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Accueil > Publications

Publications de l’I2BC

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.

  • A. Abou-Hamdan, L. Belot, A. Albertini, et Y. Gaudin, « Monomeric Intermediates Formed by Vesiculovirus Glycoprotein during Its Low-pH-induced Structural Transition », Journal of Molecular Biology, avr. 2018.
    Mots-clés : conformational change, glycoprotein, Influenza, membrane fusion, RHABDO, Vesiculovirus, VIRO.


  • 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.

  • N. Agier, S. Delmas, Q. Zhang, A. Fleiss, Y. Jaszczyszyn, E. van Dijk, C. Thermes, M. Weigt, M. Cosentino-Lagomarsino, et G. Fischer, « The evolution of the temporal program of genome replication », Nature Communications, vol. 9, nᵒ 1, p. 2199, juin 2018.
    Résumé : Genome replication is highly regulated in time and space, but the rules governing the remodeling of these programs during evolution remain largely unknown. We generated genome-wide replication timing profiles for ten Lachancea yeasts, covering a continuous evolutionary range from closely related to more divergent species. We show that replication programs primarily evolve through a highly dynamic evolutionary renewal of the cohort of active replication origins. We found that gained origins appear with low activity yet become more efficient and fire earlier as they evolutionarily age. By contrast, origins that are lost comprise the complete range of firing strength. Additionally, they preferentially occur in close vicinity to strong origins. Interestingly, despite high evolutionary turnover, active replication origins remain regularly spaced along chromosomes in all species, suggesting that origin distribution is optimized to limit large inter-origin intervals. We propose a model on the evolutionary birth, death, and conservation of active replication origins.
    Mots-clés : CHERDIR, NGS, PF.

  • 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.

  • M. Ansaldi, L. Debarbieux, S. Gandon, M. - A. Petit, P. Tavares, et P. Boulanger, « "French Phage Network"-Third Meeting Report », Viruses, vol. 10, nᵒ 3, mars 2018.
    Résumé : In its third year of existence, the French Phage Network (Phages.fr) is pursuing its expansion. With more than 25 groups, mostly based in France, working on the various aspects of phage research, the network has increased its visibility, interactivity, and activity. The third meeting of the Phages.fr network, held on November 2017 at the Gif-sur-Yvette Centre National de la Recherche Scientifique (CNRS) campus, was a great opportunity for many young scientists to present their work and interact with more senior scientists, amongst which several were invited from abroad. Here we provide a summary of the work presented at this occasion during the oral presentations and poster sessions.
    Mots-clés : bacteria, bacteriophage, co-evolution, France, genomics, infection, PHAG+, phage therapy, resistance, structural biology, T5PHAG, VIRO, virulence.

  • J. - M. Arbona, A. Goldar, O. Hyrien, A. Arneodo, et B. Audit, « The eukaryotic bell-shaped temporal rate of DNA replication origin firing emanates from a balance between origin activation and passivation », eLife, vol. 7, juin 2018.
    Résumé : The time-dependent rate I(t) of origin firing per length of unreplicated DNA presents a universal bell shape in eukaryotes that has been interpreted as the result of a complex time-evolving interaction between origins and limiting firing factors. Here we show that a normal diffusion of replication fork components towards localized potential replication origins (p-oris) can more simply account for the I(t) universal bell shape, as a consequence of a competition between the origin firing time and the time needed to replicate DNA separating two neighboring p-oris. We predict the I(t) maximal value to be the product of the replication fork speed with the squared p-ori density. We show that this relation is robustly observed in simulations and in experimental data for several eukaryotes. Our work underlines that fork-component recycling and potential origins localization are sufficient spatial ingredients to explain the universality of DNA replication kinetics.
    Mots-clés : BDG, chromosomes, computational biology, gene expression, GTR, human, S. cerevisiae, systems biology.


  • T. Avin-Wittenberg, F. Baluška, P. V. Bozhkov, P. H. Elander, A. R. Fernie, G. Galili, A. Hassan, D. Hofius, E. Isono, R. Le Bars, C. Masclaux-Daubresse, E. A. Minina, H. Peled-Zehavi, N. S. Coll, L. M. Sandalio, B. Satiat-Jeunemaitre, A. Sirko, P. S. Testillano, et H. Batoko, « Autophagy-related approaches for improving nutrient use efficiency and crop yield protection », Journal of Experimental Botany, vol. 69, nᵒ 6, p. 1335-1353, mars 2018.
    Mots-clés : BIOCELL, CYTO, DYNBSJ, PF, PHOT.

  • T. Avin-Wittenberg, F. Baluška, P. V. Bozhkov, P. H. Elander, A. R. Fernie, G. Galili, A. Hassan, D. Hofius, E. Isono, R. Le Bars, C. Masclaux-Daubresse, E. A. Minina, H. Peled-Zehavi, N. S. Coll, L. M. Sandalio, B. Satiat-Jeunemaitre, A. Sirko, P. S. Testillano, et H. Batoko, « Corrigendum: Autophagy-related approaches for improving nutrient use efficiency and crop yield protection », Journal of Experimental Botany, vol. 69, nᵒ 12, p. 3173, mai 2018.
    Mots-clés : BIOCELL, CYTO, DYNBSJ, PF, PHOT.

  • 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.

