Intermolecular Base Stacking Mediates RNA-RNA Interaction in a Crystal
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Compaction and Condensation of DNA Mediated by the C-Terminal Domain Of
i “CTR-NAR” — 2017/5/3 — 11:51 — page 1 — #1 i i i Published online 03/05/2017 Nucleic Acids Research, 2017, Vol. 00, No. 00 1–10 doi:10.1093/nar/gkn000 Compaction and condensation of DNA mediated by the C-terminal domain of Hfq 1, 2, 1,3 4 Antoine Malabirade †, Kai Jiang †, Krzysztof Kubiak , Alvaro Diaz-Mendoza , Fan Liu 2, Jeroen A. van Kan 2, Jean-François Berret 4, 1,4, 2, Véronique Arluison ú, and Johan R.C. van der Maarel ú 1Laboratoire Léon Brillouin, CEA, CNRS, Université Paris Saclay, 91191 Gif-sur-Yvette, France; 2Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542; 3Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; 4Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France. ABSTRACT it is usually needed to mediate post-transcriptional stress-response with small noncoding RNA (sRNA). This Hfq is a bacterial protein that is involved in several regulatory mechanism is based on the hybridisation of aspects of nucleic acids metabolism. It has been sRNA to its target mRNA. Accordingly, the majority described as one of the nucleoid associated proteins of known sRNA interacts nearby the ribosome binding shaping the bacterial chromosome, although it is site to prevent initiation of translation and thus favours better known to influence translation and turnover mRNA decay (4, 5, 6). Few studies have shed light of cellular RNAs. Here, we explore the role of on the importance of Hfq in DNA metabolism. It has Escherichia coli Hfq’s C-terminal domain in the been suggested that Hfq affects plasmid replication and compaction of double stranded DNA. -
Producing Hfq/Sm Proteins and Srnas for Structural and Biophysical Studies of Ribonucleoprotein Assembly
bioRxiv preprint doi: https://doi.org/10.1101/150672; this version posted June 16, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. Producing Hfq/Sm Proteins and sRNAs for Structural and Biophysical Studies of Ribonucleoprotein Assembly Kimberly A. Stanek* and Cameron Mura* Author affiliations & correspondence: Department of Chemistry; University of Virginia; Charlottesville, VA 22904 USA *Correspondence can be addressed to KS ([email protected]) or CM ([email protected]). Document information: Last modified: 15 June 2017 Running title: Producing Hfq•RNA Complexes for Structural Studies Abbreviations: 3D, three-dimensional; AU, asymmetric unit; CV, column volume; DEPC, diethyl pyrocarbonate; HDV, hepatitis δ virus; IMAC, immobilized metal affinity chroma- tography; MW, molecular weight; MWCO, molecular weight cut-off; nt, nucleotide; PDB, Protein Data Bank; RNP, ribonucleoprotein; RT, room temperature Additional notes: The main text is accompanied by 2 figures and 1 table. Journal format: Methods in Molecular Biology (Springer Protocols series); this volume is entitled "Bacterial Regulatory RNA: Methods and Protocols"; an author guide is linked at http://www.springer.com/series/7651 bioRxiv preprint doi: https://doi.org/10.1101/150672; this version posted June 16, 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 Hfq is a bacterial RNA-binding protein that plays key roles in the post–transcriptional regulation of gene expression. Like other Sm proteins, Hfq assembles into toroidal discs that bind RNAs with varying affin- ities and degrees of sequence specificity. -
Characterization of E Coli Hfq Structure and Its Rna Binding Properties
CHARACTERIZATION OF E COLI HFQ STRUCTURE AND ITS RNA BINDING PROPERTIES A thesis Presented to The Academic Faculty By Xueguang Sun In partial Fulfillment Of the Requirement for the Degree Doctor of Philosophy in the School of Biology Georgia Institute of Technology May 2006 Copyright Ó 2006 by Xueguang Sun CHARACTERIZATION OF E COLI HFQ STRUCTURE AND ITS RNA BINDING PROPERTIES Approved by : Roger M. Wartell, Chair Stephen C. Harvey School of Biology School of Biology Georgia Institute of Technology Georgia Institute of Technology Yury O. Chernoff Stephen Spiro School of Biology School of Biology Georgia Institute of Technology Georgia Institute of Technology Loren D Willimas School of