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Accueil > Publications

Publications plate-forme I2BC

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.


  • 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.


  • 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.

  • 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.


  • A. Doerflinger, N. N. Quang, E. Gravel, G. Pinna, M. Vandamme, F. Ducongé, et E. Doris, « Biotin-functionalized targeted polydiacetylene micelles », Chemical Communications, 2018.

  • A. González-Mula, J. Lang, C. Grandclément, D. Naquin, M. Ahmar, L. Soulère, Y. Queneau, Y. Dessaux, et D. Faure, « Lifestyle of the biotroph Agrobacterium tumefaciens in the ecological niche constructed on its host plant », The New Phytologist, avr. 2018.
    Résumé : Agrobacterium tumefaciens constructs an ecological niche in its host plant by transferring the T-DNA from its Ti plasmid into the host genome and by diverting the host metabolism. We combined transcriptomics and genetics for understanding the A. tumefaciens lifestyle when it colonizes Arabidopsis thaliana tumors. Transcriptomics highlighted: a transition from a motile to sessile behavior that mobilizes some master regulators (Hfq, CtrA, DivK and PleD); a remodeling of some cell surface components (O-antigen, succinoglucan, curdlan, att genes, putative fasciclin) and functions associated with plant defense (Ef-Tu and flagellin pathogen-associated molecular pattern-response and glycerol-3-phosphate and nitric oxide signaling); and an exploitation of a wide variety of host resources, including opines, amino acids, sugars, organic acids, phosphate, phosphorylated compounds, and iron. In addition, construction of transgenic A. thaliana lines expressing a lactonase enzyme showed that Ti plasmid transfer could escape host-mediated quorum-quenching. Finally, construction of knock-out mutants in A. tumefaciens showed that expression of some At plasmid genes seemed more costly than the selective advantage they would have conferred in tumor colonization. We provide the first overview of A. tumefaciens lifestyle in a plant tumor and reveal novel signaling and trophic interplays for investigating host-pathogen interactions.
    Mots-clés : Agrobacterium, Arabidopsis, horizontal transfer, MICROBIO, NGS, niche exploitation, opine, PBI, PF, plasmid, quorum-sensing, tumor.


  • B. Gronenborn, J. W. Randles, D. Knierim, Q. Barrière, H. J. Vetten, N. Warthmann, D. Cornu, T. Sileye, S. Winter, et T. Timchenko, « Analysis of DNAs associated with coconut foliar decay disease implicates a unique single-stranded DNA virus representing a new taxon », Scientific Reports, vol. 8, nᵒ 1, 2018.
    Mots-clés : MICROBIO, PBI, PF, SICAPS.

  • S. Malli, C. Bories, M. Bourge, P. M. Loiseau, et K. Bouchemal, « Surface-dependent endocytosis of poly(isobutylcyanoacrylate) nanoparticles by Trichomonas vaginalis », International Journal of Pharmaceutics, vol. 548, nᵒ 1, p. 276-287, juill. 2018.
    Résumé : Previous data from our research group showed that chitosan-coated poly(isobutylcyanoacrylate) nanoparticles (NPs) (denoted PIBCA/Chito20) exhibited intrinsic anti-Trichomonas vaginalis activity, while PIBCA/pluronic® F68 without chitosan (PIBCA/F68) were inactive. However, the mechanism of anti-T. vaginalis activity of chitosan-coated PIBCA NPs is still unknown. Our hypothesis is that chitosan-coated NPs are internalized by the parasite, contrarily to PIBCA/F68. In this investigation, the impact of NP surface on their internalization by the protozoan was studied using flow cytometry and parasite morphological changes after different incubation times with PIBCA/Chito20 NPs were monitored by electron microscopy. Flow-cytometry revealed that PIBCA/Chito20 NPs were uptaken by T. vaginalis as early as 10-min-incubation. Drastic cell morphological transformations were observed from scanning electron microscopy and transmission electron microscopy after incubation with PIBCA/Chito20 NPs. Numerous pits were seen on cell membrane since 10 min. Gradual increase in contact time increased NP endocytosis and induced proportional damages to T. vaginalis membrane. Then, investigation of whether PIBCA/Chito20 NPs can improve MTZ anti-T. vaginalis activity was studied using checkerboard experiment. Calculation of fractional inhibitory concentration index (FICI = 3.53) showed an additive effect between NPs and MTZ.
    Mots-clés : Chitosan, CYTO, Metronidazole, PF, Poly(isobutylcyanoacrylate), Trichomonas vaginalis.

  • 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.

  • D. Naquin, C. Panozzo, G. Dujardin, E. van Dijk, Y. d'Aubenton-Carafa, et C. Thermes, « Complete Sequence of the Intronless Mitochondrial Genome of the Saccharomyces cerevisiae Strain CW252 », Genome Announcements, vol. 6, nᵒ 17, avr. 2018.
    Résumé : The mitochondrial genomes of Saccharomyces cerevisiae strains contain up to 13 introns. An intronless recombinant genome introduced into the nuclear background of S. cerevisiae strain W303 gave the S. cerevisiae CW252 strain, which is used to model mitochondrial respiratory pathologies. The complete sequence of this mitochondrial genome was obtained using a hybrid assembling methodology.
    Mots-clés : BIOCELL, BIOMIT, NGS, PF.

  • 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.

