DOCSLIB.ORG

Viruses in the North Sea: Viromics and Prophage Genomics

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

VIRUSES IN THE NORTH SEA: VIROMICS AND PROPHAGE GENOMICS by Alexa Garin-Fernandez a Thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Marine Microbiology Thesis Committee: Prof. Dr. Frank Oliver GLÖCKNER (chair) Alfred Wegener Institute for Marine and Polar Research Jacobs University Bremen Dr. Antje WICHELS Alfred Wegener Institute for Marine and Polar Research Prof. Dr. Matthias ULLRICH Jacobs University Bremen Dr. Gunnar GERDTS Alfred Wegener Institute for Marine and Polar Research Date of Defense: October 30, 2019 Department of Life Sciences and Chemistry, Jacobs University Bremen II STATUTORY DECLARATION Family Name, Given/First Name Garin Fernandez, Alexa Matriculationnumber 20331313 What kind of thesis are you submitting: PhD Thesis Bachelor‐, Master‐ or PhD‐Thesis English: Declaration of Authorship I hereby declare that the thesis submitted was created and written solely by myself without any external support. Any sources, direct or indirect, are marked as such. I am aware of the fact that the contents of the thesis in digital form may be revised with regard to usage of unauthorized aid as well as whether the whole or parts of it may be identified as plagiarism. I do agree my work to be entered into a database for it to be compared with existing sources, where it will remain in order to enable further comparisons with future theses. This does not grant any rights of reproduction and usage, however. The Thesis has been written independently and has not been submitted at any other university for the conferral of a PhD degree; neither has the thesis been previously published in full. German: Erklärung der Autorenschaft (Urheberschaft) Ich erkläre hiermit, dass die vorliegende Arbeit ohne fremde Hilfe ausschließlich von mir erstellt und geschrieben worden ist. Jedwede verwendeten Quellen, direkter oder indirekter Art, sind als solche kenntlich gemacht worden. Mir ist die Tatsache bewusst, dass der Inhalt der Thesis in digitaler Form geprüft werden kann im Hinblick darauf, ob es sich ganz oder in Teilen um ein Plagiat handelt. Ich bin damit einverstanden, dass meine Arbeit in einer Datenbank eingegeben werden kann, um mit bereits bestehenden Quellen verglichen zu werden und dort auch verbleibt, um mit zukünftigen Arbeiten verglichen werden zu können. Dies berechtigt jedoch nicht zur Verwendung oder Vervielfältigung. Diese Arbeit wurde in der vorliegenden Form weder einer anderen Prüfungsbehörde vorgelegt noch wurde das Gesamtdokument bisher veröffentlicht. ………………………………………………………………………………………………………………………………………… Date, Signature III IV “What is essential is invisible to the eye” Le Petit Prince (1943) V VI THESIS ABSTRACT Viruses are the most abundant biological entity on Earth, dominating the marine environment. Despite their small size, viruses have an enormous influence on microbial population dynamics, due to lysis and horizontal gene transfer. Due the high abundance of their hosts, bacteriophages or phages comprise the majority of viruses and also provide the largest reservoirs of unexplored genetic diversity in marine environments. The rise of Next Generation Sequencing (NGS) techniques brings new opportunities to investigate the marine virus community. However, there is no current statutory pipeline applied in marine phage ecology. Therefore, this thesis proposes a virus-specific pipeline based on the integration of existing tools and state of the art techniques. The developed pipeline was applied to accomplish the two research aims of this thesis: (1) to analyze the virus community in the North Sea with viromics, and (2) to characterize lysogenic phages from potentially pathogenic Vibrio species. For the first part of this thesis, the virus community of four sampling stations were described using virus metagenomics (viromics). The results show that the virus community is dominated by phages and they are not evenly distributed throughout the North Sea. In general, the coastal virus community was genetically more diverse than the open sea community. The influence of riverine inflow and currents, for instance the English Channel flow affects the genetic virus diversity with the community carrying genes from a variety of metabolic pathways and other functions. These results offer the first insights in the virus community in the North Sea using viromics and shows the variation in virus diversity and the genetic information moved from coastal to open sea areas. Although phages of emerging Vibrio species were identified in low percentage in the North Sea virome, is possible they are lysogenic phages integrated into the host genome. The seawater temperature rise promotes the growth of potentially human pathogenic Vibrio species. In the North