Introduction

The Biological Universe

What Is Genetics?

Bacterial Genetics

Phage Genetics

A Brief History of Bacterial Molecular Genetics

What Is Ahead

1 The Bacterial Chromosome: DNA Structure, Replication, and Segregation

DNA Structure

The Mechanism of DNA Replication

Replication Errors

Impediments to DNA Replication

Replication of the Bacterial Chromosome and Cell Division

The Bacterial Nucleoid

The Bacterial Genome

2 Bacterial Gene Expression: Transcription, Translation, Protein Folding, and Localization

Overview

The Structure and Function of RNA

Transcription

RNA Degradation

The Structure and Function of Proteins

Translation

Protein Folding and Degradation

Protein Localization

Protein Secretion and Export

Regulation of Gene Expression

What You Need To Know

3 Bacterial Genetic Analysis: Fundamentals and Current Approaches

Definitions

Inheritance in Bacteria

Mutation Rates

Types of Mutations

Reversion versus Suppression

Genetic Analysis in Bacteria

Perspective

4 Plasmids

What Is a Plasmid?

Properties of Plasmids

5 Conjugation

Overview

Mechanism of DNA Transfer during Conjugation in Proteobacteria

Chromosome Transfer by Plasmids

Diversity in Transfer Systems

Integrating Conjugative Elements

6 Transformation

Natural Transformation

Artificially Induced Competence

7 Bacteriophages and Transduction

Lytic Development

Lysogenic Development

Genetic Analysis of Phages

Phage-Mediated Genetic Transfer

Host Defenses Against Phage Infection

Phages as Tools

8 Transposition, Site-Specific Recombination, and Families of Recombinases

Transposition

Mechanisms of Transposition

General Properties of Transposons

Transposon Mutagenesis

Site-Specific Recombination

Y and S Recombinases

Group II Mobile Introns: Elements that Move Using an RNA Intermediate

Importance of Transposition and Site-Specific Recombination in Bacterial Adaptation

9 Molecular Mechanisms of Homologous Recombination

Homologous Recombination and DNA Replication in Bacteria

The Molecular Basis for Recombination in E. coli

Recombination between Different DNAs in Bacteria

Recombineering: Gene Replacements in E. coli with Phage λ Recombination Functions

10 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

11 Regulation of Gene Expression: Genes and Operons

Transcriptional Regulation in Bacteria

Negative Regulation of Transcription Initiation

Positive Regulation of Transcription Initiation

Regulation by Transcription Attenuation

Regulation of mRNA Degradation

Regulation of Translation

Posttranslational Regulation

Why Are There So Many Mechanisms of Gene Regulation?

12 Global Regulation: Regulons and Stimulons

Carbon Catabolite Regulation

Regulation of Nitrogen Assimilation

Regulation of Ribosome Components and tRNA Synthesis

Ribosomal Protein Gene Regulation

Stress Responses in Bacteria

Iron Regulation in E. coli

Regulation of Virulence Genes in Pathogenic Bacteria

Developmental Regulation: Sporulation in B. subtilis

13 Genomes and Genomic Analysis

The Bacterial Genome

DNA Sequencing

Barriers to Horizontal Transfer: Genome Gatekeepers and the Molecular Biologist’s Toolkit

Glossary

End Papers

Index

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