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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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. -
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. -
Intermolecular Base Stacking Mediates RNA-RNA Interaction in a Crystal
www.nature.com/scientificreports OPEN Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA Received: 12 April 2017 Accepted: 2 August 2017 chaperone Hfq Published: xx xx xxxx Eike C. Schulz1,2,5, Markus Seiler1,6, Cecilia Zuliani1, Franka Voigt1,7, Vladimir Rybin3, Vivian Pogenberg 2, Norbert Mücke4, Matthias Wilmanns2, Toby J. Gibson1 & Orsolya Barabas1 The RNA-chaperone Hfq catalyses the annealing of bacterial small RNAs (sRNAs) with target mRNAs to regulate gene expression in response to environmental stimuli. Hfq acts on a diverse set of sRNA- mRNA pairs using a variety of diferent molecular mechanisms. Here, we present an unusual crystal structure showing two Hfq-RNA complexes interacting via their bound RNA molecules. The structure contains two Hfq6:A18 RNA assemblies positioned face-to-face, with the RNA molecules turned towards each other and connected via interdigitating base stacking interactions at the center. Biochemical data further confrm the observed interaction, and indicate that RNA-mediated contacts occur between Hfq-RNA complexes with various (ARN)X motif containing RNA sequences in vitro, including the stress response regulator OxyS and its target, flA. A systematic computational survey also shows that phylogenetically conserved (ARN)X motifs are present in a subset of sRNAs, some of which share similar modular architectures. We hypothesise that Hfq can co-opt RNA-RNA base stacking, an unanticipated structural trick, to promote the interaction of (ARN)X motif containing sRNAs with target mRNAs on a “speed-dating” fashion, thereby supporting their regulatory function. Non-coding RNAs play key roles in regulating gene expression in all domains of life. -
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). -
The International Journal of Developmental Biology
Int. J. Dev. Biol. 53: 725-731 (2009) DEVELOPMENTALTHE INTERNATIONAL JOURNAL OF doi: 10.1387/ijdb.072575mr BIOLOGY www.intjdevbiol.com Molecular tools, classic questions - an interview with Clifford Tabin MICHAEL K. RICHARDSON* Institute of Biology, Leiden University, Leiden, The Netherlands ABSTRACT Clifford J. Tabin has made pioneering contributions to several fields in biology, including retroviruses, oncogenes, developmental biology and evolution. His father, a physicist who worked in the Manhattan project, kindled his interest in science. Cliff later chose to study biology and started his research career when the world of recombinant DNA was opening up. In Robert Weinberg’s lab, he constructed the Moloney leukaemia virus (MLV-tk), the first recombi- nant retrovirus that could be used as a eukaryotic vector. He also discovered the amino acid changes leading to the activation of Ras, the first human oncogene discovered. As an independent researcher, he began in the field of urodele limb regeneration, and described the expression of retinoic acid receptor and Hox genes in the blastema. Moving to the chick model, his was one of the labs that simultaneously cloned the first vertebrate hedgehog cognates and showed that sonic hedgehog functions as a morphogen in certain developmental contexts, in particular as an organizing activity during limb development. Comparative studies by Ann Burke in his lab showed that differences in boundaries of Hox gene expression across vertebrate phylogeny correlated with differences in skeletal morphology. The Tabin lab also discovered a genetic pathway responsible for mediating left-right asymmetry in vertebrates; helped uncover the pathways leading to dorsoventral limb patterning; made contributions to our understanding of skeletal morphogenesis and identified developmental mechanisms that might underpin the diversifica- tion of the beak in Darwin’s finches. -
Biologie Moléculaire De LA CELLULE Biologie Moléculaire De Sixième Édition
Sixième édition BRUCE ALEXANDER JULIAN DAVID MARTIN KEITH PETER ALBERTS JOHNSON LEWIS MORGAN RAFF ROBERTS WALTER Biologie moléculaire de LA CELLULE Biologie moléculaire de Sixième édition LA CELLULESixième édition Biologie moléculaire de moléculaire Biologie LA CELLULE LA BRUCE ALBERTS BRUCE ALBERTS ALEXANDER JOHNSON ALEXANDER JOHNSON JULIAN LEWIS JULIAN LEWIS DAVID MORGAN DAVID MORGAN MARTIN RAFF MARTIN RAFF KEITH ROBERTS KEITH ROBERTS PETER WALTER PETER WALTER -:HSMCPH=WU[\]\: editions.lavoisier.fr 978-2-257-20678-7 20678-Albers2017.indd 1-3 08/09/2017 11:09 Chez le même éditeur Culture de cellules animales, 3e édition, par G. Barlovatz-Meimon et X. Ronot Biochimie, 7e édition, par J. M. Berg, J. L. Tymoczko, L. Stryer L’essentiel de la biologie cellulaire, 3e édition, par B. Alberts, D. Bray, K. Hopkin, A. Johnson, A. J. Lewis, M. Ra", K. Roberts et P. Walter Immunologie, par L. Chatenoud et J.-F. Bach Génétique moléculaire humaine, 4e édition, par T. Strachan et A. Read Manuel de poche de biologie cellulaire, par H. Plattner et J. Hentschel Manuel de poche de microbiologie médicale, par F. H. Kayser, E. C. Böttger, P. Deplazes, O. Haller, A. Roers Atlas de poche de génétique, par E. Passarge Atlas de poche de biotechnologie et de génie génétique, par R.D. Schmid Les biosimilaires, par J.-L. Prugnaud et J.-H. Trouvin Bio-informatique moléculaire : une approche algorithmique (Coll. IRIS), par P. A. Pevzner et N. Puech Cycle cellulaire et cytométrie en "ux, par D. Grunwald, J.-F. Mayol et X. Ronot La cytométrie en "ux, par X. Ronot, D. -
