DOCSLIB.ORG

Dna Replication in Archaea: Priming, Transferase, and Elongation Activities

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Dna Replication in Archaea: Priming, Transferase, and Elongation Activities DNA REPLICATION IN ARCHAEA: PRIMING, TRANSFERASE, AND ELONGATION ACTIVITIES by Zhongfeng Zuo Bachelor degree, Beijing Technology and Business University, 1999 Submitted to the Graduate Faculty of the Kenneth P. Dietrich School of Arts and Sciences in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Pittsburgh 2012 UNIVERSITY OF PITTSBURGH THE KENNETH P. DIETRICH SCHOOL OF ARTS AND SCIENCES This dissertation was presented by Zhongfeng Zuo It was defended on January 27, 2012 and approved by Stephen G. Weber, Professor, Department of Chemistry Billy Day, Professor, Department of Chemistry, Department of Pharmacy Renã A. S. Robinson, Assistant Professor, Department of Chemistry Dissertation Advisor: Michael A. Trakselis, Assistant Professor, Department of Chemistry ii DNA REPLICATION IN ARCHAEA: PRIMING, TRANSFERASE, AND ELONGATION ACTIVITIES Zhongfeng Zuo, Ph.D University of Pittsburgh, 2012 Copyright © by Zhongfeng Zuo 2012 iii DNA REPLICATION IN ARCHAEA: PRIMING, TRANSFERASE, AND ELONGATION ACTIVITIES Zhongfeng Zuo, Ph.D University of Pittsburgh, 2012 We have biochemically characterized the bacterial-like DnaG primase contained within the hyperthermophilic crenarchaeon Sulfolobus solfataricus (Sso ) and compared in vitro priming kinetics with those of the eukaryotic-like primase (PriS&L) also found in Sso . Sso DnaG exhibited metal- and temperature-dependent profiles consistent with priming at high temperatures. The distribution of primer products for Sso DnaG was discrete but highly similar to the distribution of primer products produced by the homologous Escherichia coli DnaG. The predominant primer length was 13 bases, although less abundant products of varying sizes are also present. Sso DnaG was found to bind DNA cooperatively as a dimer with a moderate dissociation constant. Mutation of the conserved glutamate in the active site severely inhibited priming activity, showing functional homology with E. coli DnaG. Sso DnaG was also found to have a greater than four-fold faster rate of DNA priming over that of Sso PriS&L under optimal in vitro conditions. The presence of both enzymatically functional primase families in archaea suggests that the DNA priming role may be shared on leading or lagging strands during DNA replication. iv DNA replication polymerases have the inherent ability to faithfully copy a DNA template according to Watson Crick base pairing. The primary B-family DNA replication polymerase (Dpo1) in Sso is shown here to possess a remarkable DNA stabilizing ability for maintaining weak base pairing interactions to facilitate primer extension. This thermal stabilization by Sso Dpo1 allowed for template-directed synthesis at temperatures more than 30 °C above the melting temperature of naked DNA. Surprisingly, Sso Dpo1 also displays a terminal deoxynucleotide transferase (TdT) activity unlike any other B-family DNA polymerases. Sso Dpo1 is shown to elongate single stranded DNA in template-dependent and template- independent manners. The multiple activities of this unique B-family DNA polymerase make this enzyme an essential component for DNA replication and DNA repair for the maintenance of the archaeal genome at high temperatures. Preliminary results of primer transfer studies in Sso show that Sso Dpo1 can elongate DNA primers de novo synthesized by Sso PriS&L, but elongation of RNA primers synthesized by both Sso PriS&L and Sso DnaG was not observed for Sso Dpo1. Future studies to untangle the primer transfer mechanism in archaea are discussed. v TABLE OF CONTENTS TABLE OF CONTENTS ........................................................................................................... VI LIST OF TABLES ...................................................................................................................... IX LIST OF FIGURES ..................................................................................................................... X PREFACE .................................................................................................................................. XII 1.0 INTRODUCTION ........................................................................................................ 1 1.1 DNA REPLICATION ......................................................................................... 1 1.2 PRIMASES AND PRIMING IN DNA REPLICATION ................................. 4 1.2.1 Primases and primers ....................................................................................... 4 1.2.2 Mechanism of DNA priming ........................................................................... 10 1.2.3. Primer handoff ................................................................................................. 