DOCSLIB.ORG

Funktionelle Bedeutung Nichtkodierender Rnas in Der Urothelialen Differenzierung

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Funktionelle Bedeutung Nichtkodierender Rnas in Der Urothelialen Differenzierung Funktionelle Bedeutung nichtkodierender RNAs in der urothelialen Differenzierung Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Heinrich-Heine-Universität Düsseldorf vorgelegt von Judith Dehn, geb. Heubach aus Sangerhausen Düsseldorf, August 2015 aus dem Forschungslabor der Urologischen Klinik der Heinrich-Heine-Universität Düsseldorf Gedruckt mit der Genehmigung der Mathematisch-Naturwissenschaftlichen Fakultät der Heinrich-Heine-Universität Düsseldorf Referent: Prof. Dr. Wolfgang A. Schulz, Forschungslabor der Urologischen Klinik, Heinrich-Heine-Universität Korreferent: Prof. Dr. Rüdiger Simon, Institut für Entwicklungsgenetik, Heinrich- Heine-Universität Düsseldorf Tag der mündlichen Prüfung: 23.10.2015 Publikationen Teile der Arbeit wurden veröffentlich unter dem Titel „The long noncoding RNA HOTAIR has tissue and cell type-dependent effects on HOX gene expression and phenotype of urothelial cancer cells.“; J. Heubach, J. Monsior, R. Deenen, G. Niegisch, T. Szarvas, C. Niedworok, W.A. Schulz, M.J. Hoffmann; Mol Cancer, 2015 Mai 21; 14:108. Inhalt =XVDPPHQIDVVXQJ 6XPPDU\ (LQOHLWXQJ 'DV8URWKHONDU]LQRP 'DV+2;*HQ&OXVWHU /DQJHQLFKWNRGLHUHQGH51$V *HQHPLW,PSULQWLQJ )UDJHVWHOOXQJ 0DWHULDOXQG0HWKRGHQ 0DWHULDOLHQ 8&*HZHEH =HOOOLQLHQ %DNWHULHQVWlPPH 3ODVPLGH (Q]\PH $QWLN|USHU .LWVXQG$VVD\V 6XEVWDQ]HQ /|VXQJHQXQG3XIIHU 2OLJRQXNOHRWLGH 9HUEUDXFKVPDWHULDOLHQ *HUlWH 0HWKRGHQ 3UlSDUDWLRQYRQ3ODVPLGHQ .XOWLYLHUXQJYRQKXPDQHQ=HOOHQ 0777HVW , /LPLWHG'LOXWLRQ$VVD\ 6RIW$JDU&RORQ\)RUPDWLRQ$VVD\ 6FUDWFK$VVD\ %R\GHQ&KDPEHU$VVD\ '1$7UDQVIHNWLRQ VL51$7UDQVIHNWLRQ /1$7UDQVIHNWLRQ 51$3UlSDUDWLRQ )UDNWLRQLHUWH51$3UlSDUDWLRQ 5HYHUVH7UDQVNULSWDVH3&5 4XDQWLWDWLYH5HDO7LPH3&5 T573&5 P51$0LFURDUUD\ 9HUJOHLFKGHU0LFURDUUD\'DWHQPLWSXEOL]LHUWHQ'DWHQVlW]HQ 3URWHLQ3UlSDUDWLRQ 3URWHLQNRQ]HQWUDWLRQVEHVWLPPXQJ :HVWHUQ%ORW$QDO\VHQ ,PPXQIOXRUHV]HQ] &KURPDWLQ,PPXQRSUl]LSLWDWLRQ &K,3 '1$3UlSDUDWLRQ %LVXOILW8PZDQGOXQJYRQ'1$ 3\URVHTXHQ]LHUXQJ '1$0HWK\OLHUXQJV$UUD\ ,QVLOLFR$QDO\VHQ|IIHQWOLFKHU'DWHQVlW]H (UJHEQLVVH +2;*HQH[SUHVVLRQVPXVWHULP8URWKHO +2;*HQH[SUHVVLRQVPXVWHULPQRUPDOHQ8URWKHO +2;*HQH[SUHVVLRQVPXVWHULP8URWKHONDU]LQRP ([SUHVVLRQGHUOQF51$+27$,5LQYHUVFKLHGHQHQ7XPRUHQWLWlWHQ ,, ([SUHVVLRQGHUOQF51$+27$,5LQ8URWKHONDU]LQRP*HZHEHSUREHQ ([SUHVVLRQ GHU