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" Microorganisms As Model Systems for Studying Evolution. "
Mortlock, Robert
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BL
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727368
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b547100
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Mortlock, Robert
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| Title & Author
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Microorganisms As Model Systems for Studying Evolution.\ Mortlock, Robert
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| Publication Statement
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Springer Verlag, 2013
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| ISBN
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1468448447
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: 9781468448443
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| Contents
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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.
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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.
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| LC Classification
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QR13.M678 2013
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| Added Entry
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Mortlock, Robert
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