Bacterial Metabolism

I am particularly indebted to Joan Macy, Lynne Quandt, Jan Andreesen and Peter Hillmer for reading the manuscript, for their criticisms and their suggestions, and I thank Ute Gnass for typing the manuscript and for her invaluable help with the indexing and with the preparation of the figures. Finally, I am grateful to the publishers for their patience, willing help, and cooperation. G6ttingen, 1978 GERHARD GOTTSCHALK Contents CHAPTER I Nutrition of Bacteria I. Major and Minor Bioelements I II. The Two Basic Mechanisms of ATP Synthesis 4 III. Nutrients as Energy Sources 6 IV. Growth Factor Requirements of Bacteria 9 V. Summary 10 CHAPTER 2 How Escherichia coli Synthesizes ATP during Aerobic Growth on Glucose I. Transport of D-Glucose into the E. coli Cell 13 II. Degradation of Glucose-6-Phosphate to Pyruvate via the Embden-Meyerhof- Parnas (EMP) Pathway 15 III. Oxidative Decarboxylation of Pyruvate to Acetyl-Coenzyme A 18 IV. Oxidation of Acetyl-CoA via the Tricarboxylic Acid Cycle 20 V. The Formation of ATP in the Respiratory Chain 22 VI. Summary 35 CHAPTER 3 Biosynthesis of Escherichia coli Cells from Glucose I. Composition of E. coli Cells 38 II. Assimilation of Ammonia 40 Ill. Assimilatory Reduction of Sulfate 42 IV. Biosynthesis of Amino Acids 43 V. How Pentose Phosphates and NADPH are Formed 55 xii Contents VI. Ribonucleotides and Deoxyribonucleotides 59 VII. Biosynthesis of Lipids 65 VIII. Formation of Carbohydrates 71 IX. Synthesis of Polymers 73 X. The Requirement for an Anaplerotic Sequence 92 XI.

1 Nutrition of Bacteria. - I. Major and Minor Bioelements. - II. The Two Basic Mechanisms of ATP Synthesis. - III. Nutrients as Energy Sources. - IV. Growth Factor Requirements of Bacteria. - V. Summary. - 2 How Escherichia coil Synthesizes ATP during Aerobic Growth on Glucose. - I. Transport of D-Glucose into theE. coliCell. - II. Degradation of Glucose-6-Phosphate to Pyruvate via the Embden Meyerhof Parnas (EMP) Pathway. - III. Oxidative Decarboxylation of Pyruvate to Acetyl-Coenzyme A. - IV. Oxidation of Acetyl-CoA via the Tricarboxylic Acid Cycle. - V. The Formation of ATP in the Respiratory Chain. - VI. Summary. - 3 Biosynthesis ofEscherichia colsCells from Glucose. - I. Composition of E. coli Cells. - II. Assimilation of Ammonia. - III. Assimilatory Reduction of Sulfate. - IV. Biosynthesis of Amino Acids. - V. How Pentose Phosphates and NADPH are Formed. - VI. Ribonucleotides and Deoxyribonucleotides. - VII. Biosynthesis of Lipids. - VIII. Formation of Carbohydrates. - IX. Synthesis of Polymers. - X. The Requirement for an Anaplerotic Sequence. - XI. Summary. - 4 Aerobic Growth of Escherichia coli on Substrates Other Than Glucose. - I. Fructose and Lactose as Substrates. - II. Pentoses as Substrates. - III. Acetate, Pyruvate, and L-Malate as Substrates. - IV. Summary. - 5 Metabolic Diversity of Aerobic Heterotrophs. - I. The Different Mechanisms for the Uptake of Substrates. - II. The Entner-Doudoroff Pathway. - III. Sugar Degradation via the Pentose Phosphate Cycle. - IV. The Methylglyoxal Bypass. - V. Diversity in Energy Metabolism. - VI. Dissimilatory Reduction of Nitrate. - VII. Bacterial Bioluminescence. - VIII. Alternate Anaplerotic Sequences. - IX. Biosynthesis of Monomers and Polymers. - X. Summary. - 6 Catabolic Activities of Aerobic Heterotrophs. - I. Degradation of Polymers by Exoenzymes. - II. Growth with Amino Acids. - III. Growth with Organic Acids. - IV. Growth with Aliphatic Hydrocarbons. - V. Growth with Aromatic Compounds. - VI. Growth with C1Compounds. - VII. Incomplete Oxidations. - VIII. Plasmid-Encoded Catabolic Activities. - IX. Summary. - 7 Regulation of Bacterial Metabolism. - I. Regulation of Enzyme Synthesis by Induction and Repression. - II. Regulation of Enzyme Activity. - III. Summary. - 8 Bacterial Fermentations. - I. Alcohol Fermentation. - II. Lactate Fermentation. - III. Butyrate and Butanol-Acetone Fermentation. - IV. Mixed Acid and Butanediol Fermentation. - V. Propionate and Succinate Fermentation. - VI. Acetate Fermentation. - VII. Methane Fermentation. - VIII. Sulfide Fermentation (Desulfurication). - IX. The Anaerobic Food Chain. - X. Fermentation of Nitrogenous Compounds. - Xl. Summary. - 9 Chemolithotrophic and Phototrophic Metabolism. - I. Chemolithotrophic Metabolism. - II. Assimilation of CO2. - III. Phototrophic Metabolism. - IV. Summary. - 10 Fixation of Molecular Nitrogen. - I. Nitrogen-fixing Organisms. - II. Biochemistry of Nitrogen Fixation. - III. Regulation of Nitrogenase. - IV. Summary. - Further Reading. - Index of Organisms.