Ann M. Stevens (VA Virginia Tech), Jayna L. Ditty (University of St. Thomas), Rebecca E. Parales (Davis University of California)
Microbial Physiology
Unity and Diversity
Ann M. Stevens (VA Virginia Tech), Jayna L. Ditty (University of St. Thomas), Rebecca E. Parales (Davis University of California)
Microbial Physiology
Unity and Diversity
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MICROBIAL PHYSIOLOGY UNITY AND DIVERSITY Explore the fascinating world of microbes in Microbial Physiology: Unity and Diversity. This comprehensive, advanced undergraduate-level textbook takes readers on a captivating journey through the intricate and often underappreciated world of microbial physiology, emphasizing both the common features that unify microbes and the diversity that makes them unique. In Part I: Unity, the book lays a strong foundation in the basics of microbial physiology. Delve into the three domains of life, get an intimate look at the metabolic pathways that fuel the…mehr
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MICROBIAL PHYSIOLOGY UNITY AND DIVERSITY Explore the fascinating world of microbes in Microbial Physiology: Unity and Diversity. This comprehensive, advanced undergraduate-level textbook takes readers on a captivating journey through the intricate and often underappreciated world of microbial physiology, emphasizing both the common features that unify microbes and the diversity that makes them unique. In Part I: Unity, the book lays a strong foundation in the basics of microbial physiology. Delve into the three domains of life, get an intimate look at the metabolic pathways that fuel the microbial world, and take a deep dive into the cellular components that constitute a microbe. Further, explore the principles of cellular growth, bioenergetics, and the mechanics of respiration and fermentation. The Unity section concludes with a comprehensive discussion of regulation at posttranslational and gene levels, paving the way for a rich understanding of microbial function. Part II: Diversity, takes the reader into the broad and versatile world of microbial metabolism, exploring the range of energy sources and metabolic pathways microbes employ. This section leads readers through topics such as autotrophy, phototrophy, chemotrophy, and microbial contributions to the carbon, sulfur, and nitrogen cycles. The complexity of microbial cell envelope structures, transport processes, and protein transport are explored, along with bacterial motility, chemotaxis, and the phenomenon of quorum sensing. The section concludes with an exploration of stress responses and the diverse lifestyles that bacteria can adopt. Microbial Physiology: Unity and Diversity will engage readers with its accessible yet thorough treatment of this critical field of microbiology. Each chapter contains detailed illustrations that concisely explain complex topics and concludes with robust end-of-chapter questions that not only test understanding but also provide an opportunity for readers to dig deeper into the content. This book is a must-have for students studying microbiology, as well as researchers and professionals keen to brush up their knowledge or explore new facets of microbial physiology.
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Hinweis: Dieser Artikel kann nur an eine deutsche Lieferadresse ausgeliefert werden.
Produktdetails
- Produktdetails
- ASM Books
- Verlag: American Society for Microbiology
- Seitenzahl: 496
- Erscheinungstermin: 30. April 2024
- Englisch
- Abmessung: 286mm x 216mm x 54mm
- Gewicht: 1594g
- ISBN-13: 9781683673675
- ISBN-10: 1683673670
- Artikelnr.: 63662165
- ASM Books
- Verlag: American Society for Microbiology
- Seitenzahl: 496
- Erscheinungstermin: 30. April 2024
- Englisch
- Abmessung: 286mm x 216mm x 54mm
- Gewicht: 1594g
- ISBN-13: 9781683673675
- ISBN-10: 1683673670
- Artikelnr.: 63662165
Ann M. Stevens, Professor in the Department of Biological Sciences Virginia Tech. Jayna L. Ditty, Professor and Associate Dean of College of Arts and Sciences, University of St. Thomas. Rebecca E. Parales, Professor in the Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis. Susan M. Merkel, Associate Director of the CALS Office of Academic Programs, Cornell University.
Preface xv About the Authors xvii About the Companion Website xviii Part I:
Unity 3 1 Microbial Phylogeny--The Three Domains of Life 5 Introduction 6
The Three Branches of Life: Bacteria, Archaea, and Eukarya 6 The 16S/18S
rRNA Gene as a Basis for Phylogenetic Comparisons 7 The Modern Molecular
Phylogenetic Tree of Life 12 Phylogenetics and Earth History 14 2 Metabolic
Unity--Generation of Biosynthetic Precursors 21 Making Connections 22 The
