Microbial Physiology: Unity and Diversity

TABLE OF CONTENTS TITLE PAGE COPYRIGHT DEDICATION PREFACE ABOUT THE AUTHORS ABOUT THE COMPANION WEBSITE PART I:: UNITY 1 MICROBIAL PHYLOGENY—THE THREE DOMAINS OF LIFE Introduction The Three Branches of Life: Bacteria , Archaea , and Eukarya The 16S/18S rRNA Gene as a Basis for Phylogenetic Comparisons The Modern Molecular Phylogenetic Tree of Life Phylogenetics and Earth History 2 METABOLIC UNITY—GENERATION OF BIOSYNTHETIC PRECURSORS Making Connections The Purpose of Central Metabolism The 12 Essential Precursors The Embden-Meyerhof-Parnas (EMP) Pathway/Glycolysis Structure and Energy Exchange of Key Coenzymes Controlling the Direction of Carbon Flow during Glycolysis The Pentose Phosphate Pathway (PPP) The Entner-Doudoroff (ED) Pathway The Transition Reaction: Carbon Flow into the Tricarboxylic Acid (TCA) Cycle The Tricarboxylic Acid (TCA) Cycle Anaplerotic Reactions The Branched or Incomplete Tricarboxylic Acid (TCA) Pathway The Glyoxylate Cycle Reversing Carbon Flow from the Tricarboxylic Acid (TCA) Cycle to the Embden-Meyerhof-Parnas (EMP) Pathway 3 CELLULAR COMPONENTS—WHAT’S IN A CELL Making Connections Estimating Molecular Concentrations Physiologically Relevant Protein Concentrations Measuring Enzyme Activity: Basic Principles of Enzyme Assays Michaelis-Menten Kinetics Studying the Proteome The Physiological Role and Composition of Cellular RNA The Physiological Role and Composition of Cellular DNA Studying the Genome and the Transcriptome 4 CELLULAR GROWTH Making Connections Methods to Monitor Bacterial Growth The Phases of Bacterial Growth in Batch Culture Requirements for Microbial Growth Diauxic Growth Exponential Growth Kinetics Chemostats Characteristics of Stationary-Phase Cells Proteins Important for Cell Shape and Cell Division Chromosome Segregation 5 BIOENERGETICS AND THE PROTON MOTIVE FORCE Making Connections Cellular Mechanisms for ATP Synthesis Chemiosmotic Theory ATP Synthase The Proton Motive Force (PMF) Quantifying the Proton Motive Force (PMF) Cellular Proton Levels Environmental Impacts on the Proton Motive Force (PMF) Experimentally Measuring the Proton Motive Force (PMF) 6RESPIRATION AND FERMENTATION: RESPIRATION AND FERMENTATION Making Connections The Basic Components of an Electron Transport Chain (ETC) Electrode/Reduction Potential ( E 0 ′) Brief Review of the Electron Transport Chain (ETC) in Mitochondria Q Cycle of Mitochondria Bacterial Electron Transport Chains (ETCs) Q Loop of Bacteria Electron Donors and Acceptors in Bacteria Fermentation 7 REGULATION—POSTTRANSLATIONAL CONTROL Making Connections Importance of Regulatory Processes Allosteric Regulation of Enzymes Allosteric Regulation of Branched Pathways Covalent Modifications Posttranslational Regulation in the Sugar Phosphotransferase System (PTS) 8 GENE REGULATION—TRANSCRIPTION INITIATION AND POSTTRANSCRIPTIONAL CONTROL Making Connections Transcription Terminology Bacterial Transcription Initiation and Elongation Bacterial Transcription Termination Regulatory cis - and trans -Acting Elements Impacting Transcription Examples of Different Promoter Structures Transcriptional Regulation of the lac Operon Activation and Repression by the Global Regulator Cra Attenuation Posttranscriptional Regulation Methods Used to Study Gene Regulation Methods to Demonstrate Protein–DNA Interactions INTERLUDE: FROM UNITY TO DIVERSITY Metabolic Diversity Global Nutrient Cycles Structural and Regulatory Diversity of Microbes PART II:: DIVERSITY 9 AUTOTROPHY Making Connections Autotrophy Calvin Cycle Reductive Tricarboxylic Acid (rTCA) Cycle Reductive Acetyl-CoA Pathway 3-Hydroxypropionate (3HP) Bi-cycle 3-Hydroxypropionate-4-Hydroxybutyrate (3HP-4HB) and Dicarboxylate-4-Hydroxybutyrate (DC-4HB) Cycles Why So Many CO 2 Fixation Pathways? 