  • E. L. Bastow, V. S. Garcia de la Torre, A. E. Maclean, R. T. Green, S. Merlot, S. Thomine, et J. Balk, « Vacuolar iron stores gated by NRAMP3 and NRAMP4 are the primary source of iron in germinating seeds », Plant Physiology, vol. 177, nᵒ 3, p. 1267-1276, mai 2018.
    Résumé : During seed germination, iron (Fe) stored in vacuoles is exported by the redundant NRAMP3 and NRAMP4 transporter proteins. A double nramp3 nramp4 mutant is unable to mobilize Fe stores and does not develop in the absence of external Fe. We used RNA sequencing to compare gene expression in nramp3 nramp4 and wild type during germination and early seedling development. Even though sufficient Fe was supplied, the Fe-responsive transcription factors bHLH38, 39, 100 and 101 and their downstream targets FRO2 and IRT1 mediating Fe uptake were strongly upregulated in the nramp3 nramp4 mutant. Activation of the Fe deficiency response was confirmed by increased ferric chelate reductase activity in the mutant. At early stages, genes important for chloroplast redox control (FSD1, SAPX), Fe homeostasis (FER1, SUFB) and chlorophyll metabolism (HEMA1, NYC1) were downregulated, indicating limited Fe availability in plastids. In contrast, expression of FRO3, encoding a ferric reductase involved in Fe import into the mitochondria, was maintained and Fe-dependent enzymes in the mitochondria were unaffected in nramp3 nramp4. Together these data show that a failure to mobilize Fe stores during germination triggered Fe deficiency responses and strongly affected plastids but not mitochondria.
    Mots-clés : BIOCELL, MINION.

  • A. Belyy, U. Mechold, L. Renault, et D. Ladant, « ExoY, an actin-activated nucleotidyl cyclase toxin from P. aeruginosa: A minireview », Toxicon: Official Journal of the International Society on Toxinology, vol. 149, p. 65-71, juill. 2018.
    Résumé : ExoY is one of four well-characterized Pseudomonas aeruginosa type 3 secretion system (T3SS) effectors. It is a nucleotidyl cyclase toxin that is inactive inside the bacteria, but becomes potently activated once it is delivered into the eukaryotic target cells. Recently, filamentous actin was identified as the eukaryotic cofactor that stimulates specifically ExoY enzymatic activity by several orders of magnitude. In this review, we discuss recent advances in understanding the biochemistry of nucleotidyl cyclase activity of ExoY and its regulation by interaction with filamentous actin.
    Mots-clés : ACTIN.

  • 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.

  • S. Bhullar, C. Denby Wilkes, O. Arnaiz, M. Nowacki, L. Sperling, et E. Meyer, « A mating-type mutagenesis screen identifies a zinc-finger protein required for specific DNA excision events in Paramecium », Nucleic Acids Research, août 2018.
    Résumé : In the ciliate Paramecium tetraurelia, functional genes are reconstituted during development of the somatic macronucleus through the precise excision of ∼45 000 single-copy Internal Eliminated Sequences (IESs), thought to be the degenerate remnants of ancient transposon insertions. Like introns, IESs are marked only by a weak consensus at their ends. How such a diverse set of sequences is faithfully recognized and precisely excised remains unclear: specialized small RNAs have been implicated, but in their absence up to ∼60% of IESs are still correctly excised. To get further insight, we designed a mutagenesis screen based on the hypersensitivity of a specific excision event in the mtA gene, which determines mating types. Unlike most IES-containing genes, the active form of mtA is the unexcised one, allowing the recovery of hypomorphic alleles of essential IES recognition/excision factors. Such is the case of one mutation recovered in the Piwi gene PTIWI09, a key player in small RNA-mediated IES recognition. Another mutation identified a novel protein with a C2H2 zinc finger, mtGa, which is required for excision of a small subset of IESs characterized by enrichment in a 5-bp motif. The unexpected implication of a sequence-specific factor establishes a new paradigm for IES recognition and/or excision.
    Mots-clés : ANGE, BDG, GTR.

  • J. Bischerour, S. Bhullar, C. Denby Wilkes, V. Régnier, N. Mathy, E. Dubois, A. Singh, E. Swart, O. Arnaiz, L. Sperling, M. Nowacki, et M. Bétermier, « Six domesticated PiggyBac transposases together carry out programmed DNA elimination in Paramecium », eLife, vol. 7, sept. 2018.
    Résumé : The domestication of transposable elements has repeatedly occurred during evolution and domesticated transposases have often been implicated in programmed genome rearrangements, as remarkably illustrated in ciliates. In Paramecium, PiggyMac (Pgm), a domesticated PiggyBac transposase, carries out developmentally programmed DNA elimination, including the precise excision of tens of thousands of gene-interrupting germline Internal Eliminated Sequences (IESs). Here, we report the discovery of five groups of distant Pgm-like proteins (PgmLs), all able to interact with Pgm and essential for its nuclear localization and IES excision genome-wide. Unlike Pgm, PgmLs lack a conserved catalytic site, suggesting that they rather have an architectural function within a multi-component excision complex embedding Pgm. PgmL depletion can increase erroneous targeting of residual Pgm-mediated DNA cleavage, indicating that PgmLs contribute to accurately position the complex on IES ends. DNA rearrangements in Paramecium constitute a rare example of a biological process jointly managed by six distinct domesticated transposases.
    Mots-clés : BDG, chromosomes, ciliates, DNA elimination, gene expression, GTR, IES, MICMAC, piggyBacv, transposées domestication.