Purpose of Central Metabolism 22 The 12 Essential Precursors 23 The
Embden-Meyerhof-Parnas (EMP) Pathway/Glycolysis 25 Structure and Energy
Exchange of Key Coenzymes 28 Controlling the Direction of Carbon Flow
during Glycolysis 29 The Pentose Phosphate Pathway (PPP) 31 The
Entner-Doudoroff (ED) Pathway 33 The Transition Reaction: Carbon Flow into
the Tricarboxylic Acid (TCA) Cycle 36 The Tricarboxylic Acid (TCA) Cycle 37
Anaplerotic Reactions 37 The Branched or Incomplete Tricarboxylic Acid
(TCA) Pathway 41 The Glyoxylate Cycle 41 Reversing Carbon Flow from the
Tricarboxylic Acid (TCA) Cycle to the Embden-Meyerhof-Parnas (EMP) Pathway
43 3 Cellular Components--What's In a Cell 51 Making Connections 52
Estimating Molecular Concentrations 52 Physiologically Relevant Protein
Concentrations 54 Measuring Enzyme Activity: Basic Principles of Enzyme
Assays 55 Michaelis-Menten Kinetics 58 Studying the Proteome 59 The
Physiological Role and Composition of Cellular RNA 61 The Physiological
Role and Composition of Cellular DNA 63 Studying the Genome and the
Transcriptome 64 4 Cellular Growth 73 Making Connections 74 Methods to
Monitor Bacterial Growth 74 The Phases of Bacterial Growth in Batch Culture
78 Requirements for Microbial Growth 80 Diauxic Growth 80 Exponential
Growth Kinetics 81 Chemostats 83 Characteristics of Stationary-Phase Cells
84 Proteins Important for Cell Shape and Cell Division 85 Chromosome
Segregation 86 5 Bioenergetics and the Proton Motive Force 95 Making
Connections 96 Cellular Mechanisms for ATP Synthesis 96 Chemiosmotic Theory
98 ATP Synthase 99 The Proton Motive Force (PMF) 99 Quantifying the Proton
Motive Force 99 Cellular Proton Levels 100 Environmental Impacts on the
Proton Motive Force (PMF) 100 Experimentally Measuring the Proton Motive
Force (PMF) 101 6 Respiration and Fermentation 107 Making Connections 108
The Basic Components of an Electron Transport Chain (ETC) 108
Electrode/Reduction Potential (E0') 109 Brief Review of the Electron
Transport Chain (ETC) in Mitochondria 110 Q Cycle of Mitochondria 113
Bacterial Electron Transport Chains (ETCs) 113 Q Loop of Bacteria 115
Electron Donors and Acceptors in Bacteria 115 Fermentation 117 7
Regulation--Posttranslational Control 127 Making Connections 128 Importance
of Regulatory Processes 128 Allosteric Regulation of Enzymes 129 Allosteric
Regulation of Branched Pathways 131 Covalent Modifications 134
Posttranslational Regulation in the Sugar Phosphotransferase System (PTS)
138 8 Gene Regulation--Transcription Initiation and Posttranscriptional
Control 147 Making Connections 148 Transcription Terminology 148 Bacterial
Transcription Initiation and Elongation 149 Bacterial Transcription
Termination 151 Regulatory cis- and trans-Acting Elements Impacting
Transcription 153 Examples of Different Promoter Structures 154
Transcriptional Regulation of the lac Operon 156 Activation and Repression
by the Global Regulator Cra 158 Attenuation 158 Posttranscriptional
Regulation 161 Methods Used to Study Gene Regulation 163 Methods to
Demonstrate Protein-DNA Interactions 164 Interlude: From Unity to Diversity
177 Metabolic Diversity 178 Global Nutrient Cycles 179 Structural and
Regulatory Diversity of Microbes 180 Part II: Diversity 183 9 Autotrophy
185 Making Connections 186 Autotrophy 186 Calvin Cycle 187 Reductive
Tricarboxylic Acid (rTCA) Cycle 191 Reductive Acetyl-CoA Pathway 193
3-Hydroxypropionate (3HP) Bi-cycle 195
3-Hydroxypropionate-4-Hydroxybutyrate (3HP-4HB) and
Dicarboxylate-4-Hydroxybutyrate (DC-4HB) Cycles 195 Why So Many CO2
Fixation Pathways? 197 10 Phototrophy 207 Making Connections 208
Phototrophy 208 Chlorophyll-Based Phototrophy 209 Cellular Structures
Needed for Phototrophy: Light-Harvesting Complexes, Reaction Centers, and
Unique Membrane Organizations 211 Oxygenic Photoautotrophy in the
Cyanobacteria 215 Anaerobic Anoxygenic Phototrophy in the Phototrophic
Purple Sulfur and Purple Nonsulfur Bacteria 218 Anaerobic Anoxygenic
Phototrophy in the Chlorobi and Chloroflexi (Green Sulfur and Green
Nonsulfur Bacteria, Respectively) 221 Anaerobic Anoxygenic
Photoheterotrophy in the Firmicutes 224 Aerobic Anoxygenic Phototrophy 224
Retinal-Based Phototrophy 225 11 Chemotrophy in the Carbon and Sulfur
Cycles 233 Making Connections 234 The Carbon Cycle 234 The
Chemoorganotrophic Degradation of Polymers 236 The Chemoorganotrophic
Degradation of Aromatic Acids 236 Chemoorganotrophy in Escherichia coli 241
Chemolithoautotrophy 246 Chemolithoautotrophy in Methanogens 248
Methylotrophy Enables Cycling of One-Carbon (C1) Compounds 251 One-Carbon
(C1) Chemolithotrophy in Acetogens 253 The Sulfur Cycle 256
