DOCSLIB.ORG

Mechanism for IL-15–Driven B Cell Chronic Lymphocytic Leukemia Cycling: Roles for AKT and STAT5 in Modulating Cyclin D2 and DNA Damage Response Proteins

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mechanism for IL-15–Driven B Cell Chronic Lymphocytic Leukemia Cycling: Roles for AKT and STAT5 in Modulating Cyclin D2 and DNA Damage Response Proteins Mechanism for IL-15−Driven B Cell Chronic Lymphocytic Leukemia Cycling: Roles for AKT and STAT5 in Modulating Cyclin D2 and DNA Damage Response Proteins This information is current as of September 23, 2021. Rashmi Gupta, Wentian Li, Xiao J. Yan, Jacqueline Barrientos, Jonathan E. Kolitz, Steven L. Allen, Kanti Rai, Nicholas Chiorazzi and Patricia K. A. Mongini J Immunol 2019; 202:2924-2944; Prepublished online 15 April 2019; Downloaded from doi: 10.4049/jimmunol.1801142 http://www.jimmunol.org/content/202/10/2924 http://www.jimmunol.org/ Supplementary http://www.jimmunol.org/content/suppl/2019/04/14/jimmunol.180114 Material 2.DCSupplemental References This article cites 125 articles, 55 of which you can access for free at: http://www.jimmunol.org/content/202/10/2924.full#ref-list-1 Why The JI? Submit online. by guest on September 23, 2021 • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2019 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Mechanism for IL-15–Driven B Cell Chronic Lymphocytic Leukemia Cycling: Roles for AKT and STAT5 in Modulating Cyclin D2 and DNA Damage Response Proteins Rashmi Gupta,* Wentian Li,* Xiao J. Yan,* Jacqueline Barrientos,† Jonathan E. Kolitz,*,†,‡ Steven L. Allen,*,†,‡ Kanti Rai,*,‡,x Nicholas Chiorazzi,*,‡,x and Patricia K. A. Mongini*,x Clonal expansion of B cell chronic lymphocytic leukemia (B-CLL) occurs within lymphoid tissue pseudofollicles. IL-15, a stromal cell–associated cytokine found within spleens and lymph nodes of B-CLL patients, significantly boosts in vitro cycling of blood- derived B-CLL cells following CpG DNA priming. Both IL-15 and CpG DNA are elevated in microbe-draining lymphatic tissues, and unraveling the basis for IL-15–driven B-CLL growth could illuminate new therapeutic targets. Using CpG DNA-primed human B-CLL clones and approaches involving both immunofluorescent staining and pharmacologic inhibitors, we show that Downloaded from both PI3K/AKT and JAK/STAT5 pathways are activated and functionally important for IL-15→CD122/ɣc signaling in ODN- primed cells expressing activated pSTAT3. Furthermore, STAT5 activity must be sustained for continued cycling of CFSE-labeled B-CLL cells. Quantitative RT-PCR experiments with inhibitors of PI3K and STAT5 show that both contribute to IL-15–driven upregulation of mRNA for cyclin D2 and suppression of mRNA for DNA damage response mediators ATM, 53BP1, and MDC1. Furthermore, protein levels of these DNA damage response molecules are reduced by IL-15, as indicated by Western blotting and immunofluorescent staining. Bioinformatics analysis of ENCODE chromatin immunoprecipitation sequencing data from cell lines http://www.jimmunol.org/ provides insight into possible mechanisms for STAT5-mediated repression. Finally, pharmacologic inhibitors of JAKs and STAT5 significantly curtailed B-CLL cycling when added either early or late in a growth response. We discuss how the IL-15–induced changes in gene expression lead to rapid cycling and possibly enhanced mutagenesis. STAT5 inhibitors might be an effective modality for blocking B-CLL growth in patients. The Journal of Immunology, 2019, 202: 2924–2944. cell chronic lymphocytic leukemia (B-CLL), a disease of This led to the early conjecture that B-CLL results from a gradual the elderly with a median age at diagnosis of 69 y, de- accumulation of clonal cells defective in apoptosis (2). More re- + B velops from a nonmalignant expansion of CD5 B cells cently, heightened research on B-CLL led to the recognition that a by guest on September 23, 2021 that is referred to as monoclonal B cell lymphocytosis. Approxi- sizeable component of each clone undergoes active cycling (3, 4). mately 1–2% of people with this precursor condition require