DOCSLIB.ORG

Small RNA-Mediated Regulation of Gene Expression in Escherichia Coli

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Small RNA-Mediated Regulation of Gene Expression in Escherichia Coli TILL MIN FAMILJ List of Publications Publications I-III This thesis is based on the following papers, which are referred to in the text as Paper I-III. I *Darfeuille, F., *Unoson, C., Vogel, J., and Wagner, E.G.H. (2007) An antisense RNA inhibits translation by competing with standby ribosomes. Molecular Cell, 26, 381-392 II Unoson, C., and Wagner, E.G.H. (2008) A small SOS-induced toxin is targeted against the inner membrane in Escherichia coli. Molecular Microbiology, 70(1), 258-270 III *Holmqvist, E., *Unoson, C., Reimegård, J., and Wagner, E.G.H. (2010) The small RNA MicF targets its own regulator Lrp and promotes a positive feedback loop. Manuscript *Shared first authorship Reprints were made with permission from the publishers. Some of the results presented in this thesis are not included in the publications listed above Additional publications Unoson, C., and Wagner, E.G.H. (2007) Dealing with stable structures at ribosome binding sites. RNA biology, 4:3, 113-117 (point of view) Contents Introduction................................................................................................... 11 A historical view of gene regulation and RNA research ......................... 11 Small RNAs in Escherichia coli .............................................................. 13 Antisense mechanisms ............................................................................. 14 Translation inhibition by targeting the TIR ............................................. 15 Degradation versus translation inhibition ................................................ 16 Translation activation............................................................................... 17 sRNAs targeting non-TIRs to control translation .................................... 18 Protein targeting sRNAs .......................................................................... 18 Odd sRNA characteristics........................................................................ 19 Hfq is an important player in sRNA-mediated regulation ....................... 20 CRISPR RNAs inhibit uptake of foreign DNA ....................................... 21 TA modules employ sRNAs as antitoxins ............................................... 22 Hok-Sok............................................................................................... 23 Chromosomally encoded type I TA systems....................................... 23 Implications of structured TIRs ............................................................... 24 Biological aspects: when and why to use sRNAs.................................... 26 The present investigation.............................................................................. 29 istR-tisAB; a new toxin-antitoxin module (Papers I-II) ........................... 29 Post-transcriptional regulation of tisAB (Paper I).................................... 30 Only one out of three mRNAs is active .............................................. 30 Translational coupling or structural rearrangements? ......................... 31 A ribosome standby site? .................................................................... 33 Standby required to overcome RNA structure .................................... 34 Summary ............................................................................................. 34 Characterization of TisB (Paper II).......................................................... 35 TisB is irreversibly toxic when over-expressed .................................. 35 Mode of action of TisB ....................................................................... 35 Physiological role of the IstR1-TisB system....................................... 36 Summary ............................................................................................. 37 Further studies.......................................................................................... 37 The terminator stem in tisAB mRNA is a stability determinant.......... 37 IstR-2 function..................................................................................... 38 MicF targets its own regulator Lrp, providing a positive feedback loop (Paper III)................................................................................................. 39 Lrp: a putative MicF target.................................................................. 39 MicF targeting of lrp is sequence-specific and Hfq-dependent .......... 39 MicF affects Lrp-controlled downstream target genes........................ 40 A positive feedback loop..................................................................... 40 Mixed feed-forward loop?................................................................... 41 Summary ............................................................................................. 41 Discussion..................................................................................................... 44 Benefits of using regulatory RNA ........................................................... 44 Non-coding RNAs in all kingdoms of life............................................... 45 Localization of sRNAs............................................................................. 46 Additional characteristics of riboregulation............................................. 47 Standby requirement: a common theme?................................................. 49 Relevance of chromosomally encoded TA systems?............................... 51 Persisters: dormant cells........................................................................... 