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  • 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, 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, eBio, Hydrolysis, Lipid droplets, MESMIC, MICROBIO, PF, Phosphatidic Acids, Phosphatidylcholines, Phospholipase D, Phosphotransferases (Phosphate Group Acceptor), Polyphosphate kinase, Promiscuous enzyme, Protein Conformation, Streptomyces lividans.



  • M. Descrimes, Y. Ben Zouari, M. Wery, R. Legendre, D. Gautheret, et A. Morillon, « VING: a software for visualization of deep sequencing signals », BMC research notes, vol. 8, p. 419, 2015.
    Résumé : BACKGROUND: Next generation sequencing (NGS) data treatment often requires mapping sequenced reads onto a reference genome for further analysis. Mapped data are commonly visualized using genome browsers. However, such software are not suited for a publication-ready and versatile representation of NGS data coverage, especially when multiple experiments are simultaneously treated. RESULTS: We developed 'VING', a stand-alone R script that takes as input NGS mapping files and genome annotations to produce accurate snapshots of the NGS coverage signal for any specified genomic region. VING offers multiple viewing options, including strand-specific views and a special heatmap mode for representing multiple experiments in a single figure. CONCLUSIONS: VING produces high-quality figures for NGS data representation in a genome region of interest. It is available at We also developed a Galaxy wrapper, available in the Galaxy tool shed with installation and usage instructions.
    Mots-clés : Computational Biology, eBio, Genome, Genomics, High-Throughput Nucleotide Sequencing, Internet, PF, Reproducibility of Results, Sequence Analysis, DNA, Software.

  • U. Gophna, D. M. Kristensen, Y. I. Wolf, O. Popa, C. Drevet, et E. V. Koonin, « No evidence of inhibition of horizontal gene transfer by CRISPR-Cas on evolutionary timescales », The ISME journal, vol. 9, nᵒ 9, p. 2021-2027, 2015.
    Résumé : The CRISPR (clustered, regularly, interspaced, short, palindromic repeats)-Cas (CRISPR-associated genes) systems of archaea and bacteria provide adaptive immunity against viruses and other selfish elements and are believed to curtail horizontal gene transfer (HGT). Limiting acquisition of new genetic material could be one of the sources of the fitness cost of CRISPR-Cas maintenance and one of the causes of the patchy distribution of CRISPR-Cas among bacteria, and across environments. We sought to test the hypothesis that the activity of CRISPR-Cas in microbes is negatively correlated with the extent of recent HGT. Using three independent measures of HGT, we found no significant dependence between the length of CRISPR arrays, which reflects the activity of the immune system, and the estimated number of recent HGT events. In contrast, we observed a significant negative dependence between the estimated extent of HGT and growth temperature of microbes, which could be explained by the lower genetic diversity in hotter environments. We hypothesize that the relevant events in the evolution of resistance to mobile elements and proclivity for HGT, to which CRISPR-Cas systems seem to substantially contribute, occur on the population scale rather than on the timescale of species evolution.
    Mots-clés : Adaptive Immunity, Archaea, bacteria, Biological Evolution, Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-Cas Systems, eBio, Gene Transfer, Horizontal, Genome, Bacterial, Models, Genetic, PF, Temperature, Viruses.

  • J. Li, M. - A. Poursat, D. Drubay, A. Motz, Z. Saci, A. Morillon, S. Michiels, et D. Gautheret, « A Dual Model for Prioritizing Cancer Mutations in the Non-coding Genome Based on Germline and Somatic Events », PLoS computational biology, vol. 11, nᵒ 11, p. e1004583, 2015.
    Résumé : We address here the issue of prioritizing non-coding mutations in the tumoral genome. To this aim, we created two independent computational models. The first (germline) model estimates purifying selection based on population SNP data. The second (somatic) model estimates tumor mutation density based on whole genome tumor sequencing. We show that each model reflects a different set of constraints acting either on the normal or tumor genome, and we identify the specific genome features that most contribute to these constraints. Importantly, we show that the somatic mutation model carries independent functional information that can be used to narrow down the non-coding regions that may be relevant to cancer progression. On this basis, we identify positions in non-coding RNAs and the non-coding parts of mRNAs that are both under purifying selection in the germline and protected from mutation in tumors, thus introducing a new strategy for future detection of cancer driver elements in the expressed non-coding genome.
    Mots-clés : Computational Biology, DBG, eBio, Genome, Human, Humans, Models, Genetic, Mutation, Neoplasms, PF, RNA, Untranslated, Sequence Analysis, DNA, SSFA.
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