Microorganisms as Model Systems for Studying Evolution, Softcover reprint of the original 1st ed. 1984 Monographs in Evolutionary Biology Series

The microorganisms present on the earth today possess a vast range of metabolic activities and are often able to demonstrate their surprising versatility by gaining both new enzyme activities and new metabolic path­ ways through mutations. It is generally assumed that the earliest micro­ organisms were very limited in their metabolic abilities, but as time passed they gradually expanded their range of enzymatic activities and increased both their biosynthetic and catabolic capacity. It is also believed that these primitive microorganisms increased the amount of genetic material they possessed by duplicating their existing genes and possibly by ac­ quiring genetic material from other organisms. A small group of scientists has been exploring the means by which existing microorganisms are capable of mutating to expand their bio­ chemical abilities. In recent years, more attention has been focused on this type of research, sometimes called "evolution in a test tube." The recent advances in biotechnology and modern techniques of genetic trans­ fer have generated new interest in the methods by which a microorgan­ ism's metabolic activities can be improved or deliberately changed in some specific manner.

1 The Utilization of Pentitols in Studies of the Evolution of Enzyme Pathways.- 1. Introduction.- 2. The Pentitols.- 3. The Utilization of Pentitols by Klebsiella Species.- 3.1. Growth on Xylitol and l-Arabitol.- 3.2. The Nature of the Mutations Establishing Growth on the New Pentitol Substrates.- 3.3. The Origin of the Xylitol Dehydrogenase Activity.- 3.4. The Origin of the d-Xylulokinase of the New Xylitol Pathway.- 4. The Origin of the l-Arabitol Dehydrogenase Activity.- 5. Mutations Improving the Growth Rate on Xylitol.- 5.1. Alterations in the Dehydrogenase Activity.- 5.2. Mutants with Increased Amounts of Ribitol Dehydrogenase.- 5.3. Utilization of the d-Arabitol Transport System to Facilitate the Transport of Xylitol.- 6. The Growth of Escherichia Coli Strains on Xylitol.- 6.1. The Utilization of Ribitol Dehydrogenase to Establish Growth on Xylitol.- 6.2. The Construction of a Different Route for Xylitol Catabolism.- 7. The Utilization of Xylitol by a Mutant in the Genus Erwinia.- 8. Summary.- References.- 2 Experimental Evolution of Ribitol Dehydrogenase.- 1. Introduction.- 1.1. Evolutionary Lessons from Protein Structures.- 1.2. Microbial Enzyme Evolution.- 2. Pentitol Metabolism in Klebsiella aerogenes.- 3. Chemostat Culture of Klebsiella aerogenes on Xylitol.- 4. Evolution of Ribitol Dehydrogenase in the Chemostat.- 4.1. Enzyme Superproduction.- 4.2. Mechanisms of Enzyme Superproduction.- 4.3. Improved Xylitol Dehydrogenases.- 5. Fluctuating Selective Pressure.- 6. Transfer of the Klebsiella aerogenes Ribitol Dehydrogenase Gene into Escherichia coli K12.- 6.1. Evolution of Ribitol Dehydrogenase in Escherichia coli.- 7. Evolutionary Lessons from the Chemostat Studies.- References.- 3 The Structure and Control of the Pentitol Operons.- 1. Introduction.- 1.1. Construction of ?p rbt.- 1.2. Construction of ?p rbt dal.- 2. The Structure of ?p rbt and ?p rbt dal.- 2.1. Genetic Analysis.- 2.2. Physical Analyses.- 2.3. How Did ?p rbt and ?p rbt dal Arise?.- 3. Bipolar Transcription of the Pentitol Operons.- 4. The Pentitol Operon Enzymes.- 4.1. d-Arabitol Dehydrogenase.- 4.2. d-Ribulokinase.- 4.3. d-Xylulokinase.