Microbial Physiology / Albert G. Moat.

Enhanced descriptions from Syndetics:

Microbial physiology, the understanding of cell structure, growth factors, metabolism and genetic composition of microorganisms, is a field that is experiencing growth and strong interest. However, there is a lack of solid, comprehensive, and current reference books covering this part of microbiology.Microbial Physiology, Third Edition fills that void.This new edition is completely revised and updated to reflect the most current information and latest topics. Written by two of the leading experts in the field, Albert G. Moat and John W. Foster, the new edition of Microbial Physiology integrates genetics and molecular biology with bacterial physiology and metabolism in addition to providing an in-depth coverage of all the topics central to microbial physiology.Topics covered in the Third Edition include: Macromolecular Synthesis and Processing Regulation of Prokaryotic Gene Expression Bacteriophage Genetics Subcellular Structure of Microorganisms Nitrogen Metabolism Amino Acids, Purines, and Pyrimidines Morphogenesis: Development of Dormant and Resting Forms Microbial Physiology, Third Edition is the perfect reference source for professional microbiologists and graduate students in microbiology, as well as researchers in both the pharmaceutical and biotechnology industries.

Table of contents provided by Syndetics

• Preface (p. xix)
• 1 Introduction to Microbial Physiology (p. 1)
• The Escherichia coli Paradigm (p. 1)
• Cell Structure (p. 1)
• The Cell Surface (p. 1)
• Synthesis of DNA, RNA, and Protein (p. 7)
• Metabolic and Genetic Regulation (p. 10)
• Microbial Genetics (p. 10)
• Chemical Synthesis (p. 12)
• Chemical Composition (p. 12)
• Energy (p. 13)
• Oxidation--Reduction Versus Fermentation (p. 15)
• Nitrogen Assimilation (p. 18)
• Special Topics (p. 18)
• Endospores (p. 18)
• Growth (p. 19)
• Continuous Culture (p. 22)
• Factors Affecting Growth (p. 22)
• Nutrition (p. 22)
• Oxygen (p. 24)
• Carbon Dioxide (p. 24)
• Extremophiles (p. 25)
• Microbial Stress Responses (p. 26)
• Summary (p. 26)
• 2 Macromolecular Synthesis and Processing: DNA, RNA, and Protein Synthesis (p. 27)
• Structure of DNA (p. 28)
• Bacterial Nucleoids (p. 30)
• REP Elements (p. 35)
• DNA Replication (p. 36)
• DNA Replication is Bidirectional and Semiconservative (p. 36)
• DNA Polymerase Functions as a Dimer (p. 36)
• Model of DNA Replication (p. 37)
• Initiation of DNA Replication (p. 42)
• Termination of DNA Replication and Chromosome Partitioning (p. 46)
• RNA Synthesis: Transcription (p. 47)
• RNA Synthesis (p. 47)
• RNA Turnover (p. 53)
• RNA Processing (p. 54)
• Protein Synthesis: Translation (p. 57)
• Transfer RNA (p. 58)
• Charging of tRNA (p. 62)
• Ribosome Structure and Synthesis (p. 62)
• Initiation of Polypeptide Synthesis (p. 68)
• Elongation (p. 68)
• Peptide Bond Formation (p. 71)
• Translocation (p. 71)
• Termination (p. 72)
• Posttranslational Processing (p. 73)
• When Nonsense Makes Sense (p. 74)
• Coupled Transcription and Translation (p. 74)
• Protein Folding and Chaperones (p. 74)
• Folding Stages (p. 75)
• Protein Folding and Chaperone Mechanisms Outside the Cytoplasm (p. 76)
• Quality Control (p. 76)
• Protein Trafficking (p. 77)
• Insertion of Integral Membrane Proteins and Export of Periplasmic Proteins (p. 77)