treat- Moreover, the extent of in vivo cycling is linked to patient out- ment for CLL each subsequent year (1). As the elderly population come (5, 6), with the CLL clones bearing IGHV-unmutated Ag increases, B-CLL incidence will undoubtedly rise. The personal and receptors (U-CLL) typically exhibiting faster birth rates than economic costs of living with and treating this malignancy are in- CLL clones bearing IGHV-mutated Ag receptors (M-CLL) (5). centives for continued study into its etiology and unique mecha- Importantly, cycling occurs within lymphoid tissues with a stromal nisms for growth. environment conducive to B-CLL survival and growth (5, 7). The Unlike B cell acute lymphocytic leukemia, which manifests as fact that not all tissue-localized B-CLL cells are undergoing cycling rapidly cycling, bloodborne blasts, B-CLL generally reveals itself suggests that certain stimuli must be encountered for the growth as a slow rise in relatively quiescent CD5+ B cells within blood. response. *The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY 11030; specimens used for this study and edited the paper. P.K.A.M. conceived the exper- †Department of Medicine, Northwell Health, Manhasset, NY 11030; ‡Department of iments, performed certain experiments, analyzed data, and wrote the paper. Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549; and x Address correspondence and reprint requests to Dr. Patricia K. A. Mongini at the Department of Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, current address: Pathogen and Microbiome Institute, Room 156, P.O. Box 4073, Hempstead, NY 11549 Northern Arizona University, Flagstaff, AZ 86011. E-mail address: patricia. ORCIDs: 0000-0002-3717-5803 (X.J.Y.); 0000-0003-2700-4784 (J.E.K.); 0000- [email protected] 0002-3482-3182 (S.L.A.); 0000-0002-5804-2823 (K.R.); 0000-0003-1023- The online version of this article contains supplemental material. 6650 (N.C.); 0000-0002-4966-7741 (P.K.A.M.). Abbreviations used in this article: ATM, ataxia telangiectasia mutated; B-CLL, Received for publication August 17, 2018. Accepted for publication March 13, 2019. B cell chronic lymphocytic leukemia; 53BP1, p53-binding protein 1; ChIP-seq, This work was supported by research funds from Dr. Betty Diamond (The Center for chromatin immunoprecipitation sequencing; chr, chromosome; CLL, chronic lympho- Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institute, cytic leukemia; Ct, threshold cycle; CTCF, CCCTC-binding factor; DDR, DNA Manhasset, NY), the National Cancer Institute, National Institutes of Health (NIH) damage response; F, forward; GAS, g-activated sequence; M-CLL, CLL clone (Grant CA08155C4 to N.C.), and the National Institute of Arthritis and Musculo- bearing IGHV-mutated Ag receptors; MDC1, mediator of DNA damage checkpoint skeletal and Skin Diseases, NIH (Grant AR061653 to P.K.A.M.). protein 1; MFI, median fluorescence intensity; ODN, oligodeoxynucleotide; PB, peripheral blood; Q-PCR, quantitative PCR; qRT-PCR, quantitative RT-PCR; R, R.G. performed most in vitro experiments, analyzed data, and edited the paper. W.L. reverse; TBP, TATA box–binding TF; TF, transcription factor; TP53BP1,tumor performed the bioinformatics analysis of ATM, MDC1,andTP53BP1 promoters. protein 53BP1; TSS, transcription start site; U-CLL, CLL clone bearing IGHV- X.J.Y. led the IGHV gene characterization of all B cell chronic lymphocytic leukemia unmutated Ag receptors. (B-CLL) clones. J.B. and J.E.K. provided B-CLL blood specimens and clinical information. S.L.A. and K.R. provided B-CLL blood specimens and clinical infor- Ó mation and edited the paper. N.C. led the acquisition and characterization of B-CLL Copyright 2019 by The American Association of Immunologists, Inc. 0022-1767/19/$37.50 www.jimmunol.org/cgi/doi/10.4049/jimmunol.1801142 The Journal of Immunology 2925 CpG oligodeoxynucleotides (ODN) and IL-15 are two candidate cells did show that IL-15 enhanced the phosphorylation of Shc, stimuli that manifest notable synergy in driving the in vitro cycling ERK, JAK1, JAK3, and STAT5 but not STAT3 or STAT1 (29). of many, albeit