Larry Snyder, Joseph E. Peters, Tina M. Henkin & Wendy Champness
Release at:
2013
Pages:
732
Edition:
Fourth Edition
File Size:
99 MB
File Type:
pdf
Language:
English
Description of Molecular Genetics of Bacteria 4th Edition (PDF)
Molecular Genetics of Bacteria 4th Edition by Larry Snyder, J. E. Peters is a great molecular genetics book available for PDF download. The fourth edition of the textbook Molecular Genetics of Bacteria has been substantially revised and some new sections have been added. We tried to do this without increasing the length of the book, which, at more than 700 pages, was already quite long. While the book retains the same number and order of chapters, many topics have been moved or integrated more completely into the text to reflect a more modern perspective.
The purpose was to convey more accurately how one approaches questions in modern bacterial genetics, using the full repertoire of methods now available. Also, to make room for the new material, we made the philosophical decision to condense or eliminate descriptions of methods where they seemed unnecessarily detailed for a textbook.
We have invited a group of outstanding microbiologists/ experts to contribute to this book.We believe the contents are accurate and up-to-date. However, we welcome any comments or suggestions that you may have regarding the contents of this book.
Content of Molecular Genetics of Bacteria 4th Edition (PDF)
Introduction
The Biological Universe
The Bacteria
The Archaea
The Eukaryotes
Speculations on the Origin of the Three Domains of Life
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
What Is Ahead
SUGGESTED READING
CHAPTER 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 the Bacterial Chromosome
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
Antibiotics That Affect Replication and DNA Structure
Antibiotics That Block Precursor Synthesis
Antibiotics That Block Polymerization of Deoxynucleotides
Antibiotics That Affect DNA Structure
Antibiotics That Affect Gyrase
Molecular Biology Manipulations with DNA
Restriction Endonucleases
Hybridizations
Applications of the Enzymes Used in DNA Replication
Polymerase Chain Reaction
BOX 1.1 Structural Features of Bacterial Genomes
BOX 1.2 Advanced Genome-Sequenc
Techniques
SUMMARY
QUESTIONS FOR THOUGHT
PROBLEMS
SUGGESTED READING
CHAPTER 2: Bacterial Gene Expression: Transcription, Translation, and Protein Folding
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
Protein Folding and Degradation
Protein Chaperones
Protein Degradation
Membrane Proteins and Prot
Export
Regulation of Gene Expression
Transcriptional Regulation
Posttranscriptional Regulation
Genomes and Genomics
Annotation and Comparative Genomics
What You Need To Know
Open Reading Frames
Transcriptional and Translational Fusions
Antibiotics That Block Transcription and Translation
Antibiotic Inhibitors of Transcription
Antibiotic Inhibitors of Translation
BOX 2.1 Molecular Phylogen
BOX 2.2 Mimicry in Translatio
BOX 2.3 Exceptions to the Cod
BOX 2.4 Selfish DNAs: RNA Introns and Protein Inteins
BOX 2.5 Annotation and Comparative Genomics
SUMMARY
QUESTIONS FOR THOUGHT
PROBLEMS
SUGGESTED READING
CHAPTER 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
The Lederbergs’ 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
Isolation of Tandem Duplications of the his Operon in Salmonella
Lengths of Tandem Duplications
Frequency of Spontaneous Duplications
BOX 3.1 Statistical Analysis of the Number of Mutants per Culture
BOX 3.2 Inversions and the Genetic Map
SUMMARY
QUESTIONS FOR THOUGHT
PROBLEMS
SUGGESTED READING
CHAPTER 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 Toxin-Antitoxin Systems and Plasmid Maintenance
SUMMARY
QUESTIONS FOR THOUGHT
PROBLEMS
SUGGESTED READING
CHAPTER 5: Conjugation
Overview
Classification of Self-Transmissible Plasmids
The Fertility Plasmid
Mechanism of DNA Transfer during Conjugation in Gram-Negative Bacteria
Transfer (tra) Genes
The oriT Sequence
Male-Specific Phages
Efficiency of Transfer
Interspecies Transfer of Plasmids
Conjugation and Type IV Protein Secretion
Mobilizable Plasmids
Chromosome Transfer by Plasmids
Formation of Hfr Strains
Transfer of Chromosomal DNA by Integrated Plasmids
Chromosome Mobilization
Prime Factors
Transfer Systems of Gram-Positive Bacteria
Plasmid-Attracting Pheromones
