard or stability value. The standard value is reached irrespective of sequences and 3D folds. Peptides are too short to follow the rule and frequently exist as populations of conformers; one exception are peptides in amyloid fibrils. Fibrils surpass the standard value in accordance with their uppermost stability. In parallel, we calculate median MFP values of amino acids in stably folded PDB models of proteins: median values vary from -25 for Gly to -115kcal/aa for Trp. These median values are used to score primary sequences of proteins: all sequences converge to a mean value of -63.5+/-2.5kcal/aa i.e. only 1.5kcal less than the folded model standard. Sequences from unfolded proteins have lower values. This supports the conclusion that sequences carry in an important message and more specifically that diversity of amino acids in sequences is mandatory for stability. We also use the median amino acid MFP to score residue stability in 3D folds. This demonstrates that 3D folds are compromises between fragments of high and fragments of low scores and that functional residues are often, but not always in the extreme score values. The approach opens to possibilities of evaluating any 3D model, of detecting functional residues and should help in conducting mutation assays. [less ▲]

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See detail1,6-AnhMurNAc derivatives for assay development of amidase AmiD.
Mercier, Frédéric ULg; Zervosen, Astrid ULg; Teller, Nathalie et al

in Bioorganic & Medicinal Chemistry (2010), 18(21), 7422-31

Various peptidoglycan fragments were synthesized from two anhydro-muramic acid derivatives protected with a Bn or a PMB group at the 4th position, in homogenate phase or on a solid support. In order to ... [more ▼]

Various peptidoglycan fragments were synthesized from two anhydro-muramic acid derivatives protected with a Bn or a PMB group at the 4th position, in homogenate phase or on a solid support. In order to facilitate HPLC detection, a chromophoric group was attached to the peptide chain. The periplasmic amidase sAmiD of Escherichia coli was used to cleave the amide bond between the lactyl group of the MurNAc and the alpha-amino group of L-Ala where the peptide chain was at least a dipeptide (L-Ala-gamma-D-Glu) amidated by benzylamine on the gamma-carboxyl group of D-Glu. In the presence of a tripeptide chain (L-Ala-gamma-D-Glu-L-Lys) or a tetrapeptide chain (L-Ala-gamma-D-Glu-m-A(2)pm-D-Ala) higher hydrolysis rates were observed. We have also demonstrated that the presence of TNB on the epsilon-amino group of L-Lys only has a small influence on the hydrolysis capacity of sAmiD. [less ▲]

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See detailSpecific Structural Features of the N-Acetylmuramoyl-l-Alanine Amidase AmiD from Escherichia coli and Mechanistic Implications for Enzymes of This Family.
Kerff, Frédéric ULg; Petrella, Stéphanie; Mercier, Frédéric ULg et al

in Journal of Molecular Biology (2010), 397

AmiD is the fifth identified N-acetylmuramoyl-l-alanine zinc amidase of Escherichia coli. This periplasmic lipoprotein is anchored in the outer membrane and has a broad specificity. AmiD is capable of ... [more ▼]

AmiD is the fifth identified N-acetylmuramoyl-l-alanine zinc amidase of Escherichia coli. This periplasmic lipoprotein is anchored in the outer membrane and has a broad specificity. AmiD is capable of cleaving the intact peptidoglycan (PG) as well as soluble fragments containing N-acetylmuramic acid regardless of the presence of an anhydro form or not, unlike the four other amidases, AmiA, AmiB, AmiC, and AmpD, which have some specificity. AmiD function is, however, not clearly established but it could be part of the enzymatic machinery involved in the PG turnover in E. coli. We solved three structures of the E. coli zinc amidase AmiD devoid of its lipidic anchorage: the holoenzyme, the apoenzyme in complex with the substrate anhydro-N-acetylmuramic-acid-l-Ala-gamma-d-Glu-l-Lys, and the holoenzyme in complex with the l-Ala-gamma-d-Glu-l-Lys peptide, the product of the hydrolysis of this substrate by AmiD. The AmiD structure shows a relatively flexible N-terminal extension that allows an easy reach of the PG by the enzyme inserted into the outer membrane. The C-terminal domain provides a potential extended geometrical complementarity to the substrate. AmiD shares a common fold with AmpD, the bacteriophage T7 lysozyme, and the PG recognition proteins, which are receptor proteins involved in the innate immune responses of a wide range of organisms. Analysis of the different structures reveals the similarity between the catalytic mechanism of zinc amidases of the AmiD family and the thermolysin-related zinc peptidases. [less ▲]

