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Accueil > Départements > Biochimie, Biophysique et Biologie Structurale > Herman VAN TILBEURGH : Fonction et Architecture des Assemblages Macromoléculaires

Les publications

2018


  • L. Ahmad, S. Plancqueel, V. Dubosclard, N. Lazar, W. Ghattas, I. Li de la Sierra-Gallay, H. van Tilbeurgh, et L. Salmon, « Crystal structure of phosphomannose isomerase from Candida albicans complexed with 5-phospho-d-arabinonhydrazide », FEBS letters, avr. 2018.
    Résumé : Type I phosphomannose isomerases (PMIs) are zinc-dependent monofunctional metalloenzymes catalysing the reversible isomerization of d-mannose 6-phosphate to d-fructose 6-phosphate. 5-Phospho-d-arabinonhydrazide (5PAHz), designed as an analogue of the enediolate high-energy intermediate, strongly inhibits PMI from Candida albicans (CaPMI). In this study, we report the 3D crystal structure of CaPMI complexed with 5PAHz at 1.85 Å resolution. The high-resolution structure suggests that Glu294 is the catalytic base that transfers a proton between the C1 and C2 carbon atoms of the substrate. Bidentate coordination of the inhibitor explains the stereochemistry of the isomerase activity, as well as the absence of both anomerase and C2-epimerase activities for Type I PMIs. A detailed mechanism of the reversible isomerization is proposed.
    Mots-clés : B3S, Candida albicans, enzyme mechanism, FAAM, inhibitor, phosphomannose isomerase, zinc metalloenzyme.


  • Z. Edoo, L. Iannazzo, F. Compain, I. Li de la Sierra Gallay, H. van Tilbeurgh, M. Fonvielle, F. Bouchet, E. Le Run, J. - L. Mainardi, M. Arthur, M. Ethève-Quelquejeu, et J. - E. Hugonnet, « Synthesis of avibactam derivatives and activity on β-lactamases and peptidoglycan biosynthesis enzymes of mycobacteria », Chemistry - A European Journal, mars 2018.

  • S. Missoury, S. Plancqueel, I. Li de la Sierra-Gallay, W. Zhang, D. Liger, D. Durand, R. Dammak, B. Collinet, et H. van Tilbeurgh, « The structure of the TsaB/TsaD/TsaE complex reveals an unexpected mechanism for the bacterial t6A tRNA-modification », Nucleic Acids Research, mai 2018.
    Résumé : The universal N6-threonylcarbamoyladenosine (t6A) modification at position A37 of ANN-decoding tRNAs is essential for translational fidelity. In bacteria the TsaC enzyme first synthesizes an l-threonylcarbamoyladenylate (TC-AMP) intermediate. In cooperation with TsaB and TsaE, TsaD then transfers the l-threonylcarbamoyl-moiety from TC-AMP onto tRNA. We determined the crystal structure of the TsaB-TsaE-TsaD (TsaBDE) complex of Thermotoga maritima in presence of a non-hydrolysable AMPCPP. TsaE is positioned at the entrance of the active site pocket of TsaD, contacting both the TsaB and TsaD subunits and prohibiting simultaneous tRNA binding. AMPCPP occupies the ATP binding site of TsaE and is sandwiched between TsaE and TsaD. Unexpectedly, the binding of TsaE partially denatures the active site of TsaD causing loss of its essential metal binding sites. TsaE interferes in a pre- or post-catalytic step and its binding to TsaBD is regulated by ATP hydrolysis. This novel binding mode and activation mechanism of TsaE offers good opportunities for antimicrobial drug development.
    Mots-clés : B3S, FAAM.

  • D. P. O'Brien, A. C. S. Perez, J. Karst, S. E. Cannella, V. Y. N. Enguéné, A. Hessel, D. Raoux-Barbot, A. Voegele, O. Subrini, M. Davi, J. I. Guijarro, B. Raynal, B. Baron, P. England, B. Hernandez, M. Ghomi, V. Hourdel, C. Malosse, J. Chamot-Rooke, P. Vachette, D. Durand, S. Brier, D. Ladant, et A. Chenal, « Calcium-dependent disorder-to-order transitions are central to the secretion and folding of the CyaA toxin of Bordetella pertussis, the causative agent of whooping cough », Toxicon: Official Journal of the International Society on Toxinology, janv. 2018.
    Résumé : The adenylate cyclase toxin (CyaA) plays an essential role in the early stages of respiratory tract colonization by Bordetella pertussis, the causative agent of whooping cough. Once secreted, CyaA invades eukaryotic cells, leading to cell death. The cell intoxication process involves a unique mechanism of translocation of the CyaA catalytic domain directly across the plasma membrane of the target cell. Herein, we review our recent results describing how calcium is involved in several steps of this intoxication process. In conditions mimicking the low calcium environment of the crowded bacterial cytosol, we show that the C-terminal, calcium-binding Repeat-in-ToXin (RTX) domain of CyaA, RD, is an extended, intrinsically disordered polypeptide chain with a significant level of local, secondary structure elements, appropriately sized for transport through the narrow channel of the secretion system. Upon secretion, the high calcium concentration in the extracellular milieu induces the refolding of RD, which likely acts as a scaffold to favor the refolding of the upstream domains of the full-length protein. Due to the presence of hydrophobic regions, CyaA is prone to aggregate into multimeric forms in vitro, in the absence of a chaotropic agent. We have recently defined the experimental conditions required for CyaA folding, comprising both calcium binding and molecular confinement. These parameters are critical for CyaA folding into a stable, monomeric and functional form. The monomeric, calcium-loaded (holo) toxin exhibits efficient liposome permeabilization and hemolytic activities in vitro, even in a fully calcium-free environment. By contrast, the toxin requires sub-millimolar calcium concentrations in solution to translocate its catalytic domain across the plasma membrane, indicating that free calcium in solution is actively involved in the CyaA toxin translocation process. Overall, this data demonstrates the remarkable adaptation of bacterial RTX toxins to the diversity of calcium concentrations it is exposed to in the successive environments encountered in the course of the intoxication process.
    Mots-clés : B3S, Bordetella pertussis, Calcium, CyaA toxin, Disorder-to-order transition, FAAM, Folding, Protein secretion, Whooping cough.

  • A. Pichard-Kostuch, W. Zhang, D. Liger, M. - C. Daugeron, J. Letoquart, I. Li de la Sierra-Gallay, P. Forterre, B. Collinet, H. van Tilbeurgh, et T. Basta, « Structure-function analysis of Sua5 protein reveals novel functional motifs required for the biosynthesis of the universal t6A tRNA modification », RNA (New York, N.Y.), avr. 2018.
    Résumé : N6-threonyl-carbamoyl adenosine (t6A) is a universal tRNA modification found at position 37, next to the anticodon, in almost all tRNAs decoding ANN codons (where N = A, U, G or C). t6A stabilizes the codon-anticodon interaction and hence promotes translation fidelity. The first step of the biosynthesis of t6A, the production of threonyl-carbamoyl adenylate (TC-AMP), is catalyzed by the Sua5/TsaC family of enzymes. While TsaC is a single domain protein, Sua5 enzymes are composed of the TsaC-like domain, a linker and an extra domain called SUA5 of unknown function. In the present study, we report structure-function analysis of Pyrococcus abyssi Sua5 (Pa-Sua5). Crystallographic data revealed binding sites for bicarbonate substrate and pyrophosphate product. The linker of Pa-Sua5 forms a loop structure that folds into the active site gorge and closes it. Using structure-guided mutational analysis we established that the conserved sequence motifs in the linker and the domain-domain interface are essential for the function of Pa-Sua5. We propose that the linker participates actively in the biosynthesis of TC-AMP by binding to ATP/PPi and by stabilizing the N-carboxy-L-threonine intermediate. Hence, TsaC orthologs which lack such a linker and SUA5 domain use different mechanism for TC-AMP synthesis.
    Mots-clés : ARCHEE, B3S, FAAM, MICROBIO, Sua5, t6A37, threonylcarbamoyl adenosine, tRNA modification, TsaC.

