Molecular genetics of bacteria Larry Snyder ...

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adam_text 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 vi CONTENTS A Brief History of Bacterial Molecular Genetics 9 Inheritance in Bacteria 9 Transformation 9 Conjugation 10 Transduction 10 Recombination within Genes 10 Semiconservative DNA Replication 10 mRNA 10 The Genetic Code 10 The Operan Model 10 Enzymes for Molecular Biology 10 What Is Ahead 11 SUGGESTED READING 11 CHAPTER 1____________________ The Bacterial Chromosome: DNA Structure, Replication, and Segregation 13 DNA Structure 13 The Deoxyribonucleotides 13 The DNA Chain 14 The 5 and 3 Ends 14 Base Pairing 16 Antiparallel Construction 17 The Major and Minor Grooves 17 The Mechanism of DNA Replication 17 Deoxyribonucleotide Precursor Synthesis 17 Replication of the Bacterial Chromosome 19 Replication of Double-Stranded DNA 23 26 Replication Errors Editing 26 RNA Primers and Editing 27 Impediments to DNA Replication 28 Damaged DNA and DNA Polymerase ill 28 Mechanisms To Deal with Impediments on Template DNA Strands 28 Physical Blocks to Replication Forks 30 Replication of the Bacterial Chromosome and Cell Division 31 Structure of the Bacterial Chromosome 31 Replication of the Bacterial Chromosome 31 Initiation of Chromosome Replication 32 RNA Priming of Initiation 33 Termination of Chromosome Replication 33 Chromosome Segregation 34 Coordination of Cell Division with Replication of the Chromosome 43 Timing of Initiation of Replication 45 The Bacterial Nucleoid 47 Supercoiling in the Nucleoid 47 Topoisomerases 49 The Bacterial Genome 50 Antibiotics That Affect Replication and DNA Structure 51 Antibiotics That Block Precursor Synthesis 51 Antibiotics That Block Polymerization of Deoxynucleotides 52 Antibiotics That Affect DNA Structure 52 Antibiotics That Affect Gyrase 52 Molecular Biology Manipulations with DNA 53 Restriction Endonucleases 53 Hybridizations 56 Applications of the Enzymes Used in DNA Replication 58 Polymerase Chain Reaction 58 BOX 1.1 Structural Features of Bacterial Genomes 37 BOX 1.2 Advanced Genome-Sequencing Techniques 59 SUMMARY 62 QUESTIONS FOR THOUGHT 64 PROBLEMS 64 SUGGESTED READING 65 CHAPTER 2 Bacterial Gene Expression: Transcription, Translation, and Protein Folding 67 Overview 67 The Structure and Function of RNA Types of RNA 69 RNA Precursors 69 RNA Structure 69 RNA Processing and Modification 70 68 CONTENTS vii Transcription 70 Structure of Bacterial RNA Polymerase 70 Overview of Transcription 71 Details of Transcription 75 rRNAs and tRNAs 81 RNA Degradation 82 RNases 83 The Structure and Function of Proteins 84 Protein Structure 85 Translation 86 Structure of the Bacterial Ribosome 86 Overview of Translation 88 Details of Protein Synthesis 90 The Genetic Code 97 Protein Folding and Degradation 105 Protein Chaperones 105 Protein Degradation 107 Membrane Proteins and Protein Export 108 Regulation of Gene Expression 108 Transcriptional Regulation 108 Posttranscriptional Regulation 109 Genomes and Genomics 109 Annotation and Comparative Genomics 110 What You Need To Know 110 Open Reading Frames 116 Transcriptional and Translational Fusions 116 Antibiotics That Block Transcription and Translation 116 Antibiotic Inhibitors of Transcription 117 Antibiotic Inhibitors