Bacterial and Bacteriophage Genetics

Bacterial and Bacteriophage Genetics  
Author:
Edward A. Birge
Release at: 2006
Pages: 582
Edition:
Fifth Edition
File Size: 9 MB
File Type: pdf
Language: English


Description of Bacterial and Bacteriophage Genetics


Before beginning the formal study of the genetics of bacteria and their viruses, it is important to understand the fundamentals of a microbial cell, chromosome, and DNA structures, and the basic viral processes.

Content of Bacterial and Bacteriophage Genetics



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

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

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 105


4 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

Questions for Review and Discussion 145

Suggestions for Further Reading 145

General 145

Specialized 146

5 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 175


6 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

References 218

General 218

Specialized 218


7 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 φX174 242

RNA-Containing Bacteriophages 244


Single-Stranded RNA Viruses 244

Double-Stranded RNA Viruses 250

Bacteriophages Infecting Bacillus subtilis 251

Bacteriophage SP01 251

Bacteriophage φ29 253

Bacteriophages Infecting the Archaea 255

Summary 255

Questions for Review and Discussion 256

References 257

General 257

Specialized 257


8 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 P22 288

Bacteriophages P2 and P4 290

Bacteriophage P1 293

Bacteriophage Mu 295

SSV1 and SSV2 299

Summary 299

Questions for Review and Discussion 300

References 301

General 301

Specialized 301


9 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 φ80 310

Bacteriophage P1 312

Bacteriophage P22 312

Generalized Transduction 314

Bacteriophage P22 314

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 324


10 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

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 350


11 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 381


12 Plasmids and Conjugation Systems Other than F 383


Major Chromosome-Mobilizing Plasmids 384

Salmonella 384

Pseudomonas 386

Enterococcus 388

Streptomyces 390

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 R100 403

Genetic Analysis of Plasmid R100 406

Conjugal Plasmid Interactions 409

Summary 411

Questions for Review and Discussion 412

References 413

General 413

Specialized 414


13 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 440


14 Advanced Regulatory Topics 443


Regulons 444

Maltose 444

Heat Shock Proteins 448

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 460


15 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 Tn10 470

Phage Mu Transposition 474

Summary 476

Questions for Review and Discussion 477

References 477

General 477

Specialized 477


16 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

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 503


17 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

Appendix 1 Laws of Probability and Their Application to Prokaryote Cultures 531

Appendix 2 Useful World Wide Web Sites for Bacterial Genetics 549

Appendix 3 Answers to Application Questions 551

Glossary 553

Index 567

GET THIS BOOK
Similar Books

0 comments: