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Library of Congress Cataloging-in-Publication Data

Molecular genetics of bacteria / Larry Snyder ... [et al.]. — 4th ed.
p. ; cm.
Rev. ed. of: Molecular genetics of bacteria / Larry Snyder and Wendy Champness. c2007.
Includes bibliographical references and index.
ISBN 978-1-55581-627-8 (hardcover : alk. paper) — ISBN 978-1-55581-716-9 (e-book)
I. Snyder, Larry. II. Snyder, Larry. Molecular genetics of bacteria.
[DNLM: 1. Bacteria—genetics. 2. Bacteriophages—genetics. 3. Chromosomes, Bacterial.
4. Genetics, Microbial—methods. 5. Molecular Biology—methods. QW 51]

572.8′293—dc23
2012027461

10 9 8 7 6 5 4 3 2 1
Printed in the United States of America

Address editorial correspondence to ASM Press, 1752 N St. NW,

Washington, DC 20036-2904, USA
E-mail: books@asmusa.org

Send orders to ASM Press, P.O. Box 605, Herndon, VA 20172, USA
Phone: (800) 546-2416 or (703) 661-1593
Fax: (703) 661-1501
Online: estore.asm.org

doi:10.1128/9781555817169

Illustrations: Patrick Lane, ScEYEnce Studios

Cover and interior design: Susan Brown Schmidler
Cover illustration: Terese Winslow

Cover photo: Fluorescence micrograph of Bacillus subtilis cells showing the location of the
cell membrane (red), DNA (blue), and ConE mating protein fused to green fluorescent pro-
tein (yellow-green). The ConE protein is a component of the conjugative DNA translocation
channel required for horizontal transfer of the integrating conjugative element ICEBs1. The
ConE protein is concentrated at the cell poles, but additional protein is localized around the
entire cell periphery. The lateral distribution enables cells to transfer ICEBs1 side to side, and
the high concentration at the poles may contribute to the very efficient transfer of ICEBs1
observed in chains of cells from pole to pole. See chapter 5 for details. Photo courtesy of
Melanie Berkmen and Alan Grossman. Modified from M. B. Berkmen et al., J. Bacteriol.
192:38–45, 2010.

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 Contents

Preface xv
About the Authors xix

Introduction 1
The Biological Universe 3
The Bacteria 3
The Archaea 3
The Eukaryotes 5
Speculations on the Origin of the Three Domains of Life 5

What Is Genetics? 6
Bacterial Genetics 6
Bacteria Are Haploid 7
Short Generation Times 7
Asexual Reproduction 7
Colony Growth on Agar Plates 7
Colony Purification 7
Serial Dilutions 7
Selections 8
Storing Stocks of Bacterial Strains 8
Genetic Exchange 8

Phage Genetics 8
Phages Are Haploid 8
Selections with Phages 9
Crosses with Phages 9

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 vi CONTENTS

A Brief History of Bacterial Molecular RNA Priming of Initiation 33

Genetics 9 Termination of Chromosome Replication 33
Inheritance in Bacteria 9 Chromosome Segregation 34
Transformation 9 Coordination of Cell Division with Replication of the
Conjugation 10 Chromosome 43
Transduction 10 Timing of Initiation of Replication 45
Recombination within Genes 10
The Bacterial Nucleoid 47
Semiconservative DNA Replication 10
Supercoiling in the Nucleoid 47
mRNA 10
Topoisomerases 49
The Genetic Code 10
The Operon Model 10 The Bacterial Genome 50
Enzymes for Molecular Biology 10 Antibiotics That Affect Replication and DNA
What Is Ahead 11 Structure 51
Antibiotics That Block Precursor Synthesis 51
SUGGESTED READING 11
Antibiotics That Block Polymerization of
Deoxynucleotides 52
CHAPTER 1 Antibiotics That Affect DNA Structure 52
Antibiotics That Affect Gyrase 52
The Bacterial Chromosome:
DNA Structure, Replication, and Molecular Biology Manipulations with
Segregation 13 DNA 53
Restriction Endonucleases 53
DNA Structure 13 Hybridizations 56
The Deoxyribonucleotides 13
Applications of the Enzymes Used in DNA
The DNA Chain 14 Replication 58
The 5′ and 3′ Ends 14 Polymerase Chain Reaction 58
Base Pairing 16 BOX 1.1 Structural Features of Bacterial
Antiparallel Construction 17 Genomes 37
The Major and Minor Grooves 17 BOX 1.2 Advanced Genome-Sequencing
Techniques 59
The Mechanism of DNA Replication 17
SUMMARY 62
Deoxyribonucleotide Precursor Synthesis 17
Replication of the Bacterial Chromosome 19 QUESTIONS FOR THOUGHT 64