of Translation 118 BOX 2.1 Molecular Phytogeny 82 BOX 2.2 Mimicry in Translation 96 BOX 23 Exceptions to the Code 99 BOX 2.4 Selfish DNAs: RNA Introns and Protein Inteins 102 BOX 2.5 Annotation and Comparative Genomics 110 SUMMARY 120 QUESTIONS FOR THOUGHT 122 PROBLEMS 122 SUGGESTED READING 123 CHAPTER 3 Bacterial Genetic Analysis: Fundamentals and Current Approaches 125 Definitions 125 Terms Used in Genetics 125 Genetic Names 126 Auxotrophic and Catabolic Mutants 127 Conditional-Lethal Mutants 128 Resistant Mutants 130 Inheritance in Bacteria 130 The Luria and Delbriick Experiment 131 Mutants Are Clonal 132 The Lederbergs Experiment 133 Mutation Rates 133 Calculating Mutation Rates 135 Calculating the Mutation Rate from the Rate of Increase in the Proportion of Mutants 136 Types of Mutations 137 Properties of Mutations 138 Base Pair Changes 138 Frameshift Mutations 142 Deletion Mutations 144 Tandem-Duplication Mutations 145 Inversion Mutations 147 Insertion Mutations 148 Reversion versus Suppression 149 Intragenic Suppressors 149 Intergenic Suppressors 150 Genetic Analysis in Bacteria 153 Isolating Mutants 153 Genetic Characterization of Mutants 157 Complementation Tests 161 Genetic Crosses in Bacteria 167 Mapping of Bacterial Markers by Transduction and Transformation 168 Other Uses of Transformation and Transduction 172 Genetic Mapping by Hfr Crosses 173 Isolation of Tandem Duplications of the his Operon ¡n Salmonella 176 Lengths of Tandem Duplications 178 Frequency of Spontaneous Duplications 179 viii CONTENTS BOX 3.1 Statistical Analysis of the Number of Mutants per Culture 134 BOX 3.2 Inversions and the Genetic Map 148 SUMMARY 179 QUESTIONS FOR THOUGHT 181 PROBLEMS 181 SUGGESTED READING 182 CHAPTER 4 Plasmids 183 What Is a Plasmici? 183 Naming Plasmids 184 Functions Encoded by Plasmids 184 Plasmid Structure 185 Properties of Plasmids 186 Replication 186 Functions of the ori Region 189 Plasmid Replication Control Mechanisms 194 Mechanisms To Prevent Curing of Plasmids 203 The Par Systems of Plasmids 205 Plasmid Cloning Vectors 209 Examples of Plasmid Cloning Vectors 210 Broad-Host-Range Cloning Vectors 213 BOX 4.1 Linear Chromosomes and Plasmids in Bacteria 190 BOX 4.2 Toxin-Antitoxin Systems and Plasmid Maintenance 204 SUMMARY 216 QUESTIONS FOR THOUGHT 217 PROBLEMS 217 SUGGESTED READING 217 CHAPTER 5 Conjugation 219 Overview 219 Classification of Self-Transmissible Plasmids 220 The Fertility Plasmid 220 Mechanism of DNA Transfer during Conjugation in Gram-Negative Bacteria 221 Transfer (ira) Genes 221 The oriT Sequence 225 Male-Specific Phages 226 Efficiency of Transfer 227 Interspecies Transfer of Plasmids 227 Conjugation and Type IV Protein Secretion 228 Mobiiizable Plasmids 232 Chromosome Transfer by Plasmids 235 Formation of Hfr Strains 235 Transfer of Chromosomal DNA by Integrated Plasmids 236 Chromosome Mobilization Prime Factors 236 236 Transfer Systems of Gram-Positive Bacteria 237 Plasmid-Attracting Pheromones 237 Integrating Conjugative Elements 240 BOX 5.1 Gene Exchange between Domains 230 SUMMARY 242 QUESTIONS FOR THOUGHT 243 PROBLEMS 243 SUGGESTED READING 244 CHAPTER 6 Transformation 247 Natural Transformation 248 Discovery of Transformation 248 Competence 248 DNA Processing after Uptake 252 Experimental Evidence for Models of Natural