modern microbial genetics 2d ed - uldis n. streips

MODERN MICROBIAL GENETICS Second Edition Modern Microbial Genetics, Second Edition. Edited by Uldis N. Streips, Ronald E. Yasbin Copyright # 2002 Wiley-Liss, Inc. ISBNs: 0-471-38665-0 (Hardback); 0-471-22197-X (Electronic) MODERN MICROBIAL GENETICS Second Edition EDITED BY Uldis N. St reips Department of Microbiology and Immunology School of Medicine University of Louisville Louisville, Kentucky Ronald E.Yasbin Program in Molecular Biology University of Texas at Dallas Richardson, Texas A JOHN WILEY & SONS, INC., PUBLICATION Designations used by companies to distinguish their products are often claimed as trademarks. In all instances where John Wiley & Sons, Inc., is aware of a claim, the product names appear in initial capital or ALL CAPITAL LETTERS. Readers, however, should contact the appropriate companies for more complete information regarding trademarks and registration. Copyright # 2002 by Wiley-Liss, Inc., New York. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means, electronic or mechanical, including uploading, downloading, printing, decompiling, recording or otherwise, except as permitted under Sections 107 or 108 of the 1976 United States Copyright Act, without the prior written permission of the Publisher. Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 605 Third Avenue, New York, NY 10158-0012, (212) 850-6011, fax (212) 850-6008, E-Mail: PERMREQ @ WILEY.COM. This publication is designed to provide accurate and authoritative information in regard to the subject matter covered. It is sold with the understanding that the publisher is not engaged in rendering professional services. If professional advice or other expert assistance is required, the services of a competent professional person should be sought. ISBN 0-471-22197-X This title is also available in print as ISBN 0-471-38665-0. For more information about Wiley products, visit our web site at www.Wiley.com. Contents Preface vii Preface to the First Edition ix Introduction xi Contributors xiii Section 1: DNA METABOLISM 1 CHAPTER 1. Prokaryotic DNA Replication William Firshein 3 CHAPTER 2. DNA Repair Mechanisms and Mutagenesis Ronald E. Yasbin 27 CHAPTER 3. Gene Expression and Its Regulation John D. Helmann 47 CHAPTER 4. Bacteriophage Genetics Burton S. Guttman and Elizabeth M. Kutter 85 CHAPTER 5. Bacteriophage l and Its Relatives Roger W. Hendrix 127 CHAPTER 6. Single-Stranded DNA Phages J. Eugene LeClerc 145 CHAPTER 7. Restriction-Modification Systems Robert M. Blumenthal and Xiaodong Cheng 177 CHAPTER 8. Recombination Stephen D. Levene and Kenneth E. Huffman 227 CHAPTER 9. Molecular Applications Thomas Geoghegan 243 Section 2: GENETIC RESPONSE 259 CHAPTER 10. Genetics of Quorum Sensing Circuitry in Pseudomonas aeruginosa: Implications for Control of Pathogenesis, Biofilm Formation, and Antibiotic/Biocide Resistance Daniel J. Hassett, Urs A. Ochsner, Teresa de Kievit, Barbara H. Iglewski, Luciano Passador, Thomas S. Livinghouse, Timothy R. McDermott, John J. Rowe, and Jeffrey A. Whitsett 261 v CHAPTER 11. Endospore Formation in Bacillus subtilis: An Example of Cell Differentiation by a Bacterium Charles P. Moran Jr. 273 CHAPTER 12. Stress Shock Uldis N. Streips. . 281 CHAPTER 13. Genetic Tools for Dissecting Motility and Development of Myxococcus xanthus Patricia L. Hartzell 289 CHAPTER 14. Agrobacterium Genetics Walt Ream 323 CHAPTER 15. Two-Component Regulation Kenneth W. Bayles and David F. Fujimoto . 349 CHAPTER 16. Molecular Mechanisms of Quorum Sensing Clay Fuqua and Matthew R. Parsek 361 Section 3: GENETIC EXCHANGE 385 CHAPTER 17. Bacterial TransposonsÐAn Increasingly Diverse Group of Elements Gabrielle Whittle and Abigail A. Salyers . . . 387 CHAPTER 18. Transformation Uldis N. Streips. . 