Metabolic Engineering (eBook)

Principles and Methodologies

Aristos A. Aristidou, Jens Nielsen, George Stephanopoulos (Autoren)

eBook Download: PDF | EPUB

1998 | 1. Auflage
725 Seiten
Elsevier Science (Verlag)
978-0-08-053628-6 (ISBN)

Infos

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

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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. 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

Inhalt

Front Cover 1
Metabolic Engineering: Principles and Methodologies 4
Copyright Page 5
Contents 8
Preface 14
List of Symbols 18
Chapter 1. The Essence of Metabolic Engineering???????????????????????????????????????????????????????????????????????????????????????????????????????????? 24
1.1 Importance of Metabolic Engineering???????????????????????????????????????????????????????????????????????????????????????????? 32
1.2 General Overview of the Book 38
References 43
Chapter 2. Review of Cellular Metabolism?????????????????????????????????????????????????????????????????????????????????????????????? 44
2.1 An Overview of Cellular Metabolism?????????????????????????????????????????????????????????????????????????????????????????? 45
2.2 Transport Processes???????????????????????????????????????????????????????????? 50
2.3 Fueling Reactions???????????????????????????????????????????????????????? 61
2.4 Biosynthetic Reactions?????????????????????????????????????????????????????????????????? 80
2.5 Polymerization?????????????????????????????????????????????????? 89
2.6 Growth Energetics???????????????????????????????????????????????????????? 94
References?????????????????????????????????? 99
Chapter 3. Comprehensive Models for Cellular Reactions?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 104
3.1 Stoichiometry of Cellular Reactions???????????????????????????????????????????????????????????????????????????????????????????? 105
3.2 Reaction Rates?????????????????????????????????????????????????? 113
3.3 Dynamic Mass Balances???????????????????????????????????????????????????????????????? 116
3.4 Yield Coefficients and Linear Rate Equations 125
References 137
Chapter 4. Material Balances and Data Consistency???????????????????????????????????????????????????????????????????????????????????????????????????????????????? 138
4.1 The Black Box Model???????????????????????????????????????????????????????????? 140
4.2 Elemental Balances?????????????????????????????????????????????????????????? 142
4.3 Heat Balance?????????????????????????????????????????????? 149
4.4 Analysis of Overdetermined Systems—Identification of Gross Measurement Errors 153
References?????????????????????????????????? 169
Chapter 5. Regulation of Metabolic Pathways???????????????????????????????????????????????????????????????????????????????????????????????????? 170
5.1 Regulation of Enzymatic Activity?????????????????????????????????????????????????????????????????????????????????????? 173
5.2 Regulation of Enzyme Concentration?????????????????????????????????????????????????????????????????????????????????????????? 196
5.3 Global Control: Regulation at the Whole Cell Level?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 203
5.4 Regulation of Metabolic Networks?????????????????????????????????????????????????????????????????????????????????????? 211
References?????????????????????????????????? 223
Chapter 6. Examples of Pathway Manipulations: Metabolic Engineering in Practice???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 226
6.1 Enhancement of Product Yield and Productivity???????????????????????????????????????????????????????????????????????????????????????????????????????????????? 228
6.2 Extension of Substrate Range?????????????????????????????????????????????????????????????????????????????? 247
6.3 Extension of Product Spectrum and Novel Products?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 258
6.4 Improvement of Cellular Properties?????????????????????????????????????????????????????????????????????????????????????????? 279
6.5 Xenobiotic Degradation?????????????????????????????????????????????????????????????????? 289
References 296
Chapter 7. Metabolic Pathway Synthesis?????????????????????????????????????????????????????????????????????????????????????????? 308
7.1 Metabolic Pathway Synthesis Algorithm???????????????????????????????????????????????????????????????????????????????????????????????? 311
7.2 Overview of the Algorithm???????????????????????????????????????????????????????????????????????? 318
7.3 A Case Study: Lysine Biosynthesis???????????????????????????????????????????????????????????????????????????????????????? 323
7.4 Discussion of the Algorithm 330
References 331
Chapter 8. Metabolic Flux Analysis?????????????????????????????????????????????????????????????????????????????????? 332