Transformation 252 Plasmid Transformation and Phage Transfection of Naturally Competent Bacteria 254 Regulation of Natural Competence 255 Role of Natural Transformation 257 Importance of Natural Transformation for Forward and Reverse Genetics 259 Congression 259 Artificially Induced Competence 260 Chemical Induction 260 Electroporation 261 Protoplast Transformation 261 BOX 6.1 Antigenic Variation in Neisseria gonorrhoeae 259 SUMMARY 262 CONTENTS ¡χ QUESTIONS FOR THOUGHT 262 PROBLEMS 262 SUGGESTED READING 263 CHAPTER 7 Bacteriophages: Lytic Development, Genetics, and Generalized Transduction 265 Regulation of Gene Expression during Lytic Development 270 Phages That Encode Their Own RNA Polymerases 272 17 Phage-Based Expression Vectors 273 Making Riboprobes and RNA-Processing Substrates 273 Phage T4: Transcriptional Activators, a New Sigma Factor, and Replication-Coupled Transcription 275 Phage DNA Genome Replication and Packaging 279 Phages with Single-Stranded Circular DNA 279 Replication and DNA Packaging: Linear Genomes 285 Phage T7: Linear DNA That Forms Concatemers 285 Phage T4: Another Phage That Forms Concatemers 286 Phage Lysis 289 Single-Protein Lysis 289 Timed Lysis 290 Timing of Lysis by Holins 290 Phage Display 292 Genetic Analysis of Phages 298 Infection of Cells 298 Phage Crosses 299 Recombination and Complementation Tests with Phages 299 Genetic Experiments with the rll Genes of Phage T4 301 Constructing the Genetic-Linkage Map of a Phage 307 Phage Defense Mechanisms 309 Restriction-Modification Systems 310 Abi Systems 310 CRISPRLoci 311 Generalized Transduction 314 What Makes a Transducing Phage? 315 Shuttle Phasmids 316 Role of Transduction in Bacterial Evolution 317 BOX 7.1 Phage Genomics 268 BOX 7.2 RNA Phages 271 BOX 73 Protein Priming 286 BOX 7.4 Phage Display 294 SUMMARY 318 QUESTIONS FOR THOUGHT 319 PROBLEMS 319 SUGGESTED READING 320 CHAPTER 8 Lysogeny: the λ Paradigm and the Role of Lysogenic Conversion in Bacterial Pathogenesis 323 Phage λ 324 λ Lytic Development 324 Replication of λ DNA 331 Lysogeny by Phage λ 333 The Lytic-versus-Lysogen Decision: the Roles of d, dl, and clll Gene Products 333 Phage λ Integration 334 Maintenance of λ Lysogeny 335 Immunity to Superinfection 337 Induction of λ 338 Summary of the Lytic and Lysogenic Cycles 340 Specialized Transduction 340 Selection of Η FT Particles 342 Other Lysogen-Forming Phages 343 Phage P2 343 Phage P4: a Satellite Virus 343 Prophages That Replicate as Plasmids 345 Phage Mu: a Transposon Masquerading as a Phage 345 Lysogenic Conversion and Bacterial Pathogenesis 345 E. coli and Dysentery: Shiga Toxins 346 Diphtheria 347 Cholera 347 S. aureus and Toxic Shock Syndrome 349 Synopsis 350 CONTENTS Uses of Lysogeny in Genetic Analysis and Biotechnology 350 Complementation and Gene Expression Studies 350 Use of Phage Display and Frequency of Mixed Dilysogens To Detect Protein-Protein Interactions 350 Genetic Experiments with Phage λ 351 Genetic Analysis of λ Lysogen Formation 351 Genetics of the Cl Repressor: Evidence for the Domain Structure of Proteins 353 Identification of λ nut Sites Involved in Progressive Transcription Antitermination 354 Isolation of Host nus Mutations: E. coli Functions Involved in Transcription Elongation-Termination 356 BOX 8.1 Effects of Prophage Insertion on the