Snyder and Champness Molecular Genetics of Bacteria (5th Edition)

Rs. 49,760
  • Authors: Tina M. Henkin, Joseph E. Peters
  • ISBN: 9781555819750
  • Publisher: Wiley Publishing
  • Edition: 5th
  • Publication Date: October 27, 2020
  • Format: Hardback – 640 pages
  • Language: English

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Description

The single most comprehensive and authoritative textbook on bacterial molecular genetics

Snyder & Champness Molecular Genetics of Bacteria is a new edition of a classic text, updated to address the massive advances in the field of bacterial molecular genetics and retitled as homage to the founding authors.

In an era experiencing an avalanche of new genetic sequence information, this updated edition presents important experiments and advanced material relevant to current applications of molecular genetics, including conclusions from and applications of genomics; the relationships among recombination, replication, and repair and the importance of organizing sequences in DNA; the mechanisms of regulation of gene expression; the newest advances in bacterial cell biology; and the coordination of cellular processes during the bacterial cell cycle. The topics are integrated throughout with biochemical, genomic, and structural information, allowing readers to gain a deeper understanding of modern bacterial molecular genetics and its relationship to other fields of modern biology.

Although the text is centered on the most-studied bacteria, Escherichia coli and Bacillus subtilis, many examples are drawn from other bacteria of experimental, medical, ecological, and biotechnological importance. The book’s many useful features include

  • Text boxes to help students make connections to relevant topics related to other organisms, including humans
  • A summary of main points at the end of each chapter
  • Questions for discussion and independent thought
  • A list of suggested readings for background and further investigation in each chapter
  • Fully illustrated with detailed diagrams and photos in full color
  • A glossary of terms highlighted in the text

While intended as an undergraduate or beginning graduate textbook, Molecular Genetics of Bacteria is an invaluable reference for anyone working in the fields of microbiology, genetics, biochemistry, bioengineering, medicine, molecular biology, and biotechnology.

“This is a marvelous textbook that is completely up-to-date and comprehensive, but not overwhelming. The clear prose and excellent figures make it ideal for use in teaching bacterial molecular genetics.”
—Caroline Harwood, University of Washington