SXWDWLYHQ +27$,5=LHOJHQH +2;' XQG +2;' LP 8& *HZHEHVHW ([SUHVVLRQGHUOQF51$+27$,5LQ8&=HOOOLQLHQ 9HUJOHLFK GHU ([SUHVVLRQ GHU OQF51$ +27$,5 LQ 8&=HOOOLQLHQ PLW =HOOOLQLHQ DQGHUHU7XPRUHQWLWlWHQ 0RGXODWLRQGHU([SUHVVLRQGHUOQF51$+27$,5 .QRFNGRZQGHUOQF51$+27$,5 (LQ VL51$ RGHU /1$YHUPLWWHOWHU .QRFNGRZQ YHUPLQGHUW GLH .RQ]HQWUDWLRQGHUOQF51$+27$,5LP&\WRSODVPD hEHUH[SUHVVLRQGHUOQF51$+27$,5LQ8&=HOOOLQLHQ $XVZLUNXQJHQ HLQHU VWDELOHQ +27$,5hEHUH[SUHVVLRQ LQ 8&=HOOOLQLHQ DXI GHQ 3KlQRW\S $XVZLUNXQJHLQHUVWDELOHQ+27$,5hEHUH[SUHVVLRQLQGHQ8&=HOOOLQLHQ 7XQG90&8%DXIGLH3UROLIHUDWLRQXQGGLH.ORQRJHQLWlW $XVZLUNXQJHQ HLQHU VWDELOHQ +27$,5hEHUH[SUHVVLRQ LQ GHQ 8&=HOOOLQLHQ 7XQG90&8%DXIGDV0LJUDWLRQVXQG,QYDVLRQVYHUKDOWHQ 0RUSKRORJLVFKH9HUlQGHUXQJHQQDFKVWDELOHU+27$,5hEHUH[SUHVVLRQLQGHQ 8&=HOOOLQLHQ7XQG90&8% (IIHNWHGHUVWDELOHQ+27$,5hEHUH[SUHVVLRQLQGHQ8&=HOOOLQLHQ7 XQG90&8%DXIGLH&LVSODWLQ6HQVLWLYLWlW (=+68=XQG/6'6WDWXVGHU8&=HOOOLQLHQ 9HUlQGHUXQJHQ LP *HQH[SUHVVLRQVSURILO GHU 8&=HOOOLQLHQ XQG 90&8% QDFKVWDELOHU+27$,5hEHUH[SUHVVLRQ 9HUlQGHUXQJHQ LP +2;*HQH[SUHVVLRQVSURILO GHU 8&=HOOOLQLHQ XQG 90&8%QDFKVWDELOHU+27$,5hEHUH[SUHVVLRQ 9HUJOHLFK GHU HLJHQHQ ([SUHVVLRQVGDWHQ PLW SXEOL]LHUWHQ 'DWHQ ]XP gVRSKDJXVXQG0DPPDNDU]LQRPQDFKHNWRSLVFKHU+27$,5([SUHVVLRQ (IIHNWH HLQHU VWDELOHQ +27$,5hEHUH[SUHVVLRQ LQ GHQ 8&=HOOOLQLHQ 90&8% XQGDXIGLH([SUHVVLRQYRQJHSUlJWHQ*HQHQ ,,, (IIHNWH HLQHU +27$,50RGXODWLRQ DXI GLH JHSUlJWHQ *HQH 3/$*/ &'.1& ,*)XQG+ (IIHNWH HLQHU HNWRSLVFKHQ ([SUHVVLRQ YRQ +27$,5 DXI GLH ([SUHVVLRQ YRQ 3/$*/&'.1&,*)XQG+LQ8&=HOOOLQLHQ (IIHNWHLQHUHNWRSLVFKHQ+27$,5([SUHVVLRQDXIGLHJHSUlJWHQ*HQH3/$*/ &'.1&,*)XQG+LQGHU0DPPDNDU]LQRP=HOOOLQLH6.%5 (IIHNWH HNWRSLVFKHQ +27$,5([SUHVVLRQ DXI GLH JHSUlJWHQ *HQH 3/$*/ &'.1&,*)XQG+LQGHU3URVWDWDNDU]LQRP]HOOOLQLH'8 (IIHNWH HLQHV +27$,5 .QRFNGRZQV DXI GLH ([SUHVVLRQ YRQ 3/$*/ &'.1&,*)XQG+LQ8&=HOOOLQLHQ (IIHNWH HLQHV +27$,5 .QRFNGRZQV DXI GLH ([SUHVVLRQ YRQ 3/$*/ &'.1&,*)XQG+LQGHU3URVWDWDNDU]LQRP=HOOOLQLH'8 ([SUHVVLRQ GHU JHSUlJWHQ *HQH 3/$*/ &'.1& ,*) XQG + LQ 8& =HOOOLQLHQ ([SUHVVLRQGHVJHSUlJWHQ*HQV3/$*/LQ8&=HOOOLQLHQ ([SUHVVLRQGHVJHSUlJWHQ*HQV&'.1&LQ8&=HOOOLQLHQ ([SUHVVLRQGHVJHSUlJWHQ*HQV,*)XQGGHUOQF51$+LQ8&=HOOOLQLHQ 0HFKDQLVWLVFKH 8QWHUVXFKXQJHQ GHU +LVWRQPHWK\OLHUXQJ XQG GHU '1$ 0HWK\OLHUXQJDQSRWHQWLHOOHQ+27$,5=LHOJHQHQPLWHOWHUOLFKHU3UlJXQJ 9HUlQGHUXQJHQGHU7ULPHWK\OLHUXQJDQ+.XQG+.DQJHSUlJWHQ*HQHQ '1$0HWK\OLHUXQJVYHUlQGHUXQJHQDQJHSUlJWHQ*HQHQ 9HUlQGHUXQJHQ GHV '1$0HWK\OLHUXQJVSURILOV GHU 8&=HOOOLQLHQ XQG 90 &8%QDFKVWDELOHU+27$,5hEHUH[SUHVVLRQ (IIHNWHHLQHU9HUlQGHUXQJGHU3/$*/([SUHVVLRQLQ8&=HOOOLQLHQDXI&'.1& ,*)XQG+ 'LVNXVVLRQ 'LH9HUlQGHUXQJHQGHU+2;*HQH[SUHVVLRQLP8URWKHONDU]LQRP 'LH([SUHVVLRQGHUOQF51$+27$,5LP8URWKHONDU]LQRPXQGLKU(LQIOXVVDXIGLH +2;'([SUHVVLRQ ,9 6.3 Zelllinienspezifische Effekte einer HOTAIR-Überexpression .............................. 