Chemistry and Biochmestry Georgia Institute of Technology Date Approved: November 29 2005 To my family, for their constant love and support. iii ACKNOWLEDGEMENTS There are many people I would like to thank and acknowledge for their support and help during my five-year Ph.D. study. First and foremost, I would like to thank my advisor, Dr Roger Wartell, for his guidance and assistance throughout this chapter of my career. His constantly open door, scientific insight and perspective, and technical guidance have been integral to furthering my scientific education. He also provided knowledgeable recommendations and multi-faceted support in my personal life and bridged me to a culture which I have never experienced. Without him, it would be impossible to accomplish this thesis work. I would like to acknowledge Dr. Stephen Harvey, Dr. Yury Chernoff, Dr. Stephen Spiro and Dr. Loren Williams for being on my thesis committee and helpful discussion in structural modeling. -
A Method for Producing an L-Amino Acid Using Bacterium of The
(19) & (11) EP 2 055 771 A2 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 06.05.2009 Bulletin 2009/19 C12N 1/20 (2006.01) C12P 13/04 (2006.01) (21) Application number: 08171633.4 (22) Date of filing: 22.03.2007 (84) Designated Contracting States: (72) Inventors: AT BE BG CH CY CZ DE DK EE ES FI FR GB GR • Rybak, Konstantin Vyacheslavovich HU IE IS IT LI LT LU LV MC MT NL PL PT RO SE Moscow 117149 (RU) SI SK TR • Skorokhodova, Aleksandra Yurievna Moscow 115304 (RU) (30) Priority: 23.03.2006 RU 2006109062 • Voroshilova, Elvira Borisovna 23.03.2006 RU 2006109063 Moscow 117648 (RU) 11.04.2006 RU 2006111808 • Gusyatiner, Mikhail Markovich 11.04.2006 RU 2006111809 Moscow 117648 (RU) 04.05.2006 RU 2006115067 • Leonova, Tatyana Viktorovna 04.05.2006 RU 2006115068 Moscow 123481 (RU) 04.05.2006 RU 2006115070 • Kozlov, Yury Ivanovich 02.06.2006 RU 2006119216 Deceased (RU) 04.07.2006 RU 2006123751 • Ueda, Takuji 16.01.2007 RU 2007101437 Kanagawa 210-8681 (JP) 16.01.2007 RU 2007101440 (74) Representative: HOFFMANN EITLE (62) Document number(s) of the earlier application(s) in Patent- und Rechtsanwälte accordance with Art. 76 EPC: Arabellastrasse 4 07740190.9 / 2 004 803 81925 München (DE) (71) Applicant: Ajinomoto Co., Inc. Remarks: Tokyo 104-8315 (JP) This application was filed on 15-12-2008 as a divisional application to the application mentioned under INID code 62. (54) A method for producing an L-amino acid using bacterium of the Enterobacteriaceae family with attenuated expression of a gene coding for small RNA (57) The present invention provides a method for pro- to genus Escherichia or Pantoea, which has been mod- ducing an L-amino acid using a bacterium of the Entero- ified to attenuate expression of a gene coding for sRNA. -
And Plasmid-Borne Resistance of Escherichia Coli Hfq Mutants to High Concentrations of Various Antibiotics
International Journal of Molecular Sciences Article Differential Chromosome- and Plasmid-Borne Resistance of Escherichia coli hfq Mutants to High Concentrations of Various Antibiotics Lidia Gaffke † , Krzysztof Kubiak †, Zuzanna Cyske and Grzegorz W˛egrzyn* Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; [email protected] (L.G.); [email protected] (K.K.); [email protected] (Z.C.) * Correspondence: [email protected]; Tel.: +48-58-523-6024 † These authors contributed equally to this work. Abstract: The Hfq protein is a bacterial RNA chaperone, involved in many molecular interactions, including control of actions of various small RNA regulatory molecules. We found that the presence of Hfq was required for survival of plasmid-containing Escherichia coli cells against high concentrations of chloramphenicol (plasmid p27cmr), tetracycline (pSC101, pBR322) and ampicillin (pBR322), as hfq+ strains were more resistant to these antibiotics than the hfq-null mutant. In striking contrast, production of Hfq resulted in low resistance to high concentrations of kanamycin when the antibiotic- resistance marker was chromosome-borne, with deletion of hfq resulting in increasing bacterial survival. These results were observed both in solid and liquid medium, suggesting that antibiotic resistance is an intrinsic feature of these strains rather than a consequence of adaptation. Despite its major role as RNA chaperone, which also affects mRNA stability, Hfq was not found to significantly affect kan and tet mRNAs turnover. Nevertheless, kan mRNA steady-state levels were higher in Citation: Gaffke, L.; Kubiak, K.; the hfq-null mutant compared to the hfq+ strain, suggesting that Hfq can act as a repressor of kan Cyske, Z.; W˛egrzyn,G. -