13 1.3 DNA POLYMERASES, DNA REPLICATION AND DNA REPAIR .......... 14 1.4 DNA REPLICATION IN ARCHAEA ............................................................. 18 2.0 CHARACTERIZATION OF SSO DNAG: IMPLICATIONS FOR A DUAL PRIMASE SYSTEM ................................................................................................................... 27 2.1 MATERIALS AND METHODS ...................................................................... 28 2.2 RESULTS ........................................................................................................... 34 2.2.1 Purification of SsoDnaG ................................................................................ 34 2.2.2 Conditions for Maximal Priming Activity of SsoDnaG ................................ 37 vi 2.2.3 Primer Products Synthesized by SsoDnaG .................................................... 39 2.2.4 Priming Activity of SsoDnaG ......................................................................... 40 2.2.5 DNA Binding of SsoDnaG ............................................................................. 41 2.2.6 Active Site Mutant of Sso DnaG Reduces Priming Activity ....................... 42 2.2.7 Comparison of Priming Activities of SsoDnaG to SsoPriS&L ..................... 45 2.3 DISCUSSIONS ................................................................................................... 47 2.3.1 Comparison of the DnaG Primase from Archaea and Bacterial Domains .. 48 2.3.2 Potential Roles of Each Primase in Archaea ................................................ 51 3.0 STRAND ANNEALING AND TERMINAL TRANSFERASE ACTIVITIES OF SSO DPO1 ..................................................................................................................................... 58 3.1 MATERIALS AND METHODS ...................................................................... 61 3.2 RESULTS ........................................................................................................... 64 3.2.1 Thermal Stabilization and Annealing Activity of Sso Dpo1 ....................... 64 3.2.2 Template Specific Terminal Transferase Activities ................................... 69 3.2.3 Nucleotide Specificity for TdT Activity ....................................................... 74 3.2.4 Loop Back Annealing Model for Transferase Activity .............................. 76 3.2.5 Kinetic Mechanism for TdT Activity ........................................................... 78 3.3 DISCUSSION ..................................................................................................... 82 3.3.1 Role of DNA Polymerase Strand Annealing/Stabilization in DNA Replication .................................................................................................................. 83 3.3.2 DNA Polymerase Template Slipping ........................................................... 84 3.3.3 Both Template Independent and Dependent Terminal Transferase Activities ...................................................................................................................... 85 vii 3.3.4 Looping Back as a Mechanism for Terminal Transferase Activity .......... 86 3.3.5 Role of Terminal Transferase Activity in Archaea .................................... 88 4.0 PRIMER HANDOFF IN SULFOLOBUS SOLFATARICUS TO INITIATE DNA REPLICATION .......................................................................................................................... 95 4.1 MATERIALS AND METHODS ...................................................................... 98 4.2 RESULTS ......................................................................................................... 101 4.2.1 Elongation of synthetic primers ................................................................. 101 4.2.2 De novo primer transfer from PriS&L to Dpo1 ....................................... 104 4.2.3 De novo Primer handoff from DnaG to Dpo1 ........................................... 107 4.3 DISCUSSION ................................................................................................... 109 5.0 FUTURE WORK ..................................................................................................... 114 5.1 MOLECULAR ROLE OF SSO DNAG IN DNA REPLICATION IN ARCHAEA ........................................................................................................................ 114 5.2 TDT ACTIVITY OF DPO1 IN ARCHAEAL DNA REPAIR ..................... 115 5.3 PRIMER TRANSFER IN ARCHAEA .......................................................... 116 viii LIST OF TABLES Table 1-1. Biochemical properties of purified DNA primases .................................................. 5 Table 1-2. DNA Polymerase Families......................................................................................