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See detailInteraction of ceftobiprole with the low-affinity PBP 5 of Enterococcus faecium
Henry, X.; Amoroso, Ana Maria ULg; Coyette, Jacques ULg et al

in Antimicrobial Agents and Chemotherapy (2010), 54

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See detailDynamics Characterization of Fully Hydrated Bacterial Cell Walls by Solid-State NMR: Evidence for Cooperative Binding of Metal Ions
Kern, Thomas; Giffard, Mathilde; Hediger, Sabine et al

in Journal of the American Chemical Society (2010), 132

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See detailThe diversity of clostridial hydrogenases revealed by genome sequencing projects
Calusinska, Magdalena ULg; Wilmotte, Annick ULg; Joris, Bernard ULg

Poster (2009, December 15)

Molecular hydrogen is a key intermediate in metabolomic interactions of a wide range of microorganisms. Hydrogen is also regarded as a key component in future energy systems as it is a sustainable, clean ... [more ▼]

Molecular hydrogen is a key intermediate in metabolomic interactions of a wide range of microorganisms. Hydrogen is also regarded as a key component in future energy systems as it is a sustainable, clean, and transportable energy carrier. Some microorganisms can produce hydrogen during a reversible reduction of protons to dihydrogen, a reaction which is catalyzed by the enzyme hydrogenases. On the basis of their bimetallocenter composition, hydrogenases are divided into three main groups, phylogenetically not related: [NiFe] hydrogenases, [Fe] only hydrogenases and FeS cluster free hydrogenases. The latter were described in methanogenic Archaea only. [NiFe] hydrogenases, composed of at least two subunits are well characterized and widely distributed between Archaea and Bacteria. However, only a few representatives of Clostridium sp. possess this type of enzyme. On the other hand, much less is known about the [Fe] only hydrogenases, that are usually monomeric enzymes and restricted to Bacteria and a few eukaryotic species. Genome sequencing projects gave a completely new insight into the diversity of forms of putative [Fe] only hydrogenases within the genus Clostridium. With the use of bioinformatic tools, we have described the unusual modularity of forms of these enzymes, from monomeric to tetrameric with a different number of accessory domains reacting with diverse redox partners. This fact seems to support the central role of hydrogenases in cell metabolism and quick adaptation of the host to changing environmental conditions. Moreover, the presence of multiple putative operons encoding for multisubunit [FeFe] hydrogenases is highlighting the fact that hydrogen metabolism is very complex in the Clostridium genus. [less ▲]

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See detailApplication of molecular techniques to monitor the evolution of bacterial consortia composed of Clostridium sp. in a hydrogen producing bioreactor
Calusinska, Magdalena ULg; Savichtcheva, Olga; Joris, Bernard ULg et al

Poster (2009, December 11)

Our current dependence on fossil fuels as the primary energy source contributes to global climate change, environmental degradation and health problems. Hydrogen offers a tremendous potential as a clean ... [more ▼]

Our current dependence on fossil fuels as the primary energy source contributes to global climate change, environmental degradation and health problems. Hydrogen offers a tremendous potential as a clean, renewable energy currency and it is compatible with electrochemical and combustion processes for energy conversion without producing carbon – based emissions. Many microorganisms, especially photosynthetic as well as facultative and anaerobic bacteria have been reported to produce large amounts of hydrogen from soluble and insoluble biomass. Clostridia, being obligate anaerobes, are capable of biogas production during ‘dark fermentation’ of a wide range of carbohydrates. In this ARC project, entitled Micro – H2 we have focused on a new direction in bio – hydrogen production systems which is the use of mixed cultures of microorganisms (consortia). We expect that the combination of complementary metabolisms could significantly increase the efficiencies of mixed systems compared to monocultures. However, a few fundamental studies need to be carried out in order to investigate and improve the stability of microbial populations involved in the processes. It is now recognised that molecular microbial ecology tools provide the scientific basis to monitor the processes used in environmental biotechnology. To characterize the diversity of bacterial communities, quantitative techniques such as Real – Time Quantitative PCR and FISH (Fluorescence in situ hybridization) and semi – quantitative DGGE (Denaturing Gradient Gel Electrophoresis) have been optimized and applied on different bioreactor samples. This approach enabled for the temporal monitoring of the evolution of bacterial consortia, both in terms of species dominance and their metabolic activity. Molecular analysis of bacterial consortia allowed for careful examination of interactions between different bacterial species within a consortium, which is crucial in the stabilization of the hydrogen production process. [less ▲]

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See detailIdentification and characterization of novel peptidoglycan glycosyltransferase inhibitors with antibacterial activity
Derouaux, Adeline ULg; Turk, Samo; Offant, Julien et al

Poster (2009, November)

