Snyder and Champness Molecular Genetics of Bacteria, 5th edition

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 Cover Title Page Copyright Contents Preface Acknowledgments About the Authors Introduction The Biological Universe The Bacteria The Archaea The Eukaryotes What Is Genetics? Bacterial Genetics Bacteria Are Haploid Short Generation Times Asexual Reproduction Colony Growth on Agar Plates Colony Purification Serial Dilutions Selections Storing Stocks of Bacterial Strains Genetic Exchange Phage Genetics Phages Are Haploid Selections with Phages Crosses with Phages A Brief History of Bacterial Molecular Genetics Inheritance in Bacteria Transformation Conjugation Transduction Recombination within Genes Semiconservative DNA Replication mRNA The Genetic Code The Operon Model Enzymes for Molecular Biology Synthetic Genomics What Is Ahead 1 The Bacterial Chromosome: DNA Structure, Replication, and Segregation DNA Structure The Deoxyribonucleotides The DNA Chain The 5' and 3' Ends Base Pairing Antiparallel Construction The Major and Minor Grooves The Mechanism of DNA Replication Deoxyribonucleotide Precursor Synthesis Replication of the Bacterial Chromosome Replication of Double-Stranded DNA Replication Errors Editing RNA Primers and Editing Impediments to DNA Replication Damaged DNA and DNA Polymerase III Mechanisms To Deal with Impediments on Template DNA Strands Physical Blocks to Replication Forks Replication of the Bacterial Chromosome and Cell Division Structure of Bacterial Chromosomes Replication of the Bacterial Chromosome Initiation of Chromosome Replication RNA Priming of Initiation Termination of Chromosome Replication Chromosome Segregation Coordination of Cell Division with Replication of the Chromosome Timing of Initiation of Replication The Bacterial Nucleoid Supercoiling in the Nucleoid Topoisomerases The Bacterial Genome BOX 1.1 Structural Features of Bacterial Genomes BOX 1.2 Antibiotics That Affect Replication and DNA Structure 2 Bacterial Gene Expression: Transcription, Translation, Protein Folding, and Localization Overview The Structure and Function of RNA Types of RNA RNA Precursors RNA Structure RNA Processing and Modification Transcription Structure of Bacterial RNA Polymerase Overview of Transcription Details of Transcription rRNAs and tRNAs RNA Degradation RNases The Structure and Function of Proteins Protein Structure Translation Structure of the Bacterial Ribosome Overview of Translation Details of Protein Synthesis The Genetic Code Polycistronic mRNA Protein Folding and Degradation Protein Chaperones Protein Degradation Protein Localization The Translocase System The Signal Sequence The Targeting Factors The Tat Secretion Pathway Disulfide Bonds Protein Secretion and Export Protein Secretion Systems in Bacteria with an Outer Membrane Protein Secretion in Bacteria That Lack an Outer Membrane Sortases Regulation of Gene Expression Transcriptional Regulation Posttranscriptional Regulation What You Need To Know Open Reading Frames Transcriptional and Translational Fusions BOX 2.1 Antibiotic Inhibitors of Transcription BOX 2.2 Molecular Phylogeny BOX 2.3 Antibiotic Inhibitors of Translation BOX 2.4 Mimicry in Translation BOX 2.5 Exceptions to the Code 3 Bacterial Genetic Analysis: Fundamentals and Current Approaches Definitions Terms Used in Genetics Genetic Names Auxotrophic and Catabolic Mutants Conditional-Lethal Mutants Resistant Mutants Inheritance in Bacteria The Luria and Delbrück Experiment Mutants Are Clonal Esther and Joshua Lederberg's Experiment Mutation Rates Calculating Mutation Rates Calculating the Mutation Rate from the Rate of Increase in the Proportion of Mutants Types of Mutations Properties of Mutations Base Pair Changes Frameshift Mutations Deletion Mutations Tandem-Duplication Mutations Inversion Mutations Insertion Mutations Reversion versus Suppression Intragenic Suppressors Intergenic Suppressors Genetic Analysis in Bacteria Isolating Mutants Genetic Characterization of Mutants Complementation Tests Genetic Crosses in Bacteria Mapping of Bacterial Markers by Transduction and Transformation Other Uses of Transformation and Transduction Genetic Mapping by Hfr Crosses Perspective BOX 3.1 Inversions and the Genetic Map 4 Plasmids What Is a Plasmid? Naming Plasmids Functions Encoded by Plasmids Plasmid Structure Properties of Plasmids Replication Functions of the ori Region Plasmid Replication Control Mechanisms Mechanisms To Prevent Curing of Plasmids The Par Systems of Plasmids Plasmid Cloning Vectors Examples of Plasmid Cloning Vectors Broad-Host-Range Cloning Vectors BOX 4.1 Linear Chromosomes and Plasmids in Bacteria BOX 4.2 Determining the Inc Group BOX 4.3 Toxin-Antitoxin Systems and Plasmid Maintenance 5 Conjugation Overview Classification of Self-Transmissible Plasmids and Integrating Elements