plasmids: biology and impact in biotechnology and discovery

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PLASMIDSBIOLOGY AND IMPACT IN BIOTECHNOLOGY AND DISCOVERY


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Marcelo E. TolmaskyCenter for Applied Biotechnology StudiesDepartment of Biological ScienceCollege of Natural Sciences and MathematicsCalifornia State University, Fullerton

AND

Juan C. AlonsoCentro Nacional de Biotecnología, CSICDepartamento de Biotecnología Microbiana,Madrid, Spain

PLASMIDSBIOLOGY AND IMPACT IN BIOTECHNOLOGY AND DISCOVERY

Edited by |

ASM Press, Washington, DC


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Copyright © 2015 American Society for Microbiology. All rights reserved. No part of this publication may be reproduced or transmitted in whole or in part or reused in any form or by any means, electronic or mechanical, including photocopying and recording, or by any information storage and retrieval system, without permission in writing from the publisher.

Disclaimer: To the best of the publisher’s knowledge, this publication provides informa-tion concerning the subject matter covered that is accurate as of the date of publication. The publisher is not providing legal, medical, or other professional services. Any refer-ence herein to any specific commercial products, procedures, or services by trade name, trademark, manufacturer, or otherwise does not constitute or imply endorsement, rec-ommendation, or favored status by the American Society for Microbiology (ASM). The views and opinions of the author(s) expressed in this publication do not necessarily state or reflect those of ASM, and they shall not be used to advertise or endorse any product.

Library of Congress Cataloging-in-Publication Data

Plasmids : biology and impact in biotechnology and discovery / edited by Marcelo Tolmasky, Department of Biological Sciences, California State University, Fullerton, and Juan Carlos Alonso, Centro Nacional de Biotecnología, Cantoblanco, Departamento de Biotecnología Microbiana, Madrid, Spain. pages cm Includes bibliographical references and index. ISBN 978-1-55581-897-5 (hardcover : alk. paper) 1. Plasmids. I. Tolmasky, Marcelo, editor. II. Alonso, Juan Carlos (Biotechnologist), editor. QR76.6.P563 2015 572.8'69—dc23 2015004787eISBN: 978-1-55581-898-2 doi:10.1128/9781555818982

10 9 8 7 6 5 4 3 2 1

All Rights ReservedPrinted in the United States of America

Address editorial correspondence to ASM Press, 1752 N St., N.W.,Washington, DC 20036-2904, USA

Send orders to ASM Press, P.O. Box 605, Herndon, VA 20172, USAPhone: 800-546-2416; 703-661-1593Fax: 703-661-1501E-mail: [email protected]: http://estore.asm.org

Cover images: on the front and back covers, the gold-colored ring structures in the background are atomic force microscopy (AFM) images showing one linear molecule and three covalently closed circular ones at different degrees of supercoiling (image provided by Sonia Trigueros); the spine has an electron microscopy (EM) image of a replicating plasmid (image produced by Jorge Crosa).

Cover design: Rings Leighton Design Group, Washington, DC


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Dedicated to the memory of Jorge Crosa


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vii

Contributors xiPreface xxi

I. IntroDuCtIon

1. Historical Events That Spawned the Field of Plasmid Biology 3 Clarence I. Kado

II. PLasmID rePLICatIon systems anD theIr ControL

2. Iteron Plasmids 15 Igor Konieczny, Katarzyna Bury, Aleksandra Wawrzycka,

and Katarzyna Wegrzyn

3. Mechanisms of Theta Plasmid Replication 33 Joshua Lilly and Manel Camps

4. Plasmid Rolling-Circle Replication 45 José A. Ruiz-Masó, Cristina Machón, Lorena Bordanaba-

Ruiseco, Manuel Espinosa, Miquel Coll, and Gloria del Solar

5. Replication and Maintenance of Linear Phage-Plasmid N15 71 Nikolai V. Ravin

6. Plasmid Replication Control by Antisense RNAs 83 Sabine Brantl

Contents


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viii Contents

7. Topological Behavior of Plasmid DNA 105 N. Patrick Higgins and Alexander V. Vologodskii

III. PLasmID maIntenanCe, transfer anD BarrIers

8. Plasmid Partition Mechanisms 135 Jamie C. Baxter and Barbara E. Funnell

9. Resolution of Multimeric Forms of Circular Plasmids and Chromosomes 173

Estelle Crozat, Florian Fournes, François Cornet, Bernard Hallet, and Philippe Rousseau

10. Conditional Activation of Toxin-Antitoxin Systems: Postsegregational Killing and Beyond 175

Ana María Hernández-Arriaga, Wai Ting Chan, Manuel Espinosa, and Ramón Díaz-Orejas

11. The Interplay between Different Stability Systems Contributes to Faithful Segregation: Streptococcus pyogenes pSM19035 as a Model 193

Andrea Volante, Nora E. Soberón, Silvia Ayora, and Juan C. Alonso

12. The CRISPR-Cas Immune System and Genetic Transfers: Reaching an Equilibrium 209

Julie E. Samson, Alfonso H. Magadan, and Sylvain Moineau

13. Plasmid Diversity and Adaptation Analyzed by Massive Sequencing of Escherichia coli Plasmids 219

María de Toro, M. Pilar Garcillán-Barcia and Fernando de la Cruz

14. Conjugation in Gram-Positive Bacteria 237 Nikolaus Goessweiner-Mohr, Karsten Arends,

Walter Keller, and Elisabeth Grohmann

15. Mobilizable Rolling-Circle Replicating Plasmids from Gram-Positive Bacteria: A Low-Cost Conjugative Transfer 257

Cris Fernández-López, Alicia Bravo, Sofía Ruiz-Cruz, Virtu Solano-Collado, Danielle A. Garsin, Fabián Lorenzo-Díaz, and Manuel Espinosa

IV. sPeCIfIC PLasmID systems

16. The Plasmid Mobilome of the Model Plant Symbiont Sinorhizobium meliloti: Coming up with New Questions and Answers 279

Antonio Lagares, Juan Sanjuán, and Mariano Pistorio 17. The Agrobacterium Ti Plasmids 295 Jay E. Gordon and Peter J. Christie


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Contents ix

18. The Influence of Biofilms in the Biology of Plasmids 315 Laura C. C. Cook and Gary M. Dunny

19. The Partitioning and Copy Number Control Systems of the Selfish Yeast Plasmid: An Optimized Molecular Design for Stable Persistence in Host Cells 325

Yen-Ting-Liu, Saumitra Sau, Chien-Hui Ma, Aashiq H. Kachroo, Paul A. Rowley, Keng-Ming Chang, Hsiu-Fang Fan, and Makkuni Jayaram

20. Plasmids from Euryarchaeota 349 Patrick Forterre, Mart Krupovic, Kasie Raymann, and

Nicolas Soler

V. PLasmID eCoLogy anD eVoLutIon

21. The Plasmidome of Firmicutes: Impact on the Emergence and the Spread of Resistance to Antimicrobials 381

Val Fernández Lanza, Ana P. Tedim, José Luís Martínez, Fernando Baquero, and Teresa M. Coque

22. Plasmid-Mediated Antimicrobial Resistance in Staphylococci and Other Firmicutes 421

Stefan Schwarz, Jianzhong Shen, Sarah Wendlandt, Andrea T. Feßler, Yang Wang, Kristina Kadlec, and Cong-Ming Wu

23. Plasmid Detection, Characterization, and Ecology 445 Kornelia Smalla, Sven Jechalke, and Eva M. Top

24. Plasmid-Mediated Antibiotic Resistance and Virulence in Gram-Negatives: The Klebsiella pneumoniae Paradigm 459

Maria S. Ramirez, German M. Traglia, David L. Lin, Tung Tran, and Marcelo E. Tolmasky

25. Plasmid-Mediated Quinolone Resistance 475 George A. Jacoby, Jacob Strahilevitz, and David C. Hooper

VI. sPeCIaLIzeD funCtIons meDIateD By PLasmIDs

26. Plasmid-Mediated Tolerance Toward Environmental Pollutants 507

Ana Segura, Lázaro Molina, and Juan Luis Ramos

27. Virulence Plasmids of Spore-Forming Bacteria 533 Vicki Adams, Jihong Li, Jessica A. Wisniewski,

Francisco A. Uzal, Robert J. Moore, Bruce A. McClane, and Julian I. Rood

28. Virulence Plasmids of Nonsporulating Gram-Positive

Pathogens 559 Daria Van Tyne and Michael S. Gilmore


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x Contents

29. Plasmid-Encoded Iron Uptake Systems 577 Manuela Di Lorenzo and Michiel Stork

VII. PLasmIDs as genetIC tooLs

30. DNA Assembly Tools and Strategies for the Generation of Plasmids 601

Chang-Ho Baek, Michael Liss, Kevin Clancy, Jonathan Chesnut, and Federico Katzen

31. Plasmids as Tools for Containment 615 José L. García and Eduardo Díaz

32. Mining Environmental Plasmids for Synthetic Biology Parts and Devices 633

Esteban Martínez-García, Ilaria Benedetti, Angeles Hueso, and Víctor de Lorenzo

33. Using Plasmids as DNA Vaccines for Infectious Diseases 651 John S. Tregoning and Ekaterina Kinnear

34. Plasmid Biopharmaceuticals 669 Duarte Miguel F. Prazeres and Gabriel A. Monteiro

Index 689


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xi

Vicki AdamsDepartment of Microbiology, Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Victoria 3800, Australia