  • X. Raffoux, M. Bourge, F. Dumas, O. C. Martin, et M. Falque, « High-throughput measurement of recombination rates and genetic interference in Saccharomyces cerevisiae », Yeast (Chichester, England), vol. 35, nᵒ 6, p. 431-442, 2018.
    Résumé : Allelic recombination owing to meiotic crossovers is a major driver of genome evolution, as well as a key player for the selection of high-performing genotypes in economically important species. Therefore, we developed a high-throughput and low-cost method to measure recombination rates and crossover patterning (including interference) in large populations of the budding yeast Saccharomyces cerevisiae. Recombination and interference were analysed by flow cytometry, which allows time-consuming steps such as tetrad microdissection or spore growth to be avoided. Moreover, our method can also be used to compare recombination in wild-type vs. mutant individuals or in different environmental conditions, even if the changes in recombination rates are small. Furthermore, meiotic mutants often present recombination and/or pairing defects affecting spore viability but our method does not involve growth steps and thus avoids filtering out non-viable spores.
    Mots-clés : crossing-over, CYTO, flow cytometry, fluorescent tag, meiosis, PF, yeast.

  • Á. Szabó, C. Papin, D. Cornu, E. Chélot, Z. Lipinszki, A. Udvardy, V. Redeker, U. Mayor, et F. Rouyer, « Ubiquitylation Dynamics of the Clock Cell Proteome and TIMELESS during a Circadian Cycle », Cell Reports, vol. 23, nᵒ 8, p. 2273-2282, mai 2018.
    Résumé : Circadian clocks have evolved as time-measuring molecular devices to help organisms adapt their physiology to daily changes in light and temperature. Transcriptional oscillations account for a large fraction of rhythmic protein abundance. However, cycling of various posttranslational modifications, such as ubiquitylation, also contributes to shape the rhythmic protein landscape. In this study, we used an in vivo ubiquitin labeling assay to investigate the circadian ubiquitylated proteome of Drosophila melanogaster. We find that cyclic ubiquitylation affects MEGATOR (MTOR), a chromatin-associated nucleoporin that, in turn, feeds back to regulate the core molecular oscillator. Furthermore, we show that the ubiquitin ligase subunits CULLIN-3 (CUL-3) and SUPERNUMERARY LIMBS (SLMB) cooperate for ubiquitylating the TIMELESS protein. These findings stress the importance of ubiquitylation pathways in the Drosophila circadian clock and reveal a key component of this system.
    Mots-clés : circadian clock, Drosophila, oscillation, PF, protein degradation, proteomics, SICAPS, ubiquitin, ubiquitin ligase.

  • E. L. van Dijk, Y. Jaszczyszyn, D. Naquin, et C. Thermes, « The Third Revolution in Sequencing Technology », Trends in genetics: TIG, juin 2018.
    Résumé : Forty years ago the advent of Sanger sequencing was revolutionary as it allowed complete genome sequences to be deciphered for the first time. A second revolution came when next-generation sequencing (NGS) technologies appeared, which made genome sequencing much cheaper and faster. However, NGS methods have several drawbacks and pitfalls, most notably their short reads. Recently, third-generation/long-read methods appeared, which can produce genome assemblies of unprecedented quality. Moreover, these technologies can directly detect epigenetic modifications on native DNA and allow whole-transcript sequencing without the need for assembly. This marks the third revolution in sequencing technology. Here we review and compare the various long-read methods. We discuss their applications and their respective strengths and weaknesses and provide future perspectives.
    Mots-clés : long-read sequencing, nanopore sequencing, next-generation sequencing, NGS, PF, single-molecule real-time sequencing, synthetic long-read sequencing, third-generation sequencing.

2017


  • L. Becker, S. Bellow, V. Carré, G. Latouche, A. Poutaraud, D. Merdinoglu, S. C. Brown, Z. G. Cerovic, et P. Chaimbault, « Correlative Analysis of Fluorescent Phytoalexins by Mass Spectrometry Imaging and Fluorescence Microscopy in Grapevine Leaves », Analytical Chemistry, juin 2017.
    Résumé : Plant response to their environment stresses is a complex mechanism involving secondary metabolites. Stilbene phytoalexins, namely resveratrol, pterostilbene, piceids and viniferins play a key role in grapevine (Vitis vinifera) leaf defense. Despite their well-established qualities, conventional analyses such as HPLC-DAD or LC-MS lose valuable information on metabolite localization during the extraction process. To overcome this issue, a correlative analysis combining mass spectroscopy imaging (MSI) and fluorescence imaging was developed to localize in situ stilbenes on the same stressed grapevine leaves. High-resolution images of the stilbene fluorescence provided by macroscopy were supplemented by specific distributions and structural information concerning resveratrol, pterostilbene, and piceids obtained by MSI. The two imaging techniques led to consistent and complementary data on the stilbene spatial distribution for the two stresses addressed: UV-C irradiation and infection by Plasmopara viticola. Results emphasize that grapevine leaves react differently depending on the stress. A rather uniform synthesis of stilbenes is induced after UV-C irradiation, whereas a more localized synthesis of stilbenes in stomata guard cells and cell walls is induced by P. viticola infection. Finally, this combined imaging approach could be extended to map phytoalexins of various plant tissues with resolution approaching the cellular level.
    Mots-clés : IMAGIF, PF, PHOT.

  • C. Bou-Nader, D. Cornu, V. Guerineau, T. Fogeron, M. Fontecave, et D. Hamdane, « Enzyme Activation with a Synthetic Catalytic Co-enzyme Intermediate: Nucleotide Methylation by Flavoenzymes », Angewandte Chemie (International Ed. in English), août 2017.
    Résumé : To facilitate production of functional enzymes and to study their mechanisms, especially in the complex cases of coenzyme-dependent systems, activation of an inactive apoenzyme preparation with a catalytically competent coenzyme intermediate is an attractive strategy. This is illustrated with the simple chemical synthesis of a flavin-methylene iminium compound previously proposed as a key intermediate in the catalytic cycle of several important flavoenzymes involved in nucleic acid metabolism. Reconstitution of both flavin-dependent RNA methyltransferase and thymidylate synthase apoproteins with this synthetic compound led to active enzymes for the C5-uracil methylation within their respective transfer RNA and dUMP substrate. This strategy is expected to be of general application in enzymology.
    Mots-clés : artificial enzymes, flavoenzyme mechanism, Methylation, Nucleotides, PF, reaction intermediates, SICAPS.

