RNA-Dependent RNA Polymerase Encodingartifacts in Eukaryotic
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Specific Binding of Transposase to Terminal Inverted Repeats Of
Proc. Natl. Acad. Sci. USA Vol. 84, pp. 8220-8224, December 1987 Biochemistry Specific binding of transposase to terminal inverted repeats of transposable element Tn3 (transposon/DNA binding protein/DNase I "footprinting") HITOSHI ICHIKAWA*, KAORU IKEDA*, WILLIAM L. WISHARTt, AND EIICHI OHTSUBO*t *Institute of Applied Microbiology, University of Tokyo, Bunkyo-ku, Yayoi 1-1-1, Tokyo 113, Japan; and tDepartment of Molecular Biology, Princeton University, Princeton, NJ 08544 Communicated by Norman Davidson, July 27, 1987 ABSTRACT Tn3 transposase, which is required for trans- containing the Tn3 terminal regions when 8 mM ATP is position of Tn3, has been purified by a low-ionic-strength- present (14). precipitation method. Using a nitrocellulose filter binding In this paper, we study the interaction of Tn3 transposase, assay, we have shown that transposase binds to any restriction which has been purified by a low-ionic-strength-precipitation fragment. However, binding of the transposase to specific method, with DNA. We demonstrate that the purified fragments containing the terminal inverted repeat sequences of transposase is an ATP-independent DNA binding protein, Tn3 can be demonstrated by treatment of transposase-DNA which has interesting properties that may be involved in the complexes with heparin, which effectively removes the actual transposition event of Tn3. transposase bound to the other nonspecific fragments at pH 5-6. DNase I "footprinting" analysis showed that the MATERIALS AND METHODS transposase protects an inner 25-base-pair region of the 38- base-pair terminal inverted repeat sequence of Tn3. This Bacterial Strains and Plasmids. The bacterial strains used protection is not dependent on pH. -
Chapitre Quatre La Spécificité D'hôtes Des Virophages Sputnik
AIX-MARSEILLE UNIVERSITE FACULTE DE MEDECINE DE MARSEILLE ECOLE DOCTORALE DES SCIENCES DE LA VIE ET DE LA SANTE THESE DE DOCTORAT Présentée par Morgan GAÏA Né le 24 Octobre 1987 à Aubagne, France Pour obtenir le grade de DOCTEUR de l’UNIVERSITE AIX -MARSEILLE SPECIALITE : Pathologie Humaine, Maladies Infectieuses Les virophages de Mimiviridae The Mimiviridae virophages Présentée et publiquement soutenue devant la FACULTE DE MEDECINE de MARSEILLE le 10 décembre 2013 Membres du jury de la thèse : Pr. Bernard La Scola Directeur de thèse Pr. Jean -Marc Rolain Président du jury Pr. Bruno Pozzetto Rapporteur Dr. Hervé Lecoq Rapporteur Faculté de Médecine, 13385 Marseille Cedex 05, France URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095 Directeur : Pr. Didier RAOULT Avant-propos Le format de présentation de cette thèse correspond à une recommandation de la spécialité Maladies Infectieuses et Microbiologie, à l’intérieur du Master des Sciences de la Vie et de la Santé qui dépend de l’Ecole Doctorale des Sciences de la Vie de Marseille. Le candidat est amené à respecter des règles qui lui sont imposées et qui comportent un format de thèse utilisé dans le Nord de l’Europe permettant un meilleur rangement que les thèses traditionnelles. Par ailleurs, la partie introduction et bibliographie est remplacée par une revue envoyée dans un journal afin de permettre une évaluation extérieure de la qualité de la revue et de permettre à l’étudiant de commencer le plus tôt possible une bibliographie exhaustive sur le domaine de cette thèse. Par ailleurs, la thèse est présentée sur article publié, accepté ou soumis associé d’un bref commentaire donnant le sens général du travail. -
Viruses 2011, 3, 32-46; Doi:10.3390/V3010032 OPEN ACCESS Viruses ISSN 1999-4915