Juan C. AlonsoDepartamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, 28049 Madrid, Spain

Karsten ArendsRobert Koch-Institute, Nordufer 20, 13353 Berlin, Germany

Silvia AyoraDepartamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CNB-CSIC, 28049 Madrid, Spain

Chang-Ho BaekLife Technologies, Carlsbad, CA 92008

Fernando BaqueroRamón y Cajal University Hospital, IRYCIS, 28034 Madrid, Spain

Jamie C. Baxter Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada

Ilaria BenedettiDepartamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CNB-CSIC, 3, Darwin Street, 28049 Madrid, Spain

Contributors


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xii Contributors

Lorena Bordanaba-RuisecoCentro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain

Sabine BrantlAG Bakteriengenetik, Philosophenweg 12, Friedrich-Schiller-Universität Jena, D-07743 Jena, Germany

Alicia Bravo Centro de Investigaciones Biológicas, CSIC, 28040 Madrid, Spain

Katarzyna BuryDepartment of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland

Manel CampsDepartment of Microbiology and Environmental Toxicology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064

Wai Ting ChanCentro de Investigaciones Biológicas, CSIC, 28040 Madrid, Spain

Keng-Ming ChangSection of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712

Jonathan Chesnut Life Technologies, Carlsbad, CA 92008

Peter J. ChristieDepartment of Microbiology and Molecular Genetics, University of Texas Medical School at Houston, Houston, TX 77005

Kevin ClancyLife Technologies, Carlsbad, CA 92008

Miquel CollInstitute for Research in Biomedicine (IRB-Barcelona), and Institut de Biologia Molecular de Barcelona, CSIC, Baldiri Reixac 10-12, 08028 Barcelona, Spain

Laura C.C. Cook Department of Medicinal Chemistry, University of Illinois, Chicago, IL 60607

Teresa M. CoqueDepartment of Microbiology, Ramón y Cajal University Hospital, IRYCIS, 28034 Madrid, Spain

François CornetCNRS, Laboratoire de Microbiologie et Génétique Moléculaires, F-31062 Toulouse, France

Estelle CrozatUPS, Laboratoire de Microbiologie et Génétique Moléculaires, Université de Toulouse, F-31062 Toulouse, France


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Contributors xiii

Fernando De La CruzInstituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria, CSIC, 39011 Santander, Spain

Gloria del SolarCentro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain

Eduardo DíazDepartment of Environmental Biology, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain

Ramón Díaz-OrejasCentro de Investigaciones Biológicas, CSIC, 28040 Madrid, Spain

Manuela Di LorenzoDepartment of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands

Gary M. DunnyDepartment of Microbiology, University of Minnesota, Minneapolis, MN 55455

Manuel Espinosa Consejo Superior de Investigaciones Científicas, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain

Hsiu-Fang Fan Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan

Cris Fernández-López Centro de Investigaciones Biológicas, CSIC, 28040 Madrid, Spain

Andrea T. Feßler Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany

Patrick Forterre Institut Pasteur, 75015 Paris, France

Florian FournesUPS, Laboratoire de Microbiologie et Génétique Moléculaires, Université de Toulouse, F-31062 Toulouse, France

Barbara E. FunnellDepartment of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada

José L. García Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, 28040 Madrid, Spain

M. Pilar Garcillán-BarciaInstituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria, CSIC, 39011 Santander, Spain


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xiv Contributors

Danielle A. GarsinDepartment of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, Texas

Michael S. GilmoreDepartment of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, MA 02114

Nikolaus Goessweiner-Mohr Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria

Jay E. GordonDepartment of Microbiology and Molecular Genetics, University of Texas Medical School at Houston, Houston, TX 77005

Elisabeth GrohmannFaculty of Biology, Microbiology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany

Bernard HalletInstitut des Sciences de la Vie, UC Louvain, 4/5 L7.07.06 Place Croix du Sud, B-1348 Louvain-la-Neuve, Belgium

Ana María Hernández-ArriagaCentro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain

Angeles HuesoDepartamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CNB-CSIC, 3, Darwin Street, 28049 Madrid, Spain

N. Patrick HigginsDepartment of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294

David C. HooperMassachusetts General Hospital, 55 Fruit Street, Boston, MA 02114

George A. Jacoby Lahey Hospital and Medical Center, 41 Mall Road, Burlington, MA 01805

Makkuni JayaramDepartment of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan

Sven JechalkeJulius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany

Aashiq H. Kachroo Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712

Kristina KadlecInstitute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany


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Contributors xv

Clarence I. KadoPlant Pathology, University of California, Davis, Davis, CA 95616

Federico KatzenLife Technologies, Carlsbad, CA 92008

Walter Keller Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria

Ekaterina KinnearMucosal Infection and Immunity Group, Section of Virology, Imperial College London, St Mary’s Campus, London W2 1PG,United Kingdom

Igor Konieczny Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland

Mart KrupovicInstitut Pasteur, 75015 Paris, France

Antonio Lagares Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, IBBM, Instituto de Biotecnología y Biología Molecular, CONICET, Universidad Nacional de La Plata, (1900) La Plata, Argentina

Val Fernández LanzaCentro de Investigación en Red en Epidemiología y Salud Pública (CIBER-ESP), Melchor Fernández Almagro, 3-5, 28029 Madrid, Spain

Jihong LiDepartment of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 3550 Terrace Street, Pittsburgh, PA 15261

Joshua Lilly Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064

David L. LinDepartment of Biological Science, College of Natural Sciences and Mathematics, Center for Applied Biotechnology Studies, California State University, Fullerton, 800 N. State College Blvd., Fullerton, CA 92831

Michael Liss Life Technologies, Carlsbad, CA 92008

Yen-Ting Liu Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712

Víctor de LorenzoDepartamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, 3, Darwin Street, 28049 Madrid, Spain

Fabián Lorenzo-DíazInstituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, 38071 Laguna, Spain


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xvi Contributors

Chien-Hui MaSection of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712

Cristina MachónInstitute for Research in Biomedicine (IRB-Barcelona), and Institut de Biologia Molecular de Barcelona, CSIC, Baldiri Reixac 10-12, 08028 Barcelona, Spain

Alfonso H. MagadanDépartement de Biochimie, Microbiologie et Bio-Informatique, Groupe de Recherche en Écologie Buccale, Faculté des Sciences et de Génie, et de Médecine Dentaire, Félix d’Hérelle Reference Center for Bacterial Viruses, Université Laval, Quebec City, Quebec G1V 0A6, Canada

José Luís Martínez Centro Nacional de Biotecnología, CNB, and Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (HRYC-CSIC), Madrid, Spain

Esteban Martínez-GarcíaDepartamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CNB-CSIC, 3, Darwin Street, 28049 Madrid, Spain

Bruce A. McClaneDepartment of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 3550 Terrace Street, Pittsburgh, PA 15261

Sylvain MoineauGroupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Quebec City, Quebec G1V 0A6, Canada

Lázaro Molina CIDERTA, Laboratorio de Investigación y Control Agroalimentario (LICAH), Parque Huelva Empresarial, 21007 Huelva, Spain

Gabriel A. MonteiroDepartment of Bioengineering, Centre for Biological and Chemical Engineering, IBB, Institute for Biotechnology and Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal

Robert J. MooreDepartment of Microbiology, Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Victoria 3800, Australia

Mariano PistorioDepartamento de Ciencias Biológicas, Facultad de Ciencias Exactas, IBBM, Instituto de Biotecnología y Biología Molecular, CONICET, Universidad Nacional de La Plata, (1900) La Plata, Argentina

Duarte Miguel F. PrazeresDepartment of Bioengineering, Instituto Superior Técnico, Centre for Biological and Chemical Engineering, IBB, Institute for Biotechnology and Bioengineering, Universidade de Lisboa, 1049-001 Lisboa, Portugal


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Contributors xvii

Maria S. RamirezDepartment of Biological Science, Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University, Fullerton, 800 N. State College Blvd., Fullerton, CA 92831

Juan Luis RamosEnvironmental Protection Department, Profesor Albareda, Estación Experimental del Zaidin, CSIC, 18008 Granada, Spain

