References of "Kerff, Frédéric"
     in
Bookmark and Share    
Full Text
Peer Reviewed
See detailIncreased antimicrobial resistance in a novel CMY-54 AmpC-type enzyme with a GluLeu217-218 insertion in the Ω-loop
Pérez-Llarena, Francisco José; Vázquez-Ucha, Juan Carlos; Kerff, Frédéric ULiege et al

in Microbial Drug Resistance : Mechanism, Epidemiology, & Disease (in press)

Detailed reference viewed: 78 (6 ULiège)
Full Text
Peer Reviewed
See detailCrystal Structure and Kinetic Analysis of the Class B3 Di-Zinc Metallo-β-Lactamase LRA-12 from an Alaskan Soil Metagenome
Rodríguez, María Margarita; Herman, Raphaël ULiege; Ghiglione, Barbara et al

in PLoS ONE (in press)

Detailed reference viewed: 45 (9 ULiège)
Full Text
See detailToRQuEMaDA: Tool for retrieving queried eubacteria, metadata and dereplicating assemblie
Léonard, Raphaël ULiege; Sirjacobs, Damien ULiege; Sauvage, Eric ULiege et al

Poster (2017, May 11)

The fast-growing number of available prokaryotic genomes, along with their uneven taxonomic distribution, is a problem when trying to assemble broadly sampled genome sets for phylogenomics and comparative ... [more ▼]

The fast-growing number of available prokaryotic genomes, along with their uneven taxonomic distribution, is a problem when trying to assemble broadly sampled genome sets for phylogenomics and comparative genomics. Indeed, most of the new genomes belong to the same subset of hyper-sampled phyla, such as Proteobacteria and Firmicutes, or even to single species, such as Escherichia coli (>3000 genomes as of March 2017), while the continuous flow of newly discovered phyla prompts for regular updates of in-house databases. This situation makes it difficult to maintain sets of representative genomes combining lesser known phyla, for which only few species are available, and sound subsets of highly abundant phyla. An automated method is required but none are publicly available. In this work, the kmer composition of DNA sequences, in conjunction with quality metrics for publicly available assemblies, was used to develop an automated approach for selecting a high-quality subset of representative genomes without redundancy by using our hybrid divide-and-conquer / greedy clustering method. [less ▲]

Detailed reference viewed: 18 (4 ULiège)
Full Text
Peer Reviewed
See detailCrystal structure and biochemical characterization of the transmembrane PAP2 type phosphatidylglycerol phosphate phosphatase from Bacillus subtilis.
El Ghachi, Meriem ULiege; Howe, Nicole; Auger, Rodolphe et al

in Cellular and Molecular Life Sciences : CMLS (2017)

Type 2 phosphatidic acid phosphatases (PAP2s) can be either soluble or integral membrane enzymes. In bacteria, integral membrane PAP2s play major roles in the metabolisms of glycerophospholipids ... [more ▼]

Type 2 phosphatidic acid phosphatases (PAP2s) can be either soluble or integral membrane enzymes. In bacteria, integral membrane PAP2s play major roles in the metabolisms of glycerophospholipids, undecaprenyl-phosphate (C55-P) lipid carrier and lipopolysaccharides. By in vivo functional experiments and biochemical characterization we show that the membrane PAP2 coded by the Bacillus subtilis yodM gene is the principal phosphatidylglycerol phosphate (PGP) phosphatase of B. subtilis. We also confirm that this enzyme, renamed bsPgpB, has a weaker activity on C55-PP. Moreover, we solved the crystal structure of bsPgpB at 2.25 A resolution, with tungstate (a phosphate analog) in the active site. The structure reveals two lipid chains in the active site vicinity, allowing for PGP substrate modeling and molecular dynamic simulation. Site-directed mutagenesis confirmed the residues important for substrate specificity, providing a basis for predicting the lipids preferentially dephosphorylated by membrane PAP2s. [less ▲]

Detailed reference viewed: 37 (12 ULiège)
Full Text
Peer Reviewed
See detailStructural models of the different trimers present in the core of phycobilisomes from Gracilaria chilensis based on crystal structures and sequences.
Dagnino-Leone, Jorge; Figueroa, Maximiliano; Mella, Claudia et al

in PLoS ONE (2017), 12(5), 0177540

Phycobilisomes (PBS) are accessory light harvesting protein complexes that directionally transfer energy towards photosystems. Phycobilisomes are organized in a central core and rods radiating from it ... [more ▼]

