DOCSLIB.ORG

Genetic Map of Bacteriophage Lambda

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Genetic Map of Bacteriophage Lambda MICROBIOLOGICAL REVIEWS, Sept. 1978, p. 577-591 Vol.42, No. 3 0146-0749/78/0042-0577$02.00/0 Copyright © 1978 American Society for Microbiology Printed in U.S.A. Genetic Map of Bacteriophage Lambda HARRISON ECHOLS* AND HELIOS MURIALDO Department ofMolecular Biology, University of California, Berkeley, California 94720, * and Department of Medical Genetics, University of Toronto, Toronto M5S 1A8, Canada INTRODUCTION .5..577 PHYSICAL STATES AND ACTIVITY OF THE A GENOME 577 GENETIC MAP OF THE A GENOME .577 ACTIITrY MAP OF THE A GENOME .583 COMMENTS ON GENETIC ORGANIZATION ...........5*583 LITERATURE CITED .584 INTRODUCTION that are the obligatory precursors for the The study of bacteriophage A has been a cen- cleaved, linear molecules packaged into a phage tral endeavor of molecular biology for a number head (Fig. 1). The lysogenic pathway involves a of years. Phage A has been the creature of choice repression of transcription and a site-specific for many investigators interested in deoxyribo- recombination event that inserts A DNA into nucleic acid (DNA) transcription, replication, the host Escherichia coli genome. This integra- and recombination, in nucleoprotein assembly, tive recombination between the phage and host and in the organization of these processes into attachment sites (att) generates a genetic struc- temporally regulated pathways. As a result of ture that is permuted from the linear order this intensive study, a great deal of information found in the phage particle because the phage is now available about A genes and how they attachment site (a a' or P P) is approximately work; however, the communication of this in the center of the mature DNA molecule (Fig. knowledge is sometimes hindered by a "culture 1). The prophage has structurally distinct at- gap" between "lambdologists" and those lacking tachment sites: a left attL site (b a' or B P') an understanding ofthe array ofgene names and and a right attR site (a b' or P B'); these in sites for protein activity. In an effort to remedy turn can recombine to detach the prophage this difficulty, we present an annotated genetic DNA when the virus is induced to lytic devel- map of phage A. We begin with a brief summary opment, regenerating the phage attP site (a a' of the A life cycle; present two maps, one of gene or P P') and the original host attB site (b b' or order and one of gene activity; and conclude B B'). with a short on the More detailed descriptions of the diverse life- commentary genetic orga- styles of phage A can be found in the general nization. review articles by Echols (47; in J. R. Sokatch PHYSICAL STATES AND ACTIVITY OF and L. N. Ornston, ed., The Bacteria, in press) THE X GENOME and Herskowitz (88). The lysogenic pathway has been recently reviewed by Weisberg et al. (233); The genome of phage A is a double-stranded the lytic pathway has not been selectively re- DNA molecule about 47,000 base pairs in length. viewed for some time, but the general features In the phage particle, A DNA has single- are covered in the review Echols stranded, complementary ends 12 bases in by (46). length, termed mature or cohesive ends m and m'. Within an infected cell, A DNA forms a circle GENETIC MAP OF THE X GENOME through pairing ofthe single-stranded DNA, and The order of genes along the linear A DNA is replicated and transcribed as a circular mole- molecule is shown in the upper part of Fig. 2; cule during the replication-oriented early phase the function of certain gene clusters is indicated of A development. below the map. The lower part of Fig. 2 gives a After this early stage, A development may