Nikolai V. RavinCenter of Bioengineering, Russian Academy of Sciences, Prosp. 60-let Oktiabria, Bldg. 7-1, Moscow 117312, Russia

Kasie RaymannInstitut Pasteur, 75015 Paris, France

Julian I. RoodDepartment of Microbiology, Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Victoria 3800, Australia

Philippe RousseauUPS, Laboratoire de Microbiologie et Génétique Moléculaires, Université de Toulouse, F-31062 Toulouse, France

Paul A. Rowley Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712

José A. Ruiz-MasóCentro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain

Sofía Ruiz-CruzCentro de Investigaciones Biológicas, CSIC, 28040 Madrid, Spain

Julie E. SamsonDépartement de Biochimie, Microbiologie et Bio-Informatique, Groupe de Recherche en Écologie Buccale, Faculté des Sciences et de Génie, et de Médecine Dentaire, Félix d’Hérelle Reference Center for Bacterial Viruses, Université Laval, Quebec City, Quebec G1V 0A6, Canada

Juan Sanjuán Departamento de Microbiología del Suelo y Sistemas Simbióticos. Estación Experimental del Zaidín, CSIC, Granada, Spain

Saumitra Sau Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712

Stefan SchwarzInstitute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany

Ana Segura Environmental Protection Department, Profesor Albareda, Estación Experimental del Zaidin, CSIC, 1, 18008 Granada, Spain


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xviii Contributors

Jianzhong ShenBeijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, P. R. China

Kornelia SmallaJulius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany

Nora E. SoberónDepartamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CNB-CSIC, 28049 Madrid, Spain

Virtu Solano-Collado Centro de Investigaciones Biológicas, CSIC, 28040 Madrid, Spain

Nicolas SolerDynAMic, Université de Lorraine, UMR1128, INRA, Vandoeuvre-lès-Nancy, France

Michiel StorkProcess Development, Institute for Translational Vaccinology, 3720 AL Bilthoven, The Netherlands

Jacob StrahilevitzHadassah-Hebrew University, Jerusalem 91120, Israel

Ana P. TedimDepartment of Microbiology, Ramón y Cajal University Hospital, IRYCIS, 28034 Madrid, Spain

Marcelo E. TolmaskyCenter for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University, Fullerton, 800 N. State College Blvd., Fullerton, CA 92831

Eva M. ToppDepartment of Biological Sciences, University of Idaho, 875 Perimeter, MS 3051, Moscow, Idaho 83844-3051

María De Toro Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria—CSIC, 39011 Santander, Spain

German M. TragliaInstitute of Microbiology and Medical Parasitology, National Scientific and Technical Research Council (CONICET), University of Buenos Aires, Buenos Aires, Argentina

Tung Tran Department of Biological Science, Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University, Fullerton, 800 N. State College Blvd., Fullerton, CA 92831


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Contributors xix

John S. Tregoning Mucosal Infection and Immunity Group, Section of Virology, Imperial College London, St Mary’s Campus, London, W2 1PG, United Kingdom

Francisco A. Uzal California Animal Health and Food Safety Laboratory, San Bernardino Branch, School of Veterinary Medicine, University of California, Davis, San Bernardino, CA

Daria Van Tyne Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02114

Andrea Volante Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CNB-CSIC, 28049 Madrid, Spain

Alexander V. VologodskiiDepartment of Chemistry, New York University, New York, NY 10003

Yang WangBeijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, P. R. China

Aleksandra Wawrzycka Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland

Katarzyna WegrzynDepartment of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk Poland

Sarah WendlandtInstitute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany

Jessica A. WisniewskiAustralian Research Council, Centre of Excellence in Structural and Functional Microbial Genomics, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia

Cong-Ming WuInstitute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany


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xxi

One of the biggest dreams of medicine from the 1940s, the complete defeat of infectious diseases caused by bacteria, was treated to a rough awakening with the rise and dissemination of antibiotic resistance, toxins, and pathogenicity functions. In the early 1960s it was found that this dissemination was usually associated with the acquisition of genes that were located in extrachromosomal elements analogous to those that Joshua Lederberg had called “plasmids” in 1952. The importance of the discovery led to intense research on plasmid biology, which in turn resulted in innumerable benefits to the development of science. The list of discoveries in the fields of cell and molecular biology is far too long to detail in this Preface. In addition, a monumental contribution of research on plasmids was instrumental in the development of molecular cloning and the biotechnology revolution that ensued. Their role in virulence and antibiotic resistance, together with the generalization of “omics” disciplines, has recently ignited a new wave of interest in plasmids. As models for understanding innumerable biological mecha-nisms of living cells, as tools for creating the most diverse therapies, and as inval-uable helpers to understand the dissemination of microbial populations, plasmids continue to be at the center of research.

marcelo e. tolmaskyJuan C. alonso

Preface


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Index

AAcetyltransferase, AAC(6´)-Ib-cr variant

of, 485Achromobacter xylosoxidans, 513Actinobacteria, AbR proteins in, 383, 384proteins found in plasmids and

chromosomes of, 385, 386–387Actinobacteria Arthrobacter, 511Actinomycetales, conjugative DNA

translocation in, 237Aerobactin, 579–581, 584–585as virulence factor, 581

Aerobactin iron uptake system, Klebsiellapneumoniae and, 464–465

Aerobactin system, gene cluster of, 580, 581Aggregation substance, in pheromone-

responsive plasmids, 564–566virulence of E. faecalis and, 566

Agrobacterium Ti plasmids, 295–313biotechnological applications of, 308–309conjugative transfer, regulation of,

N-acylhomoserine lactone signalsand, 307

DNA and effector protein substrateprocessing, 298–300

encoded type IV secretion systems,298–304

encoded VirD4, T4CP receptor of,300–301

fitness cost to maintenance of, 308functions of, signaling networks

controlling, 305maintenance of, 295–298nomenclature and types of, 295, 296opine catabolism and “opine concept”

and, 305opine signals and regulation of opine

catabolism, 306–307plasmid partitioning, 296–298plasmid replication, 298proteins in T-DNA transfer and plasmid

conjugation, 304–305repABC family of, 295–296, 297replication of, plant phenol, opine, and

AHL regulatory control of, 307–308T-DNA genes expressed in plant cells

and, 305T-DNA transfer to plant cell, 304–305T4SS channel of, 301–304VirA/VirG, mediated sensory perception

of, and plant wound signals, 305–306VirB/VirD4 transfer system, steps of type

IV secretion, 299, 300Aminoglycoside-aminocyclitol-streptothricin

resistance plasmids, in staphylococci,430–431

Anguibactin, biosynthesis of, 587–588uptake and structure of, 587–588

Anthrax, 548Antibiotic resistance, DNA vaccine

technologies to remove, 655, 656in Firmicutes, 381–419plasmid-mediated, in Gram-negatives,

Klebsiella pneumoniae as example of,459–474

role of plasmids in, 459spread of, plasmids in, 383

Antibiotic resistance genes, selection markersand, 637–638

Antimicrobial resistance, plasmid-mediated,in Staphylococci and otherFirmicutes, 421–444

Antimicrobial resistance genes, exchange viaillegitimate recombination, instaphylococci, 433–435

Antimicrobial resistance plasmids, ofStaphylococci, description of,421–422

Antimicrobial resistence genes, andbacterial population ecology,401–405

Archaea, description of, 349–350hyperthermophilic, rolling-circle

replication plasmids from, 51resolution of dimers in, 169

Archaeal Cdc6/Orc1 proteins, phylogenyof, 363

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Archaeal plasmids, as probes to study DNAtopology, 366–367

Archaeal RC-Rep proteins, 355, 356Archaeoglobales, plasmid from, 366ARS plasmids, 327, 331ATPase protein, 135ATPases, ParA, 144–149

higher-order complexes with ParBs, 145interactions with ATP and DNA,144–145

models for action of, 148–149structural biology of, 145–147type Ia, and transcriptional regulation,147–148

ParA-like, partition in variousprocesses, 149

ParM, and actin-like proteins, 141–144structures of, 141, 143

ParMs/ALPs, 144Atrazine, degradation of, 513

BBacillus anthracis, toxin and capsule

plasmids of, 548–550virulence factor of, 548

Bacillus cereus, food poisoning and,549–550

virulence plasmids of, 549–550Bacillus subtilis, in vivo cloning using, 605Bacillus thuringiensis, as insect and

nematode pathogen, 550virulence plasmids of, 549–550

Bacteria, chromosomes of, plasmid data canobscure, 124–125

evolution of, plasmids as spearheadof, 220

G+C low, plasmids from, 381, 382gram-positive. See Gram-positive bacteria.mechanisms to take up iron, 577multichromosomal, 168–169partition systems in, 135–136-plant interactions, Sinorhizobium meliloti

as model species for studying, 280single-recombinase Xer systems in,

168–169spore-forming, virulence plasmids of,

533–557Bacterial isolates, plasmid content in,

451–453Barnase, for inhibition of fungal

diseases, 619Beta toxin (CPB) plasmids, of Clostridium

perfringens, 541–542production of, 541–542

Beta2-toxin (CPB2) plasmids, of Clostridiumperfringens, 546–547

BioBrick assembly, to standardize DNAassembly, 603

Biodegradation, tolerance plasmids in,515–520

Biofilms, bacterial, formation of, 315, 316conjugation and development of, 317conjugative plasmids and, 250, 316–318copy-number control and maintenance in,

318–321formation of, nonconjugative plasmids

and, 321influence in biology of plasmids, 315–323

Bioformatics software, 608–610

for cloning-based projects, 609needs fulfilled by, 608

Biopharmaceuticals, plasmid. See Plasmidbiopharamceuticals.