• Secretion of Proteins Across the Outer Membrane (p. 79)
• Protein Degradation (p. 83)
• Degradation of Abnormal Proteins (p. 83)
• Energy-Dependent Proteases (p. 86)
• Antibiotics that affect Nucleic Acid and Protein Synthesis (p. 88)
• Agents affecting DNA Metabolism (p. 88)
• Agents Affecting Transcription (p. 91)
• Agents Affecting Translation (p. 92)
• Nucleoids (p. 97)
• DNA Replication (p. 98)
• Transcription and Translation (p. 98)
• Protein Folding, Trafficking, and Degradation (p. 99)
• Antibiotics (p. 100)
• 3 Bacterial Genetics: Dna Exchange, Recombination, mutagenesis, and repair (p. 101)
• Transfer of Genetic Information in Prokaryotes (p. 101)
• Plasmids (p. 102)
• Partitioning (p. 102)
• Incompatibility (p. 103)
• Nonconjugative, Mobilizable Plasmids (p. 103)
• Resistance Plasmids (p. 103)
• Plasmids in Other Bacterial Genera (p. 104)
• Plasmid Replication (p. 104)
• Addiction Modules: Plasmid Maintenance by Host Killing: The ccd Genes (p. 108)
• Conjugation (p. 108)
• F Factor (p. 108)
• cis/trans complementation Test (p. 115)
• Conjugation and Pheromones in Enterococci (p. 116)
• Conjugation, Cell-Cell Signaling, and Bacterial-Induced Tumors (p. 117)
• Transformation (p. 118)
• Gram-Positive Transformation (p. 119)
• Gram-Negative Transformation (p. 121)
• Transfection and Forced Competence (p. 124)
• Transduction (p. 124)
• Recombination (p. 127)
• General Recombination (p. 128)
• Genetics of Recombination (p. 131)
• Restriction and Modification (p. 133)
• Insertion Sequences and Transposable Elements (p. 138)
• Transposon Tn10 (p. 140)
• Transposon Tn3 (p. 143)
• Conjugative Transposition (p. 143)
• Evolutionary Consideration (p. 144)
• Integrons (p. 145)
• Mutagenesis (p. 145)
• Spontaneous Mutations (p. 147)
• The Nature of Mutational Events (p. 147)
• Suppressor Mutations (p. 148)
• DNA Repair Systems (p. 152)
• Photoreactivation (p. 152)
• Nucleotide Excision Repair (p. 152)
• Transcription-Coupled Repair (p. 155)
• Methyl-Directed Mismatch Repair (p. 156)
• Very Short-Patch Mismatch Repair (p. 157)
• DNA Glycosylases and Base Excision Repair (p. 158)
• Adaptive Response to Methylating and Ethylating Agents (p. 159)
• Postreplication Daughter Strand Gap Repair (p. 160)
• SOS-Inducible Repair (p. 162)
• Replication Restart (p. 164)
• Adaptive Mutations (p. 166)
• Plasmids (p. 167)
• Transformation (p. 167)
• Conjugation (p. 168)
• Recombination (p. 168)
• Restriction Modification (p. 168)
• Transposition (p. 169)
• Mutagenesis (p. 169)
• Repair Mechanisms (p. 169)
• 4 Microbial Physiology in the Genomic Era: A Revolutionary Tale (p. 171)
• Genomic and Proteomic Tools (p. 171)
• Cloning a Genome (p. 171)
• DNA Sequencing (p. 172)
• Web Science: Internet Tools for DNA Sequence Analysis (p. 173)
• Gene Replacement (p. 175)
• Gene Arrays (p. 177)
• Proteomics (p. 177)
• Traditional Tools (p. 181)
• Mutant Hunts (p. 181)
• Transcriptional and Translational Gene Fusions (Reporter Genes) (p. 182)
• Polymerase Chain Reaction (p. 182)
• DNA Mobility Shifts (Gel Shifts and Supershifts) (p. 185)
• Finding Transcriptional Starts by Primer Extension (p. 186)
• Detecting DNA, RNA, Protein, and DNA-Binding Proteins by Southern, Northern, Western, and Southwestern Blots (p. 187)
• Two-Hybrid Analysis (p. 188)
