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
ix Traditional Tools/181 Mutant Hunts 181 on/183 DNA Mobility Shifts (Gel Shifts and Supe shifts)/185 Finding Tran ptional Starts by Primer Exte on/186 De RNA.Proteir DNA-Bind tei Two-Hybrid Analysis /190 Summary 192 5 REGULATION OF PROKARYOTIC GENE EXPRESSION 194 /194 ding Pro 19 cOperon:A Paradigm of Gene E ion 197 ing Energy St 20 The Ca 204 tro:Th -Pa igm /206 The Help from Hu 206 The Arabinose Operon:One Regulator.Two Functions 208 Attenuation Controls 211 Transcriptional Attenuation Mechanisms /211 Translational Attenuation Control:The pyrC Strategy /215 Membrane-Mediated Regulation:The put System 216 Renof Gene Ep(llr Yi on 21 Hijacking 1220 Global Control Networks 223 Communication with the Environment:Two-Component Regulatory Systems 224 ogen Fixation: Phosphate Uptake:Communication Between Transport and Two-Component Regulatory Systems /232
ix Traditional Tools / 181 Mutant Hunts / 181 Transcriptional and Translational Gene Fusions (Reporter Genes) / 182 Polymerase Chain Reaction / 183 DNA Mobility Shifts (Gel Shifts and Supershifts) / 185 Finding Transcriptional Starts by Primer Extension / 186 Detecting DNA, RNA, Protein, and DNA-Binding Proteins by Southern, Northern, Western, and Southwestern Blots / 187 Two-Hybrid Analysis / 190 Summary / 192 5 REGULATION OF PROKARYOTIC GENE EXPRESSION 194 Transcriptional Control / 194 DNA-Binding Proteins / 195 The lac Operon: A Paradigm of Gene Expression / 197 Catabolite Control: Sensing Energy Status / 201 Class I and Class II CRP-Dependent Genes / 204 The Catabolite Repressor/Activator Protein Cra / 204 Catabolite Control: The Gram-Positive Paradigm / 206 The gal Operon: DNA Looping with a Little Help from Hu / 206 The Arabinose Operon: One Regulator, Two Functions / 208 Attenuation Controls / 211 Transcriptional Attenuation Mechanisms / 211 Translational Attenuation Control: The pyrC Strategy / 215 Membrane-Mediated Regulation: The put System / 216 Recombinational Regulation of Gene Expression (Flagellar Phase Variation) / 217 Translational Repression / 219 Anti-σ Regulation by Molecular Hijacking / 220 Titrating a Posttranscriptional Regulator: The CsrA/CsrB Carbon Storage Regulatory Team / 222 Global Control Networks / 223 Communication with the Environment: Two-Component Regulatory Systems / 224 Regulation of Nitrogen Assimilation and Nitrogen Fixation: Examples of Integrated Biochemical and Genetic Controls / 227 Phosphate Uptake: Communication Between Transport and Two-Component Regulatory Systems / 232
X CONTENTS Quorum Sensing:How Bacteria Talk to Each Other /234 Proteolytic Control /235 Summary 236 6 BACTERIOPHAGE GENETICS General Characteristics of Bacteriophages /239 T4 Phag 1245 of T4 Gene Expression /247 T4 Genome 250 A Phage /256 The Lysis-Lysogeny Decision /259 Transcrintion 259 Function of Cro Versus CI Repressor and the Structure of OL and OR 260 Establishment of Represor roof Integratio and Excis 26 a Lifestyle/66 1274 T4 Bacteriophage /274 Phage 275 bX174/275 μPhage/275 7 CELL STRUCTURE AND FUNCTION 277 The Eukaryotic Nucleus Bacterial Nucleoid Nucleoso 8 28 aces Surface of Bacteria Peptidoelycan (Murein)Hydrolases Peptidoglycan (Murein)Synthesis/295 Teichoic Acids and Lipoteichoic Acids /300 Outer Membranes of Gram-Negative Bacteria /303