Replication of Double-Stranded DNA 23 PROBLEMS 64

SUGGESTED READING 65
Replication Errors 26
Editing 26
RNA Primers and Editing 27 CHAPTER 2
Impediments to DNA Replication 28 Bacterial Gene Expression:
Damaged DNA and DNA Polymerase III 28 Transcription, Translation, and Protein
Mechanisms To Deal with Impediments on Template Folding 67
DNA Strands 28
Physical Blocks to Replication Forks 30 Overview 67

Replication of the Bacterial Chromosome and The Structure and Function of RNA 68
Cell Division 31 Types of RNA 69
Structure of the Bacterial Chromosome 31 RNA Precursors 69
Replication of the Bacterial Chromosome 31 RNA Structure 69
Initiation of Chromosome Replication 32 RNA Processing and Modification 70

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 CONTENTS vii

Transcription 70 CHAPTER 3
Structure of Bacterial RNA Polymerase 70
Overview of Transcription 71 Bacterial Genetic Analysis:
Details of Transcription 75 Fundamentals and Current
rRNAs and tRNAs 81 Approaches 125
RNA Degradation 82 Definitions 125
RNases 83 Terms Used in Genetics 125
Genetic Names 126
The Structure and Function of Proteins 84 Auxotrophic and Catabolic Mutants 127
Protein Structure 85 Conditional-Lethal Mutants 128
Translation 86 Resistant Mutants 130
Structure of the Bacterial Ribosome 86
Inheritance in Bacteria 130
Overview of Translation 88 The Luria and Delbrück Experiment 131
Details of Protein Synthesis 90 Mutants Are Clonal 132
The Genetic Code 97 The Lederbergs’ Experiment 133
Protein Folding and Degradation 105 Mutation Rates 133
Protein Chaperones 105 Calculating Mutation Rates 135
Protein Degradation 107 Calculating the Mutation Rate from the Rate of
Increase in the Proportion of Mutants 136
Membrane Proteins and Protein
Export 108 Types of Mutations 137
Regulation of Gene Expression 108 Properties of Mutations 138
Transcriptional Regulation 108 Base Pair Changes 138
Posttranscriptional Regulation 109 Frameshift Mutations 142
Deletion Mutations 144
Genomes and Genomics 109 Tandem-Duplication Mutations 145
Annotation and Comparative Genomics 110
Inversion Mutations 147
What You Need To Know 110 Insertion Mutations 148
Open Reading Frames 116
Reversion versus Suppression 149
Transcriptional and Translational Fusions 116
Intragenic Suppressors 149
Antibiotics That Block Transcription and Intergenic Suppressors 150
Translation 116
Genetic Analysis in Bacteria 153
Antibiotic Inhibitors of Transcription 117
Isolating Mutants 153
Antibiotic Inhibitors of Translation 118
Genetic Characterization of Mutants 157
BOX 2.1 Molecular Phylogeny 82
Complementation Tests 161
BOX 2.2 Mimicry in Translation 96 Genetic Crosses in Bacteria 167
BOX 2.3 Exceptions to the Code 99 Mapping of Bacterial Markers by Transduction and
BOX 2.4 Selfish DNAs: RNA Introns and Protein Transformation 168
Inteins 102 Other Uses of Transformation and
BOX 2.5 Annotation and Comparative Transduction 172
Genomics 110 Genetic Mapping by Hfr Crosses 173
SUMMARY 120
Isolation of Tandem Duplications of the his
QUESTIONS FOR THOUGHT 122 Operon in Salmonella 176
PROBLEMS 122 Lengths of Tandem Duplications 178
SUGGESTED READING 123 Frequency of Spontaneous Duplications 179

