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See detailInsertion of domain III of Bacillus subtilis and Bacillus amyloliquefaciens PBP4a in the Bacillus licheniformis BlaP β-lactamase to study the binding to peptidoglycan and whole bacteria
Van Der Heiden, Edwige ULg; Hoebreck, Charline ULg; Freichels, Régine ULg et al

Poster (2013, October 03)

Domain III of Bacillus subtilis and B. amyloliquefaciens DD-endopeptidase PBP4a was introduced in the BlaP beta-lactamse of Bacillus licheniformis. Domain III of Bacillus licheniformis binds to ... [more ▼]

Domain III of Bacillus subtilis and B. amyloliquefaciens DD-endopeptidase PBP4a was introduced in the BlaP beta-lactamse of Bacillus licheniformis. Domain III of Bacillus licheniformis binds to peptidoglycan of Bacillus subtilis 168 and to itself whole cells. [less ▲]

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See detailA Pathway closely related to the D-tagatose pathway of Gram-Negative Enterobacteria Identified in the Gram-Positive Bacterium Bacillus licheniformis
Van Der Heiden, Edwige ULg; Delmarcelle, Michaël ULg; Lebrun, Sarah ULg et al

Poster (2013, June)

We report the first identification of a gene cluster involved in d-tagatose catabolism in Bacillus licheniformis. The pathway is closely related to the d-tagatose pathway of the Gram-negative bacterium ... [more ▼]

We report the first identification of a gene cluster involved in d-tagatose catabolism in Bacillus licheniformis. The pathway is closely related to the d-tagatose pathway of the Gram-negative bacterium Klebsiella oxytoca, in contrast to the d-tagatose 6-phosphate pathway described in the Gram-positive bacterium Staphylococcus aureus. [less ▲]

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See detailA Pathway closely related to the D-tagatose pathway of Gram-Negative Enterobacteria Identified in the Gram-Positive Bacterium Bacillus licheniformis
Van Der Heiden, Edwige ULg; Delmarcelle, Michaël ULg; Lebrun, Sarah ULg et al

in Applied and Environmental microbiology (2013), 79(11), 3511-3515

We report the first identification of a gene cluster involved in d-tagatose catabolism in Bacillus licheniformis. The pathway is closely related to the d-tagatose pathway of the Gram-negative bacterium ... [more ▼]

We report the first identification of a gene cluster involved in d-tagatose catabolism in Bacillus licheniformis. The pathway is closely related to the d-tagatose pathway of the Gram-negative bacterium Klebsiella oxytoca, in contrast to the d-tagatose 6-phosphate pathway described in the Gram-positive bacterium Staphylococcus aureus. [less ▲]

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See detailBiochemical and Structural studies of the type I tagatose bisphosphate aldolases
Freichels, Régine ULg; Guarino, Carla; Delmarcelle, Michaël ULg et al

Poster (2013, February 26)

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See detailThe attachment of Bacillus amyloliquefaciens FZB42 to tomato roots is impaired in a mutant devoid of GalM and PBP4a.
Van der Heiden, Edwige; Jourdan, Emmanuel ULg; Delmarcelle, Michaël ULg et al

Poster (2011, June 20)

In vivo experiments on tomato (Lycopersicon esculentum) roots have been performed: drench of 10-day hydroponic cultures with bacterial suspensions. A second identical treatment was applied one week later ... [more ▼]

In vivo experiments on tomato (Lycopersicon esculentum) roots have been performed: drench of 10-day hydroponic cultures with bacterial suspensions. A second identical treatment was applied one week later and after 30 days of culture, the plants were collected and the bacteria detached from a precise weight of roots were diluted, plated and counted. The mutant devoid of both GalM and PBP4a (encoded by the galM and dacC operon) is affected in its capacity to colonize the tomato roots. [less ▲]

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See detailStructure of the archaeal pab87 peptidase reveals a novel self-compartmentalizing protease family.
Delfosse, Vanessa; Girard, Eric; Birck, Catherine et al

in PLoS ONE (2009), 4(3), 4712

Self-compartmentalizing proteases orchestrate protein turnover through an original architecture characterized by a central catalytic chamber. Here we report the first structure of an archaeal member of a ... [more ▼]

Self-compartmentalizing proteases orchestrate protein turnover through an original architecture characterized by a central catalytic chamber. Here we report the first structure of an archaeal member of a new self-compartmentalizing protease family forming a cubic-shaped octamer with D(4) symmetry and referred to as CubicO. We solved the structure of the Pyrococcus abyssi Pab87 protein at 2.2 A resolution using the anomalous signal of the high-phasing-power lanthanide derivative Lu-HPDO3A. A 20 A wide channel runs through this supramolecular assembly of 0.4 MDa, giving access to a 60 A wide central chamber holding the eight active sites. Surprisingly, activity assays revealed that Pab87 degrades specifically d-amino acid containing peptides, which have never been observed in archaea. Genomic context of the Pab87 gene showed that it is surrounded by genes involved in the amino acid/peptide transport or metabolism. We propose that CubicO proteases are involved in the processing of d-peptides from environmental origins. [less ▲]

