Replication and Expression of a Bacterial-Mitochondrial Hybrid
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Mobile Genetic Elements in Streptococci
Curr. Issues Mol. Biol. (2019) 32: 123-166. DOI: https://dx.doi.org/10.21775/cimb.032.123 Mobile Genetic Elements in Streptococci Miao Lu#, Tao Gong#, Anqi Zhang, Boyu Tang, Jiamin Chen, Zhong Zhang, Yuqing Li*, Xuedong Zhou* State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China. #Miao Lu and Tao Gong contributed equally to this work. *Address correspondence to: [email protected], [email protected] Abstract Streptococci are a group of Gram-positive bacteria belonging to the family Streptococcaceae, which are responsible of multiple diseases. Some of these species can cause invasive infection that may result in life-threatening illness. Moreover, antibiotic-resistant bacteria are considerably increasing, thus imposing a global consideration. One of the main causes of this resistance is the horizontal gene transfer (HGT), associated to gene transfer agents including transposons, integrons, plasmids and bacteriophages. These agents, which are called mobile genetic elements (MGEs), encode proteins able to mediate DNA movements. This review briefly describes MGEs in streptococci, focusing on their structure and properties related to HGT and antibiotic resistance. caister.com/cimb 123 Curr. Issues Mol. Biol. (2019) Vol. 32 Mobile Genetic Elements Lu et al Introduction Streptococci are a group of Gram-positive bacteria widely distributed across human and animals. Unlike the Staphylococcus species, streptococci are catalase negative and are subclassified into the three subspecies alpha, beta and gamma according to the partial, complete or absent hemolysis induced, respectively. The beta hemolytic streptococci species are further classified by the cell wall carbohydrate composition (Lancefield, 1933) and according to human diseases in Lancefield groups A, B, C and G. -
The Acinetobacter Baumannii Mla System and Glycerophospholipid
RESEARCH ARTICLE The Acinetobacter baumannii Mla system and glycerophospholipid transport to the outer membrane Cassandra Kamischke1, Junping Fan1, Julien Bergeron2,3, Hemantha D Kulasekara1, Zachary D Dalebroux1, Anika Burrell2, Justin M Kollman2, Samuel I Miller1,4,5* 1Department of Microbiology, University of Washington, Seattle, United States; 2Department of Biochemistry, University of Washington, Seattle, United States; 3Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom; 4Department of Genome Sciences, University of Washington, Seattle, United States; 5Department of Medicine, University of Washington, Seattle, United States Abstract The outer membrane (OM) of Gram-negative bacteria serves as a selective permeability barrier that allows entry of essential nutrients while excluding toxic compounds, including antibiotics. The OM is asymmetric and contains an outer leaflet of lipopolysaccharides (LPS) or lipooligosaccharides (LOS) and an inner leaflet of glycerophospholipids (GPL). We screened Acinetobacter baumannii transposon mutants and identified a number of mutants with OM defects, including an ABC transporter system homologous to the Mla system in E. coli. We further show that this opportunistic, antibiotic-resistant pathogen uses this multicomponent protein complex and ATP hydrolysis at the inner membrane to promote GPL export to the OM. The broad conservation of the Mla system in Gram-negative bacteria suggests the system may play a conserved role in OM biogenesis. The importance of the Mla system to Acinetobacter baumannii OM integrity and antibiotic sensitivity suggests that its components may serve as new antimicrobial *For correspondence: therapeutic targets. [email protected] DOI: https://doi.org/10.7554/eLife.40171.001 Competing interests: The authors declare that no competing interests exist. -
An Update on Self-Amplifying Mrna Vaccine Development
