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 rel
evant 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.
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. ...show less
Edition/Copyright:97 Cover: Hardback Publisher:American Society for Microbiology Year Published: 1997 International: No
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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
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
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
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
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
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