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See detailIND-6, a Highly Divergent IND-type Metallo-{beta}-lactamase from Chryseobacterium indologenes strain 597 isolated in Burkina Faso.
Zeba, Boularé; De Luca, Filomena; Dubus, Alain et al

in Antimicrobial Agents and Chemotherapy (2009)

Chryseobacterium and other genera belonging to the family Flavobacteriaceae include organisms that can behave as human pathogens and are known to cause different kinds of infections. Several ... [more ▼]

Chryseobacterium and other genera belonging to the family Flavobacteriaceae include organisms that can behave as human pathogens and are known to cause different kinds of infections. Several Flavobacteriaceae, including Chryseobacterium indologenes, are naturally resistant to beta-lactam antibiotics (including carbapenems), due to the production of a resident metallo-beta-lactamase. Although C. indologenes presently constitutes a limited clinical threat, the incidence of infections caused by this organism is increasing in some settings, where isolates that exhibit multidrug resistance phenotypes (that include aminoglycosides and quinolones) have been described. Here we report the identification and characterization of a new IND-type variant from a C. indologenes isolate from Burkina Faso resistant to beta-lactams and aminoglycosides. Its sequence identity with other IND-type metallo-beta-lactamases ranges from 72 to 90% (with IND-4 and IND-5, respectively). The purified enzyme exhibited N-terminal heterogeneity and a post-translational modification, consisting in the presence of a pyroglutamate residue at the N-terminus. IND-6 shows a broad substrate profile, with overall higher turnover rates than IND-5 and higher activities than IND-2 and IND-5 against ceftazidime and cefepime. [less ▲]

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See detailSpecificity and reversibility of the transpeptidation reaction catalyzed by the Streptomyces R61 D-Ala-D-Ala peptidase
Rhazi, Noureddine ULg; Delmarcelle, Michaël ULg; Sauvage, Eric ULg et al

in Protein Science (2005), 14(11), 2922-2928

The specificity of the Streptomyces R61 penicillin-sensitive D-Ala-D-Ala peptidase has been re-examined with the help of synthetic substrates. The products of the transpeptidation reactions obtained with ... [more ▼]

The specificity of the Streptomyces R61 penicillin-sensitive D-Ala-D-Ala peptidase has been re-examined with the help of synthetic substrates. The products of the transpeptidation reactions obtained with Gly-L-Xaa dipeptides as acceptor substrates are themselves poor substrates of the enzyme. This is in apparent contradiction with the classically accepted specificity rules for D-Ala-D-Ala peptidases. The Gly-L-Xaa dipeptide is regenerated by both the hydrolysis and transpeptidation reactions. The latter reaction is observed when another Gly-L-Xaa peptide or D-Alanine are supplied as acceptors. Utilization of substrates in which the terminal -COO(-) group has been esterified or amidated shows that a free carboxylate is not an absolute prerequisite for activity. The results are discussed in the context of the expected reversibility of the transpeptidation reaction. [less ▲]

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See detailInactivation of bacterial DD-peptidase by beta-sultams.
Llinas, Antonio; Ahmed, Naveed; Cordaro, Massimiliano et al

in Biochemistry (2005), 44(21), 7738-46

N-Acyl-beta-sultams are time-dependent, irreversible active site-directed inhibitors of Streptomyces R61 DD-peptidase. The rate of inactivation is first order with respect to beta-sultam concentration ... [more ▼]

N-Acyl-beta-sultams are time-dependent, irreversible active site-directed inhibitors of Streptomyces R61 DD-peptidase. The rate of inactivation is first order with respect to beta-sultam concentration, and the second-order rate constants show a dependence on pH similar to that for the hydrolysis of a substrate. Inactivation is due to the formation of a stable 1:1 enzyme-inhibitor complex as a result of the active site serine being sulfonylated by the beta-sultam as shown by ESI-MS analysis and by X-ray crystallography. A striking feature of the sulfonyl enzyme is that the inhibitor is not bound to the oxyanion hole but interacts extensively with the "roof" of the active site where the Arg 285 is located. [less ▲]

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See detailSpecificity inversion of Ochrobactrum anthropi D-aminopeptidase to a D,D-carboxypeptidase with new penicillin binding activity by directed mutagenesis
Delmarcelle, Michaël ULg; Boursoit, Marie-Caroline; Filée, Patrice ULg et al

in Protein Science : A Publication of the Protein Society (2005), 14

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See detailThe fate of the Blal repressor during the induction of the Bacillus licheniformis BlaP beta-lactamase
Filée, Patrice ULg; Benlafya, Kamal; Delmarcelle, Michaël ULg et al

in Molecular Microbiology (2002), 44(3), 685-694

The induction of the Staphylococcus aureus BlaZ and Bacillus licheniformis 749/l BIaP beta-lactamases by beta-lactam antibiotics occurs according to similar processes. In both bacteria, the products of ... [more ▼]