Host 336 SUMMARY 357 QUESTIONS FOR THOUGHT 358 PROBLEMS 358 SUGGESTED READING 359 CHAPTER 9 Transposition, Site-Specific Recombination, and Families of Recombinases 361 Transposition 361 Overview of Transposition 362 Structure of Bacterial Transposons 362 Types of Bacterial Transposons 364 Assays of Transposition 366 Mechanisms of Transposition 368 Genetic Requirements for Transposition of Tn3 368 A Molecular Model for Transposition of Tn3 372 Transposition by Tn / 0 and Tn5 373 Details of Transposition by the DDE Transposons 376 Details of the Mechanism of Transposition by Tn5 and Tn7 376 Rolling-Circle Transposons 378 Y and S Transposons 378 General Properties of Transposons 379 Target Site Specificity 379 Effects on Genes Adjacent to the Insertion Site 380 Regulation of Transposition 380 Target Immunity 381 Transposon Mutagenesis 382 Transposon Mutagenesis In Vivo 382 Transposon Mutagenesis In Vitro 382 Transposon Mutagenesis of Plasmids 385 Transposon Mutagenesis of the Bacterial Chromosome 386 Transposon Mutagenesis of All Bacteria 386 Using Transposon Mutagenesis To Make Random Gene Fusions 387 Site-Specific Recombination 387 Integrases 387 Resolvases 390 DNA Invertases 391 Y and S Recombinases 392 Y Recombinases: Mechanism 392 S Recombinases: Mechanism 397 Importance of Transposition and Site-Specific Recombination in Bacterial Adaptation 398 BOX 9.1 Transposons and Genomics 383 SUMMARY 399 QUESTIONS FOR THOUGHT 400 PROBLEMS 400 SUGGESTED READING 401 CHAPTER 10 Molecular Mechanisms of Homologous Recombination 403 Homologous Recombination and DNA Replication in Bacteria 404 Early Evidence for the Interdependence of Homologous Recombination and DNA Replication 404 The Molecular Basis for Recombination in E.coli 405 Chi (χ) Sites and the RecBCD Complex 405 The RecF Pathway 409 Synapse Formation and the RecA Protein 411 The Ruv and RecG Proteins and the Migration and Cutting of Holliday Junctions 414 CONTENTS xi Recombination between Different DNAs in Bacteria 416 How Are Linear DNA Fragments Recombined into the E. coli Chromosome? 417 Phage Recombination Pathways 417 Rec Proteins of Phages T4 and T7 417 The RecE Pathway of the rac Prophage 417 The Phage λ Red System 419 Recombineering: Gene Replacements in £. coli with Phage λ Recombination Functions 419 Genetic Analysis of Recombination in Bacteria 422 Isolating Rec~ Mutants of E. coli 422 Isolating Mutants with Mutations in Other Recombination Genes 423 Gene Conversion and Other Manifestations of Heteroduplex Formation during Recombination 426 BOX 10.1 Other Types of Double-Strand Break Repair in Bacteria 410 BOX 10.2 Breaking and Entering: Introns and Inteins Move by Double-Strand Break Repair or Retrohoming 425 SUMMARY 429 QUESTIONS FOR THOUGHT 430 PROBLEMS 430 SUGGESTED READING 431 CHAPTER Π DNA Repair and Mutagenesís 433 Evidence for DNA Repair 434 Specific Repair Pathways 435 Deamination of Bases 435 Damage Due to Reactive Oxygen 438 Damage Due to Alkylating Agents 441 Damage Due to UV Irradiation 443 General Repair Mechanisms 445 Base Analogs 445 Frameshift Mutagens 445 Methyl-Directed Mismatch Repair 445 Nucleotide Excision Repair 452 DNA Damage Tolerance Mechanisms 453 Homologous Recombination and DNA Replication 454 SOS-lnducible Repair 458 Mechanism of TLS by the Pol V Mutasome 463 Other