DOCSLIB.ORG

Identification and Characterization of Molecular Targets for Disease Management in Tree Fruit Pathogens

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Identification and Characterization of Molecular Targets for Disease Management in Tree Fruit Pathogens IDENTIFICATION AND CHARACTERIZATION OF MOLECULAR TARGETS FOR DISEASE MANAGEMENT IN TREE FRUIT PATHOGENS By Jingyu Peng A DISSERTATION Submitted to Michigan State University in partial fulfillment of the requirements for the degree of Plant Pathology – Doctor of Philosophy 2020 ABSTRACT IDENTIFICATION AND CHARACTERIZATION OF MOLECULAR TARGETS FOR DISEASE MANAGEMENT IN TREE FRUIT PATHOGENS By Jingyu Peng Fire blight, caused by Erwinia amylovora, is a devastating bacterial disease threatening the worldwide production of pome fruit trees, including apple and pear. Within host xylem vessels, E. amylovora cells restrict water flow and cause wilting symptoms through formation of biofilms, that are matrix-enmeshed surface-attached microcolonies of bacterial cells. Biofilm matrix of E. amylovora is primarily composed of several exopolysaccharides (EPSs), including amylovora, levan, and, cellulose. The final step of biofilm development is dispersal, which allows dissemination of a subpopulation of biofilm cells to resume the planktonic mode of growth and consequentially cause systemic infection. In this work, we demonstrate that identified the Hfq-dependent small RNA (sRNA) RprA positively regulates amylovoran production, T3SS, and flagellar-dependent motility, and negatively affects levansucrase activity and cellulose production. We also identified the in vitro and in vivo conditions that activate RprA, and demonstrated that RprA activation leads to decreased formation of biofilms and promotes the dispersal movement of biofilm cells. This work supports the involvement of RprA in the systemic infection of E. amylovora during its pathogenesis. Bacterial toxin-antitoxin (TA) systems are small genetic loci composed of a proteinaceous toxin and a counteracting antitoxin. In this work, we identified and characterized a chromosomally encoded hok/sok-like type I TA system in Erwinia amylovora Ea1189. Ectopic overexpression of hok caused massive cell death in E. amylovora and its toxicity can be partially reversed through co-overexpression of the cognate sRNA sok. Phenotypic and transcriptomic examination of E. amylovora cells expressing hok at subtoxic levels demonstrated that hok causes membrane rupture and proton motive force dissipation, upregulates expression levels of ATP biosynthesis genes and consequently cellular ATP levels. Hok also positively affects phage shock protein genes to protect cells from further membrane damage. Taken together, the hok/sok TA system, besides being potentially self-toxic, appears to facilitate E. amylovora to manage various stress responses when the toxin gene is expressed in low levels. The succinate dehydrogenase inhibitor (SDHI) is a broad-spectrum fungicide class that has been widely utilized in agricultural fields. Blumeriella jaapii, the causative agent of cherry leaf spot (CLS), is the most important limiting factor for tart cherry production in the Midwestern United States. In the last decade, reduced efficacy in using SDHIs, i.e. boscalid, fluopyram, and fluxapyroxad, for management of CLS has been observed in many research and commercial orchard sites. Through whole-genome sequencing of B. jaapii using both PacBio long-reads and Illumina short-reads, we identified mutations in SdhB or SdhC that are correlative to resistance of this fungus to boscalid, fluopyram, and/or fluxapyroxad. SdhB and SdhC are components of the succinate dehydrogenase complex that contributes fungal respiration. In view of the widely conserved sequences of the SdhB and SdhC genes in phytopathogenic Ascomycete fungi, we expressed the wild-type or mutated alleles of the B. jaapii Sdh gene in the soybean white mold pathogen Sclerotinia sclerotiorum. We successfully validated the functions of the mutations in Sdh genes of B. jaapii in conferring resistance to several SDHIs examined in this study. The S. sclerotiorum heterologous expression system was also validated to be highly effective in characterizing the functions of other Sdh mutations of B. cinerea, C. homoeocarpa, and M. fructicola. The approach developed in this study can potentially be widely applied to interrogate SDHI fungicide resistance mechanisms in other phytopathogenic ascomycetes. ACKNOWLEDGEMENTS I would like to thank my great wife, Xinxin Wang, who has always been by my side throughout the PhD training. Thank you for being always supportive and making me so motivated to be a good husband and, soon, a good dad. I want to express my sincere appreciation to my PhD advisor, Dr. George W Sundin, who has truly exemplified how a great scientist should look like. I thank him for always thinking the best for myself and also other