| |
| |
| Introduction | |
| |
| |
| The Biological Universe | |
| |
| |
| What Is Genetics? | |
| |
| |
| Bacterial Genetics | |
| |
| |
| Phage Genetics | |
| |
| |
| A Brief History of Bacterial Molecular Genetics | |
| |
| |
| What's Ahead | |
| |
| |
| |
| The Bacterial Chromosome: DNA Structure, Replication, and Segregation | |
| |
| |
| DNA Structure | |
| |
| |
| The Mechanism of DNA Replication | |
| |
| |
| Replication Errors | |
| |
| |
| Replication of the Bacterial Chromosome and Cell Division | |
| |
| |
| The Bacterial Nucleoid | |
| |
| |
| The Bacterial Genome | |
| |
| |
| Antibiotics That Affect Replication and DNA Structure | |
| |
| |
| Molecular Biology Manipulations with DNA | |
| |
| |
| |
| Linear Chromosomes in Bacteria | |
| |
| |
| |
| Restarting Replication Forks | |
| |
| |
| |
| The Bacterial Cytoskeleton and Bacterial Cell Biology | |
| |
| |
| |
| Features of Bacterial Genomes | |
| |
| |
| |
| Bacterial Genome Sequencing | |
| |
| |
| |
| Bacterial Gene Expression: Transcription, Translation, and Protein Folding | |
| |
| |
| Overview | |
| |
| |
| The Structure and Function of RNA | |
| |
| |
| Transcription | |
| |
| |
| Proteins | |
| |
| |
| Protein Folding | |
| |
| |
| Membrane Proteins and Protein Export | |
| |
| |
| Introns and Inteins | |
| |
| |
| Useful Concepts | |
| |
| |
| Antibiotics That Block Transcription and Translation | |
| |
| |
| |
| Molecular Phylogeny | |
| |
| |
| |
| Mimicry in Translation | |
| |
| |
| |
| Exceptions to the Code | |
| |
| |
| |
| Traffic Jams on mRNA: Removing Stalled Ribosomes with tmRNA | |
| |
| |
| |
| Stability and Degradation of mRNA | |
| |
| |
| |
| Selfish DNAs: RNA Introns and Protein Inteins | |
| |
| |
| |
| Annotation and Comparative Genomics | |
| |
| |
| |
| Bacterial Genetic Analysis: Forward and Reverse | |
| |
| |
| Definitions | |
| |
| |
| Useful Phenotypes in Bacterial Genetics | |
| |
| |
| Inheritance in Bacteria | |
| |
| |
| Mutation Rates | |
| |
| |
| Types of Mutations | |
| |
| |
| Reversion versus Suppression | |
| |
| |
| Genetic Analysis in Bacteria | |
| |
| |
| Gene Replacements and Reverse Genetics | |
| |
| |
| Isolation of Tandem Duplications of the his Operon in Salmonella enterica Serovar Typhimurium | |
| |
| |
| |
| Statistical Analysis of the Number of Mutants per Culture | |
| |
| |
| |
| Inversions and the Genetic Map | |
| |
| |
| |
| Plasmids | |
| |
| |
| What Is a Plasmid? | |
| |
| |
| Properties of Plasmids | |
| |
| |
| Constructing a Plasmid Cloning Vector | |
| |
| |
| |
| Plasmids and Bacterial Pathogenesis | |
| |
| |
| |
| Linear Plasmids | |
| |
| |
| |
| An Incompatibility Group of One's Own | |
| |
| |
| |
| Plasmid Addiction | |
| |
| |
| |
| Conjugation | |
| |
| |
| Overview | |
| |
| |
| Mechanism of DNA Transfer during Conjugation in Gram-Negative Bacteria | |
| |
| |
| Chromosome Transfer by Plasmids | |
| |
| |
| Transfer Systems of Gram-Positive Bacteria | |
| |
| |
| Other Types of Transmissible Elements | |
| |
| |
| |
| Gene Exchange between Kingdoms | |
| |
| |
| |
| Conjugation and Type IV Protein Secretion Systems | |
| |
| |
| |
| Conjugation in Streptomycetes | |
| |
| |
| |
| Conjugative Transposons (Integrating Conjugative Elements) | |
| |
| |
| |
| Transformation | |
| |
| |
| Natural Transformation | |
| |
| |
| Importance of Natural Transformation for Forward and Reverse Genetics | |
| |
| |
| Artificially Induced Competence | |
| |
| |
| |
| Antigenic Variation in Neisseria gonorrhoeae | |
| |
| |
| |
| Lytic Bacteriophages: Development, Genetics, and Generalized Transduction | |
| |
| |
| The Bacteriophage Lytic Development Cycle | |
| |
| |
| Phage DNA Replication | |
| |
| |
| Phage Lysis | |
| |
| |
| Genetic Analysis of Phages | |
| |
| |
| Generalized Transduction | |
| |
| |
| |
| RNA Phages | |
| |
| |
| |
| Phage Display | |
| |
| |
| |
| Protein Priming | |
| |
| |
| |
| Lysogeny: the ? Paradigm and the Role of Lysogenic Conversion in Bacterial Pathogenesis | |
| |