Sea, V. parahaemolyticus and non-O1/O139 V. cholerae have been isolated and characterized. These strains contain prophages that may contribute to the emergence of pathogenic strains in the marine environment (40 % of tested isolates). The genome structure and possible biological functions of four lysogenic phages were described in the second part of this thesis. The phages from V. parahaemolyticus (two tailed phages, one filamentous phage) and V. cholerae (one tailed phages) can integrate into their host genome and might have a role in pathogenicity. This study provides new insights with respect to the presence of lysogenic phages in environmental Vibrio strains, which might have a role in the emergence of new pathogenic strains in the North Sea. This thesis represents an exemplary study of the virus community in the North Sea, with special emphasis on the marine phages. The settled virus-specific pipeline as well as the obtained insights will contribute to extend the study of the virus diversity dynamics in other marine areas, including to estimate the abundance and functional diversity of novel phages. VII VIII CONTENTS Statutory Declaration .................................................................................................................................... III Thesis abstract ............................................................................................................................................. VII Contents ..................................................................................................................................................... VIII List of Figures ............................................................................................................................................... XI List of Tables .............................................................................................................................................. XII Chapter 1 Introduction ................................................................................................................................................... 1 1.1. Marine viruses: Part of the micro-universe .................................................................................... 1 1.1.1. Marine phages and other microbial inhabitants from the North Sea ..................................... 3 1.2. the host hackers vs the time bombs: Proliferation cycle of tailed phages ...................................... 5 1.2.1. Lytic cycle, the host hackers ................................................................................................. 5 1.2.2. Lysogenic cycle, the time bombs .......................................................................................... 6 1.2.3. The viral effect: role on the ecosystem and population development .................................. 8 1.2.4. Inception of infection: Phage influence in the development of human pathogenic Vibrio strains ...................................................................................... 9 1.3. You can judge a phage by the scope it’s seen: Approaches applied in marine phage ecology ............................................................................. 11 1.3.1. Methods to collect virus biomass ........................................................................................ 12 1.3.2. Methods to estimate abundance and diversity .................................................................... 12 1.4. Methods applied to tailed phage’s characterization ..................................................................... 14 1.4.1. Methods for isolation of phage–host systems ..................................................................... 15 1.4.2. Methods to characterize morphology .................................................................................. 16 1.4.3. Methods to characterize a genome ...................................................................................... 17 1.5. NGS applied in marine virus (meta)genomics ............................................................................. 18 1.5.1. Phage (meta)genomics ........................................................................................................ 18 1.5.2. The needle in the haystack: phage genomes in the databases ............................................. 20 1.5.3. Virus (meta)genomic tools .................................................................................................. 21 1.6. Motivation and research aims ...................................................................................................... 23 1.7. Content overview ......................................................................................................................... 26 Chapter 2 North Sea
Recommended publications
  • Copyrighted Material