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 viii CONTENTS

BOX 3.1 Statistical Analysis of the Number of Mutants Efficiency of Transfer 227
per Culture 134 Interspecies Transfer of Plasmids 227
BOX 3.2 Inversions and the Genetic Map 148 Conjugation and Type IV Protein Secretion 228
SUMMARY 179 Mobilizable Plasmids 232
QUESTIONS FOR THOUGHT 181
Chromosome Transfer by Plasmids 235
PROBLEMS 181 Formation of Hfr Strains 235
SUGGESTED READING 182 Transfer of Chromosomal DNA by Integrated
Plasmids 236
Chromosome Mobilization 236
CHAPTER 4 Prime Factors 236
Plasmids 183 Transfer Systems of Gram-Positive
What Is a Plasmid? 183 Bacteria 237
Naming Plasmids 184 Plasmid-Attracting Pheromones 237
Functions Encoded by Plasmids 184 Integrating Conjugative Elements 240
Plasmid Structure 185 BOX 5.1 Gene Exchange between Domains 230
Properties of Plasmids 186 SUMMARY 242
Replication 186 QUESTIONS FOR THOUGHT 243
Functions of the ori Region 189 PROBLEMS 243
Plasmid Replication Control Mechanisms 194 SUGGESTED READING 244
Mechanisms To Prevent Curing of Plasmids 203
The Par Systems of Plasmids 205
Plasmid Cloning Vectors 209
Examples of Plasmid Cloning Vectors 210
CHAPTER 6
Broad-Host-Range Cloning Vectors 213 Transformation 247
BOX 4.1 Linear Chromosomes and Plasmids in
Bacteria 190 Natural Transformation 248
Discovery of Transformation 248
BOX 4.2 Toxin-Antitoxin Systems and Plasmid
Maintenance 204 Competence 248
SUMMARY 216
DNA Processing after Uptake 252
Experimental Evidence for Models of Natural
QUESTIONS FOR THOUGHT 217
Transformation 252
PROBLEMS 217 Plasmid Transformation and Phage Transfection of
SUGGESTED READING 217 Naturally Competent Bacteria 254
Regulation of Natural Competence 255
Role of Natural Transformation 257
CHAPTER 5
Importance of Natural Transformation for
Conjugation 219 Forward and Reverse Genetics 259
Overview 219 Congression 259
Classification of Self-Transmissible Plasmids 220 Artificially Induced Competence 260
The Fertility Plasmid 220 Chemical Induction 260
Mechanism of DNA Transfer during Electroporation 261
Conjugation in Gram-Negative Bacteria 221 Protoplast Transformation 261
Transfer (tra) Genes 221 BOX 6.1 Antigenic Variation in Neisseria
The oriT Sequence 225 gonorrhoeae 259
Male-Specific Phages 226 SUMMARY 262