Phycobilisomes (PBS) are accessory light harvesting protein complexes that directionally transfer energy towards photosystems. Phycobilisomes are organized in a central core and rods radiating from it. Components of phycobilisomes in Gracilaria chilensis (Gch) are Phycobiliproteins (PBPs), Phycoerythrin (PE), and Phycocyanin (PC) in the rods, while Allophycocyanin (APC) is found in the core, and linker proteins (L). The function of such complexes depends on the structure of each component and their interaction. The core of PBS from cyanobacteria is mainly composed by cylinders of trimers of alpha and beta subunits forming heterodimers of Allophycocyanin, and other components of the core including subunits alphaII and beta18. As for the linkers, Linker core (LC) and Linker core membrane (LCM) are essential for the final emission towards photoreaction centers. Since we have previously focused our studies on the rods of the PBS, in the present article we investigated the components of the core in the phycobilisome from the eukaryotic algae, Gracilaria chilensis and their organization into trimers. Transmission electron microscopy provided the information for a three cylinders core, while the three dimensional structure of Allophycocyanin purified from Gch was determined by X-ray diffraction method and the biological unit was determined as a trimer by size exclusion chromatography. The protein sequences of all the components of the core were obtained by sequencing the corresponding genes and their expression confirmed by transcriptomic analysis. These subunits have seldom been reported in red algae, but not in Gracilaria chilensis. The subunits not present in the crystallographic structure were modeled to build the different composition of trimers. This article proposes structural models for the different types of trimers present in the core of phycobilisomes of Gch as a first step towards the final model for energy transfer in this system. [less ▲]

Detailed reference viewed: 23 (0 ULiège)
Full Text
See detailStructure of the classe D β-lactamase OXA-29, an original dimer
Kerff, Frédéric ULiege

Conference (2016, September 29)

Detailed reference viewed: 15 (2 ULiège)
See detailCHARACTERISATION OF THE STRUCTURAL, DYNAMIC AND AGGREGATION PROPERTIES OF THE W64R AMYLOIDOGENIC MUTANT OF LYSOZYME
Vettore, Nicola; Kumita, Janet; Moray, Joël ULiege et al

Poster (2016, September 15)

Detailed reference viewed: 31 (6 ULiège)
Full Text
Peer Reviewed
See detailKinetic Studies on CphA Mutants Reveal the Role of the P158-P172 Loop in Activity versus Carbapenems.
Bottoni, Carlo; Perilli, Mariagrazia; Marcoccia, Francesca et al

in Antimicrobial Agents and Chemotherapy (2016), 60(5), 3123-6

Site-directed mutagenesis of CphA indicated that prolines in the P158-P172 loop are essential for the stability and the catalytic activity of subclass B2 metallo-beta-lactamases against carbapenems. The ... [more ▼]

Site-directed mutagenesis of CphA indicated that prolines in the P158-P172 loop are essential for the stability and the catalytic activity of subclass B2 metallo-beta-lactamases against carbapenems. The sequential substitution of proline led to a decrease of the catalytic efficiency of the variant compared to the wild-type (WT) enzyme but also to a higher affinity for the binding of the second zinc ion. [less ▲]

Detailed reference viewed: 41 (11 ULiège)
Full Text
Peer Reviewed
See detailFrom "an enzyme able to destroy penicillin" to Carbapenemases: 70 Years of Beta-lactamase Misbehaviour
Frère, Jean-Marie ULiege; Sauvage, Eric ULiege; Kerff, Frederic ULiege

in Current drug targets (2016)

As early as 1940, Abraham and Chain described "an enzyme able to destroy penicillin". In the late 1940's, penicillin-resistant strains of Staphylococcus aureus were found to be a clinical problem. They ... [more ▼]

As early as 1940, Abraham and Chain described "an enzyme able to destroy penicillin". In the late 1940's, penicillin-resistant strains of Staphylococcus aureus were found to be a clinical problem. They produced a penicillinase that could hydrolyze the amide bond in the beta-lactam ring. Later, an enzyme mediated by an R-factor was isolated from Enterobacteriaceae. Methicillin and cephalosporins, both very poor substrates of the S. aureus enzyme, were found to be sensitive to this new enzyme. Third generation cephalosporins appeared to solve the problem, but further enzymes were selected that exhibited extended spectra and could for instance hydrolyze cefotaxime and/or ceftazidime. The discovery of carbapenems constituted a major advance for our antimicrobial arsenal: they inactivated most of the essential penicillin binding proteins effectively and escaped the activity of nearly all known beta-lactamases. However, the metallo-beta-lactamases, which had not been recognised as a major danger before 1990, were found to act as effective carbapenemases and started to spread in a worrying way. Moreover, carbapenem-hydrolyzing enzymes were found in each of the 3 classes of active-site serine beta-lactamases. [less ▲]