Table of Contents
  1. Preface xv
  2. Acknowledgments xix
  3. About the Authors 1
  4. Introduction 3
    1. The Biological Universe 5
    2. The Bacteria 5
    3. The Archaea 7
    4. The Eukaryotes 7
    5. What is Genetics? 8
    6. Bacterial Genetics 8
    7. Bacteria Are Haploid 9
    8. Short Generation Times 9
    9. Asexual Reproduction 9
    10. Colony Growth on Agar Plates 9
    11. Colony Purification 9
    12. Serial Dilutions 9
    13. Selections 10
    14. Storing Stocks of Bacterial Strains 10
    15. Genetic Exchange 10
    16. Phage Genetics 10
    17. Phages Are Haploid 11
    18. Selections
    19. with Phages 11
    20. Crosses with Phages 11
    21. A Brief History of Bacterial Molecular Genetics 11
    22. Inheritance in Bacteria 11
    23. Transformation 11
    24. Conjugation 12
    25. Transduction 12
    26. Recombination within Genes 12
    27. Semiconservative DNA Replication 12
    28. mRNA 12
    29. The Genetic Code 12
    30. The Operon Model 12
    31. Enzymes for Molecular Biology 12
    32. Synthetic Genomics 13
    33. What is Ahead 13
  5. The Bacterial Chromosome: DNA Structure, Replication, and Segregation 17
    1. DNA Structure 17
    2. The Deoxyribonucleotides 17
    3. The DNA Chain 18
    4. The 5’ and 3’ Ends 18
    5. Base Pairing 20
    6. Antiparallel Construction 20
    7. The Major and Minor Grooves 21
    8. The Mechanism of DNA Replication 21
    9. Deoxyribonucleotide Precursor Synthesis 21
    10. Replication of the Bacterial Chromosome 21
    11. Replication of Double- Stranded DNA 26
    12. Replication Errors 30
    13. Editing 30
    14. RNA Primers and Editing 31
    15. Impediments to DNA Replication 31
    16. Damaged DNA and DNA Polymerase III 31
    17. Mechanisms To Deal with Impediments on Template DNA Strands 32
    18. Physical Blocks to Replication Forks 32
    19. Replication of the Bacterial Chromosome and Cell Division 32
    20. Structure of Bacterial Chromosomes 34
    21. Replication of the Bacterial Chromosome 34
    22. Initiation of Chromosome Replication 34
    23. RNA Priming of Initiation 35
    24. Termination of Chromosome Replication 35
    25. Chromosome Segregation 37
    26. Coordination of Cell Division with Replication of the Chromosome 47
    27. Timing of Initiation of Replication 49
    28. The Bacterial Nucleoid 51
    29. Supercoiling in the Nucleoid 51
    30. Topoisomerases 52
    31. The Bacterial Genome 55
    32. Box 1.1 Structural Features of Bacterial Genomes 37
    33. Box 1.2 Antibiotics That Affect Replication and DNA Structure 54
  6. Bacterial Gene Expression: Transcription, Translation, Protein Folding, and Localization 61
    1. Overview 61
    2. The Structure and Function of RNA 62
    3. Types of RNA 62
    4. RNA Precursors 62
    5. RNA Structure 62
    6. RNA Processing and Modification 64
    7. Transcription 64
    8. Structure of Bacterial RNA Polymerase 64
    9. Overview of Transcription 65
    10. Details of Transcription 67
    11. rRNAs and tRNAs 74
    12. RNA Degradation 77
    13. RNases 77
    14. The Structure and Function of Proteins 78
    15. Protein Structure 78
    16. Translation 80
    17. Structure of the Bacterial Ribosome 80
    18. Overview of Translation 83
    19. Details of Protein Synthesis 84
    20. The Genetic Code 92
    21. Polycistronic mRNA 96
    22. Protein Folding and Degradation 98
    23. Protein Chaperones 98
    24. Protein Degradation 101
    25. Protein Localization 101
    26. The Translocase System 101
    27. The Signal Sequence 103
    28. The Targeting Factors 103
    29. The Tat Secretion Pathway 104
    30. Disulfide Bonds 105
    31. Protein Secretion and Export 105
    32. Protein Secretion Systems in Bacteria with an Outer Membrane 106
    33. Protein Secretion in Bacteria That Lack an Outer Membrane 110
    34. Sortases 110
    35. Regulation of Gene Expression 111
    36. Transcriptional Regulation 112
    37. Posttranscriptional Regulation 113
    38. What You Need To Know 114
    39. Open Reading Frames 115
    40. Transcriptional and Translational Fusions 115
    41. Box 2.1 Antibiotic Inhibitors of Transcription 72
    42. Box 2.2 Molecular Phylogeny 75
    43. Box 2.3 Antibiotic Inhibitors of Translation 81
    44. Box 2.4 Mimicry in Translation 91
    45. Box 2.5 Exceptions to the Code 94
  7. Bacterial Genetic Analysis: Fundamentals and Current Approaches 123