429 CHAPTER 19. Conjugation Ronald D. Porter 463 CHAPTER 20. The Subcellular Entities a.k.a. Plasmids Michael H. Perlin 507 CHAPTER 21. Transduction in Gram-Negative Bacteria George M. Weinstock 561 CHAPTER 22. Genetic Approaches in Bacteria with No Natural Genetic Systems Carolyn A. Haller and Thomas J. DiChristina 581 Index 603 vi CONTENTS Preface The impetus for this updated edition of Modern Microbial Genetics came from many discussions among the authors and editors with the leadership and participants at the lovely Wind River Conference on Prokary- otic Biology held in Estes Park, Colorado every June. The first edition, though compre- hensive, had become outdated and the need for an up-to-date, advanced textbook for microbial genetics was palpable. With the able encouragement and cooperation of our editor Luna Han, at John Wiley & Sons, Inc., the agreement was reached to publish this text. So, we welcome you to Modern Micro- bial Genetics II. We have maintained the same model for chapter authorship. Even though in some ways it would be optimal to have a single author for the entire textbook, we felt that this in-depth material could be handled far better by enlisting experts in their fields to put together chapters of their own respective insights. Moreover, we chose authors who are also excellent teachers so that the textbook could be easily adapted to classrooms in ad- vanced undergraduate and graduate courses. A quick comparison of the two editions should point out a universal truth about sci- entific publications: namely, a published book may advance information a step, or at most a few steps, ahead of other existing books, but the moment it is published, the book is miles behind where the information will ultimately lead. Because of this, in Modern Microbial Genetics II the chapters are extensively revised and updated, some are removed, and others added. This happens to be the most complete and relevant infor- mation at this point in time from our per- spective. Publication on the Web will further allow for more facile updating and diminish the inevitable dissipation of current informa- tion. As we stated in the first edition, this book presents a vibrant field of knowledge with many areas anxiously awaiting new investi- gators. After going through this text, one or another of the chapters may beguile you, the reader, enough to willingly immerse yourself in the wonderful discipline of microbial gen- etics. Again we sayÐWelcome! We wish you success in adding the exten- sive knowledge presented in this textbook to your previous experience in microbial genet- ics and applying it to your own future goals and objectives. We look forward to many of you joining us in generating information, and perhaps even chapters, for future editions and updates to this textbook. Uldis N. Streips Ronald E. Yasbin vii Preface to the First Edition The information presented in this book rep- resents the best efforts by a select group of authors, who are not only productive in re- search but who are also excellent teachers, to delineate the limits of knowledge in the vari- ous areas of microbial genetics. We feel the use of multiple authors provides not only for depth of material, but also enriches the per- spectives of this textbook. The limits of knowledge need to be stretched continuously for science to remain exciting and meaning- ful. It should be obvious that this then leaves a vast field for future work, where some of you readers will find a lifetime of productive research. Moreover, it should also be obvious that many of the areas discussed in this book still contain pathways and byways which sometimes have never been explored, and sometimes have side roads waiting for eager minds to map and meld within the pool of knowledge which we call modern microbial genetics. We expect that you will have had some previous exposure to microbial genetics and will use this text to build on that experi- ence. As you probe in depth the thought processes and experiments which were used to formulate the fundamental concepts in modern microbial genetics, one or another of the included chapters may spark the inter- est in your mind to become a traveler within this vast and exciting discipline. If that is the caseÐWelcome! We wish you success in adding the know- ledge presented in this textbook to your pre- vious experience in microbial genetics and applying it to your future goals and object- ives. We thank the many reviewers who helped to enhance the accuracy and presen- tation of this material. In this regard, Marti Kimmey was most helpful in correlating the various chapters. Uldis N. Streips Ronald E. Yasbin ix Introduction ULDIS N. STREIPS AND RONALD E. YASBIN The initial studies, which presaged the emer- gence of the capabilities for the complete sequencing of genomes and the study of whole organism proteomics in addition to various aspects of