Detailed reference viewed: 83 (36 ULiège)
Full Text
Peer Reviewed
See detailThe CebE/MsiK Transporter is a Doorway to the Cello-oligosaccharide-mediated Induction of Streptomyces scabies Pathogenicity
Jourdan, Samuel ULiege; Francis, Isolde; Kim, Min et al

in Scientific Reports (2016)

Detailed reference viewed: 35 (13 ULiège)
Full Text
Peer Reviewed
See detailKinetic Study of Laboratory Mutants of NDM-1 Metallo-beta-Lactamase and the Importance of an Isoleucine at Position 35.
Marcoccia, Francesca; Bottoni, Carlo; Sabatini, Alessia et al

in Antimicrobial agents and chemotherapy (2016), 60(4), 2366-72

Two laboratory mutants of NDM-1 were generated by replacing the isoleucine at position 35 with threonine and serine residues: the NDM-1(I35T)and NDM-1(I35S)enzymes. These mutants were well characterized ... [more ▼]

Two laboratory mutants of NDM-1 were generated by replacing the isoleucine at position 35 with threonine and serine residues: the NDM-1(I35T)and NDM-1(I35S)enzymes. These mutants were well characterized, and their kinetic parameters were compared with those of the NDM-1 wild type. Thekcat,Km, andkcat/Kmvalues calculated for the two mutants were slightly different from those of the wild-type enzyme. Interestingly, thekcat/Kmof NDM-1(I35S)for loracarbef was about 14-fold higher than that of NDM-1. Far-UV circular dichroism (CD) spectra of NDM-1 and NDM-1(I35T)and NDM-1(I35S)enzymes suggest local structural rearrangements in the secondary structure with a marked reduction of alpha-helix content in the mutants. [less ▲]

Detailed reference viewed: 41 (16 ULiège)
Full Text
See detailOn the LZ distance for dereplicating redundant prokaryotic genomes
Léonard, Raphaël ULiege; Baurain, Denis ULiege; Kerff, Frédéric ULiege et al

Poster (2015, December 07)

The fast-growing number of available prokaryotic genomes, along with their uneven taxonomic distribution, is a prob- lem when trying to assemble broadly sampled genome sets for phylogenomics and ... [more ▼]

The fast-growing number of available prokaryotic genomes, along with their uneven taxonomic distribution, is a prob- lem when trying to assemble broadly sampled genome sets for phylogenomics and comparative genomics. Indeed, most of the new genomes belong to the same subset of hyper-sampled phyla, such as Proteobacteria and Firmicutes, or even to single species, such as Escherichia coli (almost 2000 genomes as of Sept 2015), while the continuous flow of newly discovered phyla prompts for regular updates. This situation makes it difficult to maintain sets of representative genomes combining lesser known phyla, for which only few species are available, and sound subsets of highly abundant phyla. An automated straightforward method is required but none are publicly available. The LZ distance, in conjunction with the quality of the annotations, can be used to create an automated approach for selecting a subset of represen- tative genomes without redundancy. We are planning to release this tool on a website that will be made publicly available. [less ▲]

Detailed reference viewed: 41 (13 ULiège)
Full Text
See detailSPECIFICITY OF CLASS I TAGATOSE 1,6-BISPHOSPHATE ALDOLASE ENHANCED TOWARD TAGATOSE 1,6-BISPHOPHATE
Freichels, Régine ULiege; Delmarcelle, Michaël ULiege; Colarusso, Andrea et al

Poster (2015, July)

Class I tagatose 1,6-bisphosphate aldolase catalyzes the reversible condensation of dihydroxyacetone phosphate and glyceraldehyde 3-phosphate to produce four D-ketohexoses 1,6-bisphosphate: D-tagatose 1,6 ... [more ▼]