students. His unreserved support has allowed me to always think questions broadly and critically, and I will benefit from his training for the rest of my life. I also would like to thank my committee members, Dr. Martin Chilvers, Dr. Lindsay R Triplett, and Dr. Timothy Miles for their great guidance on my research projects as well as being so kind to me. I particularly would like to thank Dr. Lindsay R Triplett, who has co-authored with me in two research articles. I have benefited hugely from her critical thinking and guidance in scientific writing. Finally, I want to thank my parents for being such supportive in the last seven years, while I have been pursuing degrees oversee. Their love has made me strong and determined to achieve our family goals. iv TABLE OF CONTENTS LIST OF TABLES ....................................................................................................................... viii LIST OF FIGURES ....................................................................................................................... ix CHAPTER 1: Literature review...................................................................................................... 1 1.1 Molecular mechanism and triggering of biofilm dispersal ................................................... 2 1.1.1 Molecular mechanisms of biofilm dispersal................................................................... 2 1.1.2 Triggeration of biofilm dispersal .................................................................................... 5 1.2 Toxin-antitoxin system and antibiotic persistence ................................................................ 6 1.2.1 Classification of toxin-antitoxin (TA) systems .............................................................. 6 1.2.2 Regulation of TA systems .............................................................................................. 8 1.2.3 Implication of TA systems in bacterial persistence ........................................................ 9 1.3 Resistance mechanisms of SDHI fungicides in phytopathogenic fungi .............................. 11 1.3.1 History and current status of SDHI fungicides............................................................. 12 1.3.2 SDHI mode of action .................................................................................................... 13 1.3.3 Resistance mechanism of SDHI fungicides ................................................................. 14 1.3.4 SDHI cross resistance ................................................................................................... 16 CHAPTER 2: Orchestration of virulence factor expression and modulation of biofilm dispersal in Erwinia amylovora through activation of small RNA RprA .................................................... 18 2.1 Abstract................................................................................................................................ 19 2.2 Introduction ......................................................................................................................... 20 2.3 Results ................................................................................................................................. 23 2.3.1 RprA positively regulates amylovoran, T3SS, and motility, and negatively regulates levansucrase activity and cellulose production ..................................................................... 23 2.3.2 RprA regulates the promoter activity of virulence factor genes ................................... 27 2.3.3 RprA regulates hrpS at a post-transcriptional level ...................................................... 28 2.3.4 rprA expression is activated by native and environmental cues ................................... 30 2.3.5 rprA inhibits biofilm formation and activates dispersal of biofilm cells...................... 34 2.4 Discussion............................................................................................................................ 36 2.5 Materials and methods ......................................................................................................... 41 2.5.1 Bacterial strains, plasmids, and media ......................................................................... 41 2.5.2 DNA manipulations ...................................................................................................... 41 2.5.3 Bioinformatics .............................................................................................................. 42 2.5.4 Quantification of amylovoran ....................................................................................... 42 2.5.5 Swimming motility assay ............................................................................................. 43 2.5.6 Cellulose assay ............................................................................................................