Review An Update on Self-Amplifying mRNA Vaccine Development Anna K. Blakney 1,* , Shell Ip 2 and Andrew J. Geall 2 1 Michael Smith Laboratories, School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z4, Canada 2 Precision NanoSystems Inc., Vancouver, BC V6P 6T7, Canada; [email protected] (S.I.); [email protected] (A.J.G.) * Correspondence: [email protected] Abstract: This review will explore the four major pillars required for design and development of an saRNA vaccine: Antigen design, vector design, non-viral delivery systems, and manufacturing (both saRNA and lipid nanoparticles (LNP)). We report on the major innovations, preclinical and clinical data reported in the last five years and will discuss future prospects. Keywords: RNA; self-amplifying RNA; replicon; vaccine; drug delivery 1. Introduction: The Four Pillars of saRNA Vaccines In December 2019, the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) virus emerged, causing a respiratory illness, coronavirus disease 2019 (COVID-19), in Hubei province, China [1,2]. The virus has spread globally, with the World Health Organization (WHO) declaring it a Public Health Emergency of International concern on 30 January 2020 and a pandemic officially on 7 March 2020 [3]. There is a strong consensus globally that a COVID-19 vaccine is likely the most effective approach to sustainably controlling the COVID-19 pandemic [4]. There has been an unprecedented research effort and global Citation: Blakney, A.K.; Ip, S.; Geall, coordination which has resulted in the rapid development of vaccine candidates and A.J. An Update on Self-Amplifying initiation of human clinical trials. -
Multiple Replicons Constituting the Genome of Pseudomonas Cepacia 17616 HAI-PING Chengt and THOMAS G
JOURNAL OF BACrERIOLOGY, JUlY 1994, p. 4034-4042 Vol. 176, No. 13 0021-9193/94/$04.00+0 Copyright © 1994, American Society for Microbiology Multiple Replicons Constituting the Genome of Pseudomonas cepacia 17616 HAI-PING CHENGt AND THOMAS G. LESSIE* Department ofMicrobiology, University ofMassachusetts, Amherst, Massachusetts 01002 Received 4 February 1994/Accepted 25 April 1994 Macrorestriction fragment analysis of DNA from Pseudomonas cepacia 17616, in conjunction with Southern hybridization experiments using junction fragments containing rare restriction enzyme sites as probes, indicated that this bacterium contains three large circular replicons of 3.4, 2.5, and 0.9 megabases (Mb). Inclusion of the 170-kb cryptic plasmid present in this strain gave an overall estimate of genome size of 7 Mb. Other Southern hybridization experiments indicated that the three large replicons contained rRNA genes as well as insertion sequence elements identified previously in this strain. The distribution of Swal, PacI, and Pmel sites on the three replicons was determined. A derivative of TnS-751 carrying a SwaI site was used to inactivate and map genes on the 2.5- and 3.4-Mb replicons. Mutants were isolated in which the 2.5- and 0.9-Mb replicons had been reduced in size to 1.8 and 0.65 Mb, respectively. The loss of DNA from the 2.5-Mb replicon was associated with lysine auxotrophy, P-lactamase deficiency, and failure to utilize ribitol and trehalose as carbon and energy sources. DNA fragments corresponding in size to randomly linearized forms of the different replicons were detected in unrestricted DNA by pulsed-field gel electrophoresis. -
Single-Round Infectious Particle Production by DNA-Launched Infectious Clones of Bungowannah Pestivirus
viruses Brief Report Single-Round Infectious Particle Production by DNA-Launched Infectious Clones of Bungowannah Pestivirus Anja Dalmann 1, Kerstin Wernike 1 , Eric J. Snijder 2 , Nadia Oreshkova 2 , Ilona Reimann 1 and Martin Beer 1,* 1 Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; anja.dalmann@fli.de (A.D.); kerstin.wernike@fli.de (K.W.) 2 Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; [email protected] (E.J.S.); [email protected] (N.O.) * Correspondence: martin.beer@fli.de Received: 15 July 2020; Accepted: 31 July 2020; Published: 4 August 2020 Abstract: Reverse genetics systems are powerful tools for functional studies of viral genes or for vaccine development. Here, we established DNA-launched reverse genetics for the pestivirus Bungowannah virus (BuPV), where cDNA flanked by a hammerhead ribozyme sequence at the 50 end and the hepatitis delta ribozyme at the 30 end was placed under the control of the CMV RNA polymerase II promoter. Infectious recombinant BuPV could be rescued from pBuPV-DNA-transfected