Class I tagatose 1,6-bisphosphate aldolase catalyzes the reversible condensation of dihydroxyacetone phosphate and glyceraldehyde 3-phosphate to produce four D-ketohexoses 1,6-bisphosphate: D-tagatose 1,6-bisphosphate, D-fructose 1,6-bisphosphate, D-psicose 1,6-bisphosphate and D-sorbose 1,6-bisphosphate. These four sugars are diastereoisomers and differs from each other in their stereochemistry at carbons 3 and 4. The structure determination of three class I tagatose 1,6-bisphosphate aldolases has afforded new insight into their catalytic mechanism as well as their evolution. However, the determinant(s) that allow(s) the enzyme to be so unspecific at carbon 4 have remains unknown. The aim of this project is focused on the characterization of the structural features of tagatose 1,6-bisphosphate aldolases that determine the specificity of the enzyme towards tagatose versus fructose 1,6-bisphosphate (carbon C4). [less ▲]

Detailed reference viewed: 84 (8 ULiège)
Full Text
See detailCharacterization of YbjG, a pyrophosphate phosphatase from E. coli involved in the lipid carrier undecaprenyl phosphate metabolism
Delbrassine, François ULiege; Auger, Rodolphe; El Ghachi, Meriem ULiege et al

Poster (2015, June 08)

•Background Undecaprenyl phosphate (C55-P) is an essential lipid carrier involved in the biosynthesis of cell surface carbohydrate polymers such as the peptidoglycan. C55-P is the result of the ... [more ▼]

•Background Undecaprenyl phosphate (C55-P) is an essential lipid carrier involved in the biosynthesis of cell surface carbohydrate polymers such as the peptidoglycan. C55-P is the result of the dephosphorylation of the undecaprenyl pyrophosphate (C55-PP) by specific phosphatases. In Escherichia coli this dephosphorylation can be performed by four integral membrane proteins, BacA, and three members of the type 2 phosphatidic acid phosphatase family (PAP2), PgpB, YbjG, and LpxT. •Objectives The aim of this project is to characterize YbjG and contributes to the understanding of the physiological role and mechanism of action of this enzyme in the C55-P metabolism. The C55-PP phosphatases could become an interesting target in the search for new molecules with antibacterial activity. •Methods In parallel the stability of YbjG and its activity against C15-PP were assessed in 94 different detergents. Moreover the enzymatic activity of YbjG was studied: substrate specificity, optimum pH and temperature, effect of detergent concentration. •Conclusions For the first time, YbjG has been purified and we show its ability to dephosphorylate C15-PP, DGPP and C55-PP in vitro with respectively decreasing efficiency. No activity has been detected on five other potential substrates (PPi, PA, C5-PP, G6P & PNPP). The phosphatase activity on C15-PP is maximum at pH 6,5 and 25 °C. Moreover Cymal6, LMNG, & ωUDM are good detergent both for the stability and the C15-PP phosphatase activity of YbjG, but approximately half of the 94 tested detergents show C15-PP phosphatase activity on the qualitative enzymatic test. [less ▲]

Detailed reference viewed: 50 (5 ULiège)
Full Text
Peer Reviewed
See detailDeciphering the metabolism of polyprenyl-phosphate: The universal glycan lipid carrier at the membrane frontier
Manat, Guillaume; Roure, Sophie; El Ghachi, Meriem ULiege et al

Poster (2015, June)

Detailed reference viewed: 19 (3 ULiège)
See detailRésistance aux antibiotiques : le retour à l’ère prébiotique ?
Galleni, Moreno ULiege; Kerff, Frédéric ULiege; Rigali, Sébastien ULiege

Conference (2015, February 05)

Aujourd’hui, la résistance des bactéries aux antibiotiques relève d'une préoccupation croissante dans le domaine de la santé publique et s'impose plus que jamais comme une priorité. Ce problème a un coût ... [more ▼]

Aujourd’hui, la résistance des bactéries aux antibiotiques relève d'une préoccupation croissante dans le domaine de la santé publique et s'impose plus que jamais comme une priorité. Ce problème a un coût, sociétal et économique en Europe: 25.000 décès annuels par septicémie et 1,5 milliard d’euros d’augmentation du coût des traitements. Bien que le besoin de nouveaux agents antibactériens en milieu clinique est urgent, seules deux nouvelles classes d’antibiotiques ont pu être proposées durant ces 30 dernières années. En effet, la découverte et le développement de nouveaux antibiotiques posent des défis scientifiques, cliniques et financiers importants. [less ▲]