Bioremediation, containment systemsstrategies for, 624–625

Biphenyls, polychlorinated, chlorobenzoatesand, 513

Broad-host-range conjugative plasmids,634–636

Broad-host-range origin of replication,636–637

Burkholderia vietnamensis, 508, 516

CCarbapenemase NDM-1, in Klebsiella

pneumoniae, 468Catabolic genes, in plasmids, 513–514Catabolic plasmids, environmental, 507–515Catenanes, in DNA replication, 120,

121–123CcdA antitoxin, 178Centromere, budding yeast, and STB,

327, 330Centromere-binding protein(s) (CBP), 135DNA binding domains of, structures of,

139, 140in type III partition systems, 150RHH dimer, 139, 140–141site-specific DNA binding of, 136–137two classes of, 136type I, 138, 141type II, 138, 141with HTH DNA binding motifs, 137–140N-termini of, 140

Chlorinated compounds, degradation of,plasmids encoding, 511–513

Chloroaniline, degradation of, 513Chloroaromatic compounds, degradation of,

513, 514Chlorobenzoates, degradation of

polychlorinated biphenyls and, 513Chromosome dimers, resolution of, 165,

168–169Chromosomes, and circular plasmids,

disadvantages of, 157multimeric forms of, 157–173

and plasmids, DNA site-specificrecombination of, 159–166

bacterial, plasmid data can obscure,124–125

Clostridium, classification of, 410Clostridium acetobutylicum, 517Clostridium botulinum, neurotoxin plasmids

of, 547–548Clostridium perfringens, beta toxin (CPB)

plasmids of, 540–541beta2-toxin (CPB2) plasmids of, 546–547cpe regions of, genetic organization of,

540–541enterotoxin plasmids of, 539–541epsilon-toxin (ETX) plasmids of, 542–544iota-toxin (ITX) plasmids of, 544NetB plasmids of, 544–546ParM variants of, phylogenetic analysis of,

535, 536peptidoglycan hydrolases and, 537spore-forming bacteria of, 533TcpA as DNA translocase of, 537

TcpC of, 537TcpF of, 537toxin plasmids in, within same cell, 535toxin plasmids of, 533–547

comparative alignment of, 533, 534conjugative transfer of, 535–539replication and maintenance of,533–535

Clostridium tetani, neurotoxin plasmids of,547–548

Clustered regularly interspaced shortpalindromic repeats (CRISPR), 385

Colicin V, 578–579Colicins, toxin-antitoxin system of, 638Conjugative transfer, inhibitors of, 266plasmid-mediated, 5–6

Containment systems, active, applications of,625, 626

control elements used in, 620molecular mechanisms for, 617outlook for, 628

biological, for biodegraders, 624–625predictability of genetically modifiedorganism and, 625

circuits of, biotechnological applicationsof, 624–628

for genetically modified organisms. SeeGenetically modifiedorganism (GMO).

new generation of, 623–624rationale for, 625, 626strategies for bioremediation, 624–625strategies for fermentation process,

625–627strategies for fundamental research,

627–628strategies for vaccines, 625–626strategies to enhance, 622–623Xenobiology, 623–624

CopA, as main control element, 86–87, 93binding to CopT, 93degradation pathway of, 94

CopB, as transcriptional repressor, 92CopG, crystal structure of, 92CopT, binding of CopA to, 94Co1V plasmids, aerobactin genes in,

579–581description of, 578determinants of, heterogeneity of,

584–585iron uptake systems of, 578schematic representation of, 579, 580virulence of E. coli and, 578

Cre/loxP of P1 and ResD/rfs of F, asindividual recombination systems,163–165

CRISPR-Cas immune system, againstinvading plasmids, action of,212, 214

and genetic transfers, 209–218and plasmids, incompatibility of, 211–213effects on plasmid replication and protein

production, 215genetic organization of, and steps of

action, 211inhibition of transformation by

electroporation, 212, 214interference with transformation, 213–214mechanism of, steps of, 210, 211

690 Index


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Neisseria meningitidis and, 214organization of, 209–210role in conjugation interference,

214–215Staphylococcus aureus and, 213targets mobile genetic elements,

210–211, 212ctRNA (RNAI), dual mechanisms involving,

40–41inhibition of, single mechanisms

involving, 40structure of, 39

Cupriavidus metallidurans, in heavy metalresistance, 518, 519–520

Cytolysin, contribution to virulence ofE. faecalis, 568

expression in E. faecalis, 567in Gram-positive species, 568produced by E. faecalis, 566–568

Cytomegalovirus immediate earlypromoter, 674

transcriptional inactivation of, 674

DDisease management, plasmids versus viral

vectors in, 670role of transgene products in, 670

DNA, binding domains, of centromere-binding proteins, structure of,139, 140

circular, closed, 106, 107molecules of, knots and catenanes of,105, 106

topology of, 105–110enzymes of, 110–111

with different topology, electrophoreticseparation of, 108–110

double-stranded, circular, Streptomycesand, 248–249TraB for transfer of, 248–249

transfer in multicellular Gram-positivebacteria, 245–249

episomal, inactive forms of chromatinand, 675

genetic rearrangements of, affectingEscherichia coli, 673–674

intramolecular triplex, 113intramycelial spread, plasmid-encoded Spd

proteins for, 249linear transfer mechanism in

Streptomyces, 249–250pathogen-associated molecular patterns

in, 674phage, conversion into linear plasmid,

71, 72plasmid, constrained and unconstrained

supercoiling in vivo, 117–119case 1, 111, 115, 117case 2, 118, 119, 120case 3, 119–120

dynamic topological equilibrium of,111–112

knotted forms of, gel electrophoresisof, 110

linking status of, topoisomeraseschanging, 110

long-term gene expression of, 675resolution of catenane and precatenanelinks in, 122

supercoiling, linking number, andlinking number difference, 106–107

topological behavior of, 105–131topology in vivo, constrained andunconstrained, 114, 115

two-dimensional gel illustrating Z-DNAformation, 112–113

plasmid synthesis of, 15plasmid transfer of, 6recombinant, plasmids in development

of, 669structure of, stabilized by negative

supercoiling, 112supercoil-sensitive, 112–114

supercoiled, conformations of, 107measuring of, 108

cruciforms forming in, 113twisting and writhing of, 107–108

supercoiling of, 112total community, plasma-specific

sequences in, 446–447unmethylated cytosine-phosphate-guanine

dinucleotides in, 674DNA assembly methodologies, 603–605schematic representation of, 604

DNA cloning, plasmids in developmentof, 669

DNA gyrase, 110, 111DNA molecules, circular, multimerization of,

157–159DNA polymerases, in plasmid rolling-circle

replication, 60–61DNA replication, catenanes and

hemicatenanes in, 120, 121–123fork reversal in, 120–121, 122forks, catenanes, hemicatenanes, and

knots, 119–125knotted bubbles in, 123–124replication intermediates in, 120, 123replication repair in, 120, 121

DNA sequence, de novo synthesis of, 606DNA site-specific recombination, of

plasmids and chromosomes, 159–166DNA topoisomers, pUC19, separation by gel

electrophoresis, 109DNA topology, archaeal plasmids to study,

366–367DNA vaccines, adaptive responses to,

657–658advantages of, 651as priming immunization in prime boost

regimens, 661as prophylactic vaccines, 671clinical trials of, 652–654compaction with cationic polymers and

liposomes, 658delivery using microparticles, 659development of, 651device-mediated delivery of, 659–660disadvantages of, 655electroporation for delivery of, 659–660expression of, 656–657optimizing of, 659–660

for clinic, optimizing of, 658–660packaging for delivery, 658–659route of delivery, 658

for epitope screening, 661for generation of monoclonal

antibodies, 661

for range of diseases, 651for veterinary practice, 655history of, 651immunogenicity, lack in humans, 659–660optimizing of, chemical adjuvantsfor, 660genetic adjuvants for, 660–661

inflammation following, 651innate response to, 657liquid jet systems to deliver, 659packaged in liposomes, 658–659packaged in phospholipid bilayers,

