Fundamentals of Bacterial Physiology and Metabolism

This book provides useful information on microbial physiology and metabolism. The key aspects covered are prokaryotic diversity, growth physiology, basic metabolic pathways and their regulation, metabolic diversity with details of various unique pathways. Another focus area is stress physiology with details on varying environmental stresses, signal transduction, adaptation and survival. For instructional purposes, the book provides case studies, interesting facts, techniques etc. which help in showcasing the inter-disciplinary nature and bridge the gap between various aspects of applied microbiology. Preface Acknowledgements Contents About the Authors Authors and Coauthors Authors Coauthors Part I Prokaryotes: Bacterial and Archaeal Diversity and Cell Structure 1 Diversity of Prokaryotes 1 Three-Domain Classification 2 Classification and Discovery of Archaea 3 Phylum Euryarchaeota 4 Phylum Crenarchaeota: Hyperthermophiles 5 Newly Discovered Archaea 6 Diversity of Bacteria 7 The Deeply Branching Bacteria 8 The Proteobacteria 9 The Non-proteobacteria Gram-Negatives 10 Firmicutes: The Low G + C Gram-Positive Bacteria 11 Actinobacteria: The High G + C Gram-Positive Bacteria References 2 Prokaryotic Cell Structure and Function 1 Morphology of Bacterial Cell 2 Cell Organization 3 Bacterial Membranes 4 Cell Wall 5 Bacterial Capsule 6 Bacterial Cytoplasm 7 Extracellular Appendages References 3 Bacterial Cell Wall Biosynthesis and Inhibitors 1 Components of Bacterial Cell Wall 2 Proteins Present in Outer Membrane 3 Biosynthesis of Bacterial Cell Wall 4 Lipopolysaccharide Synthesis References Part II Bacterial Cell division and Growth 4 Cell Division 1 Bacterial Cell Cycle 2 Chromosomal Replication and Segregation 3 Cytokinesis/Cell Division 4 Membrane Constriction and Septum Progression 5 Regulation of Septum/Z-Ring Formation 6 Divisome Proteins as Antimicrobial Targets References 5 Growth Physiology and Kinetics 1 Growth Curve in Bacteria 2 Effect of Environmental Factors on Microbial Growth 3 Diauxic Growth 4 Effect of Recombinant Protein Production on Bacterial Growth 5 Measurement of Microbial Growth 6 Growth Kinetics of Batch Fermentation 7 Continuous Stirred Tank Reactor (CSTR) 8 Fed-Batch Culture 9 Applications of High-Cell-Density Cultivation Strategies References Part III Transport Across Cell Membrane 6 Solute Transport 1 Biological Membranes as Transport Barrier: A General Account 2 Transport Across Membranes: Passive and Active Transport 3 Membrane Transport Proteins 4 Specialized Channel Proteins 5 Membrane Transport Proteins: Carriers 6 Special/Unique Transport Proteins: Ionophores 7 Iron Transport in Bacteria: Concerted Action of Primary and Secondary Active Transport References 7 ABC Transporters and Group Translocation 1 Historical Background of ABC Transporters 2 ABC Transporters: Substrate Specificity, Domain Organization and Mechanism of Transport 3 Bacterial Multidrug Efflux Pumps 4 Group Translocation: PEP-PTS System References 8 Protein Secretion 1 Sec System for Transport of Unfolded Proteins 2 Tat System for Transport of Folded Proteins 3 Protein Secretion in Gram-Negative Bacteria 4 Sec-dependent Secretion Systems of Gram-Negative Bacteria 5 Sec-independent Secretion Systems of Gram-Negative Bacteria 6 Protein Secretion