MICROBIAL PHYSIOLOGY Fourth Edition Albert G.Moat John W.Foster Michael P.Spector ®WILEY-LISS A JOHN WILEY SONS,INC.,PUBLICATION
MICROBIAL PHYSIOLOGY Fourth Edition Albert G. Moat John W. Foster Michael P. Spector A JOHN WILEY & SONS, INC., PUBLICATION
CONTENTS PREFACE 桩 1 INTRODUCTION TO MICROBIAL PHYSIOLOGY The Escherichia coli Paradigm Cell Struc The Cell Su RN and Protein Regulation/ hesis /12 Chemical Composition12 /13 Nitrogen Assimilation 18 Special Topics /19 Endospores 19 Growth 19 Continuous Culture /22 Factors Affecting Growth /22 Nutrition 22 Oxygen /24 Carbon Dioxide 24
CONTENTS PREFACE xix 1 INTRODUCTION TO MICROBIAL PHYSIOLOGY 1 The Escherichia coli Paradigm / 1 Cell Structure / 1 The Cell Surface / 1 Synthesis of DNA, RNA, and Protein / 7 Metabolic and Genetic Regulation / 10 Microbial Genetics / 11 Chemical Synthesis / 12 Chemical Composition / 12 Energy / 13 Oxidation–Reduction Versus Fermentation / 15 Nitrogen Assimilation / 18 Special Topics / 19 Endospores / 19 Growth / 19 Continuous Culture / 22 Factors Affecting Growth / 22 Nutrition / 22 Oxygen / 24 Carbon Dioxide / 24 v
CONTENTS Extremophiles /25 Microbial Stress Responses 26 Summary 26 OHOTEIN VT ROCESSING 27 Structure of DNA 28 Bacterial Nucleoids /31 REP Elements 35 DNA Replication 36 DNA Replication is Bidirectional and Semiconservative /36 DNA Polymerase Functions as a Dimer /36 Model of DNA Replication /39 Initiation of DNA Replication /42 TgP6Reaiaanaecaneoac RNA Tr h。 RNA T RNA Pr ssing 54 Protein Svnthesis:Translation /57 Transfer RNA 59 Charging of tRNA 62 Ribosome Structure and Synthesis /62 Initiation of Polypeptide Syesis Elongation 69 Peptide Bond Formation 71 Translocation /71 Termination 72 Posttranslational Processing/73 When Nonsense Makes Sense /74 Coupled Transcription and Translation /74 Protein Folding and Ch aperones 74 Folding Stages 7 Protein Fol nand Chaperone Mechanisms Outside the Protein Trafficking/77 Insertion of Int Proteins ral Membrane Proteins and Export of Periplasmic Secretion of Proteins Across the Outer Membrane /81
vi CONTENTS Extremophiles / 25 Microbial Stress Responses / 26 Summary / 26 2 MACROMOLECULAR SYNTHESIS AND PROCESSING: DNA, RNA, AND PROTEIN SYNTHESIS 27 Structure of DNA / 28 Bacterial Nucleoids / 31 REP Elements / 35 DNA Replication / 36 DNA Replication is Bidirectional and Semiconservative / 36 DNA Polymerase Functions as a Dimer / 36 Model of DNA Replication / 39 Initiation of DNA Replication / 42 Termination of DNA Replication and Chromosome Partitioning / 46 RNA Synthesis: Transcription / 47 RNA Synthesis / 47 RNA Turnover / 53 RNA Processing / 54 Protein Synthesis: Translation / 57 Transfer RNA / 59 Charging of tRNA / 62 Ribosome Structure and Synthesis / 62 Initiation of Polypeptide Synthesis / 68 Elongation / 69 Peptide Bond Formation / 71 Translocation / 71 Termination / 72 Posttranslational Processing / 73 When Nonsense Makes Sense / 74 Coupled Transcription and Translation / 74 Protein Folding and Chaperones / 74 Folding Stages / 75 Protein Folding and Chaperone Mechanisms Outside the Cytoplasm / 76 Quality Control / 77 Protein Trafficking / 77 Insertion of Integral Membrane Proteins and Export of Periplasmic Proteins / 77 Secretion of Proteins Across the Outer Membrane / 81
Protein Degradation /83 Degradation of Abnormal Proteins /83 Energy-Dependent Pro eases 86 Antibiotics Acid and Protein Synthesis/88 Agents Af cting DNA M 0, 98 ption and Tran slation 98 Folding.Trafficking and Degradation /99 3 BACTERIAL GENETICS:DNA EXCHANGE RECOMBINATION,MUTAGENESIS,AND REPAIR o Transfer of Genetic Information in Prokaryotes /101 Plasmids 102 Partitioning 102 Incompatibility 103 Nonconjugative,Mobilizable Plasmids /103 Resistance Plasmids 104 Plasmids in Other Bacterial Genera /104 Plasmid Replication/104 AhemiesPoaMmneyHoKe The ced Gene comp /115 Cell-Cell Signaling.and d Ba acterial-Induced Tumors/117 Transformation 118 Gram-Positive Transformation 119 Gram-Negative Transformation /123 Transfection and Forced Competence/124 Transduction /124 Recombination 127 General Recombination 128 Genetics of Recombination /131 Restriction and Modification 133
