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Accueil > Publications

Publications Département B3S

2018


  • N. Abdollahi, A. Albani, E. Anthony, A. Baud, M. Cardon, R. Clerc, D. Czernecki, R. Conte, L. David, A. Delaune, S. Djerroud, P. Fourgoux, N. Guiglielmoni, J. Laurentie, N. Lehmann, C. Lochard, R. Montagne, V. Myrodia, V. Opuu, E. Parey, L. Polit, S. Privé, C. Quignot, M. Ruiz-Cuevas, M. Sissoko, N. Sompairac, A. Vallerix, V. Verrecchia, M. Delarue, R. Guérois, Y. Ponty, S. Sacquin-Mora, A. Carbone, C. Froidevaux, S. Le Crom, O. Lespinet, M. Weigt, S. Abboud, J. Bernardes, G. Bouvier, C. Dequeker, A. Ferré, P. Fuchs, G. Lelandais, P. Poulain, H. Richard, H. Schweke, E. Laine, et A. Lopes, « Meet-U: Educating through research immersion », PLoS computational biology, vol. 14, nᵒ 3, p. e1005992, mars 2018.
    Résumé : We present a new educational initiative called Meet-U that aims to train students for collaborative work in computational biology and to bridge the gap between education and research. Meet-U mimics the setup of collaborative research projects and takes advantage of the most popular tools for collaborative work and of cloud computing. Students are grouped in teams of 4-5 people and have to realize a project from A to Z that answers a challenging question in biology. Meet-U promotes "coopetition," as the students collaborate within and across the teams and are also in competition with each other to develop the best final product. Meet-U fosters interactions between different actors of education and research through the organization of a meeting day, open to everyone, where the students present their work to a jury of researchers and jury members give research seminars. This very unique combination of education and research is strongly motivating for the students and provides a formidable opportunity for a scientific community to unite and increase its visibility. We report on our experience with Meet-U in two French universities with master's students in bioinformatics and modeling, with protein-protein docking as the subject of the course. Meet-U is easy to implement and can be straightforwardly transferred to other fields and/or universities. All the information and data are available at www.meet-u.org.
    Mots-clés : AMIG, B3S, BDG, BIM.


  • C. Adam, R. Guérois, A. Citarella, L. Verardi, F. Adolphe, C. Béneut, V. Sommermeyer, C. Ramus, J. Govin, Y. Couté, et V. Borde, « The PHD finger protein Spp1 has distinct functions in the Set1 and the meiotic DSB formation complexes », PLOS Genetics, vol. 14, nᵒ 2, p. e1007223, févr. 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, vol. 592, nᵒ 10, p. 1667-1680, mai 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.

  • G. Annio, T. L. Jennings, O. Tagit, et N. Hildebrandt, « Sensitivity Enhancement of Förster Resonance Energy Transfer Immunoassays by Multiple Antibody Conjugation on Quantum Dots », Bioconjugate Chemistry, vol. 29, nᵒ 6, p. 2082-2089, juin 2018.
    Résumé : Quantum dots (QDs) are not only advantageous for color-tuning, improved brightness, and high stability, but their nanoparticle surfaces also allow for the attachment of many biomolecules. Because IgG antibodies (AB) are in the same size range of biocompatible QDs and the AB orientation after conjugation to the QD is often random, it is difficult to predict if few or many AB per QD will lead to an efficient AB-QD conjugate. This is particularly true for homogeneous Förster resonance energy transfer (FRET) sandwich immunoassays, for which the AB on the QD must bind a biomarker that needs to bind a second AB-FRET-conjugate. Here, we investigate the performance of Tb-to-QD FRET immunoassays against total prostate specific antigen (TPSA) by changing the number of AB per QD while leaving all the other assay components unchanged. We first characterize the AB-QD conjugation by various spectroscopic, microscopic, and chromatographic techniques and then quantify the TPSA immunoassay performance regarding sensitivity, limit of detection, and dynamic range. Our results show that an increasing conjugation ratio leads to significantly enhanced FRET immunoassays. These findings will be highly important for developing QD-based immunoassays in which the concentrations of both AB and QDs can significantly influence the assay performance.
    Mots-clés : B3S, NANO.

  • A. Barwinska-Sendra, A. Baslé, K. J. Waldron, et S. Un, « A charge polarization model for the metal-specific activity of superoxide dismutases », Physical chemistry chemical physics: PCCP, janv. 2018.
    Résumé : The pathogenicity of Staphylococcus aureus is enhanced by having two superoxide dismutases (SODs): a Mn-specific SOD and another that can use either Mn or Fe. Using 94 GHz electron-nuclear double resonance (ENDOR) and electron double resonance detected (ELDOR)-NMR we show that, despite their different metal-specificities, their structural and electronic similarities extend down to their active-site 1H- and 14N-Mn(ii) hyperfine interactions. However these interactions, and hence the positions of these nuclei, are different in the inactive Mn-reconstituted Escherichia coli Fe-specific SOD. Density functional theory modelling attributes this to a different angular position of the E. coli H171 ligand. This likely disrupts the Mn-H171-E170' triad causing a shift in charge and in metal redox potential, leading to the loss of activity. This is supported by the correlated differences in the Mn(ii) zero-field interactions of the three SOD types and suggests that the triad is important for determining metal specific activity.
    Mots-clés : B3S, BHFMR.

  • A. Berto, J. Yu, S. Morchoisne-Bolhy, C. Bertipaglia, R. Vallee, J. Dumont, F. Ochsenbein, R. Guerois, et V. Doye, « Disentangling the molecular determinants for Cenp-F localization to nuclear pores and kinetochores », EMBO reports, vol. 19, nᵒ 5, mai 2018.
    Résumé : Cenp-F is a multifaceted protein implicated in cancer and developmental pathologies. The Cenp-F C-terminal region contains overlapping binding sites for numerous proteins that contribute to its functions throughout the cell cycle. Here, we focus on the nuclear pore protein Nup133 that interacts with Cenp-F both at nuclear pores in prophase and at kinetochores in mitosis, and on the kinase Bub1, known to contribute to Cenp-F targeting to kinetochores. By combining in silico structural modeling and yeast two-hybrid assays, we generate an interaction model between a conserved helix within the Nup133 β-propeller and a short leucine zipper-containing dimeric segment of Cenp-F. We thereby create mutants affecting the Nup133/Cenp-F interface and show that they prevent Cenp-F localization to the nuclear envelope, but not to kinetochores. Conversely, a point mutation within an adjacent leucine zipper affecting the kinetochore targeting of Cenp-F KT-core domain impairs its interaction with Bub1, but not with Nup133, identifying Bub1 as the direct KT-core binding partner of Cenp-F. Finally, we show that Cenp-E redundantly contributes together with Bub1 to the recruitment of Cenp-F to kinetochores.
    Mots-clés : AMIG, B3S, Cenp‐F, in silico modeling, kinetochores, mitosin, nuclear pore.

