Snyder and Champness molecular genetics of bacteria

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