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Molecular Genetics of Bacteria

Molecular Genetics of Bacteria - 97 edition

ISBN13: 978-1555811020

Cover of Molecular Genetics of Bacteria 97 (ISBN 978-1555811020)
ISBN13: 978-1555811020
ISBN10: 1555811027
Cover type: Hardback
Edition/Copyright: 97
Publisher: American Society for Microbiology
Published: 1997
International: No

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Molecular Genetics of Bacteria - 97 edition

ISBN13: 978-1555811020

Larry Snyder

ISBN13: 978-1555811020
ISBN10: 1555811027
Cover type: Hardback
Edition/Copyright: 97
Publisher: American Society for Microbiology

Published: 1997
International: No
Summary

Molecular Genetics of Bacteria fulfills the need for a comprehensive, primary textbook in bacterial and microbial genetics. Ideally suited as a textbook for advanced undergraduate level courses and as background reading for graduate level courses, this book presents an interesting, modern perspective of the subject and offers descriptive background information, descriptions of experimental methods and data interpretation, examples of genetic analysis, and advanced material relevant to current applications of molecular genetics in biotechnology.

The theme of genetic analysis is used to integrate all of the concepts presented in the text, with recombinant DNA techniques covered in their own chapters. While the genetics of E. coli are used throughout the book because of the extensive work done with this organism, many other microbial systems are introduced in order to show the breadth and diversity of the discipline of bacterial genetics. Chapters are pedagogically constructed and end with a review of key concepts, a set of discussion questions, a set of problems for exercise and testing assignments, and answers to the questions. An end-of-book glossary reviews all of the key terms found in the text. This book, extensively reviewed and class tested by instructors over the past four years, serves as an important text for all courses in bacterial molecular genetics and as background for courses in molecular biology and biotechnology.

Table of Contents

INTRODUCTION

The Biological Universe
The Eubacteria
The Archaea
The Eukaryotes
The Prokaryotes and 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
Genetic Code
The Operon Model
Enzymes for Molecular Biology

I GENES: REPLICATION AND EXPRESSION

1. INTRODUCTION TO MACROMOLECULAR SYNTHESIS: CHROMOSOME STRUCTURE AND REPLICATION

DNA Structure
The Deoxyribonucleotides
The DNA Chain
The 5' and 3' Ends
Base Pairing
Antiparallel Construction
The Major and Minor Grooves
Mechanism of DNA Replication
Deoxyribonucleotide Precursor Synthesis
Deoxynucleotide Polymerization
Semiconservative Replication
Replication of Double-Stranded DNA
Replication Errors
Editing
Methyl-Directed Mismatch Repair
Role of Editing and Mismatch Repair in Maintaining Replication Fidelity
Replication of the Bacterial Chromosome and Cell Division
Structure of the Bacterial Chromosome
Replication of the Bacterial Chromosome
Initiation of Chromosome Replication
Termination of Chromosome Replication
Coordination of Cell Division with Replication of the Chromosome
Coordination of the Cell Cycle with Replication
Supercoiling
The Bacterial Nucleoid
Supercoiling in the Nucleoid
Topoisomerases
Antibiotics That Affect Replication and DNA Structure
Antibiotics That Block Precursor Synthesis
Antibiotics That Block Polymerization of Nucleotides
Antibiotics That Affect DNA Structure
Antibiotics That Affect Gyrase
Summary
Questions for Thought
Problems
Suggested Reading
Box 1.1 Linear Chromosomes in Bacteria

 2. INTRODUCTION TO MACROMOLECULAR SYNTHESIS: GENE EXPRESSION

Overview
The Structure and Function of RNA
Types of RNA
RNA Precursors
RNA Structure
RNA Processing and Modification
Transcription
Bacterial RNA Polymerase
Transcription Initiation
The Polymerization Reaction
Transcription Termination
rRNAs and tRNAs and Their Synthesis
Translation
Protein Structure
Ribosome Structure
Details of Protein Synthesis
The Genetic Code
Translation Initiation
Translation Termination
Polycistronic mRNA
Protein Folding
Chaperones
Protein Disulfide Isomerases
Membrane Proteins
Useful Concept
Open Reading Frame
Antibiotics That Block Transcription and Translation
Antibiotic Inhibitors of Transcription
Antibiotic Inhibitors of Translation
Summary
Questions for Thought
Problems
Suggested Reading
Box 2.1 RNA World
Box 2.2 Exceptions to the Code
Box 2.3 Molecular Phylogeny