The induction of the Staphylococcus aureus BlaZ and Bacillus licheniformis 749/l BIaP beta-lactamases by beta-lactam antibiotics occurs according to similar processes. In both bacteria, the products of the blal and blaR1 genes share a high degree of sequence homology and act as repressors and penicillin-sensory transducers respectively. It has been shown in S. aureus that the Blal repressor, which controls the expression of BlaZ negatively, is degraded after the addition of the inducer. In the present study, we followed the fate of Blal during beta-lactamase induction in B. licheniformis 749/l and in a recombinant Bacillus subtilis 168 strain harbouring the pDML995 plasmid, which carries the B. licheniformis blaP, blal and blaR1 genes. In contrast to the situation in B. licheniformis 749/l, beta-lactamase induction in B. subtilis 168/pDML995 was not correlated with the proteolysis of Blal. To exclude molecular variations undetectable by SDS-PAGE, two-dimensional gel electrophoresis was performed with cellular extracts from uninduced or induced B. subtilis 168/pDML995 cells. No variation in the Blal isoelectric point was observed in induced cells, whereas the DNA-binding property was lost. Cross-linking experiments with dithiobis(succimidylpropionate) confirmed that, in uninduced recombinant B. subtilis cells, Blat was present as a homodimer and that this situation was not altered in induced conditions. This latter result is incompatible with a mechanism of inactivation of Blal by proteolysis and suggests that the inactivation of Blal results from a non-covalent modification by a co-activator and that the subsequent proteolysis of Blal might be a secondary phenomenon. In addition to the presence of this co-activator, our results show that the presence of penicillin stress is also required for full induction of beta-lactamase biosynthesis. [less ▲]

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See detailUse of an Alfexpress DNA Sequencer to Analyze Protein-Nucleic Acid Interactions by Band Shift Assay
Filée, Patrice ULg; Delmarcelle, Michaël ULg; Thamm, Iris ULg et al

in BioTechniques (2001), 30(5), 1044-81050-1

Gel retardation analysis, or band shift assay, is technically the simplest method to investigate protein-nucleic acid interactions. In this report, we describe a nonradioactive band shift assay using a ... [more ▼]

Gel retardation analysis, or band shift assay, is technically the simplest method to investigate protein-nucleic acid interactions. In this report, we describe a nonradioactive band shift assay using a fluorescent DNA target and an ALFexpress automatic DNA sequencer in place of the current method that utilizes radioactively end-labeled DNA target and a standard electrophoresis unit. In our study, the dsDNA targets were obtained by annealing two synthetic oligonucleotides or by PCR. In both cases, a molecule of indodicarbocyanine (CY5) was attached at the 5' OH end of one of the two synthetic oligonucleotides, with a ratio of one molecule of fluorescent dye per molecule of dsDNA. To demonstrate the feasibility of this new band shift assay method, the DNA-binding proteins selected as models were the BlaI and AmpR repressors, which are involved in the induction of the Bacillus licheniformis 749/I and Citrobacter freundii beta-lactamases, respectively. The results show that the use of an automatic DNA sequencer allows easy gel retardation analysis and provides a fast, sensitive, and quantitative method. The ALFexpress DNA sequencer has the same limit of detection as a laser fluorescence scanner and can be used instead of a FluorImager or a Molecular Imager. [less ▲]

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See detailCrystal structure of a D-aminopeptidase from Ochrobactrum anthropi, a new member of the 'penicillin-recognizing enzyme' family.
Bompard-Gilles, C.; Remaut, H.; Villeret, V. et al

in Structure (2000), 8(9), 971-80

BACKGROUND: beta-Lactam compounds are the most widely used antibiotics. They inactivate bacterial DD-transpeptidases, also called penicillin-binding proteins (PBPs), involved in cell-wall biosynthesis ... [more ▼]

BACKGROUND: beta-Lactam compounds are the most widely used antibiotics. They inactivate bacterial DD-transpeptidases, also called penicillin-binding proteins (PBPs), involved in cell-wall biosynthesis. The most common bacterial resistance mechanism against beta-lactam compounds is the synthesis of beta-lactamases that hydrolyse beta-lactam rings. These enzymes are believed to have evolved from cell-wall DD-peptidases. Understanding the biochemical and mechanistic features of the beta-lactam targets is crucial because of the increasing number of resistant bacteria. DAP is a D-aminopeptidase produced by Ochrobactrum anthropi. It is inhibited by various beta-lactam compounds and shares approximately 25% sequence identity with the R61 DD-carboxypeptidase and the class C beta-lactamases. RESULTS: The crystal structure of DAP has been determined to 1.9 A resolution using the multiple isomorphous replacement (MIR) method. The enzyme folds into three domains, A, B and C. Domain A, which contains conserved catalytic residues, has the classical fold of serine beta-lactamases, whereas domains B and C are both antiparallel eight-stranded beta barrels. A loop of domain C protrudes into the substrate-binding site of the enzyme. CONCLUSIONS: Comparison of the biochemical properties and the structure of DAP with PBPs and serine beta-lactamases shows that although the catalytic site of the enzyme is very similar to that of beta-lactamases, its substrate and inhibitor specificity rests on residues of domain C. DAP is a new member of the family of penicillin-recognizing proteins (PRPs) and, at the present time, its enzymatic specificity is clearly unique. [less ▲]

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