- 5. Substrate Specificity of the Pentitol Operon Enzymes.- 6. rbt Messenger RNA.- 6.1. A Switch in rbt mRNA Translation in Mid Log Phase.- 6.2. Purification and Properties of rbt mRNA.- 6.3. Is rbt mRNA Superstable?.- 7. DNA Sequencing of the Pentitol Operons.- 7.1. The Ribitol Dehydrogenase Gene.- 7.2. The d-Arabitol Dehydrogenase Gene.- 7.3. The rbt Repressor Protein.- 7.4. The dal Repressor Protein.- 7.5. The dal Promoter.- 7.6. The rbt Promoter.- 7.7. The rbt Repressor Promoter.- 7.8. The dal Repressor Promoter.- 8. Translation of the Two Kinases.- 9. Invert Repeat Sequences Enclose the Two Operons.- 10. Structure of an Experimentally Evolved Gene Duplication.- 11. Evolutionary Lessons from the Pentitol Operons.- References.- 4 The Development of Catabolic Pathways for the Uncommon Aldopentoses.- 1. The Structure of the Aldopentoses and Their Occurrence in Nature.- 1.1. The Structure of the Aldopentoses.- 1.2. d-Ribose and l-Ribose.- 1.3. d-Xylose and l-Xylose.- 1.4. d-Arabinose and l-Arabinose.- 1.5. d-Lyxose and l-Lyxose.- 2. The Pathways of Degradation of Aldopentoses by Coliform Bacteria.- 2.1. Pathways for the Degradation of Those Sugars Commonly Found in Nature.- 2.2. Pathways for the Degradation of Those Sugars Not Commonly Found in Nature.- 2.3. Enzyme Activities Establishing Growth on the New Aldopentose Substrates.- 3. The Biochemical and Genetic Bases for the Establishment of New Enzymatic Pathways for the Degradation of Aldopentoses.- 3.1. The Utilization of d-Lyxose.- 3.2. The Utilization of d-Arabinose.- 3.3. The l-Lycose and l-Xylose Pathways in Klebsiella pneumoniae.- 4. Summary.- References.- 5 Functional Divergence of the L-Fucose System in Mutants of Escherichia coli.- 1. Introduction.- 2. Reversibility of NAD-Linked Reactions.- 3. A Mutant That Uses an NAD-Linked Dehydrogenase to Grow on l-1,2-Propanediol.- 3.1. Characterization of the Novel Biochemical Pathway in the Mutant.- 3.2. Identifying the Original Role of a Recruited Enzyme.- 3.3. Connection of the Propanediol Oxidoreductase with the Fucose System.- 4. Biochemistry of the Fucose System.- 5. Enzymic Changes in the Fucose System in Mutants and Revertants.- 5.1. Propanediol-Positive Mutants Exploit Both Branches of the Fucose System.- 5.2. A Primary Stage Mutant.- 5.3. A Secondary Mutant.- 5.4. Pseudorevertants That Regained the Ability to Grow on Fucose.- 5.5. A Mutant with Superior Scavenger Power for Propanediol.- 5.6. Changes in the Property of the Oxidoreductase.- 6. Genetic Organization and Regulation of the Fucose System.- 6.1. A Regulon Comprised of Closely Linked Operons.- 6.2. Positive Control.- 6.3. The Inducer.- 6.4. Lactaldehyde Dehydrogenase under Separate Control.- 6.5. Post Transcriptional Control of the Oxidoreductase Activity.- 7. Sequential Mutations Changing Propanediol and Fucose Utilization.- 8. Relationship of the Fucose and the Rhamnose Systems.- 9. Conversion of the Fucose System for d-Arabinose Utilization.- 10. Propanediol-Positive Mutants as Evolutionary Vanguards.- 10.1. Mutants That Grow on d-Arabitol.- 10.2. Mutants That Grow on Xylitol.- 10.3. Mutants That Grow on Ethylene Glycol.- 11. Retrospective and Prospective Views.- References.- 6 The Evolved ?-Galactosidase System of Escherichia coli.- 1. Introduction.- 2. Development of the Evolved ?-Galactosidase System as a Tool for Studying Evolution.- 3. Evolution of Multiple Functions for Evolved ?-Galactosidase Enzyme: An Evolutionary Pathway.- 4. Kinetic Analysis of Evolved ?