52 Conclusions................................................................................................... 54 Paper I ...................................................................................................... 54 Paper II..................................................................................................... 54 Paper III.................................................................................................... 54 Svensk sammanfattning................................................................................ 55 Acknowledgments ........................................................................................ 58 References..................................................................................................... 60 Abbreviations sRNA Small RNA ncRNA Non-coding RNA UTR Untranslated region TIR Translation initiation region ORF Open reading frame SD Shine-Dalgarno sequence RBS Ribosome-binding site 30S Small ribosomal subunit 50S Large ribosomal subunit 70S Ribosome (30S + 50S) TF Transcription factor TA Toxin-antitoxin Introduction A historical view of gene regulation and RNA research The central dogma in molecular biology states that DNA, the genetic material in most organisms, is transcribed into messenger RNA (mRNA), which acts as a blueprint by being subsequently translated into protein(-s). Historically, RNA was only considered to be important as an information- carrying intermediate between DNA and proteins, and as transfer RNA and ribosomal RNA involved in protein synthesis, but not to have any active/regulatory function. This view has changed dramatically in the last decades. Today, we know that RNAs can carry out many functions in the cells, such as catalysis and gene regulation. In the early 1980s, the first catalytic RNAs were discovered; the ribonucleolytic component of RNAse P, M1 RNA, required for tRNA maturation, and the self-splicing group I intron of Tetrahymena (1,2). These findings resulted in the Nobel Prize in Chemistry 1989 awarded to Sidney Altman and Thomas Cech. Jacob and Monod (3) were the first scientists who suggested that gene regulation in bacteria could be carried out by RNA. In 1981 the two first regulatory RNAs which employed the antisense mechanism (sequence complementarity to another RNA molecule) were discovered in bacteria. They were shown to be involved in copy number control of plasmids in E. coli (4,5). These were the first examples that showed that antisense RNAs could be bona fide regulators. Today, many different non-coding RNAs (ncRNAs; not coding for proteins) are known in eukaryotes and prokaryotes. In addition to the previously known ribosomal RNAs, transfer RNAs and other so-called housekeeping RNAs, we now have a growing list of RNAs that act through an antisense mechanism to regulate gene expression. In eukaryotes, processes such as gene silencing and developmental regulation all largely depend on such regulatory RNAs (6). Bacterial regulatory RNAs were identified prior to their eukaryotic counterparts, with MicF in Escherichia coli being the first to be characterized (7). This opened up a whole new field; that of so-called small RNAs (sRNAs) in bacteria. Most sRNAs base pair to translation initiation regions (TIR) in the 5’ UTR of mRNAs to affect translation and/or mRNA stability (8). 11 Two classes of eukaryotic regulatory RNAs that have expanded our view on RNA-mediated gene regulation/defense mechanisms are miRNAs and siRNAs (9). RNAi is a eukaryotic defense system, where invading or introduced dsRNA is processed into short, ≈22 base pair effector molecules, the short interfering RNAs (siRNAs). This is carried out by the enzyme Dicer, a member of the RNase III family (10). One strand of the siRNAs is incorporated into the RNA-induced silencing complex (11). This “active” strand guides the complex to the target RNA by sequence complementarity, leading to cleavage of the target RNA (9). RNAi is now frequently
Load more

Recommended publications
  • Bacterial Small Rnas in the Genus Herbaspirillum Spp
    International Journal of Molecular Sciences Article Bacterial Small RNAs in the Genus Herbaspirillum spp. Amanda Carvalho Garcia 1,* , Vera Lúcia Pereira dos Santos 1, Teresa Cristina Santos Cavalcanti 2, Luiz Martins Collaço 2 and Hans Graf 1 1 Department of Internal Medicine, Federal University of Paraná, Curitiba 80.060-240, Brazil; [email protected] (V.L.P.d.S.); [email protected] (H.G.) 2 Department of Pathology, Federal University of Paraná, PR, Curitiba 80.060-240, Brazil; [email protected] (T.C.S.C.); [email protected] (L.M.C.) * Correspondence: [email protected]; Tel.: +55-41-99833-0124 Received: 5 November 2018; Accepted: 12 December 2018; Published: 22 December 2018 Abstract: The genus Herbaspirillum includes several strains isolated from different grasses. The identification of non-coding RNAs (ncRNAs) in the genus Herbaspirillum is an important stage studying the interaction of these molecules and the way they modulate physiological responses of different mechanisms, through RNA–RNA interaction or RNA–protein interaction. This interaction with their target occurs through the perfect pairing of short sequences (cis-encoded ncRNAs) or by the partial pairing of short sequences (trans-encoded ncRNAs). However, the companion Hfq can stabilize interactions in the trans-acting class. In addition, there are Riboswitches, located at the 50 end of mRNA and less often at the 30 end, which respond to environmental signals, high temperatures, or small binder molecules. Recently, CRISPR (clustered regularly interspaced palindromic repeats), in prokaryotes, have been described that consist of serial repeats of base sequences (spacer DNA) resulting from a previous exposure to exogenous plasmids or bacteriophages.