not all, blood-derived B-CLL clones (8). Indeed, More recently, it was reported that IL-15 independently activated clonal potential for in vitro ODN + IL-15–driven growth was p38 and STAT5 in naive mouse peritoneal B-1a cells but not statistically linked to clinical outcome in patients with U-CLL (8). conventional B cells (31). Nevertheless, even M-CLL clones, which typically succumb to In this study, ODN-primed B-CLL cells with heightened IL-15R apoptosis following culture with ODN alone (9), show sustained expression are used to examine both early and late events following viability and often extended cycling (six to eight divisions) upon IL-15 signaling. We assess the involvement of PI3K/AKT and culture with both ODN and IL-15 (8). The recent documentation STAT5 pathways in IL-15–driven growth. Furthermore, we in- of IL-15–producing cells within B-CLL–infiltrated spleens (8) vestigate whether these receptor-proximal pathways influence and lymph nodes (10) and in proximity to pseudofollicles (8) mRNA levels for cyclin D2 (important for the G1 to S phase strengthens the possibility that IL-15 fosters B-CLL growth in transition) as well as mRNA/protein for several DNA damage patients. Similar to leukemic incidence, the frequency of IL-15+ response (DDR) molecules important in cell cycle checkpoint stromal cells rises with age (11, 12). Furthermore, CpG DNA is control and DNA repair: ataxia telangiectasia mutated (ATM), available in lymphoid tissues, as microbes drain into these sites, p53-binding protein 1 (53BP1), and mediator of DNA damage and stressed or apoptotic cells are locally produced (8).
Load more

Recommended publications
  • Molecular Mechanisms of Nucleosome Positioning and DNA Methylation in Chromatin
    Molecular mechanisms of nucleosome positioning and DNA methylation in chromatin Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften (Dr. rer. nat.) der Naturwissenschaftlichen Fakultät III - Biologie und vorklinische Medizin der Universität Regensburg durchgeführt am Lehrstuhl für Biochemie III der Universität Regensburg vorgelegt von: ANNA SCHRADER SENSERSTR. 8 81371 MÜNCHEN Abgabedatum: 29. Juli 2009 Die vorliegende Arbeit wurde unter der Betreuung von Prof. Dr. Gernot Längst in der Zeit von Februar 2006 bis Juli 2009 am Institut für Biochemie III der Universität Regensburg erstellt. Prüfungskomitee: Vorsitzender: Prof. Dr. Reinhard Wirth 1. Gutachter: Prof. Dr. Gernot Längst 2. Gutachter: Prof. Dr. Alexander Brehm 3. Gutachter (Prüfer): Prof. Dr. Ralf Wagner Ersatzprüfer: Prof. Dr. Michael Thomm Table of Contents Abbreviations........................................................................................... 1 A. Zusammenfassung ............................................................................... 5 B. Introduction ........................................................................................ 7 I. The Chromatin structure ............................................................................................ 7 1. In General ......................................................................................................................... 7 1.1. The nucleosome - basic packaging unit of chromatin.................................................. 7 1.2. Chromatin higher order structures
    [Show full text]
  • Transcription Factors Recognize DNA Shape Without Nucleotide Recognition
    bioRxiv preprint doi: https://doi.org/10.1101/143677; this version posted May 29, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Transcription+factors+recognize+DNA+shape+without+nucleotide+recognition++ Md.$Abul$Hassan$Samee1,$Benoit$G.$Bruneau1,2,$Katherine$S.$Pollard$1,3$ 1:$Gladstone$Institutes,$1650$Owens$St.,$San$Francisco,$CA$94158$ 2:$$Department$of$Pediatrics$and$Cardiovascular$Research$Institute,$University$of$California,$ San$Francisco,$CA$94158$ 3:$Division$of$Bioinformatics,$Institute$for$Human$Genetics,$and$Institute$for$Computational$ Health$Sciences,$University$of$California,$San$Francisco,$CA$94158$ $ + bioRxiv preprint doi: https://doi.org/10.1101/143677; this version posted May 29, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract+ We$hypothesized$that$transcription$factors$(TFs)$recognize$DNA$shape$without$nucleotide$ sequence$recognition.