Viruses 2011, 3, 32-46; doi:10.3390/v3010032 OPEN ACCESS viruses ISSN 1999-4915 www.mdpi.com/journal/viruses Commentary Another Really, Really Big Virus James L. Van Etten Department of Plant Pathology, Nebraska Center for Virology, 205 Morrison Hall, University of Nebraska, Lincoln, NE 68583, USA; Email: [email protected]; Tel. +1 402 472 3168. Received: 20 December 2010; in revised form: 13 January 2011 / Accepted: 14 January 2011 / Published: 18 January 2011 Abstract: Viruses with genomes larger than 300 kb and up to 1.2 Mb, which encode hundreds of proteins, are being discovered and characterized with increasing frequency. Most, but not all, of these large viruses (often referred to as giruses) infect protists that live in aqueous environments. Bioinformatic analyses of metagenomes of aqueous samples indicate that large DNA viruses are quite common in nature and await discovery. One issue that is perhaps not appreciated by the virology community is that large viruses, even those classified in the same family, can differ significantly in morphology, lifestyle, and gene complement. This brief commentary, which will mention some of these unique properties, was stimulated by the characterization of the newest member of this club, virus CroV (Fischer, M.G.; Allen, M.J.; Wilson, W.H.; Suttle, C.A. Giant virus with a remarkable complement of genes infects marine zooplankton. Proc. Natl. Acad. Sci. USA 2010, 107, 19508-19513 [1]). CroV has a 730 kb genome (with ~544 protein-encoding genes) and infects the marine microzooplankton Cafeteria roenbergensis producing a lytic infection. Keywords: giruses; NCLDV; huge viruses 1. -
A Sleeping Beauty Mutagenesis Screen Reveals a Tumor Suppressor Role for Ncoa2/Src-2 in Liver Cancer
A Sleeping Beauty mutagenesis screen reveals a tumor suppressor role for Ncoa2/Src-2 in liver cancer Kathryn A. O’Donnella,b,1,2, Vincent W. Kengc,d,e, Brian Yorkf, Erin L. Reinekef, Daekwan Seog, Danhua Fanc,h, Kevin A. T. Silversteinc,h, Christina T. Schruma,b, Wei Rose Xiea,b,3, Loris Mularonii,j, Sarah J. Wheelani,j, Michael S. Torbensonk, Bert W. O’Malleyf, David A. Largaespadac,d,e, and Jef D. Boekea,b,i,2 Departments of aMolecular Biology and Genetics, iOncology, jDivision of Biostatistics and Bioinformatics, and kPathology, and bThe High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21205; cMasonic Cancer Center, dDepartment of Genetics, Cell Biology, and Development, eCenter for Genome Engineering, and hBiostatistics and Bioinformatics Core, University of Minnesota, Minneapolis, MN 55455; fDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030; and gLaboratory of Experimental Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 AUTHOR SUMMARY Emerging data from cancer ge- functions are altered. This ap- fi nome-sequencing studies have Sleeping Beauty (SB) transposase proach identi ed at least 16 demonstrated that human genes/loci that contribute to liver tumors exhibit tremendous Transposon array with gene trap (GT) tumor development. complexity and heterogeneity in We next validated that the the number and nature of iden- genes identified in the SB screen tified mutations (1). Based on contribute to tumor initiation these findings, there is an in- SB mobilization and/or progression using in vitro creasing need for in vivo vali- and in vivo cancer model sys- dation of genes whose altered tems. -
RNA As a Source of Transposase for Sleeping Beauty-Mediated Gene Insertion and Expression in Somatic Cells and Tissues
doi:10.1016/j.ymthe.2005.10.014 SHORT COMMUNICATION RNA as a Source of Transposase for Sleeping Beauty-Mediated Gene Insertion and Expression in Somatic Cells and Tissues Andrew Wilber,1 Joel L. Frandsen,1 Jennifer L. Geurts,1 David A. Largaespada,1 Perry B. Hackett,1,2 and R. Scott McIvor1,* 1The Arnold and Mabel Beckman Center for Transposon Research, Gene Therapy Program, Institute of Human Genetics, and Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA 2Discovery Genomics, Inc., Minneapolis, MN 55455, USA *To whom correspondence and reprint requests should be addressed at The Department of Genetics, Cell Biology, and Development, 6-160 Jackson Hall, 321 Church Street SE, University of Minnesota, Minneapolis, MN 55455, USA. Fax: +1 612 625 9810. E-mail: [email protected]. Available online 20 December 2005 Sleeping Beauty (SB) is a DNA transposon capable of mediating gene insertion and long-term expression in vertebrate cells when co-delivered with a source of transposase. In all previous reports of SB-mediated gene insertion in somatic cells, the transposase component has been provided by expression of a co-delivered DNA molecule that has the potential for integration into the host cell genome. Integration and continued expression of a gene encoding SB transposase could be problematic if it led to transposon re-mobilization and re-integration. We addressed this potential problem by supplying the transposase-encoding molecule in the form of mRNA. We show that transposase-encoding mRNA can effectively mediate transposition in vitro in HT1080 cells and in vivo in mouse liver following co-delivery with a recoverable transposon or with a luciferase transposon. -