Genetic Basis of Metabolic Evolution in the Cave Fish Astyanax Mexicanus
Genetic Basis of Metabolic Evolution in the Cave Fish Astyanax Mexicanus The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:40050145 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 Gene�c Basis of Metabolic Evolu�on in the Cave fish Astyanax mexicanus A disserta�on presented by Ariel Cacayuran Aspiras to The Division of Medical Sciences in par�al fulfillment of the requirements for the degree of Doctor of Philosophy in the subject of Biological and Biomedical Sciences Harvard University Cambridge, Massachuse�s May 2018 ©2018 by Ariel Cacayuran Aspiras All rights reserved. iii Dissertation Advisor: Dr. Clifford Tabin Ariel Cacayuran Aspiras Genetic Basis of Metabolic Evolution in the Cave fish Astyanax mexicanus Abstract Organisms evolve to thrive in new environments. In spite of the role metabolism plays in adaptation, the genetic basis for metabolic variation remains poorly understood. Here we use independently derived populations of Astyanax mexicanus, a Mexican tetra, to interrogate the genetic basis of extreme metabolic variation between surface and cave adapted populations. In the cave environment, food is much more scarce than in nutrient-rich rivers. Cave populations of Astyanax mexicanus rely on sporadic input of food from outside the cave. As a result, cave fish populations have evolved a suite of metabolic traits such as: starvation resistance, hyperphagia, hyperglycemia, and insulin resistance. -
RNA Interaction Studies; a Pathway to the Development of a Surface-Based Technology
RNA interaction studies; a pathway to the development of a surface-based technology Jack O. Phillips March 2016 The thesis is submitted in partial fulfilment of the requirements for the award of the degree of Doctor of Philosophy of the University of Portsmouth Declaration Whilst registered as a candidate for the above degree, I have not been registered for any other research award. The results and conclusions embodied in this thesis are the work of the named candidate and have not been submitted for any other academic award. Jack Owen Phillips Date 23/03/2016 Word count: 42011 words 2 Acknowledgements The preparation of this thesis and the work summarised within has been a task I could not have completed without the help of others and I would like to mention the names of those involved and to give them due thanks for their contributions. To my incredible supervisor Anastasia. The intense personal development and guidance you have given me over the last years is something I will forever be grateful for. Although I could not ever imagine doing another PhD again, if I did, I would only ever choose to do it under your supervision as I could not imagine a better supervisor. To my second supervisor, John. You have played your own part in my development and my biggest regret from my PhD will be not solving the VcHfq structure and publishing with you. I will not dwell on it, but remember how much I learned and that crystals don't mean structures (no matter how fast they grow). -
Famed Physicist, Attorney Tabin Dies at 92
San Diego Source > News > Famed physicist, attorney Tabin dies at 92 Thursday, September 6, 2012 Follow Us: Subscribe | Log In INFORMATION NEWS | SAN DIEGO SUBSCRIBE | LOG IN News Subscribe Today! + San Diego + California + National MarketInk Famed physicist, attorney Tabin dies at 92 Water By DOUG SHERWIN, The Daily Transcript Construction Wednesday, September 5, 2012 Defense Article Comments SourceBook Data Economy Education Renowned physicist and attorney Dr. Julius Tabin, who Finance worked on the Manhattan Project and later represented Government General Atomics and the Salk Institute, passed away last month at the age of 92. Health Hospitality He died of heart failure on Aug. 25. Law Dr. Tabin's work with General Atomics and the Salk Institute Real Estate led the Chicago-based intellectual property law firm Fitch, Technology Even Tabin & Flannery LLP to open an office in San Commentary Diego. Tabin was a partner at the firm for 56 years. "He was well thought of," said San Diego attorney Jim Schumann, a partner at Fitch Even. "He was a mentor to many of us, including myself. I wouldn't be here in San Diego (if not for Tabin). It was a loss of a friend." RESOURCES Born on Nov. 8, 1919, Tabin earned his Ph.D. in physics Attorney Directory from the University of Chicago. Following the completion of his doctoral thesis, he joined a small group working on the Awards & Programs Manhattan Project as a research assistant for Enrico Fermi. Business Center While gathering a sample during testing, Tabin was exposed to excessive radiation and was forced to leave the Digital Edition profession.