    1. Definitions 123
    2. Terms Used in Genetics 123
    3. Genetic Names 124
    4. Auxotrophic and Catabolic Mutants 125
    5. Conditional- Lethal Mutants 126
    6. Resistant Mutants 128
    7. Inheritance in Bacteria 128
    8. The Luria and Delbrück Experiment 129
    9. Mutants Are Clonal 130
    10. Esther and Joshua Lederberg’s Experiment 130
    11. Mutation Rates 132
    12. Calculating Mutation Rates 133
    13. Calculating the Mutation Rate from the Rate of Increase in the Proportion of Mutants 135
    14. Types of Mutations 136
    15. Properties of Mutations 136
    16. Base Pair Changes 136
    17. Frameshift Mutations 140
    18. Deletion Mutations 141
    19. Tandem- Duplication Mutations 143
    20. Inversion Mutations 144
    21. Insertion Mutations 145
    22. Reversion versus Suppression 147
    23. Intragenic Suppressors 147
    24. Intergenic Suppressors 147
    25. Genetic Analysis in Bacteria 151
    26. Isolating Mutants 151
    27. Genetic Characterization of Mutants 155
    28. Complementation Tests 160
    29. Genetic Crosses in Bacteria 166
    30. Mapping of Bacterial Markers by Transduction and Transformation 168
    31. Other Uses of Transformation and Transduction 171
    32. Genetic Mapping by Hfr Crosses 172
    33. Perspective 176
    34. Box 3.1 Inversions and the Genetic Map 146
  8. Plasmids 181
    1. What is a Plasmid? 181
    2. Naming Plasmids 182
    3. Functions Encoded by Plasmids 182
    4. Plasmid Structure 183
    5. Properties of Plasmids 184
    6. Replication 184
    7. Functions of the ori Region 187
    8. Plasmid Replication Control Mechanisms 193
    9. Mechanisms To Prevent Curing of Plasmids 200
    10. The Par Systems of Plasmids 203
    11. Plasmid Cloning Vectors 206
    12. Examples of Plasmid Cloning Vectors 208
    13. Broad- Host- Range Cloning Vectors 210
    14. Box 4.1 Linear Chromosomes and Plasmids in Bacteria 188
    15. Box 4.2 Determining the Inc Group 191
    16. Box 4.3 Toxin- Antitoxin Systems and Plasmid Maintenance 201
  9. Conjugation 215
    1. Overview 215
    2. Classification of Self- Transmissible Plasmids and Integrating Elements 217
    3. The Fertility Plasmid 217
    4. Mechanism of DNA Transfer during Conjugation in Proteobacteria 218
    5. Transfer (tra) Genes 218
    6. The oriT Sequence 221
    7. Efficiency of Transfer 222
    8. Interspecies Transfer of Plasmids 225
    9. Conjugation and Type IV Secretion Systems Capable of Translocating Proteins 225
    10. Mobilizable Plasmids 229
    11. Chromosome Transfer by Plasmids 230
    12. Formation of Hfr Strains of E. coli 230
    13. Transfer of Chromosomal DNA by Integrated Plasmids 230
    14. Chromosome Mobilization 231
    15. Prime Factors 231
    16. Diversity in Transfer Systems 233
    17. Integrating Conjugative Elements 234
    18. SXT/R391 ICE 234
    19. ICEBs1 236
    20. Tn916 237
    21. TnGBS1 and TnGBS2 240
    22. Box 5.1 Pilus- Specific Phages 220
    23. Box 5.2 Delivery of Conditional Plasmids by Conjugation 223
    24. Box 5.3 Gene Exchange between Domains 226
    25. Box 5.4 Conjugation and Synthetic Genomics 232
  10. Transformation 245
    1. Natural Transformation 246
    2. Discovery of Transformation 246
    3. Overview of Natural Transformation 247
    4. DNA Uptake Mechanisms 247
    5. Specificity of DNA Uptake 251
    6. DNA Pro cessing after Uptake 253
    7. Natural Transformation as a Tool 253
    8. Regulation of Natural Competence 254
    9. Identification of Competence in Other Organisms 258
    10. Role of Natural Transformation 258
    11. Artificially Induced Competence 260
    12. Chemical Induction 260
    13. Electroporation 261
    14. Protoplast Transformation 261
    15. Box 6.1 Experimental Measurements of DNA Uptake 248
    16. Box 6.2 Genetic Evidence for Single- Stranded DNA Uptake 252
    17. Box 6.3 Role of Natural Transformation in Pathogens 260
  11. Bacteriophages and Transduction 265
    1. Lytic Development 268
    2. The Lytic Cycle 268
    3. Transcriptional Regulation of Phage Gene Expression 268
    4. Phage Genome Replication and Packaging 279
    5. Host Cell Lysis 289
    6. Lysogenic Development 292
    7. The λ System 292
    8. Other Lysogenic Systems 299
    9. Genetic Analysis of Phages 302
    10. Infection of Cells 302
    11. Phage Crosses 303
    12. Recombination and Complementation Tests with Phages 303