    Copyrighted Material

    CHAPTER 1 Viruses and Their Importance CHAPTER 1 AT A GLANCE Viruses infect: • Humans • Other vertebrates • Invertebrates Smallpox1 Bluetongue virus-infected sheep2 Tipula sp. larvae (leatherjackets) infected with invertebrate iridescent virus 1 • Plants • Fungi • Bacteria COPYRIGHTED MATERIAL Escherichia coli Delayed emergence of Damaged potato Mushroom virus X4 cell potato caused by tobacco (spraing) caused by with phage T4 attached5 rattle virus infection3 tobacco rattle virus infection3 1 cc01.indd01.indd 1 118/01/138/01/13 88:14:14 PPMM 2 CHAPTER 1 VIRUSES AND THEIR IMPORTANCE CHAPTER 1 AT A GLANCE (continued) Some viruses are useful: • Phage typing of bacteria • Sources of enzymes • Pesticides • Anti-bacterial agents • Anti-cancer agents • Gene vectors Viruses are parasites; they depend on cells for molecular building blocks, machinery, and energy. Virus particles are small; dimensions range approx. from 20–400 nm. A virus genome is composed of one of the following: double-stranded single-stranded double-stranded single-stranded DNA DNA RNA RNA Photographs reproduced with permission of 1 World Health Organization. 2 From Umeshappa et al . (2011) Veterinary Immunology and Immunopathology , 141, 230. Reproduced by permission of Elsevier and the authors. 3 MacFarlane and Robinson (2004) Chapter 11, Microbe-Vector Interactions in Vector-Borne Diseases , 63rd Symposium of the Society for General Microbiology, Cambridge University Press. Reprinted with permission. 4 University of Warwick. 5 Cornell Integrated Microscopy Center. The presence of viruses is obvious in host organ- 1.1 VIRUSES ARE UBIQUITOUS ON EARTH isms showing signs of disease. Many healthy organisms, however, are hosts of non-pathogenic virus infections, Viruses infect all cellular life forms: eukaryotes (ver- some of which are active, while some are quiescent.
  • Changes to Virus Taxonomy 2004

    Changes to Virus Taxonomy 2004

    Arch Virol (2005) 150: 189–198 DOI 10.1007/s00705-004-0429-1 Changes to virus taxonomy 2004 M. A. Mayo (ICTV Secretary) Scottish Crop Research Institute, Invergowrie, Dundee, U.K. Received July 30, 2004; accepted September 25, 2004 Published online November 10, 2004 c Springer-Verlag 2004 This note presents a compilation of recent changes to virus taxonomy decided by voting by the ICTV membership following recommendations from the ICTV Executive Committee. The changes are presented in the Table as decisions promoted by the Subcommittees of the EC and are grouped according to the major hosts of the viruses involved. These new taxa will be presented in more detail in the 8th ICTV Report scheduled to be published near the end of 2004 (Fauquet et al., 2004). Fauquet, C.M., Mayo, M.A., Maniloff, J., Desselberger, U., and Ball, L.A. (eds) (2004). Virus Taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp. 1258. Recent changes to virus taxonomy Viruses of vertebrates Family Arenaviridae • Designate Cupixi virus as a species in the genus Arenavirus • Designate Bear Canyon virus as a species in the genus Arenavirus • Designate Allpahuayo virus as a species in the genus Arenavirus Family Birnaviridae • Assign Blotched snakehead virus as an unassigned species in family Birnaviridae Family Circoviridae • Create a new genus (Anellovirus) with Torque teno virus as type species Family Coronaviridae • Recognize a new species Severe acute respiratory syndrome coronavirus in the genus Coro- navirus, family Coronaviridae, order Nidovirales
  • Julia Villarroel Phd Thesis 18October2017

    Julia Villarroel Phd Thesis 18October2017

    Downloaded from orbit.dtu.dk on: Oct 10, 2021 Isolation and characterization of bacteriophages with therapeutic potential Villarroel, Julia Publication date: 2018 Document Version Publisher's PDF, also known as Version of record Link back to DTU Orbit Citation (APA): Villarroel, J. (2018). Isolation and characterization of bacteriophages with therapeutic potential. Technical University of Denmark. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Ph.D. Thesis Doctor of Philosophy in Bioinformatics Isolation and characterization of bacteriophages with therapeutic potential Julia Villarroel Kongens Lyngby 2018 DTU Bioinformatics Department of Bio and Health Informatics Technical University of Denmark Kemitorvet, Building 208 2800 Kongens Lyngby, Denmark www.bioinformatics.dtu.dk There is a vitality, a life force, an energy, a quickening, that is translated through you into action, and because there is only one of you in all time, this expression is unique. And if you block it, it will never exist through any other medium and will be lost.
  • A Persistent Giant Algal Virus, with a Unique Morphology, Encodes An