blowup of the right half of the A map, designed proceed along the productive (or lytic) pathway to focus on the activity sites for the develop- or along the alternative lysogenic pathway. The mental events noted in the preceding section. encapsulation-oriented late stage of the produc- To construct Fig. 2, we used three principal tive pathway involves a transcription switch to types of information: (i) "traditional" genetic synthesis of head, tail, and lysis proteins and a mapping; (ii) physical mapping by heteroduplex replication switch to a rolling-circle mode that analysis of genetically characterized deletion generates multimeric A genomes (concatemers) mutations; and (iii) molecular weights of gene 577 578 ECHOLS AND MURIALDO MICROBIOL. REV. DNA encapsulation Phage Late proteins Monomer DNA on Injected DNA replicotion mm' Eor1yEorly~~~~~~~mm' f" proteinsEoff K> proteins o mmmiil ° C ) Lytic DNA integration Prophoge proteins mm o,f fI _110. bo' mm' oab' Integrotion on b bI FIG. 1. Developmental pathways for bacteriophage A. The injected DNA forms a covalently closed circle through pairing of the mature ends, m and mi', followed by ligation. After an early phase common to both pathways, viral development may follow the productive or lysogenic pathways. In the productive pathway, synthesis of encapsulation and lysis proteins is turned on, synthesis of early proteins is turned off, and replication switches to a rolling-circle mode that generates the multimeric DNA used as a substrate for encapsulation of linear DNA with free mature ends. In the lysogenic pathway, synthesis of lytic proteins is turned off, and the circular viral DNA is inserted into the host genome by a specific recombination event. GENETIC MAP Nu! P.u3 Ef Fl Fl z U V G rt L K i uooint xis redX redB gem i! ciiicralrox cro cl OP S R mAmtXW W-t;tX'lCO]D 4g4HS2 /aD?J 4+ 1~~~~'V ClII o$g lm 0 10 20 30 40 50 60 70 80 90 100 Phage heod Phoge tail Integration, Replication sis excision, and ReglatonRegulation Late recombination regulationlateo GENE ACTIVITY MAP Through heod and toil 00 PL CI PR CrO fg1 Cl 'np 0 or P fe2 P's int xis cmIII ILAN9 0 m 50 60 70 2 80 90 too Pt SOL! PM Pt FIG. 2. Genetic map of bacteriophage A. The genes that code forproteins of defined function are shown in the upper part of the figure; the vertical line marks the approximate center of the genes (see Table 1). The b region is silent in terms of defined viral functions, although it does code for several proteins (see text and Table 1). The regulatory sites and their function are indicated in the lower part of the figure; these are described in the text and in Table 1. The different stages of transcriptional activity and the DNA regions involved are indicated by the arrows; the actual length of DNA transcribed can be determined from the intersection of the promoter (p) and terminator (t) lines with the horizontal calibrated line representing the A genome. products. The principles (and examples) are examples of this type of overestimate exist (e.g., given in the articles by Campbell (20), Davidson the V protein has an electrophoretic estimate of and Szybalski (38), and Szybalski and Szybalski 32,000 daltons, but a calculated value from (211). The functions of the genes and sites are amino acid composition of 26,000 daltons). summarized with references in Table 1. Based on this assessment, we have reduced the Based on the physical mapping data of Par- size of some genes (3 to 10%) to conform to the kinson and Davis (156) and the estimated mo- physical map; these reduced values are used for lecular weights of the gene products (Table 1), the "Coordinates" column of Table 1. The mo- the head and tail region is "oversaturated" lecular weight values originally reported