x CONTENTS Quorum Sensing: How Bacteria Talk to Each Other / 234 Proteolytic Control / 235 Summary / 236 6 BACTERIOPHAGE GENETICS 239 General Characteristics of Bacteriophages / 239 T4 Phage / 245 Structure / 245 General Pattern of T4 Gene Expression / 247 T4 Genome / 250 λ Phage / 256 The Lysis-Lysogeny Decision / 259 Transcription / 259 Function of Cro Versus CI Repressor and the Structure of OL and OR / 260 Establishment of Repressor Synthesis / 260 Control of Integration and Excision / 262 Negative Retroregulation of int by sib / 263 λ-Phage Replication / 264 µ Phage: Transposition as a Lifestyle / 266 X174 / 271 Summary / 274 General / 274 T4 Bacteriophage / 274 λ Phage / 275 φX174 / 275 µ Phage / 275 7 CELL STRUCTURE AND FUNCTION 277 The Eukaryotic Nucleus / 277 Bacterial Nucleoids / 279 Nucleosomes / 283 Mitochondria / 287 Microbial Cell Surfaces / 288 Eukaryotic Cell Surfaces / 288 Prokaryotic Cell Surfaces / 289 Surface Layers of Bacteria / 290 Peptidoglycans of Bacterial Cell Walls / 290 Peptidoglycan (Murein) Hydrolases / 295 Peptidoglycan (Murein) Synthesis / 295 Teichoic Acids and Lipoteichoic Acids / 300 Outer Membranes of Gram-Negative Bacteria / 303
xi Lipopolysaccharide Biosynthesis/308 Enterobacterial Common Antigen/30 Cytopl smic Men branes 31 Transport 313 nous Organelles /314 Capsules /315 Microbial Biofilms /322 Organs of Locomotion /323 Cilia and Flagella of Fukarvotes 323 Bacterial (Prokaryotie)Flagella /325 Chemotaxis /328 Swarming Motility /334 Motility in Spirochetes /337 Gliding Motility/ 339 Pili or Fimbria 340 1344 (Murein)/345 ds/346 Cytoplasmic Membrane /346 Periplasm 346 Capsules /346 Biofilms /347 Cilia and Flagella of Eukaryotes /347 Bacterial Flagella 347 48 Swarming Mo ility /3 8 iae ch 1348 :1 249 8 CENTRAL PATHWAYS OF CARBOHYDRATE METABOLISM 350 Alternate Pathways of Carbohydrate Metabolism 351 Eructose Risphosnhate Aldolase pathway /351 Altemate Pathways of Glucose Utilization /354 Entner-Doudoroff or Ketogluconate Pathway /354 Phosphoketolase Pathway /356 Oxidative Pentose Phosphate Cycle /358
xi Lipopolysaccharide Biosynthesis / 308 Enterobacterial Common Antigen / 309 Cytoplasmic Membranes / 310 Permeability and Transport / 313 Periplasm / 313 Other Membranous Organelles / 314 Capsules / 315 Microbial Biofilms / 322 Organs of Locomotion / 323 Cilia and Flagella of Eukaryotes / 323 Bacterial (Prokaryotic) Flagella / 325 Chemotaxis / 328 Swarming Motility / 334 Motility in Spirochetes / 337 Gliding Motility / 339 Pili or Fimbriae / 340 Nucleus, Nucleosomes, and Nucleoids / 343 Mitochondria / 344 Eukaryotic Cell Surface / 344 Surface (S) layers / 344 Bacterial Cell Wall Peptidoglycan (Murein) / 345 Teichoic and Lipoteichoic Acids / 346 Outer Membrane / 346 Cytoplasmic Membrane / 346 Periplasm / 346 Capsules / 346 Biofilms / 347 Cilia and Flagella of Eukaryotes / 347 Bacterial Flagella / 347 Chemotaxis / 348 Swarming Motility / 348 Gliding Motility / 348 Motility in Spirochetes / 348 Pili or Fimbriae / 349 8 CENTRAL PATHWAYS OF CARBOHYDRATE METABOLISM 350 Alternate Pathways of Carbohydrate Metabolism / 351 Fructose Bisphosphate Aldolase Pathway / 351 Alternate Pathways of Glucose Utilization / 354 Entner-Doudoroff or Ketogluconate Pathway / 354 Phosphoketolase Pathway / 356 Oxidative Pentose Phosphate Cycle / 358
CONTENTS Gluconeogenesis/360 Regulation /360 Glycogen Synthesis /361 Cye1 Glyoxylate Cycle 3 9 ENERGY PRODUCTION AND METABOLITE TRANSPORT 368 rylation/369 Oxidative Ph sph 11371 Mea PME /372 1373 /377 Energy Yield /380 gen rating ATP in Alkalophiles /380 Energetics of Chemolithotrophs/380 pH Homeostasis 382 Metabolite Transport /383 Facilitated Diffusion/383 Mechanosensitive Channels /385 ATP-Binding Cassette Transporter Family/385 Chemiosmotic-Driven Transport /385 Establishing Ion Gradients Specific Tr ystems 38 ATP-Link ive Pun s/387 Phosph Production /392 Meta lite Tra /39 10 METABOLISM OF SUBSTRATES OTHER THAN GLUCOSE Utilization of Sugars other than Glucose 394 I actose 394 Galactose /396 Maltose /396