in Gram-Positive Bacteria References Part IV Central Metabolic Pathways 9 Glycolysis and Gluconeogenesis 1 Glycolysis: Embden–Meyerhoff–Parnas Pathway 2 Regulation of Glycolysis 3 Modification of Glycolysis in Pyrococcus Furiosus 4 Atypical Glycolysis in Clostridium Thermocellum 5 Methylglyoxal Pathway: An Off-Shoot of Glycolysis 6 Gluconeogenesis 7 Key Scientists and Their Contribution to EMP Pathway References 10 Pentose Phosphate Pathway 1 Reactions of Pentose Phosphate Pathway 2 Pentose Phosphate Pathway During Oxidative Stress Response 3 Pentose Phosphate Pathway in Heterofermentative Lactate Fermentation 4 Pentose Degradation in Archaea 5 Improving Regeneration of NADPH 6 Engineering E. Coli for Cometabolism of Glucose and Xylose to Yield Ethanol: A Case Study (Chiang et al. 2013) References 11 Entner–Doudoroff Pathway 1 Discovery of Entner–Doudoroff (ED) Pathway 2 Comparison Between EMP and ED Pathways 3 Key Reactions of ED Pathway 4 Modes of ED Pathway 5 Regulation of ED Pathway in E. Coli 6 Carbohydrate Metabolism in Zymomonas Mobilis, an Alternative Ethanol Producer, Using ED Pathway 7 Metabolic Fate of Pyruvate References 12 Tricarboxylic Acid Cycle 1 Historical Background of TCA Cycle 2 Bridge Between Glycolysis and TCA Cycle—Pyruvate Dehydrogenase Complex 3 Tricarboxylic Acid Pathway/Krebs’s Cycle 4 Citric Acid Production by Aspergillus Niger: An Overview References 13 Alternate Tricarboxylic Acid Cycle 1 Distribution of TCA Cycle Among Bacteria Under Microaerophilic and Anaerobic Conditions 2 Branched TCA 3 Glyoxylate Cycle 4 Role of Glyoxylate Cycle in Gluconeogenesis 5 Glyoxylate Operon and Its Regulation 6 Metabolic Engineering of E. Coli for Over-production of Succinic Acid: An Overview References Part V Electron Transport and Energy Generation 14 Electron Transport and Energy Generation 1 Primary Electron Donors 2 Terminal Electron Acceptors 3 Electron Transport Complex 4 Bacterial Electron Transport: A General Account 5 Branched Electron Transport Chain in E. coli 6 Oxidative Phosphorylation 7 Uncouplers and Inhibitors of Electron Transport and Oxidative Phosphorylation References Part VI Metabolic Diversity of Carbon and Energy Source 15 Nutritional Diversity Amongst Bacteria: Chemolithotrophy and Phototrophy 1 Nutritional Diversity Amongst Bacteria 2 Chemolithotrophy 3 Hydrogen Oxidizers 4 Carbon Monoxide Oxidizers (Carboxydobacteria) 5 Ammonia Oxidizers 6 Nitrite Oxidizers 7 Sulphur Bacteria 8 Iron Bacteria or Iron Oxidisers 9 Economic Importance of Chemolithotrophs 10 Phototrophy 11 Diversity of Photosynthetic Bacteria 12 Classification of Phototrophic Bacteria 13 Photosynthetic Pigments 14 Oxygenic Photosynthesis 15 Anoxygenic Photosynthesis 16 C1 Metabolism References Part VII Nitrogen Metabolism 16 Nitrogen Assimilation and Dissimilation 1 Nitrogen Cycle and Nitrogen Assimilation: An Overview 2 Assimilation/Utilization of Inorganic Nitrogen NO3− and NH4+ 3 De Novo Biosynthesis of Amino Acids 4 Amino Acid Utilisation References 17 Glutathione and Polyamines in Bacteria 1 Diversity of Low Molecular Weight Thiols in Bacteria 2 Structure of Glutathione 3 Glutathione Biosynthesis and Transmembrane Cycling 4 Glutathione Homeostasis 5 Glutathione for Reduction and Glutathionylation of Proteins 6 Role of Glutathione During Environmental Stress and Chemical Toxicity 