for the (codes for more amino acids than available nu- proteins are given in the "Gene function and/or cleotides). We believe that the discrepancy most protein activity" column. likely results from overestimates of protein size Most readers of this article are aware already by the standard method of polyacrylamide gel that A nomenclature has not evolved in a logi- electrophoresis in sodium dodecyl sulfate, rather cally consistent way. Genes for proteins essential than from overlapping genes, because several to productive growth were originally given up- VOL. 42, 1978 GENETIC MAP OF PHAGE LAMBDA 579 TABLE 1. Genes ofphage A and their function co- Gene symbol Approxordinatesamap Gene function and/or protein activity Referencesb m 0 Left cohesive end of the mature DNA mol- 13,31,38,57,60,61,69,87,146, ecule; the first 12 nucleotides of the 5' 147, 151, 206, 218, 228, 229, end of the I (transcribed leftward) strand 237,238 protrude as a single-stranded chain, complementary to m'. Nul 0/0.5 Involved in DNA packaging and cohesive 8, 145, D end formation; may activate A protein. A 0.5/4.7 DNA packaging into proheads and forma- 5-7, 19, 67,90, 96, 103, 109-111, tion of cohesive ends; protein is 79,000 132, 139, 144, 145, 155, 197, daltons (79K). 204, 206, 210, 226, 229, 231 w 4.7/5.0 Modifies DNA-filled heads in an unknown 28, 93, 132, 155, 205, 226 way to allow FII action; protein is 5-10K. B 5.0/8.3 Structural component of the capsid; B pro- 7, 19, 67, 85, 86, 91, 120, 139, tein and a cleaved derivative B form 140, 141, 142, 145, 155, 169, the head-tail connector-, B is 59-62K; B" 204, 223, 231, 242 is 53-56K. C 8.3/11.3 Structural component of capsid; the 7, 19, 67, 84-86, 91, 120, 139, 56-61K C protein is present in the capsid 140, 141, 142, 144, 145, 155, as two cleaved derivatives, fused to a 169, 204, 223, 231, 242 cleaved derivative of E; the two cleav- age-fusion products, termed Xl and X2, are 29 and 27K, respectively.
Load more

Recommended publications
  • Protists and the Wild, Wild West of Gene Expression
    MI70CH09-Keeling ARI 3 August 2016 18:22 ANNUAL REVIEWS Further Click here to view this article's online features: • Download figures as PPT slides • Navigate linked references • Download citations Protists and the Wild, Wild • Explore related articles • Search keywords West of Gene Expression: New Frontiers, Lawlessness, and Misfits David Roy Smith1 and Patrick J. Keeling2 1Department of Biology, University of Western Ontario, London, Ontario, Canada N6A 5B7; email: [email protected] 2Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; email: [email protected] Annu. Rev. Microbiol. 2016. 70:161–78 Keywords First published online as a Review in Advance on constructive neutral evolution, mitochondrial transcription, plastid June 17, 2016 transcription, posttranscriptional processing, RNA editing, trans-splicing The Annual Review of Microbiology is online at micro.annualreviews.org Abstract This article’s doi: The DNA double helix has been called one of life’s most elegant structures, 10.1146/annurev-micro-102215-095448 largely because of its universality, simplicity, and symmetry. The expression Annu. Rev. Microbiol. 2016.70:161-178. Downloaded from www.annualreviews.org Copyright c 2016 by Annual Reviews. Access provided by University of British Columbia on 09/24/17. For personal use only. of information encoded within DNA, however, can be far from simple or All rights reserved symmetric and is sometimes surprisingly variable, convoluted, and wantonly inefficient. Although exceptions to the rules exist in certain model systems, the true extent to which life has stretched the limits of gene expression is made clear by nonmodel systems, particularly protists (microbial eukary- otes).