2017


  • A. Bahloul, E. Pepermans, B. Raynal, N. Wolff, F. Cordier, P. England, S. Nouaille, B. Baron, A. El-Amraoui, J. - P. Hardelin, D. Durand, et C. Petit, « Conformational switch of harmonin, a submembrane scaffold protein of the hair cell mechanoelectrical transduction machinery », FEBS letters, juin 2017.
    Résumé : Mutations in the gene encoding harmonin, a multi-PDZ domain-containing submembrane protein, cause Usher syndrome type 1 (congenital deafness and balance disorder, as well as early-onset sight loss). The structure of the protein and biological activities of its three different classes of splice isoforms (a, b, and c) remain poorly understood. Combining biochemical and biophysical analyses, we show that harmonin-a1 can switch between open and closed conformations through intramolecular binding of its C-terminal PDZ-binding motif to its N-terminal supramodule NTD-PDZ1 and a flexible PDZ2-PDZ3 linker. This conformational switch presumably extends to most harmonin isoforms, and is expected to have an impact on the interaction with some binding partners, as shown here for cadherin-related 23, another component of the hair cell mechanoelectrical transduction machinery. This article is protected by copyright. All rights reserved.
    Mots-clés : B3S, conformation switch, FAAM, PDZ domain, Usher syndrome.

  • D. A. Braun, J. Rao, G. Mollet, D. Schapiro, M. - C. Daugeron, W. Tan, O. Gribouval, O. Boyer, P. Revy, T. Jobst-Schwan, J. M. Schmidt, J. A. Lawson, D. Schanze, S. Ashraf, J. F. P. Ullmann, C. A. Hoogstraten, N. Boddaert, B. Collinet, G. Martin, D. Liger, S. Lovric, M. Furlano, I. C. Guerrera, O. Sanchez-Ferras, J. F. Hu, A. - C. Boschat, S. Sanquer, B. Menten, S. Vergult, N. De Rocker, M. Airik, T. Hermle, S. Shril, E. Widmeier, H. Y. Gee, W. - I. Choi, C. E. Sadowski, W. L. Pabst, J. K. Warejko, A. Daga, T. Basta, V. Matejas, K. Scharmann, S. D. Kienast, B. Behnam, B. Beeson, A. Begtrup, M. Bruce, G. - S. Ch'ng, S. - P. Lin, J. - H. Chang, C. - H. Chen, M. T. Cho, P. M. Gaffney, P. E. Gipson, C. - H. Hsu, J. A. Kari, Y. - Y. Ke, C. Kiraly-Borri, W. - M. Lai, E. Lemyre, R. O. Littlejohn, A. Masri, M. Moghtaderi, K. Nakamura, F. Ozaltin, M. Praet, C. Prasad, A. Prytula, E. R. Roeder, P. Rump, R. E. Schnur, T. Shiihara, M. D. Sinha, N. A. Soliman, K. Soulami, D. A. Sweetser, W. - H. Tsai, J. - D. Tsai, R. Topaloglu, U. Vester, D. H. Viskochil, N. Vatanavicharn, J. L. Waxler, K. J. Wierenga, M. T. F. Wolf, S. - N. Wong, S. A. Leidel, G. Truglio, P. C. Dedon, A. Poduri, S. Mane, R. P. Lifton, M. Bouchard, P. Kannu, D. Chitayat, D. Magen, B. Callewaert, H. van Tilbeurgh, M. Zenker, C. Antignac, et F. Hildebrandt, « Mutations in KEOPS-complex genes cause nephrotic syndrome with primary microcephaly », Nature Genetics, août 2017.
    Résumé : Galloway-Mowat syndrome (GAMOS) is an autosomal-recessive disease characterized by the combination of early-onset nephrotic syndrome (SRNS) and microcephaly with brain anomalies. Here we identified recessive mutations in OSGEP, TP53RK, TPRKB, and LAGE3, genes encoding the four subunits of the KEOPS complex, in 37 individuals from 32 families with GAMOS. CRISPR-Cas9 knockout in zebrafish and mice recapitulated the human phenotype of primary microcephaly and resulted in early lethality. Knockdown of OSGEP, TP53RK, or TPRKB inhibited cell proliferation, which human mutations did not rescue. Furthermore, knockdown of these genes impaired protein translation, caused endoplasmic reticulum stress, activated DNA-damage-response signaling, and ultimately induced apoptosis. Knockdown of OSGEP or TP53RK induced defects in the actin cytoskeleton and decreased the migration rate of human podocytes, an established intermediate phenotype of SRNS. We thus identified four new monogenic causes of GAMOS, describe a link between KEOPS function and human disease, and delineate potential pathogenic mechanisms.
    Mots-clés : ARCHEE, B3S, FAAM, MICROBIO.


  • S. E. Cannella, V. Y. Ntsogo Enguéné, M. Davi, C. Malosse, A. C. Sotomayor Pérez, J. Chamot-Rooke, P. Vachette, D. Durand, D. Ladant, et A. Chenal, « Stability, structural and functional properties of a monomeric, calcium–loaded adenylate cyclase toxin, CyaA, from Bordetella pertussis », Scientific Reports, vol. 7, p. 42065, févr. 2017.


  • L. Celma, C. Corbinais, J. Vercruyssen, X. Veaute, I. L. de la Sierra-Gallay, R. Guérois, D. Busso, A. Mathieu, S. Marsin, S. Quevillon-Cheruel, et J. P. Radicella, « Structural basis for the substrate selectivity of Helicobacter pylori NucT nuclease activity », PLOS ONE, vol. 12, nᵒ 12, p. e0189049, déc. 2017.

  • A. Chevrel, A. Mesneau, D. Sanchez, L. Celma, S. Quevillon-Cheruel, A. Cavagnino, S. Nessler, I. Li de la Sierra-Gallay, H. van Tilbeurgh, P. Minard, M. Valerio-Lepiniec, et A. Urvoas, « Alpha Repeat proteins (αRep) as expression and crystallization helpers », Journal of Structural Biology, août 2017.
    Résumé : We have previously described a highly diverse library of artificial repeat proteins based on thermostable HEAT-like repeats, named αRep. αReps binding specifically to proteins difficult to crystallize have been selected and in several examples, they made possible the crystallization of these proteins. To further simplify the production and crystallization experiments we have explored the production of chimeric protein corresponding to covalent association between the targets and their specific binders strengthened by a linker. Although chimeric proteins with expression partners are classically used to enhance expression these fusions cannot usually be used for crystallization. With specific expression partners like a cognate αRep this is no longer true, and chimeric proteins can be expressed purified and crystallized. αRep selection by phage display suppose that at least a small amount of the target protein should be produced to be used as a bait for selection and this might, in some cases, be difficult. We have therefore transferred the αRep library in a new construction adapted to selection by protein complementation assay (PCA). This new procedure allows to select specific binders by direct interaction with the target in the cytoplasm of the bacteria and consequently does not require preliminary purification of target protein. αRep binders selected by PCA or by phage display can be used to enhance expression, stability, solubility and crystallogenesis of proteins that are otherwise difficult to express, purify and/or crystallize.
    Mots-clés : artificial repeat proteins, B3S, Crystallization helper, FAAM, Fusion protein, MIP, Protein complementation assay, Protein library.