  • C. Bou-Nader, L. Pecqueur, D. Cornu, M. Lombard, M. Dezi, M. Nicaise, C. Velours, M. Fontecave, et D. Hamdane, « Power of protein/tRNA functional assembly against aberrant aggregation », Physical chemistry chemical physics: PCCP, oct. 2017.
    Résumé : Understanding the mechanisms of protein oligomerization and aggregation is a major concern for biotechnology and medical purposes. However, significant challenges remain in determining the mechanism of formation of these superstructures and the environmental factors that can precisely modulate them. Notably the role that a functional ligand plays in the process of protein aggregation is largely unexplored. We herein address these issues with an original flavin-dependent RNA methyltransferase (TrmFO) used as a protein model since this protein employs a complex set of cofactors and ligands for catalysis. Here, we show that TrmFO carries an unstable protein structure that can partially mis-unfold leading to either formation of irregular and nonfunctional soluble oligomers endowed with hyper-thermal stability or large amorphous aggregates in the presence of salts. Mutagenesis confirmed that this peculiarity is an intrinsic property of a polypeptide and it is independent of the flavin coenzyme. Structural characterization and kinetic studies identified several regions of the protein that enjoy conformational changes and more particularly pinpointed the N-terminal subdomain as being a key element in the mechanisms of oligomerization and aggregation. Only stabilization of this region via tRNA suppresses these aberrant protein states. Although protein chaperones emerged as major actors against aggregation, our study emphasizes that other powerful mechanisms exist such as the stabilizing effect of functional assemblies that provide an additional layer of protection against the instability of the proteome.
    Mots-clés : PF, PIM, SICAPS.

  • S. C. Brown, M. Bourge, N. Maunoury, M. Wong, M. W. Bianchi, S. Lepers-Andrzejewski, P. Besse, S. Siljak-Yakovlev, M. Dron, et B. Satiat-Jeunemaître, « DNA remodelling by Strict Partial Endoreplication in orchids, an original process in the plant kingdom », Genome Biology and Evolution, avr. 2017.
    Résumé : DNA remodelling during endoreplication appears to be a strong developmental characteristic in orchids. In this study, we analysed DNA content and nuclei in 41 species of orchids to further map the genome evolution in this plant family. We demonstrate that the DNA remodelling observed in 36 out of 41 orchids studied corresponds to strict partial endoreplication. Such process is developmentally regulated in each wild species studied. Cytometry data analyses allowed us to propose a model where nuclear states 2C, 4E, 8E, etc. form a series comprising a fixed proportion, the euploid genome 2C, plus 2 to 32 additional copies of a complementary part of the genome. The fixed proportion ranged from 89% of the genome in Vanilla mexicana down to 19% in V. pompona, the lowest value for all 148 orchids reported. Insterspecific hybridisation did not suppress this phenomenon. Interestingly, this process was not observed in mass-produced epiphytes. Nucleolar volumes grow with the number of endocopies present, coherent with high transcription activity in endoreplicated nuclei. Our analyses suggest species-specific chromatin rearrangement. Towards understanding endoreplication, V. planifolia constitutes a tractable system for isolating the genomic sequences that confer an advantage via endoreplication from those that apparently suffice at diploid level.
    Mots-clés : BIOCELL, CYTO, cytogenetics, cytometry, DYNBSJ, endoreplication, genome imbalance, Genome Size, IMAGIF, MINION, PF, PHOT, Vanilla.


  • E. Dambroise, M. Simion, T. Bourquard, S. Bouffard, B. Rizzi, Y. Jaszczyszyn, M. Bourge, P. Affaticati, A. Heuzé, J. Jouralet, J. Edouard, S. Brown, C. Thermes, A. Poupon, E. Reiter, F. Sohm, F. Bourrat, et J. - S. Joly, « Postembryonic Fish Brain Proliferation Zones Exhibit Neuroepithelial-Type Gene Expression Profile: Features of Neuroepithelial Cells in Fish », STEM CELLS, 2017.
    Mots-clés : BMgif, CYTO, IMAGIF, NGS, PF, PHOT.

  • T. Di Meo, W. Ghattas, C. Herrero, C. Velours, P. Minard, J. - P. Mahy, R. Ricoux, et A. Urvoas, « αRep A3: A versatile artificial scaffold for metalloenzyme design », Chemistry (Weinheim an Der Bergstrasse, Germany), mai 2017.
    Résumé : αRep is a new family of artificial proteins based on a thermostable alpha-helical repeated motif. One of its members, αRep A3, forms a stable homo-dimer with a wide cleft that is able to receive metal complexes and thus appears as suitable for generating new artificial biocatalysts. Based on the crystal structure of αRep A3, two positions (F119 and Y26) were chosen and changed independently into cysteine residues. A phenanthroline ligand was covalently attached to the unique cysteine of each protein variant and the corresponding biohybrids were purified and characterized. Once mutated and coupled to phenanthroline, the protein remained folded and dimeric. Copper(II) was bound specifically by the two biohybrids with two different binding modes and, in addition, the holo biohybrid A3F119NPH was found to be able to catalyze enantioselectively the Diels-Alder (D-A) cycloaddition with up to 62% ee. This study validates the choice of the αRep A3 dimer as a protein scaffold and provides a new promising route for the design and production of new enantioselective biohybrids based on entirely artificial proteins issued from a highly diverse library.
    Mots-clés : artificial repeat proteins, B3S, Diels-Alder reaction, Enantioselective Catalysis, MIP, PF, PIM.