    [Show full text]
  • |||||||III US005478731A United States Patent (19) 11 Patent Number: 5,478,731
    |||||||III US005478731A United States Patent (19) 11 Patent Number: 5,478,731 Short 45 Date of Patent: Dec. 26,9 1995 54). POLYCOS VECTORS 56 References Cited 75) Inventor: Jay M. Short, Encinitas, Calif. PUBLICATIONS (73 Assignee: Stratagene, La Jolla, Calif. Ahmed (1989), Gene 75:315-321. 21 Appl. No.: 133,179 Evans et al. (1989), Gene 79:9-20. 22) PCT Filed: Apr. 10, 1992 Primary Examiner-Mindy B. Fleisher Assistant Examiner-Philip W. Carter 86 PCT No.: PCT/US92/03012 Attorney, Agent, or Firm-Albert P. Halluin; Pennie & S371 Date: Oct. 12, 1993 Edmonds S 102(e) Date: Oct. 12, 1993 57 ABSTRACT 87, PCT Pub. No.: WO92/18632 A bacteriophage packaging site-based vector system is describe that involves cloning vectors and methods for their PCT Pub. Date: Oct. 29, 1992 use in preparing multiple copy number bacteriophage librar O ies of cloned DNA. The vector is based on a DNA segment Related U.S. Application Data that comprises a nucleotide sequence defining a bacterioph 63 abandoned.continuationin-part of ser, No. 685.215,y Apr 12, 1991, ligationage packaging means usedsite locatedto concatamerize between twofragments termining of DNA 6 having compatible ligation means. Methods for preparing a (51) Int. Cl. ............................... C12N 1/21; C12N 7/01; concatameric DNA for packaging cloned DNA segments, C12N 15/10; C12N 15/11 and for packaging the concatamers to produce a library are 52 U.S. Cl. ................ 435/914; 435/1723; 435/252.33; also described. 435/235.1; 435/252.3; 536/23.1 58) Field of Search .............................. 435/91.32, 172.3, 435/320.1,914, 252.33, 252.3, 235.1; 536/23.1 18 Claims, 1 Drawing Sheet U.S.
    [Show full text]
  • Lessons from Nature: Microrna-Based Shrna Libraries
    PERSPECTIVE Lessons from Nature: microRNA-based shRNA libraries methods Kenneth Chang1, Stephen J Elledge2 & Gregory J Hannon1 Loss-of-function genetics has proven essential for interrogating the functions of genes .com/nature e and for probing their roles within the complex circuitry of biological pathways. In .natur many systems, technologies allowing the use of such approaches were lacking before w the discovery of RNA interference (RNAi). We have constructed first-generation short hairpin RNA (shRNA) libraries modeled after precursor microRNAs (miRNAs) and second- http://ww generation libraries modeled after primary miRNA transcripts (the Hannon-Elledge oup libraries). These libraries were arrayed, sequence-verified, and cover a substantial portion r G of all known and predicted genes in the human and mouse genomes. Comparison of first- and second-generation libraries indicates that RNAi triggers that enter the RNAi pathway lishing through a more natural route yield more effective silencing. These large-scale resources b Pu are functionally versatile, as they can be used in transient and stable studies, and for constitutive or inducible silencing. Library cassettes can be easily shuttled into vectors Nature that contain different promoters and/or that provide different modes of viral delivery. 6 200 © RNAi is an evolutionarily conserved, sequence-specific than a decade elapsed between the discovery of the first gene-silencing mechanism that is induced by dsRNA. miRNA, Caenorhabditis elegans lin-4 (refs. 11,12) and Each dsRNA silencing trigger is processed into 21–25 bp the achievement of at least a superficial understanding dsRNAs called small interfering RNAs (siRNAs)1–3 by of the biosynthesis, processing and mode of action of Dicer, a ribonuclease III family (RNase III) enzyme4.