  • A. Boussac, I. Ugur, A. Marion, M. Sugiura, V. R. I. Kaila, et A. W. Rutherford, « The low spin - high spin equilibrium in the S2-state of the water oxidizing enzyme », Biochimica Et Biophysica Acta, vol. 1859, nᵒ 5, p. 342-356, févr. 2018.
    Résumé : In Photosystem II (PSII), the Mn4CaO5-cluster of the active site advances through five sequential oxidation states (S0to S4) before water is oxidized and O2is generated. Here, we have studied the transition between the low spin (LS) and high spin (HS) configurations of S2using EPR spectroscopy, quantum chemical calculations using Density Functional Theory (DFT), and time-resolved UV-visible absorption spectroscopy. The EPR experiments show that the equilibrium between S2LSand S2HSis pH dependent, with a pKa ≈ 8.3 (n ≈ 4) for the native Mn4CaO5and pKa ≈ 7.5 (n ≈ 1) for Mn4SrO5. The DFT results suggest that exchanging Ca with Sr modifies the electronic structure of several titratable groups within the active site, including groups that are not direct ligands to Ca/Sr, e.g., W1/W2, Asp61, His332 and His337. This is consistent with the complex modification of the pKaupon the Ca/Sr exchange. EPR also showed that NH3addition reversed the effect of high pH, NH3-S2LSbeing present at all pH values studied. Absorption spectroscopy indicates that NH3is no longer bound in the S3TyrZstate, consistent with EPR data showing minor or no NH3-induced modification of S3and S0. In both Ca-PSII and Sr-PSII, S2HSwas capable of advancing to S3at low temperature (198 K). This is an experimental demonstration that the S2LSis formed first and advances to S3via the S2HSstate without detectable intermediates. We discuss the nature of the changes occurring in the S2LSto S2HStransition which allow the S2HSto S3transition to occur below 200 K. This work also provides a protocol for generating S3in concentrated samples without the need for saturating flashes.
    Mots-clés : B3S, DFT, EPR, Mn(4)CaO(5) cluster, Oxygen evolution, Photosystem II, PS2, Spin state.

  • M. Byrdin, C. Duan, D. Bourgeois, et K. Brettel, « A Long-Lived Triplet State Is the Entrance Gateway to Oxidative Photochemistry in Green Fluorescent Proteins », Journal of the American Chemical Society, vol. 140, nᵒ 8, p. 2897-2905, févr. 2018.
    Résumé : Though ubiquitously used as selective fluorescence markers in cellular biology, fluorescent proteins (FPs) still have not disclosed all of their surprising properties. One important issue, notably for single-molecule applications, is the nature of the triplet state, suggested to be the starting point for many possible photochemical reactions leading to phenomena such as blinking or bleaching. Here, we applied transient absorption spectroscopy to characterize dark states in the prototypical enhanced green fluorescent protein (EGFP) of hydrozoan origin and, for comparison, in IrisFP, a representative phototransformable FP of anthozoan origin. We identified a long-lived (approximately 5 ms) dark state that is formed with a quantum yield of approximately 1% and has pronounced absorption throughout the visible-NIR range (peak at around 900 nm). Detection of phosphorescence emission with identical kinetics and excitation spectrum allowed unambiguous identification of this state as the first excited triplet state of the deprotonated chromophore. This triplet state was further characterized by determining its phosphorescence emission spectrum, the temperature dependence of its decay kinetics and its reactivity toward oxygen and electron acceptors and donors. It is suggested that it is this triplet state that lies at the origin of oxidative photochemistry in green FPs, leading to phenomena such as so-called "oxidative redding", "primed photoconversion", or, in a manner similar to that previously observed for organic dyes, redox induced blinking control with the reducing and oxidizing system ("ROXS").
    Mots-clés : B3S, LPB.


  • M. Cardoso Dos Santos, J. Goetz, H. Bartenlian, K. - L. Wong, L. J. Charbonnière, et N. Hildebrandt, « Autofluorescence-Free Live-Cell Imaging Using Terbium Nanoparticles », Bioconjugate Chemistry, févr. 2018.

  • F. Celli, A. Petitalot, C. Samson, F. - X. Theillet, et S. Zinn-Justin, « 1 H,13C and15N backbone resonance assignment of the lamin C-terminal region specific to prelamin A », Biomolecular NMR assignments, mars 2018.
    Résumé : Lamins are the main components of the nucleoskeleton. They form a protein meshwork that underlies the inner nuclear membrane. Mutations in the LMNA gene coding for A-type lamins (lamins A and C) cause a large panel of human diseases, referred to as laminopathies. These diseases include muscular dystrophies, lipodystrophies and premature aging diseases. Lamin A exhibits a C-terminal region that is different from lamin C and is post-translationally modified. It is produced as prelamin A and it is then farnesylated, cleaved, carboxymethylated and cleaved again in order to become mature lamin A. In patients with the severe Hutchinson-Gilford progeria syndrome, a specific single point mutation in LMNA leads to an aberrant splicing of the LMNA gene preventing the post-translational processing of prelamin A. This leads to the accumulation of a permanently farnesylated lamin A mutant lacking 50 amino acids named progerin. We here report the NMR1H,15N,13CO,13Cα and13Cβ chemical shift assignment of the C-terminal region that is specific to prelamin A, from amino acid 567 to amino acid 664. We also report the NMR1H,15N,13CO,13Cα and13Cβ chemical shift assignment of the C-terminal region of the progerin variant, from amino acid 567 to amino acid 614. Analysis of these chemical shift data confirms that both prelamin A and progerin C-terminal domains are largely disordered and identifies a common partially populated α-helix from amino acid 576 to amino acid 585. This helix is well conserved from fishes to mammals.
    Mots-clés : B3S, INTGEN, Intrinsically disordered protein, NMR spectroscopy, Nuclear envelope, Nucleoskeleton.

  • H. - J. Chang, P. Mayonove, A. Zavala, A. De Visch, P. Minard, M. Cohen-Gonsaud, et J. Bonnet, « A Modular Receptor Platform To Expand the Sensing Repertoire of Bacteria », ACS synthetic biology, vol. 7, nᵒ 1, p. 166-175, janv. 2018.
    Résumé : Engineered bacteria promise to revolutionize diagnostics and therapeutics, yet many applications are precluded by the limited number of detectable signals. Here we present a general framework to engineer synthetic receptors enabling bacterial cells to respond to novel ligands. These receptors are activated via ligand-induced dimerization of a single-domain antibody fused to monomeric DNA-binding domains (split-DBDs). Using E. coli as a model system, we engineer both transmembrane and cytosolic receptors using a VHH for ligand detection and demonstrate the scalability of our platform by using the DBDs of two different transcriptional regulators. We provide a method to optimize receptor behavior by finely tuning protein expression levels and optimizing interdomain linker regions. Finally, we show that these receptors can be connected to downstream synthetic gene circuits for further signal processing. The general nature of the split-DBD principle and the versatility of antibody-based detection should support the deployment of these receptors into various hosts to detect ligands for which no receptor is found in nature.
    Mots-clés : B3S, MIP.

  • G. Chararalambidis, S. Das, A. Trapali, A. Quaranta, M. Orio, Z. Halime, P. Fertey, R. Guillot, A. Coutsolelos, W. Leibl, A. Aukauloo, et M. Sircoglou, « Water Molecules Gating a Photoinduced One Electron Two Protons Transfer in a Tyr/His model of Photosystem II », Angewandte Chemie (International Ed. in English), mai 2018.
    Résumé : In this report, we investigate on a biomimetic model of a H-bonded TyrZ/His190 pair covalently attached to a porphyrin sensitizer. Laser flash photolysis in presence of an external electron acceptor reveals the need of water molecules to unlock the light-induced oxidation of the phenol through an intramolecular pathway. Kinetics monitoring encompasses two fast phases with distinct spectral properties. The first phase is related to one-electron transfer from the phenol to the porphyrin radical cation coupled with a domino two-proton transfer leading to the ejection of a proton from the imidazole-phenol pair. The second phase concerns the convoy of the released proton to the porphyrin N4 coordinating cavity. Importantly, our study provides an unprecedented example of light induced electron transfer process in a TyrZ/His190 model of Photosystem II, evidencing the movement of both the phenol and imidazole protons along an isoenergetic pathway.
    Mots-clés : artificial photosynthesis, B3S, LPB, Proton Coupled Electron Transfer, TyrZ-His190 model.

