First Description of a Temperate Bacteriophage (Vb Fhim KIRK) of Francisella Hispaniensis Strain 3523
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Inhibition of Chloroplast DNA Recombination and Repair by Dominant Negative Mutants of Escherichia Coli Reca
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Faculty Publications from the Center for Plant Science Innovation Plant Science Innovation, Center for June 1995 Inhibition of Chloroplast DNA Recombination and Repair by Dominant Negative Mutants of Escherichia coli RecA Heriberto D. Cerutti University of Nebraska - Lincoln, [email protected] Anita M. Johnson Duke University, Durham, North Carolina John E. Boynton Duke University, Durham, North Carolina Nicholas W. Gillham Duke University, Durham, North Carolina Follow this and additional works at: https://digitalcommons.unl.edu/plantscifacpub Part of the Plant Sciences Commons Cerutti, Heriberto D.; Johnson, Anita M.; Boynton, John E.; and Gillham, Nicholas W., "Inhibition of Chloroplast DNA Recombination and Repair by Dominant Negative Mutants of Escherichia coli RecA" (1995). Faculty Publications from the Center for Plant Science Innovation. 8. https://digitalcommons.unl.edu/plantscifacpub/8 This Article is brought to you for free and open access by the Plant Science Innovation, Center for at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Faculty Publications from the Center for Plant Science Innovation by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. MOLECULAR AND CELLULAR BIOLOGY, June 1995, p. 3003–3011 Vol. 15, No. 6 0270-7306/95/$04.0010 Copyright q 1995, American Society for Microbiology Inhibition of Chloroplast DNA Recombination and Repair by Dominant Negative Mutants of Escherichia coli RecA HERIBERTO CERUTTI, ANITA M. JOHNSON, JOHN E. BOYNTON,* AND NICHOLAS W. GILLHAM Developmental, Cell and Molecular Biology Group, Departments of Botany and Zoology, Duke University, Durham, North Carolina 27708 Received 7 December 1994/Returned for modification 12 January 1995/Accepted 28 February 1995 The occurrence of homologous DNA recombination in chloroplasts is well documented, but little is known about the molecular mechanisms involved or their biological significance. -
Evaluation of Prophage Gene Revealed Population Variation Of
Evaluation of Prophage Gene Revealed Population Variation of ‘Candidatus Liberibacter Asiaticus’: Bacterial Pathogen of Citrus Huanglongbing (HLB) in Northern Thailand Jutamas Kongjak Chiang Mai University Angsana Akarapisan ( [email protected] ) Chiang Mai University https://orcid.org/0000-0002-0506-8675 Research Article Keywords: Citrus, Prophage, Bacteriophage, Huanglongbing, Candidatus Liberibacter asiaticus Posted Date: August 24th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-822974/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/15 Abstract ‘Candidatus Liberibacter asiaticus’ is a non-culturable bacterial pathogen, the causal agent of Huanglongbing (HLB, yellow shoot disease, also known as citrus greening disease), a highly destructive disease of citrus (Rutaceae). The pathogen is transmitted by the Asian citrus psyllid: Diaphorina citri Kuwayama. Recent studies, have shown that the HLB pathogen has two prophages, SC1 that has a lytic cycle and SC2 associated with bacterial virulence. This study aimed to search for SC1 and SC2 prophages of HLB in mandarin orange, sweet orange, bitter orange, kumquat, key lime, citron, caviar lime, kar lime, pomelo and orange jasmine from ve provinces in Northern Thailand. A total of 216 samples collected from Northern Thailand during 2019 and 2020 were studied. The results revealed that 62.04% (134/216) citrus samples were infected with the ‘Ca. L. asiaticus’ the bacterial pathogen associated with citrus HLB. The prophage particles are important genetic elements of bacterial genomes that are involved in lateral gene transfer, pathogenicity, environmental adaptation and interstrain genetic variability. Prophage particles were evaluated in the terminase gene of SC1 and SC2-type prophages. -
Phages for Phage Therapy: Isolation, Characterization, and Host Range Breadth