  • S. Blanchet, D. Cornu, I. Hatin, H. Grosjean, P. Bertin, et O. Namy, « Deciphering the reading of the genetic code by near-cognate tRNA », Proceedings of the National Academy of Sciences, vol. 115, nᵒ 12, p. 3018-3023, mars 2018.

  • M. Blondeau, M. Sachse, C. Boulogne, C. Gillet, J. - M. Guigner, F. Skouri-Panet, M. Poinsot, C. Ferard, J. Miot, et K. Benzerara, « Amorphous Calcium Carbonate Granules Form Within an Intracellular Compartment in Calcifying Cyanobacteria », Frontiers in Microbiology, vol. 9, p. 1768, 2018.
    Résumé : The recent discovery of cyanobacteria forming intracellular amorphous calcium carbonate (ACC) has challenged the former paradigm suggesting that cyanobacteria-mediated carbonatogenesis was exclusively extracellular. Yet, the mechanisms of intracellular biomineralization in cyanobacteria and in particular whether this takes place within an intracellular microcompartment, remain poorly understood. Here, we analyzed six cyanobacterial strains forming intracellular ACC by transmission electron microscopy. We tested two different approaches to preserve as well as possible the intracellular ACC inclusions: (i) freeze-substitution followed by epoxy embedding and room-temperature ultramicrotomy and (ii) high-pressure freezing followed by cryo-ultramicrotomy, usually referred to as cryo-electron microscopy of vitreous sections (CEMOVIS). We observed that the first method preserved ACC well in 500-nm-thick sections but not in 70-nm-thick sections. However, cell ultrastructures were difficult to clearly observe in the 500-nm-thick sections. In contrast, CEMOVIS provided a high preservation quality of bacterial ultrastructures, including the intracellular ACC inclusions in 50-nm-thick sections. ACC inclusions displayed different textures, suggesting varying brittleness, possibly resulting from different hydration levels. Moreover, an electron dense envelope of ∼2.5 nm was systematically observed around ACC granules in all studied cyanobacterial strains. This envelope may be composed of a protein shell or a lipid monolayer, but not a lipid bilayer as usually observed in other bacteria forming intracellular minerals. Overall, this study evidenced that ACC inclusions formed and were stabilized within a previously unidentified bacterial microcompartment in some species of cyanobacteria.
    Mots-clés : amorphous calcium carbonate, bacterial microcompartment, biomineralization, carboxysome, CEMOVIS, cyanobacteria, freeze-substitution, MET, PF, thylakoid.

  • S. Bouffard, E. Dambroise, A. Brombin, S. Lempereur, I. Hatin, M. Simion, R. Corre, F. Bourrat, J. - S. Joly, et F. Jamen, « Fibrillarin is essential for S-phase progression and neuronal differentiation in zebrafish dorsal midbrain and retina », Developmental Biology, févr. 2018.
    Résumé : Fibrillarin (Fbl) is a highly conserved protein that plays an essential role in ribosome biogenesis and more particularly in the methylation of ribosomal RNAs and rDNA histones. In cellular models, FBL was shown to play an important role in tumorigenesis and stem cell differentiation. We used the zebrafish as an in vivo model to study Fbl function during embryonic development. We show here that the optic tectum and the eye are severely affected by Fbl depletion whereas ventral regions of the brain are less impacted. The morphogenesis defects are associated with impaired neural differentiation and massive apoptosis. Polysome gradient experiments show that fbl mutant larvae display defects in ribosome biogenesis and activity. Strikingly, flow cytometry analyses revealed different S-phase profiles between wild-type and mutant cells, suggesting a defect in S-phase progression.
    Mots-clés : BDG, Cell cycle regulation, Danio rerio, Differentiation, GST, Neural progenitors, Optic tectum, Ribosome biogenesis.


  • G. Bourgeois, J. Seguin, M. Babin, P. Belin, M. Moutiez, Y. Mechulam, M. Gondry, et E. Schmitt, « Structural basis for partition of the cyclodipeptide synthases into two subfamilies », Journal of Structural Biology, vol. 203, nᵒ 1, p. 17-26, juill. 2018.
    Résumé : Cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides that can be further used for the synthesis of diketopiperazines. It was shown that CDPSs fall into two subfamilies, NYH and XYP, characterized by the presence of specific sequence signatures. However, current understanding of CDPSs only comes from studies of enzymes from the NYH subfamily. The present study reveals the crystal structures of three CDPSs from the XYP subfamily. Comparison of the XYP and NYH enzymes shows that the two subfamilies mainly differ in the first half of their Rossmann fold. This gives a structural basis for the partition of CDPSs into two subfamilies. Despite these differences, the catalytic residues adopt similar positioning regardless of the subfamily suggesting that the XYP and NYH motifs correspond to two structural solutions to facilitate the reactivity of the catalytic serine residue.
    Mots-clés : Aminoacyl-tRNA synthetases, BIOSYN, Cyclodipeptides, Diketopiperazines, MICROBIO, Non-ribosomal peptide synthesis, Rossmann fold, Transfer RNA.

  • 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.