152 6.4 Mechanismen der Regulation der Genexpression durch HOTAIR ........................ 155 6.5 HOTAIR reguliert elterlich geprägte Gene ............................................................ 158 6.6 HOTAIR beeinflusst die DNA-Methylierung genomweit ..................................... 164 7 Verzeichnisse ................................................................................................................. 167 7.1 Literaturverzeichnis ................................................................................................ 167 7.2 Abbildungsverzeichnis ........................................................................................... 181 7.3 Tabellenverzeichnis ................................................................................................ 186 7.4 Abkürzungen .......................................................................................................... 188 8 Erklärung ........................................................................................................................ 192 9 Danksagung .................................................................................................................... 193 10 Anhang ........................................................................................................................... 195 V Zusammenfassung 1 Zusammenfassung Das Urothelkarzinom der Harnblase (UC) zeichnet sich durch eine ausgeprägte Heterogenität aus, die Diagnostik und Therapie erschwert. Für die Heterogenität mitverantwortlich sind aberrante Differenzierungsprozesse, die durch eine Deregulation der homöotischen HOX-Gene hervorgerufen werden könnten, wie eine in vitro Analyse dreier unabhängiger Genexpressions- Microarray-Analysen von UC-Geweben ergab. Der genaue Mechanismus der Regulation von HOX-Genen beim Menschen ist bisher nicht bekannt; neu entdeckte potentielle Regulatoren sind lange nichtkodierende RNAs (lncRNAs). Die lncRNA HOTAIR ist im HOXC-Cluster lokalisiert und kann die Expression von Genen, insbesondere posterioren HOXD-Genen, über Vermittlung von repressiven Histonmodifikationen beeinflussen. Eine