pharmaceuticals Review Phages for Phage Therapy: Isolation, Characterization, and Host Range Breadth Paul Hyman Department of Biology/Toxicology, Ashland University, 401 College Ave., Ashland, OH 44805, USA; [email protected]; Tel.: +1-419-207-6309 Received: 28 December 2018; Accepted: 4 March 2019; Published: 11 March 2019 Abstract: For a bacteriophage to be useful for phage therapy it must be both isolated from the environment and shown to have certain characteristics beyond just killing strains of the target bacterial pathogen. These include desirable characteristics such as a relatively broad host range and a lack of other characteristics such as carrying toxin genes and the ability to form a lysogen. While phages are commonly isolated first and subsequently characterized, it is possible to alter isolation procedures to bias the isolation toward phages with desirable characteristics. Some of these variations are regularly used by some groups while others have only been shown in a few publications. In this review I will describe (1) isolation procedures and variations that are designed to isolate phages with broader host ranges, (2) characterization procedures used to show that a phage may have utility in phage therapy, including some of the limits of such characterization, and (3) results of a survey and discussion with phage researchers in industry and academia on the practice of characterization of phages. Keywords: phage therapy; bacteriophage isolation; host range; bacteriophage characterization; genome sequencing; enrichment culture 1. Introduction The isolation of bacteriophages for phage therapy is often presented as a fairly straightforward exercise of mixing a phage-containing sample with host bacteria, followed by a simple removal of bacterial debris by filtration and/or centrifugation the next day [1–3]. -
State of Prophage Mu DNA Upon Induction (Bacteriophage Mu/Bacteriophage X/DNA Insertion/DNA Excision/Transposable Elements) E
Proc. Nati. Acad. Sci. USA Vol. 74, No. 8, pp. 3143-3147, August 1977 Biochemistry State of prophage Mu DNA upon induction (bacteriophage Mu/bacteriophage X/DNA insertion/DNA excision/transposable elements) E. LjUNGQUIST AND A. I. BUKHARI Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 Communicated by J. D. Watson, April 18, 1977 ABSTRACT We have compared the process of prophage different host sequences. Yet, a form of Mu DNA free of host A induction with that of prophage Mu. According to the DNA has remained undetected. Campbell model, rescue of A DNA from the host DNA involves In its continuous association with host DNA, Mu resembles reversal of X integration such that the prophage DNA is excised from the host chromosome. We have monitored this event by another class of insertion elements, referred to as the trans- locating the prophage DNA with a technique in which DNA of posable elements. The transposable elements are specific the lysogenic cells is cleaved with a restriction endonuclease stretches of DNA that can be translocated from one position to and fractionated in agarose gels. The DNA fragments are de- another in host DNA (7). Mu undergoes multiple rounds of natured in gels, transferred to a nitrocellulose paper, and hy- transposition during its growth, far exceeding the transposition bridized with 32P-labeled mature phage DNA. The fragments frequency of the bonafide transposable elements. When a Mu containing prophage DNA become visible after autoradiogra- lysogen, carrying a single Mu prophage at a given site on the phy. Upon prophage A induction, the phage-host junction fragments disappear and the fragment containing the A att site host chromosome, is induced, many copies of Mu DNA are appears. -
Philympics 2021: Prophage Predictions Perplex Programs
bioRxiv preprint doi: https://doi.org/10.1101/2021.06.03.446868; this version posted June 3, 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 Philympics 2021: Prophage 2 Predictions Perplex Programs 3 Michael J. Roach1*, Katelyn McNair2, Sarah K. Giles1, Laura Inglis1, Evan Pargin1, Przemysław 4 Decewicz3, Robert A. Edwards1 5 1. Flinders Accelerator for Microbiome Exploration, Flinders University, 5042, SA, Australia 6 2. Computational Sciences Research Center, San Diego State University, San Diego, 92182, CA, USA 7 3. Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty 8 of Biology, University of Warsaw, Warsaw, 02-096, Poland 9 10 *Corresponding Author: [email protected] 11 12 Abstract 13 Most bacterial genomes contain integrated bacteriophages—prophages—in various states of decay. 14 Many are active and able to excise from the genome and replicate, while others are cryptic 15 prophages, remnants of their former selves. Over the last two decades, many computational tools 16 have been developed to identify the prophage components of bacterial genomes, and it is a 17 particularly active area for the application of machine learning approaches. However, progress is 18 hindered and comparisons thwarted because there are no manually curated bacterial genomes that 19 can be used to test new prophage prediction algorithms. 20 Here, we present a library of gold-standard bacterial genome annotations that include manually 21 curated prophage annotations, and a computational framework to compare the predictions from 22 different algorithms. -