The Fertility Plasmid Mechanism of DNA Transfer during Conjugation in Proteobacteria Transfer (tra) Genes The oriT Sequence Efficiency of Transfer Interspecies Transfer of Plasmids Conjugation and Type IV Secretion Systems Capable of Translocating Proteins Mobilizable Plasmids Chromosome Transfer by Plasmids Formation of Hfr Strains of E. coli Transfer of Chromosomal DNA by Integrated Plasmids Chromosome Mobilization Prime Factors Diversity in Transfer Systems Integrating Conjugative Elements SXT/R391 ICE ICEBs1 Tn916 TnGBS1 and TnGBS2 BOX 5.1 Pilus-Specific Phages BOX 5.2 Delivery of Conditional Plasmids by Conjugation BOX 5.3 Gene Exchange between Domains BOX 5.4 Conjugation and Synthetic Genomics 6 Transformation Natural Transformation Discovery of Transformation Overview of Natural Transformation DNA Uptake Mechanisms Specificity of DNA Uptake DNA Processing after Uptake Natural Transformation as a Tool Regulation of Natural Competence Identification of Competence in Other Organisms Role of Natural Transformation Artificially Induced Competence Chemical Induction Electroporation Protoplast Transformation BOX 6.1 Experimental Measurements of DNA Uptake BOX 6.2 Genetic Evidence for Single-Stranded DNA Uptake BOX 6.3 Role of Natural Transformation in Pathogens 7 Bacteriophages and Transduction Lytic Development The Lytic Cycle Transcriptional Regulation of Phage Gene Expression Phage Genome Replication and Packaging Host Cell Lysis Lysogenic Development The λ System Other Lysogenic Systems Genetic Analysis of Phages Infection of Cells Phage Crosses Recombination and Complementation Tests with Phages The Genetic-Linkage Map of a Phage Phage-Mediated Genetic Transfer Generalized Transduction Specialized Transduction Lysogenic Conversion and Bacterial Pathogenesis Host Defenses Against Phage Infection Restriction-Modification Systems Abi Systems CRISPR/Cas Systems Small Molecules and Phage Defense Phage versus Phage Phages as Tools Cloning Vectors Phage Display Phage Therapy BOX 7.1 Phage Genomics BOX 7.2 Phage T7-Based Tools BOX 7.3 Protein Priming 8 Transposition, Site-Specific Recombination, and Families of Recombinases Transposition Overview of Transposition Structure of Bacterial DNA Transposons Types of Bacterial DNA Transposons Assays of Transposition Mechanisms of Transposition DDE Transposons HUH Transposons General Properties of Transposons Transposition Regulation Target Site Specificity Effects on Genes Adjacent to the Insertion Site Target Immunity Transposon Mutagenesis Transposon Mutagenesis In Vivo Transposon Mutagenesis In Vitro Transposon Mutagenesis of Plasmids Transposon Mutagenesis of the Bacterial Chromosome Transposon Mutagenesis of All Bacteria Using Transposon Mutagenesis To Make Random Gene Fusions Site-Specific Recombination Integrases Resolvases DNA Invertases Y and S Recombinases Y Recombinases: Mechanism S Recombinases: Mechanism Group II Mobile Introns: Elements That Move Using an RNA Intermediate Importance of Transposition and Site-Specific Recombination in Bacterial Adaptation BOX 8.1 Mobile Elements and DNA Replication BOX 8.2 Transposons and Genomics 9 Molecular Mechanisms of Homologous Recombination Homologous Recombination and DNA Replication in Bacteria Early Evidence for the Interdependence of Homologous Recombination and DNA Replication The Molecular Basis for Recombination in E. coli chi (χ) Sites and the RecBCD Complex The RecF Pathway Synapse Formation and the RecA Protein The Ruv and RecG Proteins and the Migration and Cutting of Holliday Junctions Recombination between Different DNAs in Bacteria How Are Linear DNA Fragments Recombined into the E. coli Chromosome? Recombination during Natural Transformation Phage Recombination Pathways Rec Proteins of Phages T4 and T7 The RecE Pathway of the rac Prophage The Phage λ Red System Recombineering: Gene Replacements in E. coli with Phage λ Recombination Functions Gene Conversion and Other Manifestations of Heteroduplex Formation during Recombination BOX 9.1 Discovery of x sites BOX 9.2 Other Types of Double-Strand Break Repair in Bacteria 10 DNA Repair and Mutagenesis Evidence for DNA Repair Specific Repair Pathways Deamination of Bases Damage Due to Reactive Oxygen Damage Due to Alkylating Agents Damage Due to UV Irradiation General Repair Mechanisms Base Analogs Frameshift Mutagens Mismatch Repair Nucleotide Excision Repair DNA Damage Tolerance Mechanisms Homologous Recombination and DNA Replication SOS-Inducible Repair Mechanism of TLS by the Pol V Mutasome Other Specialized Polymerases and Their Regulation Summary of Repair Pathways in E. coli Bacteriophage Repair Pathways BOX 10.1 The Role of Reactive Oxygen Species in Cancer and Degenerative Diseases BOX 10.2 DNA Repair and Cancer BOX 10.3 The Ames Test 11 Regulation of Gene Expression: Genes and Operons