  • J. - H. Chen, L. - J. Yu, A. Boussac, Z. - Y. Wang-Otomo, T. Kuang, et J. - R. Shen, « Properties and structure of a low-potential, penta-heme cytochrome c 552 from a thermophilic purple sulfur photosynthetic bacterium Thermochromatium tepidum », Photosynthesis Research, avr. 2018.
    Résumé : The thermophilic purple sulfur bacterium Thermochromatium tepidum possesses four main water-soluble redox proteins involved in the electron transfer behavior. Crystal structures have been reported for three of them: a high potential iron-sulfur protein, cytochrome c', and one of two low-potential cytochrome c 552 (which is a flavocytochrome c) have been determined. In this study, we purified another low-potential cytochrome c 552 (LPC), determined its N-terminal amino acid sequence and the whole gene sequence, characterized it with absorption and electron paramagnetic spectroscopy, and solved its high-resolution crystal structure. This novel cytochrome was found to contain five c-type hemes. The overall fold of LPC consists of two distinct domains, one is the five heme-containing domain and the other one is an Ig-like domain. This provides a representative example for the structures of multiheme cytochromes containing an odd number of hemes, although the structures of multiheme cytochromes with an even number of hemes are frequently seen in the PDB database. Comparison of the sequence and structure of LPC with other proteins in the databases revealed several characteristic features which may be important for its functioning. Based on the results obtained, we discuss the possible intracellular function of this LPC in Tch. tepidum.
    Mots-clés : B3S, Crystal structure, Cytochrome c, Electron transfer, Multiheme, PS2, Purple sulfur bacteria, Thermochromatium tepidum.

  • R. R. Choubeh, E. Wientjes, P. C. Struik, D. Kirilovsky, et H. van Amerongen, « State transitions in the cyanobacterium Synechococcus elongatus 7942 involve reversible quenching of the photosystem II core », Biochimica Et Biophysica Acta, juin 2018.
    Résumé : Cyanobacteria use chlorophyll and phycobiliproteins to harvest light. The resulting excitation energy is delivered to reaction centers (RCs), where photochemistry starts. The relative amounts of excitation energy arriving at the RCs of photosystem I (PSI) and II (PSII) depend on the spectral composition of the light. To balance the excitations in both photosystems, cyanobacteria perform state transitions to equilibrate the excitation energy. They go to state I if PSI is preferentially excited, for example after illumination with blue light (light I), and to state II after illumination with green-orange light (light II) or after dark adaptation. In this study, we performed 77-K time-resolved fluorescence spectroscopy on wild-type Synechococcus elongatus 7942 cells to measure how state transitions affect excitation energy transfer to PSI and PSII in different light conditions and to test the various models that have been proposed in literature. The time-resolved spectra show that the PSII core is quenched in state II and that this is not due to a change in excitation energy transfer from PSII to PSI (spill-over), either direct or indirect via phycobilisomes.
    Mots-clés : B3S, Cyanobacteria, MROP, Photosystem II, State transitions, Time-resolved fluorescence spectroscopy.

  • M. David, C. Lebrun, T. Duguet, F. Talmont, R. Beech, S. Orlowski, F. André, R. K. Prichard, et A. Lespine, « Structural model, functional modulation by ivermectin and tissue localization of Haemonchus contortus P-glycoprotein-13 », International Journal for Parasitology. Drugs and Drug Resistance, vol. 8, nᵒ 1, p. 145-157, avr. 2018.
    Résumé : Haemonchus contortus, one of the most economically important parasites of small ruminants, has become resistant to the anthelmintic ivermectin. Deciphering the role of P-glycoproteins in ivermectin resistance is desirable for understanding and overcoming this resistance. In the model nematode, Caenorhabditis elegans, P-glycoprotein-13 is expressed in the amphids, important neuronal structures for ivermectin activity. We have focused on its ortholog in the parasite, Hco-Pgp-13. A 3D model of Hco-Pgp-13, presenting an open inward-facing conformation, has been constructed by homology with the Cel-Pgp-1 crystal structure. In silico docking calculations predicted high affinity binding of ivermectin and actinomycin D to the inner chamber of the protein. Following in vitro expression, we showed that ivermectin and actinomycin D modulated Hco-Pgp-13 ATPase activity with high affinity. Finally, we found in vivo Hco-Pgp-13 localization in epithelial, pharyngeal and neuronal tissues. Taken together, these data suggest a role for Hco-Pgp-13 in ivermectin transport, which could contribute to anthelmintic resistance.
    Mots-clés : ABC transporters, B3S, Haemonchus contortus, Homology modeling, Ivermectin, LPSM, LSOD, Nematode, P-glycoprotein.


  • A. De Muyt, A. Pyatnitskaya, J. Andréani, L. Ranjha, C. Ramus, R. Laureau, A. Fernandez-Vega, D. Holoch, E. Girard, J. Govin, R. Margueron, Y. Couté, P. Cejka, R. Guérois, et V. Borde, « A meiotic XPF–ERCC1-like complex recognizes joint molecule recombination intermediates to promote crossover formation », Genes & Development, vol. 32, nᵒ 3-4, p. 283-296, févr. 2018.

  • 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 (Weinheim an Der Bergstrasse, Germany), vol. 24, nᵒ 32, p. 8081-8086, juin 2018.
    Résumé : There is a renewed interest for β-lactams for treating infections due to Mycobacterium tuberculosis and M. abscessus because their β-lactamases are inhibited by classical (clavulanate) or new generation (avibactam) inhibitors, respectively. Here, access to an azido derivative of the diazabicyclooctane (DBO) scaffold of avibactam for functionalization by the Huisgen-Sharpless cycloaddition reaction is reported. The amoxicillin-DBO combinations were active, indicating that the triazole ring is compatible with drug penetration (minimal inhibitory concentration of 16 μg mL-1 for both species). Mechanistically, β-lactamase inhibition was not sufficient to account for the potentiation of amoxicillin by DBOs. Thus, the latter compounds were investigated as inhibitors of l,d-transpeptidases (Ldts), which are the main peptidoglycan polymerases in mycobacteria. The DBOs acted as slow-binding inhibitors of Ldts by S-carbamoylation indicating that optimization of DBOs for Ldt inhibition is an attractive strategy to obtain drugs selectively active on mycobacteria.
    Mots-clés : Avibactam, Azabicyclo Compounds, B3S, beta-Lactamase Inhibitors, beta-Lactamases, FAAM, l,d-transpeptidases, Mycobacterium abscessus, Mycobacterium tuberculosis, Peptidoglycan, β-lactamase.


  • J. B. Fernandes, M. Duhamel, M. Seguéla-Arnaud, N. Froger, C. Girard, S. Choinard, V. Solier, N. De Winne, G. De Jaeger, K. Gevaert, P. Andrey, M. Grelon, R. Guerois, R. Kumar, et R. Mercier, « FIGL1 and its novel partner FLIP form a conserved complex that regulates homologous recombination », PLOS Genetics, vol. 14, nᵒ 4, p. e1007317, avr. 2018.

  • M. - H. Ha-Thi, V. - T. Pham, T. Pino, V. Maslova, A. Quaranta, C. Lefumeux, W. Leibl, et A. Aukauloo, « Photoinduced electron transfer in a molecular dyad by nanosecond pump-pump-probe spectroscopy », Photochemical & Photobiological Sciences: Official Journal of the European Photochemistry Association and the European Society for Photobiology, juin 2018.
    Résumé : The design of robust and inexpensive molecular photocatalysts for the conversion of abundant stable molecules like H2O and CO2 into an energetic carrier is one of the major fundamental questions for scientists nowadays. The outstanding challenge is to couple single photoinduced charge separation events with the sequential accumulation of redox equivalents at the catalytic unit for performing multielectronic catalytic reactions. Herein, double excitation by nanosecond pump-pump-probe experiments was used to interrogate the photoinduced charge transfer and charge accumulation on a molecular dyad composed of a porphyrin chromophore and a ruthenium-based catalyst in the presence of a reversible electron acceptor. An accumulative charge transfer state is unattainable because of rapid reverse electron transfer to the photosensitizer upon the second excitation and the low driving force of the forward photodriven electron transfer reaction. Such a method allows the fundamental understanding of the relaxation mechanism after two sequential photon absorptions, deciphering the undesired electron transfer reactions that limit the charge accumulation efficiency. This study is a step toward the improvement of synthetic strategies of molecular photocatalysts for light-induced charge accumulation and more generally, for solar energy conversion.
    Mots-clés : B3S, LPB.