    A Persistent Giant Algal Virus, with a Unique Morphology, Encodes An

    bioRxiv preprint doi: https://doi.org/10.1101/2020.07.30.228163; this version posted January 13, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 A persistent giant algal virus, with a unique morphology, encodes an 2 unprecedented number of genes involved in energy metabolism 3 4 Romain Blanc-Mathieu1,2, Håkon Dahle3, Antje Hofgaard4, David Brandt5, Hiroki 5 Ban1, Jörn Kalinowski5, Hiroyuki Ogata1 and Ruth-Anne Sandaa6* 6 7 1: Institute for Chemical Research, Kyoto University, Gokasho, Uji, 611-0011, Japan 8 2: Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, 9 CNRS, INRA, IRIG, Grenoble, France 10 3: Department of Biological Sciences and K.G. Jebsen Center for Deep Sea Research, 11 University of Bergen, Bergen, Norway 12 4: Department of Biosciences, University of Oslo, Norway 13 5: Center for Biotechnology, Universität Bielefeld, Bielefeld, 33615, Germany 14 6: Department of Biological Sciences, University of Bergen, Bergen, Norway 15 *Corresponding author: Ruth-Anne Sandaa, +47 55584646, [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.30.228163; this version posted January 13, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 16 Abstract 17 Viruses have long been viewed as entities possessing extremely limited metabolic 18 capacities.
  • And Giant Guitarfish (Rhynchobatus Djiddensis)

    And Giant Guitarfish (Rhynchobatus Djiddensis)

    VIRAL DISCOVERY IN BLUEGILL SUNFISH (LEPOMIS MACROCHIRUS) AND GIANT GUITARFISH (RHYNCHOBATUS DJIDDENSIS) BY HISTOPATHOLOGY EVALUATION, METAGENOMIC ANALYSIS AND NEXT GENERATION SEQUENCING by JENNIFER ANNE DILL (Under the Direction of Alvin Camus) ABSTRACT The rapid growth of aquaculture production and international trade in live fish has led to the emergence of many new diseases. The introduction of novel disease agents can result in significant economic losses, as well as threats to vulnerable wild fish populations. Losses are often exacerbated by a lack of agent identification, delay in the development of diagnostic tools and poor knowledge of host range and susceptibility. Examples in bluegill sunfish (Lepomis macrochirus) and the giant guitarfish (Rhynchobatus djiddensis) will be discussed here. Bluegill are popular freshwater game fish, native to eastern North America, living in shallow lakes, ponds, and slow moving waterways. Bluegill experiencing epizootics of proliferative lip and skin lesions, characterized by epidermal hyperplasia, papillomas, and rarely squamous cell carcinoma, were investigated in two isolated poopulations. Next generation genomic sequencing revealed partial DNA sequences of an endogenous retrovirus and the entire circular genome of a novel hepadnavirus. Giant Guitarfish, a rajiform elasmobranch listed as ‘vulnerable’ on the IUCN Red List, are found in the tropical Western Indian Ocean. Proliferative skin lesions were observed on the ventrum and caudal fin of a juvenile male quarantined at a public aquarium following international shipment. Histologically, lesions consisted of papillomatous epidermal hyperplasia with myriad large, amphophilic, intranuclear inclusions. Deep sequencing and metagenomic analysis produced the complete genomes of two novel DNA viruses, a typical polyomavirus and a second unclassified virus with a 20 kb genome tentatively named Colossomavirus.
  • Abstract 9 10 Bacteriophages (Phages) Are Bacterial Parasites That Can Themselves Be Parasitized by Phage 11 Satellites

