| Author: |
Edward A. Birge
|
| Release at: | 2006 |
| Pages: | 582 |
| Edition: |
Fifth Edition
|
| File Size: | 9 MB |
| File Type: | |
| 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
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
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