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 CONTENTS ix

QUESTIONS FOR THOUGHT 262 Shuttle Phasmids 316

PROBLEMS 262 Role of Transduction in Bacterial
SUGGESTED READING 263 Evolution 317
BOX 7.1 Phage Genomics 268
BOX 7.2 RNA Phages 271
CHAPTER 7 BOX 7.3 Protein Priming 286
BOX 7.4 Phage Display 294
Bacteriophages: Lytic Development,
Genetics, and Generalized SUMMARY 318
Transduction 265 QUESTIONS FOR THOUGHT 319
PROBLEMS 319
Regulation of Gene Expression during Lytic
Development 270 SUGGESTED READING 320
Phages That Encode Their Own RNA Polymerases 272
T7 Phage-Based Expression Vectors 273
Making Riboprobes and RNA-Processing CHAPTER 8
Substrates 273
Phage T4: Transcriptional Activators, a New Sigma Lysogeny: the λ Paradigm and the Role
Factor, and Replication-Coupled Transcription 275 of Lysogenic Conversion in Bacterial
Phage DNA Genome Replication and
Pathogenesis 323
Packaging 279 Phage λ 324
Phages with Single-Stranded Circular DNA 279 λ Lytic Development 324
Replication and DNA Packaging: Linear Genomes 285 Replication of λ DNA 331
Phage T7: Linear DNA That Forms Concatemers 285
Phage T4: Another Phage That Forms
Lysogeny by Phage λ 333
Concatemers 286 The Lytic-versus-Lysogen Decision: the Roles of cI, cII,
and cIII Gene Products 333
Phage Lysis 289 Phage λ Integration 334
Single-Protein Lysis 289 Maintenance of λ Lysogeny 335
Timed Lysis 290 Immunity to Superinfection 337
Timing of Lysis by Holins 290 Induction of λ 338
Summary of the Lytic and Lysogenic Cycles 340
Phage Display 292
Genetic Analysis of Phages 298 Specialized Transduction 340
Infection of Cells 298 Selection of HFT Particles 342
Phage Crosses 299 Other Lysogen-Forming Phages 343
Recombination and Complementation Tests with Phage P2 343
Phages 299 Phage P4: a Satellite Virus 343
Genetic Experiments with the r II Genes of Prophages That Replicate as Plasmids 345
Phage T4 301
Phage Mu: a Transposon Masquerading as a
Constructing the Genetic-Linkage Map of a Phage 345
Phage 307
Lysogenic Conversion and Bacterial
Phage Defense Mechanisms 309
Pathogenesis 345
Restriction-Modification Systems 310
E. coli and Dysentery: Shiga Toxins 346
Abi Systems 310
Diphtheria 347
CRISPR Loci 311
Cholera 347
Generalized Transduction 314 S. aureus and Toxic Shock Syndrome 349
What Makes a Transducing Phage? 315 Synopsis 350

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 x CONTENTS

Uses of Lysogeny in Genetic Analysis and Effects on Genes Adjacent to the Insertion Site 380
Biotechnology 350 Regulation of Transposition 380
Complementation and Gene Expression Studies 350 Target Immunity 381
Use of Phage Display and Frequency of Mixed
Dilysogens To Detect Protein-Protein Interactions 350 Transposon Mutagenesis 382
Transposon Mutagenesis In Vivo 382
Genetic Experiments with Phage λ 351 Transposon Mutagenesis In Vitro 382
Genetic Analysis of λ Lysogen Formation 351 Transposon Mutagenesis of Plasmids 385
Genetics of the CI Repressor: Evidence for the Domain Transposon Mutagenesis of the Bacterial
Structure of Proteins 353 Chromosome 386
Identification of λ nut Sites Involved in Progressive Transposon Mutagenesis of All Bacteria 386
Transcription Antitermination 354
Using Transposon Mutagenesis To Make Random Gene
Isolation of Host nus Mutations: E. coli Functions Fusions 387
Involved in Transcription Elongation-Termination 356
BOX 8.1 Effects of Prophage Insertion on the Site-Specific Recombination 387
Host 336 Integrases 387
SUMMARY 357 Resolvases 390
QUESTIONS FOR THOUGHT 358 DNA Invertases 391
PROBLEMS 358
Y and S Recombinases 392
SUGGESTED READING 359 Y Recombinases: Mechanism 392
S Recombinases: Mechanism 397

CHAPTER 9 Importance of Transposition and Site-Specific

Recombination in Bacterial Adaptation 398
Transposition, Site-Specific BOX 9.1 Transposons and Genomics 383
Recombination, and Families of SUMMARY 399
Recombinases 361 QUESTIONS FOR THOUGHT 400
Transposition 361 PROBLEMS 400
Overview of Transposition 362 SUGGESTED READING 401
Structure of Bacterial Transposons 362
Types of Bacterial Transposons 364
Assays of Transposition 366
CHAPTER 10
Mechanisms of Transposition 368
Genetic Requirements for Transposition of Molecular Mechanisms of Homologous
Tn3 368 Recombination 403
A Molecular Model for Transposition of
Tn3 372 Homologous Recombination and DNA
Transposition by Tn10 and Tn5 373 Replication in Bacteria 404
Early Evidence for the Interdependence
Details of Transposition by the DDE of Homologous Recombination and DNA
Transposons 376 Replication 404
Details of the Mechanism of Transposition by Tn5 and
Tn7 376 The Molecular Basis for Recombination in
E. coli 405
Rolling-Circle Transposons 378 Chi (χ) Sites and the RecBCD Complex 405
The RecF Pathway 409
Y and S Transposons 378
Synapse Formation and the RecA Protein 411
General Properties of Transposons 379 The Ruv and RecG Proteins and the Migration and
Target Site Specificity 379 Cutting of Holliday Junctions 414

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 CONTENTS xi

Recombination between Different DNAs in SOS-Inducible Repair 458

Bacteria 416 Mechanism of TLS by the Pol V Mutasome 463
How Are Linear DNA Fragments Recombined into the Other Specialized Polymerases and Their
E. coli Chromosome? 417 Regulation 464
Phage Recombination Pathways 417
Rec Proteins of Phages T4 and T7 417 Summary of Repair Pathways in E. coli 466
The RecE Pathway of the rac Prophage 417 Bacteriophage Repair Pathways 466
The Phage λ Red System 419 BOX 11.1 The Role of Reactive Oxygen Species in
Cancer and Degenerative Diseases 439
Recombineering: Gene Replacements in E. coli
BOX 11.2 DNA Repair and Cancer 449
with Phage λ Recombination Functions 419
BOX 11.3 The Ames Test 465
Genetic Analysis of Recombination in
SUMMARY 468
Bacteria 422
Isolating Rec− Mutants of E. coli 422 QUESTIONS FOR THOUGHT 469
Isolating Mutants with Mutations in Other PROBLEMS 469
Recombination Genes 423 SUGGESTED READING 469
Gene Conversion and Other Manifestations of
Heteroduplex Formation during Recombination 426
BOX 10.1 Other Types of Double-Strand Break Repair
in Bacteria 410 CHAPTER 12
BOX 10.2 Breaking and Entering: Introns and
Inteins Move by Double-Strand Break Repair or Regulation of Gene Expression: Genes
Retrohoming 425 and Operons 471
SUMMARY 429 Transcriptional Regulation in Bacteria 472
QUESTIONS FOR THOUGHT 430 Genetic Evidence for Negative and Positive
PROBLEMS 430 Regulation 474
SUGGESTED READING 431 Negative Regulation of Transcription
Initiation 474
Negative Inducible Systems 474
CHAPTER 11 Negative Repressible Systems 484
Molecular Mechanisms of Transcriptional
DNA Repair and Mutagenesis 433 Repression 486
Evidence for DNA Repair 434 Positive Regulation of Transcription
Initiation 487
Specific Repair Pathways 435
Positive Inducible Systems 487
Deamination of Bases 435
Positive Repressible Systems 496
Damage Due to Reactive Oxygen 438
Molecular Mechanisms of Transcriptional
Damage Due to Alkylating Agents 441 Activation 496
Damage Due to UV Irradiation 443
Regulation by Transcription Attenuation 497
General Repair Mechanisms 445 Modulation of RNA Structure 497
Base Analogs 445 Changes in Processivity of RNA Polymerase 506
Frameshift Mutagens 445
Methyl-Directed Mismatch Repair 445 Regulation of mRNA Degradation 507
Nucleotide Excision Repair 452 Protein-Dependent Effects on RNA Stability 507
RNA-Dependent Effects on RNA Stability 508
DNA Damage Tolerance Mechanisms 453
Homologous Recombination and DNA Regulation of Translation 508
Replication 454 Regulation of Translation Initiation 509