Chemoheterotrophy and Chemolithoautotrophy in the Sulfur Cycle: Sulfate
Reducers 256 Chemolithoautotrophy in the Sulfur Cycle: Sulfur Oxidizers 259
The Anaerobic Food Web and Syntrophy 261 12 Microbial Contributions to the
Nitrogen Cycle 275 Making Connections 276 Overview of the Nitrogen Cycle
276 Nitrogen Fixation 277 Biochemistry of Nitrogen Fixation 278 Regulation
of Nitrogen Fixation 280 Symbiotic Plant-Microbe Interactions during
Nitrogen Fixation 282 Assimilatory Nitrate Reduction 284 Ammonia
Assimilation into Cellular Biomass 285 Nitrification: Ammonia Oxidation,
Nitrite Oxidation, and Comammox 287 Anammox: Anaerobic Ammonia Oxidation
290 Denitrification 293 13 Structure and Function of the Cell Envelope 303
Making Connections 304 Fundamental Structure of the Cytoplasmic Membrane
304 Variation in Cytoplasmic Membranes 306 Transport across Cytoplasmic
Membranes 306 Cell Wall Structures 311 Gram-Negative Outer Membrane 315
Periplasm 320 Additional Extracellular Layers 321 14 Transport and
Localization of Proteins and Cell Envelope Macromolecules 333 Making
Connections 334 Introduction to Cytoplasmic Membrane Protein Transport
Systems 334 Secretory (Sec)-Dependent Protein Transport System 334 The
Secretory (Sec)-Dependent Protein Transport Process 337 Signal Recognition
Particle (SRP)-Dependent Protein Transport Process 338 Twin-Arginine
Translocation (Tat) Protein Transport Process 339 Integration of
Cytoplasmic Membrane Proteins 340 Gram-Negative Bacterial Outer Membrane
Protein Secretion Systems 341 Secretory (Sec)- and Twin-Arginine
Translocation (Tat)-Dependent Protein Secretion Systems 341 Secretory
(Sec)-Independent and Mixed-Mechanism Protein Secretion Systems 343
Importance of Disulfide Bonds 347 Transport and Localization of Other Cell
Envelope Components 348 15 Microbial Motility and Chemotaxis 363 Making
Connections 364 Motility in Microorganisms 364 Bacterial Flagella and
Swimming Motility 364 Regulation of Flagellar Synthesis in Escherichia coli
367 Mechanism of Swimming Motility 369 Archaeal Flagella 370 Bacterial
Surface Motility 371 Chemotaxis 372 Conservation and Variation in
Chemotaxis Systems among Bacteria and Archaea 380 Methods to Study
Bacterial Motility and Chemotaxis 381 16 Quorum Sensing 389 Making
Connections 390 Fundamentals of Quorum Sensing 390 Quorum Sensing and
Bioluminescence in the Vibrio fischeri-Squid Symbiosis 391 Basic Model of
Quorum Sensing in Gram-Negative Proteobacteria 395 Basic Model of Quorum
Sensing in Gram-Positive Bacteria 398 Interspecies Communication: the LuxS
System 400 Regulatory Cascade Controlling Quorum Sensing in Vibrio cholerae
400 Quorum Quenching 402 17 Stress Responses 415 Making Connections 416
Oxidative Stress 416 Heat Shock Response 419 Sporulation 420 18 Lifestyles
Involving Bacterial Differentiation 441 Making Connections 442 A Simple
Model for Bacterial Cellular Differentiation: Caulobacter crescentus 443
Differentiation in Filamentous Cyanobacterial Species 444 Life Cycle of
Filamentous Spore-Forming Streptomyces: An Example of Bacterial
Multicellularity 447 Life Cycle of Myxobacteria: Predatory Spore-Forming
Social Bacteria 449 Biofilms: The Typical State of Microorganisms in the
Environment 452 Index 467
Unity 3 1 Microbial Phylogeny--The Three Domains of Life 5 Introduction 6
The Three Branches of Life: Bacteria, Archaea, and Eukarya 6 The 16S/18S
rRNA Gene as a Basis for Phylogenetic Comparisons 7 The Modern Molecular
Phylogenetic Tree of Life 12 Phylogenetics and Earth History 14 2 Metabolic
Unity--Generation of Biosynthetic Precursors 21 Making Connections 22 The
Purpose of Central Metabolism 22 The 12 Essential Precursors 23 The
Embden-Meyerhof-Parnas (EMP) Pathway/Glycolysis 25 Structure and Energy
Exchange of Key Coenzymes 28 Controlling the Direction of Carbon Flow
during Glycolysis 29 The Pentose Phosphate Pathway (PPP) 31 The
Entner-Doudoroff (ED) Pathway 33 The Transition Reaction: Carbon Flow into
the Tricarboxylic Acid (TCA) Cycle 36 The Tricarboxylic Acid (TCA) Cycle 37
Anaplerotic Reactions 37 The Branched or Incomplete Tricarboxylic Acid
(TCA) Pathway 41 The Glyoxylate Cycle 41 Reversing Carbon Flow from the
Tricarboxylic Acid (TCA) Cycle to the Embden-Meyerhof-Parnas (EMP) Pathway
43 3 Cellular Components--What's In a Cell 51 Making Connections 52
Estimating Molecular Concentrations 52 Physiologically Relevant Protein
Concentrations 54 Measuring Enzyme Activity: Basic Principles of Enzyme
Assays 55 Michaelis-Menten Kinetics 58 Studying the Proteome 59 The
Physiological Role and Composition of Cellular RNA 61 The Physiological
Role and Composition of Cellular DNA 63 Studying the Genome and the