Integrating Conjugative Elements
BOX 5.1 Gene Exchange between Domains
SUMMARY
QUESTIONS FOR THOUGHT
PROBLEMS
SUGGESTED READING
CHAPTER 6: Transformation
Natural Transformation
Discovery of Transformation
Competence
DNA Processing after Uptake
Experimental Evidence for Models of Natural Transformation
Plasmid Transformation and Phage Transfection of Naturally Competent Bacteria
Regulation of Natural Competence
Role of Natural Transformation
Importance of Natural Transformation for Forward and Reverse Genetics
Congression
Artificially Induced Competence
Chemical Induction
Electroporation
Protoplast Transformation
BOX 6.1 Antigenic Variation in Neisseria gonorrhoeae
SUMMARY
QUESTIONS FOR THOUGHT
PROBLEMS
SUGGESTED READING
CHAPTER 7: Bacteriophages: Lytic Development, Genetics, and Generalized Transduction
Regulation of Gene Expression during Lytic Development
Phages That Encode Their Own RNA Polymerases
T7 Phage-Based Expression Vectors
Making Riboprobes and RNA-Processing Substrates
Phage T4: Transcriptional Activators, a New Sigma Factor, and Replication-Coupled Transcription
Phage DNA Genome Replication and Packaging
Phages with Single-Stranded Circular DNA
Replication and DNA Packaging: Linear Genomes
Phage T7: Linear DNA That Forms Concatemers
Phage T4: Another Phage That Forms Concatemers
Phage Lysis
Single-Protein Lysis
Timed Lysis
Timing of Lysis by Holins
Phage Display
Genetic Analysis of Phages
Infection of Cells
Phage Crosses
Recombination and Complementation Tests with Phages
Genetic Experiments with the r II Genes of Phage T4
Constructing the Genetic-Linkage Map of a Phage
Phage Defense Mechanisms
Restriction-Modification Systems
Abi Systems
CRISPR Loci
Generalized Transduction
What Makes a Transducing Phage?
Shuttle Phasmids
Role of Transduction in Bacte
Evolution
BOX 7.1 Phage Genomics
BOX 7.2 RNA Phages
BOX 7.3 Protein Priming
BOX 7.4 Phage Display
SUMMARY
QUESTIONS FOR THOUGHT
PROBLEMS
SUGGESTED READING
CHAPTER 8: Lysogeny: the λ Paradigm and the Role of Lysogenic Conversion in Bacterial Pathogenesis
Phage λ
λ Lytic Development
Replication of λ DNA
Lysogeny by Phage λ
The Lytic-versus-Lysogen Decision: the Roles of cI,
and cIII Gene Products
Phage λ Integration
Maintenance of λ Lysogeny
Immunity to Superinfection
Induction of λ
Summary of the Lytic and Lysogenic Cycles
Specialized Transduction
Selection of HFT Particles
Other Lysogen-Forming Phages
Phage P2
Phage P4: a Satellite Virus
Prophages That Replicate as Plasmids
Phage Mu: a Transposon Masquerading as a Phage
Lysogenic Conversion and Bacterial Pathogenesis
E. coli and Dysentery: Shiga Toxins
Diphtheria
Cholera
S. aureus and Toxic Shock Syndrome
Synopsis
Uses of Lysogeny in Genetic Analysis and Biotechnology
Complementation and Gene Expression Studies
Use of Phage Display and Frequency of Mixed Dilysogens To Detect Protein-Protein Interactions
Genetic Experiments with Phage λ
Genetic Analysis of λ Lysogen Formation
Genetics of the CI Repressor: Evidence for the Domain Structure of Proteins
Identification of λ nut Sites Involved in Progressive Transcription Antitermination
Isolation of Host nus Mutations: E. coli Functions Involved in Transcription Elongation-Termination
BOX 8.1 Effects of Prophage Insertion on the Host
SUMMARY
QUESTIONS FOR THOUGHT
PROBLEMS
SUGGESTED READING
CHAPTER 9: Transposition, Site-Specific Recombination, and Families of Recombinases
Transposition
Overview of Transposition
Structure of Bacterial Transposons
Types of Bacterial Transposons
Assays of Transposition
Mechanisms of Transposition
Genetic Requirements for Transposition of Tn3
A Molecular Model for Transposition of Tn3
Transposition by Tn10 and Tn5
Details of Transposition by the DDE Transposons
Details of the Mechanism of Transposition by Tn5 and Tn7
Rolling-Circle Transposons
Y and S Transposons
General Properties of Transposons
Target Site Specificity
Effects on Genes Adjacent to the Insertion Site
Regulation of Transposition
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
Importance of Transposition and Site-Specific Recombination in Bacterial Adaptation
BOX 9.1 Transposons and Genomics
SUMMARY
QUESTIONS FOR THOUGHT
PROBLEMS
SUGGESTED READING
CHAPTER 10: Molecular Mechanisms of Homologous Recombination
Homologous Recombination and
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?