Genomic Analysis and Relatedness of P2-Like Phages of the Burkholderia Cepacia Complex Karlene H Lynch1, Paul Stothard2, Jonathan J Dennis1*
Lynch et al. BMC Genomics 2010, 11:599 http://www.biomedcentral.com/1471-2164/11/599 RESEARCH ARTICLE Open Access Genomic analysis and relatedness of P2-like phages of the Burkholderia cepacia complex Karlene H Lynch1, Paul Stothard2, Jonathan J Dennis1* Abstract Background: The Burkholderia cepacia complex (BCC) is comprised of at least seventeen Gram-negative species that cause infections in cystic fibrosis patients. Because BCC bacteria are broadly antibiotic resistant, phage therapy is currently being investigated as a possible alternative treatment for these infections. The purpose of our study was to sequence and characterize three novel BCC-specific phages: KS5 (vB_BceM-KS5 or vB_BmuZ-ATCC 17616), KS14 (vB_BceM-KS14) and KL3 (vB_BamM-KL3 or vB_BceZ-CEP511). Results: KS5, KS14 and KL3 are myoviruses with the A1 morphotype. The genomes of these phages are between 32317 and 40555 base pairs in length and are predicted to encode between 44 and 52 proteins. These phages have over 50% of their proteins in common with enterobacteria phage P2 and so can be classified as members of the Peduovirinae subfamily and the “P2-like viruses” genus. The BCC phage proteins similar to those encoded by P2 are predominantly structural components involved in virion morphogenesis. As prophages, KS5 and KL3 integrate into an AMP nucleosidase gene and a threonine tRNA gene, respectively. Unlike other P2-like viruses, the KS14 prophage is maintained as a plasmid. The P2 E+E’ translational frameshift site is conserved among these three phages and so they are predicted to use frameshifting for expression of two of their tail proteins. -
The Diversity of Bacterial Lifestyles Hampers Bacteriophage Tenacity
viruses Review The Diversity of Bacterial Lifestyles Hampers Bacteriophage Tenacity Marta Lourenço 1,2, Luisa De Sordi 1 and Laurent Debarbieux 1,* ID 1 Department of Microbiology, Institut Pasteur, F-75015 Paris, France; [email protected] (M.L.); [email protected] (L.D.S.) 2 Collège Doctoral, Sorbonne Université, F-75005 Paris, France * Correspondence: [email protected] Received: 18 May 2018; Accepted: 11 June 2018; Published: 15 June 2018 Abstract: Phage therapy is based on a simple concept: the use of a virus (bacteriophage) that is capable of killing specific pathogenic bacteria to treat bacterial infections. Since the pioneering work of Félix d’Herelle, bacteriophages (phages) isolated in vitro have been shown to be of therapeutic value. Over decades of study, a large number of rather complex mechanisms that are used by phages to hijack bacterial resources and to produce their progeny have been deciphered. While these mechanisms have been identified and have been studied under optimal conditions in vitro, much less is known about the requirements for successful viral infections in relevant natural conditions. This is particularly true in the context of phage therapy. Here, we highlight the parameters affecting phage replication in both in vitro and in vivo environments, focusing, in particular, on the mammalian digestive tract. We propose avenues for increasing the knowledge-guided implementation of phages as therapeutic tools. Keywords: virus–host interactions; bacteriophage efficacy; gastrointestinal tract; phage therapy 1. Introduction With the alarming worldwide increase in the prevalence of multidrug-resistant bacteria, phage therapy—the use of phages to target pathogenic bacteria [1]—has recently returned to the spotlight in the USA and Europe, although it had never fallen out of favour in countries such as Georgia [2]. -
Molecular Model for the Transposition and Replication of Bacteriophage