Transcriptome 64 4 Cellular Growth 73 Making Connections 74 Methods to
Monitor Bacterial Growth 74 The Phases of Bacterial Growth in Batch Culture
78 Requirements for Microbial Growth 80 Diauxic Growth 80 Exponential
Growth Kinetics 81 Chemostats 83 Characteristics of Stationary-Phase Cells
84 Proteins Important for Cell Shape and Cell Division 85 Chromosome
Segregation 86 5 Bioenergetics and the Proton Motive Force 95 Making
Connections 96 Cellular Mechanisms for ATP Synthesis 96 Chemiosmotic Theory
98 ATP Synthase 99 The Proton Motive Force (PMF) 99 Quantifying the Proton
Motive Force 99 Cellular Proton Levels 100 Environmental Impacts on the
Proton Motive Force (PMF) 100 Experimentally Measuring the Proton Motive
Force (PMF) 101 6 Respiration and Fermentation 107 Making Connections 108
The Basic Components of an Electron Transport Chain (ETC) 108
Electrode/Reduction Potential (E0') 109 Brief Review of the Electron
Transport Chain (ETC) in Mitochondria 110 Q Cycle of Mitochondria 113
Bacterial Electron Transport Chains (ETCs) 113 Q Loop of Bacteria 115
Electron Donors and Acceptors in Bacteria 115 Fermentation 117 7
Regulation--Posttranslational Control 127 Making Connections 128 Importance
of Regulatory Processes 128 Allosteric Regulation of Enzymes 129 Allosteric
Regulation of Branched Pathways 131 Covalent Modifications 134
Posttranslational Regulation in the Sugar Phosphotransferase System (PTS)
138 8 Gene Regulation--Transcription Initiation and Posttranscriptional
Control 147 Making Connections 148 Transcription Terminology 148 Bacterial
Transcription Initiation and Elongation 149 Bacterial Transcription
Termination 151 Regulatory cis- and trans-Acting Elements Impacting
Transcription 153 Examples of Different Promoter Structures 154
Transcriptional Regulation of the lac Operon 156 Activation and Repression
by the Global Regulator Cra 158 Attenuation 158 Posttranscriptional
Regulation 161 Methods Used to Study Gene Regulation 163 Methods to
Demonstrate Protein-DNA Interactions 164 Interlude: From Unity to Diversity
177 Metabolic Diversity 178 Global Nutrient Cycles 179 Structural and
Regulatory Diversity of Microbes 180 Part II: Diversity 183 9 Autotrophy
185 Making Connections 186 Autotrophy 186 Calvin Cycle 187 Reductive
Tricarboxylic Acid (rTCA) Cycle 191 Reductive Acetyl-CoA Pathway 193
3-Hydroxypropionate (3HP) Bi-cycle 195
3-Hydroxypropionate-4-Hydroxybutyrate (3HP-4HB) and
Dicarboxylate-4-Hydroxybutyrate (DC-4HB) Cycles 195 Why So Many CO2
Fixation Pathways? 197 10 Phototrophy 207 Making Connections 208
Phototrophy 208 Chlorophyll-Based Phototrophy 209 Cellular Structures
Needed for Phototrophy: Light-Harvesting Complexes, Reaction Centers, and
Unique Membrane Organizations 211 Oxygenic Photoautotrophy in the
Cyanobacteria 215 Anaerobic Anoxygenic Phototrophy in the Phototrophic
Purple Sulfur and Purple Nonsulfur Bacteria 218 Anaerobic Anoxygenic
Phototrophy in the Chlorobi and Chloroflexi (Green Sulfur and Green
Nonsulfur Bacteria, Respectively) 221 Anaerobic Anoxygenic
Photoheterotrophy in the Firmicutes 224 Aerobic Anoxygenic Phototrophy 224
Retinal-Based Phototrophy 225 11 Chemotrophy in the Carbon and Sulfur
Cycles 233 Making Connections 234 The Carbon Cycle 234 The
Chemoorganotrophic Degradation of Polymers 236 The Chemoorganotrophic
Degradation of Aromatic Acids 236 Chemoorganotrophy in Escherichia coli 241
Chemolithoautotrophy 246 Chemolithoautotrophy in Methanogens 248
Methylotrophy Enables Cycling of One-Carbon (C1) Compounds 251 One-Carbon
(C1) Chemolithotrophy in Acetogens 253 The Sulfur Cycle 256
Chemoheterotrophy and Chemolithoautotrophy in the Sulfur Cycle: Sulfate
Reducers 256 Chemolithoautotrophy in the Sulfur Cycle: Sulfur Oxidizers 259
The Anaerobic Food Web and Syntrophy 261 12 Microbial Contributions to the
Nitrogen Cycle 275 Making Connections 276 Overview of the Nitrogen Cycle
276 Nitrogen Fixation 277 Biochemistry of Nitrogen Fixation 278 Regulation
of Nitrogen Fixation 280 Symbiotic Plant-Microbe Interactions during
Nitrogen Fixation 282 Assimilatory Nitrate Reduction 284 Ammonia
Assimilation into Cellular Biomass 285 Nitrification: Ammonia Oxidation,
Nitrite Oxidation, and Comammox 287 Anammox: Anaerobic Ammonia Oxidation
290 Denitrification 293 13 Structure and Function of the Cell Envelope 303
Making Connections 304 Fundamental Structure of the Cytoplasmic Membrane
304 Variation in Cytoplasmic Membranes 306 Transport across Cytoplasmic
Membranes 306 Cell Wall Structures 311 Gram-Negative Outer Membrane 315
Periplasm 320 Additional Extracellular Layers 321 14 Transport and
Localization of Proteins and Cell Envelope Macromolecules 333 Making