Licensing RNA-Guided Genome Defense
TIBS-1023; No. of Pages 10 Review Recognizing the enemy within: licensing RNA-guided genome defense Phillip A. Dumesic and Hiten D. Madhani Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA How do cells distinguish normal genes from transpo- RNAi-related RNA silencing pathways are deeply con- sons? Although much has been learned about RNAi- served genome defense mechanisms that act in organisms related RNA silencing pathways responsible for genome from protist to human to recognize and suppress transpo- defense, this fundamental question remains. The litera- sons [8]. In all of these pathways, 20–30 nucleotide small ture points to several classes of mechanisms. In some RNAs act in complex with Argonaute family proteins to cases, double-stranded RNA (dsRNA) structures pro- silence complementary transcripts. Depending on the duced by transposon inverted repeats or antisense inte- pathway and context, silencing proceeds by a variety of gration trigger endogenous small interfering RNA mechanisms, which include RNA degradation, translation- (siRNA) biogenesis. In other instances, DNA features al repression, and the establishment of repressive histone associated with transposons – such as their unusual modifications [9,10]. The pathways also differ in the means copy number, chromosomal arrangement, and/or chro- by which they generate small RNAs. In the canonical RNAi matin environment – license RNA silencing. Finally, re- pathway, RNase-III-type Dicer enzymes convert long cent studies have identified improper transcript dsRNA into small interfering RNA (siRNA). In contrast, processing events, such as stalled pre-mRNA splicing, PIWI-interacting RNA (piRNA) pathways do not require as signals for siRNA production. -
Genomic Exploration of Individual Giant Ocean Viruses
The ISME Journal (2017) 11, 1736–1745 © 2017 International Society for Microbial Ecology All rights reserved 1751-7362/17 www.nature.com/ismej ORIGINAL ARTICLE Genomic exploration of individual giant ocean viruses William H Wilson1,2, Ilana C Gilg1, Mohammad Moniruzzaman3, Erin K Field1,4, Sergey Koren5, Gary R LeCleir3, Joaquín Martínez Martínez1, Nicole J Poulton1, Brandon K Swan1,6, Ramunas Stepanauskas1 and Steven W Wilhelm3 1Bigelow Laboratory for Ocean Sciences, Boothbay, ME, USA; 2School of Marine Science and Engineering, Plymouth University, Plymouth, UK; 3Department of Microbiology, The University of Tennessee, Knoxville, TN, USA; 4Department of Biology, Howell Science Complex, East Carolina University, Greenville, NC, USA; 5Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA and 6National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA Viruses are major pathogens in all biological systems. Virus propagation and downstream analysis remains a challenge, particularly in the ocean where the majority of their microbial hosts remain recalcitrant to current culturing techniques. We used a cultivation-independent approach to isolate and sequence individual viruses. The protocol uses high-speed fluorescence-activated virus sorting flow cytometry, multiple displacement amplification (MDA), and downstream genomic sequencing. We focused on ‘giant viruses’ that are readily distinguishable by flow cytometry. From a single- milliliter sample of seawater collected from off the dock at Boothbay Harbor, ME, USA, we sorted almost 700 single virus particles, and subsequently focused on a detailed genome analysis of 12. A wide diversity of viruses was identified that included Iridoviridae, extended Mimiviridae and even a taxonomically novel (unresolved) giant virus. -
Exploring the Interplay of Telomerase Reverse Transcriptase and Β-Catenin in Hepatocellular Carcinoma