Load more

Recommended publications
  • Arthur Kornberg Discovered (The First) DNA Polymerase Four
    Arthur Kornberg discovered (the first) DNA polymerase Using an “in vitro” system for DNA polymerase activity: 1. Grow E. coli 2. Break open cells 3. Prepare soluble extract 4. Fractionate extract to resolve different proteins from each other; repeat; repeat 5. Search for DNA polymerase activity using an biochemical assay: incorporate radioactive building blocks into DNA chains Four requirements of DNA-templated (DNA-dependent) DNA polymerases • single-stranded template • deoxyribonucleotides with 5’ triphosphate (dNTPs) • magnesium ions • annealed primer with 3’ OH Synthesis ONLY occurs in the 5’-3’ direction Fig 4-1 E. coli DNA polymerase I 5’-3’ polymerase activity Primer has a 3’-OH Incoming dNTP has a 5’ triphosphate Pyrophosphate (PP) is lost when dNMP adds to the chain E. coli DNA polymerase I: 3 separable enzyme activities in 3 protein domains 5’-3’ polymerase + 3’-5’ exonuclease = Klenow fragment N C 5’-3’ exonuclease Fig 4-3 E. coli DNA polymerase I 3’-5’ exonuclease Opposite polarity compared to polymerase: polymerase activity must stop to allow 3’-5’ exonuclease activity No dNTP can be re-made in reversed 3’-5’ direction: dNMP released by hydrolysis of phosphodiester backboneFig 4-4 Proof-reading (editing) of misincorporated 3’ dNMP by the 3’-5’ exonuclease Fidelity is accuracy of template-cognate dNTP selection. It depends on the polymerase active site structure and the balance of competing polymerase and exonuclease activities. A mismatch disfavors extension and favors the exonuclease.Fig 4-5 Superimposed structure of the Klenow fragment of DNA pol I with two different DNAs “Fingers” “Thumb” “Palm” red/orange helix: 3’ in red is elongating blue/cyan helix: 3’ in blue is getting edited Fig 4-6 E.
    [Show full text]
  • Artificial Human Telomeres from DNA Nanocircle Templates
    Artificial human telomeres from DNA nanocircle templates Ulf M. Lindstro¨ m*, Ravi A. Chandrasekaran*, Lucian Orbai*, Sandra A. Helquist*, Gregory P. Miller*, Emin Oroudjev†, Helen G. Hansma†, and Eric T. Kool*‡ *Department of Chemistry, Stanford University, Stanford, CA 94305-5080; and †Department of Physics, University of California, Santa Barbara, CA 93106 Edited by Peter B. Dervan, California Institute of Technology, Pasadena, CA, and approved October 9, 2002 (received for review July 3, 2002) Human telomerase is a reverse-transcriptase enzyme that synthe- sizes the multikilobase repeating hexamer telomere sequence (TTAGGG)n at the ends of chromosomes. Here we describe a designed approach to mimicry of telomerase, in which synthetic DNA nanocircles act as essentially infinite catalytic templates for efficient synthesis of long telomeres by DNA polymerase enzymes. Results show that the combination of a nanocircle and a DNA polymerase gives a positive telomere-repeat amplification proto- col assay result for telomerase activity, and similar to the natural enzyme, it is inhibited by a known telomerase inhibitor. We show that artificial telomeres can be engineered on human chromo- somes by this approach. This strategy allows for the preparation of synthetic telomeres for biological and structural study of telomeres and proteins that interact with them, and it raises the possibility of telomere engineering in cells without expression of telomerase itself. Finally, the results provide direct physical support for a recently proposed rolling-circle mechanism for telomerase- independent telomere elongation. rolling-circle replication ͉ primer extension ͉ telomerase ͉ TRAP assay he telomerase enzyme synthesizes the multikilobase repeat- Ting hexamer telomere sequence (TTAGGG)n at the ends of chromosomes (1–3).