xii CONTENTS Gluconeogenesis / 360 Regulation / 360 Glycogen Synthesis / 361 Tricarboxylic Acid Cycle / 361 Glyoxylate Cycle / 365 9 ENERGY PRODUCTION AND METABOLITE TRANSPORT 368 Energy Production / 368 Substrate-Level Phosphorylation / 369 Oxidative Phosphorylation / 371 Measurement of PMF / 372 Electron Transport Systems / 373 Anaerobic Respiration / 376 Conversion of PMF to Energy / 377 Structure of F1F0 and the atp Operon / 379 Energy Yield / 380 Generating ATP in Alkalophiles / 380 Energetics of Chemolithotrophs / 380 pH Homeostasis / 382 Metabolite Transport / 383 Facilitated Diffusion / 383 Mechanosensitive Channels / 385 ATP-Binding Cassette Transporter Family / 385 Chemiosmotic-Driven Transport / 385 Establishing Ion Gradients / 387 Specific Transport Systems / 387 ATP-Linked Ion Motive Pumps / 387 The Histidine Permease / 389 Iron / 389 Phosphotransferase System / 390 Summary / 392 Energy Production / 392 Metabolite Transport / 392 10 METABOLISM OF SUBSTRATES OTHER THAN GLUCOSE 394 Utilization of Sugars other than Glucose / 394 Lactose / 394 Galactose / 396 Maltose / 396
Mannitol/396 1397 Raffinose.Sta chyose.and Gu ur Gum /399 Pathways /400 1403 Pectin Utilization /4 410 Utilization of starch.gly and Related Compounds /411 Utilization of Aromatic H carbons /411 11 FERMENTATION PATHWAYS 412 Fermentation Balances /412 Yeast Fermentation 415 Lactic Acid-Producing Fermentations /417 Butyric Acid-and Solvent-Producing Fermentations /423 Fermentations of the Mixed-Acid Type /425 Propionic Acid Fermentation /428 Acetic Acid Fermentation /430 Fermentation Pathways 431 431 ntation /3 Acid and Solvent-Produ cing Fermentations /43 /43 Propionic Acid Ferment 43 d Fermentatio 3 12 PHOTOSYNTHESIS AND INORGANIC METABOLISM 434 Characteristics and Metabolism of Autotro h8/434 hetic Bacteria and Cva /434 d mechanis ns of Photosynthesis/437 Hydrogen Bacteria 440 Nitrifying Bacteria 442 Sulfur Bacteria/442 Iron Bacteria 443 Methylotrophs /44 Methanogens 446
xiii Mannitol / 396 Fucose and Rhamnose / 397 Mellibiose, Raffinose, Stachyose, and Guar Gum / 399 Pectin and Aldohexuronate Pathways / 400 Cellulose Degradation / 402 Starch, Glycogen, and Related Compounds / 403 Metabolism of Aromatic Compounds / 407 Pectin Utilization / 410 Cellulose Utilization / 410 Utilization of Starch, Glycogen, and Related Compounds / 411 Utilization of Aromatic Hydrocarbons / 411 11 FERMENTATION PATHWAYS 412 Fermentation Balances / 412 Yeast Fermentation / 415 Lactic Acid–Producing Fermentations / 417 Butyric Acid — and Solvent-Producing Fermentations / 423 Fermentations of the Mixed-Acid Type / 425 Propionic Acid Fermentation / 428 Acetic Acid Fermentation / 430 Fermentation Pathways / 431 Yeast Fermentation / 431 Lactic Acid Fermentation / 432 Butyric Acid and Solvent-Producing Fermentations / 432 Mixed-Acid Fermentations / 433 Propionic Acid Fermentation / 433 Acetic Acid Fermentation / 433 12 PHOTOSYNTHESIS AND INORGANIC METABOLISM 434 Characteristics and Metabolism of Autotrophs / 434 Photosynthetic Bacteria and Cyanobacteria / 434 Autotrophic CO2 Fixation and Mechanisms of Photosynthesis / 437 Hydrogen Bacteria / 440 Nitrifying Bacteria / 442 Sulfur Bacteria / 442 Iron Bacteria / 443 Methylotrophs / 444 Methanogens / 446