Load more

Recommended publications
  • Interplay Between Ompa and Rpon Regulates Flagellar Synthesis in Stenotrophomonas Maltophilia
    microorganisms Article Interplay between OmpA and RpoN Regulates Flagellar Synthesis in Stenotrophomonas maltophilia Chun-Hsing Liao 1,2,†, Chia-Lun Chang 3,†, Hsin-Hui Huang 3, Yi-Tsung Lin 2,4, Li-Hua Li 5,6 and Tsuey-Ching Yang 3,* 1 Division of Infectious Disease, Far Eastern Memorial Hospital, New Taipei City 220, Taiwan; [email protected] 2 Department of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; [email protected] 3 Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; [email protected] (C.-L.C.); [email protected] (H.-H.H.) 4 Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei 112, Taiwan 5 Department of Pathology and Laboratory Medicine, Taipei Veterans General Hosiptal, Taipei 112, Taiwan; [email protected] 6 Ph.D. Program in Medical Biotechnology, Taipei Medical University, Taipei 110, Taiwan * Correspondence: [email protected] † Liao, C.-H. and Chang, C.-L. contributed equally to this work. Abstract: OmpA, which encodes outer membrane protein A (OmpA), is the most abundant transcript in Stenotrophomonas maltophilia based on transcriptome analyses. The functions of OmpA, including adhesion, biofilm formation, drug resistance, and immune response targets, have been reported in some microorganisms, but few functions are known in S. maltophilia. This study aimed to elucidate the relationship between OmpA and swimming motility in S. maltophilia. KJDOmpA, an ompA mutant, Citation: Liao, C.-H.; Chang, C.-L.; displayed compromised swimming and failure of conjugation-mediated plasmid transportation. The Huang, H.-H.; Lin, Y.-T.; Li, L.-H.; hierarchical organization of flagella synthesis genes in S.
    [Show full text]
  • Subunit of RNA Polymerase and the Transcriptional Regulators Rsd from Escherichia Coli and Algq from Pseudomonas Aeruginosa
    Bacterial two-hybrid analysis of interactions between region 4 of the sigma(70) subunit of RNA polymerase and the transcriptional regulators Rsd from Escherichia coli and AlgQ from Pseudomonas aeruginosa. The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Dove, S. L., and A. Hochschild. 2001. “Bacterial Two-Hybrid Analysis of Interactions between Region 4 of the 70 Subunit of RNA Polymerase and the Transcriptional Regulators Rsd from Escherichia Coli and AlgQ from Pseudomonas Aeruginosa.” Journal of Bacteriology 183 (21): 6413–21. https://doi.org/10.1128/ jb.183.21.6413-6421.2001. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:41483172 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA JOURNAL OF BACTERIOLOGY, Nov. 2001, p. 6413–6421 Vol. 183, No. 21 0021-9193/01/$04.00ϩ0 DOI: 10.1128/JB.183.21.6413–6421.2001 Copyright © 2001, American Society for Microbiology. All Rights Reserved. Bacterial Two-Hybrid Analysis of Interactions between Region 4 of the ␴70 Subunit of RNA Polymerase and the Transcriptional Regulators Rsd from Escherichia coli and AlgQ from Pseudomonas aeruginosa SIMON L. DOVE AND ANN HOCHSCHILD* Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115 Received 3 May 2001/Accepted 6 August 2001 A number of transcriptional regulators mediate their effects through direct contact with the ␴70 subunit of Escherichia coli RNA polymerase (RNAP).
    [Show full text]
  • Subcellular Localization in Bacteria: from Envz/Ompr to Transertion
    University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations Summer 2011 Subcellular Localization in Bacteria: From EnvZ/OmpR to Transertion Elizabeth Libby University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Biological and Chemical Physics Commons, and the Microbiology Commons Recommended Citation Libby, Elizabeth, "Subcellular Localization in Bacteria: From EnvZ/OmpR to Transertion" (2011). Publicly Accessible Penn Dissertations. 974. https://repository.upenn.edu/edissertations/974 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/974 For more information, please contact [email protected]. Subcellular Localization in Bacteria: From EnvZ/OmpR to Transertion Abstract The internal structures of the bacterial cell and the associated dynamic changes as a function of physiological state have only recently begun to be characterized. Here we explore two aspects of subcellular localization in E. coli cells: the cytoplasmic distribution of the response regulator OmpR and its regulated chromosomal genes, and the subcellular repositioning of chromosomal loci encoding membrane proteins upon induction. To address these questions by quantitative fluorescence microscopy, we developed a simple system to tag virtually any chromosomal location with arrays of lacO or tetO by extending and modifying existing tools. An unexplained subcellular localization was reported for a functional fluorescent protein fusion to the response regulator OmpR in Escherichia coli. The pronounced regions of increased fluorescence, or foci, are dependent on OmpR phosphorylation, and do not occupy fixed, easily identifiable positions, such as the poles or midcell. Here we show that the foci are due to OmpR-YFP binding specific sites in the chromosome.
