Table of Contents
Introduction
The Biological Universe
What Is Genetics?
Bacterial Genetics
Phage Genetics
A Brief History of Bacterial Molecular Genetics
What’s Ahead
1. 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
BOX 1.1 Linear Chromosomes in Bacteria
BOX 1.2 Restarting Replication Forks
BOX 1.3 The Bacterial Cytoskeleton and Bacterial Cell Biology
BOX 1.4 Features of Bacterial Genomes
BOX 1.5 Bacterial Genome Sequencing
2. 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
BOX 2.1 Molecular Phylogeny
BOX 2.2 Mimicry in Translation
BOX 2.3 Exceptions to the Code
BOX 2.4 Traffic Jams on mRNA: Removing Stalled Ribosomes with tmRNA
BOX 2.5 Stability and Degradation of mRNA
BOX 2.6 Selfish DNAs: RNA Introns and Protein Inteins
BOX 2.7 Annotation and Comparative Genomics
3. 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
BOX 3.1 Statistical Analysis of the Number of Mutants per Culture
BOX 3.2 Inversions and the Genetic Map
4. Plasmids
What Is a Plasmid?
Properties of Plasmids
Constructing a Plasmid Cloning Vector
BOX 4.1 Plasmids and Bacterial Pathogenesis
BOX 4.2 Linear Plasmids
BOX 4.3 An Incompatibility Group of One’s Own
BOX 4.4 Plasmid Addiction
5. 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
BOX 5.1 Gene Exchange between Kingdoms
BOX 5.2 Conjugation and Type IV Protein Secretion Systems
BOX 5.3 Conjugation in Streptomycetes
BOX 5.4 Conjugative Transposons (Integrating Conjugative Elements)
6. Transformation
Natural Transformation
Importance of Natural Transformation for Forward and Reverse Genetics
Artificially Induced Competence
BOX 6.1 Antigenic Variation in Neisseria gonorrhoeae
7. Lytic Bacteriophages: Development, Genetics, and Generalized Transduction
The Bacteriophage Lytic Development Cycle
Phage DNA Replication
Phage Lysis
Genetic Analysis of Phages
Generalized Transduction
BOX 7.1 RNA Phages
BOX 7.2 Phage Display
BOX 7.3 Protein Priming
8. Lysogeny: the ë 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
BOX 8.1 Effects of Prophage Integration on the Host
BOX 8.2 Retroregulation
BOX 8.3 How a Pathogenicity Island Gets Around
9. 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
BOX 9.1 Phage Mu: a Transposon Masquerading as a Phage
BOX 9.2 Transposon Mutagenesis In Vitro
10. 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
BOX 10.1 Breaking and Entering: Introns and Inteins Move by Double-Strand Break Repair or Retrohoming
BOX 10.2 The Three R’s: Recombination, Replication, and Repair
BOX 10.3 Recombineering: Gene Replacements in E. coli with Phage ëRecombination Functions
11. 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
BOX 11.1 Oxygen: the Enemy Within
BOX 11.2 Cancer and Mismatch Repair
BOX 11.3 Transcription-Repair Coupling
BOX 11.4 Translesion Synthesis and Cancer
BOX 11.5 The Ames Test
12. 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
BOX 12.1 The Helix-Turn-Helix Motif of DNA-Binding Proteins
BOX 12.2 Families of Regulators
13. 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
BOX 13.1 cAMP-Independent Catabolite Repression
BOX 13.2 Nitrogen Fixation
BOX 13.3 Sigma Factors
BOX 13.4 Signal Transduction Systems in Bacteria
BOX 13.5 Regulatory RNAs
14. 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
BOX 14.1 Secretion Systems and Motility
BOX 14.2 Phosphorelay Activation of the Transcription Factor Spo0A
Answers to Questions for Thought and Problems
Glossary
Figure and Table Credits
Index