• Summary (p. 192)
• 5 Regulation of Prokaryotic Gene Expression (p. 194)
• Transcriptional Control (p. 194)
• DNA-Binding Proteins (p. 195)
• The lac Operon: A Paradigm of Gene Expression (p. 197)
• Catabolite Control: Sensing Energy Status (p. 201)
• Class I and Class II CRP-Dependent Genes (p. 204)
• The Catabolite Repressor/Activator Protein Cra (p. 204)
• Catabolite Control: The Gram-Positive Paradigm (p. 206)
• The gal Operon: DNA Looping with a Little Help from Hu (p. 206)
• The Arabinose Operon: One Regulator, Two Functions (p. 206)
• Attenuation Controls (p. 211)
• Transcriptional Attenuation Mechanisms (p. 211)
• Translational Attenuation Control: The pyrC Strategy (p. 215)
• Membrane-Mediated Regulation: The put System (p. 216)
• Recombinational Regulation of Gene Expression (Flagellar Phase Variation) (p. 217)
• Translational Repression (p. 219)
• Anti-[sigma] Regulation by Molecular Hijacking (p. 220)
• Titrating a Posttranscriptional Regulator: The CsrA/CsrB Carbon Storage Regulatory Team (p. 222)
• Global Control Networks (p. 223)
• Communication with the Environment: Two-Component Regulatory Systems (p. 223)
• Regulation of Nitrogen Assimilation and Nitrogen Fixation: Examples of Integrated Biochemical and Genetic Controls (p. 227)
• Phosphate Uptake: Communication Between Transport and Two-Component Regulatory Systems (p. 232)
• Quorum Sensing: How Bacteria Talk to Each Other (p. 234)
• Proteolytic Control (p. 235)
• Summary (p. 236)
• 6 Bacteriophage Genetics (p. 239)
• General Characteristics of Bacteriophages (p. 239)
• T4 Phage (p. 245)
• Structure (p. 245)
• General Pattern of T4 Gene Expression (p. 247)
• T4 Genome (p. 250)
• [lambda]Phage (p. 256)
• The Lysis-Lysogeny Decision (p. 256)
• Transcription (p. 259)
• Function of Cro Versus CI Repressor and the Structure of O[subscript L] and O[subscript R] (p. 259)
• Establishment of Repressor Synthesis (p. 260)
• Control of Integration and Excision (p. 262)
• Negative Retroregulation of int by sib (p. 263)
• [lambda]-Phage Replication (p. 264)
• [mu]Phage: Transposition as a Lifestyle (p. 266)
• [Phi]X174 (p. 271)
• Summary (p. 274)
• General (p. 274)
• T4 Bacteriophage (p. 274)
• [lambda] Phage (p. 275)
• [phi]X174 (p. 275)
• [mu] Phage (p. 275)
• 7 Cell Structure and Function (p. 277)
• The Eukaryotic Nucleus (p. 277)
• Bacterial Nucleoids (p. 278)
• Nucleosomes (p. 282)
• Mitochondria (p. 287)
• Microbial Cell Surfaces (p. 288)
• Eukaryotic Cell Surfaces (p. 288)
• Prokaryotic Cell Surfaces (p. 289)
• Surface Layers of Bacteria (p. 290)
• Peptidoglycans of Bacterial Cell Walls (p. 290)
• Peptidoglycan (Murein) Hydrolases (p. 294)
• Peptidoglycan (Murein) Synthesis (p. 295)
• Teichoic Acids and Lipoteichoic Acids (p. 300)
• Outer Membranes of Gram-Negative Bacteria (p. 303)
• Lipopolysaccharide Biosynthesis (p. 308)
• Enterobacterial Common Antigen (p. 309)
• Cytoplasmic Membranes (p. 310)
• Permeability and Transport (p. 313)
• Periplasm (p. 313)
• Other Membranous Organelles (p. 313)
• Capsules (p. 315)
• Microbial Biofilms (p. 322)
• Organs of Locomotion (p. 323)
• Cilia and Flagella of Eukaryotes (p. 323)
• Bacterial (Prokaryotic) Flagella (p. 324)
• Chemotaxis (p. 327)
• Swarming Motility (p. 334)
• Motility in Spirochetes (p. 337)
• Gliding Motility (p. 339)
• Pili or Fimbriae (p. 340)