    [Show full text]
  • Biological Circuits with Small RNA Switches
    Downloaded from genesdev.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW Stealth regulation: biological circuits with small RNA switches Susan Gottesman Laboratory of Molecular Biology, National Cancer Institute, Bethesda, Maryland 20892, USA So you thinkyou finally understand the regulation of temporal RNAs (stRNAs) or microRNAs, and that these your favorite gene? The transcriptional regulators have RNAs are processed by some of the same protein cofac- been identified; the signaling cascades that regulate syn- tors as is RNAi, have put regulatory RNAs in the spot- thesis and activity of the regulators have been found. light in eukaryotes as well. Recent searches have con- Possibly you have found that the regulator is itself un- firmed that flies, worms, plants, and humans all harbor stable, and that instability is necessary for proper regu- significant numbers of small RNAs likely to play regu- lation. Time to lookfor a new project, or retire and rest latory roles. on your laurels? Not so fast—there’s more. It is rapidly Along with the rapid expansion in RNAs doing inter- becoming apparent that another whole level of regula- esting things, has come a proliferation of nomenclature. tion lurks, unsuspected, in both prokaryotic and eukary- Noncoding RNAs (ncRNA) has been used recently, as otic cells, hidden from our notice in part by the tran- the most general term (Storz 2002). Among the noncod- scription-based approaches that we usually use to study ing RNAs, the subclass of relatively small RNAs that gene regulation, and in part because these regulators are frequently act as regulators have been called stRNAs very small targets for mutagenesis and are not easily (small temporal RNAs, eukaryotes) and sRNAs (small found from genome sequences alone.
    [Show full text]
  • Fur Is the Master Regulator of the Extraintestinal Pathogenic
    Downloaded from RESEARCH ARTICLE crossmark Fur Is the Master Regulator of the Extraintestinal Pathogenic mbio.asm.org Escherichia coli Response to Serum on August 3, 2015 - Published by Sagi Huja,a Yaara Oren,a Dvora Biran,a Susann Meyer,b Ulrich Dobrindt,c Joerg Bernhard,b Doerte Becher,b Michael Hecker,b Rotem Sorek,d Eliora Z. Rona,e Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israela; Institute for Microbiology, Ernst-Moritz-Arndt-Universität, Greifswald, Germanyb; Institute of Hygiene, Westfälische Wilhelms-Universität, Münster, Germanyc; Department of Molecular Genetics Weizmann Institute of Science, Rehovot, Israeld; MIGAL, Galilee Research Center, Kiriat Shmona, Israele ABSTRACT Drug-resistant extraintestinal pathogenic Escherichia coli (ExPEC) strains are the major cause of colisepticemia (coli- bacillosis), a condition that has become an increasing public health problem in recent years. ExPEC strains are characterized by high resistance to serum, which is otherwise highly toxic to most bacteria. To understand how these bacteria survive and grow in serum, we performed system-wide analyses of their response to serum, making a clear distinction between the responses to nu- tritional immunity and innate immunity. Thus, mild heat inactivation of serum destroys the immune complement and abolishes mbio.asm.org the bactericidal effect of serum (inactive serum), making it possible to examine nutritional immunity. We used a combination of deep RNA sequencing and proteomics in order to characterize ExPEC genes whose expression is affected by the nutritional stress of serum and by the immune complement. The major change in gene expression induced by serum—active and inactive—in- volved metabolic genes.