  • C. Corbinais, A. Mathieu, P. P. Damke, T. Kortulewski, D. Busso, M. Prado-Acosta, J. P. Radicella, et S. Marsin, « ComB proteins expression levels determine Helicobacter pylori competence capacity », Scientific Reports, vol. 7, p. 41495, janv. 2017.
    Résumé : Helicobacter pylori chronically colonises half of the world's human population and is the main cause of ulcers and gastric cancers. Its prevalence and the increase in antibiotic resistance observed recently reflect the high genetic adaptability of this pathogen. Together with high mutation rates and an efficient DNA recombination system, horizontal gene transfer through natural competence makes of H. pylori one of the most genetically diverse bacteria. We show here that transformation capacity is enhanced in strains defective for recN, extending previous work with other homologous recombination genes. However, inactivation of either mutY or polA has no effect on DNA transformation, suggesting that natural competence can be boosted in H. pylori by the persistence of DNA breaks but not by enhanced mutagenesis. The transformation efficiency of the different DNA repair impaired strains correlates with the number of transforming DNA foci formed on the cell surface and with the expression of comB8 and comB10 competence genes. Overexpression of the comB6-B10 operon is sufficient to increase the transformation capacity of a wild type strain, indicating that the ComB complex, present in the bacterial wall and essential for DNA uptake, can be a limiting factor for transformation efficiency.
    Mots-clés : B3S, FAAM.

  • M. Ma, I. Li de La Sierra Gallay, N. Lazar, O. Pellegrini, J. Lepault, C. Condon, D. Durand, et H. van Tilbeurgh, « Trz1, the long form RNase Z from yeast, forms a stable heterohexamer with endonuclease Nuc1 and mutarotase », The Biochemical Journal, sept. 2017.
    Résumé : Proteomic studies haves established that Trz1, Nuc1 and mutarotase form a complex in yeast. Trz1 is a b-lactamase type RNase composed of two b-lactamase type domains connected by a long linker that is responsible for the endonucleolytic cleavage at the 3'-end of tRNAs during the maturation process (RNase Z activity); Nuc1 is a dimeric mitochondrial nuclease involved in apoptosis, while mutarotase (encoded by YMR099C) catalyzes the conversion between the a- and b-configuration of glucose-6-phosphate. Using gel-filtration, SAXS and electron microscopy we demonstrated that Trz1, Nuc1 and mutarotase form a very stable heterohexamer, composed of two copies of each of the three subunits. A Nuc1 homodimer is at the centre of the complex, creating a two-fold symmetry and interacting with both Trz1 and mutarotase. Enzymatic characterization of the ternary complex revealed that the activities of Trz1 and mutarotase are not affected by complex formation, but that the Nuc1 activity is completely inhibited by mutarotase and partially by Trz1. This suggests that mutarotase and Trz1 might be regulators of the Nuc1 apoptotic nuclease activity.
    Mots-clés : B3S, complex, CRYOEM, endoglucanase, FAAM, mutarotase, PF, RNASeZ, Structure.


  • M. Ma, I. Li de la Sierra-Gallay, N. Lazar, O. Pellegrini, D. Durand, A. Marchfelder, C. Condon, et H. van Tilbeurgh, « The crystal structure of Trz1, the long form RNase Z from yeast », Nucleic Acids Research, avr. 2017.


  • W. Mao, P. Daligaux, N. Lazar, T. Ha-Duong, C. Cavé, H. van Tilbeurgh, P. M. Loiseau, et S. Pomel, « Biochemical analysis of leishmanial and human GDP-Mannose Pyrophosphorylases and selection of inhibitors as new leads », Scientific Reports, vol. 7, nᵒ 1, 2017.

  • D. P. O'Brien, S. Brier, D. Ladant, D. Durand, A. Chenal, et P. Vachette, « SEC-SAXS and HDX-MS: a powerful combination. The case of the calcium-binding domain of a bacterial toxin », Biotechnology and Applied Biochemistry, août 2017.
    Résumé : Small-angle X-ray Scattering (SAXS) is a relatively simple experimental technique that provides information on the global conformation of macromolecules in solution, be they fully structured, partially, or extensively unfolded. Size Exclusion chromatography in line with a SAXS measuring cell considerably improves the mono-dispersity and ideality of solutions, the two main requirements of a "good" SAXS sample. Hydrogen/Deuterium eXchange monitored by Mass Spectrometry (HDX-MS) offers a wealth of information regarding the solvent accessibility at the local (peptide) level. It constitutes a sensitive probe of local flexibility and, more generally, of structural dynamics. The combination of both approaches presented here is very powerful, as illustrated by the case of RD, a calcium binding protein that is part of a bacterial virulence factor. This article is protected by copyright. All rights reserved.
    Mots-clés : B3S, Calcium, FAAM, Hydrogen/Deuterium eXchange Mass Spectrometry, RTX motif, Size-Exclusion Chromatography, small-angle X-ray scattering.

  • D. P. O'Brien, D. Durand, A. Voegele, V. Hourdel, M. Davi, J. Chamot-Rooke, P. Vachette, S. Brier, D. Ladant, et A. Chenal, « Calmodulin fishing with a structurally disordered bait triggers CyaA catalysis », PLoS biology, vol. 15, nᵒ 12, p. e2004486, déc. 2017.
    Résumé : Once translocated into the cytosol of target cells, the catalytic domain (AC) of the adenylate cyclase toxin (CyaA), a major virulence factor of Bordetella pertussis, is potently activated by binding calmodulin (CaM) to produce supraphysiological levels of cAMP, inducing cell death. Using a combination of small-angle X-ray scattering (SAXS), hydrogen/deuterium exchange mass spectrometry (HDX-MS), and synchrotron radiation circular dichroism (SR-CD), we show that, in the absence of CaM, AC exhibits significant structural disorder, and a 75-residue-long stretch within AC undergoes a disorder-to-order transition upon CaM binding. Beyond this local folding, CaM binding induces long-range allosteric effects that stabilize the distant catalytic site, whilst preserving catalytic loop flexibility. We propose that the high enzymatic activity of AC is due to a tight balance between the CaM-induced decrease of structural flexibility around the catalytic site and the preservation of catalytic loop flexibility, allowing for fast substrate binding and product release. The CaM-induced dampening of AC conformational disorder is likely relevant to other CaM-activated enzymes.
    Mots-clés : B3S, FAAM.

  • J. Pérez et P. Vachette, « A Successful Combination: Coupling SE-HPLC with SAXS », Advances in Experimental Medicine and Biology, vol. 1009, p. 183-199, 2017.
    Résumé : A monodispersed and ideal solution is a central (unique?) requirement of SAXS to allow one to extract structural information from the recorded pattern. On-line Size Exclusion Chromatography (SEC) marked a major breakthrough, separating particles present in solution according to their size. Identical frames under an elution peak can be averaged and further processed free from contamination. However, this is not always straightforward, separation is often incomplete and software have been developed to deconvolve the contributions from the different species (molecules or oligomeric forms) within the sample. In this chapter, we present the general workflow of a SEC-SAXS experiment. We present recent instrumental and data analysis improvements that have improved the quality of recorded data, extended its potential and turn it into a mainstream approach. We describe into some details two specific applications of SEC-SAXS that provide more than just separating associated forms from the particle of interest.
    Mots-clés : B3S, FAAM, Membrane protein-detergent complex, Monodispersity, Size exclusion chromatography, small-angle X-ray scattering.


  • A. Talagas, L. Fontaine, L. Ledesma-García, J. Mignolet, I. Li de la Sierra-Gallay, N. Lazar, M. Aumont-Nicaise, M. J. Federle, G. Prehna, P. Hols, et S. Nessler, « Correction: Structural Insights into Streptococcal Competence Regulation by the Cell-to-Cell Communication System ComRS », PLOS Pathogens, vol. 13, nᵒ 2, p. e1006208, févr. 2017.
    Mots-clés : B3S, FAAM, PF, PIM.