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See detailHigh-level biosynthesis of the anteiso-C(17) isoform of the antibiotic mycosubtilin in Bacillus subtilis and characterization of its candidacidal activity.
Fickers, Patrick ULg; Guez, Jean-Sebastien; Damblon, Christian ULg et al

in Applied and Environmental Microbiology (2009), 75(13), 4636-40

High-level production (880 mg liter(-1)) and isolation of the anteiso-C(17) isoform of the lipopeptide mycosubtilin produced by a genetically engineered Bacillus subtilis strain are reported. Antifungal ... [more ▼]

High-level production (880 mg liter(-1)) and isolation of the anteiso-C(17) isoform of the lipopeptide mycosubtilin produced by a genetically engineered Bacillus subtilis strain are reported. Antifungal activity of this isoform, as determined via culture and fluorometric and cell leakage assays, suggests its potential therapeutic use as an antifungal agent, in particular against Candida spp. [less ▲]

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See detailStructural basis of the inhibition of class A beta-lactamases and penicillin-binding proteins by 6-beta-iodopenicillanate
Sauvage, Eric ULg; Zervosen, Astrid ULg; Dive, Georges ULg et al

in Journal of the American Chemical Society (2009), 131(42), 15262-15269

6-Beta-halogenopenicillanates are powerful, irreversible inhibitors of various beta-lactamases and penicillin-binding proteins. Upon acylation of these enzymes, the inhibitors are thought to undergo a ... [more ▼]

6-Beta-halogenopenicillanates are powerful, irreversible inhibitors of various beta-lactamases and penicillin-binding proteins. Upon acylation of these enzymes, the inhibitors are thought to undergo a structural rearrangement associated with the departure of the iodide and formation of a dihydrothiazine ring, but, to date, no structural evidence has proven this. 6-Beta-iodopenicillanic acid (BIP) is shown here to be an active antibiotic against various bacterial strains and an effective inhibitor of the class A beta-lactamase of Bacillus subtilis BS3 (BS3) and the D,D-peptidase of Actinomadura R39 (R39). Crystals of BS3 and of R39 were soaked with a solution of BIP and their structures solved at 1.65 and 2.2 A, respectively. The beta-lactam and the thiazolidine rings of BIP are indeed found to be fused into a dihydrothiazine ring that can adopt two stable conformations at these active sites. The rearranged BIP is observed in one conformation in the BS3 active site and in two monomers of the asymmetric unit of R39, and is observed in the other conformation in the other two monomers of the asymmetric unit of R39. The BS3 structure reveals a new mode of carboxylate interaction with a class A beta-lactamase active site that should be of interest in future inhibitor design. [less ▲]

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See detailCharacterisation of an Antilisterial Bacteriocin Produced by Lactobacillus sakei CWBI-B1365 Isolated from Raw Poultry Meat and Determination of Factors Controlling its Production
Dortu, C.; Fickers, P.; Franz, C.M.A.P. et al

in Probiotics and Antimicrobial Proteins (2009), 1

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See detailBacillus amyloliquefaciens GA1 as a source of potent antibiotics and other secondary metabolites for biocontrol of plant pathogens.
Arguelles-Arias, A.; Ongena, MARC ULg; Halimi, B. et al

in Microbial Cell Factories (2009), 8(1), 63

ABSTRACT: BACKGROUND: Phytopathogenic fungi affecting crop and post-harvested vegetables are a major threat to food production and food storage. To face these drawbacks, producers have become increasingly ... [more ▼]

ABSTRACT: BACKGROUND: Phytopathogenic fungi affecting crop and post-harvested vegetables are a major threat to food production and food storage. To face these drawbacks, producers have become increasingly dependent on agrochemicals. However, intensive use of these compounds has led to the emergence of pathogen resistance and severe negative environmental impacts. There are also a number of plant diseases for which chemical solutions are ineffective or non-existent as well as an increasing demand by consumers for pesticide-free food. Thus, biological control through the use of natural antagonistic microorganisms has emerged as a promising alternative to chemical pesticides for more rational and safe crop management. RESULTS: The genome of the plant-associated B. amyloliquefaciens GA1 was sample sequenced. Several gene clusters involved in the synthesis of biocontrol agents were detected. Four gene clusters were shown to direct the synthesis of the cyclic lipopeptides surfactin, iturin A and fengycin as well as the iron-siderophore bacillibactin. Beside these non-ribosomaly synthetised peptides, three additional gene clusters directing the synthesis of the antibacterial polyketides macrolactin, bacillaene and difficidin were identified. Mass spectrometry analysis of culture supernatants led to the identification of these secondary metabolites, hence demonstrating that the corresponding biosynthetic gene clusters are functional in strain GA1. In addition, genes encoding enzymes involved in synthesis and export of the dipeptide antibiotic bacilysin were highlighted. However, only its chlorinated derivative, chlorotetaine, could be detected in culture supernatants. On the contrary, genes involved in ribosome-dependent synthesis of bacteriocin and other antibiotic peptides were not detected as compared to the reference strain B. amyloliquefaciens FZB42. CONCLUSION: The production of all of these antibiotic compounds highlights B. amyloliquefaciens GA1 as a good candidate for the development of biocontrol agents. [less ▲]

