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