Snyder and Champness Molecular Genetics of Bacteria

ISBN-13: 9781555819750 / Angielski / Twarda / 2020 / 640 str.

Tina M. Henkin; Joseph E. Peters

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Preface xvAcknowledgments xixAbout the Authors 1Introduction 3The Biological Universe 5The Bacteria 5The Archaea 7The Eukaryotes 7What is Genetics? 8Bacterial Genetics 8Bacteria Are Haploid 9Short Generation Times 9Asexual Reproduction 9Colony Growth on Agar Plates 9Colony Purification 9Serial Dilutions 9Selections 10Storing Stocks of Bacterial Strains 10Genetic Exchange 10Phage Genetics 10Phages Are Haploid 11Selectionswith Phages 11Crosses with Phages 11A Brief History of Bacterial Molecular Genetics 11Inheritance in Bacteria 11Transformation 11Conjugation 12Transduction 12Recombination within Genes 12Semiconservative DNA Replication 12mRNA 12The Genetic Code 12The Operon Model 12Enzymes for Molecular Biology 12Synthetic Genomics 13What is Ahead 131 The Bacterial Chromosome: DNA Structure, Replication, and Segregation 17DNA Structure 17The Deoxyribonucleotides 17The DNA Chain 18The 5' and 3' Ends 18Base Pairing 20Antiparallel Construction 20The Major and Minor Grooves 21The Mechanism of DNA Replication 21Deoxyribonucleotide Precursor Synthesis 21Replication of the Bacterial Chromosome 21Replication of Double- Stranded DNA 26Replication Errors 30Editing 30RNA Primers and Editing 31Impediments to DNA Replication 31Damaged DNA and DNA Polymerase III 31Mechanisms To Deal with Impediments on Template DNA Strands 32Physical Blocks to Replication Forks 32Replication of the Bacterial Chromosome and Cell Division 32Structure of Bacterial Chromosomes 34Replication of the Bacterial Chromosome 34Initiation of Chromosome Replication 34RNA Priming of Initiation 35Termination of Chromosome Replication 35Chromosome Segregation 37Coordination of Cell Division with Replication of the Chromosome 47Timing of Initiation of Replication 49The Bacterial Nucleoid 51Supercoiling in the Nucleoid 51Topoisomerases 52The Bacterial Genome 55Box 1.1 Structural Features of Bacterial Genomes 37Box 1.2 Antibiotics That Affect Replication and DNA Structure 542 Bacterial Gene Expression: Transcription, Translation, Protein Folding, and Localization 61Overview 61The Structure and Function of RNA 62Types of RNA 62RNA Precursors 62RNA Structure 62RNA Processing and Modification 64Transcription 64Structure of Bacterial RNA Polymerase 64Overview of Transcription 65Details of Transcription 67rRNAs and tRNAs 74RNA Degradation 77RNases 77The Structure and Function of Proteins 78Protein Structure 78Translation 80Structure of the Bacterial Ribosome 80Overview of Translation 83Details of Protein Synthesis 84The Genetic Code 92Polycistronic mRNA 96Protein Folding and Degradation 98Protein Chaperones 98Protein Degradation 101Protein Localization 101The Translocase System 101The Signal Sequence 103The Targeting Factors 103The Tat Secretion Pathway 104Disulfide Bonds 105Protein Secretion and Export 105Protein Secretion Systems in Bacteria with an Outer Membrane 106Protein Secretion in Bacteria That Lack an Outer Membrane 110Sortases 110Regulation of Gene Expression 111Transcriptional Regulation 112Posttranscriptional Regulation 113What You Need To Know 114Open Reading Frames 115Transcriptional and Translational Fusions 115Box 2.1 Antibiotic Inhibitors of Transcription 72Box 2.2 Molecular Phylogeny 75Box 2.3 Antibiotic Inhibitors of Translation 81Box 2.4 Mimicry in Translation 91Box 