    [Show full text]
  • Site Directed Mutagensis of Bacteriophage HK639 and Identification of Its Integration Site Madhuri Jonnalagadda Western Kentucky University
    Western Kentucky University TopSCHOLAR® Masters Theses & Specialist Projects Graduate School 12-2008 Site Directed Mutagensis of Bacteriophage HK639 and Identification of Its Integration Site Madhuri Jonnalagadda Western Kentucky University Follow this and additional works at: http://digitalcommons.wku.edu/theses Part of the Cell and Developmental Biology Commons, Genetics Commons, Immunopathology Commons, and the Molecular Genetics Commons Recommended Citation Jonnalagadda, Madhuri, "Site Directed Mutagensis of Bacteriophage HK639 and Identification of Its Integration Site" (2008). Masters Theses & Specialist Projects. Paper 42. http://digitalcommons.wku.edu/theses/42 This Thesis is brought to you for free and open access by TopSCHOLAR®. It has been accepted for inclusion in Masters Theses & Specialist Projects by an authorized administrator of TopSCHOLAR®. For more information, please contact [email protected]. SITE DIRECTED MUTAGENESIS OF BACTERIOPHAGE HK639 AND IDENTIFICATION OF ITS INTEGRATION SITE A Thesis presented to The faculty of the Department of Biology Western Kentucky University Bowling Green, Kentucky. In Partial Fulfillment Of the Requirement for the Degree Master of Science By Madhuri Jonnalagadda December, 2008 Site Directed Mutagenesis of Bacteriophage HK639 and Identification of its Integration Site Date Recommended 12/4/08 Dr.Rodney A. King Director of Thesis __Dr.Jeffery Marcus Dr. Sigrid Jacobshagen _____________________________________ Dean, Graduate Studies and Research Date DEDICATION I would like to dedicate my thesis to my dear father Dr. J. Padmanabha Rao, my mother, Dr.V. Lakshmi, my sister Dr. J. Sushma for their support and encouragement. i ACKNOWLEDGEMENTS I wish to express my heartfelt gratitude to my graduate committee in the Department of Biology, Western Kentucky University. Primarily, I am thankful to my advisor, Dr.
    [Show full text]
  • Purification and Propertiesof a DNA-Binding Protein With
    Proc. Natl. Acad. Sci. USA Vol. 73, No. 7, pp. 2249-2253, July 1976 Biochemistry Purification and properties of a DNA-binding protein with characteristics expected for the Cro protein of bacteriophage X, a repressor essential for lytic growth (bacteriophage X cro gene/promoter-operator DNA) ATIS FOLKMANIS, YOSHINORI TAKEDA, JOSEF SIMUTH, GARY GUSSIN*, AND HARRISON ECHOLS Department of Molecular Biology, University of California, Berkeley, Calif. 94720, and * Department of Zoology, University of Iowa, Iowa City, Iowa 52242 Communicated by A. D. Kaiser, April 14, 1976 ABSTRACT The Cro protein specified by bacteriophage X viously (8), X DNA was labeled with P2p by growth of phage in is a repressor essential for normal lytic growth of the virus, thus low phosphate medium containing 5 ,Ci/ml of UP-labeled having a physiological role distinct from that of cI, the repressor that maintains lyso We have purified a X-specific DNA- inorganic phosphate. Phage were purified by precipitation with binding protein witheny.the requirements for synthesis and bio- polyethylene glycol and centrifugation to equilibrium in a CsCI chemical activities expected for Cro protein from studies in vivo. density gradient (2-3 times). DNA was extracted with redis- As isolated, the protein appears to be a dimer of molecular tilled phenol, the phenol was removed by extraction with ether, weight approximately 18,000 with DNA-binding properties that and the DNA was dialyzed into and stored in 10mM Tris-HCl, are very similar, but not identical, to those of the cI protein. We 0.2 mM EDTA, at pH 7.3. infer that bacteriophage X uses the same regulatory region of DNA for two different DNA-binding repressor proteins with DNA-Binding Assay.