cancers Review Exploring the Interplay of Telomerase Reverse Transcriptase and β-Catenin in Hepatocellular Carcinoma Srishti Kotiyal and Kimberley Jane Evason * Department of Oncological Sciences, Department of Pathology, and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-801-587-4606 Simple Summary: Liver cancer is one of the deadliest human cancers. Two of the most common molecular aberrations in liver cancer are: (1) activating mutations in the gene encoding β-catenin (CTNNB1); and (2) promoter mutations in telomerase reverse transcriptase (TERT). Here, we review recent findings regarding the interplay between TERT and β-catenin in order to better understand their role in liver cancer. Abstract: Hepatocellular carcinoma (HCC) is one of the deadliest human cancers. Activating muta- tions in the telomerase reverse transcriptase (TERT) promoter (TERTp) and CTNNB1 gene encoding β-catenin are widespread in HCC (~50% and ~30%, respectively). TERTp mutations are predicted to increase TERT transcription and telomerase activity. This review focuses on exploring the role of TERT and β-catenin in HCC and the current findings regarding their interplay. TERT can have contradictory effects on tumorigenesis via both its canonical and non-canonical functions. As a critical regulator of proliferation and differentiation in progenitor and stem cells, activated β-catenin drives HCC; however, inhibiting endogenous β-catenin can also have pro-tumor effects. Clinical studies revealed a significant concordance between TERTp and CTNNB1 mutations in HCC. In Citation: Kotiyal, S.; Evason, K.J. stem cells, TERT acts as a co-factor in β-catenin transcriptional complexes driving the expression Exploring the Interplay of Telomerase of WNT/β-catenin target genes, and β-catenin can bind to the TERTp to drive its transcription. -
Molecular Bases and Role of Viruses in the Human Microbiome
Review IMF YJMBI-64492; No. of pages: 15; 4C: 7 Molecular Bases and Role of Viruses in the Human Microbiome Shira R. Abeles 1 and David T. Pride 1,2 1 - Department of Medicine, University of California, San Diego, CA 92093, USA 2 - Department of Pathology, University of California, San Diego, CA 92093, USA Correspondence to David T. Pride: Department of Pathology, University of California, San Diego, CA 92093, USA. [email protected] http://dx.doi.org/10.1016/j.jmb.2014.07.002 Edited by J. L. Sonnenburg Abstract Viruses are dependent biological entities that interact with the genetic material of most cells on the planet, including the trillions within the human microbiome. Their tremendous diversity renders analysis of human viral communities (“viromes”) to be highly complex. Because many of the viruses in humans are bacteriophage, their dynamic interactions with their cellular hosts add greatly to the complexities observed in examining human microbial ecosystems. We are only beginning to be able to study human viral communities on a large scale, mostly as a result of recent and continued advancements in sequencing and bioinformatic technologies. Bacteriophage community diversity in humans not only is inexorably linked to the diversity of their cellular hosts but also is due to their rapid evolution, horizontal gene transfers, and intimate interactions with host nucleic acids. There are vast numbers of observed viral genotypes on many body surfaces studied, including the oral, gastrointestinal, and respiratory tracts, and even in the human bloodstream, which previously was considered a purely sterile environment. The presence of viruses in blood suggests that virome members can traverse mucosal barriers, as indeed these communities are substantially altered when mucosal defenses are weakened. -
A Survey of Transposable Element Classification Systems Â
Molecular Phylogenetics and Evolution 86 (2015) 90–109 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev Review A survey of transposable element classification systems – A call for a fundamental update to meet the challenge of their diversity and complexity ⇑ ⇑ Benoît Piégu a, Solenne Bire a,b, Peter Arensburger a,c, , Yves Bigot a, a UMR INRA-CNRS 7247, PRC, Centre INRA de Nouzilly, 37380 Nouzilly, France b Institute of Biotechnology, University of Lausanne, Center for Biotechnology UNIL-EPFL, 1015 Lausanne, Switzerland c Biological Sciences Department, California State Polytechnic University, Pomona, CA 91768, United States article info abstract Article history: The increase of publicly available sequencing data has allowed for rapid progress in our understanding of Received 24 December 2014 genome composition. As new information becomes available we should constantly be updating and Revised 11 March 2015 reanalyzing existing and newly acquired data. In this report we focus on transposable elements (TEs) Accepted 12 March 2015 which make up a significant portion of nearly all sequenced genomes. Our ability to accurately identify Available online 20 March 2015 and classify these sequences is critical to understanding their impact on host genomes. At the same time, as we demonstrate in this report, problems with existing classification schemes have led to significant Keywords: misunderstandings of the evolution of both TE sequences and their host genomes. In a pioneering pub- Transposon lication Finnegan (1989) proposed classifying all TE sequences into two classes based on transposition Mobility Host range mechanisms and structural features: the retrotransposons (class I) and the DNA transposons (class II). -