Detailed reference viewed: 171 (17 ULiège)
Full Text
Peer Reviewed
See detailStructural and Kinetic Insights into the "Ceftazidimase" Behavior of the Extended-Spectrum beta-Lactamase CTX-M-96.
Ghiglione, Barbara; Rodriguez, Maria Margarita; Herman, Raphaël ULiege et al

in Biochemistry (2015), 54(32), 5072-82

Diversification of the CTX-M beta-lactamases led to the emergence of variants responsible for decreased susceptibility to ceftazidime, like the Asp240Gly-harboring "ceftazidimases". We solved the ... [more ▼]

Diversification of the CTX-M beta-lactamases led to the emergence of variants responsible for decreased susceptibility to ceftazidime, like the Asp240Gly-harboring "ceftazidimases". We solved the crystallographic structure of the Asp240Gly variant CTX-M-96 at 1.2 A and evaluated the role of Asp240 in the activity toward oxyimino-cephalosporins through simulated models and kinetics. There seem to be subtle changes in the conformation of the active site cavity of CTX-M-96, compared to enzyme variants harboring the Asp240, and these small rearrangements could be due to localized shifts in the environment of the beta3 strand. According to the crystallographic evidence, CTX-M-96 presents a "compact" active site, which in spite of its reduced cavity seems to allow the proper interaction with oxyimino-cephalosporins, as suggested by simulated models. The term "ceftazidimases" that is currently applied for the Asp240Gly-harboring CTX-M variants should be used carefully. Structural differences between CTX-M harboring the Asp240Gly mutation (and also probably others like those at Pro167) do not seem to be conclusive to determine the "ceftazidimase" behavior observed in vivo, which is in turn partially supported by the mild improvement in the catalytic efficiency toward ceftazidime by CTX-M-96 and similar enzymes, compared to "parental" Asp240-harboring variants. In addition, it is observed that alterations in OmpF expression could act synergistically with CTX-M-96 for yielding clinical resistance toward ceftazidime. We therefore propose that the observed resistance in vivo is due to the sum of synergic mechanisms, and the term "cefotaximases associated with ceftazidime resistance" could be conveniently used to describe CTX-M harboring the Asp240Gly substitution. [less ▲]

Detailed reference viewed: 44 (12 ULiège)
Full Text
Peer Reviewed
See detailMembrane Topology and Biochemical Characterization of the Escherichia coli BacA Undecaprenyl-Pyrophosphate Phosphatase.
Manat, Guillaume; El Ghachi, Meriem ULiege; Auger, Rodolphe et al

in PloS one (2015), 10(11), 0142870

Several integral membrane proteins exhibiting undecaprenyl-pyrophosphate (C55-PP) phosphatase activity were previously identified in Escherichia coli that belonged to two distinct protein families: the ... [more ▼]

Several integral membrane proteins exhibiting undecaprenyl-pyrophosphate (C55-PP) phosphatase activity were previously identified in Escherichia coli that belonged to two distinct protein families: the BacA protein, which accounts for 75% of the C55-PP phosphatase activity detected in E. coli cell membranes, and three members of the PAP2 phosphatidic acid phosphatase family, namely PgpB, YbjG and LpxT. This dephosphorylation step is required to provide the C55-P carrier lipid which plays a central role in the biosynthesis of various cell wall polymers. We here report detailed investigations of the biochemical properties and membrane topology of the BacA protein. Optimal activity conditions were determined and a narrow-range substrate specificity with a clear preference for C55-PP was observed for this enzyme. Alignments of BacA protein sequences revealed two particularly well-conserved regions and several invariant residues whose role in enzyme activity was questioned by using a site-directed mutagenesis approach and complementary in vitro and in vivo activity assays. Three essential residues Glu21, Ser27, and Arg174 were identified, allowing us to propose a catalytic mechanism for this enzyme. The membrane topology of the BacA protein determined here experimentally did not validate previous program-based predicted models. It comprises seven transmembrane segments and contains in particular two large periplasmic loops carrying the highly-conserved active site residues. Our data thus provide evidence that all the different E. coli C55-PP phosphatases identified to date (BacA and PAP2) catalyze the dephosphorylation of C55-PP molecules on the same (outer) side of the plasma membrane. [less ▲]

Detailed reference viewed: 18 (1 ULiège)