2.5 Exceptions to the Code 943 Bacterial Genetic Analysis: Fundamentals and Current Approaches 123Definitions 123Terms Used in Genetics 123Genetic Names 124Auxotrophic and Catabolic Mutants 125Conditional- Lethal Mutants 126Resistant Mutants 128Inheritance in Bacteria 128The Luria and Delbrück Experiment 129Mutants Are Clonal 130Esther and Joshua Lederberg's Experiment 130Mutation Rates 132Calculating Mutation Rates 133Calculating the Mutation Rate from the Rate of Increase in the Proportion of Mutants 135Types of Mutations 136Properties of Mutations 136Base Pair Changes 136Frameshift Mutations 140Deletion Mutations 141Tandem- Duplication Mutations 143Inversion Mutations 144Insertion Mutations 145Reversion versus Suppression 147Intragenic Suppressors 147Intergenic Suppressors 147Genetic Analysis in Bacteria 151Isolating Mutants 151Genetic Characterization of Mutants 155Complementation Tests 160Genetic Crosses in Bacteria 166Mapping of Bacterial Markers by Transduction and Transformation 168Other Uses of Transformation and Transduction 171Genetic Mapping by Hfr Crosses 172Perspective 176Box 3.1 Inversions and the Genetic Map 1464 Plasmids 181What is a Plasmid? 181Naming Plasmids 182Functions Encoded by Plasmids 182Plasmid Structure 183Properties of Plasmids 184Replication 184Functions of the ori Region 187Plasmid Replication Control Mechanisms 193Mechanisms To Prevent Curing of Plasmids 200The Par Systems of Plasmids 203Plasmid Cloning Vectors 206Examples of Plasmid Cloning Vectors 208Broad- Host- Range Cloning Vectors 210Box 4.1 Linear Chromosomes and Plasmids in Bacteria 188Box 4.2 Determining the Inc Group 191Box 4.3 Toxin- Antitoxin Systems and Plasmid Maintenance 2015 Conjugation 215Overview 215Classification of Self- Transmissible Plasmids and Integrating Elements 217The Fertility Plasmid 217Mechanism of DNA Transfer during Conjugation in Proteobacteria 218Transfer (tra) Genes 218The oriT Sequence 221Efficiency of Transfer 222Interspecies Transfer of Plasmids 225Conjugation and Type IV Secretion Systems Capable of Translocating Proteins 225Mobilizable Plasmids 229Chromosome Transfer by Plasmids 230Formation of Hfr Strains of E. coli 230Transfer of Chromosomal DNA by Integrated Plasmids 230Chromosome Mobilization 231Prime Factors 231Diversity in Transfer Systems 233Integrating Conjugative Elements 234SXT/R391 ICE 234ICEBs1 236Tn916 237TnGBS1 and TnGBS2 240Box 5.1 Pilus- Specific Phages 220Box 5.2 Delivery of Conditional Plasmids by Conjugation 223Box 5.3 Gene Exchange between Domains 226Box 5.4 Conjugation and Synthetic Genomics 2326 Transformation 245Natural Transformation 246Discovery of Transformation 246Overview of Natural Transformation 247DNA Uptake Mechanisms 247Specificity of DNA Uptake 251DNA Pro cessing after Uptake 253Natural Transformation as a Tool 253Regulation of Natural Competence 254Identification of Competence in Other Organisms 258Role of Natural Transformation 258Artificially Induced Competence 260Chemical Induction 260Electroporation 261Protoplast Transformation 261Box 6.1 Experimental Measurements of DNA Uptake 248Box 6.2 Genetic Evidence for Single- Stranded DNA Uptake 252Box 6.3 Role of Natural Transformation in Pathogens 2607 Bacteriophages and Transduction 265Lytic Development 268The Lytic Cycle 268Transcriptional Regulation of Phage Gene Expression 268Phage Genome Replication and Packaging 279Host Cell Lysis 289Lysogenic Development 292The lambda System 292Other Lysogenic Systems 299Genetic Analysis