    [Show full text]
  • Family a and B DNA Polymerases in Cancer: Opportunities for Therapeutic Interventions
    biology Review Family A and B DNA Polymerases in Cancer: Opportunities for Therapeutic Interventions Vinit Shanbhag 1,2, Shrikesh Sachdev 2,3, Jacqueline A. Flores 2,3, Mukund J. Modak 4 and Kamalendra Singh 2,3,4,5,* 1 Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; [email protected] 2 The Christopher S. Bond Life Science Center, University of Missouri, Columbia, MO 65211, USA; [email protected] (S.S.); [email protected] (J.A.F.) 3 Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65211, USA 4 Department of Microbiology, Biochemistry and Molecular Genetics 225 Warren Street, NJ 07103, USA; [email protected] 5 Department of Laboratory Medicine, Karolinska Institutet, Stockholm 141 86, Sweden * Correspondence: [email protected]; Tel.: +1-573-882-9024 Received: 13 November 2017; Accepted: 29 December 2017; Published: 2 January 2018 Abstract: DNA polymerases are essential for genome replication, DNA repair and translesion DNA synthesis (TLS). Broadly, these enzymes belong to two groups: replicative and non-replicative DNA polymerases. A considerable body of data suggests that both groups of DNA polymerases are associated with cancer. Many mutations in cancer cells are either the result of error-prone DNA synthesis by non-replicative polymerases, or the inability of replicative DNA polymerases to proofread mismatched nucleotides due to mutations in 30-50 exonuclease activity. Moreover, non-replicative, TLS-capable DNA polymerases can negatively impact cancer treatment by synthesizing DNA past lesions generated from treatments such as cisplatin, oxaliplatin, etoposide, bleomycin, and radiotherapy. Hence, the inhibition of DNA polymerases in tumor cells has the potential to enhance treatment outcomes.
    [Show full text]
  • DNA Or RNA Priming of Bacteriophage G4 DNA Synthesis By
    Proc. Nati. Acad. Sci. USA Vol. 74, No. 7, pp. 2815-2819, July 1977 Biochemistry DNA or RNA priming of bacteriophage G4 DNA synthesis by Escherichia coli dnaG protein (ADP/DNA binding protein/bacteriophage ST-1 DNA/DNA replication) SUE WICKNER Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20014 Communicated by Jerard Hurwitz, May 6, 1977 ABSTRACT Escherichia coli dnaG protein is involved in wild-type and thermolabile) were purified by procedures in the initiation of DNA synthesis dependent on G4 or ST-1 sin- refs. 13, 14, 15, 16, 5, and 17, respectively. Assay conditions and gle-stranded phage DNAs [Bouche, J.-P., Zechel, K. & Kornberg, definitions of units for DNA polymerase III are in ref. A. (1975)1. Biol. Chem. 250,5995-60011. The reaction occurs by 3; those the following mechanism: dnaG protein binds to specific sites for the other proteins are in the above references. DNA EF I on the DNA in a reaction requiring E. coli DNA binding protein. and DNA EF III were purified by procedures to be published An oligonucleotide is synthesized in a reaction involving dnaG elsewhere using the assay described in ref. 4. By native poly- protein, DNA binding protein, and DNA. With G4 DNA this acrylamide gel electrophoresis (18), the DNA binding protein reaction requires ADP, dTTP (or UTP), and dGTP (or GTP). was 80% pure and the dnaG protein from wild-type cells was Elongation of the oligonucleotide can be catalyzed by DNA 30% polymerase II or III in combination with dnaZ protein and pure.