molecular biology, are now almost 90 years old. The early reports on bacteriophage by Twort (1915), d'Herelle (1917), and Ellis and Delbruck (1939) and the initial description of the pneumococcal type ``transformation'' by Griffith (1928) presha- dowed this explosion of information by laying down a solid foundation on which to build layer upon layer of new ideas and facts. Even though these early workers had no basis for concluding more than their time in the flow of events allowed them to conjec- ture, we can envision that an unbreakable thread was formulated by their work. The scientists in the many subsequent decades have woven this initially thin thread into an extensive and mutlicolored tapestry in which are embedded the stories of the research that is described in Modern Microbial Genetics II. It is fascinating that for the first years the major debate was on the existence and function of DNA. Entering the New Millen- ium, not only can we reproducibly obtain DNA, deliver it to any cell we choose, but we can also unlock every secret in that molecule. In the 1940s and 1950s two major research thrusts permanently changed the perspectives on microbial genetics and provided the basis for the explosion of information in the field of molecular biology. These were, first, the documentation of DNA as the carrier of an organism's genetic information by Avery and coworkers (1944) and the subsequent de- ciphering of the chemical structure of this molecule by Watson and Crick (1953), and second, the discovery of mobile genetic elem- ents by McClintock (1956). The seminal work on proving that DNA is the stuff of heredity, can be manipulated, and indeed is self-manipulating, rapidly led to the description in 1950s and 1960s of genetic ex- change in bacteria and in subsequent years to modern microbial genetics. In this textbook there are detailed descriptions of three major areas. The first is DNA Metabolism: how DNA replicates (Firshein), how DNA is repaired (Yasbin), how DNA is transcribed and the transcription regulated (Helmann) and how DNA recombines (Levene and Huff- man). This section also includes the genetics of bacteriophage including the T-even phages (Guttman and Kutter), the lambdoid phages (Hendrix), the phages with nucleic acids other than double stranded DNA (Leclerc), and how restriction and modification directs mi- crobial existence (Blumenthal and Cheng). A chapter (Geoghegan) on DNA manipula- tion techniques and application to molecular biology completes the DNA Metabolism section. The second section is on Genetic Response and includes several chapters on how micro- organisms interact with the environment. The role and mechanism of bacteria in establish- ing disease states is discussed by Hassett and coauthors. How cells react to environmental stress is shown in the chapters by Moran on sporulation and Streips on stress shock. Two environmental organisms that depend on gen- etic versatility are discussed in the chapters on Myxococcus by Hartzell and Agrobacterium xi by Ream. The ability of microorganisms to constantly sense their environment is revealed in chapters on two-component sensing by Bayles and Fujimoto and quorum sensing by Parsek and Fuqua. The last section on Genetic Exchange in- cludes the latest information on the classic exchange mechanisms (see the Chapters by Streips on transformation, Porter on conjuga- tion, and Weinstock on transduction). Perlin discusses the genetics of plasmids that do not belong to the F family. In addition this section also includes recent information about trans- posons and their ability to move from cell to cell (Whittle and Salyers). Finally, the mo- lecular study of bacteria which have no stand- ard genetic systems is described by Haller and DiChristina and concludes this book. The elucidation of global regulatory sys- tems, which control everything from DNA uptake to emergency responses and overall microbial development, are widely discussed in various chapters in this book and they help to bring the study of molecular biology full circle. As described by Helmann, Streips, and Moran, there are genes and operons in bacteria which are coordinately regulated and defined as regulons. So, from the initial consideration about the existence and nature of DNA, now assumptions are made about how genes network and cooperate in