$Motivating$an$independent$role$for$shape,$many$TF$binding$sites$lack$ a$sequenceZmotif,$DNA$shape$adds$specificity$to$sequenceZmotifs,$and$different$sequences$ can$ encode$ similar$ shapes.$ We$ therefore$ asked$ if$ binding$ sites$ of$ a$ TF$ are$ enriched$ for$ specific$patterns$of$DNA$shapeZfeatures,$e.g.,$helical$twist.$We$developed$ShapeMF,$which$ discovers$ these$ shapeZmotifs$ de%novo%without$ taking$ sequence$ information$ into$ account.$
    [Show full text]
  • Forscher Ernst
    10/2016 be INSPIRED drive DISCOVERY stay GENUINE Molekularbiologie ist keine Hexerei Gleicht Ihr Labor manchmal einer Hexenküche? Oder scheinen bestimmte Experimente nur bei Qualität & Performance sind kein Zufall: Vollmond zu gelingen? NEB bietet Ihnen besonders saubere Enyzme ohne unerwünschte Fremdaktivitäten! Beispiel: T4 DNA Ligase Nutzen Sie lieber die besonders zuverlässigen www.laborjournal.de Reagenzien und Kits von New England Biolabs! NEB NEB HERSTELLER M Lot 101 Lot 102 A B C D Denn Qualität und Zuverlässigkeit sind bei uns kein Zufall, sondern das Ergebnis aus über 40 Jahren kontinuierlicher Forschung & Entwicklung von exzellenten Werkzeugen für die Molekularbiologie. Egal ob Sie DNA Cloning, Gene Editing, PCR, Next-Gen-Seq, RNA-Biologie, Protein-Analyse oder andere moderne Methoden betreiben – bei NEB finden Sie die große Auswahl an hochqualitativen und zuverlässigen Produkten für Ihre Experimente. Und dass Sie dabei stets auf technische und logistische Äquivalente Proteinmengen von T4 DNA Ligase verschiedener Hersteller wurden im SDS-PAGE (angefärbt mit SilverXpress®) analysiert. Unterstützung noch am gleichen Tag bauen dürfen, Spur M ist ein Protein Standard. grenzt dann doch an Hexerei! SILVERXPRESS® is a registered trademark of Invitrogen (LIFE TECHNOLOGIES CORPORATION). Besuchen Sie www.neb-online.de/hexerei und erfahren Sie mehr! MolBio-ist-keine-Hexerei.indd 1 14.09.16 10:03 LJ_1016_OC_OC.indd 2 04.10.16 18:51 no more service4 hi.pdf 1 9/8/16 8:43 AM Liquid Handling von ROTH Perfekt gelaufen! C M Y CM MY CY CMY K www.laborjournal.de • Höchste Präzision und Qualität • Für jede Applikation das optimale Gerät • Persönliche Expertenberatung • Extrem kurze Lieferzeiten • Von unseren Pipettenspitzen erhalten Sie gerne kostenlose Muster! • Faire Preise bei höchster Qualität Wir sind die Experten für Laborbedarf, Chemikalien und Life Science.
    [Show full text]
  • Ncrna Synthesis Ny RNA Polymerase
    “The functional characterization of mammalian non-coding Y RNAs” Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften (Dr. rer. nat.) der Naturwissenschaftlichen Fakultät I – Biowissenschaften – der Martin-Luther-Universität Halle-Wittenberg, vorgelegt von Herrn Marcel Köhn geb. am 04.01.1983 in Wolgast Öffentlich verteidigt am 30.10.2015 Gutachter: Prof. Dr. Stefan Hüttelmaier (Halle, Deutschland) Prof. Dr. Elmar Wahle (Halle, Deutschland) Prof. Dr. Daniel Zenklusen (Montreal, Kanada) Contents Abstract 1. Non-coding RNAs (ncRNAs) 2. NcRNA synthesis by RNA polymerase III 2.1. NcRNAs transcribed from type I and II POLIII-genes 2.2. NcRNAs transcribed from type III POLIII-genes 3. The non-coding Y RNAs 3.1. Evolution of Y RNAs 3.2. Y RNA genes and expression patterns 3.3. Processing of Y RNAs 3.4. Subcellular localization of Y RNAs 3.5. Y RNA-associated proteins 3.6. The Y RNA core proteins – La and Ro60 3.7. A paradigm of accessory Y RNA-binding proteins – IGF2BPs 3.8. The characterization of Y RNPs 3.9. The association of Y3/Y3** with mRNA 3’-end processing factors 4. Y RNA functions 4.1. The role of Y RNAs in DNA replication and cell growth 4.2. Y RNAs as modulators of Ro60 function and cellular stress 5. The role of Y3/Y3** in the 3’-end processing of histone mRNAs 5.1. The depletion of Y RNAs and their impact on pre-mRNA processing 5.2. The evolutionary conservation of Y3’s role in histone mRNA processing 5.3. Y3** ncRNA is essential for histone mRNA processing 5.4.