  • J. Trewhella, A. P. Duff, D. Durand, F. Gabel, J. M. Guss, W. A. Hendrickson, G. L. Hura, D. A. Jacques, N. M. Kirby, A. H. Kwan, J. Pérez, L. Pollack, T. M. Ryan, A. Sali, D. Schneidman-Duhovny, T. Schwede, D. I. Svergun, M. Sugiyama, J. A. Tainer, P. Vachette, J. Westbrook, et A. E. Whitten, « 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update », Acta Crystallographica. Section D, Structural Biology, vol. 73, nᵒ Pt 9, p. 710-728, sept. 2017.
    Résumé : In 2012, preliminary guidelines were published addressing sample quality, data acquisition and reduction, presentation of scattering data and validation, and modelling for biomolecular small-angle scattering (SAS) experiments. Biomolecular SAS has since continued to grow and authors have increasingly adopted the preliminary guidelines. In parallel, integrative/hybrid determination of biomolecular structures is a rapidly growing field that is expanding the scope of structural biology. For SAS to contribute maximally to this field, it is essential to ensure open access to the information required for evaluation of the quality of SAS samples and data, as well as the validity of SAS-based structural models. To this end, the preliminary guidelines for data presentation in a publication are reviewed and updated, and the deposition of data and associated models in a public archive is recommended. These guidelines and recommendations have been prepared in consultation with the members of the International Union of Crystallography (IUCr) Small-Angle Scattering and Journals Commissions, the Worldwide Protein Data Bank (wwPDB) Small-Angle Scattering Validation Task Force and additional experts in the field.
    Mots-clés : B3S, biomolecular structure, DNA, FAAM, hybrid structural modelling, integrative structural biology, Proteins, publication guidelines, RNA, SANS, SAXS, small-angle scattering, structural modelling.

  • E. Vernhes, M. Renouard, B. Gilquin, P. Cuniasse, D. Durand, P. England, S. Hoos, A. Huet, J. F. Conway, A. Glukhov, V. Ksenzenko, E. Jacquet, N. Nhiri, S. Zinn-Justin, et P. Boulanger, « Erratum: High affinity anchoring of the decoration protein pb10 onto the bacteriophage T5 capsid », Scientific Reports, vol. 7, p. 43977, avr. 2017.


  • E. Vernhes, M. Renouard, B. Gilquin, P. Cuniasse, D. Durand, P. England, S. Hoos, A. Huet, J. F. Conway, A. Glukhov, V. Ksenzenko, E. Jacquet, N. Nhiri, S. Zinn-Justin, et P. Boulanger, « High affinity anchoring of the decoration protein pb10 onto the bacteriophage T5 capsid », Scientific Reports, vol. 7, p. 41662, févr. 2017.

2016


  • T. Bizien, D. Durand, P. Roblina, A. Thureau, P. Vachette, et J. Pérez, « A Brief Survey of State-of-the-Art BioSAXS », Protein and Peptide Letters, vol. 23, nᵒ 3, p. 217-231, 2016.
    Résumé : In the field of structural biology, Small Angle X-ray Scattering (SAXS) has undergone a tremendous evolution in the last two decades. From a craft reserved to a few experts in the late 80's, it has now turned into a high-throughput technique, following the same trend as macromolecular crystallography. Synchrotron radiation has played a key role in this evolution, by providing intense X-ray beams of high optical quality that made possible the recording of statistically meaningful data from weakly scattering biological solutions in a reasonable time. This, in turn, prompted the development of powerful and specific software for data analysis and modeling. In this mini-review, mainly addressed towards a broad readership, representing as many potential users, we try to summarize the latest aspects of evolution of BioSAXS, both conceptually and from the point of view of instrumentation. We emphasize the need for complementary experimental or computational techniques used in combination with SAXS. The great potential of these multi-pronged approaches is illustrated by a series of very recent studies covering the various ways and means of using BioSAXS.
    Mots-clés : B3S, Computational Biology, FAAM, Macromolecular Substances, Models, Molecular, Molecular Structure, Scattering, Small Angle, Software, Synchrotrons, X-Ray Diffraction.

  • P. Brézellec, I. Vallet-Gely, C. Possoz, S. Quevillon-Cheruel, et J. - L. Ferat, « DciA is an ancestral replicative helicase operator essential for bacterial replication initiation », Nature Communications, vol. 7, p. 13271, nov. 2016.
    Résumé : Delivery of the replicative helicase onto DNA is an essential step in the initiation of replication. In bacteria, DnaC (in Escherichia coli) and DnaI (in Bacillus subtilis) are representative of the two known mechanisms that assist the replicative helicase at this stage. Here, we establish that these two strategies cannot be regarded as prototypical of the bacterial domain since dnaC and dnaI (dna[CI]) are present in only a few bacterial phyla. We show that dna[CI] was domesticated at least seven times through evolution in bacteria and at the expense of one gene, which we rename dciA (dna[CI] antecedent), suggesting that DciA and Dna[CI] share a common function. We validate this hypothesis by establishing in Pseudomonas aeruginosa that DciA possesses the attributes of the replicative helicase-operating proteins associated with replication initiation.
    Mots-clés : B3S, DBG, EMC2, FAAM, OCB.

  • E. Brookes, P. Vachette, M. Rocco, et J. Pérez, « US-SOMO HPLC-SAXS module: dealing with capillary fouling and extraction of pure component patterns from poorly resolved SEC-SAXS data », Journal of Applied Crystallography, vol. 49, nᵒ Pt 5, p. 1827-1841, oct. 2016.
    Résumé : Size-exclusion chromatography coupled with SAXS (small-angle X-ray scattering), often performed using a flow-through capillary, should allow direct collection of monodisperse sample data. However, capillary fouling issues and non-baseline-resolved peaks can hamper its efficacy. The UltraScan solution modeler (US-SOMO) HPLC-SAXS (high-performance liquid chromatography coupled with SAXS) module provides a comprehensive framework to analyze such data, starting with a simple linear baseline correction and symmetrical Gaussian decomposition tools [Brookes, Pérez, Cardinali, Profumo, Vachette & Rocco (2013 ▸). J. Appl. Cryst.46, 1823-1833]. In addition to several new features, substantial improvements to both routines have now been implemented, comprising the evaluation of outcomes by advanced statistical tools. The novel integral baseline-correction procedure is based on the more sound assumption that the effect of capillary fouling on scattering increases monotonically with the intensity scattered by the material within the X-ray beam. Overlapping peaks, often skewed because of sample interaction with the column matrix, can now be accurately decomposed using non-symmetrical modified Gaussian functions. As an example, the case of a polydisperse solution of aldolase is analyzed: from heavily convoluted peaks, individual SAXS profiles of tetramers, octamers and dodecamers are extracted and reliably modeled.
    Mots-clés : aldolase supramolecular complexes, asymmetric modified Gaussian decomposition, B3S, CorMap analysis, FAAM, multi-resolution modeling, P-value analysis, poorly resolved chromatographic peaks, US-SOMO HPLC-SAXS module.

  • C. Corbinais, A. Mathieu, T. Kortulewski, J. P. Radicella, et S. Marsin, « Following transforming DNA in Helicobacter pylori from uptake to expression », Molecular Microbiology, vol. 101, nᵒ 6, p. 1039-1053, sept. 2016.
    Résumé : Natural transformation is a potent driver for genetic diversification in bacterial populations. It involves exogenous DNA binding, uptake, transport and internalization into the cytoplasm, where DNA can be processed and integrated into the host chromosome. Direct visualisation of transforming DNA (tDNA) has been limited to its binding to the surface or, in the case of Gram-negative species, to its entrance into the periplasm. We present here for the first time the direct visualisation of tDNA entering the bacterial cytoplasm. We used as a model the Gram-negative pathogen Helicobacter pylori, characterised by a large intraspecies variability that results from high mutation rates and efficient horizontal gene transfer. Using fluorescently labelled DNA, we followed for up to 3 h the fate of tDNA foci formed in the periplasm and eventually internalised into the cytoplasm. By tracking at the single cell level the expression of a fluorescent protein coded by the tDNA, we show that up to 50% of the cells express the transforming phenotype. The overall transformation process in H. pylori, from tDNA uptake to expression of the recombinant gene, can take place in less than 1 h, without requiring a growth arrest, and prior to the replication of the chromosome.
    Mots-clés : B3S, DNA, Bacterial, FAAM, gene expression, Gene Transfer, Horizontal, Helicobacter pylori, Transformation, Bacterial.