    [Show full text]
  • Journal of Microbiological Methods a Proteome-Wide Screen to Identify Transcription Factors Interacting with the Vibrio Cholerae
    Journal of Microbiological Methods 165 (2019) 105702 Contents lists available at ScienceDirect Journal of Microbiological Methods journal homepage: www.elsevier.com/locate/jmicmeth Note A proteome-wide screen to identify transcription factors interacting with the Vibrio cholerae rpoS promoter T ⁎ ⁎ Julio C. Ayala1, Jorge A. Benitez , Anisia J. Silva Morehouse School of Medicine, Department of Microbiology, Biochemistry and Immunology, 720 Westview Dr., SW, Atlanta, GA 30310, USA ABSTRACT We describe a proteomic approach to identify transcription factors binding to a target promoter. The method's usefulness was tested by identifying proteins binding to the Vibrio cholerae rpoS promoter in response to cell density. Proteins identified in this screen included the nucleoid-associated protein Fis and the quorum sensing regulator HapR. Isolation of regulatory mutants has played a major role in increasing with agitation at 37 °C to stationary phase. Culture media were sup- our understanding of the regulation of gene expression (Shuman and plemented with ampicillin (Amp, 100 μg/mL), kanamycin (Km, 25 μg/ Silhavy, 2003). There are cases, however, in which the above approach mL), polymyxin B (PolB, 100 units/mL) or L-arabinose (0.2%) as re- can encounter significant obstacles. For instance, the methods used to quired. Chromosomal deletions of fis and/or hapR were created in strain genetically manipulate model organisms are not always equally effec- C7258ΔlacZ by allelic exchange as described previously (Wang et al., tive in less studied microorganisms; some regulatory mutations can be 2011; Wang et al., 2012; Wang et al., 2014). Briefly, genomic DNA highly pleiotropic, often be deleterious, unstable and difficult to select.
    [Show full text]
  • Genome-Wide Transcriptional Response to Varying Rpos Levels
    RESEARCH ARTICLE crossm Genome-Wide Transcriptional Response Downloaded from to Varying RpoS Levels in Escherichia coli K-12 Garrett T. Wong,a* Richard P. Bonocora,b Alicia N. Schep,a* Suzannah M. Beeler,a* Anna J. Lee Fong,a* Lauren M. Shull,a* Lakshmi E. Batachari,a Moira Dillon,a Ciaran Evans,c* Carla J. Becker,a Eliot C. Bush,a Johanna Hardin,c http://jb.asm.org/ Joseph T. Wade,b,d Daniel M. Stoebela Department of Biology, Harvey Mudd College, Claremont, California, USAa; Wadsworth Center, New York State Department of Health, Albany, New York, USAb; Department of Mathematics, Pomona College, Claremont, California, USAc; Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, New York, USAd ABSTRACT The alternative sigma factor RpoS is a central regulator of many stress on April 17, 2017 by CALIFORNIA INSTITUTE OF TECHNOLOGY responses in Escherichia coli. The level of functional RpoS differs depending on the Received 21 October 2016 Accepted 12 stress. The effect of these differing concentrations of RpoS on global transcriptional January 2017 Accepted manuscript posted online 23 responses remains unclear. We investigated the effect of RpoS concentration on the January 2017 transcriptome during stationary phase in rich media. We found that 23% of genes in Citation Wong GT, Bonocora RP, Schep AN, the E. coli genome are regulated by RpoS, and we identified many RpoS-transcribed Beeler SM, Lee Fong AJ, Shull LM, Batachari LE, genes and promoters. We observed three distinct classes of response to RpoS by Dillon M, Evans C, Becker CJ, Bush EC, Hardin J, Wade JT, Stoebel DM.