Connections 334 Introduction to Cytoplasmic Membrane Protein Transport
Systems 334 Secretory (Sec)-Dependent Protein Transport System 334 The
Secretory (Sec)-Dependent Protein Transport Process 337 Signal Recognition
Particle (SRP)-Dependent Protein Transport Process 338 Twin-Arginine
Translocation (Tat) Protein Transport Process 339 Integration of
Cytoplasmic Membrane Proteins 340 Gram-Negative Bacterial Outer Membrane
Protein Secretion Systems 341 Secretory (Sec)- and Twin-Arginine
Translocation (Tat)-Dependent Protein Secretion Systems 341 Secretory
(Sec)-Independent and Mixed-Mechanism Protein Secretion Systems 343
Importance of Disulfide Bonds 347 Transport and Localization of Other Cell
Envelope Components 348 15 Microbial Motility and Chemotaxis 363 Making
Connections 364 Motility in Microorganisms 364 Bacterial Flagella and
Swimming Motility 364 Regulation of Flagellar Synthesis in Escherichia coli
367 Mechanism of Swimming Motility 369 Archaeal Flagella 370 Bacterial
Surface Motility 371 Chemotaxis 372 Conservation and Variation in
Chemotaxis Systems among Bacteria and Archaea 380 Methods to Study
Bacterial Motility and Chemotaxis 381 16 Quorum Sensing 389 Making
Connections 390 Fundamentals of Quorum Sensing 390 Quorum Sensing and
Bioluminescence in the Vibrio fischeri-Squid Symbiosis 391 Basic Model of
Quorum Sensing in Gram-Negative Proteobacteria 395 Basic Model of Quorum
Sensing in Gram-Positive Bacteria 398 Interspecies Communication: the LuxS
System 400 Regulatory Cascade Controlling Quorum Sensing in Vibrio cholerae
400 Quorum Quenching 402 17 Stress Responses 415 Making Connections 416
Oxidative Stress 416 Heat Shock Response 419 Sporulation 420 18 Lifestyles
Involving Bacterial Differentiation 441 Making Connections 442 A Simple
Model for Bacterial Cellular Differentiation: Caulobacter crescentus 443
Differentiation in Filamentous Cyanobacterial Species 444 Life Cycle of
Filamentous Spore-Forming Streptomyces: An Example of Bacterial
Multicellularity 447 Life Cycle of Myxobacteria: Predatory Spore-Forming
Social Bacteria 449 Biofilms: The Typical State of Microorganisms in the
Environment 452 Index 467
Preface xv About the Authors xvii About the Companion Website xviii Part I:
Unity 3 1 Microbial Phylogeny--The Three Domains of Life 5 Introduction 6
The Three Branches of Life: Bacteria, Archaea, and Eukarya 6 The 16S/18S
rRNA Gene as a Basis for Phylogenetic Comparisons 7 The Modern Molecular
Phylogenetic Tree of Life 12 Phylogenetics and Earth History 14 2 Metabolic
Unity--Generation of Biosynthetic Precursors 21 Making Connections 22 The
Purpose of Central Metabolism 22 The 12 Essential Precursors 23 The
Embden-Meyerhof-Parnas (EMP) Pathway/Glycolysis 25 Structure and Energy
Exchange of Key Coenzymes 28 Controlling the Direction of Carbon Flow
during Glycolysis 29 The Pentose Phosphate Pathway (PPP) 31 The
Entner-Doudoroff (ED) Pathway 33 The Transition Reaction: Carbon Flow into
the Tricarboxylic Acid (TCA) Cycle 36 The Tricarboxylic Acid (TCA) Cycle 37
Anaplerotic Reactions 37 The Branched or Incomplete Tricarboxylic Acid
(TCA) Pathway 41 The Glyoxylate Cycle 41 Reversing Carbon Flow from the
Tricarboxylic Acid (TCA) Cycle to the Embden-Meyerhof-Parnas (EMP) Pathway
43 3 Cellular Components--What's In a Cell 51 Making Connections 52
Estimating Molecular Concentrations 52 Physiologically Relevant Protein
Concentrations 54 Measuring Enzyme Activity: Basic Principles of Enzyme
Assays 55 Michaelis-Menten Kinetics 58 Studying the Proteome 59 The
Physiological Role and Composition of Cellular RNA 61 The Physiological
Role and Composition of Cellular DNA 63 Studying the Genome and the
Transcriptome 64 4 Cellular Growth 73 Making Connections 74 Methods to
Monitor Bacterial Growth 74 The Phases of Bacterial Growth in Batch Culture
78 Requirements for Microbial Growth 80 Diauxic Growth 80 Exponential
Growth Kinetics 81 Chemostats 83 Characteristics of Stationary-Phase Cells
84 Proteins Important for Cell Shape and Cell Division 85 Chromosome
Segregation 86 5 Bioenergetics and the Proton Motive Force 95 Making
Connections 96 Cellular Mechanisms for ATP Synthesis 96 Chemiosmotic Theory
98 ATP Synthase 99 The Proton Motive Force (PMF) 99 Quantifying the Proton
Motive Force 99 Cellular Proton Levels 100 Environmental Impacts on the
Proton Motive Force (PMF) 100 Experimentally Measuring the Proton Motive
Force (PMF) 101 6 Respiration and Fermentation 107 Making Connections 108
The Basic Components of an Electron Transport Chain (ETC) 108
Electrode/Reduction Potential (E0') 109 Brief Review of the Electron
Transport Chain (ETC) in Mitochondria 110 Q Cycle of Mitochondria 113
Bacterial Electron Transport Chains (ETCs) 113 Q Loop of Bacteria 115