  • C. Cragnell, D. Durand, B. Cabane, et M. Skepö, « Coarse-grained modeling of the intrinsically disordered protein Histatin 5 in solution: Monte Carlo simulations in combination with SAXS », Proteins, vol. 84, nᵒ 6, p. 777-791, 2016.
    Résumé : Monte Carlo simulations and coarse-grained modeling have been used to analyze Histatin 5, an unstructured short cationic salivary peptide known to have anticandidical properties. The calculated scattering functions have been compared with intensity curves and the distance distribution function P(r) obtained from small angle X-ray scattering (SAXS), at both high and low salt concentrations. The aim was to achieve a molecular understanding and a physico-chemical insight of the obtained SAXS results and to gain information of the conformational changes of Histatin 5 due to altering salt content, charge distribution, and net charge. From a modeling perspective, the accuracy of the electrostatic interactions are of special interest. The used coarse-grained model was based on the primitive model in which charged hard spheres differing in charge and in size represent the ionic particles, and the solvent only enters the model through its relative permittivity. The Hamiltonian of the model comprises three different contributions: (i) excluded volumes, (ii) electrostatic, and (iii) van der Waals interactions. Even though the model can be considered as gross omitting all atomistic details, a great correspondence is obtained with the experimental results. Proteins 2016; 84:777-791. © 2016 Wiley Periodicals, Inc.
    Mots-clés : antimicrobial activity, B3S, cationic protein, Computer Simulation, FAAM, Histatins, Humans, intrinsically disordered proteins, Models, Biological, Monte Carlo Method, Monte Carlo simulations, Osmolar Concentration, Protein Conformation, Scattering, Small Angle, small angle X-ray scattering, Static Electricity, unstructured proteins, X-Ray Diffraction.

  • A. Devigne, P. Guérin, J. Lisboa, S. Quevillon-Cheruel, J. Armengaud, S. Sommer, C. Bouthier de la Tour, et P. Servant, « PprA Protein Is Involved in Chromosome Segregation via Its Physical and Functional Interaction with DNA Gyrase in Irradiated Deinococcus radiodurans Bacteria », mSphere, vol. 1, nᵒ 1, févr. 2016.
    Résumé : PprA, a radiation-induced Deinococcus-specific protein, was previously shown to be required for cell survival and accurate chromosome segregation after exposure to ionizing radiation. Here, we used an in vivo approach to determine, by shotgun proteomics, putative PprA partners coimmunoprecipitating with PprA when cells were exposed to gamma rays. Among them, we found the two subunits of DNA gyrase and, thus, chose to focus our work on characterizing the activities of the deinococcal DNA gyrase in the presence or absence of PprA. Loss of PprA rendered cells hypersensitive to novobiocin, an inhibitor of the B subunit of DNA gyrase. We showed that treatment of bacteria with novobiocin resulted in induction of the radiation desiccation response (RDR) regulon and in defects in chromosome segregation that were aggravated by the absence of PprA. In vitro, the deinococcal DNA gyrase, like other bacterial DNA gyrases, possesses DNA negative supercoiling and decatenation activities. These two activities are inhibited in vitro by novobiocin and nalidixic acid, whereas PprA specifically stimulates the decatenation activity of DNA gyrase. Together, these results suggest that PprA plays a major role in chromosome decatenation via its interaction with the deinococcal DNA gyrase when D. radiodurans cells are recovering from exposure to ionizing radiation. IMPORTANCE D. radiodurans is one of the most radiation-resistant organisms known. This bacterium is able to cope with high levels of DNA lesions generated by exposure to extreme doses of ionizing radiation and to reconstruct a functional genome from hundreds of radiation-induced chromosomal fragments. Here, we identified partners of PprA, a radiation-induced Deinococcus-specific protein, previously shown to be required for radioresistance. Our study leads to three main findings: (i) PprA interacts with DNA gyrase after irradiation, (ii) treatment of cells with novobiocin results in defects in chromosome segregation that are aggravated by the absence of PprA, and (iii) PprA stimulates the decatenation activity of DNA gyrase. Our results extend the knowledge of how D. radiodurans cells survive exposure to extreme doses of gamma irradiation and point out the link between DNA repair, chromosome segregation, and DNA gyrase activities in the radioresistant D. radiodurans bacterium.
    Mots-clés : B3S, DBG, Deinococcus radiodurans, DNA decatenation, DNA gyrase, FAAM, PprA, RBA.


  • M. Figueroa, M. Sleutel, M. Vandevenne, G. Parvizi, S. Attout, O. Jacquin, J. Vandenameele, A. W. Fischer, C. Damblon, E. Goormaghtigh, M. Valerio-Lepiniec, A. Urvoas, D. Durand, E. Pardon, J. Steyaert, P. Minard, D. Maes, J. Meiler, A. Matagne, J. A. Martial, et C. Van de Weerdt, « The unexpected structure of the designed protein Octarellin V.1 forms a challenge for protein structure prediction tools », Journal of Structural Biology, vol. 195, nᵒ 1, p. 19-30, 2016.

  • M. de Frutos, A. Leforestier, J. Degrouard, N. Zambrano, F. Wien, P. Boulanger, S. Brasilès, M. Renouard, D. Durand, et F. Livolant, « Can Changes in Temperature or Ionic Conditions Modify the DNA Organization in the Full Bacteriophage Capsid? », The Journal of Physical Chemistry. B, vol. 120, nᵒ 26, p. 5975-5986, juill. 2016.
    Résumé : We compared four bacteriophage species, T5, λ, T7, and Φ29, to explore the possibilities of DNA reorganization in the capsid where the chain is highly concentrated and confined. First, we did not detect any change in DNA organization as a function of temperature between 20 to 40 °C. Second, the presence of spermine (4+) induces a significant enlargement of the typical size of the hexagonal domains in all phages. We interpret these changes as a reorganization of DNA by slight movements of defects in the structure, triggered by a partial screening of repulsive interactions. We did not detect any signal characteristic of a long-range chiral organization of the encapsidated DNA in the presence and in the absence of spermine.
    Mots-clés : B3S, FAAM, T5PHAG, VIRO.


  • D. Liger, L. Mora, N. Lazar, S. Figaro, J. Henri, N. Scrima, R. H. Buckingham, H. van Tilbeurgh, V. Heurgué-Hamard, et M. Graille, « Mechanism of activation of methyltransferases involved in translation by the Trm112 ‘hub’ protein », Nucleic Acids Research, vol. 44, nᵒ 3, p. 1482-1482, févr. 2016.
    Mots-clés : B3S, FAAM, RHABDO, VIRO.


  • S. Perchat, A. Talagas, S. Poncet, N. Lazar, I. Li de la Sierra-Gallay, M. Gohar, D. Lereclus, et S. Nessler, « Correction: How Quorum Sensing Connects Sporulation to Necrotrophism in Bacillus thuringiensis », PLOS Pathogens, vol. 12, nᵒ 10, p. e1006009, oct. 2016.


  • S. Perchat, A. Talagas, S. Poncet, N. Lazar, I. Li de la Sierra-Gallay, M. Gohar, D. Lereclus, et S. Nessler, « How Quorum Sensing Connects Sporulation to Necrotrophism in Bacillus thuringiensis », PLOS Pathogens, vol. 12, nᵒ 8, p. e1005779, août 2016.