    [Show full text]
  • Regulatory Interplay Between Small Rnas and Transcription Termination Factor Rho Lionello Bossi, Nara Figueroa-Bossi, Philippe Bouloc, Marc Boudvillain
    Regulatory interplay between small RNAs and transcription termination factor Rho Lionello Bossi, Nara Figueroa-Bossi, Philippe Bouloc, Marc Boudvillain To cite this version: Lionello Bossi, Nara Figueroa-Bossi, Philippe Bouloc, Marc Boudvillain. Regulatory interplay be- tween small RNAs and transcription termination factor Rho. Biochimica et Biophysica Acta - Gene Regulatory Mechanisms , Elsevier, 2020, pp.194546. 10.1016/j.bbagrm.2020.194546. hal-02533337 HAL Id: hal-02533337 https://hal.archives-ouvertes.fr/hal-02533337 Submitted on 6 Nov 2020 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. Regulatory interplay between small RNAs and transcription termination factor Rho Lionello Bossia*, Nara Figueroa-Bossia, Philippe Bouloca and Marc Boudvillainb a Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France b Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans cedex 2, France * Corresponding author: [email protected] Highlights Repression
    [Show full text]
  • Osmosensing by the Bacterial Phoq/Phop Two-Component System
    Osmosensing by the bacterial PhoQ/PhoP two-component system Jing Yuana,b,1, Fan Jina,b, Timo Glattera, and Victor Sourjika,b,1 aMax Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; and bLOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany Edited by Susan Gottesman, National Institutes of Health, Bethesda, MD, and approved November 6, 2017 (received for review October 5, 2017) The PhoQ/PhoP two-component system plays an essential role in domain and the cytoplasmic domains (10, 11), with the latter the response of enterobacteria to the environment of their mam- detecting the cytoplasmic pH change. The PhoQ TM domain is a malian hosts. It is known to sense several stimuli that are poten- dimer of two TM helices that form a four-helix bundle (12). tially associated with the host, including extracellular magnesium Upon activation of the sensory domain, the periplasmic ends of limitation, low pH, and the presence of cationic antimicrobial the two TM1 helices move closer to each other and push the two peptides. Here, we show that the PhoQ/PhoP two-component TM2 helices farther apart, accompanied by a TM2 rotation, systems of Escherichia coli and Salmonella can also perceive an which requires the solvation of a semichannel in the four-helix osmotic upshift, another key stimulus to which bacteria become bundle (12). Asn202, located near the center of the TM2 helix exposed within the host. In contrast to most previously estab- and proximal to this semichannel, affects the solvation of the lished stimuli of PhoQ, the detection of osmotic upshift does not cavity, and mutations of Asn202 to a nonpolar residue lock PhoQ require its periplasmic sensor domain.
    [Show full text]
  • Identification of Small Regulatory Rnas and Their Targets in Bacteria
    Identification of Small Regulatory RNAs and Their Targets in Bacteria Dissertation zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) der Technischen Fakultat¨ der Universitat¨ Bielefeld vorgelegt von Cynthia Mira Sharma Bielefeld, im Mai 2009 Dissertation zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) der Technischen Fakultat¨ der Universitat¨ Bielefeld. Vorgelegt von: Dipl.-Biol. Cynthia Mira Sharma Angefertigt im: Max-Planck-Institut fur¨ Infektionsbiologie, Berlin Tag der Einreichung: 04. Mai 2009 Tag der Verteidigung: 22. Juli 2009 Gutachter: Prof. Dr. Robert Giegerich, Universitat¨ Bielefeld Dr. Jorg¨ Vogel, Max-Planck-Institut fur¨ Infektionsbiologie, Berlin Prof. Dr. Wolfgang Hess, Universitat¨ Freiburg Prufungsausschuss:¨ Prof. Dr. Jens Stoye, Universitat¨ Bielefeld Prof. Dr. Robert Giegerich, Universitat¨ Bielefeld Dr. Jorg¨ Vogel, Max-Planck-Institut fur¨ Infektionsbiologie, Berlin Prof. Dr. Wolfgang Hess, Universitat¨ Freiburg Dr. Marilia Braga, Universitat¨ Bielefeld Gedruckt auf alterungsbestandigem¨ Papier nach ISO 9706. Dedicated to my parents, Ingrid Sharma and Som Deo Sharma ACKNOWLEDGEMENTS At this point, I would like to thank everybody who contributed in whatever form to this thesis. In particular, I am grateful to the following persons: . my supervisor Dr. Jorg¨ Vogel for giving me the opportunity to work in a superb scientific environment and for his continuous support and guidance throughout the past several years, . Prof. Dr. Robert Giegerich for enabling me to submit this thesis to the University of Bielefeld and for valuable suggestions during several visits to his institute, . Prof. Dr. Wolfgang Hess for his willingness to evaluate this thesis, . Dr. Fabien Darfeuille (a. k. a. the “master of the gels”) for a great stay in his lab in Bordeaux and many fruitful discussions, .
