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Accueil > Départements > Biologie des Génomes > Yoshiharu YAMAICHI : Intégrité du génome et de la polarité cellulaire chez la bactérie

Publications de l’équipe


  • I. Altinoglu, C. J. Merrifield, et Y. Yamaichi, « Single molecule super-resolution imaging of bacterial cell pole proteins with high-throughput quantitative analysis pipeline », Scientific Reports, vol. 9, nᵒ 1, p. 6680, avr. 2019.
    Résumé : Bacteria show sophisticated control of their cellular organization, and many bacteria deploy different polar landmark proteins to organize the cell pole. Super-resolution microscopy, such as Photo-Activated Localization Microscopy (PALM), provides the nanoscale localization of molecules and is crucial for better understanding of organization and dynamics in single-molecule. However, analytical tools are not fully available yet, in particular for bacterial cell biology. For example, quantitative and statistical analyses of subcellular localization with multiple cells from multiple fields of view are lacking. Furthermore, brightfield images are not sufficient to get accurate contours of small and low contrast bacterial cells, compared to subpixel presentation of target molecules. Here we describe a novel analytic tool for PALM which integrates precisely drawn cell outlines, of either inner membrane or periplasm, labelled by PALM-compatible fluorescent protein fusions, with molecule data for >10,000 molecules from >100 cells by fitting each cell into an oval arc. In the vibrioid bacterium Vibrio cholerae, the polar anchor HubP constitutes a big polar complex which includes multiple proteins involved in chemotaxis and the flagellum. With this pipeline, HubP is shown to be slightly skewed towards the inner curvature side of the cell, while its interaction partners showed rather loose polar localization.
    Mots-clés : BIOCELL, DBG, EQYY.

  • M. A. Hanson, A. Dostálová, C. Ceroni, M. Poidevin, S. Kondo, et B. Lemaitre, « Synergy and remarkable specificity of antimicrobial peptides in vivo using a systematic knockout approach », eLife, vol. 8, févr. 2019.
    Résumé : Antimicrobial peptides (AMPs) are host-encoded antibiotics that combat invading microorganisms. These short, cationic peptides have been implicated in many biological processes, primarily involving innate immunity. In vitro studies have shown AMPs kill bacteria and fungi at physiological concentrations, but little validation has been done in vivo. We utilized CRISPR gene editing to delete all known immune-inducible AMPs of Drosophila, namely: 4 Attacins, 4 Cecropins, 2 Diptericins, Drosocin, Drosomycin, Metchnikowin and Defensin. Using individual and multiple knockouts, including flies lacking all 14 AMP genes, we characterize the in vivo function of individual and groups of AMPs against diverse bacterial and fungal pathogens. We found that Drosophila AMPs act primarily against Gram-negative bacteria and fungi, contributing either additively or synergistically. We also describe remarkable specificity wherein certain AMPs contribute the bulk of microbicidal activity against specific pathogens, providing functional demonstrations of highly specific AMP-pathogen interactions in an in vivo setting.
    Mots-clés : AMP, D. melanogaster, DBG, Diptericin, Drosocin, EQYY, Imd, immunology, inflammation, PF, systemic immunity, Toll.