• Nucleus, Nucleosomes, and Nucleoids (p. 343)
• Mitochondria (p. 344)
• Eukaryotic Cell Surface (p. 344)
• Surface (S) layers (p. 344)
• Bacterial Cell Wall Peptidoglycan (Murein) (p. 345)
• Teichoic and Lipoteichoic Acids (p. 346)
• Outer Membrane (p. 346)
• Cytoplasmic Membrane (p. 346)
• Periplasm (p. 346)
• Capsules (p. 346)
• Biofilms (p. 346)
• Cilia and Flagella of Eukaryotes (p. 347)
• Bacterial Flagella (p. 347)
• Chemotaxis (p. 348)
• Swarming Motility (p. 348)
• Gliding Motility (p. 348)
• Motility in Spirochetes (p. 348)
• Pili or Fimbriae (p. 349)
• 8 Central Pathways of Carbohydrate Metabolism (p. 350)
• Alternate Pathways of Carbohydrate Metabolism (p. 350)
• Fructose Bisphosphate Aldolase Pathway (p. 350)
• Alternate Pathways of Glucose Utilization (p. 353)
• Entner-Doudoroff or Ketogluconate Pathway (p. 354)
• Phosphoketolase Pathway (p. 356)
• Oxidative Pentose Phosphate Cycle (p. 358)
• Gluconeogenesis (p. 360)
• Regulation (p. 360)
• Glycogen Synthesis (p. 361)
• Tricarboxylic Acid Cycle (p. 361)
• Glyoxylate Cycle (p. 365)
• 9 Energy Production and Metabolite Transport (p. 368)
• Energy Production (p. 368)
• Substrate-Level Phosphorylation (p. 369)
• Oxidative Phosphorylation (p. 371)
• Measurement of PMF (p. 372)
• Electron Transport Systems (p. 373)
• Anaerobic Respiration (p. 375)
• Conversion of PMF to Energy (p. 377)
• Structure of F[subscript 1]F[subscript 0] and the atp Operon (p. 379)
• Energy Yield (p. 380)
• Generating ATP in Alkalophiles (p. 380)
• Energetics of Chemolithotrophs (p. 380)
• pH Homeostasis (p. 381)
• Metabolite Transport (p. 382)
• Facilitated Diffusion (p. 382)
• Mechanosensitive Channels (p. 384)
• ATP-Binding Cassette Transporter Family (p. 385)
• Chemiosmotic-Driven Transport (p. 385)
• Establishing Ion Gradients (p. 386)
• Specific Transport Systems (p. 387)
• ATP-Linked Ion Motive Pumps (p. 387)
• The Histidine Permease (p. 389)
• Iron (p. 389)
• Phosphotransferase System (p. 390)
• Summary (p. 392)
• Energy Production (p. 392)
• Metabolite Transport (p. 392)
• 10 Metabolism of Substrates Other Than Glucose (p. 394)
• Utilization of Sugars Other Than Glucose (p. 394)
• Lactose (p. 394)
• Galactose (p. 396)
• Maltose (p. 396)
• Mannitol (p. 396)
• Fucose and Rhamnose (p. 397)
• Mellibiose, Raffinose, Stachyose, and Guar Gum (p. 399)
• Pectin and Aldohexuronate Pathways (p. 400)
• Cellulose Degradation (p. 402)
• Starch, Glycogen, and Related Compounds (p. 402)
• Metabolism of Aromatic Compounds (p. 407)
• Pectin Utilization (p. 410)
• Cellulose Utilization (p. 410)
• Utilization of Starch, Glycogen, and Related Compounds (p. 411)
• Utilization of Aromatic Hydrocarbons (p. 411)
• 11 Fermentation Pathways (p. 412)
• Fermentation Balances (p. 412)
• Yeast Fermentation (p. 414)
• Lactic Acid-Producing Fermentations (p. 417)
• Butyric Acid--and Solvent-Producing Fermentations (p. 423)
• Fermentations of the Mixed-Acid Type (p. 425)
• Propionic Acid Fermentation (p. 428)
• Acetic Acid Fermentation (p. 430)
• Fermentation Pathways (p. 431)
• Yeast Fermentation (p. 431)
• Lactic Acid Fermentation (p. 432)
• Butyric Acid and Solvent-Producing Fermentations (p. 432)
• Mixed-Acid Fermentations (p. 433)
• Propionic Acid Fermentation (p. 433)
• Acetic Acid Fermentation (p. 433)
• 12 Photosynthesis and Inorganic Metabolism (p. 434)