    [Show full text]
  • Pamela L. Mellon, Ph.D
    Pamela L. Mellon, Ph.D. Vice-Chair for Research, Department of Reproductive Medicine Distinguished Professor, Departments of Reproductive Medicine and Neurosciences Director, Center for Reproductive Science and Medicine University of California, San Diego, School of Medicine 3A14 Leichtag Biomedical Research Building 9500 Gilman Drive, La Jolla, CA 92093-0674 (858) 534-1312, Fax (858) 534-1438, e-mail: [email protected] Departmental Web page: http://repromed.ucsd.edu/divisions/endocrinology/mellon.shtml Laboratory Web Page: http://repro.ucsd.edu/Mellon/SitePages/home.aspx ORCID 0000-0002-8856-0410 EDUCATION B.A., 1975, University of California at Santa Cruz Degrees in both Biology and Chemistry with Highest Honors Ph.D., 1979, University of California at Berkeley Department of Molecular Biology Dissertation: Two Transforming Genes and Three Replicative Genes of Avian RNA Tumor Viruses: Identification, Gene Order, and Gene Expression APPOINTMENTS Research Associate, 1975, University of California at Berkeley Department of Molecular Biology with Dr. Harrison Echols Postdoctoral Fellow with Dr. Tom Maniatis 1979-1980, California Institute of Technology, Division of Biology 1980-1984, Harvard University, Department of Biochemistry and Molecular Biology Assistant Professor 1984-1990, The Salk Institute for Biological Studies, Regulatory Biology Laboratory Assistant Adjunct Professor 1988-1991, University of California, San Diego Associate Professor 1990-1991, The Salk Institute for Biological Studies, Regulatory Biology Laboratory Associate
    [Show full text]
  • Journal of Virology
    JOURNAL OF VIROLOGY VOLUME 37 0 NUMBER 1 0 JANUARY 1981 EDITORIAL BOARD Robert R. Wagner, Editor-in-Chief (1982) University of Virginia School of Medicine, Charlottesville Dwight L. Anderson, Editor (1983) Haold S. Ginsberg, Editor (1984) School ofDentistry, Columbia University University of Minnesota, New York, N. Y. Minneapolis David T. Denhardt, Editor (1982) Edward M. Scolnick, Editor (1982) University of Western Ontario National Cancer Institute London, Ontario, Canada Bethesda, Md. David Baltimore (1981) Calderon Howe (1982) Dan S. Ray (1983) Amiya K. Banerjee (1982) Alice S. Huang (1981) M. E. Reichmann (1982) Kenneth I. Berns (1982) Tony Hunter (1983) Bernard E. Reilly (1983) David H. L. Bishop (1982) D. C. Kelly (1982) Wiliam S. Robinson (1983) David Botstein (1982) Thomas J. Kelly, Jr. (1982) Bernard Roizman (1982) Dennis T. Brown (1981) George Khoury (1981) Roland R. Rueckert (1982) Ahmad 1. Bukhari (1981) Jonathan A. King (1981) Norman P. Salzman (1981) Purnell Cboppin (1983) David W. Kingsbury (1982) Joseph Sambrook (1982) John M. Coffin (1983) Daniel Kolakofsky (1983) PrisciUa A. Schaffer (1981) Richard W. Compans (1982) Lloyd M. Kozboff (1982) Sondra Schlesinger (1983) Geoffrey M. Cooper (1981) Robert M. Krug (1983) June R. Scott (1983) Clive Dickson (1981) Robert A. Lazzarini 1981) Phillip A. Sharp (1982) Walter Doerfler (1983) Richard A. Lerner (1981) Aaron J. Shatkin (1982) Harrison Echols (1981) Myron Levine (1982) Saul J. Sllverstein (1982) Elvera Ehrenfeld (1983) Tomas Lindahl (1981) Lee D. Simon (1981) Robert N. Eisenman (1982) Douglas R. Lowy (1983) Kai Simons (1981) Suzanne U. Emerson (1983) Ronald B. Luftig (1981) Patrcia G. Spear (1981) Lynn Enquist (1981) Robert Martin (1981) Mark F.