8.1 Theory?????????????????????????????????? 336
8.2 Overdetermined Systems?????????????????????????????????????????????????????????????????? 356
8.3 Underdetermined Systems—Linear Programming 364
8.4 Sensitivity Analysis?????????????????????????????????????????????????????????????? 370
References?????????????????????????????????? 373
Chapter 9. Methods for the Experimental Determination of Metabolic Fluxes by Isotope Labeling???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 376
9.1 Direct Flux Determination from Fractional Label Enrichment?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 379
9.2 Applications Involving Complete Enumeration of Metabolite Isotopomers???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 390
9.3 Carbon Metabolite Balances?????????????????????????????????????????????????????????????????????????? 420
References 432
Chapter 10. Applications of Metabolic Flux Analysis???????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 434
10.1 Amino Acid Production by Glutamic Acid Bacteria?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 436
10.2 Metabolic Fluxes in Mammalian Cell Cultures?????????????????????????????????????????????????????????????????????????????????????????????????????????????? 468
References?????????????????????????????????? 481
Chapter 11. Metabolic Control Analysis?????????????????????????????????????????????????????????????????????????????????????????? 484
11.1 Fundamentals of Metabolic Control Analysis???????????????????????????????????????????????????????????????????????????????????????????????????????????? 487
11.2 Determination of Flux Control Coefficients???????????????????????????????????????????????????????????????????????????????????????????????????????????? 498
11.3 MCA of Linear Pathways???????????????????????????????????????????????????????????????????? 515
11.4 MCA of Branched Pathways???????????????????????????????????????????????????????????????????????? 522
11.5 Theory of Large Deviations???????????????????????????????????????????????????????????????????????????? 536
References 553
Chapter 12. Analysis of Structure of Metabolic Networks???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 558
12.1 Control of Flux Distribution at a Single Branch Point?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 562
12.2 Grouping of Reactions?????????????????????????????????????????????????????????????????? 568
12.3 Case Study: Aromatic Amino Acid Biosynthetic Pathway???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 577
References?????????????????????????????????? 603
Chapter 13. Flux Analysis of Metabolic Networks???????????????????????????????????????????????????????????????????????????????????????????????????????????? 604
13.1 Relationships among Group and Individual Control Coefficients (Bottom-Up Approach)???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 605
13.2 Determination of Group Control Coefficients from Flux Measurements (Top-Down Approach)???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 608
13.3 Case Study???????????????????????????????????????????? 615
13.4 Extension of Control Analysis to Intermetabolite Reaction Groups???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 627
13.5 Optimization of Flux Amplification???????????????????????????????????????????????????????????????????????????????????????????? 632
13.6 Consistency Tests and Experimental Validation?????????????????????????????????????????????????????????????????????????????????????????????????????????????????? 639
References 649
Chapter 14. Thermodynamics of Cellular Processes?????????????????????????????????????????????????????????????????????????????????????????????????????????????? 652
14.1 Thermodynamic Principles: A Review???????????????????????????????????????????????????????????????????????????????????????????? 653
14.2 Thermodynamic Feasibility?????????????????????????????????????????????????????????????????????????? 662
14.3 Nonequilibrium Thermodynamics?????????????????????????????????????????????????????????????????????????????????? 686
14.4 Application of Thermokinetics to MCA 709
References 715
Glossary?????????????????????????????? 718
Index???????????????????????? 730

Produkt-Details

• Erscheint lt. Verlag: 17.10.1998
• Sprache: englisch
• Themenwelt: Medizin / Pharmazie ► Pflege
• Themenwelt: Medizin / Pharmazie ► Physiotherapie / Ergotherapie ► Orthopädie
• Themenwelt: Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
• Themenwelt: Naturwissenschaften ► Biologie ► Mikrobiologie / Immunologie
• Themenwelt: Naturwissenschaften ► Biologie ► Zellbiologie
• Themenwelt: Naturwissenschaften ► Chemie ► Technische Chemie
• Themenwelt: Technik ► Bauwesen
• Themenwelt: Technik ► Medizintechnik
• Themenwelt: Technik ► Umwelttechnik / Biotechnologie
• ISBN-10: 0-08-053628-X / 008053628X
• ISBN-13: 978-0-08-053628-6 / 9780080536286