• Characteristics and Metabolism of Autotrophs (p. 434)
• Photosynthetic Bacteria and Cyanobacteria (p. 434)
• Autotrophic CO[subscript 2] Fixation and Mechanisms of Photosynthesis (p. 437)
• Hydrogen Bacteria (p. 440)
• Nitrifying Bacteria (p. 442)
• Sulfur Bacteria (p. 442)
• Iron Bacteria (p. 443)
• Methylotrophs (p. 444)
• Methanogens (p. 446)
• 13 Lipids and Sterols (p. 450)
• Lipid Composition of Microorganisms (p. 450)
• Straight-Chain Fatty Acids (p. 451)
• Branched-Chain Fatty Acids (p. 453)
• Ring-Containing Fatty Acids (p. 454)
• Alk-1-enyl Ethers (Plasmalogens) (p. 455)
• Alkyl Ethers (p. 455)
• Phospholipids (Phosphoglycerides) (p. 457)
• Glycolipids (p. 458)
• Biosynthesis of Fatty Acids (p. 459)
• Degradation of Fatty Acids (p. 464)
• Biosynthesis of Phospholipids (p. 465)
• Biosynthesis of Isoprenoids (p. 468)
• 14 Nitrogen Metabolism (p. 475)
• Biological Nitrogen Fixation (p. 475)
• The Nitrogen Fixation Process (p. 479)
• Components of the Nitrogenase System (p. 480)
• Symbiotic Nitrogen Fixation (p. 483)
• Inorganic Nitrogen Metabolism (p. 487)
• Assimilation of Inorganic Nitrogen (p. 492)
• General Reactions of Amino Acids (p. 494)
• Amino Acid Decarboxylases (p. 494)
• Amino Acid Deaminases (p. 494)
• Amino Acid Transaminases (Aminotransferases) (p. 497)
• Amino Acid Racemases (p. 498)
• Role of Pyridoxal-5'-Phosphate in Enzymatic Reactions with Amino Acids (p. 499)
• The Stickland Reaction (p. 500)
• Nitrogen Fixation (p. 501)
• Inorganic Nitrogen (p. 502)
• Urease (p. 502)
• Assimilation of Inorganic Nitrogen (p. 502)
• 15 Biosynthesis and Metabolism of Amino Acids (p. 503)
• The Glutamate or [alpha]-Ketoglutarate Family (p. 503)
• Glutamine and Glutathione Synthesis (p. 503)
• The Proline Pathway (p. 504)
• Aminolevulinate Synthesis (p. 504)
• The Arginine Pathway (p. 504)
• Polyamine Biosynthesis (p. 509)
• The [alpha]-Ketoadipate Pathway to Lysine (p. 510)
• The Asparate and Pyruvate Families (p. 513)
• Asparagine Synthesis (p. 513)
• The Aspartate Pathway (p. 514)
• The Bacterial Pathway to Lysine (p. 515)
• Threonine, Isoleucine, and Methionine Formation (p. 516)
• Isoleucine, Valine, and Leucine Biosynthesis (p. 518)
• Regulation of the Aspartate Family (p. 518)
• The Serine-Glycine Family (p. 520)
• Aminolevulinate and the Pathway to Tetrapyrroles (p. 523)
• The Aromatic Amino Acid Pathway (p. 523)
• Phenylalanine, Tyrosine, and Tryptophan (p. 523)
• The Common Aromatic Amino Acid Pathway (p. 525)
• Pathways to Tyrosine and Phenylalanine (p. 526)
• p-Aminobenzoate and Folate Biosynthesis (p. 531)
• Enterobactin Biosynthesis (p. 533)
• The Pathway to Ubiquinone (p. 534)
• Menaquinone (Vitamin K) Biosynthesis (p. 534)
• Biosynthesis of Nicotinamide Adenine Dinucleotide (NAD) (p. 534)
• Histidine Biosynthesis (p. 539)
• Amino Acids (p. 541)
• Glutamate ([alpha]-Ketoglutarate) Family (p. 541)
• Aspartate and Pyruvate Families (p. 542)
• Serine-Glycine Family (p. 543)
• Aromatic Amino Acid Family (p. 543)
• Histidine (p. 544)
• 16 Purines and Pyrimidines (p. 545)
• Biosynthesis of Purines (p. 545)
• Biosynthesis of Pyrimidines (p. 550)
• Interconversion of Nucleotides, Nucleosides, and Free Bases: Salvage Pathways (p. 554)
• Regulation of Purine and Pyrimidine Biosynthesis (p. 555)
• Purines and Pyrimidines (p. 559)