    [Show full text]
  • The Impact of the Integrated Stress Response on DNA Replication
    The impact of the integrated stress response on DNA replication ____________________________________________________ Dissertation for the award of the degree "Doctor of Philosophy" (Ph.D.) Division of Mathematics and Natural Sciences of the Georg-August-Universität Göttingen within the doctoral program Molecular Biology of Cells of the Georg-August University School of Science (GAUSS) submitted by Josephine Ann Mun Yee Choo from Selangor, Malaysia Göttingen 2019 Thesis Committee 1. Prof. Dr. Matthias Dobbelstein, Institute of Molecular Oncology, University Medical Center Göttingen (UMG) 2. PD Dr. Halyna Shcherbata, Research Group – Gene Expression and Signaling, Max Planck Institute for Biophysical Chemistry (MPI-BPC) 3. Prof. Dr. Steven Johnsen, Clinic for General, Visceral and Pediatric Surgery, University Medical Center Göttingen (UMG) Members of the Examination Board 1st reviewer: Prof. Dr. Matthias Dobbelstein, Institute of Molecular Oncology, University Medical Center Göttingen (UMG) 2nd reviewer: PD Dr. Halyna Shcherbata, Research Group – Gene Expression and Signalling, Max Planck Institute for Biophysical Chemistry (MPI-BPC) External members of the Examination Board 1. Dr. Roland Dosch, Department of Developmental Biochemistry, University Medical Center Göttingen (UMG) 2. Prof. Dr. Heidi Hahn, Department of Human Genetics, University Medical Center Göttingen (UMG) 3. Prof. Dr. Dieter Kube, Department of Hematology and Oncology, University Medical Center Göttingen (UMG) 4. Dr. Nuno Raimundo, Department of Cellular Biochemistry,
    [Show full text]
  • 6.Start.Stop.07.Ppt [Read-Only]
    Accessory factors summary 1. DNA polymerase can’t replicate a genome. Solution ATP? No single stranded template Helicase + The ss template is unstable SSB (RPA (euks)) - No primer Primase (+) No 3’-->5’ polymerase Replication fork Too slow and distributive SSB and sliding clamp - Sliding clamp can’t get on Clamp loader (γ/RFC) + Lagging strand contains RNA Pol I 5’-->3’ exo, RNAseH - Lagging strand is nicked DNA ligase + Helicase introduces + supercoils Topoisomerase II + and products tangled 2. DNA replication is fast and processive DNA polymerase holoenzyme 1 Maturation of Okazaki fragments Topoisomerases control chromosome topology Catenanes/knots Topos Relaxed/disentangled •Major therapeutic target - chemotherapeutics/antibacterials •Type II topos transport one DNA through another 2 Starting and stopping summary 1. DNA replication is controlled at the initiation step. 2. DNA replication starts at specific sites in E. coli and yeast. 3. In E. coli, DnaA recognizes OriC and promotes loading of the DnaB helicase by DnaC (helicase loader) 4. DnaA and DnaC reactions are coupled to ATP hydrolysis. 5. Bacterial chromosomes are circular, and termination occurs opposite OriC. 6. In E. coli, the helicase inhibitor protein, tus, binds 7 ter DNA sites to trap the replisome at the end. 7. Eukaryotic chromosomes are linear, and the chromosome ends cannot be replicated by the replisome. 8. Telomerase extends the leading strand at the end. 9. Telomerase is a ribonucleoprotein (RNP) with RNA (template) and reverse-transcriptase subunits. Isolating DNA sequences that mediate initiation 3 Different origin sequences in different organisms E. Coli (bacteria) OriC Yeast ARS (Autonomously Replicating Sequences) Metazoans ???? Initiation in prokaryotes and eukaryotes Bacteria Eukaryotes ORC + other proteins load MCM hexameric helicases MCM (helicase) + RPA (ssbp) Primase + DNA pol α PCNA:pol δ + RFC MCM (helicase) + RPA (ssbp) PCNA:pol δ + RFC (clamp loader) Primase + DNA pol α PCNA:pol δ + DNA ligase 4 Crystal structure of DnaA:ATP revealed mechanism of origin assembly 1.