  • N. Hildebrandt et O. Tagit, « Colloidal Nanoparticles for Signal Enhancement in Optical Diagnostic Assays », Journal of Nanoscience and Nanotechnology, vol. 18, nᵒ 10, p. 6671-6679, oct. 2018.
    Résumé : The use of nanotechnologies for the development of highly sensitive and affordable diagnostic assays has significantly improved the ability to detect and characterize multiple types of biomarkers. Semiconductor and metal nanoparticles with unique optical properties have been successfully integrated within biomarker detection schemes for the generation and enhancement of optical signals in label-based and label-free assays. Highly sensitive label-based diagnostics has been realized particularly via using quantum dots (QDs) as labeling probes. Similarly, many label-free techniques that are emerging as potential complements to label-based approaches benefit from signal enhancement strategies using e.g., metal nanoparticles. This review presents a concise overview of recent advances in diagnostic assays that utilize nanoparticles for the generation and enhancement of optical signals in fluorescence- and surface plasmon resonance-based techniques. Advanced diagnostic assays that utilize nanoparticles provide major improvements in detection sensitivity, which can potentially meet the challenging requirements of clinical diagnostics.
    Mots-clés : B3S, NANO.

  • G. Hutinet, A. Besle, O. Son, S. McGovern, R. Guerois, M. - A. Petit, F. Ochsenbein, et F. Lecointe, « Sak4 of Phage HK620 Is a RecA Remote Homolog With Single-Strand Annealing Activity Stimulated by Its Cognate SSB Protein », Frontiers in Microbiology, vol. 9, p. 743, 2018.
    Résumé : Bacteriophages are remarkable for the wide diversity of proteins they encode to perform DNA replication and homologous recombination. Looking back at these ancestral forms of life may help understanding how similar proteins work in more sophisticated organisms. For instance, the Sak4 family is composed of proteins similar to the archaeal RadB protein, a Rad51 paralog. We have previously shown that Sak4 allowed single-strand annealing in vivo, but only weakly compared to the phage λ Redβ protein, highlighting putatively that Sak4 requires partners to be efficient. Here, we report that the purified Sak4 of phage HK620 infecting Escherichia coli is a poorly efficient annealase on its own. A distant homolog of SSB, which gene is usually next to the sak4 gene in various species of phages, highly stimulates its recombineering activity in vivo. In vitro, Sak4 binds single-stranded DNA and performs single-strand annealing in an ATP-dependent way. Remarkably, the single-strand annealing activity of Sak4 is stimulated by its cognate SSB. The last six C-terminal amino acids of this SSB are essential for the binding of Sak4 to SSB-covered single-stranded DNA, as well as for the stimulation of its annealase activity. Finally, expression of sak4 and ssb from HK620 can promote low-level of recombination in vivo, though Sak4 and its SSB are unable to promote strand exchange in vitro. Regarding its homology with RecA, Sak4 could represent a link between two previously distinct types of recombinases, i.e., annealases that help strand exchange proteins and strand exchange proteins themselves.
    Mots-clés : AMIG, annealase, B3S, bacteriophage, Rad51 paralog, RecA, recombineering, Sak4, SSB, strand exchange protein.

  • S. M. Kapetanaki, M. J. Burton, J. Basran, C. Uragami, P. C. E. Moody, J. S. Mitcheson, R. Schmid, N. W. Davies, P. Dorlet, M. H. Vos, N. M. Storey, et E. Raven, « A mechanism for CO regulation of ion channels », Nature Communications, vol. 9, nᵒ 1, p. 907, 2018.
    Résumé : Despite being highly toxic, carbon monoxide (CO) is also an essential intracellular signalling molecule. The mechanisms of CO-dependent cell signalling are poorly defined, but are likely to involve interactions with heme proteins. One such role for CO is in ion channel regulation. Here, we examine the interaction of CO with KATP channels. We find that CO activates KATP channels and that heme binding to a CXXHX16H motif on the SUR2A receptor is required for the CO-dependent increase in channel activity. Spectroscopic and kinetic data were used to quantify the interaction of CO with the ferrous heme-SUR2A complex. The results are significant because they directly connect CO-dependent regulation to a heme-binding event on the channel. We use this information to present molecular-level insight into the dynamic processes that control the interactions of CO with a heme-regulated channel protein, and we present a structural framework for understanding the complex interplay between heme and CO in ion channel regulation.
    Mots-clés : B3S, LSOD.

  • F. Kong, A. Burlacot, Y. Liang, B. Legeret, S. Alseekh, Y. Brotman, A. R. Fernie, A. Krieger-Liszkay, F. Beisson, G. Peltier, et Y. Li-Beisson, « Interorganelle Communication: Peroxisomal MALATE DEHYDROGENASE 2 Connects Lipid Catabolism to Photosynthesis through Redox Coupling in Chlamydomonas », The Plant Cell, juill. 2018.
    Résumé : Plants and algae must tightly coordinate photosynthetic electron transport and metabolic activities given that they often face fluctuating light and nutrient conditions. The exchange of metabolites and signaling molecules between organelles is thought to be central to this regulation but evidence for this is still fragmentary. Here we show that knocking out the peroxisome-located MALATE DEHYDROGENASE 2 (MDH2) of Chlamydomonas reinhardtii results in dramatic alterations not only in peroxisomal fatty acid breakdown but also in chloroplast starch metabolism and photosynthesis. mdh2 mutants accumulated 50% more storage lipid and two-fold more starch than wild type during nitrogen deprivation. In parallel, mdh2 showed increased PSII yield and photosynthetic CO2 fixation. Metabolite analyses revealed a >60% reduction in malate, together with increased levels of NADPH and H2O2 in mdh2. Similar phenotypes were found upon high light exposure. Furthermore, based on the lack of starch accumulation in a knock-out mutant of the H2O2-producing peroxisomal ACYL-COA OXIDASE 2 and on the effects of H2O2 supplementation, we propose that peroxisome-derived H2O2 acts as a regulator of chloroplast metabolism. We conclude that peroxisomal MDH2 helps photoautotrophs cope with nitrogen scarcity and high light by transmitting the redox state of the peroxisome to the chloroplast by means of malate shuttle- and H2O2-based redox signaling.
    Mots-clés : B3S, MROP.


  • H. Kubota-Kawai, R. Mutoh, K. Shinmura, P. Sétif, M. M. Nowaczyk, M. Rögner, T. Ikegami, H. Tanaka, et G. Kurisu, « X-ray structure of an asymmetrical trimeric ferredoxin–photosystem I complex », Nature Plants, vol. 4, nᵒ 4, p. 218-224, 2018.