10 PHOTOTROPHY Making Connections Phototrophy Chlorophyll-Based Phototrophy Cellular Structures Needed for Phototrophy: Light-Harvesting Complexes, Reaction Centers, and Unique Membrane Organizations Oxygenic Photoautotrophy in the Cyanobacteria Anaerobic Anoxygenic Phototrophy in the Phototrophic Purple Sulfur and Purple Nonsulfur Bacteria P870 REACTIONS Anaerobic Anoxygenic Phototrophy in the Chlorobi and Chloroflexi (Green Sulfur and Green Nonsulfur Bacteria, Respectively) Anaerobic Anoxygenic Photoheterotrophy in the Firmicutes Aerobic Anoxygenic Phototrophy Retinal-Based Phototrophy 11 CHEMOTROPHY IN THE CARBON AND SULFUR CYCLES Making Connections The Carbon Cycle The Chemoorganotrophic Degradation of Polymers The Chemoorganotrophic Degradation of Aromatic Acids Chemoorganotrophy in Escherichia coli Chemolithoautotrophy Chemolithoautotrophy in Methanogens Methylotrophy Enables Cycling of One-Carbon (C1) Compounds One-Carbon (C1) Chemolithotrophy in Acetogens The Sulfur Cycle Chemoheterotrophy and Chemolithoautotrophy in the Sulfur Cycle: Sulfate Reducers Chemolithoautotrophy in the Sulfur Cycle: Sulfur Oxidizers The Anaerobic Food Web and Syntrophy 12 MICROBIAL CONTRIBUTIONS TO THE NITROGEN CYCLE Making Connections Overview of the Nitrogen Cycle Nitrogen Fixation Biochemistry of Nitrogen Fixation Regulation of Nitrogen Fixation Symbiotic Plant-Microbe Interactions during Nitrogen Fixation Assimilatory Nitrate Reduction Ammonia Assimilation into Cellular Biomass Nitrification: Ammonia Oxidation, Nitrite Oxidation, and Comammox Anammox: Anaerobic Ammonia Oxidation Denitrification 13 STRUCTURE AND FUNCTION OF THE CELL ENVELOPE Making Connections Fundamental Structure of the Cytoplasmic Membrane Variation in Cytoplasmic Membranes Transport across Cytoplasmic Membranes Cell Wall Structures Gram-Negative Outer Membrane Periplasm Additional Extracellular Layers 14 TRANSPORT AND LOCALIZATION OF PROTEINS AND CELL ENVELOPE MACROMOLECULES Making Connections Introduction to Cytoplasmic Membrane Protein Transport Systems Secretory (Sec)-Dependent Protein Transport System The Secretory (Sec)-Dependent Protein Transport Process Signal Recognition Particle (SRP)-Dependent Protein Transport Process Twin-Arginine Translocation (Tat) Protein Transport Process Integration of Cytoplasmic Membrane Proteins Gram-Negative Bacterial Outer Membrane Protein Secretion Systems Secretory (Sec)- and Twin-Arginine Translocation (Tat)-Dependent Protein Secretion Systems Secretory (Sec)-Independent and Mixed-Mechanism Protein Secretion Systems Importance of Disulfide Bonds Transport and Localization of Other Cell Envelope Components 15 MICROBIAL MOTILITY AND CHEMOTAXIS Making Connections Motility in Microorganisms Bacterial Flagella and Swimming Motility Regulation of Flagellar Synthesis in Escherichia coli Mechanism of Swimming Motility Archaeal Flagella Bacterial Surface Motility Chemotaxis Conservation and Variation in Chemotaxis Systems among Bacteria and Archaea Methods to Study Bacterial Motility and Chemotaxis 16 QUORUM SENSING Making Connections Fundamentals of Quorum Sensing Quorum Sensing and Bioluminescence in the Vibrio fischeri -Squid Symbiosis Basic Model of Quorum Sensing in Gram-Negative Proteobacteria Basic Model of Quorum Sensing in Gram-Positive Bacteria Interspecies Communication: the LuxS System Regulatory Cascade Controlling Quorum Sensing in Vibrio cholerae Quorum Quenching 17 STRESS RESPONSES Making Connections Oxidative Stress Heat Shock Response Sporulation 18 LIFESTYLES INVOLVING BACTERIAL DIFFERENTIATION Making Connections A Simple Model for Bacterial Cellular Differentiation: Caulobacter crescentus Differentiation in Filamentous Cyanobacterial Species Life Cycle of Filamentous Spore-Forming Streptomyces : An Example of Bacterial Multicellularity Life Cycle of Myxobacteria: Predatory Spore-Forming Social Bacteria Biofilms: The Typical State of Microorganisms in the Environment Index End User License Agreement