II GENES AND GENETIC ELEMENTS

3. MUTATIONS IN BACTERIA

Definitions
Terms Used in Genetics
Genetic Names
Useful Phenotypes in Bacterial Genetics
Auxotrophic Mutant
Conditional Lethal Mutants
Resistant Mutants
Inheritance in Bacteria
The Luria and Delbrück Experiment
The Newcombe Experiment
The Lederbergs' Experiment
Mutation Rates
Calculating Mutation Rates
Using the Increase in the Fraction of Mutants To Measure Mutation Rates
Summary
Types of Mutations
Base Pair Changes
Frameshift Mutations
Deletion Mutations
Inversion Mutations
Tandem Duplication Mutations
Insertion Mutations
Reversion versus Suppression
Intragenic Suppressors
Intergenic Suppressors
Nonsense Suppressors
Summary
Questions for Thought
Problems
Suggested Reading
Box 3.1 Statistical Analysis of the Number of Mutants per Culture
Box 3.2 The Directed- or Adaptive-Mutation Controversy
Box 3.3 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
Mechanisms to Prevent Curing of Plasmids
Incompatibility
Plasmid Genetics
Methods for Detecting and Isolating Plasmids
Determining the Incompatibility Group
Maintaining Plasmids Belonging to the Same Incompatibility Group
Determining the Host Range
Finding the Plasmid ori Region
Studying the Requirements for Plasmid Replication
Plasmid Cloning Vectors
Desirable Features of Plasmid Cloning Vectors
Broad-Host-Range Cloning Vectors
Summary
Questions for Thought
Problems
Suggested Reading
Box 4.1 Linear Plasmids
Box 4.2 Plasmids and Bacterial
Pathogenesis
Box 4.3 Plasmid Addiction

5. CONJUGATION

Overview
Classification of Self-Transmissible Plasmids
Interspecies Transfer of Plasmids
Mechanism of DNA Transfer during Conjugation in Gram-Negative Bacteria
Transfer (tra) Genes
The oriT Sequence
Function of Plasmid Primases in Transfer
Efficiency of Transfer
Mobilizable Plasmids
Chromosome Transfer by Plasmids
Formation of Hfr Strains
Transfer of Chromosomal DNA by Integrated Plasmids
Chromosome Mobilization
Prime Factors
Genetics of Plasmid Transmission
Determining Whether a Plasmid Is Self-Transmissible
Determining Whether a Plasmid Is Promiscuous
Determining Whether a Plasmid Is Mobilizable
Triparental Matings
Mapping Plasmid Functions
Experiments to Demonstrate Transfer of Primase Protein
Transfer Systems of Gram-Positive Bacteria
Plasmid-Attracting Pheromones
Other Types of Transmissible Elements
Summary
Questions for Thought
Problems
Suggested Reading
Box 5.1 Gene Exchange Between Kingdoms

6. TRANSFORMATION

Natural Transformation
Discovery of Transformation
Competence
Uptake of DNA during Natural Transformation
Mechanism of DNA Uptake during Transformation
Genetic Evidence for Single-Strand Uptake
Plasmid Transformation and Transfection of Naturally Competent Bacteria
The Role of Natural Transformation
Artificially Induced Competence
Calcium Ion Induction
Electroporation
Summary
Questions for Thought
Problems
Suggested reading
Box 6.1 Antigenic Variation in Neisseria Gonorrhoeae

7. BACTERIOPHAGES

Bacteriophage Lytic Development Cycle
Phage T7: a Phage-Encoded RNA Polymerase
Phage T4: a New Sigma Factor and Replication-Coupled Transcription
Phage l: Transcription Antitermination
Phage DNA Replication
Phage M13: Single-Stranded Circular DNA
Phage l: Linear DNA That Replicates as a Circle
Phage T7: Linear DNA That Never Cyclizes
Phage T4: Another Linear DNA That Never Cyclizes
Generalized Transduction
What Makes a Transducing Phage?
The Role of Transduction in Bacterial Evolution
Lysogeny
Phage l Lysogeny
Specialized Transduction
Other Lysogenic Phages
Use of Lysogenic Phages as Cloning Vectors
Lysogenic Phages and Bacterial Pathogenesis
Summary
Questions for Thought
Problems
Suggested reading
Box 7.1 RNA Phages
Box 7.2 Protein Priming
Box 7.3 Phages That Integrate into Essential Genes of the Host
Box 7.4 Retroregulation