658–659regulatory requirements for, 655technologies to remove antibiotic

resistance, 655, 656use as experimental vaccines, 661use in humans, 655virosomes used in, 659

EEitABCD iron transport system, 583Enterobacteriaceae transconjugants, toluene

degradation of, 520–521Enterococcal plasmids, RepA_N, 397–401Enterococci, dendrogram of plasmids from,

392–393pheromone-responsive plasmids in,

563–564Enterococcus faecalis, cytolysin expression

in, 567cytolysin produced by, 566–568hospital-acquired infection and, 561virulence of, aggregation substance

and, 566and pathogenesis of, 561–563

virulence plasmids in, 561–568Enterococcus sex pheromone plasmids,

conjugative transfer of, 241–242Enterococcus spp., plasmids from, 394Enterotoxin plasmids, of Clostridium

perfringens, 539–541Enterotoxins, staphylococcal, 559–560,

561, 562Environmental pollutants, contaminating

waters and soils, 507plasmid-mediated tolerance toward,

507–531perspectives on, 521–523

Epsilon toxin (ETX), as neurotoxin, 542etx locus of comparative alignment of, 543production of, regulation of, 542

Epsilon-toxin (ETX) plasmids, ofClostridium perfringens, 542–544

Escherichia coli, BIDMC43a genome,reconstruction of, 224, 225

Co1E1 type replicon in, from plasmid, 602fluoroquinolone concentrations of,

486, 487genetic rearrangements of DNA and,

673–674in vivo cloning using, 605multimer formation in, 161, 165, 168narrow host range origins of replication

and, 636proteins constraining topology in, 114–117proteins in, 516quinolone susceptibility of, 486virulence of, Co1V plasmids and, 578

Index 691


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Escherichia coli incompatibility group Qplasmids, 37–38

Escherichia coli plasmids, 255-, Inc/Reptypes in, 228

MOB types in, 229plasmid sizes in, 221, 222

genomes sequenced to establish, 220pangenome evolution in, 219plasmid diversity and adaptation and,

219–235prevalent plasmid groups in, 226–229

Euryarchaeota, diversity of, 350–351examples of evolution in, 368–369group I, plasmids from, 351–358group II, plasmids from, 359–365phylogeny of, 351plasmids and genetic tools for, 367–368plasmids from, 349–377biological roles of, 369–370perspectives on, 370–371

rolling circle plasmids from, 353Exfoliative toxins, produced by S. aureus,

560–561, 562Expression vectors, based on pMV158

replicon, 269

FFactor for inversion stimulation (FIS), 116Fermentation process, containment systems

strategies for, 627Firmicutes, evolutionary ecology of, gene

and plasmid flow shapes in, 401–410gene pool of, mobile resistance genes

within, 436–437horizontal gene transfer in, analysis of,

383–385Inc18 family of plasmids in, 393–396multidrug resistance plasmids in, 385plasmid diversity in, 385–387plasmid-mediated antimicrobial resistance

in, 421–444plasmidome of, 381–419plasmids of, and bacterial population

ecology, 405and population biology, 405–410

pMG1/pHT plasmids of, 396, 407–408proteins found in plasmids and

chromosomes of, 385, 386–387Rep_1 family of plasmids in, 389–391,

398–399Rep_3 family of plasmids in, 390, 391,

404–405Rep_2 group of plasmids in, 391, 402RepA_N family of plasmids in, 396–397,

408–409Rep_L family of plasmids in, 391, 403Rep_trans group of plasmids in, 391,

400–401theta-replicating plasmids in, 391–397

Flp, misregulation of, plasmid amplificationand, 327, 330

R308A, extracatalytic role for,338–340, 341

Flp active site, mechanism of, probing of,337–338, 340

organization and mechanism of,335–337, 339

Flp reaction pathway, single molecule TPManalysis of, 340–343

Flp site-specific recombination system, and2-micron plasmid, 330, 335, 338

in vitro analyses of, 335, 339

GGel electrophoresis, of knotted forms of

plasmid DNA, 109separation of pUC19 DNA topoisomers

by, 109Gene gun, for delivery of plasmid

biopharmaceuticals, 677Gene synthesis, de novo, 606–608product ligation, into minimal cloning

vector, 607workflow of, schematic overview of, 607

Gene transfer, horizontal, dimer resolutionand, 169

Genetic transfers, and CRISPR-Cas immunesystem, 209–218

Genetically modified organism (GMO),containment of, active, 616–617

and genetic safeguard circuits, 615–622biological and gene, 616lethal functions for, 617–619

affecting cell envelope, 618affecting chemical control, 619–620affecting cytoplasm, 618–619affecting periplasm, 618

maintenance of contained cells and,622–623

passive, 616control element of, biological interaction-

dependent, 621cell density-dependent, 622chemical, 619–620environmental stress, 620–621gene transfer, 622stochastic, 621

control of, containment approachesfor, 615

control of lethal gene and, 619Genome sequencing, plasmid, 447–448Genomic bioaugmentation, as biotechnical

application, 520–523Gram-negative bacteria, motor protein

family in, 238–239T4SSs, 238

Gram-positive bacteria, conjugation in,237–256

conjugative transfer mechanisms in, 238in biofilms, conjugation between, 250mobilizable rolling-circle replicating

plasmids from, 257–276multicellular, double-stranded DNA

transfer in, 245–249single-stranded DNA transfer in, 238–245

Green fluorescent bacteria, constructionusing pMV158 replicon, 267,268–269, 270

GTPase protein, 135, 136

HHaloarchaea, plasmids and megaplasmids

from, 359–365Haloarchaeal rolling-circle plasmids, of

pGRB family, 361–363Haloarcula sp., pSCM201 plasmid

from, 363Halobacterium salinarum, 360

Halophiles, 350Halorubrum saccharovorum, pZMX101

plasmid from, 363Heavy metal tolerance, plasmids in, 517–520Helicases, group 1 superfamily, plasmid-

encoded Rep initiator and, 61–63Hemagglutinin Tsh, temperature-

sensitive, 583Hemicatenanes, in DNA replication,

121–123Hemolysin, in iron uptake, 580, 583–584Heteroaromatic compounds, degradation of,

plasmids and, 509–511degradation pathways of, 511, 512

Horizontal gene transfer (HGH), biofilmsin, 318

in Firmicutes, 383–385HTH DNA binding motifs, centromere-

binding proteins with, 137–140N-termini of, 140

Hydrocarbons, polycyclic aromatic,degradation of, plasmids and,509–511

IIncB plasmid pMU720, 90, 91IncIα and IncB group plasmids, 91IncIα/IncB case, inhibition of pseudoknot

formation, 90–92Integration host factor (IHF), 116Integrative and conjugative elements (ICEs),

actions of, 641organization of, 641

Integrons, as site-specific recombinationsystem, 639

Iota-toxin (ITX) plasmids, of Clostridiumperfringens, 544

Iron, transport of, 578Iron transport system, EitABCD, 583SitABCD, 582

Iron uptake, hemolysin in, 580, 583–584mechanisms of bacteria for, 577pJM1-type plasmids in, 585

Iron uptake system(s), Co1V plasmidsof, 578

of bacterial pathogens, 464–465, 466pJM1-type plasmids, 587plasmid-encoded, 577–597salmochelin, 581–582

Iteron plasmids, 15–32AT-rich and, 16, 17control mechanisms of replication in,

activation and proteolysis of Rep,25–26

auto-repression, 24–25, 26handcuffing, 24

DNA replication initiation, helicasedelivery and loading, 22–23

origin opening mechanism, 20–22origin recognition mechanism, 20–22

structure of, 15, 16Iterons, Rep proteins and, 15

KKlebsiella pneumoniae, 475aerobactin iron uptake system and,

464–465and Escherichia coli, genetic maps of,

463, 465

692 Index


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as cause of hospital-acquiredinfections, 460

as example of plasmid-mediatedantibiotic resistance and virulence,459–474

carbapenemase NDM-1 in, 468ColE1-type plasmids in, 460, 461large plasmids of, 464–468mortality of, resistance to antibiotics

and, 468plasmids in, 460pMET1 plasmid of, 466–468small plasmids of, 460–463, 464, 465transposon Tn4401 in, 468XerD binding sites of, 461–463, 464