SK-6 cells and it had very similar growth characteristics to BuPV generated by conventional RNA-based reverse genetics and wild type BuPV. Subsequently, DNA-based ERNS deleted BuPV split genomes (pBuPVDERNS/ERNS)—co-expressing the ERNS protein from a separate synthetic CAG promoter—were constructed and characterized in vitro. Overall, DNA-launched BuPV genomes enable a rapid and cost-effective generation of recombinant BuPV and virus mutants, however, the protein expression efficiency of the DNA-launched systems after transfection is very low and needs further optimization in the future to allow the use e.g., as vaccine platform. -
Ribozyme-Mediated, Multiplex CRISPR Gene Editing and Crispri in Plasmodium Yoelii
bioRxiv preprint doi: https://doi.org/10.1101/481416; this version posted November 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Ribozyme-Mediated, Multiplex CRISPR Gene Editing and CRISPRi in Plasmodium yoelii Michael P. Walker1 and Scott E. Lindner1 * 1Department of Biochemistry and Molecular Biology, the Huck Center for Malaria Research, Pennsylvania State University, University Park, PA. *Correspondence: Scott E. Lindner, [email protected] Running Title: CRISPR-RGR in Plasmodium yoelii Keywords: Plasmodium, CRISPR, CRISPRi, Ribozyme, HDR, ALBA bioRxiv preprint doi: https://doi.org/10.1101/481416; this version posted November 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Abstract 2 Functional characterization of genes in Plasmodium parasites often relies on genetic 3 manipulations to disrupt or modify a gene-of-interest. However, these approaches are limited by 4 the time required to generate transgenic parasites for P. falciparum and the availability of a 5 single drug selectable marker for P. yoelii. In both cases, there remains a risk of disrupting native 6 gene regulatory elements with the introduction of exogenous sequences. To address these 7 limitations, we have developed CRISPR-RGR, a SpCas9-based gene editing system for 8 Plasmodium that utilizes a Ribozyme-Guide-Ribozyme (RGR) sgRNA expression strategy. 9 Using this system with P. yoelii, we demonstrate that both gene disruptions and coding sequence 10 insertions are efficiently generated, producing marker-free and scar-free parasites with homology 11 arms as short as 80-100bp. -
Double-Stranded RNA Killer Plasmid Replication in Saccharomyces Cerevisiae (Ski Mutants/Mak Mutants) Akio TOH-E* and REED B
Proc. Natl. Acad. Sci. USA Vol. 77, No. 1, pp. 527-530, January 1980 Genetics "Superkiller" mutations suppress chromosomal mutations affecting double-stranded RNA killer plasmid replication in Saccharomyces cerevisiae (ski mutants/mak mutants) AKIo TOH-E* AND REED B. WICKNERt Laboratory of Biochemical Pharmacology, National Institute of Arthritis, Metabolism, and Digestive Diseases, National Institutes of Health, Bethesda, Maryland 20205 Communicated by G. Gilbert Ashwell, October 17,1979 ABSTRACT Saccharomyces cerevisiae strains carrying a MATERIALS AND METHODS 1.5 X 106-dalton double-stranded RNA genome in virus-like particles (killer plasmid) secrete a protein toxin that kills strains Strains. Some of the strains of Saccharomyces cerevsiae used not carrying this plasmid. At least 28 chromosomal genes (mak in this study are listed in Table 1. Description of the phenotype genes) are required to maintain or replicate this plasmid. Re- and genotype of killer strains was presented previously (21). cessive mutations in any of four other chromosomal genes (ski Curing of the killer plasmid is done by growing killer strains for superkiller) result in enhanced toxin production. We report at an elevated temperature (37°C) (23). Mitochondrial DNA that many ski- mak- double mutants are able to maintain the killer plasmid, indicating that the SKIproducts have an effect was eliminated from strains by streaking to single colonies on on plasmid replication. The skil-) mutation suppresses (by- YPAD medium containing ethidium bromide at 30 ug/ml passes) all mak mutations tested except makl6-l. A variant killer (24). plasmid is described that confers the superkiller phenotype and, Media. YPAD, YPG, SD, presporulation medium, sporula- like chromosomal ski mutations, makes several mak genes tion medium, MB medium, and various omission media were dispensable for plasmid replication. -