  • P. Lafite, F. André, J. P. Graves, D. C. Zeldin, P. M. Dansette, et D. Mansuy, « Role of Arginine 117 in Substrate Recognition by Human Cytochrome P450 2J2 », International Journal of Molecular Sciences, vol. 19, nᵒ 7, juill. 2018.
    Résumé : The influence of Arginine 117 of human cytochrome P450 2J2 in the recognition of ebastine and a series of terfenadone derivatives was studied by site-directed mutagenesis. R117K, R117E, and R117L mutants were produced, and the behavior of these mutants in the hydroxylation of ebastine and terfenadone derivatives was compared to that of wild-type CYP2J2. The data clearly showed the importance of the formation of a hydrogen bond between R117 and the keto group of these substrates. The data were interpreted on the basis of 3D homology models of the mutants and of dynamic docking of the substrates in their active site. These modeling studies also suggested the existence of a R117-E222 salt bridge between helices B' and F that would be important for maintaining the overall folding of CYP2J2.
    Mots-clés : B3S, CYP2J2, docking, homology modeling, human cytochrome P450, inhibitor, LSOD, mutants, regioselectivity.

  • F. Lallemand, A. Petitalot, S. Vacher, L. de Koning, K. Taouis, B. S. Lopez, S. Zinn-Justin, N. Dalla-Venezia, W. Chemlali, A. Schnitzler, R. Lidereau, I. Bieche, et S. M. Caputo, « Involvement of the FOXO6 transcriptional factor in breast carcinogenesis », Oncotarget, vol. 9, nᵒ 7, p. 7464-7475, janv. 2018.
    Résumé : In mammals, FOXO transcriptional factors form a family of four members (FOXO1, 3, 4, and 6) involved in the modulation proliferation, apoptosis, and carcinogenesis. The role of the FOXO family in breast cancer remains poorly elucidated. According to the cellular context and the stage of the disease, FOXOs can have opposite effects on carcinogenesis. To study the role of FOXOs in breast carcinogenesis in more detail, we examined their expression in normal tissues, breast cell lines, and a large series of breast tumours of human origin. We found a very low physiological level ofFOXO6expression in normal adult tissues and high levels of expression in foetal brain.FOXOgene expressions fluctuate specifically in breast cancer cells compared to normal cells, suggesting that these genes may have different roles in breast carcinogenesis. For the first time, we have shown that, among the variousFOXOgenes, onlyFOXO6was frequently highly overexpressed in breast cell lines and tumours. We also found that inhibition of the endogenous expression of FOXO6 by a specific siRNA inhibited the growth of the human breast cell lines MDA-MB-468 and HCC-38. FACS and Western blot analysis showed that inhibition of endogenous expression of FOXO6 induced accumulation of cells in G0/G1 phase of the cell cycle, but not apoptosis. These results tend to demonstrate that the overexpression of the humanFOXO6gene that we highlighted in the breast tumors stimulates breast carcinogenesis by activating breast cancer cell proliferation.
    Mots-clés : B3S, cervical squamous cell carcinoma, endometrial adenocarcinoma, gynecological cancers, INTGEN, prognosis, uc.189.

  • S. Leach, N. C. Jones, S. V. Hoffmann, et S. Un, « VUV Absorption Spectra of Gas-Phase Quinoline in the 3.5-10.7 eV Photon Energy Range », The Journal of Physical Chemistry. A, juill. 2018.
    Résumé : The absorption spectrum of quinoline was measured in the gas phase between 3.5 and 10.7 eV using a synchrotron photon source. A large number of sharp and broad spectral features were observed, some of which have plasmon-type collective π-electron modes contributing to their intensities. Eight valence electronic transitions were assigned, considerably extending the number of π-π* transitions previously observed mainly in solution. The principal factor in solution red-shifts is found to be the Lorentz-Lorenz polarizability parameter. Rydberg bands, observed for the first time, are analyzed into eight different series, converging to the D0 ground and two excited electronic states, namely, D3 and D4, of the quinoline cation. The R1 series limit is 8.628 eV for the first ionization energy of quinoline, a value more precise than previously published. This value, combined with cation electronic transition data, provides precise energies, respectively, 10.623 and 11.355 eV, for the D3 and D4 states. The valence transition assignments are based on density functional theory (DFT) calculations as well as on earlier Pariser-Parr-Pople (P-P-P) self-consistent field linear combination of atomic orbitals molecular orbital results. The relative quality of the P-P-P and DFT data is discussed. Both are far from spectroscopic accuracy concerning electronic excited states but were nevertheless useful for our assignments. Our time-dependent DFT calculations of quinoline are excellent for its ground-state properties such as geometry, rotational constants, dipole moment, and vibrational frequencies, which agree well with experimental observations. Vibrational components of the valence and Rydberg transitions mainly involve C-H bend and C═C and C═N stretch modes. Astrophysical applications of the vacuum UV absorption of quinoline are briefly discussed.
    Mots-clés : B3S, BHFMR.

  • L. Lecoq, S. Wang, T. Wiegand, S. Bressanelli, M. Nassal, B. H. Meier, et A. Böckmann, « Localizing Conformational Hinges by NMR: Where Do Hepatitis B Virus Core Proteins Adapt for Capsid Assembly? », Chemphyschem: A European Journal of Chemical Physics and Physical Chemistry, vol. 19, nᵒ 11, p. 1336-1340, juin 2018.
    Résumé : The hepatitis B virus (HBV) icosahedral nucleocapsid is assembled from 240 chemically identical core protein molecules and, structurally, comprises four groups of symmetrically nonequivalent subunits. We show here that this asymmetry is reflected in solid-state NMR spectra of the capsids, in which peak splitting is observed for a subset of residues. We compare this information to dihedral angle variations from available 3D structures and also to computational predictions of "dynamic" domains and molecular hinges. We find that although, at the given resolution, dihedral angles variations directly obtained from the X-ray structures are not precise enough to be interpreted, the chemical-shift information from NMR correlates, and interestingly goes beyond, information from bioinformatics approaches. Our study reveals the high sensitivity with which NMR can detect the residues allowing the subtle conformational adaptations needed in lattice formation. Our findings are important for understanding the formation and modulation of protein assemblies in general.
    Mots-clés : asymmetric unit, B3S, core protein, hepatitis B virus, IMAPP, nucleocapsid, solid-state NMR.

  • L. Lecoq, S. Wang, T. Wiegand, S. Bressanelli, M. Nassal, B. H. Meier, et A. Böckmann, « Solid-state [13C-15N] NMR resonance assignment of hepatitis B virus core protein », Biomolecular NMR assignments, vol. 12, nᵒ 1, p. 205-214, avr. 2018.
    Résumé : Each year, nearly 900,000 deaths are due to serious liver diseases caused by chronic hepatitis B virus infection. The viral particle is composed of an outer envelope and an inner icosahedral nucleocapsid formed by multiple dimers of a ~ 20 kDa self-assembling core protein (Cp). Here we report the solid-state 13C and 15N resonance assignments of the assembly domain, Cp149, of the core protein in its capsid form. A secondary chemical shift analysis of the 140 visible residues suggests an overall alpha-helical three-dimensional fold matching that derived for Cp149 from the X-ray crystallography of the capsid, and from solution-state NMR of the Cp149 dimer. Interestingly, however, at three distinct regions the chemical shifts in solution differ significantly between core proteins in the capsid state versus in the dimer state, strongly suggesting the respective residues to be involved in capsid assembly.
    Mots-clés : AMIG, Assignments, B3S, Core protein, Hepatitis B virus, IMAPP, Nucleocapsid, Solid-state NMR.

  • G. Lenoir, T. Dieudonné, A. Lamy, M. Lejeune, J. - L. Vazquez-Ibar, et C. Montigny, « Screening of Detergents for Stabilization of Functional Membrane Proteins », Current Protocols in Protein Science, p. e59, juill. 2018.
    Résumé : Membrane protein studies usually require use of detergents to extract and isolate proteins from membranes and manipulate them in a soluble context for their functional or structural characterization. However, solubilization with detergent may interfere with MP stability and may directly affect MP function or structure. Moreover, detergent properties can be affected such as critical micellar concentration (CMC) can be affected by the experimental conditions. Consequently, the experimenter must pay attention to both the protein and the behavior of the detergent. This article provides a convenient protocol for estimating the CMC of detergents in given experimental conditions. Then, it presents two protocols aimed at monitoring the function of a membrane protein in the presence of detergent. Such experiments may help to test various detergents for their inactivating or stabilizing effects on long incubation times, ranging from few hours to some days. © 2018 by John Wiley & Sons, Inc.
    Mots-clés : B3S, detergents, Drs2p/Cdc50p, lipids, LMNG, LPSM, membrane protein, SERCA1a, stabilization.