of Phages 302Infection of Cells 302Phage Crosses 303Recombination and Complementation Tests with Phages 303The Genetic- Linkage Map of a Phage 305Phage- Mediated Genetic Transfer 306Generalized Transduction 306Specialized Transduction 308Lysogenic Conversion and Bacterial Pathogenesis 310Host Defenses Against Phage Infection 313Restriction- Modification Systems 313Abi Systems 313CRISPR/Cas Systems 314Small Molecules and Phage Defense 314Phage versus Phage 314Phages as Tools 315Cloning Vectors 315Phage Display 315Phage Therapy 317Box 7.1 Phage Genomics 266Box 7.2 Phage T7- Based Tools 271Box 7.3 Protein Priming 2858 Transposition, Site- Specific Recombination, and Families of Recombinases 321Transposition 321Overview of Transposition 322Structure of Bacterial DNA Transposons 322Types of Bacterial DNA Transposons 323Assays of Transposition 326Mechanisms of Transposition 328DDE Transposons 328HUH Transposons 332General Properties of Transposons 334Transposition Regulation 334Target Site Specificity 335Effects on Genes Adjacent to the Insertion Site 337Target Immunity 337Transposon Mutagenesis 337Transposon Mutagenesis In Vivo 339Transposon Mutagenesis In Vitro 340Transposon Mutagenesis of Plasmids 341Transposon Mutagenesis of the Bacterial Chromosome 341Transposon Mutagenesis of All Bacteria 342Using Transposon Mutagenesis To Make Random Gene Fusions 342Site- Specific Recombination 343Integrases 343Resolvases 345DNA Invertases 345Y and S Recombinases 347Y Recombinases: Mechanism 347S Recombinases: Mechanism 351Group II Mobile Introns: Elements That Move Using an RNA Intermediate 352Importance of Transposition and Site- Specific Recombination in Bacterial Adaptation 354Box 8.1 Mobile Elements and DNA Replication 333Box 8.2 Transposons and Genomics 3389 Molecular Mechanisms of Homologous Recombination 359Homologous Recombination and DNA Replication in Bacteria 360Early Evidence for the Interdependence of Homologous Recombination and DNA Replication 361The Molecular Basis for Recombination in E. coli 361chi (chi) Sites and the RecBCD Complex 361The RecF Pathway 367Synapse Formation and the RecA Protein 368The Ruv and RecG Proteins and the Migration and Cutting of Holliday Junctions 371Recombination between Different DNAs in Bacteria 373How Are Linear DNA Fragments Recombined into the E. coli Chromosome? 373Recombination during Natural Transformation 375Phage Recombination Pathways 375Rec Proteins of Phages T4 and T7 375The RecE Pathway of the rac Prophage 375The Phage lambda Red System 375Recombineering: Gene Replacements in E. coli with Phage lambda Recombination Functions 376Gene Conversion and Other Manifestations of Heteroduplex Formation during Recombination 379Box 9.1 Discovery of chi sites 364Box 9.2 Other Types of Double- Strand Break Repair in Bacteria 36510 DNA Repair and Mutagenesis 385Evidence for DNA Repair 386Specific Repair Pathways 387Deamination of Bases 387Damage Due to Reactive Oxygen 389Damage Due to Alkylating Agents 393Damage Due to UV Irradiation 395General Repair Mechanisms 396Base Analogs 396Frameshift Mutagens 397Mismatch Repair 398Nucleotide Excision Repair 403DNA Damage Tolerance Mechanisms 405Homologous Recombination and DNA Replication 405SOS- Inducible Repair 409Mechanism of TLS by the Pol V Mutasome 416Other Specialized Polymerases and Their Regulation 417Summary of Repair Pathways in E. coli 418Bacteriophage Repair Pathways 418Box 10.1 The Role of Reactive Oxygen Species in Cancer and Degenerative Diseases 