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 xii CONTENTS

Translational Regulation in the Exit Channel of the Extracytoplasmic (Envelope) Stress Responses 563
Ribosome 511
Regulation of Translation Termination 512 Iron Regulation in E. coli 568
The Fur Regulon 568
Posttranslational Regulation 514 The RyhB sRNA 569
Posttranslational Protein Modification 514 The Aconitase Translational Repressor 570
Regulation of Protein Turnover 514
Feedback Inhibition of Enzyme Activity 515 Regulation of Virulence Genes in Pathogenic
Bacteria 571
Why Are There So Many Mechanisms of Gene Diphtheria 572
Regulation? 520 Cholera and Quorum Sensing 572
Operon Analysis for Sequenced Genomes 521 Whooping Cough 578
BOX 12.1 The Helix-Turn-Helix Motif of DNA-Binding From Genes to Regulons to Networks 579
Proteins 473
BOX 13.1 cAMP-Independent Carbon Catabolite
BOX 12.2 Families of Regulators 488 Regulation in E. coli 529
BOX 12.3 Special Problems in Genetic Analysis of BOX 13.2 A Bacterial Two-Hybrid System Based on
Operons 516 Adenylate Cyclase 531
SUMMARY 521 BOX 13.3 Nitrogen Fixation 537
QUESTIONS FOR THOUGHT 522 BOX 13.4 Signal Transduction Systems in
PROBLEMS 522 Bacteria 539
SUGGESTED READING 523 BOX 13.5 Sigma Factors 542
BOX 13.6 Regulatory RNAs 560

CHAPTER 13 BOX 13.7 Tools for Studying Global

Regulation 571
Global Regulation: Regulons and SUMMARY 580
Stimulons 525 QUESTIONS FOR THOUGHT 582

Carbon Catabolite Regulation 526 PROBLEMS 582

Catabolite Regulation in E. coli: Catabolite Activator SUGGESTED READING 582
Protein (CAP) and cAMP 526
Carbon Catabolite Regulation in B. subtilis: CcpA and
Hpr 535
CHAPTER 14
Regulation of Nitrogen Assimilation 536
Pathways for Nitrogen Assimilation 536 Bacterial Cell Biology and
Regulation of Nitrogen Assimilation Pathways in E. coli Development 585
by the Ntr System 537
Regulation of Nitrogen Assimilation in B. subtilis 547
Membrane Proteins and Protein Export 585
The Translocase System 586
Regulation of Ribosome and tRNA The Signal Sequence 586
Synthesis 547 The Targeting Factors 588
Ribosomal Protein Gene Regulation 548 The Tat Secretion Pathway 590
Regulation of rRNA and tRNA Synthesis 550 Disulfide Bonds 590
The Stringent Response 551 Use of mal-lac Fusions To Study Protein Transport in
E. coli 591
Stress Responses in Bacteria 554
Heat Shock Regulation 555 Genetic Analysis of Transmembrane Domains
General Stress Response in Gram-Negative of Inner Membrane Proteins in Gram-Negative
Bacteria 558 Bacteria 594
General Stress Response in Gram-Positive Identification of Genes for Inner Membrane Proteins
Bacteria 559 by Random phoA Fusions 595

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 CONTENTS xiii

Protein Secretion 595 Finding Sporulation Genes: Mutant Hunts, Suppressor

Protein Secretion Systems in Gram-Negative Analysis, and Functional Genomics 635
Bacteria 595 BOX 14.1 Secretion Systems and Motility 599
Protein Secretion in Gram-Positive Bacteria 602 BOX 14.2 Example of a Sortase-Dependent Pathway:
Sortases 603 Sporulation in S. coelicolor 605
BOX 14.3 Evolutionary Origin of the Eukaryotic
Bacterial Cell Biology and the Cell Cycle 605 Cytoskeleton 612
The Bacterial Cell Wall 606
BOX 14.4 Phosphorelay Activation of the
Septum Formation 615 Transcription Factor Spo0A 625
The FtsZ Protein and the Septal Ring 616
SUMMARY 636
Regulation of FtsZ Ring Formation in
C. crescentus 619 QUESTIONS FOR THOUGHT 637
PROBLEMS 637
Genetic Analysis of Sporulation in SUGGESTED READING 638
B. subtilis 621
Identification of Genes That Regulate Sporulation 622 Answers to Problems and Questions for
Regulation of Initiation of Sporulation 623 Thought 641
Compartmentalized Regulation of Sporulation
Genes 627 Glossary 655
Analysis of the Role of Sigma Factors in Sporulation
Regulation 627 Figure and Table Credits 685
Intercompartmental Regulation during
Development 630 Index 689

