Bacterial and Bacteriophage Genetics. Fifth Edition

Transcription

1 Bacterial and Bacteriophage Genetics Fifth Edition

2 Bacterial and Bacteriophage Genetics Fifth Edition Edward A. Birge With 167 Illustrations

3 Edward A. Birge School of Life Sciences Arizona State University Tempe, AZ USA Cover illustration: Micrographs courtesy of Dr. Yuri Lyubchenko and Dr. Luda Shlyakhtenko, Department of Pharmaceutical Sciences, College of Pharmacy, Nebraska Medical Center, Omaha, Nebraska. Library of Congress Control Number: ISBN-10: ISBN-13: Printed on acid-free paper. 2006, 2000, 1994, 1988, 1984 Springer Science+Business Media, Inc. All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer Science+Business Media, Inc., 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. Printed in the United States of America. (SPI/MVY) springeronline.com

4 For Lori, Anna, and Mara

5 Preface I t has been exactly 25 years since I completed the first edition of this text, and its evolution is not yet complete. Continued from the previous edition are some boxed questions for students to read and think about before moving on to the next section. The Thinking Ahead boxes are intended to prod the students to make predictions based on their existing knowledge before reading the new material. The Applications boxes are intended to encourage the students to try their hands at experimental design. The answers to these latter questions are provided in an appendix, usually in the form of a reference to a research paper that addressed that specific question. For instructors who have used the fourth edition of this book, there is only one major rearrangement of material. The material on DNA and chromosome structure has moved from Chapter 2 to Chapter 1 to allow room for more discussion of analytic techniques. Once again, the final four chapters are shorter and much less dependent on each other, so they can be used in any order or vii

6 Preface omitted at an instructor s discretion. All chapters contain updated material, but there are significant additions to Chapters 14, 16, and 17. I have tried to convey the concept of the Age of Phage as a theme throughout the book. There is an appendix that provides Internet addresses where current information about maps and organisms is located because the amount of detail now available precludes publishing current maps in a book of this size. A supporting Web site for this book is located at Once again, it is a pleasure to acknowledge the support and able assistance of Paula Callaghan, Andrea Macaluso, Francine McNeill, and the other members of the editorial and production staff at Springer Science+Business Media, Inc. I am also grateful to my family for their patience while I was closeted with this manuscript. Edward A. Birge Yakima, Washington viii

7 Preface vii 1 Fundamentals of Bacterial and Viral Genetics 1 Nomenclature 2 Prokaryotic Cells and Eukaryotic Cells 5 Structure 5 Ploidy 8 DNA Structure 10 Chromosome Structure 13 Eukaryotes 13 Prokaryotes 15 Selection: An Essential Element of Microbial Genetics 22 ix

8 Major Genetic Transfer Processes Observed in Microorganisms and Their Viruses 23 Genetic Transformation 23 Transduction 24 Conjugation 25 Protoplast Fusion 25 Electroporation 26 Bacteriophage Genetic Exchange 26 Summary 27 Questions for Review and Discussion 27 References 27 General 27 Specialized 28 Reference Books for Specific Organisms 29 2 Replication and Analysis of DNA 31 DNA Replication 32 Linking DNA in Arbitrary Ways 42 Enzymology of DNA Restriction and Modification 43 Use of Restriction Fragments to Make New DNA Molecules 47 Analytical Techniques for DNA Molecules 49 Electrophoresis 49 Atomic Force Microscopy 50 Detection of Specific DNA Sequences 50 Polymerase Chain Reaction 54 DNA Sequence Analysis 56 Custom Synthesis of DNA 61 Footprinting 62 Gel Mobility Shift Analysis 64 Yeast Two-Hybrid Systems 65 Summary 65 Questions for Review and Discussion 66 References 67 General 67 Specialized 68 3 Mutations and Mutagenesis 69 Bacterial Variation 70 Plate Spreading 70 x

