Metabolic Engineering: Principles and Methodologies
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Table of contents
- Cover
- Contentsvii
- Prefacexiii
- List of Symbolsxvii
- Chapter 1. The Essence of Metabolic Engineering1
- 1.1 Importance of Metabolic Engineering9
- 1.2 General Overview of the Book15
- References20
- Chapter 2. Review of Cellular Metabolism21
- 2.1 An Overview of Cellular Metabolism22
- 2.2 Transport Processes27
- 2.3 Fueling Reactions38
- 2.4 Biosynthetic Reactions57
- 2.5 Polymerization66
- 2.6 Growth Energetics71
- References76
- Chapter 3. Comprehensive Models for Cellular Reactions81
- 3.1 Stoichiometry of Cellular Reactions82
- 3.2 Reaction Rates90
- 3.3 Dynamic Mass Balances93
- 3.4 Yield Coefficients and Linear Rate Equations102
- References114
- Chapter 4. Material Balances and Data Consistency115
- 4.1 The Black Box Model117
- 4.2 Elemental Balances119
- 4.3 Heat Balance126
- 4.4 Analysis of Overdetermined Systems„Identification of Gross Measurement Errors130
- References146
- Chapter 5. Regulation of Metabolic Pathways147
- 5.1 Regulation of Enzymatic Activity150
- 5.2 Regulation of Enzyme Concentration173
- 5.3 Global Control: Regulation at the Whole Cell Level180
- 5.4 Regulation of Metabolic Networks188
- References200
- Chapter 6. Examples of Pathway Manipulations: Metabolic Engineering in Practice203
- 6.1 Enhancement of Product Yield and Productivity205
- 6.2 Extension of Substrate Range224
- 6.3 Extension of Product Spectrum and Novel Products235
- 6.4 Improvement of Cellular Properties256
- 6.5 Xenobiotic Degradation266
- References273
- Chapter 7. Metabolic Pathway Synthesis285
- 7.1 Metabolic Pathway Synthesis Algorithm288
- 7.2 Overview of the Algorithm295
- 7.3 A Case Study: Lysine Biosynthesis300
- 7.4 Discussion of the Algorithm307
- References308
- Chapter 8. Metabolic Flux Analysis309
- 8.1 Theory313
- 8.2 Overdetermined Systems333
- 8.3 Underdetermined Systems„Linear Programming341
- 8.4 Sensitivity Analysis347
- References350
- Chapter 9. Methods for the Experimental Determination of Metabolic Fluxes by Isotope Labeling353
- 9.1 Direct Flux Determination from Fractional Label Enrichment356
- 9.2 Applications Involving Complete Enumeration of Metabolite Isotopomers367
- 9.3 Carbon Metabolite Balances397
- References409
- Chapter 10. Applications of Metabolic Flux Analysis411
- 10.1 Amino Acid Production by Glutamic Acid Bacteria413
- 10.2 Metabolic Fluxes in Mammalian Cell Cultures445
- References458
- Chapter 11. Metabolic Control Analysis461
- 11.1 Fundamentals of Metabolic Control Analysis464
- 11.2 Determination of Flux Control Coefficients475
- 11.3 MCA of Linear Pathways492
- 11.4 MCA of Branched Pathways499
- 11.5 Theory of Large Deviations513
- References530
- Chapter 12. Analysis of Structure of Metabolic Networks535
- 12.1 Control of Flux Distribution at a Single Branch Point539
- 12.2 Grouping of Reactions545
- 12.3 Case Study: Aromatic Amino Acid Biosynthetic Pathway554
- References580
- Chapter 13. Flux Analysis of Metabolic Networks581
- 13.1 Relationships among Group and Individual Control Coefficients (Bottom-Up Approach)582
- 13.2 Determination of Group Control Coefficients from Flux Measurements (Top-Down Approach)585
- 13.3 Case Study592
- 13.4 Extension of Control Analysis to Intermetabolite Reaction Groups604
- 13.5 Optimization of Flux Amplification609
- 13.6 Consistency Tests and Experimental Validation616
- References626
- Chapter 14. Thermodynamics of Cellular Processes629
- 14.1 Thermodynamic Principles: A Review630
- 14.2 Thermodynamic Feasibility639
- 14.3 Nonequilibrium Thermodynamics663
- 14.4 Application of Thermokinetics to MCA686
- References692
- Glossary695
- Index707
Metabolic engineering is a new field with applications in the production of chemicals, fuels, materials, pharmaceuticals, and medicine at the genetic level. The field's novelty is in the synthesis of molecular biology techniques and the tools of mathematical analysis, which allow rational selection of targets for genetic modification through measurements and control of metabolic fluxes. The objective is to identify specific genetics or environmental manipulations that result in improvements in yield and productivities of biotechnological processes.
Key features of the book are pathway integration and the focus on metabolic flux as a fundamental determinant of cell physiology. The book keeps mathematical complexity to a minimum, and provides a glossary of biological terms to facilitate use of the book by a broader spectrum of readers. A web page exists to communicate updates of the codes and homework problems.
Key Features
* Demonstrates metabolic engineering in action with numerous examples of pathway modification
* Includes methods for identifying key enzymes in metabolic networks
* Contains a comprehensive review of metabolic biochemistry
* Discusses metabolic regulation at the gene, enzyme, operon, and cell levels
* Explains concepts of stoichiometry, kinetics, and thermodynamics of metabolic pathways
* Minimizes mathematical complexity
* Links to a Web page to communicate updates of the software code and homework problems
Key features of the book are pathway integration and the focus on metabolic flux as a fundamental determinant of cell physiology. The book keeps mathematical complexity to a minimum, and provides a glossary of biological terms to facilitate use of the book by a broader spectrum of readers. A web page exists to communicate updates of the codes and homework problems.
Key Features
* Demonstrates metabolic engineering in action with numerous examples of pathway modification
* Includes methods for identifying key enzymes in metabolic networks
* Contains a comprehensive review of metabolic biochemistry
* Discusses metabolic regulation at the gene, enzyme, operon, and cell levels
* Explains concepts of stoichiometry, kinetics, and thermodynamics of metabolic pathways
* Minimizes mathematical complexity
* Links to a Web page to communicate updates of the software code and homework problems