    [Show full text]
  • Chloroplast and Cytosolic Triosephosphate Isomerases from Spinach: Purification, Microsequencing and Cdna Cloning of the Chloroplast Enzyme
    Plant Molecular Biology 26: 1961-1973, 1994. © 1994 KIuwer Academic Publishers. Printed in Belgium. 1961 Chloroplast and cytosolic triosephosphate isomerases from spinach: purification, microsequencing and cDNA cloning of the chloroplast enzyme Katrin Henze 1, Claus Schnarrenberger 2, Josef Kellermann 3 and William Martin 1,, l lnstitutfiir Genetik, Technische Universitiit Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, FRG (* author for correspondence); 2Institut fiir Pflanzenphysiologie und Mikrobiologie, Freie Universitiit Berlin, KOnigin-Luise-Strasse 12-16a, D-14195 Berlin, Germany; 3Max Planck Institut fiir Biochemie, Am Klopferspitz, D-82152 Martinsried, Germany Received 27 September 1994; accepted 25 October 1994 Key words: triosephosphate isomerase, isoenzyme purification, Calvin cycle enzyme, cDNA cloning, gene phylogeny Abstract Chloroplast and cytosolic triosephosphate isomerases from spinach were separated and purified to homogeneity. Bothenzymes were partially sequenced by Edman degradation. Using degenerate prim- ers designed against the amino acid sequences, a homologous probe for the chloroplast enzyme was amplified and used to isolate several full-size cDNA clones. Chloroplast triosephosphate isomerase is encoded by a single gene in spinach. Analysis of the chloroplast cDNA sequence in the context of its homologues from eukaryotes and eubacteria reveals that the gene arose through duplication of its pre- existing nuclear counterpart for the cytosolic enzyme during plant evolution. Abbreviations: TPI, triosephosphate
    [Show full text]
  • DNA Replication
    Semiconservative Replication DNA Replication Chapter 11 Wikipedia Kornberg’s DNA Polymerase I DNA Polymerase Reaction Requirements for DNA synthesis DNA Polymerase Mg++ dNTP single stranded DNA template Priming 3’ OH Consider how the active site descriminates among the dNTP’s. Other Enzymatic Activities Origin of Replication E. coli DNA Polymerases 9 mers- TTATTTCCAC Enzymatic Activities I II III . 5’-3’ synthesis + + + Pair 13mers GATCTCTTATTAG Required Primer + + + Order of Interaction 1. dnaA binds 9mers 3’-5’ Exonuclease + + + 2. dnaBC bind dnaA and 13mer -dnaB ATP dependent (Proofreading Activity) helicase 3. ssbp bind unwound DNA stabilizing it 5’-3’ Exonuclease 4. Gyrase (topoisomerase) relieves torsional stress (Replacement Activity) + - - . 5. Primase (dnaG) synthesizes short primers 6. DNA polymerase III initiates synthesis DNA Polymerase III mutation lethal – essential to replication DNA Polymerase I mutation viable – higher rate of mutation DNA Polymerase II mutation viable – function unknown 1 dnaA Discontinuous Replication DNA Polymerase synthesizes 5’-3’ only http://oregonstate.edu/instruction/bb492/figletters/FigH3.html Two Replication Forks Replication Fork http://oregonstate.edu/instruction/bb492/figletters/FigH2.html DNA Polymerase Clamp Replication Fork Improved Processivity http://www.wehi.edu.au/education/wehi-tv/dna/replication.html 2 Simultaneous Synthesis Eukaryotic Issues • Size of Genome • Ends of Linear Chromosomes Movie Size of Eukaryotic Genome Multiple Origins of Replication Genome Size – E coli 4.6 Mbp
    [Show full text]
  • Analysis of DNA Polymerases II and III in Mutants of Escherichia Coli Thermosensitive for DNA Synthesis (Polal Mutants/Phosphocellulose Chromatography/Dnae Locus)