  • S. Perchat, A. Talagas, S. Zouhir, S. Poncet, L. Bouillaut, S. Nessler, et D. Lereclus, « NprR, a moonlighting quorum sensor shifting from a phosphatase activity to a transcriptional activator », Microbial Cell (Graz, Austria), vol. 3, nᵒ 11, p. 573-575, nov. 2016.
    Résumé : Regulation of biological functions requires factors (proteins, peptides or chemicals) able to sense and translate environmental conditions or any circumstances in order to modulate the transcription of a gene, the stability of a transcript or the activity of a protein. Quorum sensing is a regulation mechanism connecting cell density to the physiological state of a single cell. In bacteria, quorum sensing coordinates virulence, cell fate and commitment to sporulation and other adaptation properties. The critical role of such regulatory systems was demonstrated in pathogenicity and adaptation of bacteria from the Bacillus cereus group (i.e. B. cereus and Bacillus thuringiensis). Furthermore, using insects as a model of infection, it was shown that sequential activation of several quorum sensing systems allowed bacteria to switch from a virulence state to a necrotrophic lifestyle, allowing their survival in the host cadaver, and ultimately to the commitment into sporulation. The chronological development of these physiological states is directed by quorum sensors forming the RNPP family. Among them, NprR combines two distinct functions connecting sporulation to necrotrophism in B. thuringiensis. In the absence of its cognate signaling peptide (NprX), NprR negatively controls sporulation by acting as a phosphatase. In the presence of NprX, it acts as a transcription factor regulating a set of genes involved in the survival of the bacteria in the insect cadaver.
    Mots-clés : B3S, Bacillus, bifunctional protein, FAAM, phosphatase, Quorum Sensing, sporulation.


  • E. Shanker, D. A. Morrison, A. Talagas, S. Nessler, M. J. Federle, et G. Prehna, « Pheromone Recognition and Selectivity by ComR Proteins among Streptococcus Species », PLOS Pathogens, vol. 12, nᵒ 12, p. e1005979, déc. 2016.


  • A. Talagas, L. Fontaine, L. Ledesma-Garca, J. Mignolet, I. Li de la Sierra-Gallay, N. Lazar, M. Aumont-Nicaise, M. J. Federle, G. Prehna, P. Hols, et S. Nessler, « Structural Insights into Streptococcal Competence Regulation by the Cell-to-Cell Communication System ComRS », PLOS Pathogens, vol. 12, nᵒ 12, p. e1005980, déc. 2016.
    Mots-clés : B3S, FAAM, PF, PIM.

  • J. Urbonavičius, R. Rutkienė, A. Lopato, D. Tauraitė, J. Stankevičiūtė, A. Aučynaitė, L. Kaliniene, H. van Tilbeurgh, et R. Meškys, « Evolution of tRNAPhe:imG2 methyltransferases involved in the biosynthesis of wyosine derivatives in Archaea », RNA (New York, N.Y.), vol. 22, nᵒ 12, p. 1871-1883, déc. 2016.
    Résumé : Tricyclic wyosine derivatives are found at position 37 of eukaryotic and archaeal tRNA(Phe) In Archaea, the intermediate imG-14 is targeted by three different enzymes that catalyze the formation of yW-86, imG, and imG2. We have suggested previously that a peculiar methyltransferase (aTrm5a/Taw22) likely catalyzes two distinct reactions: N(1)-methylation of guanosine to yield m(1)G; and C(7)-methylation of imG-14 to yield imG2. Here we show that the recombinant aTrm5a/Taw22-like enzymes from both Pyrococcus abyssi and Nanoarchaeum equitans indeed possess such dual specificity. We also show that substitutions of individual conservative amino acids of P. abyssi Taw22 (P260N, E173A, and R174A) have a differential effect on the formation of m(1)G/imG2, while replacement of R134, F165, E213, and P262 with alanine abolishes the formation of both derivatives of G37. We further demonstrate that aTrm5a-type enzyme SSO2439 from Sulfolobus solfataricus, which has no N(1)-methyltransferase activity, exhibits C(7)-methyltransferase activity, thereby producing imG2 from imG-14. We thus suggest renaming such aTrm5a methyltransferases as Taw21 to distinguish between monofunctional and bifunctional aTrm5a enzymes.
    Mots-clés : Archaea, B3S, bifunctional enzyme, evolution, FAAM, tRNA modification, wyosine.

2015


  • K. Blondeau, F. Blaise, M. Graille, S. D. Kale, J. Linglin, B. Ollivier, A. Labarde, N. Lazar, G. Daverdin, M. - H. Balesdent, D. H. Y. Choi, B. M. Tyler, T. Rouxel, H. van Tilbeurgh, et I. Fudal, « Crystal structure of the effector AvrLm4-7 of Leptosphaeria maculans reveals insights into its translocation into plant cells and recognition by resistance proteins », The Plant Journal: For Cell and Molecular Biology, vol. 83, nᵒ 4, p. 610-624, août 2015.
    Résumé : The avirulence gene AvrLm4-7 of Leptosphaeria maculans, the causal agent of stem canker in Brassica napus (oilseed rape), confers a dual specificity of recognition by two resistance genes (Rlm4 and Rlm7) and is strongly involved in fungal fitness. In order to elucidate the biological function of AvrLm4-7 and understand the specificity of recognition by Rlm4 and Rlm7, the AvrLm4-7 protein was produced in Pichia pastoris and its crystal structure was determined. It revealed the presence of four disulfide bridges, but no close structural analogs could be identified. A short stretch of amino acids in the C terminus of the protein, (R/N)(Y/F)(R/S)E(F/W), was well-conserved among AvrLm4-7 homologs. Loss of recognition of AvrLm4-7 by Rlm4 is caused by the mutation of a single glycine to an arginine residue located in a loop of the protein. Loss of recognition by Rlm7 is governed by more complex mutational patterns, including gene loss or drastic modifications of the protein structure. Three point mutations altered residues in the well-conserved C-terminal motif or close to the glycine involved in Rlm4-mediated recognition, resulting in the loss of Rlm7-mediated recognition. Transient expression in Nicotiana benthamiana (tobacco) and particle bombardment experiments on leaves from oilseed rape suggested that AvrLm4-7 interacts with its cognate R proteins inside the plant cell, and can be translocated into plant cells in the absence of the pathogen. Translocation of AvrLm4-7 into oilseed rape leaves is likely to require the (R/N)(Y/F)(R/S)E(F/W) motif as well as an RAWG motif located in a nearby loop that together form a positively charged region.
    Mots-clés : 3D structure, Ascomycota, avirulence protein, B3S, Brassica napus, effector, FAAM, Fungal Proteins, Leptosphaeria maculans, plant cell translocation, plant disease resistance, Plant Diseases, Virulence.


  • E. Chabrol, M. Thépaut, C. Dezutter-Dambuyant, C. Vivès, J. Marcoux, R. Kahn, J. Valladeau-Guilemond, P. Vachette, D. Durand, et F. Fieschi, « Alteration of the Langerin Oligomerization State Affects Birbeck Granule Formation », Biophysical Journal, vol. 108, nᵒ 3, p. 666-677, 2015.
    Mots-clés : Animals, Antigens, CD, B3S, Cell Line, Chromatography, High Pressure Liquid, Cross-Linking Reagents, Crystallography, X-Ray, Cytoplasmic Granules, FAAM, Fibroblasts, HIV Envelope Protein gp120, Humans, Lectins, C-Type, Mannans, Mannose-Binding Lectins, Mice, Models, Molecular, Mutant Proteins, Mutation, Protein Binding, Protein Multimerization, Protein Structure, Tertiary, Scattering, Small Angle, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Transfection.


  • A. Chevrel, A. Urvoas, I. L. de la Sierra-Gallay, M. Aumont-Nicaise, S. Moutel, M. Desmadril, F. Perez, A. Gautreau, H. van Tilbeurgh, P. Minard, et M. Valerio-Lepiniec, « Specific GFP-binding artificial proteins ( Rep): a new tool for in vitro to live cell applications », Bioscience Reports, vol. 35, nᵒ 4, p. e00223-e00223, août 2015.
    Mots-clés : B3S, FAAM, MIP, PF, PIM.


  • A. Derouiche, L. Shi, V. Bidnenko, M. Ventroux, N. Pigonneau, M. Franz-Wachtel, A. Kalantari, S. Nessler, M. - F. Noirot-Gros, et I. Mijakovic, « Bacillus subtilis SalA is a phosphorylation-dependent transcription regulator that represses scoC and activates the production of the exoprotease AprE: SalA is a transcription factor phosphorylated by PtkA », Molecular Microbiology, vol. 97, nᵒ 6, p. 1195-1208, 2015.
    Mots-clés : Adenosine Triphosphate, B3S, Bacillus subtilis, Bacterial Proteins, DNA-Binding Proteins, Exopeptidases, FAAM, Membrane Transport Proteins, Phosphorylation, Promoter Regions, Genetic, Protein Interaction Domains and Motifs, Protein Kinases, Transcription Factors, Tyrosine.