    Abstract 9 10 Bacteriophages (Phages) Are Bacterial Parasites That Can Themselves Be Parasitized by Phage 11 Satellites

    bioRxiv preprint doi: https://doi.org/10.1101/2021.03.30.437493; this version posted March 30, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 To catch a hijacker: abundance, evolution and genetic diversity of 2 P4-like bacteriophage satellites 3 Jorge A. Moura de Sousa1,*& Eduardo P.C. Rocha1,* 4 5 1Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris 75015, France 6 * corresponding authors: [email protected], [email protected] 7 8 Abstract 9 10 Bacteriophages (phages) are bacterial parasites that can themselves be parasitized by phage 11 satellites. The molecular mechanisms used by satellites to hijack phages are sometimes 12 understood in great detail, but the origins, abundance, distribution, and composition of these 13 elements are poorly known. Here, we show that P4-like elements are present in more than 14 10% of the genomes of Enterobacterales, and in almost half of those of Escherichia coli, 15 sometimes in multiple distinct copies. We identified over 1000 P4-like elements with very 16 conserved genetic organization of the core genome and a few hotspots with highly variable 17 genes. These elements are never found in plasmids and have very little homology to known 18 phages, suggesting an independent evolutionary origin. Instead, they are scattered across 19 chromosomes, possibly because their integrases are often exchanged with other elements. 20 The rooted phylogenies of hijacking functions are correlated and suggest longstanding co- 21 evolution.
  • Keizo Nagasaki and Gunnar Bratbak. Isolation of Viruses Infecting

    Keizo Nagasaki and Gunnar Bratbak. Isolation of Viruses Infecting

    MANUAL of MAVE Chapter 10, 2010, 92–101 AQUATIC VIRAL ECOLOGY © 2010, by the American Society of Limnology and Oceanography, Inc. Isolation of viruses infecting photosynthetic and nonphotosynthetic protists Keizo Nagasaki1* and Gunnar Bratbak2† 1National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan 2University of Bergen, Department of Biology, Box 7800, N-5020 Bergen, Norway Abstract Viruses are the most abundant biological entities in aquatic environments and our understanding of their eco- logical significance has increased tremendously since the first discovery of their high abundance in natural waters. About 40 viruses infecting eukaryotic algae and 4 viruses infecting nonphotosynthetic protists have so far been isolated and characterized to different extents. The isolated viruses infecting phytoplankton (Chlorophyceae, Prasinophyceae, Haptophyceae, Dinophyceae, Pelagophyceae, Raphidophyceae, and Bacillariophyceae) and heterotrophic protists (Bicosoecophyceae, Acanthamoebidae, and Thraustochytriaceae) are all lytic. Some of the brown algal phaeoviruses, which infect host spores or gametes, have also been found in a latent form (lysogeny) in vegetative cells. Viruses infecting eukaryotic photosynthetic and nonphotosynthetic protists are highly diverse both in size (ca. 20–220 nm in diameter), genome type (double-strand deoxyribonu- cleic acid [dsDNA], single-strand [ss]DNA, ds–ribonucleic acid [dsRNA], ssRNA), and genome size [4.4–560 kb]). Availability of host–virus laboratory cultures is a necessary prerequisite for characterization of the viruses and for investigation of host–virus interactions. In this report we summarize and comment on the techniques used for preparation of host cultures and for screening, cloning, culturing, and maintaining viruses in the laboratory.
  • Soybean Thrips (Thysanoptera: Thripidae) Harbor Highly Diverse Populations of Arthropod, Fungal and Plant Viruses

    Soybean Thrips (Thysanoptera: Thripidae) Harbor Highly Diverse Populations of Arthropod, Fungal and Plant Viruses