• Riboflavin Biosynthesis (p. 560)
• Thiamine Biosynthesis (p. 560)
• 17 Bacterial Cell Division (p. 561)
• Cell Division in Gram-Negative Rods (p. 561)
• Cell Division in Gram-Positive Cocci (p. 570)
• Cell Division in Gram-Positive Bacilli (p. 575)
• General Reviews (p. 578)
• Cell Division in Gram-Negative Rods (p. 579)
• Cell Division in Gram-Positive Cocci (p. 580)
• Cell Division in Gram-Positive Bacilli (p. 581)
• 18 Microbial Stress Responses (p. 582)
• Osmotic Stress and Osmoregulation (p. 582)
• High Osmolality (p. 583)
• Low Osmolality (p. 584)
• Osmotic Control of Gene Expression (p. 585)
• Aerobic to Anaerobic Transitions (p. 587)
• Formate Nitrate Regulation (p. 589)
• Nitrate Response (p. 589)
• ArcAB System (p. 591)
• Oxidative Stress (p. 592)
• Regulation of the Oxidative Stress Response (p. 594)
• pH Stress and Acid Tolerance (p. 596)
• Thermal Stress and the Heat Shock Response (p. 597)
• Nutrient Stress and the Starvation--Stress Response (p. 601)
• Starvation--Stress Response (p. 601)
• Stringent Control (p. 602)
• Extremophiles (p. 605)
• Summary (p. 608)
• Osmotic Stress and Osmoregulation (p. 608)
• Aerobic to Anaerobic Transitions (p. 609)
• Oxidative Stress (p. 609)
• pH Stress and Acid Tolerance (p. 610)
• Thermal Stress and the Heat Shock Response (p. 610)
• Nutrient Stress and the Starvation Stress Response (p. 611)
• Stringent Control (p. 611)
• Extremophiles (p. 611)
• 19 Bacterial Differentiation (p. 612)
• Bacillus Endospore Formation (p. 612)
• Life Cycle of Bacillus (p. 613)
• Stages of Sporulation (p. 614)
• Physiological and Genetic Aspects of Sporulation (p. 616)
• Sporulation Genes (p. 616)
• Initiation (p. 617)
• Transition from Stage II to Stage III (p. 619)
• Forespore Development (p. 620)
• Final Stages of Sporulation (p. 621)
• Spore Cortex Synthesis (p. 622)
• Spore Coat Protein Synthesis (p. 622)
• Activation, Germination, and Outgrowth of Bacterial
• Endospores (p. 623)
• Activation (p. 624)
• Germination (p. 624)
• Outgrowth (p. 627)
• Myxobacterial Developmental Cycle (p. 628)
• Life Cycle of Myxobacteria (p. 628)
• Aggregation and Fruiting Body Formation (p. 629)
• Genetics of Myxococcus xanthus Development (p. 632)
• Caulobacter Differentiation (p. 637)
• Life Cycle of Caulobacter crescentus (p. 637)
• The Stalk, the Holdfast, and the Flagellum: Structure, Genetics, and Regulation (p. 638)
• Regulation and Checkpoints of the Cell Cycle of C. crescentus (p. 642)
• Endospore Formation (p. 644)
• Germination and Outgrowth of Endospores (p. 645)
• Myxobacterial Developmental Cycle (p. 646)
• Caulobacter Differentiation (p. 647)
• 20 Host-Parasite Interactions (p. 648)
• Overview of Host-Parasite Relationships (p. 648)
• Structures and Functions Involved in Host-Parasite Interactions (p. 650)
• Adherence/Colonization (p. 650)
• Virulence Factor Secretion Systems (p. 653)
• Exotoxins (p. 658)
• Quorum Sensing (p. 664)
• Paradigms of Bacterial Pathogenesis (p. 669)
• Enteropathogenic Escherichia coli (p. 669)
• Salmonella Enterica Serovars (p. 669)
• Listeria Monocytogenes (p. 670)
• Chlamydia spp (p. 672)
• Overview (p. 672)
• Adherence/Colonization (p. 672)
• Virulence Factor Secretion Systems (p. 673)
• Exotoxins (p. 673)
• Quorum Sensing (p. 674)
• Paradigms of Bacterial Pathogenesis (p. 675)
• Index (p. 676)