Proc. Natl. Acad. Sci. USA Vol. 76, No. 4, pp. 1933-1937, April 1979 Genetics Molecular model for the transposition and replication of bacteriophage Mu and other transposable elements (DNA insertion elements/nonhomologous recombination/site-specific recombination/replicon fusion/topoisomerases) JAMES A. SHAPIRO Department of Microbiology, The University of Chicago, Chicago, Illinois 60637 Communicated by Hewson Swift, December 11, 1978 ABSTRACT A series of molecular events will explain how B genetic elements can transpose from one DNA site to another, B y generate a short oligonucleotide duplication at both ends of the I % new insertion site, and replicate in the transposition process. I These events include the formation of recombinant molecules A a% /; C which have been postulated to be intermediates in the trans- position process. The model explains how the replication of bacteriophage Mu is obligatorily associated with movement to z x x new genetic sites. It postulates that all transposable elements replicate in the transposition process so that they remain at their z original site while moving to new sites. According to this model, the mechanism of transposition is very different from the in- V sertion and excision of bacteriophage X. y FIG. 1. Replicon fusion. The boxes with an arrow indicate copies Recent research on transposable elements in bacteria has pro- of a transposable element. The letters mark arbitrary regions of the vided important insights into the role of nonhomologous re- two replicons to indicate the relative positions of the elements in the combination in genetic rearrangements (1-4). These elements donor and cointegrate molecules. include small insertion sequences (IS elements), transposable resistance determinants (Tn elements), and bacteriophage Mu results in the duplication of a short oligonucleotide sequence (3). -
Geographic Differences in Sexual Reassortment in Rna Phage
ORIGINAL ARTICLE doi:10.1111/j.1558-5646.2010.01040.x GEOGRAPHIC DIFFERENCES IN SEXUAL REASSORTMENT IN RNA PHAGE Kara J. O’Keefe,1,2 Olin K. Silander,3 Helen McCreery,4 Daniel M. Weinreich,5 Kevin M. Wright,6 Lin Chao,7 Scott V. Edwards,2 Susanna K. Remold,8 and Paul E. Turner1,9 1Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520-8106 2Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138 3Core Program Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland 4Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 5Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912 6Department of Biology, Duke University, Durham, North Carolina 27708 7Section of Ecology, Evolution and Behavior, University of California, San Diego, La Jolla, California 92093 8Department of Biology, University of Louisville, Louisville, Kentucky 40292 9E-mail: [email protected] Received November 5, 2008 Accepted April 20, 2010 The genetic structure of natural bacteriophage populations is poorly understood. Recent metagenomic studies suggest that phage biogeography is characterized by frequent migration. Using virus samples mostly isolated in Southern California, we recently showed that very little population structure exists in segmented RNA phage of the Cystoviridae family due to frequent segment reassortment (sexual genetic mixis) between unrelated virus individuals. Here we use a larger genetic dataset to examine the structure of Cystoviridae phage isolated from three geographic locations in Southern New England. We document extensive natural variation in the physical sizes of RNA genome segments for these viruses. -
Elucidating Viral Communities During a Phytoplankton Bloom on the West Antarctic Peninsula
fmicb-10-01014 May 10, 2019 Time: 14:46 # 1 ORIGINAL RESEARCH published: 14 May 2019 doi: 10.3389/fmicb.2019.01014 Elucidating Viral Communities During a Phytoplankton Bloom on the West Antarctic Peninsula Tomás Alarcón-Schumacher1,2†, Sergio Guajardo-Leiva1†, Josefa Antón3 and Beatriz Díez1,4* 1 Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile, 2 Max Planck Institute for Marine Microbiology, Bremen, Germany, 3 Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain, 4 Center for Climate and Resilience Research (CR2), University of Chile, Santiago, Chile In Antarctic coastal waters where nutrient limitations are low, viruses are expected to play a major role in the regulation of bloom events. Despite this, research in viral identification and dynamics is scarce, with limited information available for the Southern Ocean (SO). This study presents an integrative-omics approach, comparing variation in the viral and microbial active communities on two contrasting sample conditions from Edited by: a diatom-dominated phytoplankton bloom occurring in Chile Bay in the West Antarctic David Velazquez, Autonomous