    Proc. Nat. Acad. Sci. USA Vol. 68, No. 12, pp. 3150-3153, December 1971 Analysis of DNA Polymerases II and III in Mutants of Escherichia coli Thermosensitive for DNA Synthesis (polAl mutants/phosphocellulose chromatography/dnaE locus) MALCOLM L. GEFTER, YUKINORI HIROTA*, THOMAS KORNBERG, JAMES A. WECHSLER, AND C. BARNOUX* Department of Biological Sciences, Columbia University, New York, N.Y. 10027; and * Service de G6n6tique Cellulaire de l'Institut Pasteur, Paris Communicated by Cyrus Levinthal, October 18, 1971 ABSTRACT A series of double mutants carrying one of (5) PC79: F- his- strr malA xyl- mtlh thi- polAl sup- the thermosensitive mutations for DNA synthesis (dnaA, dnaD7 B, C, D, E, F, and G) and the polAl mutation of DeLucia and Cairns, were constructed. Enzyme activities of DNA (6) E5111: F- his- strr malA xylh mtlh arg- thi- sup- Polymerases II and III were measured in each mutant. polAl dnaE511 DNA Polymerase II activity was normal in all strains (7) E4860: F- his- str' malA xylh mtlh arg- thi- sup- tested. DNA Polymerase III activity is thermosensitive dnaE486 specifically in those strains having thermosensitive muta- tions at the dnaE locus. From these results we conclude (8) E4868: F- his- strr malA xyl- mtlh arg thi- sup- that DNA Polymerases II and III are independent en- polAl dnaE486 zymes and that DNA Polymerase III is an enzyme required (9) BT1026: H560thy-endoI- polAl dnaE for DNA replication in Escherichia coli. (10) BT1040: H560 thy endoI polAl dnaE (11) E1011: F- his- strr malA xyl- mtl- arg- thi- sup- The isolation by DeLucia and Cairns (1) of an Escherichia polAl dnaFI01 coli mutant that lacks DNA Polymerase I activity (polA1) (12) JW207: thy-rha-strrpolAl dnaF101 has prompted many investigations into the nature of the (13) NY73: leu- thy- metE rifr strr polAl dnaG3 DNA synthetic capacity of such strains.
    [Show full text]
  • Rnase HI Is Essential for Survival of Mycobacterium Smegmatis
    RESEARCH ARTICLE RNase HI Is Essential for Survival of Mycobacterium smegmatis Alina E. Minias1*, Anna M. Brzostek1, Malgorzata Korycka- Machala1, Bozena Dziadek2, Piotr Minias3, Malini Rajagopalan4, Murty Madiraju4, Jaroslaw Dziadek1* 1 Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland, 2 Department of Immunoparasitology, University of Lodz, Lodz, Poland, 3 Department of Teacher Training and Biodiversity Studies, University of Lodz, Lodz, Poland, 4 Department of Microbiology, University of Texas Health Center at Tyler, Tyler, Texas, United States of America * [email protected] (AM); [email protected] (JD) Abstract RNases H are involved in the removal of RNA from RNA/DNA hybrids. Type I RNases H are thought to recognize and cleave the RNA/DNA duplex when at least four ribonucleo- tides are present. Here we investigated the importance of RNase H type I encoding genes OPEN ACCESS for model organism Mycobacterium smegmatis. By performing gene replacement through homologous recombination, we demonstrate that each of the two presumable RNase H Citation: Minias AE, Brzostek AM, Korycka- Machala M, Dziadek B, Minias P, Rajagopalan M, et al. (2015) type I encoding genes, rnhA and MSMEG4305, can be removed from M. smegmatis ge- RNase HI Is Essential for Survival of Mycobacterium nome without affecting the growth rate of the mutant. Further, we demonstrate that deletion smegmatis. PLoS ONE 10(5): e0126260. of both RNases H type I encoding genes in M. smegmatis leads to synthetic lethality. Final- doi:10.1371/journal.pone.0126260 ly, we question the possibility of existence of RNase HI related alternative mode of initiation Academic Editor: Anil Kumar Tyagi, University of of DNA replication in M.