Überexpression von HOTAIR korreliert in vielen Tumoren mit einem aggressiven Phänotyp und einer schlechten Prognose. Auch in einer in dieser Arbeit untersuchten großen Serie von UC-Gewebeproben waren die 25 % der Fälle mit der höchsten HOTAIR-Expression mit einer schlechten Prognose assoziiert. Die Effekte einer ektopischen HOTAIR-Überexpression in UC-Zelllinien variierten stark. In VM-CUB1 Zellen wurde durch stabile HOTAIR-Überexpression der erwartete aggressivere Phänotyp mit Markern einer epithelial-mesenchymalen Transition, verstärkter Proliferation und Invasionsfähigkeit induziert. Die Effekte der Überexpression in 5637 waren teilweise entgegengesetzt, mit Anzeichen einer Seneszenz-Induktion. Eine Mikroarray-Expressionsanalyse bestätigte die zelllinienabhängigen Effekte von HOTAIR auf HOX-Gene, Zellzyklusregulatoren und Differenzierung. Auch ein breiterer bioinformatischer Vergleich mit Ösophagus- und Mammakarzinom-Zelllinien erbrachte nur eine sehr kleine Schnittmenge gemeinsamer HOTAIR- Zielgene. Eines davon war PLAGL1, ein Schlüsselregulator eines Netzwerkes von elterlich geprägten Genen (IGN), das - mindestens in Mäusen - das embryonale Wachstum reguliert. Auch weitere Gene des IGN wurden in UC-Zelllinien durch HOTAIR beeinflusst, zum Teil vermittelt über PLAGL1. Diese Ergebnisse deuten auf eine Funktion von HOTAIR bei der Regulation von elterlich geprägten Genen. An IGN- und HOX-Genen wurden nach HOTAIR-Überexpression mittels Chromatin-Immunpräzipitation Veränderungen von Histonmethylierungen festgestellt, darunter jedoch auch transkriptionsaktivierende. Dies deutet auf weitere, bisher unbekannte Interaktionspartner von HOTAIR hin. Neu war auch die Beobachtung, dass Überexpression von HOTAIR zu einer verstärkten DNA-Methylierung des PLAGL1-Promotors führt. Ein DNA- Methylierungsarray ergab, dass sich nach HOTAIR-Überexpression die Methylierung an bestimmten CpG-Stellen über das gesamte Genom hinweg verändert. Somit scheint HOTAIR die Expression von Genen nicht nur über die Modulation von Histonmodifikationen, sondern auch der DNA-Methylierung zu regulieren. 1 Summary 2 Summary Urothelial carcinoma (UC) is characterized by pronounced heterogeneity that complicate diagnosis and therapy. One factor contributing to heterogeneity may be aberrant differentiation
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]
  • 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.
    [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]