Review Article Proteins with RNA Chaperone Activity: a World of Diverse Proteins with a Common Task—Impediment of RNA Misfolding
Hindawi Publishing Corporation Biochemistry Research International Volume 2011, Article ID 532908, 11 pages doi:10.1155/2011/532908 Review Article Proteins with RNA Chaperone Activity: A World of Diverse Proteins with a Common Task—Impediment of RNA Misfolding Katharina Semrad Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9/5, 1030 Vienna, Austria Correspondence should be addressed to Katharina Semrad, [email protected] Received 19 July 2010; Revised 12 November 2010; Accepted 19 November 2010 Academic Editor: Andrei Surguchov Copyright © 2011 Katharina Semrad. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Proteins with RNA chaperone activity are ubiquitous proteins that play important roles in cellular mechanisms. They prevent RNA from misfolding by loosening misfolded structures without ATP consumption. RNA chaperone activity is studied in vitro and in vivo using oligonucleotide- or ribozyme-based assays. Due to their functional as well as structural diversity, a common chaperoning mechanism or universal motif has not yet been identified. A growing database of proteins with RNA chaperone activity has been established based on evaluation of chaperone activity via the described assays. Although the exact mechanism is not yet understood, it is more and more believed that disordered regions within proteins play an important role. This possible mechanism and which proteins were found to possess RNA chaperone activity are discussed here. 1. Introduction In the cellular environment, RNA molecules do not appear as “naked” nucleic acids but always are found in Among all biological macromolecules, RNAs represent one conjunction with proteins. -
Back Matter (PDF)
JOBNAME: RNA 12#12 2006 PAGE: 1 OUTPUT: November 10 14:27:49 2006 csh/RNA/125784/reviewers-index RNA: Reviewers for Volume 12, 2006 The editors wish to thank the following individuals whose efforts in reviewing papers for RNA in the past year are greatly appreciated. Juan Alfonzo Donald Burke Fritz Eckstein Carol Greider Frederic Allain John Burke Martin Egli Sam Griffiths-Jones Emily Allen Samuel Butcher Sherif Abou Elela Claudio Gualerzi Sidney Altman Ronald Emeson Alexander Gultyaev Victor Ambros Gail Emilsson Samuel Gunderson Mark Caprara James Anderson Luis Enjuanes Christine Guthrie Paul Anderson Massimo Caputi Anne Ephrussi Raul Andino James Carrington Jay Evans Charles Carter Gordon Hager Mohammed Ararzguioui Eduardo Eyras Paul Hagerman Manuel Ares Richard Carthew Jamie Cate Stephen Hajduk Jean Armengaud Dan Fabris Jean Cavarelli Kathleen Hall Brandon Ason Philip Farabaugh Guillaume Chanfreau Michelle Hamm Gil Ast Jean Feagin Tien-Hsien Chang Scott Hammond Pascal Auffinger Martha Fedor Lawrence Chasin Maureen Hanson Johanna Avis Yuriy Fedorov Chang-Zheng Chen Eoghan Harrington Juli Feigon Eric Christian Michael Harris James Fickett Kristian Baker Christine Clayton Roland Hartmann Carol Fierke Alice Barkan Peter Clote Stephen Harvey Susan Baserga Witold Filipowicz Jeffery Coller Michelle Hastings Brenda Bass Andrew Fire Kathleen Collins Christopher Hayes Christoph Flamm David Bartel Richard Collins Christopher Hellen William Folk Robert Batey Elena Conti Matthias Hentze Maurille Fournier Peter Becker Howard Cooke Thomas Herdegen -
FARE2021WINNERS Sorted by Institute