    [Show full text]
  • Global Analysis of Small RNA and Mrna Targets of Hfq
    Blackwell Science, LtdOxford, UKMMIMolecular Microbiology 1365-2958Blackwell Publishing Ltd, 200350411111124Original ArticleA. Zhang et al.Global analysis of Hfq targets Molecular Microbiology (2003) 50(4), 1111–1124 doi:10.1046/j.1365-2958.2003.03734.x Global analysis of small RNA and mRNA targets of Hfq Aixia Zhang,1 Karen M. Wassarman,2 greatly expanded over the past few years (reviewed in Carsten Rosenow,3 Brian C. Tjaden,4† Gisela Storz1* Gottesman, 2002; Grosshans and Slack, 2002; Storz, and Susan Gottesman5* 2002; Wassarman, 2002; Massé et al., 2003). A subset of 1Cell Biology and Metabolism Branch, National Institute of these small RNAs act via short, interrupted basepairing Child Health and Development, Bethesda MD 20892, interactions with target mRNAs. How do these small USA. RNAs find and anneal to their targets? In Escherichia coli, 2Department of Bacteriology, University of Wisconsin, at least part of the answer lies in their association with Madison, WI 53706, USA. and dependence upon the RNA chaperone, Hfq. The 3Affymetrix, Santa Clara, CA 95051, USA. abundant Hfq protein was identified originally as a host 4Department of Computer Science, University of factor for RNA phage Qb replication (Franze de Fernan- Washington, Seattle, WA 98195, USA. dez et al., 1968), but later hfq mutants were found to 5Laboratory of Molecular Biology, National Cancer exhibit multiple phenotypes (Brown and Elliott, 1996; Muf- Institute, Bethesda, MD 20892, USA. fler et al., 1996). These defects are, at least in part, a reflection of the fact that Hfq is required for the function of several small RNAs including DsrA, RprA, Spot42, Summary OxyS and RyhB (Zhang et al., 1998; Sledjeski et al., Hfq, a bacterial member of the Sm family of RNA- 2001; Massé and Gottesman, 2002; Møller et al., 2002).
    [Show full text]
  • RNAIII of the Staphylococcus Aureus Agr System Activates Global Regulator Mgra by Stabilizing Mrna
    Correction MICROBIOLOGY Correction for “RNAIII of the Staphylococcus aureus agr system (112:14036–14041; first published October 26, 2015; 10.1073/ activates global regulator MgrA by stabilizing mRNA,” by Ravi pnas.1509251112). Kr. Gupta, Thanh T. Luong, and Chia Y. Lee, which appeared The authors note that Fig. 2 appeared incorrectly. The cor- in issue 45, November 10, 2015, of Proc Natl Acad Sci USA rected figure and its legend appear below. A B 6 6 * * * 5 ** ** * 5 * 4 4 3 3 2 2 1 1 Half-life (min) 0 Half-life (min) 0 agr agr agr (11346) Newman P1 UTR P2 UTR P1 UTR P1 UTR P2 UTR P2 UTR (1844) (1845) +RNAIII +pML100 +RNAIII 5-nt mutant(12916) (A22) +pML100 (12501) (12502) P1 UTR P2 UTR 5-nt revertant Fig. 2. Stability of mgrA mRNA. (A) Stability in various chromosomal mutants. (B) RNAIII complementation of deletion mutations in mgrA UTR. mRNA stability expressed as half-life in minutes. The numbers in parentheses represent strain number. *P < 0.05, **P < 0.01 (unpaired two-tailed Student t test between Newman and each mutant, n = 3). www.pnas.org/cgi/doi/10.1073/pnas.1523895113 E7306 | PNAS | December 29, 2015 | vol. 112 | no. 52 www.pnas.org Downloaded by guest on September 26, 2021 RNAIII of the Staphylococcus aureus agr system activates global regulator MgrA by stabilizing mRNA Ravi Kr. Gupta, Thanh T. Luong, and Chia Y. Lee1 Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR 72205 Edited by Richard P. Novick, New York University School of Medicine, New York, NY, and approved September 9, 2015 (received for review May 12, 2015) RNAIII, the effector of the agr quorum-sensing system, plays a key (13) to postulate that RNAIII must interact with one or more role in virulence gene regulation in Staphylococcus aureus, but how pleiotropic regulators.