    viruses Article Soybean Thrips (Thysanoptera: Thripidae) Harbor Highly Diverse Populations of Arthropod, Fungal and Plant Viruses Thanuja Thekke-Veetil 1, Doris Lagos-Kutz 2 , Nancy K. McCoppin 2, Glen L. Hartman 2 , Hye-Kyoung Ju 3, Hyoun-Sub Lim 3 and Leslie. L. Domier 2,* 1 Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; [email protected] 2 Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL 61801, USA; [email protected] (D.L.-K.); [email protected] (N.K.M.); [email protected] (G.L.H.) 3 Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 300-010, Korea; [email protected] (H.-K.J.); [email protected] (H.-S.L.) * Correspondence: [email protected]; Tel.: +1-217-333-0510 Academic Editor: Eugene V. Ryabov and Robert L. Harrison Received: 5 November 2020; Accepted: 29 November 2020; Published: 1 December 2020 Abstract: Soybean thrips (Neohydatothrips variabilis) are one of the most efficient vectors of soybean vein necrosis virus, which can cause severe necrotic symptoms in sensitive soybean plants. To determine which other viruses are associated with soybean thrips, the metatranscriptome of soybean thrips, collected by the Midwest Suction Trap Network during 2018, was analyzed. Contigs assembled from the data revealed a remarkable diversity of virus-like sequences. Of the 181 virus-like sequences identified, 155 were novel and associated primarily with taxa of arthropod-infecting viruses, but sequences similar to plant and fungus-infecting viruses were also identified.
  • The Ins and Outs of Nondestructive Cell-To-Cell and Systemic Movement of Plant Viruses

    The Ins and Outs of Nondestructive Cell-To-Cell and Systemic Movement of Plant Viruses

    Critical Reviews in Plant Sciences, 23(3):195–250 (2004) Copyright C Taylor and Francis Inc. ISSN: 0735-2689 print / 1549-7836 online DOI: 10.1080/07352680490452807 The Ins and Outs of Nondestructive Cell-to-Cell and Systemic Movement of Plant Viruses Elisabeth Waigmann Max F. Perutz Laboratories, University Departments at the Vienna Biocenter, Institute of Medical Biochemistry, Medical University of Vienna, Dr. Bohrgasse 9 A-1030, Vienna, Austria Shoko Ueki Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY 11794-5215 Kateryna Trutnyeva Max F. Perutz Laboratories, University Departments at the Vienna Biocenter, Institute of Medical Biochemistry, Medical University of Vienna, Dr. Bohrgasse 9 A-1030, Vienna, Austria Vitaly Citovsky∗ Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY 11794-5215 Referee: Dr. Ernest Hiebert, Professor, Department of Plant Pathology, University of Florida/IFAS, P.O. Box 110680, 1541 Fifield Hall, Gainesville, FL 32611-0680, USA. Table of Contents 1. Introduction ..........................................................................................................................................................196 2. Structure and Composition of Plasmodesmata, the Intercellular Conduits for Viral Movement ..............................198 3. Cell-to-Cell Transport of Plant Viruses: Have Movement Protein, Will Travel ........................................................200 3.1. MP Structure: Are Common Functions Supported by
  • High Variety of Known and New RNA and DNA Viruses of Diverse Origins in Untreated Sewage

    High Variety of Known and New RNA and DNA Viruses of Diverse Origins in Untreated Sewage

    Edinburgh Research Explorer High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage Citation for published version: Ng, TF, Marine, R, Wang, C, Simmonds, P, Kapusinszky, B, Bodhidatta, L, Oderinde, BS, Wommack, KE & Delwart, E 2012, 'High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage', Journal of Virology, vol. 86, no. 22, pp. 12161-12175. https://doi.org/10.1128/jvi.00869-12 Digital Object Identifier (DOI): 10.1128/jvi.00869-12 Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: Journal of Virology Publisher Rights Statement: Copyright © 2012, American Society for Microbiology. All Rights Reserved. General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 09. Oct. 2021 High Variety of Known and New RNA and DNA Viruses of Diverse Origins in Untreated Sewage Terry Fei Fan Ng,a,b Rachel Marine,c Chunlin Wang,d Peter Simmonds,e Beatrix Kapusinszky,a,b Ladaporn Bodhidatta,f Bamidele Soji Oderinde,g K.
  • United States Patent ( 10 ) Patent No.: US 10,676,721 B2 Collins Et Al