    [Show full text]
  • Duplication Mutation As an SOS Response in Escherichia Coli
    Copyright 0 1989 by the Genetics Society of America Duplication Mutation as anSOS Response in Escherichia coli: Enhanced Duplication Formationby a Constitutively Activated RecA Joan Dimpfl and Harrison Echols Department of Molecular Biology, University of CaE$ornia, Berkeley, California 94720 Manuscript received March 10, 1989 Accepted for publication July 6, 1989 ABSTRACT The SOS response in Escherichia coli involves the induction of a multioperon regulatory system, which copes withthe presence of DNA lesions that interfere with DNA replication. Induction depends on activation of the RecA protein to cleave the LexA repressor of SOS operons. In addition to inducible DNA repair, the SOS system producesa large increasein the frequency of point mutations. To examine the possibility that other types of mutations are induced as partof the SOS response, we have studied the production of tandem duplications.To avoid the complications of indirect effectsof the DNA lesions, we have activated the SOS response by a constitutive mutation in the recA gene, recA730. The introduction of the recA730 mutation results in an increase in duplications in the range of tenfold or greater, as judged by two different criteria. Based on its genetic requirements, the pathway for induced duplication formation is distinct from the point mutation pathway and also differs from the major normal recombination pathway.The induction of pathways for both duplica- tions and point mutationsshows that the SOS system produces a broad mutagenic response.We have suggested previously that many typesof mutations might be inducedby severe environmental stress, thereby enhancing genetic variationin an endangered population. HE introduction of a replication-inhibitinglesion deletions, translocations) (ECHOLS198 1 ; 1982; Mc- T (by UV light or a chemical mutagen) into the DONALD1984).
    [Show full text]
  • MORC1 Represses Transposable Elements in the Mouse Male Germline
    ARTICLE Received 12 Sep 2014 | Accepted 7 Nov 2014 | Published 12 Dec 2014 DOI: 10.1038/ncomms6795 OPEN MORC1 represses transposable elements in the mouse male germline William A. Pastor1,*, Hume Stroud1,*,w, Kevin Nee1, Wanlu Liu1, Dubravka Pezic2, Sergei Manakov2, Serena A. Lee1, Guillaume Moissiard1, Natasha Zamudio3,De´borah Bourc’his3, Alexei A. Aravin2, Amander T. Clark1,4 & Steven E. Jacobsen1,4,5 The Microrchidia (Morc) family of GHKL ATPases are present in a wide variety of prokaryotic and eukaryotic organisms but are of largely unknown function. Genetic screens in Arabidopsis thaliana have identified Morc genes as important repressors of transposons and other DNA-methylated and silent genes. MORC1-deficient mice were previously found to display male-specific germ cell loss and infertility. Here we show that MORC1 is responsible for transposon repression in the male germline in a pattern that is similar to that observed for germ cells deficient for the DNA methyltransferase homologue DNMT3L. Morc1 mutants show highly localized defects in the establishment of DNA methylation at specific classes of transposons, and this is associated with failed transposon silencing at these sites. Our results identify MORC1 as an important new regulator of the epigenetic landscape of male germ cells during the period of global de novo methylation. 1 Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, 4028 Terasaki Life Sciences Building, 610 Charles E. Young Drive East, Los Angeles, California 90095, USA. 2 Division of Biology and Biochemical Engineering, California Institute of Technology, 1200 E California Boulevard, Pasadena, California 91125, USA. 3 Unite´ de ge´ne´tique et biologie du de´veloppement, Instititute Curie, CNRS UMR3215, INSERM U934, Paris 75005, France.
    [Show full text]
  • The Roles of Moron Genes in the Escherichia Coli Enterobacteria Phage Phi-80
    THE ROLES OF MORON GENES IN THE ESCHERICHIA COLI ENTEROBACTERIA PHAGE PHI-80 Yury V. Ivanov A Dissertation Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY December 2012 Committee: Ray A. Larsen, Advisor Craig L. Zirbel Graduate Faculty Representative Vipa Phuntumart Scott O. Rogers George S. Bullerjahn © 2012 Yury Ivanov All Rights Reserved iii ABSTRACT Ray Larsen, Advisor The TonB system couples cytoplasmic membrane-derived proton motive force energy to drive ferric siderophore transport across the outer membrane of Gram-negative bacteria. While much effort has focused on this process, how energy is harnessed to provide for transport of ligands remains unknown. Several bacterial viruses (“phage”) are known to require the TonB system to irreversibly adsorb (i.e., establish infection) in the model organism Escherichia coli. One such phage is φ80, a “cousin” of the model temperate phage λ. Determining how φ80 is using the TonB system for infection should provide novel insights to the mechanisms of TonB-dependent processes. It had long been known that recombination between λ and φ80 results in a λ-like phage for whom TonB is now required; and this recombination involved the λ J gene, which encodes the tail-spike protein required for irreversible adsorption of λ to E. coli. Thus, we suspected that a φ80 homologue of the λ J gene product was responsible for the TonB dependence of φ80. While φ80 has long served as a tool for assaying TonB activity, it has not received the scrutiny afforded λ.