    [Show full text]
  • Outer Membrane Protein Genes and Their Small Non-Coding RNA Regulator Genes in Photorhabdus Luminescens Dimitris Papamichail1 and Nicholas Delihas*2
    Biology Direct BioMed Central Research Open Access Outer membrane protein genes and their small non-coding RNA regulator genes in Photorhabdus luminescens Dimitris Papamichail1 and Nicholas Delihas*2 Address: 1Department of Computer Sciences, SUNY, Stony Brook, NY 11794-4400, USA and 2Department of Molecular Genetics and Microbiology, School of Medicine, SUNY, Stony Brook, NY 11794-5222, USA Email: Dimitris Papamichail - [email protected]; Nicholas Delihas* - [email protected] * Corresponding author Published: 22 May 2006 Received: 08 May 2006 Accepted: 22 May 2006 Biology Direct 2006, 1:12 doi:10.1186/1745-6150-1-12 This article is available from: http://www.biology-direct.com/content/1/1/12 © 2006 Papamichail and Delihas; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Introduction: Three major outer membrane protein genes of Escherichia coli, ompF, ompC, and ompA respond to stress factors. Transcripts from these genes are regulated by the small non-coding RNAs micF, micC, and micA, respectively. Here we examine Photorhabdus luminescens, an organism that has a different habitat from E. coli for outer membrane protein genes and their regulatory RNA genes. Results: By bioinformatics analysis of conserved genetic loci, mRNA 5'UTR sequences, RNA secondary structure motifs, upstream promoter regions and protein sequence homologies, an ompF -like porin gene in P. luminescens as well as a duplication of this gene have been predicted.
    [Show full text]
  • Life's Origins
    THE SEARCH FOR LIFE'S ORIGINS Progress and Future Directions in Planetary Biology and Chemical Evolution SPACE STUDIES BOARD Committee on Planetary Biology and Chemical Evolution Commission on Physical Sciences, Mathematics, and Applications National Research Council (NASA-CR-190929) THE SEARCH FCR N93-11603 LIFF'S nRIGINS: PROGRESS AND FUTURE DTR_CTI_NS IN PLANETARY biOLOgY AND CHEMICAL FVOLUTION (NAS-NRC) Unclas i59 p G3191 0125180 NATIONAL ACADEMY PRESS Washington, D.C. 1990 NATIONAL ACADEMY PRESS - 2101 Constitution Avenue, N.W. • Washington, D.C. 20418 NOTICE: The project that is the subject of this report was approved by the Governing Board of the National l_esearch Council, whose members are drawn from the councils of the National Academy of Sciences, the National Academy of Engineering, and the Institute of Medicine. The members of the committee responsible for the report were chosen for their special compe- tences and with regard for appropriate balance. This report has been reviewed by a group other than the authors according to procedures approved by a Report Review Committee consisting of members of the National Academy of Sciences, the National Academy of Engineering, and the Institute of Medicine. Support for this project was provided by Contract NASW 4102 between the National Academy of Sciences and the National Aeronautics and Space Administration. Library of Congress Cataloging-in-Publication Data The Search for life's origins : progress and future directions in planetary biology and chemical evolution / Committee on Planetary Biology and Chemical Evolution. p. cm. Includes bibliographical references. Includes index. ISBN 0-309-04246-1 1. Life--Origin. 2. Space biology.