  • T. Candelli, D. Challal, J. - B. Briand, J. Boulay, O. Porrua, J. Colin, et D. Libri, « High-resolution transcription maps reveal the widespread impact of roadblock termination in yeast », The EMBO journal, janv. 2018.
    Résumé : Transcription termination delimits transcription units but also plays important roles in limiting pervasive transcription. We have previously shown that transcription termination occurs when elongating RNA polymerase II (RNAPII) collides with the DNA-bound general transcription factor Reb1. We demonstrate here that many different DNA-binding proteins can induce termination by a similar roadblock (RB) mechanism. We generated high-resolution transcription maps by the direct detection of RNAPII upon nuclear depletion of two essential RB factors or when the canonical termination pathways for coding and non-coding RNAs are defective. We show that RB termination occurs genomewide and functions independently of (and redundantly with) the main transcription termination pathways. We provide evidence that transcriptional readthrough at canonical terminators is a significant source of pervasive transcription, which is controlled to a large extent by RB termination. Finally, we demonstrate the occurrence of RB termination around centromeres and tRNA genes, which we suggest shields these regions from RNAPII to preserve their functional integrity.
    Mots-clés : BDG, DBG, pervasive transcription, Rap1, roadblock termination, TENOR, transcription readthrough, transcription termination mechanism.

  • N. Canu, P. Belin, R. Thai, I. Correia, O. Lequin, J. Seguin, M. Moutiez, et M. Gondry, « Incorporation of Non-canonical Amino Acids into 2,5-Diketopiperazines by Cyclodipeptide Synthases », Angewandte Chemie (International Ed. in English), vol. 57, nᵒ 12, p. 3118-3122, mars 2018.
    Résumé : The manipulation of natural product biosynthetic pathways is a powerful means of expanding the chemical diversity of bioactive molecules. 2,5-diketopiperazines (2,5-DKPs) have been widely developed by medicinal chemists, but their biological production is yet to be exploited. We introduce an in vivo method for incorporating non-canonical amino acids (ncAAs) into 2,5-DKPs using cyclodipeptide synthases (CDPSs), the enzymes responsible for scaffold assembly in many 2,5-DKP biosynthetic pathways. CDPSs use aminoacyl-tRNAs as substrates. We exploited the natural ability of aminoacyl-tRNA synthetases to load ncAAs onto tRNAs. We found 26 ncAAs to be usable as substrates by CDPSs, leading to the enzymatic production of approximately 200 non-canonical cyclodipeptides. CDPSs constitute an efficient enzymatic tool for the synthesis of highly diverse 2,5-DKPs. Such diversity could be further expanded, for example, by using various cyclodipeptide-tailoring enzymes found in 2,5-DKP biosynthetic pathways.
    Mots-clés : biocatalysis, BIOSYN, biosynthesis, Cyclodipeptide synthases, cyclodipeptides, Diketopiperazines, MICROBIO, Natural product engineering, Non-canonical amino acid.


  • 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.


  • D. Carmona-Gutierrez, M. A. Bauer, A. Zimmermann, A. Aguilera, N. Austriaco, K. Ayscough, R. Balzan, S. Bar-Nun, A. Barrientos, P. Belenky, M. Blondel, R. J. Braun, M. Breitenbach, W. C. Burhans, S. Buettner, D. Cavalieri, M. Chang, K. F. Cooper, M. Côrte-Real, V. Costa, C. Cullin, I. Dawes, J. Dengjel, M. B. Dickman, T. Eisenberg, B. Fahrenkrog, N. Fasel, K. - U. Froehlich, A. Gargouri, S. Giannattasio, P. Goffrini, C. W. Gourlay, C. M. Grant, M. T. Greenwood, N. Guaragnella, T. Heger, J. Heinisch, E. Herker, J. M. Herrmann, S. Hofer, A. Jiménez-Ruiz, H. Jungwirth, K. Kainz, D. P. Kontoyiannis, P. Ludovico, S. Manon, E. Martegani, C. Mazzoni, L. A. Megeney, C. Meisinger, J. Nielsen, T. Nystroem, H. D. Osiewacz, T. F. Outeiro, H. - O. Park, T. Pendl, D. Petranovic, S. Picot, P. Polčic, T. Powers, M. Ramsdale, M. Rinnerthaler, P. Rockenfeller, C. Ruckenstuhl, R. Schaffrath, M. Segovia, F. F. Severin, A. Sharon, S. J. Sigrist, C. Sommer-Ruck, M. J. Sousa, J. M. Thevelein, K. Thevissen, V. Titorenko, M. B. Toledano, M. Tuite, F. - N. Voegtle, B. Westermann, J. Winderickx, S. Wissing, S. Woelfl, Z. J. Zhang, R. Y. Zhao, B. Zhou, L. Galluzzi, G. Kroemer, et F. Madeo, « Guidelines and recommendations on yeast cell death nomenclature », Microbial Cell, vol. 5, nᵒ 1, p. 4-31, janv. 2018.