LLAB, plasmids from, 397Lactococcus garvieae, virulence plasmids

in, 569Leader peptide translation, inhibition of,

93–94Lederberg, Joshua, 3, 4Lipids, cationic, and polymers, in delivery

of plasmid biopharmaceuticals,677, 678

Listeria spp., plasmids from, 396

MMacrolide-lincosamide-streptogramin

resistance plasmids, in staphylococci,427–429

Metagenomes, plasmid-specific sequences in,449, 450

Metamobilomes, plasmid-specific sequencesin, 449, 450

Methanobacteriales, plasmids from,358–359

Methanococcales, plasmids from, 358–359pT26-2 and TKV2/3 genes shared

between, 357Methanogens, 350group I, plasmids from, 358–359

Methanosarcinales, plasmids from,365–366

MfpA protein, 476Microparticles, plasmid-loaded, in delivery

of plasmid biopharmaceuticals,677, 678

Minimalistic Immunogenically Defined GeneExpression (MIDGE) vectors, 676

Mobile genetic elements, nature anddiversity of, 258–259

Mobilization (MOB) systems, to classifyplasmids, 387

MobM protein, 263–265Mono- and biaromatic compounds,

degradation pathways of, 510–511Monoaromatic compounds, degradation of,

plasmids and, 508–509Multidrug resistance (MDR) plasmids, in

Firmicutes, 385Multimer resolution system, as site-specific

recombination system, 638–639Multiplex-PCR typing system, 385–387Mupirocin resistance plasmids, in

staphylococci, 431–432Mutagenesis, commercial kits for, 606site-directed, 605–606

NNalidixic acid, 475Naphthalene, degradation by bacteria, 509Neisseria meningitidis, and CRISPR-Cas

immune system, 214NetB plasmids, of Clostridium perfringens,

544–546Neurotoxin plasmids, of Clostridium

botulinum, 547–548of Clostridium tetani, 547–548

NTPase protein, 135–136NTPases, partition, partition dynamics

promoted by, 141–149Nucleases, in active containment

systems, 619

OOligo- or multiresistance plasmids, in

Staphylococci, formation of, 433–435OqxAB efflux pump, 485–486Oxazolidinone resistance plasmids, in

staphylococci, 423–426

Pp33701, virulence plasmid, map of, 568,

569Pathogen-associated molecular patterns, 674pCAR plasmids, degradation of carbazole/

dioxin and, 511PCR amplicons, 446Penicillin resistance plasmids, in

staphylococci, 432–433Peptidoglycan hydrolases, Clostridium

perfringens and, 537pGRT1 plasmid, 516–517Phage plasmid(s), linear N15-like,

biotechnological applications of, 79centromere sites of, 76–77control of lysogeny and replication of,74–75

covalently closed telomeres, generationof, 77–78

map of prophage of, 73organization of genomes of, 72–74origin of, 79–80prophage, partitioning system, 75–77stable inheritance of, 76

protelomerases, 72, 77–78replication mechanism of, 78–79

Phage-plasmid(s), linear, conversion of phageDNA into, 71, 72

discovery of, 71–72linear N15-like, family of, 71–72isolation of, 71replication and maintenance of, 71–82

Phages, and alternative RNApolymerases, 634

Phenanthrene, degradation by bacteria, 509Phenicol resistance plasmids, in

staphylococci, 423Phenol, degradation of, 515pIB485, plasmid map of, 560pJM1-type plasmids, 585–589determinants of, heterogeneity of, 589in iron uptake, 585iron transport and biosynthesis operon of,

588–589iron uptake system of, 587regulation of, 587–589

replication and transfer of, 585–587schematic representation of, 586–587transport of, 586–587, 588

Plasmid addiction systems, 638Plasmid and resistance gene integration, via

insertion sequences, instaphylococci, 435

Plasmid biology, field of, birth of, 3, 4historical events spawning, 3–11

future of, 7–8Plasmid biopharmaceuticals, administration

and delivery of, barriers to, 676, 677combined cationic lipids and polymersfor, 677, 678

via electroporation, 678via gene gun, 677via plasmid DNA, 676–677with plasmid-loaded microparticles andnanoparticles, 677, 678

delivery of transgene to target cells,672, 673

development of, 669–670for disease prophylaxis, 672in cancer, 672in disease management, 670–672in hereditary disorders, 671in multifactorial diseases, 671–672in vivo plasmid stability and, 673–674maximizing immune response to, 675molecular aspects of, 672–676safety issues associated with, 678–679transgene expression and, 674

Plasmid bioplarmaceuticals, veterinary, roadto market, 680

Plasmid copy number, control of, plasmid-and host-mediated regulatorymechanisms in, 326–327, 328–329

Plasmid copy number control, antisense-RNA-mediated mechanisms of, 85,86–87

Plasmid detection, characterization, andecology, 445–458

Plasmid dimers, formation of, 157, 158Plasmid diversity, and classification systems,

385–401Plasmid DNA, for delivery of plasmid

biopharmaceuticals, 676–677Plasmid DNA synthesis, 15Plasmid DNA transfer, 6Plasmid-encoded iron uptake systems,

577–597Plasmid genome sequencing, 447–448Plasmid-mediated antibiotic resistance, in

Gram-negatives, Klebsiellapneumoniae as example of, 459–474

Plasmid-mediated conjugative transfer, 5–6Plasmid-mediated quinolone resistance,

clinical importance of, 487determinants, resistance produced by,

486–487varieties of, 487

Plasmid-mediated quinolone resistancegenes, distribution of, 478, 480–482

transmissible, plasmids and, 478, 479Plasmid-mediated tolerance, toward

environmental pollutants, 507–531perspectives on, 521–523

Plasmid mobilization, tripartite matingsfor, 640

Index 693


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Plasmid multimers, formation and incidenceof, 157–159

Plasmid N15, linear phage-. See Phage-plasmid(s), linear N15-like.

Plasmid partition mechanisms, 135–155diffusion-ratchet, 148, 149filamentation, 141, 142nomenclature in, 137partition complex recognition and

assembly, 136–137promoted by partition NTPases, 141–149proteins of, structure of, 138questions remaining concerning, 150–151type III (tubulin-like), 149–150

Plasmid-related parts and devices,repositories of, 642–644

Plasmid replicons, assembly of, 453Plasmid resolution systems, of serine

recombinase family, 159–163of tyrosine recombinase family, 163–166

Plasmid-specific sequences, in totalcommunity DNA, 446–447

Plasmid vectors, devoid of bacterialsequences, 673, 675

immune response to, 674optimized, 674–676physical characteristics of, 672, 673

Plasmid(s), 83–842-micron, as optimized and miniaturized

selfish DNA element, 326, 328–329chromosome-coupled segration of,327–329

contributions to biology andbioengineering applications, 343

organization of, 332segregation of, 327, 330

and chromosomes, DNA site-specificrecombination of, 159–166

and CRISPR-Cas immune system,incompatibility of, 211–213

and degradation of monoaromaticcompounds, 508–509

and degradation of polycyclic aromatichydrocarbons and heteroaromaticcompounds, 509–511

annotation of, 448antimicrobial-resistant. See specific

plasmids.antisense-RNA-mediated, copy number

control, 83–84, 86–87as DNA vaccines, for infectious diseases.

See DNA vaccines.as means of bacterial adaptation and

diversification, 445–446as spearhead of bacterial evolution, 220as tools for containment, 615–631assembly strategy for, 601beta toxin (CPB), of Clostridium

perfringens, 541–542production of, 541–542

beta2-toxin (CPB2), of Clostridiumperfringens, 546–547

biology of, influence of biofilms in,315–323

boosting of endogenous protein by, 671broad-host-range, conjugative transfer of,

238–245broad-host-range conjugative, 634–636catabolic genes in, 513–514

circular, and chromosomes, disadvantagesof, 157multimeric forms of, 157–173

replication of, 33–44initiation of, 35

ColE1, 89ColE2, 95–96conjugation and transfer functions of,

639–641conjugative, and biofilms, 250broad-host-range, 634–635in biofilms, 316–318transfer of, monitoring of, 250–251type IV secretion system of, 237

construction of, tools for, 601containment systems for. See Containment

systems.degradation of chlorinated compounds

and, 511–513dissemination of, limiting of, 229–230DNA. See DNA, plasmid.ennvironmental, outlook for, 644–645enterotoxin, of Clostridium perfringens,

539–541environmental, broad-host-range,

biological parts in, 635expression systems of, 641–642

chemically inducible, 642effector-triggered, 641–642mining of transcriptional factors/cognate chemical inducers, 641–642

mining of, for synthetic biology partsand devices, 633–649

self-transmissible, 640epsilon-toxin (ETX), of Clostridium

perfringens, 542–544Escherichia coli. See Escherichia coli

plasmids.exogenous capturing of, by biparental and

triparental matings, 449–451,452–453

F factors, F pilus, 3, 5–6fluorescence-tagged STB reporter, 332single copy, 332–334

fluorescent marker-tagged, host rangeof, 454

for immune stimulation, 671from Euryarchaeota. See Euryarchaeota,

plasmids from.from low G+C bacteria, 381, 382from Thermococcales, 351–358generation of, DNA assembly tools for,

601–613horizontal gene transfer by, 639–640host range of, and plasmid costs and

benefits, 453–455in antibiotic resistance, 459in development of DNA cloning and

recombinant DNA, 669in heavy metal tolerance, 517–520in silico design tools for, 608–610in solvent/aromatic compound tolerance,