9 Replica Plating 71 Fluctuation Test 72 Measurement of Mutation Rate 76 Expression and Selection of Mutant Cell Phenotypes 81 Expression 81 Selection 85 Genetic Code 87 Kinds of Mutation 88 Base Substitutions 89 Insertion and Deletion Mutations 92 Frameshift Mutations 93 Suppressors of Mutations 94 Mutagens 97 Radiation 98 Chemical Modifiers 98 Base Analogs 99 Cross-Linking Agents 100 Transposons 100 Mutator Mutations 101 Site-Directed Mutagenesis 101 Summary 103 Questions for Review and Discussion 104 References 104 General 104 Specialized Transcription and Translation: Processes and Basic Regulation 107 RNA Structure 108 Transcription 109 RNA Processing 113 Translation of the Genetic Message 116 Ribosome Function 116 Protein Folding 121 Regulation 123 Examples of Regulation in Simple Functional Units 124 Operon: The Basic Regulatory Unit 124 Lactose Operon 125 Galactose Operon 132 Tryptophan Operon 135 Summary 144 xi

10 Questions for Review and Discussion 145 Suggestions for Further Reading 145 General 145 Specialized DNA Repair and Simple Recombination 149 DNA Repair 150 Mismatch Repair: An Example of Intrareplicational Repair 153 Ultraviolet-Irradiated DNA as a Model Repair System 154 The SOS Global Regulatory Network 157 A Conceptual Model for Generalized Recombination 160 Genetic and Functional Analysis of Recombination 164 RecA and Similar Proteins 164 Other Genes Affecting Recombination 168 A Model for General Recombination 170 Interrelation of Repair and Recombination Pathways 172 Summary 173 Questions for Review and Discussion 174 References 175 General 175 Specialized T4 Bacteriophage as a Model Genetic System 177 Morphology and Composition 178 Experimental Methods Used to Study Phage Infection 181 Genetic Organization of T4 186 Types of Mutations Observed in the T4 Genome 186 Genetic Crosses 188 Visconti Delbrück Analysis 196 Phage Heterozygotes 199 DNA Replication 202 Molecular Biology of T4 Phage Infection 204 Initial Stages of Infection 204 Regulatory Issues 206 Morphogenesis and Maturation 214 Summary 216 Questions for Review and Discussion 217 xii

11 References 218 General 218 Specialized Genetics of Other Intemperate Bacteriophages 221 Other Members of the T Series 224 Bacteriophages T2 and T6 224 Bacteriophage T1 227 Bacteriophage T5 228 Bacteriophages T7 and T3 230 Bacteriophages Containing Single-Strand DNA 235 Bacteriophages Belonging to the Ff Group 235 Bacteriophage φx RNA-Containing Bacteriophages 244 Single-Stranded RNA Viruses 244 Double-Stranded RNA Viruses 250 Bacteriophages Infecting Bacillus subtilis 251 Bacteriophage SP Bacteriophage φ Bacteriophages Infecting the Archaea 255 Summary 255 Questions for Review and Discussion 256 References 257 General 257 Specialized Genetics of Temperate Bacteriophages 261 General Nature of the Temperate Response 264 Bacteriophage Lambda as the Archetypal Temperate Phage 265 Lytic Life Cycle 266 Temperate Life Cycle 277 Genetic Map of Lambda 285 Other Lambdoid Phages 286 Bacteriophage P Bacteriophages P2 and P4 290 Bacteriophage P1 293 Bacteriophage Mu 295 SSV1 and SSV2 299 Summary 299 xiii

12 Questions for Review and Discussion 300 References 301 General 301 Specialized Transduction 305 Bacteriophage Lambda: A Specialized Transducing Phage 306 Production of Transducing Particles 306 Physiology and Genetic Consequences of Transduction 309 Lambda Phages That Transduce Additional Genetic Markers 310 Specialized Transducing Phages Other than Lambda 310 Bacteriophage φ Bacteriophage P1 312 Bacteriophage P Generalized Transduction 314 Bacteriophage P Bacteriophage P1 317 Other Phages 318 Analysis of Transductional Data 319 Generalized Transduction 319 Specialized Transduction 322 Summary 323 Questions for Review and Discussion 323 References 324 General 324 Specialized Genetic Transformation 327 Standard Genetic Transformation Systems 328 Discovery of Genetic Transformation 328 Competent Cells 330 DNA Uptake and Entry 333 Establishment of Donor DNA in the Recipient Cell 335 Other Transformation Systems 339 Escherichia coli 339 Electroporation 340 Transfection 341 E. coli as a Recipient 342 B. subtilis as a Recipient 343 xiv

