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Metabolic Engineering of Escherichia Coli for the Efficient Utilization of Plant Sugar Mixture Madhuresh Kumar Choudhary Iowa State University

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Metabolic Engineering of Escherichia Coli for the Efficient Utilization of Plant Sugar Mixture Madhuresh Kumar Choudhary Iowa State University Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 2008 Metabolic engineering of Escherichia coli for the efficient utilization of plant sugar mixture Madhuresh Kumar Choudhary Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Chemical Engineering Commons Recommended Citation Choudhary, Madhuresh Kumar, "Metabolic engineering of Escherichia coli for the efficient utilization of plant sugar mixture" (2008). Retrospective Theses and Dissertations. 15312. https://lib.dr.iastate.edu/rtd/15312 This Thesis is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Metabolic engineering of Escherichia coli for the efficient utilization of plant sugar mixture by Madhuresh Kumar Choudhary A thesis submitted to the graduate faculty in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Major: Chemical Engineering Program of Study Committee: Jacqueline V. Shanks (Major Professor) Monica H. Lamm Julie A. Dickerson Iowa State University Ames, Iowa 2008 Copyright © Madhuresh Kumar choudhary, 2008. All rights reserved. UMI Number: 1453128 UMI Microform 1453128 Copyright 2008 by ProQuest Information and Learning Company. All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code. ProQuest Information and Learning Company 300 North Zeeb Road P.O. Box 1346 Ann Arbor, MI 48106-1346 ii Table of contents List of Figures.................................................................................................................... iv List of Tables ...................................................................................................................... v Abbreviations..................................................................................................................... vi Abstract............................................................................................................................. vii 1 Introduction................................................................................................................. 1 1.1 Metabolic Engineering and Metabolic Fluxes.................................................... 2 1.2 Metabolic flux analysis....................................................................................... 4 1.3 Organization of the report................................................................................... 7 1.4 References........................................................................................................... 7 2 Literature Review........................................................................................................ 9 2.5 Metabolic flux analysis....................................................................................... 9 2.6 Conventional flux Analysis............................................................................... 11 2.7 Carbon labeling experiment.............................................................................. 13 2.8 Measurement Procedures.................................................................................. 16 2.9 NMR techniques ............................................................................................... 17 2.10 MS techniques review....................................................................................... 18 2.11 Flux determination methodology...................................................................... 19 2.12 Flux Identifiability and the Design of optimal experiment............................... 23 2.13 Labeling based metabolic flux analysis in Escherichia coli ............................. 26 2.14 References:........................................................................................................ 28 3 Sugar Utilization Regulatory System in Escherichia coli .................................. 31 3.1 Introduction....................................................................................................... 31 3.2 PTS system........................................................................................................ 31 3.3 Xylose and Arabinose utilization...................................................................... 34 3.4 PTS as signal transduction mechanism............................................................. 38 3.5 Regulation of PTS genes................................................................................... 41 3.6 Post-transcriptional regulation of ptsG............................................................. 42 3.7 Adenylate Cyclase ............................................................................................ 43 3.8 CRP................................................................................................................... 44 3.9 CRA .................................................................................................................. 44 3.10 Expression of Mlc............................................................................................. 45 3.11 Autoregulation of Carbohydrate uptake............................................................ 45 3.12 Engineering and utilization of PTS- strains...................................................... 46 3.13 Proposed Research Approach ........................................................................... 48 3.14 References......................................................................................................... 49 4 Metabolic Flux Analysis of Escherichia coli under Anaerobic Conditions and Design of 13C labeling Experiments ................................................................................. 53 4.1 Introduction....................................................................................................... 53 4.2 Material and Methods ....................................................................................... 54 4.3 Results and Discussion ..................................................................................... 62 4.4 Conclusion ........................................................................................................ 73 4.5 References......................................................................................................... 83 5 Metabolic Flux analysis of Escherichia coli ptsG Mutant and Wild Type Consuming Glucose/Xylose under Anaerobic Conditions................................................................... 86 iii 5.1 Introduction....................................................................................................... 86 5.2 Material and Methods ....................................................................................... 88 5.3 Results and Discussion ..................................................................................... 92 5.4 Conclusion ........................................................................................................ 99 5.5 Reference: ......................................................................................................... 99 Conclusion ...................................................................................................................... 107 Future directions ..................................................................................................... 107 Appendix......................................................................................................................... 108 Acknowledgements......................................................................................................... 122 iv List of Figures Figure 1.1: Metabolic engineering strategy for improving a microorganism..................... 4 Figure 2.2: Different levels of metabolic flux analysis..................................................... 11 Figure 3.2: Principles of metabolic flux analysis. ........................................................... 12 Figure 2.4: Typical situations in which stoichiometric MFA fails .................................. 13 Figure 2.5: The ratio of 3-13C Pyruvate and U-12C Pyruvate is dependent on the flux ... 14 Figure 2.6: Isotopomer possibilities of three carbon metabolite. ..................................... 15 Figure 2.7: Relationship between isotopomer and multiplet pattern. ............................... 16 Figure 2.8: (a) NMR cannot distinguish between two isotopomers ................................ 19 Figure 2.9: One-Dimensional illustration of the flux identifiability problem. ................ 25 Figure 3.10: Galactose symporter GalP............................................................................ 35 Figure 3.11: Organization of arabinose operon. .............................................................. 37 Figure 3.12: Model for the regulation by the PTS. .......................................................... 40 Figure 3.13: Schematic diagram showing the regulatory circuit of promoters................. 42 Figure 4.1 : Metabolic network representing central carbon metabolism in E. coli......... 85 Figure 4.2: Comparison of experimental and simulated NMR intensities ....................... 85 Figure 4.3: The metabolic flux map of
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