multi- gene regulons to suit the needs of the bacter- ial cell. McClintock's early work showed that DNA was not merely a static chemical mol- ecule, but rather a dynamic structure which can be amplified to a myriad of genetic pos- sibilities. So it is once the fundamental aspects of bacterial genes and their exchange were elucidated, it became apparent that bac- teria, bacteriophage, and also eukaryotes, through mutation, evolution, and genetic ex- change have arranged and rearranged their genetic material to take an optimal advan- tage of their niche in the environment. This theme is the constant thread that connects the various sections and subject areas of Modern Microbial Genetics II. This textbook is our approach to link the pioneering work of the past to the modern technology available today and to start answering some of the major questions about the molecular mechanisms operating in mi- crobial cells. REFERENCES Avery OT, MacLeod CM, McCarty M (1944): Studies on the chemical nature of the substance inducing transformation of pneumococcal types. Induction of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III. J Exp Med 79:137±158. D'Herelle F (1917): Sur un microbe invisible antagoniste des bacilles dysenteriques. CR Acad Sci 165:373. Griffith F (1928): The significance of pneumococcal types. J Hyg 27:113±159. McClintock B (1956): Controlling elements in the gene. Cold Spring Harbor Symp Quant Biol 21:197±216. Twort FW (1915): An investigation on the nature of the ultramicroscopic viruses. Lancet 11:1241. Watson JD, Crick FHC (1953): Molecular structure of nucleic acids. Nature 171:737±738. xii INTRODUCTION Contributors Kenneth W. Bayles, Department of Micro- biology, Molecular, and Biochemistry, The College of Agriculture, University of Idaho, Moscow, ID 83844±3052 Robert M. Blumenthal, Department of Micro- biology and Immunology, Medical College of Ohio, Toledo, OH 43614±5806 Xiaodong Cheng, Biochemistry Department, Emory University, Atlanta, GA 30322±4218 Thomas J. DiChristina, School of Biology, Georgia Institute of Technology, Atlanta, GA 30332 William Firshein, Department of Molecular Biology and Biochemistry, Wesleyan Univer- sity, Middletown, CT 06459 David F. Fujimoto, Biology Department LS± 416, San Diego State University, San Diego, CA 92182 Clay Fuqua, Department of Biology, Indiana University, Bloomington, IN 47405 Thomas Geoghegan, Department of Bio- chemistry and Molecular Biology, University of Louisville School of Medicine, Louisville, KY 40292 Burton S. Guttman, The Evergreen State Col- lege, Olympia, WA 98505 Carolyn A. Haller, School of Biology, Geor- gia Institute of Technology, Atlanta, GA 30332 Patricia L. Hartzell, Department of Micro- biology, Molecular Biology, and Biochemis- try, University of Idaho, Moscow, ID 83844± 3052 Daniel J. Hassett, Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, College of Medi- cine, Cincinnati, OH 45267±0524 John D. Helmann, Department of Microbiol- ogy, Cornell University, Ithaca, New York 14853±8101 Roger W. Hendrix, Pittsburgh Bacteriophage Institute, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 Kenneth E. Huffman, Department of Molecu- lar and Cell Biology, University of Texas at Dallas, Richardson, TX 75083±0688 Barbara H. Iglewski, Department of Micro- biology and Immunology, University of Ro- chester School of Medicine, Rochester, NY 14642 Teresa de Kievit, Department of Microbiol- ogy and Immunology, University of Roches- ter School of Medicine, Rochester, NY 14642 Elizabeth M. Kutter, The Evergreen State College, Olympia, WA 98505 J. Eugene LeClerc, Molecular Biology Div- ision, Center for Food Safety and Applied Nutrition, US Food and Drug Administra- tion, Washington, DC 20204 Stephen D. Levene, Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083±0688 Thomas S. Livinghouse, Department of Chemistry and Biochemistry, and Depart- ment of Land Resources and Environmental Sciences, Montana State University, Boze- man, MT 59717 xiii [...]