515–517in vivo cloning of, 605inc18 family, and pT181 family, 84–89inc18 family, genetic organization of,

193–194, 195replicating segment of, 195

inc18 family of, 197–199

encoding by, 202initiation proteins, 4, 5iota-toxin (ITX), of Clostridium

perfringens, 544iteron-containing. See Iteron plasmids.large, carrying antimicrobial resistance

genes, 426, 427of Klebsiella pneumoniae, 464–468

larger than 150 kb, 399–401low-copy, 193

long-term maintenance of, 193manufacturing of, 679–680

activities and steps in, 680cell culture in, 679downstream processing of, 679–680

mobilizable rolling-circle replicating, fromGram-positive bacteria, 257–276

mobilome, Sinorhizobium meliloti, modelplant-symbiont, 279–293

NetB, of Clostridium perfringens,544–546

neurotoxin, of Clostridium botulinum,547–548

of Clostridium tetani, 547–548nonconjugative, and biofilm

formation, 321P1, phd-doc system of, 180pAD1, aggregation substance in, 564–566pAMß1 replication, 88pCF10, protein encoding by, 242pE194, 92persistence and survival of, functional

attributes required for, 7pheromone-responsive, 397–399

in enterococci, 563–564pIP501, 87–88

DNA transfer pathway of, 240peptidoglycan hydrolase family of,239–241Gram-positive, 242

transfer region of, 238–240T4SS proteins, channel/putative corecomplex component, 242channel/putative core complexcomponent of, 241homology-based classification schemefor, 243surface factor/adhesin family of, 241,242–243

VirB1 protein family of, 243–245VirB6 protein family of, 245VirB8 protein family of, 245pJM1-type. See pJM1-type plasmids.pLS1, 92

control component of, 92pMV158, 261, 263. See pMV158 replicon.

and its derivative pLS1, 92promiscuous, host-independent biological

functions of, 634–636propagation pf, genetic determinants and

phenotypes of, 222–224pRUM-like, 399pSK41 and pSK1, 94pSM19035, 88

genome organization of, 193, 194long IR segments of, 197segA locus of, 196segB locus of, 197segB1 locus of, 197–199

694 Index


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Plasmids (continued)segB2 locus of, 199–202protein structures of, 199–201

segC locus of, 196–197segD locus of, 202–203in formation of plasmidcointegrate, 203

stability systems of, 195TA system in stabilization of, 199

pT181, 84, 87quinolone resistance (Qnr), 478–483regulation of, 485spread of, 483–484

R1, hok-sok of, 178–179kis-kid TA of, 179

R388, conjugation genes of, 220, 221RC-replicating, 258RCR, mobility of, high-throughput

assessment of, 269–271mobilizable, 259–260, 261, 263MOBp family of, 262MOBv family of, 260–262promiscuity of, factors contributingto, 265

recombinant, 601selection of, antibiotic resistance genesand, 637–638

reconstruction of, for biotechnology andbiomedical applications, 7, 8

from whole-genome sequencingdatasets, 224–226, 227

repC and repABC, 95replace of protein, by transfer of correct

gene, 671replication and partitioning systems,

recognition of, 4–5replication of, antisense-RNA control in,

83–84broad-host-range of, 636–637by strand-displacement mechanism,38, 39

duplex melting and replisome assembly,34–35

effects of CRISPR-Cas system on, 215initiation of, 33–35regulation of, 38–41

narrow host range origins of, 636origins of, 33–34theta and strand-displacement modes of,compared, 37–38

replicons commonly used in, 602rhizospheric, 521RK2, parDE system of, 179–180rolling-circle replication, 45–69accessory genes of, 47and structural and segregationalinstability, 49

control of, 55–58copy number control systems in, 56copy number regulation in, 57DNA and RNA polymerases in, 60–61double-strand origin of, 49–51functional organization of, 47, 48general aspects of, 45–49host proteins involved in, 60–63in Firmicutes, 388–389model for, 46promiscuous replicons of, 47–48RNA-mediated systems of control of, 56

single-strand origin and, 58–60size of, 47vectors for gene cloning and, 48–49

selfish yeast, partitioning and copynumber control systems of, 325–347

sequence-dependent cloning in vitro,602–603

sequence-independent cloning in vitro,603–605

single copy reporter, segregation of, duringmonopolin-directed mitosis,336–337

sister, and sister chromatids, hitchhikingmodel, 334–335, 336–337

site-specific recombination of, 638–639small, carrying antimicrobial resistance

genes, 423, 426of Klebsiella pneumoniae, 460–463,464, 465

steric hindrance of, 41structural studies and genetic mapping of, 4theta. See Theta plasmids.theta-replicating, in Firmicutes, 391–397Ti, Agrobacterium. See Agrobacterium Ti

plasmids.to block disease-related genes, 671to kill malignant cells, 671tolerance, in biodegradation, 515–520toxin, of Clostridium perfringens,

533–547toxin and capsule, of Bacillus anthracis,

548–550transformation into minimal-size gene

transfer units, 676type of, imposed by choice of replicon,

601–602virulence. See Virulence plasmids.

Pleolipoviridae, 360Pleuromutilin resistance plasmids, in

staphylococci, 429–430pMV158 replicon, applications of, 266–267construction of green fluorescent bacteria

using, 267, 268–269, 270expression vectors based on, 269lagging-strand origins, 60model for plasmid rolling-circle replication

based on, 46promotor-probe vector construction based

on, 267–269Pollutants, environmental, plasmid-mediated

tolerance toward, 507–531perspectives on, 521–523Polymerase chain reaction (PCR), sequence-

dependent cloning and, 603Postsegregational killing. See PSK.Promotor-probe vector, construction based

on pMV158 replicon, 267–269Proteins, actin-like, ParM class of ATPases

and, 141–144ATPase, 5centromere-binding. See Centromere-

binding protein(s) (CBP).histone-like nucleoid structuring (H-NS),

116–117in rolling-circle replication, 60–63nucleoid-associated, 115of plasmid partition mechanisms,

structures of, 138P1 ParB family of, 139, 140

plasmid-encoded, in suicide gene therapy,671–672

plasmid-encoded Spd, for intramycelialDNA spread, 249

plasmid initiator, 4, 5production of, effects of CRISPR-Cas

system on, 215Rep, in replication initiation, 51–55

domain structure of, 51, 52iterons and, 15plasmid, as dimers, 19–20iteron-containing, polymerasecomplex assembly, 23–24Rep-helicase interaction of, 23leucine zipper-like motif of, 20structure of, 18–20two winged helix of, 18–20

restriction to single replication event,57–58

synthesis of, mechanisms forcontrolling, 55–57

RepB, in replication initiation, 53–55replication initiator, 387plasmid-encoded Rep, 61–63

TubR/tubC, 150TubZ, 149–150

Proteobacteria, MOB and MPF families in,221–222, 223

Proteobacterial transfer systems, diversityand classification of, 220–222

Pseudoknot formation, inhibition of,Incla/IncB case, 90–92

Pseudomonas, degradation of phenoland, 515

Pseudomonas knackmussii, integrative andconjugative elements in, 641

Pseudomonas putida, mineralization oftoluene, 507

Pseudomonas resinovorans, 507, 511, 515,516, 521, 522

PSK, by TA in broad-host-range plasmid,179–180

by TA in lysogenic bacteriophage, 180in antibiotic resistance factor, 179mediated by plasmid-encoded TAs,

178–183mediated by TA present in multiresistance

conjugative plasmid, 178–179of TAs, comparative analysis of, 180–181protects from bacteriophage infection,

180success of, 181–182TAs determining plasmid maintenance by,

175, 176via chromosomally encoded TAs,

183–184, 186–187pSM19035 and pAMß1 resolution system,

162–163pTN2 plasmid family, 356–357Pyrococcus strain JT1, pRT1/pAMT11

from, 358

QQepA efflux pump, 485Quinaldine, 511Quinolone resistance, plasmid-mediated,

475–503Quinolone resistance alleles, genetic

environment of, 478, 483–484

Index 695


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Quinolone resistance protein, dimer,protection of DNA gyrase, 476, 477

rod-like structure of, 476, 477origin of, 476–478structure and function of, 475–476

RRecombination reaction, resolution

selectivity on, 166Recombinational synapses, topology of,

164, 167rep mRNA, translational inhibitionof, 92–96

RepH plasmids family, 363Research, fundamental, containment systems

strategies for, 627–628Resistance plasmids, recombination via

site-specific recombination, 433in staphylococci, 433

Resolvases, of serine recombinase family,synapse architecture for, 164,166–167

Restriction-modification (RM) systems, 385RHH dimer, of centromere-binding

protein(s) (CBP), 139, 140–141Rhizobium etli, 516–517Rhodococcus equi, virulence plasmids

in, 568RK2/RP4 resolution systems, 159–162RNA, transcription of, DNA rotation

and, 112RNA binding, antisense/sense, of IncIα and

IncB group plasmids, 90–92RNA control, antisense, in plasma

replication, 84RNA-DNA hybrids, stable, 118, 120RNA inhibition, countertranscribed,

38–41RNA polymerase(s), 115alterative, phages and, 634in plasmid rolling-circle replication,

60–61RNAI. See ctRNA (RNAI).RNAs, antisense, 85

plasmid replication control by, 83–103RNAI, 85degradation of, 85intracelllular concentrations of, 85

RNAII, 85, 92intracellular concentrations of, 85

RNAIII, 85, 88Sok, 178–179

from accessory DNA elements, 83plasmid-encoded, 83small regulatory, 83

Rolling-circle replication. See Plasmid(s),rolling-circle replication.