  • R. El Helou, G. Pinna, O. Cabaud, J. Wicinski, R. Bhajun, L. Guyon, C. Rioualen, P. Finetti, A. Gros, B. Mari, P. Barbry, F. Bertucci, G. Bidaut, A. Harel-Bellan, D. Birnbaum, E. Charafe-Jauffret, et C. Ginestier, « miR-600 Acts as a Bimodal Switch that Regulates Breast Cancer Stem Cell Fate through WNT Signaling », Cell Reports, vol. 18, nᵒ 9, p. 2256-2268, 2017.

  • C. Esnault, D. Leiber, C. Toffano-Nioche, Z. Tanfin, et M. - J. Virolle, « Another example of enzymatic promiscuity: the polyphosphate kinase of Streptomyces lividans is endowed with phospholipase D activity », Applied Microbiology and Biotechnology, vol. 101, nᵒ 1, p. 139-145, janv. 2017.
    Résumé : Polyphosphate kinases (PPK) from different bacteria, including that of Streptomyces lividans, were shown to contain the typical HKD motif present in phospholipase D (PLD) and showed structural similarities to the latter. This observation prompted us to investigate the PLD activity of PPK of S. lividans, in vitro. The ability of PPK to catalyze the hydrolysis of phosphatidylcholine (PC), the PLD substrate, was assessed by the quantification of [(3)H]phosphatidic acid (PA) released from [(3)H]PC-labeled ELT3 cell membranes. Basal cell membrane PLD activity as well as GTPγS-activated PLD activity was higher in the presence than in absence of PPK. After abolition of the basal PLD activity of the membranes by heat or tryptic treatment, the addition of PPK to cell membranes was still accompanied by an increased production of PA demonstrating that PPK also bears a PLD activity. PLD activity of PPK was also assessed by the production of choline from hydrolysis of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) in the presence of the Amplex Red reagent and compared to two commercial PLD enzymes. These data demonstrated that PPK is endowed with a weak but clearly detectable PLD activity. The question of the biological signification, if any, of this enzymatic promiscuity is discussed.
    Mots-clés : Amino Acid Motifs, Cell Membrane, Choline, DBG, eBio, Hydrolysis, Lipid droplets, MESMIC, MICROBIO, PF, Phosphatidic Acids, Phosphatidylcholines, Phospholipase D, Phosphotransferases (Phosphate Group Acceptor), Polyphosphate kinase, Promiscuous enzyme, Protein Conformation, SSFA, Streptomyces lividans.

  • R. Grzela, J. Nusbaum, S. Fieulaine, F. Lavecchia, M. Desmadril, N. Nhiri, A. Van Dorsselaer, S. Cianferani, E. Jacquet, T. Meinnel, et C. Giglione, « Peptide deformylases from Vibrio parahaemolyticus phage and bacteria display similar deformylase activity and inhibitor binding clefts », Biochimica Et Biophysica Acta, oct. 2017.
    Résumé : Unexpected peptide deformylase (PDF) genes were recently retrieved in numerous marine phage genomes. While various hypotheses dealing with the occurrence of these intriguing sequences have been made, no further characterization and functional studies have been described thus far. In this study, we characterize the bacteriophage Vp16 PDF enzyme, as representative member of the newly identified C-terminally truncated viral PDFs. We show here that conditions classically used for bacterial PDFs lead to an enzyme exhibiting weak activity. Nonetheless, our integrated biophysical and biochemical approaches reveal specific effects of pH and metals on Vp16 PDF stability and activity. A novel purification protocol taking in account these data allowed strong improvement of Vp16 specific activity to values similar to those of bacterial PDFs. We next show that Vp16PDF is as sensitive to the natural inhibitor compound of PDFs, actinonin, as bacterial PDFs. Comparison of the 3D structures of Vp16 and E. coli PDFs bound to actinonin also reveals that both PDFs display identical substrate binding mode. We conclude that bacteriophage Vp16 PDF protein has functional peptide deformylase activity and we suggest that encoded phage PDFs might be important for viral fitness.
    Mots-clés : AMIG, B3S, BDG, DBG, Enzyme mechanism, IMAPP, MIP, N-terminal methionine excision, Peptide deformylase, PF, PIM, PROMTI, Structure, Virus.


  • P. P. Weil, Y. Jaszczyszyn, A. Baroin-Tourancheau, J. Postberg, et L. Amar, « Holistic and Affordable Analyses of MicroRNA Expression Profiles Using Tagged cDNA Libraries and a Multiplex Sequencing Strategy », in Functional Genomics, vol. 1654, M. Kaufmann, C. Klinger, et A. Savelsbergh, Éd. New York, NY: Springer New York, 2017, p. 179-196.


  • J. Lang, A. Vigouroux, A. El Sahili, A. Kwasiborski, M. Aumont-Nicaise, Y. Dessaux, J. A. Shykoff, S. Moréra, et D. Faure, « Fitness costs restrict niche expansion by generalist niche-constructing pathogens », The ISME Journal, vol. 11, nᵒ 2, p. 374-385, 2017.
    Mots-clés : B3S, MESB3S, MICROBIO, PBI, PF, PIM.


  • T. N. Le Lam, C. Morvan, W. Liu, C. Bohn, Y. Jaszczyszyn, et P. Bouloc, « Finding sRNA-associated phenotypes by competition assays: An example with Staphylococcus aureus », Methods, vol. 117, p. 21-27, 2017.
    Mots-clés : DBG, NGS, PF, SRRB.