  • M. Poidevin, M. Sato, I. Altinoglu, M. Delaplace, C. Sato, et Y. Yamaichi, « Mutation in ESBL Plasmid fromEscherichia coliO104:H4 Leads Autoagglutination and Enhanced Plasmid Dissemination. », Front Microbiol, vol. 9, p. 130, 2018.
    Résumé : Conjugative plasmids are one of the main driving force of wide-spreading of multidrug resistance (MDR) bacteria. They are self-transmittable via conjugation as carrying the required set of genes andcis-acting DNA locus for direct cell-to-cell transfer. IncI incompatibility plasmids are nowadays often associated with extended-spectrum beta-lactamases producing Enterobacteria in clinic and environment. pESBL-EA11 was isolated fromEscherichia coliO104:H4 outbreak strain in Germany in 2011. During the previous study identifying transfer genes of pESBL-EA11, it was shown that transposon insertion at certain DNA region of the plasmid, referred to as Hft, resulted in great enhancement of transfer ability. This suggested that genetic modifications can enhance dissemination of MDR plasmids. Such 'superspreader' mutations have attracted little attention so far despite their high potential to worsen MDR spreading. Present study aimed to gain our understanding on regulatory elements that involved pESBL transfer. While previous studies of IncI plasmids indicated that immediate downstream gene of Hft,traA, is not essential for conjugative transfer, here we showed that overexpression of TraA in host cell elevated transfer rate of pESBL-EA11. Transposon insertion or certain nucleotide substitutions in Hft led strong TraA overexpression which resulted in activation of essential regulator TraB and likely overexpression of conjugative pili. Atmospheric Scanning Electron Microscopy observation suggested that IncI pili are distinct from other types of conjugative pili (such as long filamentous F-type pili) and rather expressed throughout the cell surface. High transfer efficiency in the mutant pESBL-EA11 was involved with hyperpiliation which facilitates cell-to-cell adhesion, including autoagglutination. The capability of plasmids to evolve to highly transmissible mutant is alarming, particularly it might also have adverse effect on host pathogenicity
    Mots-clés : DBG, EQYY.


  • A. Dostálová, S. Rommelaere, M. Poidevin, et B. Lemaitre, « Thioester-containing proteins regulate the Toll pathway and play a role in Drosophila defence against microbial pathogens and parasitoid wasps », BMC biology, vol. 15, nᵒ 1, p. 79, sept. 2017.
    Résumé : BACKGROUND: Members of the thioester-containing protein (TEP) family contribute to host defence in both insects and mammals. However, their role in the immune response of Drosophila is elusive. In this study, we address the role of TEPs in Drosophila immunity by generating a mutant fly line, referred to as TEPq (Δ) , lacking the four immune-inducible TEPs, TEP1, 2, 3 and 4. RESULTS: Survival analyses with TEPq (Δ) flies reveal the importance of these proteins in defence against entomopathogenic fungi, Gram-positive bacteria and parasitoid wasps. Our results confirm that TEPs are required for efficient phagocytosis of bacteria, notably for the two Gram-positive species tested, Staphylococcus aureus and Enterococcus faecalis. Furthermore, we show that TEPq (Δ) flies have reduced Toll pathway activation upon microbial infection, resulting in lower expression of antimicrobial peptide genes. Epistatic analyses suggest that TEPs function upstream or independently of the serine protease ModSP at an initial stage of Toll pathway activation. CONCLUSIONS: Collectively, our study brings new insights into the role of TEPs in insect immunity. It reveals that TEPs participate in both humoral and cellular arms of immune response in Drosophila. In particular, it shows the importance of TEPs in defence against Gram-positive bacteria and entomopathogenic fungi, notably by promoting Toll pathway activation.
    Mots-clés : Beauveria, Complement, DBG, Drosophila, Entomopathogenic fungus, EQYY, innate immunity, Insect, Parasitoid wasp, Phagocytosis.

  • M. Poidevin, E. Galli, Y. Yamaichi, et F. - X. Barre, « WGADseq: Whole Genome Affinity Determination of Protein-DNA Binding Sites », in The Bacterial Nucleoid, vol. 1624, O. Espéli, Éd. New York, NY: Springer New York, 2017, p. 53-60.

  • Y. Yamaichi et T. Dörr, « Transposon Insertion Site Sequencing for Synthetic Lethal Screening », in The Bacterial Nucleoid, vol. 1624, O. Espéli, Éd. New York, NY: Springer New York, 2017, p. 39-49.