    [Show full text]
  • The Emerging Role of Ncrnas and RNA-Binding Proteins in Mitotic Apparatus Formation
    non-coding RNA Review The Emerging Role of ncRNAs and RNA-Binding Proteins in Mitotic Apparatus Formation Kei K. Ito, Koki Watanabe and Daiju Kitagawa * Department of Physiological Chemistry, Graduate School of Pharmaceutical Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan; [email protected] (K.K.I.); [email protected] (K.W.) * Correspondence: [email protected] Received: 11 November 2019; Accepted: 13 March 2020; Published: 20 March 2020 Abstract: Mounting experimental evidence shows that non-coding RNAs (ncRNAs) serve a wide variety of biological functions. Recent studies suggest that a part of ncRNAs are critically important for supporting the structure of subcellular architectures. Here, we summarize the current literature demonstrating the role of ncRNAs and RNA-binding proteins in regulating the assembly of mitotic apparatus, especially focusing on centrosomes, kinetochores, and mitotic spindles. Keywords: ncRNA; centrosome; kinetochore; mitotic spindle 1. Introduction Non-coding RNAs (ncRNAs) are defined as a class of RNA molecules that are transcribed from genomic DNA, but not translated into proteins. They are mainly classified into the following two categories according to their length—small RNA (<200 nt) and long non-coding RNA (lncRNA) (>200 nt). Small RNAs include traditional RNA molecules, such as transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), PIWI-interacting RNA (piRNA), and micro RNA (miRNA), and they have been studied extensively [1]. Research on lncRNA is behind that on small RNA despite that recent transcriptome analysis has revealed that more than 120,000 lncRNAs are generated from the human genome [2–4].
    [Show full text]
  • The Srna Dicf Integrates Oxygen Sensing to Enhance Enterohemorrhagic Escherichia Coli Virulence Via Distinctive RNA Control Mechanisms
    The sRNA DicF integrates oxygen sensing to enhance enterohemorrhagic Escherichia coli virulence via distinctive RNA control mechanisms Elizabeth M. Melsona and Melissa M. Kendalla,1 aDepartment of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908 Edited by Susan Gottesman, National Institutes of Health, Bethesda, MD, and approved May 29, 2019 (received for review February 17, 2019) To establish infection, enteric pathogens integrate environmental major operons that encode a type three secretion system (T3SS) cues to navigate the gastrointestinal tract (GIT) and precisely and effectors (7, 10). The LEE-encoded ler gene encodes the control expression of virulence determinants. During passage master regulator of the LEE (11). EHEC uses the T3SS to through the GIT, pathogens encounter relatively high levels of translocate LEE- and non-LEE encoded effectors to hijack the oxygen in the small intestine before transit to the oxygen-limited host machinery, culminating in AE lesion formation, which is environment of the colon. However, how bacterial pathogens required for host colonization and overall pathogenesis (12). sense oxygen availability and coordinate expression of virulence The very low infectious dose of EHEC (as low as 50 colony traits is not resolved. Here, we demonstrate that enterohemor- forming units) is a major factor contributing to outbreaks (7) and rhagic Escherichia coli O157:H7 (EHEC) regulates virulence via the suggests that EHEC has evolved mechanisms to efficiently reg- oxygen-responsive small RNA DicF. Under oxygen-limited condi- ulate traits important for host colonization. Indeed, ler is a hub of tions, DicF enhances global expression of the EHEC type three transcriptional regulation that is responsive to numerous signals, secretion system, which is a key virulence factor required for host such as metabolites and hormones (13, 14).