  • X. Liang, C. Guo, S. Liu, Z. Dang, Y. Wei, X. Yi, et S. Abel, « Cosolubilization of phenanthrene and pyrene in surfactant micelles: Experimental and atomistic simulations studies », Journal of Molecular Liquids, vol. 263, p. 1-9, août 2018.
    Résumé : Solubilization of mixed phenanthrene (PHE) and pyrene (PYR) in Triton X-100 (TX), sodium dodecyl sulfate (SDS) and mixed TX-SDS surfactant solutions were done to observe their cosolubilization effect. Moreover, molecular dynamics (MD) simulations were performed to reveal how polycyclic aromatic hydrocarbons (PAHs) coexist in the micelle. Cosolubilization of PHE and PYR exhibited synergism along with decreasing synergistic extent with increasing SDS in mixed micelle. MD simulations verified the distribution of PHE and PYR in the shell and core regions of pure SDS and mixed SDS-TX micelles (with molar ratio of 1: 1), which were chosen as the representative systems for simulation study. The movement of PHE and PYR inside the micelle along with their different probability to contact with SDS non‑hydrogen atoms in pure SDS and mixed SDS-TX solubilization systems suggests the different solubilization sites of the two PAHs inside the micelle leading to their coexistence in the micelle. This study implies the significance of considering cosolubilization effects between PAH mixtures in determining surfactant concentration for environmental remediation.
    Mots-clés : B3S, Cosolubilization, LBMS, Molecular dynamics simulations, Phenanthrene, Pyrene, Surfactant.


  • M. J. Llansola-Portoles, K. Redeckas, S. Streckaité, C. Ilioaia, A. A. Pascal, A. Telfer, M. Vengris, L. Valkunas, et B. Robert, « Lycopene crystalloids exhibit singlet exciton fission in tomatoes », Physical Chemistry Chemical Physics, vol. 20, nᵒ 13, p. 8640-8646, 2018.

  • E. Ma, P. Dupaigne, L. Maloisel, R. Guerois, E. Le Cam, et E. Coïc, « Rad52-Rad51 association is essential to protect Rad51 filaments against Srs2, but facultative for filament formation », eLife, vol. 7, juill. 2018.
    Résumé : Homology search and strand exchange mediated by Rad51 nucleoprotein filaments are key steps of the homologous recombination process. In budding yeast, Rad52 is the main mediator of Rad51 filament formation, thereby playing an essential role. The current model assumes that Rad51 filament formation requires the interaction between Rad52 and Rad51. However, we report here that Rad52 mutations that disrupt this interaction do not affect γ-ray- or HO endonuclease-induced gene conversion frequencies. In vivo and in vitro studies confirmed that Rad51 filaments formation is not affected by these mutations. Instead, we found that Rad52-Rad51 association makes Rad51 filaments toxic in Srs2-deficient cells after exposure to DNA damaging agents, independently of Rad52 role in Rad51 filament assembly. Importantly, we also demonstrated that Rad52 is essential for protecting Rad51 filaments against dissociation by the Srs2 DNA translocase. Our findings open new perspectives in the understanding of the role of Rad52 in eukaryotes.
    Mots-clés : AMIG, B3S, biochemistry, chemical biology, chromosomes, gene expression, S. cerevisiae.

  • A. Mahuzier, A. Shihavuddin, C. Fournier, P. Lansade, M. Faucourt, N. Menezes, A. Meunier, M. Garfa-Traoré, M. - F. Carlier, R. Voituriez, A. Genovesio, N. Spassky, et N. Delgehyr, « Ependymal cilia beating induces an actin network to protect centrioles against shear stress », Nature Communications, vol. 9, nᵒ 1, p. 2279, juin 2018.
    Résumé : Multiciliated ependymal cells line all brain cavities. The beating of their motile cilia contributes to the flow of cerebrospinal fluid, which is required for brain homoeostasis and functions. Motile cilia, nucleated from centrioles, persist once formed and withstand the forces produced by the external fluid flow and by their own cilia beating. Here, we show that a dense actin network around the centrioles is induced by cilia beating, as shown by the disorganisation of the actin network upon impairment of cilia motility. Moreover, disruption of the actin network, or specifically of the apical actin network, causes motile cilia and their centrioles to detach from the apical surface of ependymal cell. In conclusion, cilia beating controls the apical actin network around centrioles; the mechanical resistance of this actin network contributes, in turn, to centriole stability.
    Mots-clés : ACTIN, B3S.

  • L. Marichal, J. - P. Renault, S. Chédin, G. Lagniel, G. Klein, J. - C. Aude, C. Tellier-Lebegue, J. Armengaud, S. Pin, J. Labarre, et Y. Boulard, « Importance of Post-translational Modifications in the Interaction of Proteins with Mineral Surfaces: The Case of Arginine Methylation and Silica surfaces », Langmuir: the ACS journal of surfaces and colloids, vol. 34, nᵒ 18, p. 5312-5322, mai 2018.
    Résumé : Understanding the mechanisms involved in the interaction of proteins with inorganic surfaces is of major interest for both basic research and practical applications involving nanotechnology. From the list of cellular proteins with the highest affinity for silica nanoparticles, we highlighted the group of proteins containing arginine-glycine-glycine (RGG) motifs. Biochemical experiments confirmed that RGG motifs interact strongly with the silica surfaces. The affinity of these motifs is further increased when the R residue is asymmetrically, but not symmetrically, dimethylated. Molecular dynamics simulations show that the asymmetrical dimethylation generates an electrostatic asymmetry in the guanidinium group of the R residue, orientating and stabilizing it on the silica surface. The RGG motifs (methylated or not) systematically target the siloxide groups on the silica surface through an ionic interaction, immediately strengthened by hydrogen bonds with proximal silanol and siloxane groups. Given that, in vivo, RGG motifs are often asymmetrically dimethylated by specific cellular methylases, our data add support to the idea that this type of methylation is a key mechanism for cells to regulate the interaction of the RGG proteins with their cellular partners.
    Mots-clés : B3S, BDG, BIM, IMAPP, PEPS.


  • A. A. Nadaradjane, R. Guerois, et J. Andreani, « Protein-Protein Docking Using Evolutionary Information », in Protein Complex Assembly, vol. 1764, J. A. Marsh, Éd. New York, NY: Springer New York, 2018, p. 429-447.

  • E. Martin, M. Amar, C. Dalle, I. Youssef, C. Boucher, C. Le Duigou, M. Brückner, A. Prigent, V. Sazdovitch, A. Halle, J. M. Kanellopoulos, B. Fontaine, B. Delatour, et C. Delarasse, « New role of P2X7 receptor in an Alzheimer's disease mouse model », Molecular Psychiatry, juin 2018.
    Résumé : Extracellular aggregates of amyloid β (Aβ) peptides, which are characteristic of Alzheimer's disease (AD), act as an essential trigger for glial cell activation and the release of ATP, leading to the stimulation of purinergic receptors, especially the P2X7 receptor (P2X7R). However, the involvement of P2X7R in the development of AD is still ill-defined regarding the dual properties of this receptor. Particularly, P2X7R activates the NLRP3 inflammasome leading to the release of the pro-inflammatory cytokine, IL-1β; however, P2X7R also induces cleavage of the amyloid precursor protein generating Aβ peptides or the neuroprotective fragment sAPPα. We thus explored in detail the functions of P2X7R in AD transgenic mice. Here, we show that P2X7R deficiency reduced Aβ lesions, rescued cognitive deficits and improved synaptic plasticity in AD mice. However, the lack of P2X7R did not significantly affect the release of IL-1β or the levels of non-amyloidogenic fragment, sAPPα, in AD mice. Instead, our results show that P2X7R plays a critical role in Aβ peptide-mediated release of chemokines, particularly CCL3, which is associated with pathogenic CD8+ T cell recruitment. In conclusion, our study highlights a novel detrimental function of P2X7R in chemokine release and supports the notion that P2X7R may be a promising therapeutic target for AD.
    Mots-clés : B3S, PIM.