Electron Donors and Acceptors in Bacteria 115 Fermentation 117 7
Regulation--Posttranslational Control 127 Making Connections 128 Importance
of Regulatory Processes 128 Allosteric Regulation of Enzymes 129 Allosteric
Regulation of Branched Pathways 131 Covalent Modifications 134
Posttranslational Regulation in the Sugar Phosphotransferase System (PTS)
138 8 Gene Regulation--Transcription Initiation and Posttranscriptional
Control 147 Making Connections 148 Transcription Terminology 148 Bacterial
Transcription Initiation and Elongation 149 Bacterial Transcription
Termination 151 Regulatory cis- and trans-Acting Elements Impacting
Transcription 153 Examples of Different Promoter Structures 154
Transcriptional Regulation of the lac Operon 156 Activation and Repression
by the Global Regulator Cra 158 Attenuation 158 Posttranscriptional
Regulation 161 Methods Used to Study Gene Regulation 163 Methods to
Demonstrate Protein-DNA Interactions 164 Interlude: From Unity to Diversity
177 Metabolic Diversity 178 Global Nutrient Cycles 179 Structural and
Regulatory Diversity of Microbes 180 Part II: Diversity 183 9 Autotrophy
185 Making Connections 186 Autotrophy 186 Calvin Cycle 187 Reductive
Tricarboxylic Acid (rTCA) Cycle 191 Reductive Acetyl-CoA Pathway 193
3-Hydroxypropionate (3HP) Bi-cycle 195
3-Hydroxypropionate-4-Hydroxybutyrate (3HP-4HB) and
Dicarboxylate-4-Hydroxybutyrate (DC-4HB) Cycles 195 Why So Many CO2
Fixation Pathways? 197 10 Phototrophy 207 Making Connections 208
Phototrophy 208 Chlorophyll-Based Phototrophy 209 Cellular Structures
Needed for Phototrophy: Light-Harvesting Complexes, Reaction Centers, and
Unique Membrane Organizations 211 Oxygenic Photoautotrophy in the
Cyanobacteria 215 Anaerobic Anoxygenic Phototrophy in the Phototrophic
Purple Sulfur and Purple Nonsulfur Bacteria 218 Anaerobic Anoxygenic
Phototrophy in the Chlorobi and Chloroflexi (Green Sulfur and Green
Nonsulfur Bacteria, Respectively) 221 Anaerobic Anoxygenic
Photoheterotrophy in the Firmicutes 224 Aerobic Anoxygenic Phototrophy 224
Retinal-Based Phototrophy 225 11 Chemotrophy in the Carbon and Sulfur
Cycles 233 Making Connections 234 The Carbon Cycle 234 The
Chemoorganotrophic Degradation of Polymers 236 The Chemoorganotrophic
Degradation of Aromatic Acids 236 Chemoorganotrophy in Escherichia coli 241
Chemolithoautotrophy 246 Chemolithoautotrophy in Methanogens 248
Methylotrophy Enables Cycling of One-Carbon (C1) Compounds 251 One-Carbon
(C1) Chemolithotrophy in Acetogens 253 The Sulfur Cycle 256
Chemoheterotrophy and Chemolithoautotrophy in the Sulfur Cycle: Sulfate
Reducers 256 Chemolithoautotrophy in the Sulfur Cycle: Sulfur Oxidizers 259
The Anaerobic Food Web and Syntrophy 261 12 Microbial Contributions to the
Nitrogen Cycle 275 Making Connections 276 Overview of the Nitrogen Cycle
276 Nitrogen Fixation 277 Biochemistry of Nitrogen Fixation 278 Regulation
of Nitrogen Fixation 280 Symbiotic Plant-Microbe Interactions during
Nitrogen Fixation 282 Assimilatory Nitrate Reduction 284 Ammonia
Assimilation into Cellular Biomass 285 Nitrification: Ammonia Oxidation,
Nitrite Oxidation, and Comammox 287 Anammox: Anaerobic Ammonia Oxidation
290 Denitrification 293 13 Structure and Function of the Cell Envelope 303
Making Connections 304 Fundamental Structure of the Cytoplasmic Membrane
304 Variation in Cytoplasmic Membranes 306 Transport across Cytoplasmic
Membranes 306 Cell Wall Structures 311 Gram-Negative Outer Membrane 315
Periplasm 320 Additional Extracellular Layers 321 14 Transport and
Localization of Proteins and Cell Envelope Macromolecules 333 Making
Connections 334 Introduction to Cytoplasmic Membrane Protein Transport
Systems 334 Secretory (Sec)-Dependent Protein Transport System 334 The
Secretory (Sec)-Dependent Protein Transport Process 337 Signal Recognition
Particle (SRP)-Dependent Protein Transport Process 338 Twin-Arginine
Translocation (Tat) Protein Transport Process 339 Integration of
Cytoplasmic Membrane Proteins 340 Gram-Negative Bacterial Outer Membrane
Protein Secretion Systems 341 Secretory (Sec)- and Twin-Arginine
Translocation (Tat)-Dependent Protein Secretion Systems 341 Secretory
(Sec)-Independent and Mixed-Mechanism Protein Secretion Systems 343
Importance of Disulfide Bonds 347 Transport and Localization of Other Cell
Envelope Components 348 15 Microbial Motility and Chemotaxis 363 Making
Connections 364 Motility in Microorganisms 364 Bacterial Flagella and
Swimming Motility 364 Regulation of Flagellar Synthesis in Escherichia coli
367 Mechanism of Swimming Motility 369 Archaeal Flagella 370 Bacterial
Surface Motility 371 Chemotaxis 372 Conservation and Variation in