    [Show full text]
  • HERPESVIRAL MICRORNAS by SUNANTHA SETHURAMAN A
    DEREGULATION OF HUMAN LONG NONCODING RNAS BY ONCOGENIC GAMMA- HERPESVIRAL MICRORNAS By SUNANTHA SETHURAMAN A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2017 © 2017 Sunantha Sethuraman To my parents, S Vijaya and K Sethuraman, and my brother S Srinivasan. ACKNOWLEDGMENTS I would like to acknowledge and thank all the people who have contributed directly and indirectly to my doctoral education and the work presented in this thesis. I would like to thank the members of the Renne laboratory, Dr. Rolf Renne, Dr. Peter Turner, Dr. Vaibhav Jain, Lauren Gay, Jackie Serfecz, Natalie Martinez and Merin Thomas, for making the lab an inspiring and fun environment. I am extremely thankful to my advisor Dr. Rolf Renne for being a mentor, a friend and a critique through the four years I have worked with him. I am also thankful to Dr. Peter Turner for carefully reviewing my manuscripts and this thesis. I would like to acknowledge the past members of the Renne laboratory, Dr. Irina Haecker and Dr. Hong Seok Choi. Dr. Irina Haecker is one of the most inspirational scientists I have met, who mentored me as a rotation student on the project that has now developed into my dissertation work. Dr. Hong Seok Choi, Dr. Vaibhav Jain and Lauren Gay have guided me with my experiments and made me a better scientist through the many scientific discussions. Jackie, Natalie and Merin have been amazing friends, and they make even a stressful day in the lab seem easy.
    [Show full text]
  • Regulatory Rnas in Staphylococcus Aureus: Function and Mechanism
    Regulatory RNAs in Staphylococcus aureus : Function and Mechanism Thao Nguyen Le Lam To cite this version: Thao Nguyen Le Lam. Regulatory RNAs in Staphylococcus aureus : Function and Mechanism. Agri- cultural sciences. Université Paris Sud - Paris XI, 2015. English. NNT : 2015PA112216. tel- 01424170 HAL Id: tel-01424170 https://tel.archives-ouvertes.fr/tel-01424170 Submitted on 2 Jan 2017 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 PARIS SACLAY - UNIVERSITÉ PARIS SUD UFR SCIENTIFIQUE D’ORSAY - ÉCOLE DOCTORALE STRUCTURE ET DYNAMIQUE DES SYSTÈMES VIVANTS Thèse Présentée pour obtenir le grade de DOCTEUR EN SCIENCES DE L’UNIVERSITÉ PARIS SUD Le 24 septembre 2015 Characterization of regulatory RNAs in Staphylococcus aureus Thao Nguyen LE LAM Directeur de thèse : Dr. Philippe BOULOC Laboratoire d’accueil : Signalisation et Réseaux de Régulations Bactériens Institute for Integrative Biology of the Cell (I2BC) CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Orsay, France Composition du jury : Président du jury Pr. Nicolas BAYAN Rapporteur Dr. Maude GUILLIER Rapporteur Dr. Francis REPOILA Examinateur Pr. Brice FELDEN Examinateur Dr. Nara FIGUEROA-BOSSI Directeur de thèse Dr. Philippe BOULOC 1 2 TABLE OF CONTENTS FIGURES AND TABLES .........................................................................................................
    [Show full text]
  • Differential RNA-Seq of Vibrio Cholerae Identifies the Vqmr Small RNA As a Regulator of Biofilm Formation
    Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA as a regulator of biofilm formation Kai Papenforta, Konrad U. Förstnerb, Jian-Ping Conga, Cynthia M. Sharmab, and Bonnie L. Basslera,c,1 aDepartment of Molecular Biology and cHoward Hughes Medical Institute, Princeton University, Princeton, NJ 08544; and bResearch Center for Infectious Diseases (ZINF), University of Würzburg, D-97080 Würzburg, Germany Contributed by Bonnie L. Bassler, January 6, 2015 (sent for review October 30, 2014; reviewed by Brian K. Hammer) Quorum sensing (QS) is a process of cell-to-cell communication ther diversified the possible uses of RNA-seq. One such that enables bacteria to transition between individual and collec- technology is called differential RNA sequencing (dRNA-seq), tive lifestyles. QS controls virulence and biofilm formation in Vib- in which enrichment of primary transcript termini can be com- rio cholerae, the causative agent of cholera disease. Differential bined with strand-specific generation of cDNA libraries to ach- V. cholerae RNA sequencing (RNA-seq) of wild-type and a locked ieve genome-wide identification of transcriptional start sites low-cell-density QS-mutant strain identified 7,240 transcriptional (TSSs) (10). ∼ start sites with 47% initiated in the antisense direction. A total of In this study, we applied dRNA-seq to the study of QS in 107 of the transcripts do not appear to encode proteins, suggest- V. cholerae. We performed dRNA-seq on wild-type V. cholerae ing they specify regulatory RNAs. We focused on one such tran- under conditions of low and high cell density. We performed script that we name VqmR.