  • L. Loiseau, C. Fyfe, L. Aussel, M. Hajj Chehade, S. B. Hernández, B. Faivre, D. Hamdane, C. Mellot-Draznieks, B. Rascalou, L. Pelosi, C. Velours, D. Cornu, M. Lombard, J. Casadesús, F. Pierrel, M. Fontecave, et F. Barras, « The UbiK protein is an accessory factor necessary for bacterial ubiquinone (UQ) biosynthesis and forms a complex with the UQ biogenesis factor UbiJ », The Journal of Biological Chemistry, mai 2017.
    Résumé : Ubiquinone (UQ), also referred to as coenzyme Q, is a widespread lipophilic molecule in both prokaryotes and eukaryotes in which it primarily acts as an electron carrier. Eleven proteins are known to participate in UQ biosynthesis in Escherichia coli, and we recently demonstrated that UQ biosynthesis requires additional, nonenzymatic factors, some of which are still unknown. Here, we report on the identification of a bacterial gene, yqiC, which is required for efficient UQ biosynthesis, and which we have renamed ubiK. Using several methods, we demonstrated that the UbiK protein forms a complex with the C-terminal part of UbiJ, another UQ biogenesis factor we previously identified. We found that both proteins are likely to contribute to global UQ biosynthesis rather than to a specific biosynthetic step, since both ubiK and ubiJ mutants accumulated octaprenylphenol, an early intermediate of the UQ biosynthetic pathway. Interestingly, we found that both proteins are dispensable for UQ biosynthesis under anaerobiosis, even though they were expressed in the absence of oxygen. We also provide evidence that the UbiK-UbiJ complex interacts with palmitoleic acid, a major lipid in E. coli. Last, in Salmonella enterica, ubiK was required for proliferation in macrophages and virulence in mice. We conclude that although the role of the UbiK-UbiJ complex remains unknown, our results support the hypothesis that UbiK is an accessory factor of Ubi enzymes and facilitates UQ biosynthesis by acting as an assembly factor, a targeting factor, or both.
    Mots-clés : bioenergetics, coenzyme Q10 (CoQ10), Electron transfer, Escherichia coli (E. coli), Microbiology, PF, PIM, SICAPS, Ubiquinone.

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


  • J. Marion, R. Le Bars, B. Satiat-Jeunemaitre, et C. Boulogne, « Optimizing CLEM protocols for plants cells: GMA embedding and cryosections as alternatives for preservation of GFP fluorescence in Arabidopsis roots », Journal of Structural Biology, 2017.
    Mots-clés : Arabidopsis, BIOCELL, Correlative microscopy, DYNBSJ, GFP, GMA resin, IMAGIF, MET, PF, PHOT, Tokuyasu, Transmission electron microscopy.

  • T. Q. Nguyen, M. Chenon, F. Vilela, C. Velours, M. Aumont-Nicaise, J. Andreani, P. F. Varela, P. Llinas, et J. Ménétrey, « Structural plasticity of the N-terminal capping helix of the TPR domain of kinesin light chain », PloS One, vol. 12, nᵒ 10, p. e0186354, 2017.
    Résumé : Kinesin1 plays a major role in neuronal transport by recruiting many different cargos through its kinesin light chain (KLC). Various structurally unrelated cargos interact with the conserved tetratricopeptide repeat (TPR) domain of KLC. The N-terminal capping helix of the TPR domain exhibits an atypical sequence and structural features that may contribute to the versatility of the TPR domain to bind different cargos. We determined crystal structures of the TPR domain of both KLC1 and KLC2 encompassing the N-terminal capping helix and show that this helix exhibits two distinct and defined orientations relative to the rest of the TPR domain. Such a difference in orientation gives rise, at the N-terminal part of the groove, to the formation of one hydrophobic pocket, as well as to electrostatic variations at the groove surface. We present a comprehensive structural analysis of available KLC1/2-TPR domain structures that highlights that ligand binding into the groove can be specific of one or the other N-terminal capping helix orientations. Further, structural analysis reveals that the N-terminal capping helix is always involved in crystal packing contacts, especially in a TPR1:TPR1' contact which highlights its propensity to be a protein-protein interaction site. Together, these results underline that the structural plasticity of the N-terminal capping helix might represent a structural determinant for TPR domain structural versatility in cargo binding.
    Mots-clés : AMIG, Amino Acid Motifs, Amino Acid Sequence, Animals, B3S, Conserved Sequence, Humans, Ligands, Mice, Microtubule-Associated Proteins, MIKICA, Models, Molecular, PF, PIM, Protein Conformation, alpha-Helical, Protein Domains.

  • J. Nikolic, R. Le Bars, Z. Lama, N. Scrima, C. Lagaudrière-Gesbert, Y. Gaudin, et D. Blondel, « Negri bodies are viral factories with properties of liquid organelles », Nature Communications, vol. 8, nᵒ 1, p. 58, juill. 2017.
    Résumé : Replication of Mononegavirales occurs in viral factories which form inclusions in the host-cell cytoplasm. For rabies virus, those inclusions are called Negri bodies (NBs). We report that NBs have characteristics similar to those of liquid organelles: they are spherical, they fuse to form larger structures, and they disappear upon hypotonic shock. Their liquid phase is confirmed by FRAP experiments. Live-cell imaging indicates that viral nucleocapsids are ejected from NBs and transported along microtubules to form either new virions or secondary viral factories. Coexpression of rabies virus N and P proteins results in cytoplasmic inclusions recapitulating NBs properties. This minimal system reveals that an intrinsically disordered domain and the dimerization domain of P are essential for Negri bodies-like structures formation. We suggest that formation of liquid viral factories by phase separation is common among Mononegavirales and allows specific recruitment and concentration of viral proteins but also the escape to cellular antiviral response.Negative strand RNA viruses, such as rabies virus, induce formation of cytoplasmic inclusions for genome replication. Here, Nikolic et al. show that these so-called Negri bodies (NBs) have characteristics of liquid organelles and they identify the minimal protein domains required for NB formation.
    Mots-clés : IMAGIF, PF, PHOT, RHABDO, VIRO.