Chemotaxis Systems among Bacteria and Archaea 380 Methods to Study
Bacterial Motility and Chemotaxis 381 16 Quorum Sensing 389 Making
Connections 390 Fundamentals of Quorum Sensing 390 Quorum Sensing and
Bioluminescence in the Vibrio fischeri-Squid Symbiosis 391 Basic Model of
Quorum Sensing in Gram-Negative Proteobacteria 395 Basic Model of Quorum
Sensing in Gram-Positive Bacteria 398 Interspecies Communication: the LuxS
System 400 Regulatory Cascade Controlling Quorum Sensing in Vibrio cholerae
400 Quorum Quenching 402 17 Stress Responses 415 Making Connections 416
Oxidative Stress 416 Heat Shock Response 419 Sporulation 420 18 Lifestyles
Involving Bacterial Differentiation 441 Making Connections 442 A Simple
Model for Bacterial Cellular Differentiation: Caulobacter crescentus 443
Differentiation in Filamentous Cyanobacterial Species 444 Life Cycle of
Filamentous Spore-Forming Streptomyces: An Example of Bacterial
Multicellularity 447 Life Cycle of Myxobacteria: Predatory Spore-Forming
Social Bacteria 449 Biofilms: The Typical State of Microorganisms in the
Environment 452 Index 467
Unity 3 1 Microbial Phylogeny--The Three Domains of Life 5 Introduction 6
The Three Branches of Life: Bacteria, Archaea, and Eukarya 6 The 16S/18S
rRNA Gene as a Basis for Phylogenetic Comparisons 7 The Modern Molecular
Phylogenetic Tree of Life 12 Phylogenetics and Earth History 14 2 Metabolic
Unity--Generation of Biosynthetic Precursors 21 Making Connections 22 The
Purpose of Central Metabolism 22 The 12 Essential Precursors 23 The
Embden-Meyerhof-Parnas (EMP) Pathway/Glycolysis 25 Structure and Energy
Exchange of Key Coenzymes 28 Controlling the Direction of Carbon Flow
during Glycolysis 29 The Pentose Phosphate Pathway (PPP) 31 The
Entner-Doudoroff (ED) Pathway 33 The Transition Reaction: Carbon Flow into
the Tricarboxylic Acid (TCA) Cycle 36 The Tricarboxylic Acid (TCA) Cycle 37
Anaplerotic Reactions 37 The Branched or Incomplete Tricarboxylic Acid
(TCA) Pathway 41 The Glyoxylate Cycle 41 Reversing Carbon Flow from the
Tricarboxylic Acid (TCA) Cycle to the Embden-Meyerhof-Parnas (EMP) Pathway
43 3 Cellular Components--What's In a Cell 51 Making Connections 52
Estimating Molecular Concentrations 52 Physiologically Relevant Protein
Concentrations 54 Measuring Enzyme Activity: Basic Principles of Enzyme
Assays 55 Michaelis-Menten Kinetics 58 Studying the Proteome 59 The
Physiological Role and Composition of Cellular RNA 61 The Physiological
Role and Composition of Cellular DNA 63 Studying the Genome and the
Transcriptome 64 4 Cellular Growth 73 Making Connections 74 Methods to
Monitor Bacterial Growth 74 The Phases of Bacterial Growth in Batch Culture
78 Requirements for Microbial Growth 80 Diauxic Growth 80 Exponential
Growth Kinetics 81 Chemostats 83 Characteristics of Stationary-Phase Cells
84 Proteins Important for Cell Shape and Cell Division 85 Chromosome
Segregation 86 5 Bioenergetics and the Proton Motive Force 95 Making
Connections 96 Cellular Mechanisms for ATP Synthesis 96 Chemiosmotic Theory
98 ATP Synthase 99 The Proton Motive Force (PMF) 99 Quantifying the Proton
Motive Force 99 Cellular Proton Levels 100 Environmental Impacts on the
Proton Motive Force (PMF) 100 Experimentally Measuring the Proton Motive
Force (PMF) 101 6 Respiration and Fermentation 107 Making Connections 108
The Basic Components of an Electron Transport Chain (ETC) 108
Electrode/Reduction Potential (E0') 109 Brief Review of the Electron
Transport Chain (ETC) in Mitochondria 110 Q Cycle of Mitochondria 113
Bacterial Electron Transport Chains (ETCs) 113 Q Loop of Bacteria 115
Electron Donors and Acceptors in Bacteria 115 Fermentation 117 7
Regulation--Posttranslational Control 127 Making Connections 128 Importance
of Regulatory Processes 128 Allosteric Regulation of Enzymes 129 Allosteric
Regulation of Branched Pathways 131 Covalent Modifications 134
Posttranslational Regulation in the Sugar Phosphotransferase System (PTS)
138 8 Gene Regulation--Transcription Initiation and Posttranscriptional
Control 147 Making Connections 148 Transcription Terminology 148 Bacterial
Transcription Initiation and Elongation 149 Bacterial Transcription
Termination 151 Regulatory cis- and trans-Acting Elements Impacting
Transcription 153 Examples of Different Promoter Structures 154
Transcriptional Regulation of the lac Operon 156 Activation and Repression
by the Global Regulator Cra 158 Attenuation 158 Posttranscriptional
Regulation 161 Methods Used to Study Gene Regulation 163 Methods to
Demonstrate Protein-DNA Interactions 164 Interlude: From Unity to Diversity
177 Metabolic Diversity 178 Global Nutrient Cycles 179 Structural and