7 Distribution of Common and Unusual Polyamines in Bacteria 8 Putrescine and Cadaverine Biosynthesis 9 Spermidine and Spermine Biosynthesis 10 Polyamines Transport and Their Role in Cell Physiology 11 Polyamine Inhibitors and Disease Prevention 12 Industrial Application of Polyamines and Overproduction Strategies for Cadaverin Synthesis References Part VIII Lipid Metabolism and Nucleotide Biosynthesis 18 Lipid Biosynthesis and Degradation 1 Distribution of Lipids in Microbes and Their Biological Significance 2 Bacterial Lipids 3 Archaeal Lipids 4 Biosynthesis of Lipids 5 Lipid Accumulation in Yeasts 6 Fatty Acid Biosynthesis Pathway Enzymes as Drug Targets 7 Lipid Degradation 8 Regulation of Fatty Acid Degradation in E. coli References 19 Nucleotide Biosynthesis and Regulation 1 Purines and Pyrimidines 2 Synthesis of Purine Ribonucleotides 3 Regulation of Purine De Novo Synthesis 4 Synthesis of Pyrimidine Ribonucleotides 5 Regulation of Pyrimidine Synthesis in E. coli 6 Synthesis of Deoxyribonucleotides 7 Inhibitors of Nucleotide Biosynthesis 8 Nucleotide Salvage Pathway 9 Diseases Related to Nucleotide Biosynthetic Pathways References Part IX Response to Environmental Signalling 20 Two-Component Systems 1 Diversity of Two-Component Systems in Three Domains of Life 2 Types of Two-Component Systems 3 Sensor Kinases 4 Mechanism of Signal Sensing by Sensor Kinases 5 Response Regulators References 21 Bacterial Response to Oxygen Availability 1 Introduction to Oxygen Sensors in E. coli 2 Rapid Response Sensors 3 Delayed Response Sensors 4 ArcAB- and FNR-Regulated Carbon Metabolism in E. coli in Response to Oxygen Availability References 22 Regulation of Anaerobic Respiration 1 Anaerobic Respiration: An Introduction 2 Nitrate Respiration 3 Nitrate Reductases 4 Nitrite Reductases 5 Nitrate and Nitrite Transport in E. Coli 6 Two-Component System for NO3−/NO2− Sensing 7 Coregulation of Formate Dehydrogenase in Presence of Nitrate, Nitrite and Formate 8 Fumarate Respiration 9 DMSO and TMAO Respiration References 23 Response to Phosphate Starvation and Osmotic Homeostasis 1 Response to Phosphate Starvation 2 Components of Pho Regulon 3 Two-Component PhoBR Regulates Pho Regulon in E. Coli 4 Cross-Regulation: Pi-Independent Regulation of Pho Regulon 5 Osmohomeostasis 6 Osmotic Stress and Turgor 7 Primary Response to Osmohomeostasis: ATP-Driven K+ Uptake 8 Secondary Response: Osmoprotectant Accumulation References Part X Cell to Cell Signalling 24 Quorum Sensing, Bioluminescence and Chemotaxis 1 What is Quorum Sensing and Why do Bacteria Talk? 2 Discovery of Quorum Sensing 3 Signaling Molecules: Autoinducers 4 Quorum Sensing in Gram-Negative Bacteria: Bioluminescence 5 Quorum Quenching 6 Chemotaxis 7 Bacterial Movement 8 Proteins Required for Chemotaxis 9 Chemotactic Response References 25 Competence and Sporulation in Bacillus subtilis 1 Competence: An Introduction 2 Competence Development in Different Bacteria 3 Genetic Basis of Competence in B. Subtilis 4 ComK: The Master Competence Regulator 5 Molecular Mechanism of Competence: Induction by Quorum Sensing 6 Sporulation in Bacillus Subtilis References Correction to: Fundamentals of Bacterial Physiology and Metabolism Correction to: R. Gupta and N. Gupta, Fundamentals of Bacterial Physiology and Metabolism, https://doi.org/10.1007/978-981-16-0723-3