Transcriptional Regulation in Bacteria Genetic Evidence for Negative and Positive Regulation Negative Regulation of Transcription Initiation Negative Inducible Systems Negative Repressible Systems Molecular Mechanisms of Transcriptional Repression Positive Regulation of Transcription Initiation Positive Inducible Systems Positive Repressible Systems Molecular Mechanisms of Transcriptional Activation Regulation by Transcription Attenuation Modulation of RNA Structure Changes in Processivity of RNA Polymerase Regulation of mRNA Degradation Protein-Dependent Effects on RNA Stability RNA-Dependent Effects on RNA Stability Regulation of Translation Regulation of Translation Initiation Translational Regulation in the Exit Channel of the Ribosome Regulation of Translation Termination Posttranslational Regulation Posttranslational Protein Modification Regulation of Protein Turnover Feedback Inhibition of Enzyme Activity Why Are There So Many Mechanisms of Gene Regulation? BOX 11.1 The Helix-Turn-Helix Motif of DNA-Binding Proteins BOX 11.2 Families of Regulators 12 Global Regulation: Regulons and Stimulons Carbon Catabolite Regulation Carbon Catabolite Regulation in E. coli: Catabolite Activator Protein (CAP) and cAMP Carbon Catabolite Regulation in B. subtilis: CcpA and Hpr Regulation of Nitrogen Assimilation Pathways for Nitrogen Assimilation Regulation of Nitrogen Assimilation Pathways in E. coli by the Ntr System Regulation of Nitrogen Assimilation in B. subtilis Regulation of Ribosome Components and tRNA Synthesis Ribosomal Protein Gene Regulation Regulation of rRNA and tRNA Synthesis Stringent Response Stress Responses in Bacteria Heat Shock Regulation General Stress Response in Enteric Bacteria General Stress Response in Firmicutes Extracytoplasmic (Envelope) Stress Responses Iron Regulation in E. coli The Fur Regulon The RyhB sRNA The Aconitase Translational Repressor Regulation of Virulence Genes in Pathogenic Bacteria Diphtheria Cholera and Quorum Sensing Whooping Cough Developmental Regulation: Sporulation in B. subtilis Identification of Genes That Regulate Sporulation Regulation of Sporulation Initiation Compartmentalized Regulation of Sporulation Genes The Role of Sigma Factors in Sporulation Regulation Intercompartmental Regulation during Development Other Sporulation Systems BOX 12.1 cAMP-Independent Carbon Catabolite Regulation in E. coli BOX 12.2 Nitrogen Fixation BOX 12.3 Signal Transduction Systems in Bacteria BOX 12.4 Sigma Factors BOX 12.5 Regulatory RNAs 13 Genomes and Genomic Analysis The Bacterial Genome DNA Sequencing Advanced Genome-Sequencing Techniques Polymerase Chain Reaction Barriers to Horizontal Transfer: Genome Gatekeepers and Molecular Biologist's Toolkit Restriction Endonucleases Techniques for Nontraditional Cloning and Assembly CRISPR/Cas Systems Final Thoughts BOX 13.1 Annotation and Comparative Genomics BOX 13.2 Special Problems in Genetic Analysis of Operons BOX 13.3 Synthesizing and Cloning Complete Bacterial Genomes Glossary Index EULA 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 WashingtonWatch an interview with the authors as they discuss their book further: https://www.youtube.com/watch?v=NEl-dfatWUU 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 eld 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 elds 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 While intended as an undergraduate or beginning graduate textbook, Molecular Genetics of Bacteria is an invaluable reference for anyone working in the elds 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 gures make it ideal for use in teaching bacterial molecular genetics." Caroline Harwood , University of Washington Watch an interview with the authors as they discuss their book The Science Of Molecular Genetics Began With The Determination Of The Structure Of Dna. Experiments With Bacteria And Phages (i.e., Viruses That Infect Bacteria) In The Late 1940s And Early 1950s, As Well As The Presence Of Dna In Chromosomes Of Higher Organisms, Had Implicated This Macromolecule As The Hereditary Material (see The Introduction). In The 1930s, Biochemical Studies Of The Base Composition Of Dna By Erwin Chargaff Established That The Amount Of Guanine Always Equals The Amount Of Cytosine And That The Amount Of Adenine Always Equals The Amount Of Thymine, Independent Of The Total Base Composition Of The Dna. In The Early 1950s, X-ray Diffraction Studies By Rosalind Franklin And Maurice Wilkins Showed That Dna Is A Double Helix. Finally, In 1953, Francis Crick And James Watson Put Together The Chemical And X-ray Diffraction Information In Their Famous Model Of The Structure Of Dna. This Story Is One Of The Most Dramatic In The History Of Science And Has Been The Subject Of Many Historical Treatments, Some Of Which Are Listed At The End Of This Chapter--