| |
| Phage ? | |
| |
| |
| Replication of ? DNA | |
| |
| |
| Lysogeny | |
| |
| |
| Specialized Transduction | |
| |
| |
| Other Lysogen-Forming Phages | |
| |
| |
| Lysogenic Conversion and Bacterial Pathogenesis | |
| |
| |
| Genetic Experiments with Phage ? | |
| |
| |
| |
| Effects of Prophage Integration on the Host | |
| |
| |
| |
| Retroregulation | |
| |
| |
| |
| How a Pathogenicity Island Gets Around | |
| |
| |
| |
| Transposition, Site-Specific Recombination, and Families of Recombinases | |
| |
| |
| Transposition | |
| |
| |
| Mechanisms of Transposition | |
| |
| |
| Details of Transposition by the DDE Transposons | |
| |
| |
| Rolling-Circle Transposons | |
| |
| |
| Y and S Transposons | |
| |
| |
| General Properties of Transposons | |
| |
| |
| Transposon Mutagenesis | |
| |
| |
| Site-Specific Recombination | |
| |
| |
| Y and S Recombinases | |
| |
| |
| Importance of Transposition and Site-Specific Recombination in Bacterial Adaptation | |
| |
| |
| |
| Phage Mu: a Transposon Masquerading as a Phage | |
| |
| |
| |
| Transposon Mutagenesis In Vitro | |
| |
| |
| |
| Molecular Mechanisms of Homologous Recombination | |
| |
| |
| Overview of Recombination | |
| |
| |
| Molecular Models of Recombination | |
| |
| |
| The Molecular Basis for Recombination in E. coli | |
| |
| |
| Phage Recombination Pathways | |
| |
| |
| Genetic Analysis of Recombination in Bacteria | |
| |
| |
| |
| Breaking and Entering: Introns and Inteins Move by Double-Strand Break Repair or Retrohoming | |
| |
| |
| |
| The Three R's: Recombination, Replication, and Repair | |
| |
| |
| |
| Recombineering: Gene Replacements in E. coli with Phage ? Recombination Functions | |
| |
| |
| |
| DNA Repair and Mutagenesis | |
| |
| |
| Evidence for DNA Repair | |
| |
| |
| Specific Repair Pathways | |
| |
| |
| General Repair Mechanisms | |
| |
| |
| DNA Damage Tolerance Mechanisms | |
| |
| |
| Summary of Repair Pathways in E. coli | |
| |
| |
| Bacteriophage Repair Pathways | |
| |
| |
| |
| Oxygen: the Enemy Within | |
| |
| |
| |
| Cancer and Mismatch Repair | |
| |
| |
| |
| Transcription-Repair Coupling | |
| |
| |
| |
| Translesion Synthesis and Cancer | |
| |
| |
| |
| The Ames Test | |
| |
| |
| |
| Regulation of Gene Expression: Operons | |
| |
| |
| Transcriptional Regulation in Bacteria | |
| |
| |
| Negative Transcriptional Regulation | |
| |
| |
| Positive Regulation | |
| |
| |
| Regulation by Attenuation of Transcription | |
| |
| |
| Posttranslational Regulation: Feedback Inhibition | |
| |
| |
| Operon Analysis for Sequenced Genomes | |
| |
| |
| |
| The Helix-Turn-Helix Motif of DNA-Binding Proteins | |
| |
| |
| |
| Families of Regulators | |
| |
| |
| |
| Global Regulation: Regulons and Stimulons | |
| |
| |
| Catabolite-Sensitive Operons | |
| |
| |
| Regulation of Nitrogen Assimilation | |
| |
| |
| Stress Responses in Bacteria | |
| |
| |
| Extracytoplasmic (Envelope) Stress Responses | |
| |
| |
| Iron Regulation in E. coli | |
| |
| |
| Regulation of Virulence Genes in Pathogenic Bacteria | |
| |
| |
| Regulation of Ribosome and tRNA Synthesis | |
| |
| |
| Microarray and Proteomic Analysis of Regulatory Networks | |
| |
| |
| |
| cAMP-Independent Catabolite Repression | |
| |
| |
| |
| Nitrogen Fixation | |
| |
| |
| |
| Sigma Factors | |
| |
| |
| |
| Signal Transduction Systems in Bacteria | |
| |
| |
| |
| Regulatory RNAs | |
| |
| |
| |
| Bacterial Cell Compartmentalization and Sporulation | |
| |
| |
| Analysis of Protein Transport in Escherichia coli | |
| |
| |
| Genetic Analysis of Transmembrane Domains of Inner Membrane Proteins in Gram-Negative Bacteria | |
| |
| |
| Protein Secretion | |
| |
| |
| Genetic Analysis of Sporulation in Bacillus subtilis | |
| |
| |
| |
| Secretion Systems and Motility | |
| |
| |
| |
| Phosphorelay Activation of the Transcription Factor Spo0A | |
| |
| |
| Answers to Questions for Thought and Problems | |
| |
| |
| Glossary | |
| |
| |
| Figure and Table Credits | |
| |
| |
| Index | |