    [Show full text]
  • Ptrr (Ynej) Is a Novel E
    bioRxiv preprint doi: https://doi.org/10.1101/2020.04.27.065417; this version posted April 29, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. PtrR (YneJ) is a novel E. coli transcription factor regulating the putrescine stress response and glutamate utilization. Irina A. Rodionova 1, 2*, Ye Gao1,2, Anand Sastry1, Jonathan Monk1, Nicholas Wong2, Richard Szubin1, Hyungyu Lim1, Zhongge Zhang2, Milton H. Saier, Jr. 2* and Bernhard Palsson1,3,4* 1Department of Bioengineering, Division of Engineering, University of California at San Diego, La Jolla, CA 92093-0116, USA. 2Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA. 3Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA 4Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark *To whom correspondence should be addressed: Prof. Bernhard Palsson, Prof. Milton Saier and Dr. I. Rodionova, 1Department of Bioengineering, Division of Engineering, and 2Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 – 0116; E-mail: [email protected], [email protected], [email protected]. Running title: YneJ (PtrR) is regulator in putrescine stress response ABSTRACT Although polyamines, such as putrescine (Ptr), induce envelope stress for bacteria, they are important as nitrogen and carbon sources. Ptr utilization in Escherichia coli involves protein glutamylation, and glutamate stands at a crossroads between catabolism and anabolism. This communication reports that the transcription factor YneJ, here renamed PtrR, is involved in the regulation of a small regulatory RNA gene, fnrS, and an operon, yneIHGF, encoding succinate- semialdehyde dehydrogenase, Sad (YneI), glutaminase, GlsB (YneH), and several other genes.
    [Show full text]
  • Genome-Wide CRISPR-Dcas9 Screens in E. Coli
    Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors Francois Rousset, Lun Cui, Elise Siouve, Christophe Bécavin, Florence Depardieu, David Bikard To cite this version: Francois Rousset, Lun Cui, Elise Siouve, Christophe Bécavin, Florence Depardieu, et al.. Genome- wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors. PLoS Genetics, Public Library of Science, 2018, 14 (11), pp.e1007749. 10.1371/journal.pgen.1007749. pasteur- 01975438 HAL Id: pasteur-01975438 https://hal-pasteur.archives-ouvertes.fr/pasteur-01975438 Submitted on 9 Jan 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License RESEARCH ARTICLE Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors 1,2☯ 1☯ 1¤ 3 FrancËois RoussetID , Lun CuiID , Elise Siouve , Christophe Becavin , 1 1 Florence DepardieuID , David BikardID * 1 Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France, 2 Sorbonne UniversiteÂ, Collège Doctoral, Paris, France, 3 Hub Bioinformatique et Biostatistique, Institut Pasteur - C3BI, USR 3756 IP CNRS, Paris, France a1111111111 a1111111111 ☯ These authors contributed equally to this work.
    [Show full text]
  • Probing the Role of Pparα in the Small Intestine
    Probing the role of PPARα in the small intestine A functional nutrigenomics approach Meike Bünger Promotor Prof. dr. Michael Müller Hoogleraar Nutrition, Metabolism and Genomics Humane Voeding, Wageningen Universiteit Co-promotor Dr. Guido J.E.J. Hooiveld Universitair docent Humane Voeding, Wageningen Universiteit Promotiecommissie Prof. dr. Jaap Keijer Wageningen University Prof. dr. Ulrich Beuers University of Amsterdam Prof. dr. Hannelore Daniel Technical University of Munich Prof. dr. Ivonne Rietjens Wageningen University Dit onderzoek is uitgevoerd binnen de onderzoeksschool VLAG. Probing the role of PPARα in the small intestine A functional nutrigenomics approach Meike Bünger Proefschrift ter verkrijging van de graad van doctor op gezag van de rector magnificus van Wageningen Universiteit, Prof. dr. M.J. Kropff, in het openbaar te verdedigen op vrijdag 12 september 2008 des namiddags te vier uur in de Aula. Meike Bünger. Probing the role of PPARα in the small intestine: A functional nutrigenomics approach. PhD Thesis. Wageningen University and Research Centre, The Netherlands, 2008. With summaries in English and Dutch. ISBN 978-90-8504973-9 Abstract Background The peroxisome proliferator-activated receptor alpha (PPARα) is a ligand- activated transcription factor known for its control of metabolism in response to diet. Although functionally best characterized in liver, PPARα is also abundantly expressed in small intestine, the organ by which nutrients, including lipids, enter the body. Dietary fatty acids, formed during the digestion of triacylglycerols, are able to profoundly influence gene expression by activating PPARα. Since the average Western diet contains a high amount of PPARα ligands, knowledge on the regulatory and physiological role of PPARα in the small intestine is of particular interest.