8. TRANSPOSITION AND NONHOMOLOGOUS RECOMBINATION

Transposition
Overview of Transposition
Structure of Bacterial Transposons
Types of Bacterial Transposons
Assays of Transposition
Molecular Models for Transposition
Site-Specific Recombination
Developmentally Regulated Excision of Intervening DNA
Integrases
Resolvases
DNA Invertases
Topoisomerases
Summary
Questions for Thought
Problems
Suggested Reading
Box 8.1 Phage MU: A Transposon Masquerading as a Phage
Box 8.2 Conjugative Transposons

III GENES IN ACTION

9. MOLECULAR BASIS OF RECOMBINATION

Overview of Recombination
Requirement 1: Identical or Very Similar Sequences in the Crossover Region
Requirement 2: Complementary Base Pairing between Double-Stranded DNA Molecules
Requirement 3: Recombination Enzymes
Requirement 4: Heteroduplex Formation
Molecular Models of Recombination
The Holliday Double-Strand Invasion Model
Single-Strand Invasion Model
Double-Strand Break Repair Model
Molecular Basis for Recombination in E. coli
Chi Sites and the RecBCD Nuclease
Synapse Formation and the RecA Protein
The Ruv and RecG Proteins and the Migration and Cutting of Holliday Junctions
Phage Recombination Pathways
Rec Proteins of Phages T4 and T7
The RecE Pathway of the rac Prophage
The Phage l red System
Genetic Analysis of Recombination in Bacteria
Isolating Rec- Mutants of E. coli
Other Recombination Genes
Gene Conversion and Other Manifestations of Heteroduplex Formation during Recombination
Summary
Questions for Thought
Problems
Suggested Reading
Box 9.1 Homing Enzymes, Introns, and Inteins

10. DNA REPAIR AND MUTAGENESIS

Evidence for DNA Repair
Specific Repair Pathways
Deamination of Bases
Damage Due to Reactive Oxygen
Alkylation
Pyrimidine Dimers
General Repair Mechanisms
The Methyl-Directed Mismatch Repair System
Nucleotide Excision Repair
Postreplication or Recombination Repair
SOS Inducible Repair
Other din Genes
Summary of Repair Pathways in E. coli
Bacteriophage Repair Pathways
Summary
Questions for Thought
Problems
Suggested reading
Box 10.1 Oxygen: The Enemy Within
Box 10.2 Cancer and Mismatch Repair
Box 10.3 Transcription-Repair Coupling
Box 10.4 The Ames Test

11. REGULATION OF GENE EXPRESSION

Transcriptional Regulation in Bacteria
The Bacterial Operon
Repressors and Activators
Negative and Positive Regulation
Inducers and Corepressors
Genetic Evidence for Negative and Positive Regulation
Negative Regulation
The E. coli lac Operon
The E. coli gal Operon
Regulation of Biosynthetic Operons: Aporepressors and Corepressors
Positive Regulation
The E. coli l-ara
Operon
The E. coli Maltose Operons
The tol Operons
Regulation by Attenuation of Transcription
Genetic Evidence for Attenuation
Feedback Inhibition
Tryptophan Operon
Isoleucine-Valine Operon
Summary
Questions for Thought
Problems
Suggested Reading
Box 11.1 The Helix-Turn-Helix Motif of DNA-Binding Proteins
Box 11.2 Families of Activators
Box 11.3 Regulation by Attenuation: The Aminoacyl-tRNA Synthetase Genes of bacillus subtilis

12. GLOBAL REGULATORY MECHANISMS

Catabolite-Sensitive Operons
cAMP and the cAMP-Binding Protein
Genetic Analysis of Catabolite Regulation in E. coli
Uses of cAMP in Other Organisms
Regulation of Nitrogen Assimilation
Pathways for Nitrogen Assimilation
Coordination of Catabolite Repression, the Ntr System, and the Regulation of Amino Acid Degradative Operons
Genetic Analysis of Nitrogen Regulation in Enteric Bacteria
Regulation of Porin Synthesis
Genetic Analysis of Porin Osmoregulation
Regulation of Virulence Genes in Pathogenic Bacteria
Diphtheria
Cholera
Whooping Cough
The Heat Shock Regulon
Heat Shock Response in E. coli
Genetic Analysis of the E. coli Heat Shock Regulon
Regulation of s32 Synthesis
Regulation of Ribosome and tRNA Synthesis
Ribosomal Proteins
rRNA and tRNA Regulation
Summary
Questions for Thought
Problems
Suggested Reading
Box 12.1 Camp-Independent Catabolite Repression
Box 12.2 Nitrogen Fixation
Box 12.3 Sensor-Response Regulator Two-Component Systems
Box 12.4 Evolutionary Conservation of Heat Shock Proteins