  • P. Houtz, A. Bonfini, X. Liu, J. Revah, A. Guillou, M. Poidevin, K. Hens, H. - Y. Huang, B. Deplancke, Y. - C. Tsai, et N. Buchon, « Hippo, TGF-β, and Src-MAPK pathways regulate transcription of the upd3 cytokine in Drosophila enterocytes upon bacterial infection. », PLoS Genet, vol. 13, p. e1007091, nov. 2017.
    Résumé : Cytokine signaling is responsible for coordinating conserved epithelial regeneration and immune responses in the digestive tract. In the Drosophila midgut, Upd3 is a major cytokine, which is induced in enterocytes (EC) and enteroblasts (EB) upon oral infection, and initiates intestinal stem cell (ISC) dependent tissue repair. To date, the genetic network directing upd3 transcription remains largely uncharacterized. Here, we have identified the key infection-responsive enhancers of the upd3 gene and show that distinct enhancers respond to various stresses. Furthermore, through functional genetic screening, bioinformatic analyses and yeast one-hybrid screening, we determined that the transcription factors Scalloped (Sd), Mothers against dpp (Mad), and D-Fos are principal regulators of upd3 expression. Our study demonstrates that upd3 transcription in the gut is regulated by the activation of multiple pathways, including the Hippo, TGF-β/Dpp, and Src, as well as p38-dependent MAPK pathways. Thus, these essential pathways, which are known to control ISC proliferation cell-autonomously, are also activated in ECs to promote tissue turnover the regulation of upd3 transcription
    Mots-clés : Animals, Bacterial Infections, Cell Proliferation, DBG, Drosophila, Drosophila Proteins, Enterocytes, EQYY, Female, Gene Expression Regulation, Gene Regulatory Networks, Intestines, Intracellular Signaling Peptides and Proteins, Male, MAP Kinase Signaling System, Pectobacterium carotovorum, Protein-Serine-Threonine Kinases, Pseudomonas, Signal Transduction, Stem Cells, Transcription Factors, Transforming Growth Factor beta.



  • Y. Yamaichi, M. C. Chao, J. Sasabe, L. Clark, B. M. Davis, N. Yamamoto, H. Mori, K. Kurokawa, et M. K. Waldor, « High-resolution genetic analysis of the requirements for horizontal transmission of the ESBL plasmid from Escherichia coli O104:H4 », Nucleic Acids Research, vol. 43, nᵒ 1, p. 348-360, janv. 2015.
    Résumé : Horizontal dissemination of the genes encoding extended spectrum beta-lactamases (ESBLs) via conjugative plasmids is facilitating the increasingly widespread resistance of pathogens to beta-lactam antibiotics. However, there is relatively little known about the regulatory factors and mechanisms that govern the spread of these plasmids. Here, we carried out a high-throughput, transposon insertion site sequencing analysis (TnSeq) to identify genes that enable the maintenance and transmission of pESBL, an R64 (IncI1)-related resistance plasmid that was isolated from Escherichia coli O104:H4 linked to a recent large outbreak of gastroenteritis. With a few exceptions, the majority of the genes identified as required for maintenance and transmission of pESBL matched those of their previously defined R64 counterparts. However, our analyses of the high-density transposon insertion library in pESBL also revealed two very short and linked regions that constitute a previously unrecognized regulatory system controlling spread of IncI1 plasmids. In addition, we investigated the function of the pESBL-encoded M.EcoGIX methyltransferase, which is also encoded by many other IncI1 and IncF plasmids. This enzyme proved to protect pESBL from restriction in new hosts, suggesting it aids in expanding the plasmid's host range. Collectively, our work illustrates the power of the TnSeq approach to enable rapid and comprehensive analyses of plasmid genes and sequences that facilitate the dissemination of determinants of antibiotic resistance.
    Mots-clés : DBG, DNA Transposable Elements, EQYY, Escherichia coli, Gene Library, Gene Transfer, Horizontal, Genes, Bacterial, High-Throughput Nucleotide Sequencing, Plasmids, Sequence Analysis, DNA, yoyo.
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