    [Show full text]
  • Chapter 20974
    Genome Replication of Bacterial and Archaeal Viruses Česlovas Venclovas, Vilnius University, Vilnius, Lithuania r 2019 Elsevier Inc. All rights reserved. Glossary RNA-primed DNA replication Conventional DNA Negative sense ( À ) strand A negative-sense DNA or RNA replication used by all cellular organisms whereby a strand has a nucleotide sequence complementary to the primase synthesizes a short RNA primer with a free 3′-OH messenger RNA and cannot be directly translated into protein. group which is subsequently elongated by a DNA Positive sense (+) strand A positive sense DNA or RNA polymerase. strand has a nucleotide sequence, which is the same as that Rolling-circle DNA replication DNA replication whereby of the messenger RNA, and the RNA version of this sequence the replication initiation protein creates a nick in the circular is directly translatable into protein. double-stranded DNA and becomes covalently attached to Protein-primed DNA replication DNA replication whereby the 5′ end of the nicked strand. The free 3′-OH group at the a DNA polymerase uses the 3′-OH group provided by the nick site is then used by the DNA polymerase to synthesize specialized protein as a primer to synthesize a new DNA strand. the new strand. Genomes of Prokaryotic Viruses At present, all identified archaeal viruses have either double-stranded (ds) or single-stranded (ss) DNA genomes. Although metagenomic analyzes suggested the existence of archaeal viruses with RNA genomes, this finding remains to be substantiated. Bacterial viruses, also refered to as bacteriophages or phages for short, have either DNA or RNA genomes, including circular ssDNA, circular or linear dsDNA, linear positive-sense (+)ssRNA or segmented dsRNA (Table 1).
    [Show full text]
  • Activity of the Hsp7o Chaperone Complex-Dnak, Dnaj, And
    Proc. Natl. Acad. Sci. USA Vol. 89, pp. 12108-12111, December 1992 Biochemistry Activity of the Hsp7O chaperone complex-DnaK, DnaJ, and GrpE- in initiating phage A DNA replication by sequestering and releasing A P protein (heat shock proteins/DNA replication/protein-protein interaction) HEIDI J. HOFFMANN, SUSAN K. LYMAN, CHI Lu, MARIE-AGNES PETIT, AND HARRISON ECHOLS Division of Biochemistry and Molecular Biology, University of California, Berkeley, CA 94720 Contributed by Harrison Echols, September 24, 1992 ABSTRACT Initiation of DNA replication by phage A occurs efficiently with less DnaK, and the unwinding reaction requires the ordered assembly and disassembly ofa specialized is more often bidirectional, indicating a more efficient disas- nucleoprotein structure at the origin of replication. In the sembly reaction (C. Wyman, C. Vasilikiotis, D. Ang, C. disasembly pathway, a set of Escherichia coli heat shock Georgopoulos, and H.E., unpublished work). Based on a proteins termed the Hsp7O complex-DnaK, DnaJ, and variety of data, the three-protein set of heat shock proteins GrpE-act with ATP to release A P protein from the nucleo- appears likely to function typically together. DnaJ and GrpE protein complex, freeing the DnaB helicase for its DNA- markedly stimulate the ATPase activity of DnaK, the bac- unwinding reaction. To investigate the mechanism of the terial homolog ofthe eukaryotic -70-kDa heat shock protein release reaction, we have exmned the interaction between P Hsp7O (14). Moreover, the three-protein set ("Hsp7O com- and the three heat shock proteins by glycerol gradient sedi- plex") acts together in other reactions, including control of mentation and gel electrophoresis.
    [Show full text]