    13. The Genetic- Linkage Map of a Phage 305
    14. Phage- Mediated Genetic Transfer 306
    15. Generalized Transduction 306
    16. Specialized Transduction 308
    17. Lysogenic Conversion and Bacterial Pathogenesis 310
    18. Host Defenses Against Phage Infection 313
    19. Restriction- Modification Systems 313
    20. Abi Systems 313
    21. CRISPR/Cas Systems 314
    22. Small Molecules and Phage Defense 314
    23. Phage versus Phage 314
    24. Phages as Tools 315
    25. Cloning Vectors 315
    26. Phage Display 315
    27. Phage Therapy 317
    28. Box 7.1 Phage Genomics 266
    29. Box 7.2 Phage T7- Based Tools 271
    30. Box 7.3 Protein Priming 285
  12. Transposition, Site- Specific Recombination, and Families of Recombinases 321
    1. Transposition 321
    2. Overview of Transposition 322
    3. Structure of Bacterial DNA Transposons 322
    4. Types of Bacterial DNA Transposons 323
    5. Assays of Transposition 326
    6. Mechanisms of Transposition 328
    7. DDE Transposons 328
    8. HUH Transposons 332
    9. General Properties of Transposons 334
    10. Transposition Regulation 334
    11. Target Site Specificity 335
    12. Effects on Genes Adjacent to the Insertion Site 337
    13. Target Immunity 337
    14. Transposon Mutagenesis 337
    15. Transposon Mutagenesis In Vivo 339
    16. Transposon Mutagenesis In Vitro 340
    17. Transposon Mutagenesis of Plasmids 341
    18. Transposon Mutagenesis of the Bacterial Chromosome 341
    19. Transposon Mutagenesis of All Bacteria 342
    20. Using Transposon Mutagenesis To Make Random Gene Fusions 342
    21. Site- Specific Recombination 343
    22. Integrases 343
    23. Resolvases 345
    24. DNA Invertases 345
    25. Y and S Recombinases 347
    26. Y Recombinases: Mechanism 347
    27. S Recombinases: Mechanism 351
    28. Group II Mobile Introns: Elements That Move Using an RNA Intermediate 352
    29. Importance of Transposition and Site- Specific Recombination in Bacterial Adaptation 354
    30. Box 8.1 Mobile Elements and DNA Replication 333
    31. Box 8.2 Transposons and Genomics 338
  13. Molecular Mechanisms of Homologous Recombination 359
    1. Homologous Recombination and DNA Replication in Bacteria 360
    2. Early Evidence for the Interdependence of Homologous Recombination and DNA Replication 361
    3. The Molecular Basis for Recombination in E. coli 361
    4. chi (χ) Sites and the RecBCD Complex 361
    5. The RecF Pathway 367
    6. Synapse Formation and the RecA Protein 368
    7. The Ruv and RecG Proteins and the Migration and Cutting of Holliday Junctions 371
    8. Recombination between Different DNAs in Bacteria 373
    9. How Are Linear DNA Fragments Recombined into the E. coli Chromosome? 373
    10. Recombination during Natural Transformation 375
    11. Phage Recombination Pathways 375
    12. Rec Proteins of Phages T4 and T7 375
    13. The RecE Pathway of the rac Prophage 375
    14. The Phage λ Red System 375
    15. Recombineering: Gene Replacements in E. coli with Phage λ Recombination Functions 376
    16. Gene Conversion and Other Manifestations of Heteroduplex Formation during Recombination 379
    17. Box 9.1 Discovery of χ sites 364
    18. Box 9.2 Other Types of Double- Strand Break Repair in Bacteria 365
  14. DNA Repair and Mutagenesis 385
    1. Evidence for DNA Repair 386
    2. Specific Repair Pathways 387
    3. Deamination of Bases 387
    4. Damage Due to Reactive Oxygen 389
    5. Damage Due to Alkylating Agents 393
    6. Damage Due to UV Irradiation 395
    7. General Repair Mechanisms 396
    8. Base Analogs 396
    9. Frameshift Mutagens 397
    10. Mismatch Repair 398
    11. Nucleotide Excision Repair 403
    12. DNA Damage Tolerance Mechanisms 405
    13. Homologous Recombination and DNA Replication 405
    14. SOS- Inducible Repair 409
    15. Mechanism of TLS by the Pol V Mutasome 416
    16. Other Specialized Polymerases and Their Regulation 417
    17. Summary of Repair Pathways in E. coli 418
    18. Bacteriophage Repair Pathways 418
    19. Box 10.1 The Role of Reactive Oxygen Species in Cancer and Degenerative Diseases 391
    20. Box 10.2 DNA Repair and Cancer 401
    21. Box 10.3 The Ames Test 417
  15. Regulation of Gene Expression: Genes and Operons 425
    1. Transcriptional Regulation in Bacteria 426
    2. Genetic Evidence for Negative and Positive Regulation 427
