Molecular Genetics of Bacteria 4th Edition (PDF)

Molecular Genetics

Author:
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
  • SUMMARY
  • QUESTIONS FOR THOUGHT
  • PROBLEMS
  • SUGGESTED READING
  • Answers to Problems and Questions for Thought
  • Glossary

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