IV GENES IN PRACTICE

13. GENETIC ANALYSIS IN PHAGE

Steps in a Genetic Analysis with Phages
Infection of Cells
Virus Crosses
Recombination and Complementation Tests with Viruses
Recombination Tests
Complementation Tests
Experiments with the r II Genes of Phage T4
Complementation Tests with r II Mutants
Recombination Tests with r II Mutants
Ordering r II Mutations by Three-Factor Crosses
The r II Genes and the Nature of the Genetic Code
Isolating Duplication Mutations of the r II Region
Constructing the Genetic Linkage Map of a Phage
Identifying Phage Genes by Complementation Tests
Mapping Phage Genes
Genetic Linkage Maps of Some Phages
Factors That Determine the Form of the Linkage Map
Genetic Experiments with Phage l
Genetics of l Lysogeny
Genetics of the l CI Repressor
trans- versus cis-Acting Functions in l DNA Replication
Isolation of l nut Mutations
Summary
Problems
Suggested Reading

14. GENETIC ANALYSIS IN BACTERIA

Isolating Bacterial Mutants
To Mutagenize or Not to Mutagenize?
Isolating Independent Mutations
Selecting Mutants
Genetic Mapping of Mutations
Genetic Markers
Mapping by Hfr Crosses
Mapping by Transduction or Transformation
Mapping Other Types of Markers
Complementation Tests in Bacteria
Selecting Prime Factors
Complementation by Specialized Transducing Phages
Complementation from Plasmid Clones
Examples of Genetic Analysis in Bacteria
Deletion Mapping of lacI Missense Mutations
Isolating Tandem Duplications of the his Operon in Salmonella typhimurium
Genetic Analysis of Repair Pathways
Genetic Analysis of Protein Transport
Summary
Problems
Suggested Reading
Box 14.1 Specific Protein Translocation Systems

15. RECOMBINANT DNA TECHNIQUES AND CLONING BACTERIAL GENES

Restriction Endonucleases and Recombinant DNA
Biological Role of Restriction Modification Systems
Types of Restriction Modification Systems
Physical Mapping with Restriction Endonucleases
Correlating Genetic and Physical Maps
Restriction Fragment Length Polymorphisms
Joining DNA Fragments Cut with Restriction Endonucleases
DNA Cloning with Restriction Endonucleases
Cloning Vectors
Cloning DNA into a Cloning Vector
Tricks for Optimizing Cloning
Cloning Bacterial Genes
Constructing DNA Libraries
Identifying Clones in a Library
Locating Genes on Cloned DNA
Applications Involving Cloned Genes
DNA Sequencing
Expression Vectors
Site-Specific Mutagenesis
Polymerase Chain Reaction
Uses of PCR
Summary
Questions for Thought
Problems
Suggested Reading
Cloning Manuals
Box 15.1 Applications of Restriction Endonucleases and Methyltransferases
Box 15.2 Bacterial Genomics

16. MOLECULAR GENETIC ANALYSIS AND BIOTECHNOLOGY

Deletion Mapping of Protein Functional Domains
Mapping the Thymidylate Synthetase Enzyme
Regulation of Plasmid Replication
Replication Control of ColE1-Derived Plasmids
Replication Control of Iteron Plasmids
Molecular Genetics and Transposition
Genetic Requirements for Transposition
Transposon Mutagenesis
In Vivo Cloning
Gene Replacement and Reverse Genetics
Selecting Gene Replacements in Bacteria
Genetics of All Bacteria
Cloning Genes of Uncharacterized Bacteria
DNA Libraries
Cloning Transposon Insertions
Complementation in the Host of Origin
Manufacturing Bioproducts
Agrobacterium tumefaciens and the Genetic Engineering of Plants
Making New Antibiotics
Horizons for Molecular Genetics Applications
Summary
Problems
Suggested Reading
Answers to End-of-Chapter Questions and Problems

Glossary
Index

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