391Box 10.2 DNA Repair and Cancer 401Box 10.3 The Ames Test 41711 Regulation of Gene Expression: Genes and Operons 425Transcriptional Regulation in Bacteria 426Genetic Evidence for Negative and Positive Regulation 427Negative Regulation of Transcription Initiation 428Negative Inducible Systems 428Negative Repressible Systems 437Molecular Mechanisms of Transcriptional Repression 439Positive Regulation of Transcription Initiation 439Positive Inducible Systems 440Positive Repressible Systems 447Molecular Mechanisms of Transcriptional Activation 447Regulation by Transcription Attenuation 449Modulation of RNA Structure 449Changes in Processivity of RNA Polymerase 459Regulation of mRNA Degradation 460Protein- Dependent Effects on RNA Stability 460RNA- Dependent Effects on RNA Stability 461Regulation of Translation 461Regulation of Translation Initiation 462Translational Regulation in the Exit Channel of the Ribosome 464Regulation of Translation Termination 465Posttranslational Regulation 467Posttranslational Protein Modification 467Regulation of Protein Turnover 467Feedback Inhibition of Enzyme Activity 468Why Are There So Many Mechanisms of Gene Regulation? 469Box 11.1 The Helix- Turn- Helix Motif of DNA- Binding Proteins 427Box 11.2 Families of Regulators 44212 Global Regulation: Regulons and Stimulons 473Carbon Catabolite Regulation 474Carbon Catabolite Regulation in E. coli: Catabolite Activator Protein (CAP) and cAMP 474Carbon Catabolite Regulation in B. subtilis: CcpA and Hpr 481Regulation of Nitrogen Assimilation 482Pathways for Nitrogen Assimilation 483Regulation of Nitrogen Assimilation Pathways in E. coli by the Ntr System 484Regulation of Nitrogen Assimilation in B. subtilis 491Regulation of Ribosome Components and tRNA Synthesis 491Ribosomal Protein Gene Regulation 492Regulation of rRNA and tRNA Synthesis 493Stringent Response 494Stress Responses in Bacteria 498Heat Shock Regulation 498General Stress Response in Enteric Bacteria 501General Stress Response in Firmicutes 505Extracytoplasmic (Envelope) Stress Responses 506Iron Regulation in E. coli 510The Fur Regulon 510The RyhB sRNA 512The Aconitase Translational Repressor 512Regulation of Virulence Genes in Pathogenic Bacteria 513Diphtheria 513Cholera and Quorum Sensing 514Whooping Cough 519Developmental Regulation: Sporulation in B. subtilis 520Identification of Genes That Regulate Sporulation 522Regulation of Sporulation Initiation 522Compartmentalized Regulation of Sporulation Genes 524The Role of Sigma Factors in Sporulation Regulation 524Intercompartmental Regulation during Development 525Other Sporulation Systems 529Box 12.1 cAMP-Independent Carbon Catabolite Regulation in E. coli 477Box 12.2 Nitrogen Fixation 483Box 12.3 Signal Transduction Systems in Bacteria 486Box 12.4 Sigma Factors 488Box 12.5 Regulatory RNAs 50313 Genomes and Genomic Analysis 535The Bacterial Genome 535DNA Sequencing 537Advanced Genome-Sequencing Techniques 545Polymerase Chain Reaction 547Barriers to Horizontal Transfer: Genome Gatekeepers and Molecular Biologist's Toolkit 549Restriction Endonucleases 549Techniques for Nontraditional Cloning and Assembly 553CRISPR/Cas Systems 559Final Thoughts 568Box 13.1 Annotation and Comparative Genomics 538Box 13.2 Special Problems in Genetic Analysis of Operons 542Box 13.3 Synthesizing and Cloning Complete Bacterial Genomes 560Glossary 573Index 599

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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.