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See detailSubstrate-induced inactivation of the Escherichia coli AmiD N-acetylmuramoyl-L-alanine amidase highlights a new strategy to inhibit this class of enzyme.
Pennartz, Anne; Genereux, Catherine ULg; Parquet, Claudine et al

in Antimicrobial Agents and Chemotherapy (2009), 53(7), 2991-7

In the eubacterial cell, the peptidoglycan is perpetually hydrolyzed throughout the cell cycle by different enzymes such as lytic transglycosylases, endopeptidases, and amidases. In Escherichia coli, four ... [more ▼]

In the eubacterial cell, the peptidoglycan is perpetually hydrolyzed throughout the cell cycle by different enzymes such as lytic transglycosylases, endopeptidases, and amidases. In Escherichia coli, four N-acetylmuramoyl-l-alanine amidases, AmiA, -B, -C, and -D, are present in the periplasm. AmiA, -B, and -C are soluble enzymes, whereas AmiD is a lipoprotein anchored in the outer membrane. To determine more precisely the specificity and the kinetic parameters of AmiD, we overproduced and purified the native His-tagged AmiD in the presence of detergent and a soluble truncated form of this enzyme by removing its signal peptide and the cysteine residue responsible for its lipidic anchorage. AmiD is a zinc metalloenzyme and is inactivated by a metal chelator such as EDTA. Native His-tagged and truncated AmiD hydrolyzes peptidoglycan fragments that have at least three amino acids in their peptide chains, and the presence of an anhydro function on the N-acetylmuramic acid is not essential for its activity. The soluble truncated AmiD exhibits a biphasic kinetic time course that can be explained by the inactivation of the enzyme by the substrate. This behavior highlights a new strategy to inhibit this class of enzymes. [less ▲]

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See detailActivities of ceftobiprole and other cephalosporins against extracellular and intracellular (THP-1 macrophages and keratinocytes) forms of methicillin-susceptible and methicillin-resistant Staphylococcus aureus.
Lemaire, Sandrine; Glupczynski, Youri; Duval, Valerie et al

in Antimicrobial Agents and Chemotherapy (2009), 53(6), 2289-97

Staphylococcus aureus is an opportunistic intracellular organism. Although they poorly accumulate in eukaryotic cells, beta-lactams show activity against intracellular methicillin (methicillin ... [more ▼]

Staphylococcus aureus is an opportunistic intracellular organism. Although they poorly accumulate in eukaryotic cells, beta-lactams show activity against intracellular methicillin (methicillin)-susceptible S. aureus (MSSA) if the exposure times and the drug concentrations are sufficient. Intraphagocytic methicillin-resistant S. aureus (MRSA) strains are susceptible to penicillins and carbapenems because the acidic pH favors the acylation of PBP 2a by these beta-lactams through pH-induced conformational changes. The intracellular activity (THP-1 macrophages and keratinocytes) of ceftobiprole, which shows almost similar in vitro activities against MRSA and MSSA in broth, was examined against a panel of hospital-acquired and community-acquired MRSA strains (MICs, 0.5 to 2.0 mg/liter at pH 7.4 and 0.25 to 1.0 mg/liter at pH 5.5) and was compared with its activity against MSSA isolates. The key pharmacological descriptors {relative maximal efficacy (E(max)), relative potency (the concentration causing a reduction of the inoculum halfway between E(0) and E(max) [EC(50)]), and static concentration (C(s))} were measured. All strains showed sigmoidal dose-responses, with E(max) being about a 1 log(10) CFU decrease from the postphagocytosis inoculum, and EC(50) and C(s) being 0.2 to 0.3x and 0.6 to 0.9x the MIC, respectively. Ceftobiprole effectively competed with Bocillin FL (a fluorescent derivative of penicillin V) for binding to PBP 2a at both pH 5.5 and pH 7.4. In contrast, cephalexin, cefuroxime, cefoxitin, or ceftriaxone (i) were less potent in PBP 2a competitive binding assays, (ii) showed only partial restoration of the activity against MRSA in broth at acidic pH, and (iii) were collectively less effective against MRSA in THP-1 macrophages and were ineffective in keratinocytes. The improved activity of ceftobiprole toward intracellular MRSA compared with the activities of conventional cephalosporins can be explained, at least in part, by its greater ability to bind to PBP 2a not only at neutral but also at acidic pH. [less ▲]

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