    [Show full text]
  • Mechanisms of Theta Plasmid Replication in Enterobacteria and Implications for Adaptation to Its Host JAY W
    DOMAIN 7 GENETICS AND GENETIC TOOLS Mechanisms of Theta Plasmid Replication in Enterobacteria and Implications for Adaptation to Its Host JAY W. KIM, VEGA BUGATA, GERARDO CORTÉS-CORTÉS, GISELLE QUEVEDO-MARTÍNEZ AND MANEL CAMPS Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, 95064 ABSTRACT Plasmids are autonomously replicating sequences that help cells adapt to diverse stresses. Theta plasmids are the most frequent plasmid class in enterobacteria. They co-opt two host replication mechanisms: replication at oriC, a DnaA-dependent pathway leading to replisome assembly (theta class A), and replication fork restart, a PriA- dependent pathway leading to primosome assembly through primer extension and D-loop formation (theta classes B, C, and D). To ensure autonomy from the host’s replication and to facilitate copy number regulation, theta plasmids have unique mechanisms of replication initiation at the plasmid origin of replication (ori). Tight plasmid copy number regulation is Received: 26 March 2020 essential because of the major and direct impact plasmid gene dosage has on gene Accepted: 07 October 2020 expression. The timing of plasmid replication and segregation are also critical for opti- Posted: 18 November 2020 mizing plasmid gene expression. Therefore, we propose that plasmid replication needs to Editor: James M. Slauch, The School of be understood in its biological context, where complex origins of replication (redundant Molecular and Cellular Biology, University of origins, mosaic and cointegrated replicons), plasmid segregation, and toxin-antitoxin sys- Illinois at Urbana-Champaign, Urbana, IL; Gregory ori Phillips, College of Veterinary Medicine, Iowa tems are often present. Highlighting their tight functional integration with function, we State University, Ames, IA show that both partition and toxin-antitoxin systems tend to be encoded in close physical Citation: EcoSal Plus 2020; doi:10.1128/ proximity to the ori in a large collection of Escherichia coli plasmids.
    [Show full text]
  • T7 DNA Polymerase
    Europaisches Patentamt 19 European Patent Office Office europeen des brevets © Publication number: 0 386 858 B1 12 EUROPEAN PATENT SPECIFICATION © Date of publication of patent specification © int. ci.5: C12N 9/12, // C12N15/54, 13.04.94 Bulletin 94/15 C12N15/34, C12Q1/68 © Application number: 90201139.4 @ Date of filing : 24.12.87 (54) T7 DNA polymerase. feg) Priority: 14.01.87 US 3227 © Publication number of the earlier application in 14.12.87 US 132569 accordance with Art. 76 EPC : 0 265 293 @ Date of publication of application © Proprietor : THE PRESIDENT AND FELLOWS 12.09.90 Bulletin 90/37 OF HARVARD COLLEGE 17 Quincy Street Cambridge, MA 02138 (US) © Publication of the grant of the patent : 13.04.94 Bulletin 94/15 © Inventor : Tabor, Stanley 37 Fayerweather Street @ Designated Contracting States : Cambridge, Massachusetts 02138 (US) AT BE CH DE ES FR GB GR IT LI LU NL SE Inventor : Richardson, Charles C. 78 Chestnut Hill Road Chestnut Hill, Massachusetts 02167 (US) © References cited : THE JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 262, no. 32, 15th November 1987,pages © Representative : Moon, Donald Keith et al 15330-15333, US; S. TABOR et al.: Selective BREWER & SON Quality House Quality Court oxidation of the exonuclease domain of bac- Chancery Lane teriophage T7 DNA polymerase" London WC2A 1HT (GB) PROC. NATL. ACAD. SCI. USA, vol. 84, July 1987, pages 4767-4771; S. TABOR et al.: DNA-sequence analysis with a modified bacteriophage T7 DNA polymerase" IDEM Virology, Vol. 95, No. 1, May 1979 CO 00 If) 00 CO 00 CO Note : Within nine months from the publication of the mention of the grant of the European patent, any person may give notice to the European Patent Office of opposition to the European patent granted.
    [Show full text]