  • B. Castrec, C. Dian, S. Ciccone, C. L. Ebert, W. V. Bienvenut, J. - P. Le Caer, J. - M. Steyaert, C. Giglione, et T. Meinnel, « Structural and genomic decoding of human and plant myristoylomes reveals a definitive recognition pattern », Nature Chemical Biology, juin 2018.
    Résumé : An organism's entire protein modification repertoire has yet to be comprehensively mapped. N-myristoylation (MYR) is a crucial eukaryotic N-terminal protein modification. Here we mapped complete Homo sapiens and Arabidopsis thaliana myristoylomes. The crystal structures of human modifier NMT1 complexed with reactive and nonreactive target-mimicking peptide ligands revealed unexpected binding clefts and a modifier recognition pattern. This information allowed integrated mapping of myristoylomes using peptide macroarrays, dedicated prediction algorithms, and in vivo mass spectrometry. Global MYR profiling at the genomic scale identified over a thousand novel, heterogeneous targets in both organisms. Surprisingly, MYR involved a non-negligible set of overlapping targets with N-acetylation, and the sequence signature marks for a third proximal acylation-S-palmitoylation-were genomically imprinted, allowing recognition of sequences exhibiting both acylations. Together, the data extend the N-end rule concept for Gly-starting proteins to subcellular compartmentalization and reveal the main neighbors influencing protein modification profiles and consequent cell fate.
    Mots-clés : BDG, PROMTI.

  • R. Catchpole, A. Gorlas, J. Oberto, et P. Forterre, « A series of new E. coli-Thermococcus shuttle vectors compatible with previously existing vectors », Extremophiles: Life Under Extreme Conditions, vol. 22, nᵒ 4, p. 591-598, juill. 2018.
    Résumé : Hyperthermophilic microorganisms are an important asset in the toolkits of biotechnologists, biochemists and evolutionary biologists. The anaerobic archaeon, Thermococcus kodakarensis, has become one of the most useful hyperthermophilic model species, not least due to its natural competence and genetic tractability. Despite this, the range of genetic tools available for T. kodakarensis remains limited. Using sequencing and phylogenetic analyses, we determined that the rolling-circle replication origin of the cryptic mini-plasmid pTP2 from T. prieurii is suitable for plasmid replication in T. kodakarensis. Based on this replication origin, we present a novel series of replicative E. coli-T. kodakarensis shuttle vectors. These shuttle vectors have been constructed with three different selectable markers, allowing selection in a range of T. kodakarensis backgrounds. Moreover, these pTP2-derived plasmids are compatible with the single-existing E. coli-T. kodakarensis shuttle vector, pLC70. We show that both pTP2-derived and pLC70-derived plasmids replicate faithfully while cohabitating in T. kodakarensis cells. These plasmids open the door for new areas of research in plasmid segregation, DNA replication and gene expression.
    Mots-clés : Archaea, ARCHEE, Cloning, Gene cloning and expression, Genetics of extremophiles, Hyperthermophiles, MICROBIO, Molecular biology, Molecular biology of archaea.

  • F. Celli, A. Petitalot, C. Samson, F. - X. Theillet, et S. Zinn-Justin, « H-1, C-13 and N-15 backbone resonance assignment of the lamin C-terminal region specific to prelamin A », Biomolecular Nmr Assignments, vol. 12, nᵒ 2, p. 225-229, oct. 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 NMR H-1, N-15, (CO)-C-13, C-13 and C-13 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 NMR H-1, N-15, (CO)-C-13, C-13 and C-13 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 -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, mutations, networks, NMR spectroscopy, NMR spectroscopy, Nuclear envelope, Nucleoskeleton.


  • C. Chaintreuil, X. Perrier, G. Martin, J. Fardoux, G. P. Lewis, L. Brottier, R. Rivallan, M. Gomez-Pacheco, M. Bourges, L. Lamy, B. Thibaud, H. Ramanankierana, H. Randriambanona, H. Vandrot, P. Mournet, E. Giraud, et J. - F. Arrighi, « Naturally occurring variations in the nod-independent model legume Aeschynomene evenia and relatives: a resource for nodulation genetics », BMC Plant Biology, vol. 18, nᵒ 1, 2018.

  • 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.

  • M. Chaumorcel, M. Lussignol, L. Mouna, Y. Cavignac, K. Fahie, J. Cotte-Laffitte, A. Geballe, W. Brune, I. Beau, P. Codogno, et A. Esclatine, « Correction for Chaumorcel et al., "The Human Cytomegalovirus Protein TRS1 Inhibits Autophagy via Its Interaction with Beclin 1" », Journal of Virology, vol. 92, nᵒ 9, 2018.

  • C. Chen, L. Ao, Y. - T. Wu, V. Cifliku, M. Cardoso Dos Santos, E. Bourrier, M. Delbianco, D. Parker, J. Zwier, L. Huang, et N. Hildebrandt, « Single-Nanoparticle Cell Barcoding by Tunable FRET from Lanthanides to Quantum Dots », Angewandte Chemie (International Ed. in English), août 2018.
    Résumé : Fluorescence barcoding based on nanoparticles provides many advantages for multiparameter imaging. However, creating different concentration-independent codes without mixing various nanoparticles and by using single wavelength excitation and emission for multiplexed cellular imaging is extremely challenging. Here, we report the development of quantum dots (QDs) with two different SiO2 shell thicknesses (6 and 12 nm) and coated with two different lanthanide complexes (Tb and Eu). FRET from Tb or Eu donors to the QD acceptors resulted in four distinct photoluminescence (PL) decays, which were encoded by simple time-gated (TG) PL intensity detection in three individual temporal detection windows. The well-defined single-nanoparticle codes were used for live cell imaging and a one-measurement distinction of four different cells in a single field of view. This single-color barcoding strategy opens new opportunities for multiplexed labeling and tracking of cells.
    Mots-clés : B3S, FRET, imaging, Lanthanides, Lifetime, NANO, quantum dots.

  • 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.