  • J. - A. Pedroza-García, C. Mazubert, I. del Olmo, M. Bourge, S. Domenichini, R. Bounon, Z. Tariq, E. Delannoy, M. Piñeiro, J. A. Jarillo, C. Bergounioux, M. Benhamed, et C. Raynaud, « Function of the Plant DNA Polymerase Epsilon in Replicative Stress Sensing, a Genetic Analysis », Plant Physiology, vol. 173, nᵒ 3, p. 1735-1749, 2017.


  • P. Pétriacq, L. de Bont, L. Genestout, J. Hao, C. Laureau, I. Florez-Sarasa, T. Rzigui, G. Queval, F. Gilard, C. Mauve, F. Guérard, M. Lamothe-Sibold, J. Marion, C. Fresneau, S. Brown, A. Danon, A. Krieger-Liszkay, R. Berthomé, M. Ribas-Carbo, G. Tcherkez, G. Cornic, B. Pineau, B. Gakière, et R. De Paepe, « Photoperiod Affects the Phenotype of Mitochondrial Complex I Mutants », Plant Physiology, vol. 173, nᵒ 1, p. 434-455, 2017.
    Mots-clés : B3S, BIOCELL, DYNBSJ, IMAGIF, MROP, PF, PHOT.

  • J. Pirrello, C. Deluche, N. Frangne, F. Gévaudant, E. Maza, A. Djari, M. Bourge, J. - P. Renaudin, S. Brown, C. Bowler, M. Zouine, C. Chevalier, et N. Gonzalez, « Transcriptome profiling of sorted endoreduplicated nuclei from tomato fruits: how global shift in expression ascribed to DNA ploidy influences RNA-Seq data normalization and interpretation », The Plant Journal: For Cell and Molecular Biology, nov. 2017.
    Résumé : As part of normal development most eukaryotic organisms ranging from insects to mammals and plants display variations in nuclear ploidy levels resulting from somatic endopolyploidy. Endoreduplication is the major source of endopolyploidy in higher plants. Endoreduplication is a remarkable characteristic of the fleshy pericarp tissue of developing tomato fruits, where it establishes a highly integrated cellular system that acts as a morphogenetic factor supporting cell growth. However, the functional significance of endoreduplication is not fully understood. Although endoreduplication is thought to increase metabolic activity due to a global increase in transcription, the issue of gene-specific ploidy-regulated transcription remains opened. To investigate the influence of endoreduplication on transcription in tomato fruit, we tested the feasibility of a RNA-Seq approach using total nuclear RNA extracted from purified populations of flow cytometry-sorted nuclei based on their DNA content. Here we show that cell-based approaches to study RNA-Seq profiles need to take into account the putative global shift in expression between samples for correct analysis and interpretation of the data. From ploidy-specific expression profiles we found that the activity of cells inside the pericarp is related both to the ploidy level and their tissue location. This article is protected by copyright. All rights reserved.
    Mots-clés : CYTO, data interpretation, endoreduplication, fruit development, PF, RNA-Seq profiling, Solanum lycopersicum, sorted nuclei, technical Advance, tomato.

  • S. Robinson, J. Nevalainen, G. Pinna, A. Campalans, J. P. Radicella, et L. Guyon, « Incorporating interaction networks into the determination of functionally related hit genes in genomic experiments with Markov random fields », Bioinformatics (Oxford, England), vol. 33, nᵒ 14, p. i170-i179, juill. 2017.
    Résumé : Motivation: Incorporating gene interaction data into the identification of 'hit' genes in genomic experiments is a well-established approach leveraging the 'guilt by association' assumption to obtain a network based hit list of functionally related genes. We aim to develop a method to allow for multivariate gene scores and multiple hit labels in order to extend the analysis of genomic screening data within such an approach. Results: We propose a Markov random field-based method to achieve our aim and show that the particular advantages of our method compared with those currently used lead to new insights in previously analysed data as well as for our own motivating data. Our method additionally achieves the best performance in an independent simulation experiment. The real data applications we consider comprise of a survival analysis and differential expression experiment and a cell-based RNA interference functional screen. Availability and implementation: We provide all of the data and code related to the results in the paper. Contact: sean.j.robinson@utu.fi or laurent.guyon@cea.fr. Supplementary information: Supplementary data are available at Bioinformatics online.
    Mots-clés : PARI, PF.


  • C. Samson, F. Celli, K. Hendriks, M. Zinke, N. Essawy, I. Herrada, A. - A. Arteni, F. - X. Theillet, B. Alpha-Bazin, J. Armengaud, C. Coirault, A. Lange, et S. Zinn-Justin, « Emerin self-assembly mechanism: role of the LEM domain », The FEBS Journal, vol. 284, nᵒ 2, p. 338-352, 2017.
    Mots-clés : B3S, CRYOEM, INTGEN, PF.


  • P. V. Sauer, J. Timm, D. Liu, D. Sitbon, E. Boeri-Erba, C. Velours, N. Mücke, J. Langowski, F. Ochsenbein, G. Almouzni, et D. Panne, « Insights into the molecular architecture and histone H3-H4 deposition mechanism of yeast Chromatin assembly factor 1 », eLife, vol. 6, mars 2017.
    Mots-clés : AMIG, B3S, PF, PIM.