Specialized Polymerases and Their Regulation 464 Summary of Repair Pathways in f . coli 466 Bacteriophage Repair Pathways 466 BOX 11.1 The Role of Reactive Oxygen Species in Cancer and Degenerative Diseases 439 BOX 11.2 DNA Repair and Cancer 449 BOX 11.3 The Ames Test 465 SUMMARY 468 QUESTIONS FOR THOUGHT 469 PROBLEMS 469 SUGGESTED READING 469 CHAPTER 12 Regulation of Gene Expression: Genes and Opérons 471 Transcriptional Regulation in Bacteria 472 Genetic Evidence for Negative and Positive Regulation 474 Negative Regulation of Transcription Initiation 474 Negative Inducible Systems 474 Negative Repressible Systems 484 Molecular Mechanisms of Transcriptional Repression 486 Positive Regulation of Transcription Initiation 487 Positive Inducible Systems 487 Positive Repressible Systems 496 Molecular Mechanisms of Transcriptional Activation 496 Regulation by Transcription Attenuation 497 Modulation of RNA Structure 497 Changes in Processivity of RNA Polymerase 506 Regulation of mRNA Degradation 507 Protein-Dependent Effects on RNA Stability 507 RNA-Dependent Effects on RNA Stability 508 Regulation of Translation 508 Regulation of Translation Initiation 509 xii CONTENTS Translational Regulation in the Exit Channel of the Ribosome 511 Regulation of Translation Termination 512 Posttranslational Regulation 514 Posttranslational Protein Modification 514 Regulation of Protein Turnover 514 Feedback Inhibition of Enzyme Activity 515 Why Are There So Many Mechanisms of Gene Regulation? 520 Operon Analysis for Sequenced Genomes 521 BOX 12.1 The Helix-Turn-Helix Motif of DNA-Binding Proteins 473 BOX 12.2 Families of Regulators 488 BOX 123 Special Problems in Genetic Analysis of Opérons 516 SUMMARY 521 QUESTIONS FOR THOUGHT 522 PROBLEMS 522 SUGGESTED READING 523 CHAPTER 13_____________________ Global Regulation: Régulons and Stimulons 525 Carbon Catabolite Regulation 526 Catabolite Regulation in £ coli: Catabolite Activator Protein (CAP) and cAMP 526 Carbon Catabolite Regulation in ß. subtilis: CcpA and Hpr 535 Regulation of Nitrogen Assimilation 536 Pathways for Nitrogen Assimilation 536 Regulation of Nitrogen Assimilation Pathways in £ coli by the Ntr System 537 Regulation of Nitrogen Assimilation in ß. subtilis 547 Regulation of Ribosome and tRNA Synthesis 547 Ribosomal Protein Gene Regulation 548 Regulation of rRNA and tRNA Synthesis 550 The Stringent Response 551 Stress Responses in Bacteria 554 Heat Shock Regulation 555 General Stress Response in Gram-Negative Bacteria 558 General Stress Response in Gram-Positive Bacteria 559 Extracytoplasmic (Envelope) Stress Responses 563 Iron Regulation in E. coli 568 The Fur Regulon 568 TheRyhBsRNA 569 The Aconitase Translational Repressor 570 Regulation of Virulence Genes in Pathogenic Bacteria 571 Diphtheria 572 Cholera and Quorum Sensing 572 Whooping Cough 578 From Genes to Régulons to Networks 579 BOX 13.1 cAMP-lndependent Carbon Catabolite Regulation in E. coli 529 BOX 13.2 A Bacterial Two-Hybrid System Based on Adenylate Cyclase 531 BOX 13.3 Nitrogen Fixation 537 BOX 13.4 Signal Transduction Systems in Bacteria 539 BOX 13.5 Sigma Factors 542 BOX 13.6 Regulatory RNAs 560 BOX 13.7 Tools for Studying Global Regulation 571 SUMMARY 580 QUESTIONS FOR THOUGHT 582 PROBLEMS 582 SUGGESTED READING 582 CHAPTER 14 Bacterial Cell Biology