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9781555816278_00i-xx_FM.indd xiv 11/6/12 2:06 PM
 Preface

W
ITH THE ADDITION OF TWO NEW COAUTHORS, the fourth edition of
the textbook Molecular Genetics of Bacteria has been substan-
tially revised and some new sections have been added. We tried
to do this without increasing the length of the book, which, at more than
700 pages, was already quite long. While the book retains the same number
and order of chapters, many topics have been moved or integrated more
completely into the text to reflect a more modern perspective. The purpose
was to convey more accurately how one approaches questions in modern
bacterial genetics, using the full repertoire of methods now available. Also,
to make room for the new material, we made the philosophical decision to
condense or eliminate descriptions of methods where they seemed unneces-
sarily detailed for a textbook.
Chapter 1, on DNA structure, DNA replication, and chromosome seg-
regation, was expanded to include updates in our understanding, including
how replication proceeds through obstacles typically found during normal
DNA replication in bacteria, while some aspects of repair-associated rep-
lication were moved to later chapters. The chapter was also significantly
expanded with new information about how numerous cell processes co-
ordinate for the efficient processing and organizing of chromosomes after
DNA replication. Scientists now more fully appreciate how sequences “hid-
den” in the structure guide a variety of systems that aid in repairing, seg-
regating, packaging, and pumping the chromosome for exquisite genome
stability in bacteria. In chapter 2, which covers bacterial gene expression,
the translation section has been reorganized to follow the same order as
the transcription section. It begins with initiation of translation and then
discusses elongation followed by termination, rather than following the
more historical order with the genetic code coming first. We reasoned that
this order makes more sense since most students already have had some
exposure to translation and the genetic code. More information on RNA
degradation is now included, and the sections on gene regulation have been
moved to chapter 12. The protein transport section has been moved from
chapter 2 to chapter 14 (see below), where it can be better integrated with
other topics of protein export. Chapter 3, on bacterial genetic analysis, also
xv