vii Protein Degradation / 83 Degradation of Abnormal Proteins / 83 Energy-Dependent Proteases / 86 Antibiotics that affect Nucleic Acid and Protein Synthesis / 88 Agents Affecting DNA Metabolism / 88 Agents Affecting Transcription / 91 Agents Affecting Translation / 92 Nucleoids / 98 DNA Replication / 98 Transcription and Translation / 98 Protein Folding, Trafficking, and Degradation / 99 Antibiotics / 100 3 BACTERIAL GENETICS: DNA EXCHANGE, RECOMBINATION, MUTAGENESIS, AND REPAIR 101 Transfer of Genetic Information in Prokaryotes / 101 Plasmids / 102 Partitioning / 102 Incompatibility / 103 Nonconjugative, Mobilizable Plasmids / 103 Resistance Plasmids / 104 Plasmids in Other Bacterial Genera / 104 Plasmid Replication / 104 Addiction Modules: Plasmid Maintenance by Host Killing: The ccd Genes / 108 Conjugation / 108 F Factor / 108 cis/trans complementation Test / 115 Conjugation and Pheromones in Enterococci / 116 Conjugation, Cell–Cell Signaling, and Bacterial-Induced Tumors / 117 Transformation / 118 Gram-Positive Transformation / 119 Gram-Negative Transformation / 123 Transfection and Forced Competence / 124 Transduction / 124 Recombination / 127 General Recombination / 128 Genetics of Recombination / 131 Restriction and Modification / 133
viii CONTENTS Insertion Sequences and Transposable Elements /138 Transposon Tn10 7140 Transposon Tn3 143 Conjugative Transposition /144 ntegrons M 14 /147 1147 Mutations 149 115 /152 Nucleotide Exci ion Repair 152 Transcrintion-Coupled r air 155 Methyl-Directed Mismatch Repair 156 Very Short-Patch Mismatch Repair /158 DNA Glycosylases and Base Excision Repair 158 Adaptive Response to Methylating and Ethylating Agents /160 Postreplication Daughter Strand Gap Repair /160 SOS-Inducible Repair /162 Replication Restart /165 Adaptive Mutations/166 Plasmids 167 Transformation Conjugation 168 Recombination Restriction Modific 0m1169 169 echanisms/170 AEVOLONA IN THE GENOMIC ERA 4 MICROBIAL PHY Genomie and Proteomie Tools/172 me/172 DNA S ncing 172 Web Science:Internet Tools for DNA Sequence Analysis/173 Gene Repl acement /176 s177 Proteomies/177
viii CONTENTS Insertion Sequences and Transposable Elements / 138 Transposon Tn10 / 140 Transposon Tn3 / 143 Conjugative Transposition / 144 Evolutionary Consideration / 144 Integrons / 145 Mutagenesis / 145 Spontaneous Mutations / 147 The Nature of Mutational Events / 147 Suppressor Mutations / 149 DNA Repair Systems / 152 Photoreactivation / 152 Nucleotide Excision Repair / 152 Transcription-Coupled Repair / 155 Methyl-Directed Mismatch Repair / 156 Very Short-Patch Mismatch Repair / 158 DNA Glycosylases and Base Excision Repair / 158 Adaptive Response to Methylating and Ethylating Agents / 160 Postreplication Daughter Strand Gap Repair / 160 SOS-Inducible Repair / 162 Replication Restart / 165 Adaptive Mutations / 166 Plasmids / 167 Transformation / 167 Conjugation / 168 Recombination / 168 Restriction Modification / 169 Transposition / 169 Mutagenesis / 169 Repair Mechanisms / 170 4 MICROBIAL PHYSIOLOGY IN THE GENOMIC ERA: A REVOLUTIONARY TALE 171 Genomic and Proteomic Tools / 172 Cloning a Genome / 172 DNA Sequencing / 172 Web Science: Internet Tools for DNA Sequence Analysis / 173 Gene Replacement / 176 Gene Arrays / 177 Proteomics / 177