Plasmids : biology and impact in biotechnology and discovery

720 Pages·2015·54.414 MB·English

by  Marcelo E. Tolmasky, Juan Carlos Alonso

PLASMIDS
BIOLOGY AND IMPACT IN BIOTECHNOLOGY AND DISCOVERY

PLASMIDS
BIOLOGY AND IMPACT IN BIOTECHNOLOGY AND DISCOVERY
Edited by | Marcelo E. Tolmasky
Center for Applied Biotechnology Studies
Department of Biological Science
College of Natural Sciences and Mathematics
California State University, Fullerton
AND
Juan C. Alonso
Centro Nacional de Biotecnología, CSIC
Departamento de Biotecnología Microbiana,
Madrid, Spain
ASM Press, Washington, DC
Copyright © 2015 American Society for Microbiology. All rights reserved. No part of
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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
2015004787
eISBN: 978-1-55581-898-2 doi:10.1128/9781555818982
10 9 8 7 6 5 4 3 2 1
All Rights Reserved
Printed 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, USA
Phone: [phone]
Fax: [phone]
E-mail: [email protected]
Online: 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
Dedicated to the memory of Jorge Crosa

Contents
Contributors xi
Preface 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
vii
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
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