SSaccharomyces cerevisiae, in in vivo cloning,

602, 605Salmochelin iron uptake system, 581–582Salmochelins, as catechol siderophores, 581biosynthesis of, 581genes coding for, 581

Salmonella enterica, 516Selfish yeast elements, 325–326Serine recombinase family, plasmid

resolution systems of, 159–163

Serine recombinase famity, resolvases of,synapse architecture for, 164,166–167

Serine recombinase(s), caralyzed resolution,mechanism of, 160, 162–163

catalyzed resolution systems, geneticorganization of, 159–162

site-specific recombination by, 159, 160Siderophore-mediated systems, of iron

uptake, 577–578Sinorhizobium medicae, 281Sinorhizobium meliloti, as model species for

studying plant-bacteriainteractions, 280

conjugative modules in, genetics of,283–287

extrachromosomal replicons in, 279–280model plant-symbiont, plasmid mobilome

of, 279–293non-pSym plasmid compartment at OMC

scale, 289–290non-pSym plasmid mobilome in,

282–283, 284non-pSym plasmid replicons in, 281non-pSym plasmids in, and pSym in,

replication systems in, 282diversity of, 281–282

plasmid pSmeLPU88b, mobilization of,284, 287

plasmid pSmeLPU88b transfer to,283–285, 286–287

strain 1021, conjugative transfer ofmegaplasmids in, 287–289

symbiotic (mega) plasmids of, 280–281symbiotic plasmids, conjugative transfer

of, 288SitABCD iron transport system, 582Solvent/aromatic compound tolerance,

plasmids in, 515–517Sphingomonas, xenobiotics and, 509–511Sphingomonas aromaticivorans F199, genes

encoded by, 509, 510–511Spore-forming bacteria, toxin plasmids from,

plasmid maps of, 538–539virulence plasmids of, 533–557

sRNAs, regulatory, acting on chromosomallyencoded targets, 96

in plasmid replication control, 96Stability systems, interplay between,

contributes to segregation, 193–207Standard European Vector Architecture

(SEVA), database, 643–644pipeline, 644

Staphylococcal plasmids, RepA_N, 390, 397Staphylococci, aminoglycoside-

aminocyclitol-streptothricin resistanceplasmids in, 430–431

and other Firmicutes, plasmid-mediatedantimicrobial resistance in, 421–444

antibicrobial resistance plasmids of,description of, 421–422

antimicrobial resistance genes in, exchangevia illegitimate recombination,433–435

plasmid-borne, 422–433contact with Firmicutes, 409fusidic acid resistance plasmids in, 432macrolide-lincosamide-streptogramin

resistance plasmids in, 427–429

mupirocin resistance plasmids in, 431–432oligo- or multiresistance plasmids in,

formation of, 433–435oxazolidinone resistance plasmids in,

423–426penicillin resistance plasmids in, 432–433phenicol resistance plasmids in, 423plasmid and resistance integration via

insertion sequences in, 435plasmid-borne antimicrobial resistance

genes in, 424–425pleuromutilin resistance plasmids in,

429–430resistance plasmids in, recombination via

site-specific recombination, 433tetracycline resistance plasmids in,

422–423trimethoprim resistance plasmids in, 432vancomycin resistance plasmids in, 432

Staphylococcus aureus, CRISPR-Cas systemand, 213

exfoliative toxins produced by, 560–561, 562

plasmid pT181, plasmid rolling-circlereplication and, 47

production of extracellular toxins, 559pT181 replicon, model for plasmid

rolling-circle replication based on, 46virulence and pathogenesis of, 559virulence plasmids in, 559–561

Staphylococcus spp., plasmids from, 390STB plasmid partitioning locus, as site for

assembly of protein factors, 328–329budding yeast centromere and, 332centromeres and chromosome segregation

at, 329two regions of, 329

Streptococcus, within phyla Firmicutes,405–407

Streptococcus pyogenes pSM19035, asmodel of segregation, 193–207

Streptococcus spp., plasmids from, 395Streptomyces, classical mode, circular

double-stranded DNA transfer in,248–249

conjugative transfer in, 245–249linear DNA transfer mechanism in,

249–250Synaptosome and topology, 166–168

TTA maintenance molecules, coupling plasmid

replication and, 181TA system, as stabilization function of

pSM19035, 199of inc18 plasmids, 197–199

TAs, as plasmid-chromosome cross-talk,185–187

chromosomally encoded, 184PSK via, 183–184, 186–187

classification of, 176, 177in plasmids and chromosomes, 177interactions, evolutionary considerations

on, 182–183plasmid-encoded, PSK mediated by, 178PSK of, comparative analysis of, 180–181regulation and activation of, 177

Tetracycline resistance plasmids, instaphylococci, 422–423

696 Index


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Thermoacidophiles, 350Thermococcales, plasmids from, 351–358rolling circle plasmids from, 353–355

Thermococcales plasmids, replicating byTheta mode, 355–356

Thermococcus, pT26-2 (TKV2,3) plasmidfamily from, 357, 358

Thermococcus faecalis, biofilm cells, ratiosof plasmids/chromosome in, 319, 320

biofilm growth of, 319conjugative plasmid of, copy number

of, 319Thermococcus kodakaraensis, 352, 355–356Thermococcus nautili, 355pTN3 (TKV4) in, 358

Thermoplasmatales, plasmids from, 366Theta plasmids, class A, replication of,

35–36transcriptional regulation by Repbinding, 41

class B, replication of, 36–37classes C and D, replication of, 37feedback regulatory mechanisms in, 38replication of, mechanisms of, 33–44

Ti plasmids, Agrobacterium. SeeAgrobacterium Ti plasmids.

TOL plasmids, toluene and, 508Toluene, degradation of, 508degradation of Enterobacteriaceae

transconjugants, 520–521mineralization by Pseudomonas

putida, 507TOL plasmids and, 508

toxIN, 180

Toxin and capsule plasmids, of Bacillusanthracis, 548–550

Toxin-antitoxin genes. See TAs.Toxin-antitoxin systems, 638conditional activation of, 175–192

Tra regulon, enterococcal, in pheromonesensing, 565

Transcriptional attenuation, antisense-RNA-mediated, 84–89

Transcriptional regulation, type Ia ParAsand, 147–148

Transcriptional repressor CopR, 85–87functions of, 85

Transglycosylases, lytic, structure-basedclassification of, 243–245, 246–247

Translational inhibition, 92–95Transposon Tn4401, in Klebsiella

pneumoniae, 468Trimethoprim resistance plasmids, in

staphylococci, 432Tyrosine recombinase family, plasmid

resolution systems of, 163–166Xe recombination of, topological

selectivity in, 164, 167–168Tyrosine recombinase(s), catalyzed

resolution, mechanism of, 161,165–166

catalyzed resolution systems, geneticresolution of, 161, 163–165

site-specific recombination by, 159, 161

UUnmethlylated cytosine-phosphate-guanine

dinucleotides, in DNAs, 674, 675

VVaccines, containment systems strategies for,

625–626Vancomycin resistance plasmids, in

staphylococci, 432Vibrio anguillarum, 587Virulence, and antibiotic resistance,

plasmid-mediated, Klebsiellapneumoniae as example of,459–474

Virulence plasmids, in Enterococcus faecalis,561–568

in Lactococcus garvieae, 569in Rhodococcus equi, 568in Staphylococcus aureus, 559–561of Bacillus cereus, 549–550of Bacillus thuringiensis, 549–550of nonsporulating Gram-positive

pathogens, 559–576of spore-forming bacteria, 533–557

WWhole genome sequencing, 387

XXenobiology, 623–624Xenobiotics, Sphingomonas and, 509–511Xer systems, as multipurpose recombination

systems, 163single-recombinase, in bacteria, 168–169

YYeast plasmid, genetic organizatio of, and

copy number of, 328–329

Index 697

plasmids: biology and impact in biotechnology and discovery

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