FARE2021WINNERS Sorted By Institute Swati Shah Postdoctoral Fellow CC Radiology/Imaging/PET and Neuroimaging Characterization of CNS involvement in Ebola-Infected Macaques using Magnetic Resonance Imaging, 18F-FDG PET and Immunohistology The Ebola (EBOV) virus outbreak in Western Africa resulted in residual neurologic abnormalities in survivors. Many case studies detected EBOV in the CSF, suggesting that the neurologic sequelae in survivors is related to viral presence. In the periphery, EBOV infects endothelial cells and triggers a “cytokine stormâ€. However, it is unclear whether a similar process occurs in the brain, with secondary neuroinflammation, neuronal loss and blood-brain barrier (BBB) compromise, eventually leading to lasting neurological damage. We have used in vivo imaging and post-necropsy immunostaining to elucidate the CNS pathophysiology in Rhesus macaques infected with EBOV (Makona). Whole brain MRI with T1 relaxometry (pre- and post-contrast) and FDG-PET were performed to monitor the progression of disease in two cohorts of EBOV infected macaques from baseline to terminal endpoint (day 5-6). Post-necropsy, multiplex fluorescence immunohistochemical (MF-IHC) staining for various cellular markers in the thalamus and brainstem was performed. Serial blood and CSF samples were collected to assess disease progression. The linear mixed effect model was used for statistical analysis. Post-infection, we first detected EBOV in the serum (day 3) and CSF (day 4) with dramatic increases until euthanasia. The standard uptake values of FDG-PET relative to whole brain uptake (SUVr) in the midbrain, pons, and thalamus increased significantly over time (p<0.01) and positively correlated with blood viremia (p≤0.01). -
Functional Characterization of Bacterial Srnas Using a Network Biology Approach
Functional characterization of bacterial sRNAs using a network biology approach Sheetal R. Modia,1, Diogo M. Camachoa,1, Michael A. Kohanskia,b, Graham C. Walkerc, and James J. Collinsa,b,d,2 aThe Howard Hughes Medical Institute, Department of Biomedical Engineering, and Center for BioDynamics, Boston University, Boston, MA 02215; bBoston University School of Medicine, Boston, MA 02118; cDepartment of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; and dThe Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115 Edited* by Susan Gottesman, National Cancer Institute, Bethesda, MD, and approved August 3, 2011 (received for review March 19, 2011) Small RNAs (sRNAs) are important components of posttranscriptional sRNAs in bacteria (see Fig. S1 and SI Materials and Methods for regulation. These molecules are prevalent in bacterial and eukaryotic a more complete overview of this method). As a first step, we organisms, and involved in a variety of responses to environmental used the Context Likelihood of Relatedness (CLR) algorithm stresses. The functional characterization of sRNAs is challenging and (16) to infer the sRNA regulatory network in E. coli. The CLR requires highly focused and extensive experimental procedures. algorithm is an inference approach based on mutual information fi Here, using a network biology approach and a compendium of gene and allows for the identi cation of regulatory relationships be- expression profiles, we predict functional roles and regulatory inter- tween biomolecular entities. This algorithm previously has been actions for sRNAs in Escherichia coli. We experimentally validate pre- used to infer transcriptional regulatory networks (17) by exam- dictions for three sRNAs in our inferred network: IsrA, GlmZ, and ining the functional relationships between transcription factors GcvB. -
Protein Targeting Via Mrna in Bacteria☆
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Biochimica et Biophysica Acta 1843 (2014) 1457–1465 Contents lists available at ScienceDirect Biochimica et Biophysica Acta journal homepage: www.elsevier.com/locate/bbamcr Protein targeting via mRNA in bacteria☆ Shanmugapriya Kannaiah, Orna Amster-Choder ⁎ Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University – Faculty of Medicine, P.O.Box 12272, Jerusalem 91120, Israel article info abstract Article history: Proteins of all living organisms must reach their subcellular destination to sustain the cell structure and function. Received 8 September 2013 The proteins are transported to one of the cellular compartments, inserted into the membrane, or secreted across Received in revised form 9 November 2013 the membrane to the extracellular milieu. Cells have developed various mechanisms to transport proteins across Accepted 11 November 2013 membranes, among them localized translation. Evidence