-Galactosidase Enzymes.- 5. Evolution by Intragenic Recombination.- 6. Allolactose Synthesis: Another New Function for Class IV Enzyme.- 7. The Role of Regulatory Mutations in the Evolution of Lactose Utilization.- 8. Directed Evolution of a Repressor.- 9. The Fully Evolved EBG Operon.- 10. A Model for Evolution in Diploid Organisms.- 11. Future Perspectives.- References.- 7 Amidases of Pseudomonas aeruginosa.- 1. Introduction.- 1.1. Biochemical Activities of Pseudomonas Species.- 1.2. Choice of Enzyme System.- 1.3. Growth of Pseudomonas aeruginosa on Acetamide.- 1.4. The Wild-Type Amidase of Pseudomonas aeruginosa PAC1.- 2. Amidase Regulatory Mutants.- 2.1. Isolation of Mutants from Succinate/Formamide Medium.- 2.2. Isolation of Mutants from Succinate/Lactamide Medium.- 2.3. Isolation of Mutants with Altered Inducibility.- 3. Amidase-Negative Mutants.- 3.1. Isolation of Acetamide-Negative Mutants.- 3.2. Mutations in the amiE Gene.- 3.3. Mutations in the amiR Gene.- 3.4. Promoter Mutations.- 4. Mutants with Altered Enzymes.- 4.1. Butyramide-Utilizing Mutants: B Group.- 4.2. Valeramide-Utilizing Mutants: V Group.- 4.3. Phenylacetamide-Utilizing Mutants: Ph Group.- 4.4. Acetanilide-Utilizing Mutants: AI Group.- 5. Properties of Wild-Type and Mutant Amidases.- 5.1. Enzyme Structure.- 5.2. Catalytic Activities.- 6. Amidase Genes and Enzymes.- 6.1. Gene Mapping.- 6.2. Mutation.- 6.3. Role of Recombination.- 6.4. Alignment of amiE Gene and Protein.- 6.5. Amidase Gene Capture.- 6.6. How Many More Amidases?.- References.- 8 Structural Evolution of Yeast Alcohol Dehydrogenase in the Laboratory.- 1. Introduction.- 2. The Biochemistry and Regulation of Yeast Alcohol Dehydrogenase.- 3. The Mechanism of Allyl Alcohol Resistance.- 4. Amino Acid Substitutions in the Mutant ADHs.- 5. Altered Kinetics of the Mutants.- 6. Evolutionary Implications.- References.- 9 Gene Recruitment for a Subunit of Isopropylmalate Isomerase.- 1. The Leucine Operon in Salmonella typhimurium Wild-Type Strains.- 2. The Wild-Type Isopropylmalate Isomerase.- 3. Strains Carrying leuD Mutations Revert to Leucine Prototrophy.- 4. Model for Leucine Biosynthesis in leuD—supQ Mutant Strains.- 5. Leucine Biosynthesis in leuD—supQ Mutant Strains.- 6. Genetic Characterization of the leuD—newD Isopropylmalate Isomerase.- 6.1. A Free leuC Polypeptide Is Needed.- 6.2. supQ Mutations Result in Availability of the newD Gene Product.- 6.3. Nature of supQ Mutations.- 6.4. Direction of Transcription in the supQ newD Region.- 6.5. What Is the Original Function of supQ newD?.- 6.6. Are supQ newD Genes Existing or Functional in Escherichia coli?.- 7. Biochemical Characterization of the leuC—newD Isopropylmalate Isomerase.- 7.1. In Vitro Specific Activity of the Hybrid leuC—newD Isopropylmalate Isomerase.- 7.2. Mutant Isopropylmalate Isomerase Activity Is Limited by the Endogenous Concentration of ?-Isopropylmalate.- 7.3. Growth Limitations in Strains with an Unbridled Leucine Biosynthesis Pathway.- 8. Theoretical Steps in the Evolution of a Complex Enzyme.- 9. Characterization of the newD (and supQ) Gene(s).- References.- 10 Arrangement and Rearrangement of Bacterial Genomes.- 1. Introduction.- 2. Chromosomal Rearrangements: Mechanisms of Change.- 2.1. Duplications.- 2.2. Transpositions.- 2.3. Inversions.- 2.4. Additions and Deletions.- 3. Conservation of Global Gene Order: Mechanisms of Stability.- 3.1. Integrity of Taxonomic Groupings.- 3.2. Genetic Maps.- 3.3. Possible Stabilizing Factors.- 4. Conclusion.- References.