  • S. Julien, P. Tondl, F. Durand, A. Dagkessamanskaia, H. van Tilbeurgh, J. M. François, L. Mourey, D. Zerbib, H. Martin-Yken, et L. Maveyraud, « Crystallographic studies of the structured core domain of Knr4 from Saccharomyces cerevisiae », Acta Crystallographica. Section F, Structural Biology Communications, vol. 71, nᵒ Pt 9, p. 1120-1124, sept. 2015.
    Résumé : The potentially structured core domain of the intrinsically disordered protein Knr4 from Saccharomyces cerevisiae, comprising residues 80-340, was expressed in Escherichia coli and crystallized using the hanging-drop vapour-diffusion method. Selenomethionine-containing (SeMet) protein was also purified and crystallized. Crystals of both proteins belonged to space group P6522, with unit-cell parameters a = b = 112.44, c = 265.21 Å for the native protein and a = b = 112.49, c = 262.21 Å for the SeMet protein, and diffracted to 3.50 and 3.60 Å resolution, respectively. There are two molecules in the asymmetric unit related by a twofold axis. The anomalous signal of selenium was recorded and yielded an electron-density map of sufficient quality to allow the identification of secondary-structure elements.
    Mots-clés : B3S, cell-wall biogenesis regulation, Cloning, Molecular, Crystallization, Crystallography, X-Ray, FAAM, hub proteins, intrinsically disordered proteins, Protein Structure, Tertiary, Recombinant Proteins, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Spectrometry, Fluorescence, Static Electricity, Transcription Factors, Ultraviolet Rays.


  • J. Létoquart, N. van Tran, V. Caroline, A. Aleksandrov, N. Lazar, H. van Tilbeurgh, D. Liger, et M. Graille, « Insights into molecular plasticity in protein complexes from Trm9-Trm112 tRNA modifying enzyme crystal structure », Nucleic Acids Research, vol. 43, nᵒ 22, p. 10989-11002, déc. 2015.


  • E. Mastrangelo, P. Vachette, F. Cossu, F. Malvezzi, M. Bolognesi, et M. Milani, « The Activator of Apoptosis Smac-DIABLO Acts as a Tetramer in Solution », Biophysical Journal, vol. 108, nᵒ 3, p. 714-723, 2015.


  • D. P. O’Brien, B. Hernandez, D. Durand, V. Hourdel, A. - C. Sotomayor-Pérez, P. Vachette, M. Ghomi, J. Chamot-Rooke, D. Ladant, S. Brier, et A. Chenal, « Structural models of intrinsically disordered and calcium-bound folded states of a protein adapted for secretion », Scientific Reports, vol. 5, p. 14223, sept. 2015.


  • S. Pilotto, V. Speranzini, M. Tortorici, D. Durand, A. Fish, S. Valente, F. Forneris, A. Mai, T. K. Sixma, P. Vachette, et A. Mattevi, « Interplay among nucleosomal DNA, histone tails, and corepressor CoREST underlies LSD1-mediated H3 demethylation », Proceedings of the National Academy of Sciences, vol. 112, nᵒ 9, p. 2752-2757, mars 2015.

  • D. Sanchez, M. Boudes, H. van Tilbeurgh, D. Durand, et S. Quevillon-Cheruel, « Modeling the ComD/ComE/comcde interaction network using small angle X-ray scattering », The FEBS journal, vol. 282, nᵒ 8, p. 1538-1553, avr. 2015.
    Résumé : The ComD-ComE two-component system controls the competence state of Streptococcus pneumoniae via the phospho-regulation of ComE, which fluctuates between monomeric and dimeric states. We previously showed that the non-phosphorylatable ComE(D) (58A) mutant is monomeric in solution, whereas the ComE(D) (58E) active mimic mutant dimerizes via its REC domains. The crystal structure of ComE(D) (58A) revealed an asymmetric dimer that may represent the activated form of ComE. Here, we investigated the binding between the catalytic domain of ComD, ComE and the promoter region comcde, using small angle X-ray scattering. ComD(catdom) is a dimer that adapts two monomers of ComE, one on each side, placing (Com) (E) D58 residue in front of (Com) (D) H248, a location that is convenient for the intermolecular transfer reaction of the phosphoryl group. The LytTR, ComE(D) (58A) and ComE(D) (58E) complexed with comcde are composed of two protein molecules per DNA duplex. Modeling the complexes against small angle X-ray scattering data indicated that ComE(D) (58E) bound to comcde forms a compact dimer similar to the crystal structure, whereas ComE(D) (58A) -comcde adopts more than one conformation with or without dimer contacts. The various oligomeric states of ComE induce different bending angles of the promoter, which provides a mechanistic scenario for the activation of ComE: the phosphorylation of ComE forces additional bending of comcde, and the release of this bending strain on DNA via the disruption of the ComE dimer may signal the shut-off of the competence state. DATABASE: The molecular models and experimental SAXS data have been deposited on SASBDB (Small Angle Scattering Biological Data Bank) (see http://www.sasbdb.org/aboutSASBDB/) under the SAS codes SASDAA7, SASDAB7 and SASDAC7.
    Mots-clés : Amino Acid Sequence, B3S, Bacterial Proteins, Base Sequence, ComD-ComE two-component system, competence, DNA, Bacterial, DNA-protein complexes, FAAM, Gene Expression Regulation, Bacterial, Models, Molecular, Molecular Sequence Data, Phosphorylation, Protein Conformation, Scattering, Small Angle, Sequence Homology, Amino Acid, Sequence Homology, Nucleic Acid, small-angle X-ray scattering, Streptococcus pneumoniae, Streptococcus pneumoniae, X-Ray Diffraction.


  • D. Soroka, I. Li de la Sierra-Gallay, V. Dubée, S. Triboulet, H. van Tilbeurgh, F. Compain, L. Ballell, D. Barros, J. - L. Mainardi, J. - E. Hugonnet, et M. Arthur, « Hydrolysis of Clavulanate by Mycobacterium tuberculosis β-Lactamase BlaC Harboring a Canonical SDN Motif », Antimicrobial Agents and Chemotherapy, vol. 59, nᵒ 9, p. 5714-5720, 2015.


  • C. Taveneau, K. Blondeau, et S. Bressanelli, « Definition and expression in E. coli of large fragments from the human lipid kinase phosphatidylinositol 4-kinase type III alpha, and purification of a 1100-residue N-terminal module », Protein Expression and Purification, vol. 114, p. 121-127, 2015.


  • M. A. Tortorici, S. Duquerroy, J. Kwok, C. Vonrhein, J. Perez, B. Lamp, G. Bricogne, T. Rümenapf, P. Vachette, et F. A. Rey, « X-Ray Structure of the Pestivirus NS3 Helicase and Its Conformation in Solution », Journal of Virology, vol. 89, nᵒ 8, p. 4356-4371, avr. 2015.


  • M. Valerio-Lepiniec, A. Urvoas, A. Chevrel, A. Guellouz, Y. Ferrandez, A. Mesneau, I. L. de la Sierra-Gallay, M. Aumont-Nicaise, M. Desmadril, H. van Tilbeurgh, et P. Minard, « The αRep artificial repeat protein scaffold: a new tool for crystallization and live cell applications », Biochemical Society Transactions, vol. 43, nᵒ 5, p. 819-824, oct. 2015.
    Mots-clés : B3S, FAAM, MIP, PF, PIM.

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Gruszczyk J, Olivares-Illana V, Nourikyan J, Fleurie A, Béchet E, Gueguen-Chaignon V, Freton C, Aumont-Nicaise M, Moréra S, Grangeasse C, Nessler S.
PLoS One. 2013 Oct 11 ;8(10):e75958.