The Obscure World of Integrative and Mobilizable Elements Gérard Guédon, Virginie Libante, Charles Coluzzi, Sophie Payot-Lacroix, Nathalie Leblond-Bourget
The obscure world of integrative and mobilizable elements Gérard Guédon, Virginie Libante, Charles Coluzzi, Sophie Payot-Lacroix, Nathalie Leblond-Bourget To cite this version: Gérard Guédon, Virginie Libante, Charles Coluzzi, Sophie Payot-Lacroix, Nathalie Leblond-Bourget. The obscure world of integrative and mobilizable elements: Highly widespread elements that pirate bacterial conjugative systems. Genes, MDPI, 2017, 8 (11), pp.337. 10.3390/genes8110337. hal- 01686871 HAL Id: hal-01686871 https://hal.archives-ouvertes.fr/hal-01686871 Submitted on 26 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License G C A T T A C G G C A T genes Review The Obscure World of Integrative and Mobilizable Elements, Highly Widespread Elements that Pirate Bacterial Conjugative Systems Gérard Guédon *, Virginie Libante, Charles Coluzzi, Sophie Payot and Nathalie Leblond-Bourget * ID DynAMic, Université de Lorraine, INRA, 54506 Vandœuvre-lès-Nancy, France; [email protected] (V.L.); [email protected] (C.C.); [email protected] (S.P.) * Correspondence: [email protected] (G.G.); [email protected] (N.L.-B.); Tel.: +33-037-274-5142 (G.G.); +33-037-274-5146 (N.L.-B.) Received: 12 October 2017; Accepted: 15 November 2017; Published: 22 November 2017 Abstract: Conjugation is a key mechanism of bacterial evolution that involves mobile genetic elements. -
Indirect Selection Against Antibiotic Resistance Via Specialized Plasmid-Dependent Bacteriophages
microorganisms Perspective Indirect Selection against Antibiotic Resistance via Specialized Plasmid-Dependent Bacteriophages Reetta Penttinen 1,2 , Cindy Given 1 and Matti Jalasvuori 1,* 1 Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Survontie 9C, P.O.Box 35, FI-40014 Jyväskylä, Finland; reetta.k.penttinen@jyu.fi (R.P.); cindy.j.given@jyu.fi (C.G.) 2 Department of Biology, University of Turku, FI-20014 Turku, Finland * Correspondence: matti.jalasvuori@jyu.fi; Tel.: +358-504135092 Abstract: Antibiotic resistance genes of important Gram-negative bacterial pathogens are residing in mobile genetic elements such as conjugative plasmids. These elements rapidly disperse between cells when antibiotics are present and hence our continuous use of antimicrobials selects for elements that often harbor multiple resistance genes. Plasmid-dependent (or male-specific or, in some cases, pilus-dependent) bacteriophages are bacterial viruses that infect specifically bacteria that carry certain plasmids. The introduction of these specialized phages into a plasmid-abundant bacterial community has many beneficial effects from an anthropocentric viewpoint: the majority of the plasmids are lost while the remaining plasmids acquire mutations that make them untransferable between pathogens. Recently, bacteriophage-based therapies have become a more acceptable choice to treat multi-resistant bacterial infections. Accordingly, there is a possibility to utilize these specialized phages, which are not dependent on any particular pathogenic species or strain but rather on the resistance-providing elements, in order to improve or enlengthen the lifespan of conventional antibiotic approaches. Here, Citation: Penttinen, R.; Given, C.; we take a snapshot of the current knowledge of plasmid-dependent bacteriophages. -
Virus World As an Evolutionary Network of Viruses and Capsidless Selfish Elements
Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Koonin, E. V., & Dolja, V. V. (2014). Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements. Microbiology and Molecular Biology Reviews, 78(2), 278-303. doi:10.1128/MMBR.00049-13 10.1128/MMBR.00049-13 American Society for Microbiology Version of Record http://cdss.library.oregonstate.edu/sa-termsofuse Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Eugene V. Koonin,a Valerian V. Doljab National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USAa; Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USAb Downloaded from SUMMARY ..................................................................................................................................................278 INTRODUCTION ............................................................................................................................................278 PREVALENCE OF REPLICATION SYSTEM COMPONENTS COMPARED TO CAPSID PROTEINS AMONG VIRUS HALLMARK GENES.......................279 CLASSIFICATION OF VIRUSES BY REPLICATION-EXPRESSION STRATEGY: TYPICAL VIRUSES AND CAPSIDLESS FORMS ................................279 EVOLUTIONARY RELATIONSHIPS BETWEEN VIRUSES AND CAPSIDLESS VIRUS-LIKE GENETIC ELEMENTS ..............................................280 Capsidless Derivatives of Positive-Strand RNA Viruses....................................................................................................280 -
RNA Viruses As Tools in Gene Therapy and Vaccine Development
G C A T T A C G G C A T genes Review RNA Viruses as Tools in Gene Therapy and Vaccine Development Kenneth Lundstrom PanTherapeutics, Rte de Lavaux 49, CH1095 Lutry, Switzerland; [email protected]; Tel.: +41-79-776-6351 Received: 31 January 2019; Accepted: 21 February 2019; Published: 1 March 2019 Abstract: RNA viruses have been subjected to substantial engineering efforts to support gene therapy applications and vaccine development. Typically, retroviruses, lentiviruses, alphaviruses, flaviviruses rhabdoviruses, measles viruses, Newcastle disease viruses, and picornaviruses have been employed as expression vectors for treatment of various diseases including different types of cancers, hemophilia, and infectious diseases. Moreover, vaccination with viral vectors has evaluated immunogenicity against infectious agents and protection against challenges with pathogenic organisms. Several preclinical studies in animal models have confirmed both immune responses and protection against lethal challenges. Similarly, administration of RNA viral vectors in animals implanted with tumor xenografts resulted in tumor regression and prolonged survival, and in some cases complete tumor clearance. Based on preclinical results, clinical trials have been conducted to establish the safety of RNA virus delivery. Moreover, stem cell-based lentiviral therapy provided life-long production of factor VIII potentially generating a cure for hemophilia A. Several clinical trials on cancer patients have generated anti-tumor activity, prolonged survival, and -
Lentivirus and Lentiviral Vectors Fact Sheet
Lentivirus and Lentiviral Vectors Family: Retroviridae Genus: Lentivirus Enveloped Size: ~ 80 - 120 nm in diameter Genome: Two copies of positive-sense ssRNA inside a conical capsid Risk Group: 2 Lentivirus Characteristics Lentivirus (lente-, latin for “slow”) is a group of retroviruses characterized for a long incubation period. They are classified into five serogroups according to the vertebrate hosts they infect: bovine, equine, feline, ovine/caprine and primate. Some examples of lentiviruses are Human (HIV), Simian (SIV) and Feline (FIV) Immunodeficiency Viruses. Lentiviruses can deliver large amounts of genetic information into the DNA of host cells and can integrate in both dividing and non- dividing cells. The viral genome is passed onto daughter cells during division, making it one of the most efficient gene delivery vectors. Most lentiviral vectors are based on the Human Immunodeficiency Virus (HIV), which will be used as a model of lentiviral vector in this fact sheet. Structure of the HIV Virus The structure of HIV is different from that of other retroviruses. HIV is roughly spherical with a diameter of ~120 nm. HIV is composed of two copies of positive ssRNA that code for nine genes enclosed by a conical capsid containing 2,000 copies of the p24 protein. The ssRNA is tightly bound to nucleocapsid proteins, p7, and enzymes needed for the development of the virion: reverse transcriptase (RT), proteases (PR), ribonuclease and integrase (IN). A matrix composed of p17 surrounds the capsid ensuring the integrity of the virion. This, in turn, is surrounded by an envelope composed of two layers of phospholipids taken from the membrane of a human cell when a newly formed virus particle buds from the cell.