  • M. Messant, S. Timm, A. Fantuzzi, W. Weckwerth, H. Bauwe, B. Rutherford, et A. Krieger-Liszkay, « Glycolate induces redox tuning of photosystem II in vivo: study of a photorespiration mutant », Plant Physiology, mai 2018.
    Résumé : Bicarbonate removal from the non-heme iron at the acceptor side of photosystem II (PSII) was recently shown to shift the midpoint potential of the primary quinone acceptor QA to a more positive potential and lowers the yield of singlet oxygen (1O2) production. The presence of QA- results in weaker binding of bicarbonate, suggesting a redox-based regulatory and protective mechanism where loss of bicarbonate or exchange of bicarbonate by other small carboxylic acids may protect PSII against 1O2 in vivo under photorespiratory conditions. Here we compared the properties of QA in the Arabidopsis (Arabidopsis thaliana) photorespiration mutant hpr1-1, deficient in NADH-dependent, peroxisomal hydroxypyruvate reductase 1 (HPR1), which accumulates glycolate in leaves, to the wild type. Photosynthetic electron transport was affected in the mutant, and chlorophyll fluorescence showed slower electron transport between QA and QB in the mutant. Glycolate induced an increase in the temperature maximum of thermoluminescence emission indicating a shift of the midpoint potential of QA to a more positive value. The yield of 1O2 production was lowered in thylakoid membranes isolated from hpr1-1 compared to the wild type, consistent with a higher potential of QA/QA-. In addition, electron donation to photosystem I was affected in hpr1-1 at higher light intensities consistent with diminished electron transfer out of photosystem II. This study indicates that replacement of bicarbonate at the non-heme iron by a small carboxylate anion occurs in plants in vivo. These findings suggested that replacement of the bicarbonate on the non-heme iron by glycolate may represent a regulatory mechanism that protects PSII against photo-oxidative stress under low CO2 conditions.
    Mots-clés : B3S, MROP.


  • T. Meyer, S. Renoud, A. Vigouroux, A. Miomandre, V. Gaillard, I. Kerzaon, C. Prigent-Combaret, G. Comte, S. Moréra, L. Vial, et C. Lavire, « Regulation of hydroxycinnamic acid degradation drives Agrobacterium fabrum lifestyles. », Molecular Plant-Microbe Interactions, févr. 2018.

  • T. Meyer, A. Vigouroux, M. Aumont-Nicaise, G. Comte, L. Vial, C. Lavire, et S. Moréra, « The plant defense signal galactinol is specifically used as a nutrient by the bacterial pathogen Agrobacterium fabrum », The Journal of Biological Chemistry, vol. 293, nᵒ 21, p. 7930-7941, mai 2018.
    Résumé : The bacterial plant pathogen Agrobacterium fabrum uses periplasmic-binding proteins (PBPs) along with ABC transporters to import a wide variety of plant molecules as nutrients. Nonetheless, how A. fabrum acquires plant metabolites is incompletely understood. Using genetic approaches and affinity measurements, we identified here the PBP MelB and its transporter as being responsible for the uptake of the raffinose family of oligosaccharides (RFO), which are the most widespread d-galactose-containing oligosaccharides in higher plants. We also found that the RFO precursor galactinol, recently described as a plant defense molecule, is imported into Agrobacterium via MelB with nanomolar range affinity. Structural analyses and binding mode comparisons of the X-ray structures of MelB in complex with raffinose, stachyose, galactinol, galactose, and melibiose (a raffinose degradation product) revealed how MelB recognizes the nonreducing end galactose common to all these ligands and that MelB has a strong preference for a two-unit sugar ligand. Of note, MelB conferred a competitive advantage to A. fabrum in colonizing the rhizosphere of tomato plants. Our integrative work highlights the structural and functional characteristics of melibiose and galactinol assimilation by A. fabrum, leading to a competitive advantage for these bacteria in the rhizosphere. We propose that the PBP MelB, which is highly conserved among both symbionts and pathogens from Rhizobiace family, is a major trait in these bacteria required for early steps of plant colonization.
    Mots-clés : ABC transporter, agrobacterium, Agrobacterium fabrum, B3S, bacteria, crystal structure, galactinol, MESB3S, microbiology, periplasmic binding protein, PF, PIM, plant defense, RFOs, sugar transport.

  • E. Mileo, M. Ilbert, A. Barducci, P. Bordes, M. - P. Castanié-Cornet, C. Garnier, P. Genevaux, R. Gillet, P. Goloubinoff, F. Ochsenbein, G. Richarme, C. Iobbi-Nivol, M. - T. Giudici-Orticoni, B. Gontero, et O. Genest, « Emerging fields in chaperone proteins: A French workshop », Biochimie, vol. 151, p. 159-165, août 2018.
    Résumé : The "Bioénergétique et Ingénierie des Protéines (BIP)" laboratory, CNRS (France), organized its first French workshop on molecular chaperone proteins and protein folding in November 2017. The goal of this workshop was to gather scientists working in France on chaperone proteins and protein folding. This initiative was a great success with excellent talks and fruitful discussions. The highlights were on the description of unexpected functions and post-translational regulation of known molecular chaperones (such as Hsp90, Hsp33, SecB, GroEL) and on state-of-the-art methods to tackle questions related to this theme, including Cryo-electron microscopy, Nuclear Magnetic Resonance (NMR), Electron Paramagnetic Resonance (EPR), simulation and modeling. We expect to organize a second workshop in two years that will include more scientists working in France in the chaperone field.
    Mots-clés : Aggregation, AMIG, B3S, Chaperone proteins, Folding/misfolding, Multifunctionality, Plasticity, Structural dynamics.

  • 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.


  • P. Müller, E. Ignatz, S. Kiontke, K. Brettel, et L. - O. Essen, « Sub-nanosecond tryptophan radical deprotonation mediated by a protein-bound water cluster in class II DNA photolyases », Chemical Science, vol. 9, nᵒ 5, p. 1200-1212, 2018.

  • M. Nakamura, A. Boussac, et M. Sugiura, « Consequences of structural modifications in cytochrome b559 on the electron acceptor side of Photosystem II », Photosynthesis Research, mai 2018.
    Résumé : Cytb559 in Photosystem II is a heterodimeric b-type cytochrome. The subunits, PsbE and PsbF, consist each in a membrane α-helix. Mutants were previously designed and studied in Thermosynechococcus elongatus (Sugiura et al., Biochim Biophys Acta 1847:276-285, 2015) either in which an axial histidine ligand of the haem-iron was substituted for a methionine, the PsbE/H23M mutant in which the haem was lacking, or in which the haem environment was modified, the PsbE/Y19F and PsbE/T26P mutants. All these mutants remained active showing that the haem has no structural role provided that PsbE and PsbF subunits are present. Here, we have carried on the characterization of these mutants. The following results were obtained: (i) the Y19F mutation hardly affect the Em of Cytb559, whereas the T26P mutation converts the haem into a form with a Em much below 0 mV (so low that it is likely not reducible by QB-) even in an active enzyme; (ii) in the PsbE/H23M mutant, and to a less extent in PsbE/T26P mutant, the electron transfer efficiency from QA- to QB is decreased; (iii) the lower Em of the QA/QA- couple in the PsbE/H23M mutant correlates with a higher production of singlet oxygen; (iv) the superoxide and/or hydroperoxide formation was not increased in the PsbE/H23M mutant lacking the haem, whereas it was significantly larger in the PsbE/T26P. These data are discussed in view of the literature to discriminate between structural and redox roles for the haem of Cytb559 in the production of reactive oxygen species.
    Mots-clés : Acceptor side, B3S, Cytb 559, Haem axial ligand, Photosystem II, PS2, Redox.