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 xvi PREFACE

now takes a less historical approach. Rather than be- A more comprehensive treatment for how DNA dou-
ginning with a review of classical genetic analysis and ble-strand breaks are repaired across different types of
then contrasting it with bacterial genetic analysis as in bacteria, using systems found in all domains of life, is
previous editions, the chapter now begins with bacte- also included. Chapter 11 was updated to discuss many
rial genetic analysis, again assuming that students have advances in the field of repair, including an expanded
already had some general genetics. Furthermore, rather understanding of the regulation of multiple DNA poly-
than putting more recently developed methods such as merases found in bacteria with the SOS response. Chap-
site-specific mutagenesis, recombineering, etc., into a ters 12 and 13 have been reorganized so that chapter
separate section, we have integrated throughout the text 12 is now focused on mechanisms of regulation of indi-
all the methods available nowadays to use in a genetic vidual genes and operons and chapter 13 is mostly con-
analysis. The discussion of mapping by Hfr crosses has cerned with examples of global regulatory systems that
been sharply condensed, since it is likely that no one utilize these mechanisms. There is also more emphasis
will ever again perform the laborious task of construct- on posttranscriptional regulation in both chapters, and
ing the genetic map of a bacterium. The relative ease of global regulatory mechanisms in Escherichia coli are
DNA sequencing now allows the placing of mutations contrasted with those in Bacillus subtilis. Chapter 14
on the sequenced genomes of bacteria by direct compari- is probably the most changed chapter. It now contains
son of sequences rather than by Hfr mapping. Transduc- our entire discussion of protein export, including the Sec
tion and transformation (including electroporation) are and Tat systems as well as the secretion systems of gram-
used extensively for genetic manipulations, so their use negative (i.e., Proteobacteria) and gram-positive (i.e.,
is still covered in some detail. Chapter 4 has been up- Firmicutes) bacteria. Most notably, it now contains a
dated with more information about how plasmids are new section on bacterial cell biology, including cell wall
typically used in the laboratory setting in work with synthesis and cell division and their regulation, as well
model organisms and beyond as well, including updates as a new box on the evolution of cytoskeletal filaments,
on our understanding of partitioning systems. Chapter and it introduces the use of Caulobacter crescentus as a
5 was extensively updated to illustrate the hodgepodge model system for these studies. Chapter 14 finishes with
organization of conjugal elements and advances in our sporulation in B. subtilis, probably the best understood
understanding of conjugation and to more fully inte- bacterial developmental system.
grate the important role of integrating conjugative ele- As in earlier editions, we do not mention the names
ments in bacterial genomes (including a focus on one of most investigators who have made major contribu-
of these elements from B. subtilis on the front cover). tions to bacterial molecular genetics. We include only
Chapter 6 is updated throughout and focuses on simi- those names that have become icons in the field because
larities and differences between different transformation they are associated with certain seminal experiments
systems. The bacteriophage chapters (chapters 7 and 8) (e.g., Meselson and Stahl or Luria and Delbrück), mod-
have been updated, and new material has been added. els (e.g., Jacob and Monod), or structures (e.g., Watson
Some highlights from phage genomics are now covered, and Crick). Many other names are available in the sug-
as are phage defense mechanisms, including CRISPR. gested reading lists, where we give some of the original
The section on phage lysis is expanded, as is the text box references to the developments under discussion, and in
on phage display, whose power is now demonstrated the credit lines for sources of figures and tables, which
with some current uses. The interaction between lyso- are given at the end of the book.
genic phages and genetic islands has been updated and Again we are indebted to a number of people who
moved into the text, as have some more recently devel- helped us in various ways. Some read sections of the
oped techniques using lysogenic phages, for example, in book at our request and made valuable suggestions.
detecting protein-protein interactions. Chapter 9, which Some, who have used the book for teaching, have
covers transposable elements and site-specific recombi- pointed out ways to make it more useful for them and
nation, has been updated to clarify the basic molecular their students. Others have noticed factual errors or er-
biology of these elements, and it includes updated sec- rors of omission and have pointed out references that
tions describing how they are used in the laboratory to- helped us check our facts. In addition to those who
day. Chapter 10 was significantly reorganized to stress commented on earlier editions, many of whose contri-
the role of homologous recombination in the repair of butions have carried over, this list includes Dennis Ar-
DNA double-strand breaks that occur at interruptions vidson, Dominique Belin, Melanie Berkmen, Helmut
in the template DNA during replication. The role of ho- Bertrand, Lindsay Black, Rob Britton, Yves Brun, Rich
mologous recombination in repair explains the under- Calendar, George Chaconas, Dhruba Chattoraj, Carton
pinning of the evolution of the process and also clarifies Chen, Todd Ciche, Laszlo Csonka, Gary Dunny, Marie
how the process works in concert with DNA replication. Elliot, Laura Frost, Barbara Funnell, Peter Geiduschek,

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 PREFACE xvii

Graham Hatfull, John Helmann, Ann Hochschild, Su- manager, who coordinated the entire project. We have
san Lovett, Ken Marinas, Norman Pace, Steven Sandler, also had the good fortune to work again with two of
Joel Schildbach, Linda Sherwood, Chris Waters, Robert the same professionals who did a masterful job with the
Weiss, Joanne Willey, Steve Winans, Ry Young, and Steve first three editions: Susan Brown Schmidler, who created
Zinder. Special thanks go to Lee Kroos, who agreed to the book and cover design; Terese Winslow, who created
update an entire section. Yet others furnished original the cover illustration; and Elizabeth McGillicuddy, who
figures that we could incorporate into the text; some of copyedited the manuscript. We also thank Patrick Lane
them are mentioned in the figure credits. However, in the of ScEYEnce Studios for bringing an attractive aestheti-
end, any mistakes and omissions were all ours. cism to the rendering of our hand-drawn illustrations
As with the first three editions, it was a great plea- into the final figures.
sure to work with the professionals at ASM Press. The Larry Snyder
former director of ASM Press, Jeff Holtmeier, helped us Joe Peters
prepare for the fourth edition. We have been fortunate Tina Henkin
to continue to work with Kenneth April, the production Wendy Champness

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