    United States Patent ( 10 ) Patent No.: US 10,676,721 B2 Collins Et Al

    US010676721B2 United States Patent ( 10 ) Patent No.: US 10,676,721 B2 Collins et al. (45 ) Date of Patent : Jun . 9 , 2020 ( 54 ) BACTERIOPHAGES EXPRESSING 6,699,701 B1 3/2004 Sulakvelidze et al . ANTIMICROBIAL PEPTIDES AND USES 6,759,229 B2 * 7/2004 Schaak 435 /235.1 7,211,426 B2 5/2007 Bruessow et al. THEREOF 8,153,119 B2 4/2012 Collins et al. 8,182,804 B1 5/2012 Collins et al. ( 75 ) Inventors : James J. Collins, Newton , MA (US ) ; 2001/0026795 A1 10/2001 Merril et al . Michael Koeris , Natick , MA (US ) ; 2002/0013671 Al 1/2002 Ananthaiyer et al. 2004/0161141 A1 8/2004 Dewaele Timothy Kuan - Ta Lu , Charlestown, 2005/0004030 A1 1/2005 Fischetti et al . MA (US ) ; Tanguy My Chau , Palo 2007/0020240 A1 1/2007 Jayasheela et al. Alto , CA ( US ) ; Gregory 2007/0134207 Al 6/2007 Bruessow et al . Stephanopoulos , Winchester , MA (US ) ; 2007/0207209 A1 * 9/2007 Murphy A61K 9/06 Christopher Jongsoo Yoon , Seoul 424/484 (KR ) 2007/0248724 Al 10/2007 Sulakvelidze et al. 2008/0194000 Al 8/2008 Pasternack et al. ( 73 ) Assignees : Trustees of Boston University , Boston , 2008/0247997 Al 10/2008 Reber et al . MA (US ) ; Massachusetts Institute of 2008/0311643 A1 12/2008 Sulakvelidze et al. Technology , Cambridge, MA (US ) 2008/0318867 A1 12/2008 Loessner et al. FOREIGN PATENT DOCUMENTS ( * ) Notice: Subject to any disclaimer , the term of this patent is extended or adjusted under 35 EP 0403458 A1 12/1990 CO7K 7/10 WO 2002/034892 Al 5/2002 U.S.C.
  • Article Differential Codon Adaptation

    Article Differential Codon Adaptation

    Differential Codon Adaptation between dsDNA and ssDNA Phages in Escherichia coli Shivapriya Chithambaram,1 Ramanandan Prabhakaran,1 and Xuhua Xia*,1 1Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Ontario, Canada *Corresponding author: E-mail: [email protected]. Associate editor: Helen Piontkivska Abstract Because phages use their host translation machinery, their codon usage should evolve toward that of highly expressed host genes. We used two indices to measure codon adaptation of phages to their host, rRSCU (thecorrelationinrelative synonymous codon usage [RSCU] between phages and their host) and Codon Adaptation Index (CAI) computed with highly expressed host genes as the reference set (because phage translation depends on host translation machinery). These indices used for this purpose are appropriate only when hosts exhibit little mutation bias, so only phages para- Downloaded from sitizing Escherichia coli were included in the analysis. For double-stranded DNA (dsDNA) phages, both rRSCU and CAI decrease with increasing number of transfer RNA genes encoded by the phage genome. rRSCU is greater for dsDNA phages than for single-stranded DNA (ssDNA) phages, and the low rRSCU values are mainly due to poor concordance in RSCU values for Y-ending codons between ssDNA phages and the E. coli host, consistent with the predicted effect of C!T mutation bias in the ssDNA phages. Strong C!T mutation bias would improve codon adaptation in codon families (e.g., Gly) where U-ending codons are favored over C-ending codons (“U-friendly” codon families) by highly expressed host http://mbe.oxfordjournals.org/ genes but decrease codon adaptation in other codon families where highly expressed host genes favor C-ending codons against U-ending codons (“U-hostile” codon families).