  • M. Chevreuil, D. Law-Hine, J. Chen, S. Bressanelli, S. Combet, D. Constantin, J. Degrouard, J. Möller, M. Zeghal, et G. Tresset, « Nonequilibrium self-assembly dynamics of icosahedral viral capsids packaging genome or polyelectrolyte », Nature Communications, vol. 9, nᵒ 1, p. 3071, août 2018.
    Résumé : The survival of viruses partly relies on their ability to self-assemble inside host cells. Although coarse-grained simulations have identified different pathways leading to assembled virions from their components, experimental evidence is severely lacking. Here, we use time-resolved small-angle X-ray scattering to uncover the nonequilibrium self-assembly dynamics of icosahedral viral capsids packaging their full RNA genome. We reveal the formation of amorphous complexes via an en masse pathway and their relaxation into virions via a synchronous pathway. The binding energy of capsid subunits on the genome is moderate (~7kBT0, with kB the Boltzmann constant and T0 = 298 K, the room temperature), while the energy barrier separating the complexes and the virions is high (~ 20kBT0). A synthetic polyelectrolyte can lower this barrier so that filled capsids are formed in conditions where virions cannot build up. We propose a representation of the dynamics on a free energy landscape.
    Mots-clés : B3S, disassembly, IMAPP, kinetic pathway, Modeling, time-resolved small-angle X-ray scattering, Virus.

  • 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.

  • C. Cohen, A. Corpet, S. Roubille, M. A. Maroui, N. Poccardi, A. Rousseau, C. Kleijwegt, O. Binda, P. Texier, N. Sawtell, M. Labetoulle, et P. Lomonte, « Promyelocytic leukemia (PML) nuclear bodies (NBs) induce latent/quiescent HSV-1 genomes chromatinization through a PML NB/Histone H3.3/H3.3 Chaperone Axis », PLoS pathogens, vol. 14, nᵒ 9, p. e1007313, sept. 2018.
    Résumé : Herpes simplex virus 1 (HSV-1) latency establishment is tightly controlled by promyelocytic leukemia (PML) nuclear bodies (NBs) (or ND10), although their exact contribution is still elusive. A hallmark of HSV-1 latency is the interaction between latent viral genomes and PML NBs, leading to the formation of viral DNA-containing PML NBs (vDCP NBs), and the complete silencing of HSV-1. Using a replication-defective HSV-1-infected human primary fibroblast model reproducing the formation of vDCP NBs, combined with an immuno-FISH approach developed to detect latent/quiescent HSV-1, we show that vDCP NBs contain both histone H3.3 and its chaperone complexes, i.e., DAXX/ATRX and HIRA complex (HIRA, UBN1, CABIN1, and ASF1a). HIRA also co-localizes with vDCP NBs present in trigeminal ganglia (TG) neurons from HSV-1-infected wild type mice. ChIP and Re-ChIP show that vDCP NBs-associated latent/quiescent viral genomes are chromatinized almost exclusively with H3.3 modified on its lysine (K) 9 by trimethylation, consistent with an interaction of the H3.3 chaperones with multiple viral loci and with the transcriptional silencing of HSV-1. Only simultaneous inactivation of both H3.3 chaperone complexes has a significant impact on the deposition of H3.3 on viral genomes, suggesting a compensation mechanism. In contrast, the sole depletion of PML significantly impacts the chromatinization of the latent/quiescent viral genomes with H3.3 without any overall replacement with H3.1. vDCP NBs-associated HSV-1 genomes are not definitively silenced since the destabilization of vDCP NBs by ICP0, which is essential for HSV-1 reactivation in vivo, allows the recovery of a transcriptional lytic program and the replication of viral genomes. Consequently, the present study demonstrates a specific chromatin regulation of vDCP NBs-associated latent/quiescent HSV-1 through an H3.3-dependent HSV-1 chromatinization involving the two H3.3 chaperones DAXX/ATRX and HIRA complexes. Additionally, the study reveals that PML NBs are major actors in latent/quiescent HSV-1 H3.3 chromatinization through a PML NB/histone H3.3/H3.3 chaperone axis.


  • F. Coll, J. Phelan, G. A. Hill-Cawthorne, M. B. Nair, K. Mallard, S. Ali, A. M. Abdallah, S. Alghamdi, M. Alsomali, A. O. Ahmed, S. Portelli, Y. Oppong, A. Alves, T. B. Bessa, S. Campino, M. Caws, A. Chatterjee, A. C. Crampin, K. Dheda, N. Furnham, J. R. Glynn, L. Grandjean, D. Minh Ha, R. Hasan, Z. Hasan, M. L. Hibberd, M. Joloba, E. C. Jones-López, T. Matsumoto, A. Miranda, D. J. Moore, N. Mocillo, S. Panaiotov, J. Parkhill, C. Penha, J. Perdigão, I. Portugal, Z. Rchiad, J. Robledo, P. Sheen, N. T. Shesha, F. A. Sirgel, C. Sola, E. Oliveira Sousa, E. M. Streicher, P. V. Helden, M. Viveiros, R. M. Warren, R. McNerney, A. Pain, et T. G. Clark, « Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis », Nature Genetics, janv. 2018.