Regulatory Diversity of Microbes 180 Part II: Diversity 183 9 Autotrophy
185 Making Connections 186 Autotrophy 186 Calvin Cycle 187 Reductive
Tricarboxylic Acid (rTCA) Cycle 191 Reductive Acetyl-CoA Pathway 193
3-Hydroxypropionate (3HP) Bi-cycle 195
3-Hydroxypropionate-4-Hydroxybutyrate (3HP-4HB) and
Dicarboxylate-4-Hydroxybutyrate (DC-4HB) Cycles 195 Why So Many CO2
Fixation Pathways? 197 10 Phototrophy 207 Making Connections 208
Phototrophy 208 Chlorophyll-Based Phototrophy 209 Cellular Structures
Needed for Phototrophy: Light-Harvesting Complexes, Reaction Centers, and
Unique Membrane Organizations 211 Oxygenic Photoautotrophy in the
Cyanobacteria 215 Anaerobic Anoxygenic Phototrophy in the Phototrophic
Purple Sulfur and Purple Nonsulfur Bacteria 218 Anaerobic Anoxygenic
Phototrophy in the Chlorobi and Chloroflexi (Green Sulfur and Green
Nonsulfur Bacteria, Respectively) 221 Anaerobic Anoxygenic
Photoheterotrophy in the Firmicutes 224 Aerobic Anoxygenic Phototrophy 224
Retinal-Based Phototrophy 225 11 Chemotrophy in the Carbon and Sulfur
Cycles 233 Making Connections 234 The Carbon Cycle 234 The
Chemoorganotrophic Degradation of Polymers 236 The Chemoorganotrophic
Degradation of Aromatic Acids 236 Chemoorganotrophy in Escherichia coli 241
Chemolithoautotrophy 246 Chemolithoautotrophy in Methanogens 248
Methylotrophy Enables Cycling of One-Carbon (C1) Compounds 251 One-Carbon
(C1) Chemolithotrophy in Acetogens 253 The Sulfur Cycle 256
Chemoheterotrophy and Chemolithoautotrophy in the Sulfur Cycle: Sulfate
Reducers 256 Chemolithoautotrophy in the Sulfur Cycle: Sulfur Oxidizers 259
The Anaerobic Food Web and Syntrophy 261 12 Microbial Contributions to the
Nitrogen Cycle 275 Making Connections 276 Overview of the Nitrogen Cycle
276 Nitrogen Fixation 277 Biochemistry of Nitrogen Fixation 278 Regulation
of Nitrogen Fixation 280 Symbiotic Plant-Microbe Interactions during
Nitrogen Fixation 282 Assimilatory Nitrate Reduction 284 Ammonia
Assimilation into Cellular Biomass 285 Nitrification: Ammonia Oxidation,
Nitrite Oxidation, and Comammox 287 Anammox: Anaerobic Ammonia Oxidation
290 Denitrification 293 13 Structure and Function of the Cell Envelope 303
Making Connections 304 Fundamental Structure of the Cytoplasmic Membrane
304 Variation in Cytoplasmic Membranes 306 Transport across Cytoplasmic
Membranes 306 Cell Wall Structures 311 Gram-Negative Outer Membrane 315
Periplasm 320 Additional Extracellular Layers 321 14 Transport and
Localization of Proteins and Cell Envelope Macromolecules 333 Making
Connections 334 Introduction to Cytoplasmic Membrane Protein Transport
Systems 334 Secretory (Sec)-Dependent Protein Transport System 334 The
Secretory (Sec)-Dependent Protein Transport Process 337 Signal Recognition
Particle (SRP)-Dependent Protein Transport Process 338 Twin-Arginine
Translocation (Tat) Protein Transport Process 339 Integration of
Cytoplasmic Membrane Proteins 340 Gram-Negative Bacterial Outer Membrane
Protein Secretion Systems 341 Secretory (Sec)- and Twin-Arginine
Translocation (Tat)-Dependent Protein Secretion Systems 341 Secretory
(Sec)-Independent and Mixed-Mechanism Protein Secretion Systems 343
Importance of Disulfide Bonds 347 Transport and Localization of Other Cell
Envelope Components 348 15 Microbial Motility and Chemotaxis 363 Making
Connections 364 Motility in Microorganisms 364 Bacterial Flagella and
Swimming Motility 364 Regulation of Flagellar Synthesis in Escherichia coli
367 Mechanism of Swimming Motility 369 Archaeal Flagella 370 Bacterial
Surface Motility 371 Chemotaxis 372 Conservation and Variation in
Chemotaxis Systems among Bacteria and Archaea 380 Methods to Study
Bacterial Motility and Chemotaxis 381 16 Quorum Sensing 389 Making
Connections 390 Fundamentals of Quorum Sensing 390 Quorum Sensing and
Bioluminescence in the Vibrio fischeri-Squid Symbiosis 391 Basic Model of
Quorum Sensing in Gram-Negative Proteobacteria 395 Basic Model of Quorum
Sensing in Gram-Positive Bacteria 398 Interspecies Communication: the LuxS
System 400 Regulatory Cascade Controlling Quorum Sensing in Vibrio cholerae
400 Quorum Quenching 402 17 Stress Responses 415 Making Connections 416
Oxidative Stress 416 Heat Shock Response 419 Sporulation 420 18 Lifestyles
Involving Bacterial Differentiation 441 Making Connections 442 A Simple
Model for Bacterial Cellular Differentiation: Caulobacter crescentus 443
Differentiation in Filamentous Cyanobacterial Species 444 Life Cycle of
Filamentous Spore-Forming Streptomyces: An Example of Bacterial
Multicellularity 447 Life Cycle of Myxobacteria: Predatory Spore-Forming
Social Bacteria 449 Biofilms: The Typical State of Microorganisms in the
Environment 452 Index 467