for targeting of Messenger RNA for the sake of transla- Available online 19 November 2013 tion of their respective protein products at specific subcellular sites in many eukaryotic model organisms have been accumulating in recent years. Cis-acting RNA localizing elements, termed RNA zip-codes, which are embed- Keywords: Protein targeting ded within the mRNA sequence, are recognized by RNA-binding proteins, which in turn interact with motor pro- Protein export teins, thus coordinating the intracellular transport of the mRNA transcripts. Despite the rareness of conventional RNA localization organelles, first and foremost a nucleus, pieces of evidence for mRNA localization to specific subcellular domains, RNA zip-code where their protein products function, have also been obtained for prokaryotes. -
Rnase III Participates in Gady-Dependent Cleavage of the Gadx-Gadw Mrna
doi:10.1016/j.jmb.2010.12.009 J. Mol. Biol. (2011) 406,29–43 Contents lists available at www.sciencedirect.com Journal of Molecular Biology journal homepage: http://ees.elsevier.com.jmb RNase III Participates in GadY-Dependent Cleavage of the gadX-gadW mRNA Jason A. Opdyke†, Elizabeth M. Fozo†, Matthew R. Hemm and Gisela Storz⁎ Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA Received 28 August 2010; The adjacent gadX and gadW genes encode transcription regulators that are received in revised form part of a complex regulatory circuit controlling the Escherichia coli response 2 December 2010; to acid stress. We previously showed that the small RNA GadY positively accepted 3 December 2010 regulates gadX mRNA levels. The gadY gene is located directly downstream Available online of the gadX coding sequence on the opposite strand of the chromosome. We 13 December 2010 now report that gadX is transcribed in an operon with gadW, although this full-length mRNA does not accumulate. Base pairing of the GadY small Edited by M. Gottesman RNA with the intergenic region of the gadX-gadW mRNA results in directed processing events within the region of complementarity. The resulting two Keywords: halves of the cleaved mRNA accumulate to much higher levels than the antisense RNA; unprocessed mRNA. We examined the ribonucleases required for this acid response; processing, and found that multiple enzymes are involved in the GadY- ribonuclease; directed cleavage including the double-strand RNA-specific endoribonu- OOP RNA clease RNase III. Published by Elsevier Ltd. -
Regulatory Rnas in Bacteria
CORE Metadata, citation and similar papers at core.ac.uk Provided by Elsevier - Publisher Connector Leading Edge Review Regulatory RNAs in Bacteria Lauren S. Waters1 and Gisela Storz1,* 1Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA *Correspondence: [email protected] DOI 10.1016/j.cell.2009.01.043 Bacteria possess numerous and diverse means of gene regulation using RNA molecules, including mRNA leaders that affect expression in cis, small RNAs that bind to proteins or base pair with target RNAs, and CRISPR RNAs that inhibit the uptake of foreign DNA. Although examples of RNA regu- lators have been known for decades in bacteria, we are only now coming to a full appreciation of their importance and prevalence. Here, we review the known mechanisms and roles of regulatory RNAs, highlight emerging themes, and discuss remaining questions. Introduction logical responses were not initially appreciated. In 2001–2002, RNA regulators in bacteria are a heterogeneous group of mole- four groups reported the identification of many new small cules that act by various mechanisms to modulate a wide range RNAs through systematic computational searches for conserva- of physiological responses. One class comprises riboswitches, tion and orphan promoter and terminator sequences in the inter- which are part of the mRNAs that they regulate. These leader genic regions of E. coli (reviewed in Livny and Waldor, 2007). sequences fold into structures amenable to conformational Additional RNAs were discovered by direct detection using changes upon the binding of small molecules. Riboswitches cloning-based techniques or microarrays with probes in inter- thus sense and respond to the availability of various nutrients genic regions (reviewed in Altuvia, 2007).