  • T. Q. Nguyen, M. Aumont-Niçaise, J. Andreani, C. Velours, M. Chenon, F. Vilela, C. Geneste, P. F. Varela, P. Llinas, et J. Menetrey, « Characterization of the binding mode of JNK-interacting protein 1 (JIP1) to kinesin-light chain 1 (KLC1) », The Journal of Biological Chemistry, juill. 2018.
    Résumé : JIP1 was first identified as scaffold protein for the MAP kinase JNK and is a cargo protein for the kinesin1 molecular motor. JIP1 plays significant and broad roles in neurons, mainly as a regulator of kinesin1-dependent transport, and is associated with human pathologies such as cancer and Alzheimer disease. JIP1 is specifically recruited by the kinesin-light chain 1 (KLC1) of kinesin1, but the details of this interaction are not yet fully elucidated. Here, using calorimetry, we extensively biochemically characterized the interaction between KLC1 and JIP1. Using various truncated fragments of the tetratricopeptide repeat (TPR) domain of KLC1, we narrowed down its JIP1-binding region and identified seven KLC1 residues critical for JIP1 binding. These ITC-based binding data enabled us to footprint the JIP1-binding site on KLC1-TPR. This footprint was used to uncover the structural basis for the marginal inhibition of JIP1 binding by the autoinhibitory LFP-acidic motif of KLC1, as well as for the competition between JIP1 and another cargo protein of kinesin1, the W-acidic motif-containing Alcadein-α. Also, we examined the role of each of these critical residues of KLC1 for JIP1 binding in the light of the previously reported crystal structure of the KLC1-TPR:JIP1 complex. Finally, sequence search in eukaryotic genomes identified several proteins, among which SH2D6 that exhibit similar motif to the KLC1-binding motif of JIP1. Overall, our extensive biochemical characterization of the KLC:JIP1 interaction, as well as identification of potential KLC1-binding partners improve the understanding of how this growing family of cargos is recruited to kinesin1 by KLC1.
    Mots-clés : Alcadein, AMIG, B3S, isothermal titration calorimetry (ITC), kinesin, MIKICA, MST, PF, PIM, protein engineering, protein-protein interaction, SH2D6, site-directed mutagenesis, TPR domain, Y-acidic motif.

  • T. Q. Nguyen, M. Chenon, F. Vilela, C. Velours, M. Aumont-Nicaise, J. Andreani, P. F. Varela, P. Llinas, et J. Ménétrey, « Correction: Structural plasticity of the N-terminal capping helix of the TPR domain of kinesin light chain », PloS One, vol. 13, nᵒ 5, p. e0197193, 2018.
    Résumé : [This corrects the article DOI: 10.1371/journal.pone.0186354.].
    Mots-clés : AMIG, B3S, MIKICA, PF, PIM.

  • D. J. Nürnberg, J. Morton, S. Santabarbara, A. Telfer, P. Joliot, L. A. Antonaru, A. V. Ruban, T. Cardona, E. Krausz, A. Boussac, A. Fantuzzi, et A. W. Rutherford, « Photochemistry beyond the red limit in chlorophyll f-containing photosystems », Science (New York, N.Y.), vol. 360, nᵒ 6394, p. 1210-1213, 2018.
    Résumé : Photosystems I and II convert solar energy into the chemical energy that powers life. Chlorophyll a photochemistry, using red light (680 to 700 nm), is near universal and is considered to define the energy "red limit" of oxygenic photosynthesis. We present biophysical studies on the photosystems from a cyanobacterium grown in far-red light (750 nm). The few long-wavelength chlorophylls present are well resolved from each other and from the majority pigment, chlorophyll a. Charge separation in photosystem I and II uses chlorophyll f at 745 nm and chlorophyll f (or d) at 727 nm, respectively. Each photosystem has a few even longer-wavelength chlorophylls f that collect light and pass excitation energy uphill to the photochemically active pigments. These photosystems function beyond the red limit using far-red pigments in only a few key positions.
    Mots-clés : B3S, PS2.

  • 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.

  • C. Orelle, C. Durmort, K. Mathieu, B. Duchêne, S. Aros, F. Fenaille, F. André, C. Junot, T. Vernet, et J. - M. Jault, « A multidrug ABC transporter with a taste for GTP », Scientific Reports, vol. 8, nᵒ 1, p. 2309, févr. 2018.
    Résumé : During the evolution of cellular bioenergetics, many protein families have been fashioned to match the availability and replenishment in energy supply. Molecular motors and primary transporters essentially need ATP to function while proteins involved in cell signaling or translation consume GTP. ATP-Binding Cassette (ABC) transporters are one of the largest families of membrane proteins gathering several medically relevant members that are typically powered by ATP hydrolysis. Here, a Streptococcus pneumoniae ABC transporter responsible for fluoroquinolones resistance in clinical settings, PatA/PatB, is shown to challenge this concept. It clearly favors GTP as the energy supply to expel drugs. This preference is correlated to its ability to hydrolyze GTP more efficiently than ATP, as found with PatA/PatB reconstituted in proteoliposomes or nanodiscs. Importantly, the ATP and GTP concentrations are similar in S. pneumoniae supporting the physiological relevance of GTP as the energy source of this bacterial transporter.
    Mots-clés : B3S, LSOD.

  • M. Parlato, F. Charbit-Henrion, J. Pan, C. Romano, R. Duclaux-Loras, M. - H. Le Du, N. Warner, P. Francalanci, J. Bruneau, M. Bras, M. Zarhrate, B. Bègue, N. Guegan, S. Rakotobe, N. Kapel, P. De Angelis, A. M. Griffiths, K. Fiedler, E. Crowley, F. Ruemmele, A. M. Muise, et N. Cerf-Bensussan, « Human ALPI deficiency causes inflammatory bowel disease and highlights a key mechanism of gut homeostasis », EMBO molecular medicine, mars 2018.
    Résumé : Herein, we report the first identification of biallelic-inherited mutations inALPIas a Mendelian cause of inflammatory bowel disease in two unrelated patients.ALPIencodes for intestinal phosphatase alkaline, a brush border metalloenzyme that hydrolyses phosphate from the lipid A moiety of lipopolysaccharides and thereby drastically reduces Toll-like receptor 4 agonist activity. Prediction tools and structural modelling indicate that all mutations affect critical residues or inter-subunit interactions, and heterologous expression in HEK293T cells demonstrated that allALPImutations were loss of function.ALPImutations impaired either stability or catalytic activity of ALPI and rendered it unable to detoxify lipopolysaccharide-dependent signalling. Furthermore, ALPI expression was reduced in patients' biopsies, and ALPI activity was undetectable in ALPI-deficient patient's stool. Our findings highlight the crucial role of ALPI in regulating host-microbiota interactions and restraining host inflammatory responses. These results indicate thatALPImutations should be included in screening for monogenic causes of inflammatory bowel diseases and lay the groundwork for ALPI-based treatments in intestinal inflammatory disorders.
    Mots-clés : B3S, inflammatory bowel diseases, intestinal phosphatase alkaline, INTGEN, monogenic disease.

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