  • M. Comisso, A. Hadchouel, J. de Blic, et M. Mirande, « Mutations in MARS identified in a specific type of pulmonary alveolar proteinosis alter methionyl-tRNA synthetase activity », The FEBS journal, mai 2018.
    Résumé : Biallelic missense mutations in MARS are responsible for rare but severe cases of pulmonary alveolar proteinosis (PAP) prevalent on the island of La Réunion. MARS encodes cytosolic methionyl-tRNA synthetase (MetRS), an essential translation factor. The multisystemic effects observed in patients with this form of PAP are consistent with a loss-of-function defect in an ubiquitously expressed enzyme. The pathophysiological mechanisms involved in MARS-related PAP are currently unknown. In this work, we analyzed the effect of the PAP-related mutations in MARS on the thermal stability and on the catalytic parameters of the MetRS mutants, relative to wild-type. The effect of these mutations on the structural integrity of the enzyme as a member of the cytosolic multisynthetase complex was also investigated. Our results establish that the PAP-related substitutions in MetRS impact the tRNAMet -aminoacylation reaction especially at the level of methionine recognition, and suggest a direct link between the loss of activity of the enzyme and the pathological disorders in PAP.
    Mots-clés : aminoacylation kinetics, BDG, MARS, methionyl-tRNA synthetase, pulmonary alveolar proteinosis.

  • D. Couvin, A. Bernheim, C. Toffano-Nioche, M. Touchon, J. Michalik, B. Néron, E. P. C Rocha, G. Vergnaud, D. Gautheret, et C. Pourcel, « CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins », Nucleic Acids Research, mai 2018.
    Résumé : CRISPR (clustered regularly interspaced short palindromic repeats) arrays and their associated (Cas) proteins confer bacteria and archaea adaptive immunity against exogenous mobile genetic elements, such as phages or plasmids. CRISPRCasFinder allows the identification of both CRISPR arrays and Cas proteins. The program includes: (i) an improved CRISPR array detection tool facilitating expert validation based on a rating system, (ii) prediction of CRISPR orientation and (iii) a Cas protein detection and typing tool updated to match the latest classification scheme of these systems. CRISPRCasFinder can either be used online or as a standalone tool compatible with Linux operating system. All third-party software packages employed by the program are freely available. CRISPRCasFinder is available at https://crisprcas.i2bc.paris-saclay.fr.
    Mots-clés : BDG, LGBMB, MICROBIO, SSFA.

  • M. Crüsemann, R. Reher, I. Schamari, A. O. Brachmann, T. Ohbayashi, M. Kuschak, D. Malfacini, A. Seidinger, M. Pinto-Carbó, R. Richarz, T. Reuter, S. Kehraus, A. Hallab, M. Attwood, H. B. Schiöth, P. Mergaert, Y. Kikuchi, T. F. Schäberle, E. Kostenis, D. Wenzel, C. E. Müller, J. Piel, A. Carlier, L. Eberl, et G. M. König, « Heterologous Expression, Biosynthetic Studies, and Ecological Function of the Selective Gq-Signaling Inhibitor FR900359 », Angewandte Chemie (International Ed. in English), vol. 57, nᵒ 3, p. 836-840, janv. 2018.
    Résumé : The cyclic depsipeptide FR900359 (FR), isolated from the tropical plant Ardisia crenata, is a strong and selective inhibitor of Gq proteins, making it an indispensable pharmacological tool to study Gq-related processes, as well as a promising drug candidate. Gq inhibition is a novel mode of action for defense chemicals and crucial for the ecological function of FR, as shown by in vivo experiments in mice, its affinity to insect Gq proteins, and insect toxicity studies. The uncultured endosymbiont of A. crenata was sequenced, revealing the FR nonribosomal peptide synthetase (frs) gene cluster. We here provide a detailed model of FR biosynthesis, supported by in vitro enzymatic and bioinformatic studies, and the novel analogue AC-1, which demonstrates the flexibility of the FR starter condensation domains. Finally, expression of the frs genes in E. coli led to heterologous FR production in a cultivable, bacterial host for the first time.
    Mots-clés : biosynthesis, FR900359, G proteins, G proteins, Heterologous expression, MICROBIO, natural products, PBI.


  • V. Da Cunha, M. Gaia, A. Nasir, et P. Forterre, « Asgard archaea do not close the debate about the universal tree of life topology », PLOS Genetics, vol. 14, nᵒ 3, p. e1007215, mars 2018.

  • C. Dard-Dascot, D. Naquin, Y. d'Aubenton-Carafa, K. Alix, C. Thermes, et E. van Dijk, « Systematic comparison of small RNA library preparation protocols for next-generation sequencing », BMC genomics, vol. 19, nᵒ 1, p. 118, 2018.
    Résumé : BACKGROUND: Next-generation sequencing technologies have revolutionized the study of small RNAs (sRNAs) on a genome-wide scale. However, classical sRNA library preparation methods introduce serious bias, mainly during adapter ligation steps. Several types of sRNA including plant microRNAs (miRNA), piwi-interacting RNAs (piRNA) in insects, nematodes and mammals, and small interfering RNAs (siRNA) in insects and plants contain a 2'-O-methyl (2'-OMe) modification at their 3' terminal nucleotide. This inhibits 3' adapter ligation and makes library preparation particularly challenging. To reduce bias, the NEBNext kit (New England Biolabs) uses polyethylene glycol (PEG), the NEXTflex V2 kit (BIOO Scientific) uses both randomised adapters and PEG, and the novel SMARTer (Clontech) and CATS (Diagenode) kits avoid ligation altogether. Here we compared these methods with Illumina's classical TruSeq protocol regarding the detection of normal and 2' OMe RNAs. In addition, we modified the TruSeq and NEXTflex protocols to identify conditions that improve performance. RESULTS: Among the five kits tested with their respective standard protocols, the SMARTer and CATS kits had the lowest levels of bias but also had a strong formation of side products, and as a result performed relatively poorly with biological samples; NEXTflex detected the largest numbers of different miRNAs. The use of a novel type of randomised adapters called MidRand-Like (MRL) adapters and PEG improved the detection of 2' OMe RNAs both in the TruSeq as well as in the NEXTflex protocol. CONCLUSIONS: While it is commonly accepted that biases in sRNA library preparation protocols are mainly due to adapter ligation steps, the ligation-free protocols were not the best performing methods. Our modified versions of the TruSeq and NEXTflex protocols provide an improved tool for the study of 2' OMe RNAs.
    Mots-clés : 2’-O-methyl RNA, ANGE, Bias, CHERDIR, DBG, Library preparation, Next-generation sequencing, NGS, PF, Small RNA.