  • A. K. Sinha, A. Durand, J. - M. Desfontaines, I. Iurchenko, H. Auger, D. R. F. Leach, F. - X. Barre, et B. Michel, « Division-induced DNA double strand breaks in the chromosome terminus region of Escherichia coli lacking RecBCD DNA repair enzyme », PLoS genetics, vol. 13, nᵒ 10, p. e1006895, oct. 2017.
    Résumé : Marker frequency analysis of the Escherichia coli recB mutant chromosome has revealed a deficit of DNA in a specific zone of the terminus, centred on the dif/TerC region. Using fluorescence microscopy of a marked chromosomal site, we show that the dif region is lost after replication completion, at the time of cell division, in one daughter cell only, and that the phenomenon is transmitted to progeny. Analysis by marker frequency and microscopy shows that the position of DNA loss is not defined by the replication fork merging point since it still occurs in the dif/TerC region when the replication fork trap is displaced in strains harbouring ectopic Ter sites. Terminus DNA loss in the recB mutant is also independent of dimer resolution by XerCD at dif and of Topo IV action close to dif. It occurs in the terminus region, at the point of inversion of the GC skew, which is also the point of convergence of specific sequence motifs like KOPS and Chi sites, regardless of whether the convergence of GC skew is at dif (wild-type) or a newly created sequence. In the absence of FtsK-driven DNA translocation, terminus DNA loss is less precisely targeted to the KOPS convergence sequence, but occurs at a similar frequency and follows the same pattern as in FtsK+ cells. Importantly, using ftsIts, ftsAts division mutants and cephalexin treated cells, we show that DNA loss of the dif region in the recB mutant is decreased by the inactivation of cell division. We propose that it results from septum-induced chromosome breakage, and largely contributes to the low viability of the recB mutant.
    Mots-clés : DBG, EMC2, NGS, PF, STABAC.


  • Z. M. Song, L. Bouchab, E. Hudik, R. Le Bars, O. Nüsse, et S. Dupré-Crochet, « Phosphoinositol 3-phosphate acts as a timer for reactive oxygen species production in the phagosome », Journal of Leukocyte Biology, p. jlb.1A0716-305R, janv. 2017.


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

  • Y. Wu, V. Pons, A. Goudet, L. Panigai, A. Fischer, J. - A. Herweg, S. Kali, R. A. Davey, J. Laporte, C. Bouclier, R. Yousfi, C. Aubenque, G. Merer, E. Gobbo, R. Lopez, C. Gillet, S. Cojean, M. R. Popoff, P. Clayette, R. Le Grand, C. Boulogne, N. Tordo, E. Lemichez, P. M. Loiseau, T. Rudel, D. Sauvaire, J. - C. Cintrat, D. Gillet, et J. Barbier, « ABMA, a small molecule that inhibits intracellular toxins and pathogens by interfering with late endosomal compartments », Scientific Reports, vol. 7, nᵒ 1, p. 15567, nov. 2017.
    Résumé : Intracellular pathogenic microorganisms and toxins exploit host cell mechanisms to enter, exert their deleterious effects as well as hijack host nutrition for their development. A potential approach to treat multiple pathogen infections and that should not induce drug resistance is the use of small molecules that target host components. We identified the compound 1-adamantyl (5-bromo-2-methoxybenzyl) amine (ABMA) from a cell-based high throughput screening for its capacity to protect human cells and mice against ricin toxin without toxicity. This compound efficiently protects cells against various toxins and pathogens including viruses, intracellular bacteria and parasite. ABMA provokes Rab7-positive late endosomal compartment accumulation in mammalian cells without affecting other organelles (early endosomes, lysosomes, the Golgi apparatus, the endoplasmic reticulum or the nucleus). As the mechanism of action of ABMA is restricted to host-endosomal compartments, it reduces cell infection by pathogens that depend on this pathway to invade cells. ABMA may represent a novel class of broad-spectrum compounds with therapeutic potential against diverse severe infectious diseases.
    Mots-clés : MET, PF.

2016



  • S. Ahmad, L. Pecqueur, B. Dreier, D. Hamdane, M. Aumont-Nicaise, A. Plückthun, M. Knossow, et B. Gigant, « Destabilizing an interacting motif strengthens the association of a designed ankyrin repeat protein with tubulin », Scientific Reports, vol. 6, p. 28922, juill. 2016.
    Mots-clés : B3S, MIKICA, PF, PIM.

  • C. Aillaud, C. Bosc, Y. Saoudi, E. Denarier, L. Peris, L. Sago, N. Taulet, A. Cieren, O. Tort, M. M. Magiera, C. Janke, V. Redeker, A. Andrieux, et M. - J. Moutin, « Evidence for new C-terminally truncated variants of α- and β-tubulins », Molecular Biology of the Cell, vol. 27, nᵒ 4, p. 640-653, févr. 2016.
    Résumé : Cellular α-tubulin can bear various carboxy-terminal sequences: full-length tubulin arising from gene neosynthesis is tyrosinated, and two truncated variants, corresponding to detyrosinated and Δ2 α‑tubulin, result from the sequential cleavage of one or two C-terminal residues, respectively. Here, by using a novel antibody named 3EG that is highly specific to the -EEEG C-terminal sequence, we demonstrate the occurrence in neuronal tissues of a new αΔ3‑tubulin variant corresponding to α1A/B‑tubulin deleted of its last three residues (EEY). αΔ3‑tubulin has a specific distribution pattern: its quantity in the brain is similar to that of αΔ2-tubulin around birth but is much lower in adult tissue. This truncated α1A/B-tubulin variant can be generated from αΔ2-tubulin by the deglutamylases CCP1, CCP4, CCP5, and CCP6 but not by CCP2 and CCP3. Moreover, using 3EG antibody, we identify a C‑terminally truncated β-tubulin form with the same -EEEG C-terminal sequence. Using mass spectrometry, we demonstrate that β2A/B-tubulin is modified by truncation of the four C-terminal residues (EDEA). We show that this newly identified βΔ4-tubulin is ubiquitously present in cells and tissues and that its level is constant throughout the cell cycle. These new C-terminally truncated α- and β-tubulin variants, both ending with -EEEG sequence, are expected to regulate microtubule physiology. Of interest, the αΔ3-tubulin seems to be related to dynamic microtubules, resembling tyrosinated-tubulin rather than the other truncated variants, and may have critical function(s) in neuronal development.
    Mots-clés : Amino Acid Sequence, Animals, Brain, Carboxypeptidases, cell cycle, Gene Knockdown Techniques, HEK293 Cells, HeLa Cells, Humans, Mass Spectrometry, Mice, Microtubules, Molecular Sequence Data, Neurogenesis, Neurons, Peptide Synthases, PF, Protein Processing, Post-Translational, SICAPS, Tubulin, Tyrosine.