Characterization of the First Cultured Representative of Verrucomicrobia Subdivision 5 Indicates the Proposal of a Novel Phylum
The ISME Journal (2016) 10, 2801–2816 OPEN © 2016 International Society for Microbial Ecology All rights reserved 1751-7362/16 www.nature.com/ismej ORIGINAL ARTICLE Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum Stefan Spring1, Boyke Bunk2, Cathrin Spröer3, Peter Schumann3, Manfred Rohde4, Brian J Tindall1 and Hans-Peter Klenk1,5 1Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; 2Department Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; 3Department Central Services, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany and 4Central Facility for Microscopy, Helmholtz-Centre of Infection Research, Braunschweig, Germany The recently isolated strain L21-Fru-ABT represents moderately halophilic, obligately anaerobic and saccharolytic bacteria that thrive in the suboxic transition zones of hypersaline microbial mats. Phylogenetic analyses based on 16S rRNA genes, RpoB proteins and gene content indicated that strain L21-Fru-ABT represents a novel species and genus affiliated with a distinct phylum-level lineage originally designated Verrucomicrobia subdivision 5. A survey of environmental 16S rRNA gene sequences revealed that members of this newly recognized phylum are wide-spread and ecologically important in various anoxic environments ranging from hypersaline sediments to wastewater and the intestine of animals. Characteristic phenotypic traits of the novel strain included the formation of extracellular polymeric substances, a Gram-negative cell wall containing peptidoglycan and the absence of odd-numbered cellular fatty acids. Unusual metabolic features deduced from analysis of the genome sequence were the production of sucrose as osmoprotectant, an atypical glycolytic pathway lacking pyruvate kinase and the synthesis of isoprenoids via mevalonate. -
Molecular Architecture of a Eukaryotic DNA Transposase
ARTICLES Molecular architecture of a eukaryotic DNA transposase Alison B Hickman1, Zhanita N Perez1, Liqin Zhou2, Primrose Musingarimi1,4, Rodolfo Ghirlando1, Jenny E Hinshaw3, Nancy L Craig2 & Fred Dyda1 Mobile elements and their inactive remnants account for large proportions of most eukaryotic genomes, where they have had central roles in genome evolution. Over 50 years ago, McClintock reported a form of stress-induced genome instability in maize in which discrete DNA segments move between chromosomal locations. Our current mechanistic understanding of enzymes catalyzing transposition is largely limited to prokaryotic transposases. The Hermes transposon from the housefly is part of the eukaryotic hAT superfamily that includes hobo from Drosophila, McClintock’s maize Activator and Tam3 from snapdragon. We http://www.nature.com/nsmb report here the three-dimensional structure of a functionally active form of the transposase from Hermes at 2.1-A˚ resolution. The Hermes protein has some structural features of prokaryotic transposases, including a domain with a retroviral integrase fold. However, this domain is disrupted by the insertion of an additional domain. Finally, transposition is observed only when Hermes assembles into a hexamer. Genome sequencing efforts have yielded many unanticipated results, particularly interested in the biochemistry and mechanism of the among them the realization that large proportions of many eukaryotic Hermes hAT transposase from the housefly Musca domestica7. Hermes genomes originated as mobile elements. These mobile elements are is a 2,749-bp element that contains 17-bp terminal inverted repeats discrete pieces of DNA that can either move from one place to another and encodes a 70-kDa transposase7.