    [Show full text]
  • Beyond DNA Origami: the Unfolding Prospects of Nucleic Acid Nanotechnology Nicole Michelotti,1 Alexander Johnson-Buck,2 Anthony J
    Opinion Beyond DNA origami: the unfolding prospects of nucleic acid nanotechnology Nicole Michelotti,1 Alexander Johnson-Buck,2 Anthony J. Manzo,2 and Nils G. Walter2,∗ Nucleic acid nanotechnology exploits the programmable molecular recognition properties of natural and synthetic nucleic acids to assemble structures with nanometer-scale precision. In 2006, DNA origami transformed the field by providing a versatile platform for self-assembly of arbitrary shapes from one long DNA strand held in place by hundreds of short, site-specific (spatially addressable) DNA ‘staples’. This revolutionary approach has led to the creation of a multitude of two-dimensional and three-dimensional scaffolds that form the basis for functional nanodevices. Not limited to nucleic acids, these nanodevices can incorporate other structural and functional materials, such as proteins and nanoparticles, making them broadly useful for current and future applications in emerging fields such as nanomedicine, nanoelectronics, and alternative energy. 2011 Wiley Periodicals, Inc. How to cite this article: WIREs Nanomed Nanobiotechnol 2012, 4:139–152. doi: 10.1002/wnan.170 INTRODUCTION Inspired by nature, researchers over the past four decades have explored nucleic acids as convenient ucleic acid nanotechnology has been utilized building blocks to assemble novel nanodevices.1,10 by nature for billions of years.1,2 DNA in N Because they are composed of only four different particular is chemically inert enough to reliably chemical building blocks and follow relatively store
    [Show full text]
  • An E. Coli Small Rna Inhibits Translation Initiation from a Distance
    AN E. COLI SMALL RNA INHIBITS TRANSLATION INITIATION FROM A DISTANCE BY MUHAMMAD SHAFIUL AZAM DISSERTATION Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Microbiology in the Graduate College of the University of Illinois at Urbana-Champaign, 2019 Urbana, Illinois Doctoral Committee: Professor Carin K. Vanderpool, Chair Professor Rachel J. Whitaker Professor James M. Slauch Professor Gary J. Olsen ABSTRACT In bacterial systems, small RNA (sRNA)-dependent translational repression is commonly carried out via sRNA-mRNA base pairing interactions near the Shine- Dalgarno (SD) region. In this so-called “canonical” mechanism, the sRNA is the direct regulator; it competes with the initiating ribosomes while the chaperone protein Hfq plays a supporting role. Contrary to this widely accepted model, there are a few examples in the literature where the sRNA base pairs far from the SD region, yet translation of the target mRNA is still inhibited. Mechanistically, non-canonical translation regulation is one of the least understood aspects of sRNA biology. In the targetome of an E. coli sRNA SgrS, manXYZ is a non-canonical target where SgrS base pairs at two distinct sites that are far from the SD regions of manX and manY , yet translation of these two cistrons are repressed by SgrS. We found that manX translation is controlled by a molecular role- reversal mechanism where an Hfq binding site is directly adjacent to the manX ribosome binding site. In this regulatory mechanism, SgrS plays the role of a guide to recruit Hfq to the appropriate binding site to form the silencing complex.
    [Show full text]