    3. Negative Regulation of Transcription Initiation 428
    4. Negative Inducible Systems 428
    5. Negative Repressible Systems 437
    6. Molecular Mechanisms of Transcriptional Repression 439
    7. Positive Regulation of Transcription Initiation 439
    8. Positive Inducible Systems 440
    9. Positive Repressible Systems 447
    10. Molecular Mechanisms of Transcriptional Activation 447
    11. Regulation by Transcription Attenuation 449
    12. Modulation of RNA Structure 449
    13. Changes in Processivity of RNA Polymerase 459
    14. Regulation of mRNA Degradation 460
    15. Protein- Dependent Effects on RNA Stability 460
    16. RNA- Dependent Effects on RNA Stability 461
    17. Regulation of Translation 461
    18. Regulation of Translation Initiation 462
    19. Translational Regulation in the Exit Channel of the Ribosome 464
    20. Regulation of Translation Termination 465
    21. Posttranslational Regulation 467
    22. Posttranslational Protein Modification 467
    23. Regulation of Protein Turnover 467
    24. Feedback Inhibition of Enzyme Activity 468
    25. Why Are There So Many Mechanisms of Gene Regulation? 469
    26. Box 11.1 The Helix- Turn- Helix Motif of DNA- Binding Proteins 427
    27. Box 11.2 Families of Regulators 442
  16. Global Regulation: Regulons and Stimulons 473
    1. Carbon Catabolite Regulation 474
    2. Carbon Catabolite Regulation in E. coli: Catabolite Activator Protein (CAP) and cAMP 474
    3. Carbon Catabolite Regulation in B. subtilis: CcpA and Hpr 481
    4. Regulation of Nitrogen Assimilation 482
    5. Pathways for Nitrogen Assimilation 483
    6. Regulation of Nitrogen Assimilation Pathways in E. coli by the Ntr System 484
    7. Regulation of Nitrogen Assimilation in B. subtilis 491
    8. Regulation of Ribosome Components and tRNA Synthesis 491
    9. Ribosomal Protein Gene Regulation 492
    10. Regulation of rRNA and tRNA Synthesis 493
    11. Stringent Response 494
    12. Stress Responses in Bacteria 498
    13. Heat Shock Regulation 498
    14. General Stress Response in Enteric Bacteria 501
    15. General Stress Response in Firmicutes 505
    16. Extracytoplasmic (Envelope) Stress Responses 506
    17. Iron Regulation in E. coli 510
    18. The Fur Regulon 510
    19. The RyhB sRNA 512
    20. The Aconitase Translational Repressor 512
    21. Regulation of Virulence Genes in Pathogenic Bacteria 513
    22. Diphtheria 513
    23. Cholera and Quorum Sensing 514
    24. Whooping Cough 519
    25. Developmental Regulation: Sporulation in B. subtilis 520
    26. Identification of Genes That Regulate Sporulation 522
    27. Regulation of Sporulation Initiation 522
    28. Compartmentalized Regulation of Sporulation Genes 524
    29. The Role of Sigma Factors in Sporulation Regulation 524
    30. Intercompartmental Regulation during Development 525
    31. Other Sporulation Systems 529
    32. Box 12.1 cAMP-Independent Carbon Catabolite Regulation in E. coli 477
    33. Box 12.2 Nitrogen Fixation 483
    34. Box 12.3 Signal Transduction Systems in Bacteria 486
    35. Box 12.4 Sigma Factors 488
    36. Box 12.5 Regulatory RNAs 503
  17. Genomes and Genomic Analysis 535
    1. The Bacterial Genome 535
    2. DNA Sequencing 537
    3. Advanced Genome-Sequencing Techniques 545
    4. Polymerase Chain Reaction 547
    5. Barriers to Horizontal Transfer: Genome Gatekeepers and Molecular Biologist’s Toolkit 549
    6. Restriction Endonucleases 549
    7. Techniques for Nontraditional Cloning and Assembly 553
    8. CRISPR/Cas Systems 559
    9. Final Thoughts 568
    10. Box 13.1 Annotation and Comparative Genomics 538
    11. Box 13.2 Special Problems in Genetic Analysis of Operons 542
    12. Box 13.3 Synthesizing and Cloning Complete Bacterial Genomes 560
    13. Glossary 573
    14. Index 599
Authors Biography

Tina M. Henkin is Professor of Microbiology and Robert W. and Estelle S. Bingham Professor of Biological Sciences at Ohio State University, where she has been teaching since 1995. Dr. Henkin received a PhD in genetics at the University of Wisconsin.

Joseph E. Peters is Professor of Microbiology and Director of the Graduate Program in Microbiology at Cornell University, where he has been teaching since 2002. Dr. Peters received a PhD in microbiology at the University of Maryland.

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