  • 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.

  • E. H. Dawson, T. P. M. Bailly, J. Dos Santos, C. Moreno, M. Devilliers, B. Maroni, C. Sueur, A. Casali, B. Ujvari, F. Thomas, J. Montagne, et F. Mery, « Social environment mediates cancer progression in Drosophila », Nature Communications, vol. 9, nᵒ 1, p. 3574, sept. 2018.
    Résumé : The influence of oncogenic phenomena on the ecology and evolution of animal species is becoming an important research topic. Similar to host-pathogen interactions, cancer negatively affects host fitness, which should lead to the selection of host control mechanisms, including behavioral traits that best minimize the proliferation of malignant cells. Social behavior is suggested to influence tumor progression. While the ecological benefits of sociality in gregarious species are widely acknowledged, only limited data are available on the role of the social environment on cancer progression. Here, we exposed adult Drosophila, with colorectal-like tumors, to different social environments. We show how subtle variations in social structure have dramatic effects on the progression of tumor growth. Finally, we reveal that flies can discriminate between individuals at different stages of tumor development and selectively choose their social environment accordingly. Our study demonstrates the reciprocal links between cancer and social interactions and how sociality may impact health and fitness in animals and its potential implications for disease ecology.
    Mots-clés : BIOCELL, METABO.


  • 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.

  • T. Denecker et G. Lelandais, « Empowering the detection of ChIP-seq "basic peaks" (bPeaks) in small eukaryotic genomes with a web user-interactive interface », BMC research notes, vol. 11, nᵒ 1, p. 698, oct. 2018.
    Résumé : OBJECTIVE: bPeaks is a peak calling program to detect protein DNA-binding sites from ChIPseq data in small eukaryotic genomes. The simplicity of the bPeaks method is well appreciated by users, but its use via an R package is challenging and time-consuming for people without programming skills. In addition, user feedback has highlighted the lack of a convenient way to carefully explore bPeaks result files. In this context, the development of a web user interface represents an important added value for expanding the bPeaks user community. RESULTS: We developed a new bPeaks application (bPeaks App). The application allows the user to perform all the peak-calling analysis steps with bPeaks in a few mouse clicks via a web browser. We added new features relative to the original R package, particularly the possibility to import personal annotation files to compare the location of the detected peaks with specific genomic elements of interest of the user, in any organism, and a new organization of the result files which are directly manageable via a user-interactive genome browser. This significantly improves the ability of the user to explore all detected basic peaks in detail.
    Mots-clés : bPeaks, ChIP-seq, Peak calling, Protein DNA-binding sites, Small eukaryotic genomes.

  • Y. Dessaux et D. Faure, « Niche Construction and Exploitation by Agrobacterium: How to Survive and Face Competition in Soil and Plant Habitats », Berlin, Heidelberg: Springer Berlin Heidelberg, 2018.

  • Y. Dessaux et D. Faure, « Quorum Sensing and Quorum Quenching in Agrobacterium: A "Go/No Go System"? », Genes, vol. 9, nᵒ 4, avr. 2018.
    Résumé : The pathogen Agrobacterium induces gall formation on a wide range of dicotyledonous plants. In this bacteria, most pathogenicity determinants are borne on the tumour inducing (Ti) plasmid. The conjugative transfer of this plasmid between agrobacteria is regulated by quorum sensing (QS). However, processes involved in the disturbance of QS also occur in this bacteria under the molecular form of a protein, TraM, inhibiting the sensing of the QS signals, and two lactonases BlcC (AttM) and AiiB that degrade the acylhomoserine lactone (AHL) QS signal. In the model Agrobacteriumfabrum strain C58, several data, once integrated, strongly suggest that the QS regulation may not be reacting only to cell concentration. Rather, these QS elements in association with the quorum quenching (QQ) activities may constitute an integrated and complex “go/no go system” that finely controls the biologically costly transfer of the Ti plasmid in response to multiple environmental cues. This decision mechanism permits the bacteria to sense whether it is in a gall or not, in a living or decaying tumor, in stressed plant tissues, etc. In this scheme, the role of the lactonases selected and maintained in the course of Ti plasmid and agrobacterial evolution appears to be pivotal.
    Mots-clés : (p)ppGpp, Agrobacterium, GABA, lactonase, MICROBIO, PBI, proline, quorum quenching, quorum sensing, Ti plasmid.

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