  • M. Benincasa, Q. Barrière, G. Runti, O. Pierre, M. Bourge, M. Scocchi, et P. Mergaert, « Single Cell Flow Cytometry Assay for Peptide Uptake by Bacteria », BIO-PROTOCOL, vol. 6, nᵒ 23, 2016.
    Mots-clés : CYTO, IMAGIF, MICROBIO, PBI, PF.

  • C. Chaintreuil, D. Gully, C. Hervouet, P. Tittabutr, H. Randriambanona, S. C. Brown, G. P. Lewis, M. Bourge, F. Cartieaux, M. Boursot, H. Ramanankierana, A. D'Hont, N. Teaumroong, E. Giraud, et J. - F. Arrighi, « The evolutionary dynamics of ancient and recent polyploidy in the African semiaquatic species of the legume genus Aeschynomene », The New Phytologist, vol. 211, nᵒ 3, p. 1077-1091, août 2016.
    Résumé : The legume genus Aeschynomene is notable in the ability of certain semiaquatic species to develop nitrogen-fixing stem nodules. These species are distributed in two clades. In the first clade, all the species are characterized by the use of a unique Nod-independent symbiotic process. In the second clade, the species use a Nod-dependent symbiotic process and some of them display a profuse stem nodulation as exemplified in the African Aeschynomene afraspera. To facilitate the molecular analysis of the symbiotic characteristics of such legumes, we took an integrated molecular and cytogenetic approach to track occurrences of polyploidy events and to analyze their impact on the evolution of the African species of Aeschynomene. Our results revealed two rounds of polyploidy: a paleopolyploid event predating the African group and two neopolyploid speciations, along with significant chromosomal variations. Hence, we found that A. afraspera (8x) has inherited the contrasted genomic properties and the stem-nodulation habit of its parental lineages (4x). This study reveals a comprehensive picture of African Aeschynomene diversification. It notably evidences a history that is distinct from the diploid Nod-independent clade, providing clues for the identification of the specific determinants of the Nod-dependent and Nod-independent symbiotic processes, and for comparative analysis of stem nodulation.
    Mots-clés : Aeschynomene, CYTO, dysploidy, genome downsizing, IMAGIF, PF, PHOT, Polyploidy, stem nodulation, Symbiosis.

  • A. de Saint Germain, G. Clavé, M. - A. Badet-Denisot, J. - P. Pillot, D. Cornu, J. - P. Le Caer, M. Burger, F. Pelissier, P. Retailleau, C. Turnbull, S. Bonhomme, J. Chory, C. Rameau, et F. - D. Boyer, « An histidine covalent receptor and butenolide complex mediates strigolactone perception », Nature Chemical Biology, vol. 12, nᵒ 10, p. 787-794, oct. 2016.
    Résumé : Strigolactone plant hormones control plant architecture and are key players in both symbiotic and parasitic interactions. They contain an ABC tricyclic lactone connected to a butenolide group, the D ring. The DWARF14 (D14) strigolactone receptor belongs to the superfamily of α/β-hydrolases, and is known to hydrolyze the bond between the ABC lactone and the D ring. Here we characterized the binding and catalytic functions of RAMOSUS3 (RMS3), the pea (Pisum sativum) ortholog of rice (Oryza sativa) D14 strigolactone receptor. Using new profluorescent probes with strigolactone-like bioactivity, we found that RMS3 acts as a single-turnover enzyme that explains its apparent low enzymatic rate. We demonstrated the formation of a covalent RMS3-D-ring complex, essential for bioactivity, in which the D ring was attached to histidine 247 of the catalytic triad. These results reveal an undescribed mechanism of plant hormone reception in which the receptor performs an irreversible enzymatic reaction to generate its own ligand.
    Mots-clés : PF, SICAPS.


  • E. Deforzh, T. Vargas, J. Kropp, M. Vandamme, G. Pinna, et A. Polesskaya, « IMP-3 protects the mRNAs of cyclins D1 and D3 from GW182/AGO2-dependent translational repression », International Journal of Oncology, oct. 2016.
    Mots-clés : DBG, PARI, PF, RPTEG.

  • T. Eychenne, E. Novikova, M. - B. Barrault, O. Alibert, C. Boschiero, N. Peixeiro, D. Cornu, V. Redeker, L. Kuras, P. Nicolas, M. Werner, et J. Soutourina, « Functional interplay between Mediator and TFIIB in preinitiation complex assembly in relation to promoter architecture », Genes & Development, vol. 30, nᵒ 18, p. 2119-2132, sept. 2016.
    Résumé : Mediator is a large coregulator complex conserved from yeast to humans and involved in many human diseases, including cancers. Together with general transcription factors, it stimulates preinitiation complex (PIC) formation and activates RNA polymerase II (Pol II) transcription. In this study, we analyzed how Mediator acts in PIC assembly using in vivo, in vitro, and in silico approaches. We revealed an essential function of the Mediator middle module exerted through its Med10 subunit, implicating a key interaction between Mediator and TFIIB. We showed that this Mediator-TFIIB link has a global role on PIC assembly genome-wide. Moreover, the amplitude of Mediator's effect on PIC formation is gene-dependent and is related to the promoter architecture in terms of TATA elements, nucleosome occupancy, and dynamics. This study thus provides mechanistic insights into the coordinated function of Mediator and TFIIB in PIC assembly in different chromatin contexts.
    Mots-clés : DBG, GTR, Mediator, PEPS, PF, preinitiation complex, promoter architecture, RNA polymerase II transcription, Saccharomyces cerevisiae, SICAPS, TFIIB.

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