... Actinobacillus, type III restriction-modification systems in, 194 Activator binding sites, in transcriptional regulation, 56 Activators response regulators as, 64 in transcriptional regulation, 56±57, 59±61 Active-partition system, for prokaryote plasmids, 546 Acyl-ACP (acylated-acyl carrier protein) acyl-HSL synthesis and, 365, 368 Tn7 transposon and, 402 Acyl-HSL (acylated-homoserine lactone or HSL) as... DNA repair, 42±43 Adaptive-phase induced mutations, 29 Adaptor molecules, in translation, 53 Addiction modules, restriction-modification systems as, 186±188 Adenine in DNA methylation, 197±198 hypoxanthine from, 30 mispairing of, 29 Adenine-thymine base pairs, in DNA, 3 Adhesin, from plasmids, 538 AdoMet (S-adenosyl-l -methionine) in acyl-HSL synthesis, 367 in restriction-modification systems, 179,... translation, 113±114 hmdCTP (deoxy-5-hydroxymethylcytosine triphosphate), in bacteriophage T4 translation, 113 hmdUDP (deoxy-5-hydroxymethyluracil diphosphate), in Bacillus subtilis phages, 121 INDEX hmdUMP (deoxy-5-hydroxymethyluracil monophosphate), in Bacillus subtilis phages, 121 hmdUTP (deoxy-5-hydroxymethyluracil triphosphate), in Bacillus subtilis phages, 121 hmU-containing DNA phages, 121±122... molecules, 261±262 Butyryl-ACP, acyl-HSL and, 365±366 Butyryl-HSL acyl-HSL and, 365±366 in Pseudomonas aeruginosa, 375±376 C proteins, transcription regulation via, 213 CA (catalytic ATP-binding) subdomain, in sensor protein transmitter domain, 351±352 Caenorhabditis elegans, reduced Pseudomonas aeruginosa virulence in, 265 Cag proteins, secretion of, 328 Cairns, John, 28±29 Cairns intermediate form with supercoils,... coli, 465±471 F factor fertility in, 467±468 of F-like plasmids, 482±483 F-prime, 478±482 in Hfr strains, 471±478 history of, 464 mapping via, 496±499 INDEX nonconjugative mobilizable plasmids and, 483±484 non-F plasmids and, 486±488 plasmid-based, 488±494 requirements for, 464 self-transmissible plasmids and, 484±486 T-DNA transfer via, 328±336 unanswered questions concerning, 496 Conjugative transfer,... LuxR-type proteins and, 374 Erwinia spp., acyl-HSL based quorum sensing in, 362 Erwinia stewartii, EsaR protein of, 375 Erwinia uredovora, genetically engineered rice and, 339±340 EsaR protein, of Erwinia, 375 Escherichia wX phages of, 146 retrotransposons in, 407 Escherichia coli, 281 acyl-HSL from, 364±365, 367 adaptive DNA repair in, 42±43 arabinose operon in, 60±61 in artificial chromosome-based... method, in plant genetic engineering, 337 fMET-tRNA complex, in translation, 71±72 FokI unit, in type IIS restriction-modification systems, 191, 194, 208 Forespores, in sporulation, 274 Formyl-methionine (fMET), in translation, 55 4-Nitroquinoline-1-oxide (4NQO), Escherichia coli mutagenesis via, 42 4poS-dependent gene expression, in adaptive response, 42 F-prime factors in conjugation, 478±482 properties... enzymes and, 178±179 restriction-modification system as protection against, 182±186 restriction-modification system countermeasures of, 183 single-stranded DNA, 145±164, 165±170, 170±171 single-stranded RNA, 165 site-directed mutagenesis via, 168±169 standardization of studies of, 88±89 structure of, 90, 91 target-recognizing domains and, 209 therapeutic uses of, 123 transformation and, 431±432 as transposons,... 155 VirB pilus and, 334±335 F plasmids, T-odd coliphages and, 120 F protein of bacteriophage wX, 156 in phage assembly and release, 161±162 in single-stranded DNA phages, 147±148 F42lac factor formation of, 479 in F-prime conjugation, 482 Factor-independent sites, in RNA synthesis, 50 Farlow Reference Library, 291 fecI gene, s factor from, 61 621 Fertility-inhibited plasmids, conjugation of, 482±483 Ff... gene expression, 76±78 Episomes, plasmids as, 508 EPSP (5-enolpyruvylshikimic acid-3-phosphate) synthase, glyphosate and, 339 Epstein, R H., 97 Error-prone polymerases, 28 Error-prone repair, translesion DNA synthesis as, 39 Erwinia, EsaR protein of, 375 Erwinia carotovora acyl-HSL synthase genes in, 377 inhibiting quorum sensing in, 265 LuxR-type proteins and, 370, 372±373, 374 surrogate gene strategies . MODERN MICROBIAL GENETICS Second Edition Modern Microbial Genetics, Second Edition. Edited by Uldis N. Streips, Ronald E. Yasbin Copyright # 2002 Wiley-Liss, Inc. ISBNs: 0-4 7 1-3 866 5-0 (Hardback);. (Firshein), how DNA is repaired (Yasbin), how DNA is transcribed and the transcription regulated (Helmann) and how DNA recombines (Levene and Huff- man). This section also includes the genetics of. 97 Antisense RNA, in translation, 71 Anti-sigma factors, in sporulation, 277±278 Antitermination in bacteriophage l transcription, 132 in transcription regulation, 66±67 Antiterminators, in transcription