    [Show full text]
  • Epigenetic Control of Ribosome Biogenesis Homeostasis Jerôme Deraze
    Epigenetic control of ribosome biogenesis homeostasis Jerôme Deraze To cite this version: Jerôme Deraze. Epigenetic control of ribosome biogenesis homeostasis. Cellular Biology. Université Pierre et Marie Curie - Paris VI, 2017. English. NNT : 2017PA066342. tel-01878354 HAL Id: tel-01878354 https://tel.archives-ouvertes.fr/tel-01878354 Submitted on 21 Sep 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Université Pierre et Marie Curie Ecole doctorale : Complexité du Vivant IBPS – UMR7622 Laboratoire de Biologie du Développement UPMC CNRS Epigenetic control of developmental homeostasis and plasticity Epigenetic Control of Ribosome Biogenesis Homeostasis Par Jérôme Deraze Thèse de doctorat de Biologie Moléculaire et Cellulaire Dirigée par Frédérique Peronnet et Sébastien Bloyer Présentée et soutenue publiquement le 19 Septembre 2017 Devant un jury composé de : Pr Anne-Marie MARTINEZ Professeur Rapporteur Dr Jacques MONTAGNE Directeur de Recherche Rapporteur Dr Olivier JEAN-JEAN Directeur de Recherche Examinateur Dr Michel COHEN-TANNOUDJI Directeur de Recherche Examinateur Dr Françoise JAMEN Maître de Conférences Examinateur Dr Nicolas NEGRE Maître de Conférences Examinateur Dr Frédérique PERONNET Directrice de Recherche Directrice de thèse Pr Sébastien BLOYER Professeur Co-directeur de thèse Table of contents Table of contents ....................................................................................................................................
    [Show full text]
  • Membrane Transport Metabolons
    Biochimica et Biophysica Acta 1818 (2012) 2687–2706 Contents lists available at SciVerse ScienceDirect Biochimica et Biophysica Acta journal homepage: www.elsevier.com/locate/bbamem Review Membrane transport metabolons Trevor F. Moraes, Reinhart A.F. Reithmeier ⁎ Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8 article info abstract Article history: In this review evidence from a wide variety of biological systems is presented for the genetic, functional, and Received 15 November 2011 likely physical association of membrane transporters and the enzymes that metabolize the transported Received in revised form 28 May 2012 substrates. This evidence supports the hypothesis that the dynamic association of transporters and enzymes Accepted 5 June 2012 creates functional membrane transport metabolons that channel substrates typically obtained from the Available online 13 June 2012 extracellular compartment directly into their cellular metabolism. The immediate modification of substrates on the inner surface of the membrane prevents back-flux through facilitated transporters, increasing the Keywords: fi Channeling ef ciency of transport. In some cases products of the enzymes are themselves substrates for the transporters Enzyme that efflux the products in an exchange or antiport mechanism. Regulation of the binding of enzymes to Membrane protein transporters and their mutual activities may play a role in modulating flux through transporters and entry Metabolic pathways of substrates into metabolic pathways. Examples showing the physical association of transporters and Metabolon enzymes are provided, but available structural data is sparse. Genetic and functional linkages between mem- Operons, protein interactions brane transporters and enzymes were revealed by an analysis of Escherichia coli operons encoding polycistronic Transporter mRNAs and provide a list of predicted interactions ripe for further structural studies.