    [Show full text]
  • Sral Srna Interaction Regulates the Terminator by Preventing Premature Transcription Termination of Rho Mrna
    SraL sRNA interaction regulates the terminator by preventing premature transcription termination of rho mRNA Inês Jesus Silvaa,1, Susana Barahonaa,2, Alex Eyraudb,2, David Lalaounab, Nara Figueroa-Bossic, Eric Masséb, and Cecília Maria Arraianoa,1 aInstituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal; bRNA Group, Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada; and cInstitute for Integrative Biology of the Cell (I2BC), Commissariat à l’énergie atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France Edited by Tina M. Henkin, The Ohio State University, Columbus, OH, and approved December 28, 2018 (received for review July 5, 2018) Transcription termination is a critical step in the control of gene sequence, leading to changes in translation and/or mRNA degra- expression. One of the major termination mechanisms is mediated dation (9–11). However, distinct mechanisms of action have been by Rho factor that dissociates the complex mRNA-DNA-RNA poly- increasingly reported in the literature (11). For instance, the Sal- merase upon binding with RNA polymerase. Rho promotes termina- monella sRNA ChiX was shown to induce premature transcription tion at the end of operons, but it can also terminate transcription termination within the coding sequence of chiP as a result of its within leader regions, performing regulatory functions and avoiding interaction with 5′-UTR of the operon chiPQ, thus affecting the pervasive transcription. Transcription of rho is autoregulated through expression of both genes of the operon (12). Conversely, it was a Rho-dependent attenuation in the leader region of the transcript.
    [Show full text]
  • Transcriptional Occlusion Caused by Overlapping Promoters
    Transcriptional occlusion caused by overlapping promoters M. Ammar Zafara,1, Valerie J. Carabettab,1, Mark J. Mandelc, and Thomas J. Silhavya,2 aDepartment of Molecular Biology, Princeton University, Princeton, NJ 08544; bPublic Health Research Institute at New Jersey Medical School, Rutgers University, Newark, NJ 07103; and cDepartment of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 Contributed by Thomas J. Silhavy, December 17, 2013 (sent for review November 6, 2013) RpoS (σ38) is required for cell survival under stress conditions, but has as its basis two overlapping promoters and a long noncoding it can inhibit growth if produced inappropriately and, consequently, RNA (lncRNA). Expression of the shorter transcript blocks ex- its production and activity are elaborately regulated. Crl, a transcrip- pression of the longer, but the former cannot be translated be- tional activator that does not bind DNA, enhances RpoS activity by cause it lacks a ribosome-binding site (rbs). This simple, but stimulating the interaction between RpoS and the core polymerase. economical, mechanism allows a near instantaneous reduction crl The gene has two overlapping promoters, a housekeeping, RpoD- in Crl synthesis without the need to produce any transacting σ70 σ54 ( ) dependent promoter, and an RpoN ( )promoterthatis regulatory factor. strongly up-regulated under nitrogen limitation. However, transcrip- tion from the RpoN promoter prevents transcription from the RpoD Results promoter, and the RpoN-dependent transcript lacks a ribosome- The Role of Crl Under Nitrogen-Stress Conditions. In rapidly growing binding site. Thus, activation of the RpoN promoter produces cells, RpoS is made but it is directed by the adaptor protein SprE a long noncoding RNA that silences crl gene expression simply by being made.
    [Show full text]