13 Genetic Mapping Using Transformation 345 Analysis of Transformational Data 345 Genetic Map for B. subtilis 345 Summary 346 Questions for Review and Discussion 349 References 349 General 349 Specialized Conjugation and the Escherichia coli Paradigm 351 Basic Properties of the E. coli Conjugation System 352 Discovery of Conjugation 352 Discovery of Efficient Donor Strains and Partial Transfer 353 Nature of the Transfer Process 355 Recombination Following Conjugation 358 Construction of the First Genetic Map 359 Interactions of the F Plasmid with the Bacterial Chromosome 362 Integration of the F Plasmid 362 Excision of the F Plasmid 365 Physiology of Conjugation 367 Formation of Mating Aggregates 367 Transfer DNA Synthesis 370 Analysis of the F Plasmid 373 General Structure 373 Genetic Analysis of the F Plasmid 375 Something Completely Different Possible Diploidy 379 Summary 379 Questions for Review and Discussion 380 References 381 General 381 Specialized Plasmids and Conjugation Systems Other than F 383 Major Chromosome-Mobilizing Plasmids 384 Salmonella 384 Pseudomonas 386 Enterococcus 388 Streptomyces 390 xv

14 Agrobacterium 392 Sulfolobus 395 Bacteriocins 396 General Properties 396 Colicins: The Best-Studied Bacteriocins 398 Conjugative Colicin Plasmids 400 Nonconjugative Colicin Plasmids 401 Resistance Plasmids 402 General Properties 402 Plasmid R Genetic Analysis of Plasmid R Conjugal Plasmid Interactions 409 Summary 411 Questions for Review and Discussion 412 References 413 General 413 Specialized Plasmid Molecular Biology 417 Plasmid DNA Replication 418 Interactions Between Plasmid and Host 418 DNA Replication Processes 420 Control of Copy Number 422 Partitioning 426 Incompatibility 430 Conjugal Functions 431 Pilus Production 431 Transfer DNA Replication 434 Broad Host Range Plasmids 436 Summary 438 Questions for Review and Discussion 439 References 439 General 439 Specialized Advanced Regulatory Topics 443 Regulons 444 Maltose 444 Heat Shock Proteins 448 xvi

15 Global Regulatory Networks 450 Nitrogen Regulation 450 Endospore Formation in Bacillus 453 Inteins 457 Small RNA Molecules 458 Summary 458 Questions for Review and Discussion 459 References 459 Generalized 459 Specialized Site-Specific Recombination 463 General Principles 464 Double Site-Specific Recombination 464 Phage Lambda Integration 464 Circular Chromosome Segregation 466 Inversion Systems 467 Integrons 468 Transposons: Single Site-Specific Recombination 470 Transposon Tn Phage Mu Transposition 474 Summary 476 Questions for Review and Discussion 477 References 477 General 477 Specialized Applied Bacterial Genetics 479 More Information About Recombinant DNA Technology 480 Restriction Mapping 480 Sources of DNA for Linking 481 Safety Considerations 484 Difficulties with the Expression of Cloned DNA 487 Cloning Vectors 488 Phage λ Vectors 489 Phage M13 Vectors 490 Expression Vectors 491 Broad Host Range Vectors 494 xvii

16 Runaway Replication Vectors 494 Artificial Chromosomes 495 Applications of DNA Cloning 496 Peptide Display Systems 496 Laboratory Reagents 497 Phage as Therapeutic Agents 498 Other Applications of Bacterial Genetics 498 Mutagenicity Testing 498 Recombineering 500 Genetic Transfer in Nature 501 Ecogenomics 501 Summary 502 Questions for Review and Discussion 502 References 503 General 503 Specialized Bacterial and Bacteriophage Evolution 505 What Is Evolution? 506 Implications of Strain Differences 506 Cryptic Genes 507 Expression of Evolutionary Relationships 510 Genomics and Proteomics 519 Bacteria 519 Bacteriophage 520 Specific Examples of Evolution 520 Evolution of Genomes 521 Evolution of the Genetic Code 522 Evolution of Proteins 522 Evolution of Regulatory Sequences 523 Evolution of Mitochondria and Other Endosymbionts 523 Genetic Structure of the Chromosome 525 Bacteria 525 Bacteriophage 526 Summary 526 Questions for Review and Discussion 527 References 528 General 528 Specialized 529 xviii

17 Appendix 1 Appendix 2 Laws of Probability and Their Application to Prokaryote Cultures 531 Useful World Wide Web Sites for Bacterial Genetics 549 Appendix 3 Answers to Application Questions 551 Glossary 553 Index 567 xix