- Peptide-binding dependent conformational changes regulate the transcriptional activity of the quorum-sensor NprR.
Zouhir S, Perchat S, Nicaise M, Perez J, Guimaraes B, Lereclus D, Nessler S.
Nucleic Acids Res. 2013 Sep ;41(16):7920-33.

- Activity of the Bacillus thuringiensis NprR-NprX cell-cell communication system is coordinated to the physiological stage through a complex transcriptional regulation.
Dubois T, Perchat S, Verplaetse E, Gominet M, Lemy C, Aumont-Nicaise M, Grenha R, Nessler S, Lereclus D.
Mol Microbiol. 2013 Apr ;88(1):48-63.

- Structural basis for the activation mechanism of the PlcR virulence regulator by the quorumsensing signal peptide PapR.
Grenha R, Slamti L, Nicaise M, Refes Y, Lereclus D, Nessler S.
Proc Natl Acad Sci U S A. 2013 Jan 15 ;110(3):1047-52.

- Intermediate conformations during viral fusion glycoprotein structural transition.
Baquero E, Albertini AA, Vachette P, Lepault J, Bressanelli S, Gaudin Y.
Curr Opin Virol. 2013 Apr ;3(2):143-50.

- A two-state cooperative expansion converts the procapsid shell of bacteriophage T5 into a
highly stable capsid isomorphous to the final virion head.
Preux O, Durand D, Huet A, Conway JF, Bertin A, Boulogne C, Drouin-Wahbi J, Trévarin D, Pérez J, Vachette P, Boulanger P.
J Mol Biol. 2013 Jun 12 ;425(11):1999-2014.

- Processive steps in the reverse direction require uncoupling of the lead head lever arm of myosin VI.
Ménétrey J, Isabet T, Ropars V, Mukherjea M, Pylypenko O, Liu X, Perez J, Vachette P, Sweeney HL, Houdusse AM.
Mol Cell. 2012 Oct 12 ;48(1):75-86. doi : 10.1016/j.molcel.2012.07.034. Epub 2012 Aug 30.

- Characterization of monomeric intermediates during VSV glycoprotein structural transition.
Albertini AA, Mérigoux C, Libersou S, Madiona K, Bressanelli S, Roche S, Lepault J, Melki R, Vachette P, Gaudin Y.
PLoS Pathog. 2012 Feb ;8(2):e1002556.

- Bacterial tyrosine kinases : evolution, biological function and structural insights.
Grangeasse C, Nessler S, Mijakovic I.
Philos Trans R Soc Lond B Biol Sci. 2012 Sep 19 ;367(1602):2640-55

- Selection of specific protein binders for pre-defined targets from an optimized library of artificial helicoidal repeat proteins (alphaRep).
Guellouz A, Valerio-Lepiniec M, Urvoas A, Chevrel A, Graille M, Fourati-Kammoun Z, Desmadril M, van Tilbeurgh H, Minard P.
PLoS One. 2013 Aug 27 ;8(8):e71512.

- A network of HMG-box transcription factors regulates sexual cycle in the fungus Podospora anserina.
Ait Benkhali J, Coppin E, Brun S, Peraza-Reyes L, Martin T, Dixelius C, Lazar N, van Tilbeurgh H, Debuchy R.
PLoS Genet. 2013 ;9(7):e1003642.

- The structure of FemX(Wv) in complex with a peptidyl-RNA conjugate : mechanism of aminoacyl transfer from Ala-tRNA(Ala) to peptidoglycan precursors.
Fonvielle M, Li de La Sierra-Gallay I, El-Sagheer AH, Lecerf M, Patin D, Mellal D, Mayer C, Blanot D, Gale N, Brown T, van Tilbeurgh H, Ethève-Quelquejeu M, Arthur M.
Angew Chem Int Ed Engl. 2013 Jul 8 ;52(28):7278-81.

- The carboxy-terminal aN helix of the archaeal XerA tyrosine recombinase is a molecular switch to control site-specific recombination.
Serre MC, El Arnaout T, Brooks MA, Durand D, Lisboa J, Lazar N, Raynal B, van Tilbeurgh H, Quevillon-Cheruel S.
PLoS One. 2013 May 7 ;8(5):e63010.

- Mechanistic and structural basis for inhibition of thymidylate synthase ThyX.
Basta T, Boum Y, Briffotaux J, Becker HF, Lamarre-Jouenne I, Lambry JC, Skouloubris S, Liebl U, Graille M, van Tilbeurgh H, Myllykallio H.
Open Biol. 2012 Oct ;2(10):120120.

- Structure-function analysis of pneumococcal DprA protein reveals that dimerization is crucial for loading RecA recombinase onto DNA during transformation.
Quevillon-Cheruel S, Campo N, Mirouze N, Mortier-Barrière I, Brooks MA, Boudes M, Durand D, Soulet AL, Lisboa J, Noirot P, Martin B, van Tilbeurgh H, Noirot-Gros MF, Claverys JP, Polard P.
Proc Natl Acad Sci U S A. 2012 Sep 11 ;109(37):E2466-75.

- The structure of the NasR transcription antiterminator reveals a one-component system with a NIT nitrate receptor coupled to an ANTAR RNA-binding effector.
Boudes M, Lazar N, Graille M, Durand D, Gaidenko TA, Stewart V, van Tilbeurgh H.
Mol Microbiol. 2012 Aug ;85(3):431-44.

- Found : the elusive ANTAR transcription antiterminator.
Stewart V, van Tilbeurgh H.
PLoS Genet. 2012 ;8(6):e1002773.

- A cell-cell communication system regulates protease production during sporulation in bacteria of the Bacillus cereus group.
Perchat S, Dubois T, Zouhir S, Gominet M, Poncet S, Lemy C, Aumont-Nicaise M, Deutscher J, Gohar M, Nessler S, Lereclus D.
Mol Microbiol. 2011 Nov ;82(3):619-33.

- Structure analysis of the Staphylococcus aureus UDP-N-acetyl-mannosamine
dehydrogenase Cap5O involved in capsular polysaccharide biosynthesis.
Gruszczyk J, Fleurie A, Olivares-Illana V, Béchet E, Zanella-Cleon I, Moréra S, Meyer P, Pompidor G, Kahn R, Grangeasse C, Nessler S.
J Biol Chem. 2011 May 13 ;286(19):17112-21. doi : 10.1074/jbc.M110.216002. Epub 2011 Mar 23.

- Strategies for the structural analysis of multi-protein complexes : lessons from the 3DRepertoire project.
Collinet B, Friberg A, Brooks MA, van den Elzen T, Henriot V, Dziembowski A, Graille M, Durand D, Leulliot N, Saint André C, Lazar N, Sattler M, Séraphin B, van Tilbeurgh H.
J Struct Biol. 2011 Aug ;175(2):147-58. 29.

- Bacterial tyrosine-kinases : structure-function analysis and therapeutic potential.
Grangeasse C, Terreux R, Nessler S.
Biochim Biophys Acta. 2010 Mar ;1804(3):628-34.

- Dissection of Dom34-Hbs1 reveals independent functions in two RNA quality control pathways.
van den Elzen AM, Henri J, Lazar N, Gas ME, Durand D, Lacroute F, Nicaise M, van Tilbeurgh H, Séraphin B, Graille M.
Nat Struct Mol Biol. 2010 Dec ;17(12):1446-52.

- Zinc induces structural reorganization of gelatin binding domain from human fibronectin and affects collagen binding.
Graille M, Pagano M, Rose T, Ravaux MR, van Tilbeurgh H.
Structure. 2010 Jun 9 ;18(6):710-8.

- Structural basis for the regulation mechanism of the tyrosine kinase CapB from Staphylococcus aureus.
Olivares-Illana V, Meyer P, Bechet E, Gueguen-Chaignon V, Soulat D, Lazereg-Riquier S, Mijakovic I, Deutscher J, Cozzone AJ, Laprévote O, Morera S, Grangeasse C, Nessler S.
PLoS Biol. 2008 Jun 10 ;6(6):e143.

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