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
Genetic Analysis of Recombination in Bacteria
Isolating Rec − Mutants of E. coli
Isolating Mutants with Mutations in Other Recombination Genes
Gene Conversion and Other Manifestations of Heteroduplex Formation during Recombination
BOX 10.1 Other Types of Double-Strand Break Repair in Bacteria
BOX 10.2 Breaking and Entering: Introns and Inteins Move by Double-Strand Break Repair or Retrohoming
SUMMARY
QUESTIONS FOR THOUGHT
PROBLEMS
SUGGESTED READING
CHAPTER 11: 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
Methyl-Directed Mismatch Repair
Nucleotide Excision Repair
DNA Damage Tolerance Mechanisms
Homologous Recombination and
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 11.1 The Role of Reactive Oxygen Species in Cancer and Degenerative Diseases
BOX 11.2 DNA Repair and Cancer
BOX 11.3 The Ames Test
SUMMARY
QUESTIONS FOR THOUGHT
PROBLEMS
SUGGESTED READING
CHAPTER 12: 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 Transcripti
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?
Operon Analysis for Sequenced Genomes
BOX 12.1 The Helix-Turn-Helix Motif of DNA- Binding Proteins
BOX 12.2 Families of Regulators
BOX 12.3 Special Problems in Genetic Analysis of Operons
SUMMARY
QUESTIONS FOR THOUGHT
PROBLEMS
SUGGESTED READING
CHAPTER 13: Global Regulation: Regulons and Stimulons
Carbon Catabolite Regulation
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 and tRNA Synthesis
Ribosomal Protein Gene Regulation
Regulation of rRNA and tRNA Synthesis
The Stringent Response
Stress Responses in Bacteria
Heat Shock Regulation
General Stress Response in Gram- Negative Bacteria
General Stress Response in Gram- Positive Bacteria
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
From Genes to Regulons to Networks
BOX 13.1 cAMP-Independent Carbon Catabolite Regulation in E. coli
BOX 13.2 A Bacterial Two- Hybrid System Based on Adenylate Cyclase
BOX 13.3 Nitrogen Fixation
BOX 13.4 Signal Transduction Systems in Bacteria
BOX 13.5 Sigma Factors
BOX 13.6 Regulatory RNAs
BOX 13.7 Tools for Studying Global-Regulation
SUMMARY
QUESTIONS FOR THOUGHT
PROBLEMS
SUGGESTED READING
CHAPTER 14: Bacterial Cell Biology and Development
Membrane Proteins and Protein Export
The Translocase System
The Signal Sequence
The Targeting Factors
The Tat Secretion Pathway
Disulfide Bonds
Use of mal- lac Fusions To Study Protein Transport in E. coli
Genetic Analysis of Transmembrane Domains of Inner Membrane Proteins in Gram-Negative Bacteria
Identification of Genes for Inner Membrane Proteins by Random phoA Fusions
Protein Secretion
Protein Secretion Systems in Gram-Negative Bacteria
Protein Secretion in Gram-Positive Bacteria
Sortases
Bacterial Cell Biology and the Cell Cycle
The Bacterial Cell Wall
Septum Formation
The FtsZ Protein and the Septal Ring
Regulation of FtsZ Ring Formation in C. crescentus
Genetic Analysis of Sporulation in B. subtilis
Identification of Genes That Regulate Sporulation
Regulation of Initiation of Sporulation
Compartmentalized Regulation of Sporulation Genes
Analysis of the Role of Sigma Factors in Sporulation Regulation
Intercompartmental Regulation during Development
Finding Sporulation Genes: Mutant Hunts, Suppressor Analysis, and Functional Genomics
BOX 14.1 Secretion Systems and Motility
BOX 14.2 Example of a Sortase- Dependent Pathway: Sporulation in S. coelicolor
BOX 14.3 Evolutionary Origin of the Eukaryotic Cytoskeleton
BOX 14.4 Phosphorelay Activation of the Transcription Factor Spo0A
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