and Development 585 Membrane Proteins and Protein Export 585 The Translocase System 586 The Signal Sequence 586 The Targeting Factors 588 The Tat Secretion Pathway 590 Disulfide Bonds 590 Use of mal-lac Fusions To Study Protein Transport in £ coli 591 Genetic Analysis of Transmembrane Domains of Inner Membrane Proteins in Gram-Negative Bacteria 594 Identification of Genes for Inner Membrane Proteins by Random phoA Fusions 595 CONTENTS xiii Protein Secretion 595 Protein Secretion Systems in Gram-Negative Bacteria 595 Protein Secretion in Gram-Positive Bacteria 602 Sortases 603 Bacterial Cell Biology and the Cell Cycle 605 The Bacterial Cell Wall 606 Septum Formation 615 The FtsZ Protein and the Šeptal Ring 616 Regulation of FtsZ Ring Formation in С crescentus 619 Genetic Analysis of Sporulation in ß. subtilis 621 Identification of Genes That Regulate Sporulation 622 Regulation of Initiation of Sporulation 623 Compartmentalized Regulation of Sporulation Genes 627 Analysis of the Role of Sigma Factors in Sporulation Regulation 627 Intercompartmental Regulation during Development 630 Finding Sporulation Genes: Mutant Hunts, Suppressor Analysis, and Functional Genomics 635 BOX 14.1 Secretion Systems and Motility 599 BOX 14.2 Example of a Sortase-Dependent Pathway: Sporulation in 5. coelicolor 605 BOX 14.3 Evolutionary Origin of the Eukaryotic Cytoskeleton 612 BOX 14.4 Phosphorelay Activation of the Transcription Factor SpoOA 625 SUMMARY 636 QUESTIONS FOR THOUGHT 637 PROBLEMS 637 SUGGESTED READING 638 Answers to Problems and Questions for Thought 641 Glossary 655 Figure and Table Credits 685 Index 689
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illustrated Illustrated
indexdate 2024-11-25T17:37:10Z
institution BVB
isbn 1555816274
9781555816278
language English
oai_aleph_id oai:aleph.bib-bvb.de:BVB01-025306442
oclc_num 815945016
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owner DE-20
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physical XX, 707 S. Ill., graph. Darst.
publishDate 2013
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publisher ASM Press
record_format marc
spellingShingle Molecular genetics of bacteria Larry Snyder ...
Gentechnologie (DE-588)4071722-7 gnd
Bakteriophagen (DE-588)4125508-2 gnd
Bakterien (DE-588)4004296-0 gnd
Molekulargenetik (DE-588)4039987-4 gnd
subject_GND (DE-588)4071722-7
(DE-588)4125508-2
(DE-588)4004296-0
(DE-588)4039987-4
title Molecular genetics of bacteria Larry Snyder ...
title_auth Molecular genetics of bacteria Larry Snyder ...
title_exact_search Molecular genetics of bacteria Larry Snyder ...
title_full Molecular genetics of bacteria Larry Snyder ...
title_fullStr Molecular genetics of bacteria Larry Snyder ...
title_full_unstemmed Molecular genetics of bacteria Larry Snyder ...
title_short Molecular genetics of bacteria
title_sort molecular genetics of bacteria larry snyder
title_sub Larry Snyder ...
topic Gentechnologie (DE-588)4071722-7 gnd
Bakteriophagen (DE-588)4125508-2 gnd
Bakterien (DE-588)4004296-0 gnd
Molekulargenetik (DE-588)4039987-4 gnd
topic_facet Gentechnologie
Bakteriophagen
Bakterien
Molekulargenetik
url http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025306442&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA
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