University of Madrid, Peninsula (WAP) in the summer of 2014. The known viral community, initially dominated Spain by Myoviridae family (∼82% of the total assigned reads), changed to become dominated Reviewed by: by Phycodnaviridae (∼90%), while viral activity was predominantly driven by dsDNA Carole Anne Llewellyn, ∼ ∼ Swansea University, United Kingdom members of the Phycodnaviridae ( 50%) and diatom infecting ssRNA viruses ( 38%), Márcio Silva de Souza, becoming more significant as chlorophyll a increased. A genomic and phylogenetic Fundação Universidade Federal do characterization allowed the identification of a new viral lineage within the Myoviridae Rio Grande, Brazil family. -
Pioneering Soil Viromics to Elucidate Viral Impacts on Soil Ecosystem Services
Pioneering Soil Viromics to Elucidate Viral Impacts on Soil Ecosystem Services DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Gareth Trubl Graduate Program in Microbiology The Ohio State University 2018 Dissertation Committee: Virginia Rich, Advisor Matthew Sullivan, Co-Advisor Kelly Wrighton Matthew Anderson Copyrighted by Gareth Trubl 2018 Abstract Permafrost contains 30–50% of global soil carbon (C) and is rapidly thawing. While the fate of this C is unknown, it will be shaped in part by microbes and their associated viruses, which modulate microbial activities via mortality and metabolic control. To date, viral research in soils has been outpaced by that in aquatic environments due to the technical challenges of accessing soil viruses, compounded by the dramatic physicochemical heterogeneity in soils. The Stordalen Mire long-term ecological field site in Arctic Sweden encompasses a mosaic of natural permafrost thaw stages, and has been well characterized biogeochemically and microbiologically, making it an ideal site to characterize the soil virosphere and its potential impacts on the C cycle. A viral resuspension protocol was developed to generate quantitatively- amplified dsDNA viromes. The protocol yielded ~108 virus-like particles (VLPs) g−1 of soil across three thaw-stage habitats, and seven resulting viromes yielded 53 vOTUs. Viral-specific bioinformatics methods were used to recover viral populations, define their gene content, connect them to other related viruses (globally) and potential hosts (locally). Only 15% of these vOTUs had genetic similarity to publicly available viruses in the RefSeq database, and ∼30% of the genes could be annotated, supporting the concept of soils as reservoirs of substantial undescribed viral genetic diversity. -
Exploration Des Communautés Virales Thermophiles Dans Les Écosystèmes
présentée par THÈSE / UNIVERSITÉ DE BRETAGNE OCCIDENTALE Kaarle Joonas Parikka sous le sceau de l’Université européenne de Bretagne Préparée à l'Institut Universitaire pour obtenir le titre de Européen de la Mer, au sein du DOCTEUR DE L’UNIVERSITÉ DE BRETAGNE OCCIDENTALE Mention :Microbiologie Laboratoire de Microbiologie des École Doctorale des Sciences de la Mer Environnements Extrêmes Thèse soutenue le 28 mars 2013 devant le jury composé de : Exploration des communautés Hélène Montanié (Rapporteur) virales thermophiles dans Maître de Conférences, HDR, Université de La Rochelle les écosystèmes chauds des Michael DuBow (Rapporteur) Professeur, Université Paris-Sud 11 Terres australes et Stéphan Jacquet (Examinateur) antarctiques françaises Directeur de Recherche, INRA, UMR CARRTEL Thierry Bouvier (Examinateur) Chargé de Recherche CNRS, Université de Montpellier 2 Christine Paillard (Examinateur) Directrice de Recherche CNRS, Université de Bretagne Occidentale Marc Le Romancer (Directeur de thèse) Maître de Conférences, HDR, Université de Bretagne Occidentale Remerciements Cette thèse a été financée par le Ministère de l’Enseignement Supérieur et de la Recherche. Je voudrais remercier l’ancienne et la nouvelle direction du LM2E : Daniel Prieur, Anne Godfroy et Mohamed Jebbar (qui m’a lancé dans la génomique), de m’avoir accueilli au sein du laboratoire afin de pouvoir effectuer ce travail. Merci Daniel Prieur également d’avoir été mon directeur de thèse la première année de ma thèse. J’aimerais exprimer ma gratitude à Marc Le Romancer, qui m’a recruté du Plat Pays pour venir travailler sur un sujet de thèse très exotique, qui m’a permis de découvrir la virologie extrêmophile. Je lui suis reconnaissant également pour m’avoir pris avec lui à 13 000 Km de Brest pour échantillonner aux Terres australes et antarctiques françaises, la terre des « oubliés ».