    [Show full text]
  • Genome-Wide CRISPR-Dcas9 Screens in E. Coli Identify Essential 2 Genes and Phage Host Factors
    bioRxiv preprint doi: https://doi.org/10.1101/308916; this version posted April 26, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Genome-wide CRISPR-dCas9 screens in E. coli identify essential 2 genes and phage host factors 3 François Rousset1,2,†, Lun Cui1,†, Elise Siouve1, Florence Depardieu1 & David Bikard1,* 4 1 Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, 75015, France 5 2 Sorbonne Université, Collège Doctoral, F-75005 Paris, France 6 * To whom correspondence should be addressed. Tel: +33140613924; Email: 7 [email protected] 8 † François Rousset and Lun Cui contributed equally to this work. 9 10 11 Running title: Genome-wide CRISPR-dCas9 screens in E. coli 12 Keywords: CRISPR-dCas9, Escherichia coli, genome-wide screen, phage host factors, CRISPRi 1 bioRxiv preprint doi: https://doi.org/10.1101/308916; this version posted April 26, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 13 Abstract 14 High-throughput genetic screens are powerful methods to identify genes linked to a given 15 phenotype. The catalytic null mutant of the Cas9 RNA-guided nuclease (dCas9) can be conveniently 16 used to silence genes of interest in a method also known as CRISPRi.
    [Show full text]
  • The X-Ray Crystal Structure of Escherichia Coli Succinic Semialdehyde Dehydrogenase; Structural Insights Into NADP+/Enzyme Interactions
    The X-Ray Crystal Structure of Escherichia coli Succinic Semialdehyde Dehydrogenase; Structural Insights into NADP+/Enzyme Interactions Christopher G. Langendorf1, Trevor L. G. Key1,2, Gustavo Fenalti1,3, Wan-Ting Kan1,4, Ashley M. Buckle1, Tom Caradoc-Davies5, Kellie L. Tuck2, Ruby H. P. Law1,4*, James C. Whisstock1,4* 1 Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria, Australia, 2 School of Chemistry, Monash University, Clayton Campus, Melbourne, Victoria, Australia, 3 Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America, 4 ARC Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Melbourne, Victoria, Australia, 5 Australian Synchrotron, Clayton, Victoria, Australia Abstract Background: In mammals succinic semialdehyde dehydrogenase (SSADH) plays an essential role in the metabolism of the inhibitory neurotransmitter c-aminobutyric acid (GABA) to succinic acid (SA). Deficiency of SSADH in humans results in elevated levels of GABA and c-Hydroxybutyric acid (GHB), which leads to psychomotor retardation, muscular hypotonia, non-progressive ataxia and seizures. In Escherichia coli, two genetically distinct forms of SSADHs had been described that are essential for preventing accumulation of toxic levels of succinic semialdehyde (SSA) in cells. Methodology/Principal Findings: Here we structurally characterise SSADH encoded by the E coli gabD gene by X-ray crystallographic studies and compare these data with the structure of human SSADH. In the E. coli SSADH structure, electron density for the complete NADP+ cofactor in the binding sites is clearly evident; these data in particular revealing how the nicotinamide ring of the cofactor is positioned in each active site.
    [Show full text]
  • Ygae Regulates out Membrane Proteins in Salmonella Enterica Serovar Typhi Under Hyperosmotic Stress
    Hindawi Publishing Corporation e Scientific World Journal Volume 2014, Article ID 374276, 9 pages http://dx.doi.org/10.1155/2014/374276 Research Article YgaE Regulates Out Membrane Proteins in Salmonella enterica Serovar Typhi under Hyperosmotic Stress Min Wang,1 Ping Feng,1 Xun Chen,2 Haifang Zhang,3 Bin Ni,3 Xiaofang Xie,1 and Hong Du1 1 Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China 2 Clinical Laboratory Center, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China 3 Department of Biochemistry and Molecular Biology, School of Medical Technology, Jiangsu University, Zhenjiang 212013, China Correspondence should be addressed to Hong Du; hong [email protected] Received 31 August 2013; Accepted 30 October 2013; Published 23 January 2014 Academic Editors: R. Tofalo and J. Yoon Copyright © 2014 Min Wang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Salmonella enterica serovar Typhi (S. Typhi) is a human-specific pathogen that causes typhoid fever. In this study, we constructed ΔygaE mutant and a microarray was performed to investigate the role of ygaE in regulation of gene expression changes in response to hyperosmotic stress in S. Typhi. qRT-PCR was performed to validate the microarray results. Our data indicated that ygaE was the repressor of gab operon in S. Typhi as in Escherichia coli (E. coli), though the sequence of ygaE is totally different from gabC (formerly ygaE)inE. coli. OmpF, OmpC, and OmpA are the most abundant out membrane proteins in S.Typhi.Herewereport that YgaE is a repressor of both OmpF and OmpC at the early stage of hyperosmotic stress.
    [Show full text]