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Metabolic Engineering Strategies for High-Level Production of Aromatic Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2017 Metabolic engineering strategies for high-level production of aromatic amino acid pathway derivatives in Saccharomyces cerevisiae Jose Miguel Suastegui Pastrana Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Chemical Engineering Commons Recommended Citation Suastegui Pastrana, Jose Miguel, "Metabolic engineering strategies for high-level production of aromatic amino acid pathway derivatives in Saccharomyces cerevisiae" (2017). Graduate Theses and Dissertations. 15431. https://lib.dr.iastate.edu/etd/15431 This Dissertation 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 Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Metabolic engineering strategies for high-level production of aromatic amino acid pathway derivatives in Saccharomyces cerevisiae by José Miguel Suástegui Pastrana A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Chemical Engineering Program of Study Committee: Zengyi Shao, Major Professor Julie A. Dickerson Laura R. Jarboe Basil J. Nikolau Brent H. Shanks The student author and the program of study committee are solely responsible for the content of this dissertation. The Graduate College will ensure this dissertation is globally accessible and will not permit alterations after a degree is conferred. Iowa State University Ames, Iowa 2017 Copyright © José Miguel Suástegui Pastrana, 2017. All rights reserved. ii TABLE OF CONTENTS Page NOMENCLATURE .................................................................................................. vi ACKNOWLEDGMENTS ......................................................................................... vii ABSTRACT………………………………. .............................................................. ix CHAPTER 1 INTRODUCTION .......................................................................... 1 1. Motivation ........................................................................................................ 1 2. Objectives ........................................................................................................ 3 3. Approach ......................................................................................................... 4 4. Report Organization ......................................................................................... 5 CHAPTER 2 YEAST FACTORIES FOR THE PRODUCTION OF AROMATIC COMPOUNDS: FROM BUILDING BLOCKS TO PLANT SECONDARY METABOLITES ....................................................................................................... 7 Abstract ......................................................................................................... 7 1. Introduction .................................................................................................... 7 2. The Aromatic Amino Acid Biosynthetic Pathway ........................................ 10 2.1. Initiation, shikimic acid pathway, and aromatic branches ...................... 10 2.2. Transcriptional regulation ....................................................................... 11 2.3. Allosteric regulation ............................................................................... 12 3. Metabolic Engineering Strategies for Production of Aromatic Compounds . 14 3.1. Engineering the shikimic acid pathway .................................................. 14 3.1.1.Muconic acid ................................................................................... 14 3.1.2.Shikimic acid .................................................................................. 15 3.1.3.Vanillin ........................................................................................... 18 3.2. Engineering the L-tyr and L-phe branches .............................................. 20 3.2.1.Phenylethanol .................................................................................. 21 3.2.2.Coumaric acid ................................................................................. 22 3.2.3.Flavonoids and stilbenoids .............................................................. 25 3.2.4.Benzylisoquinoline alkaloids .......................................................... 27 3.3. Engineering the L-trp branch .................................................................. 31 3.3.1.Monoterpene indole alkaloids ......................................................... 31 3.3.2.Melatonin ........................................................................................ 32 4. Remarks and Future Directions ..................................................................... 34 5. Bibliography .................................................................................................. 37 iii CHAPTER 3 BUILDING A METABOLIC ENGINEERING AND ELECTROCATALYSIS PIPELINE FOR THE PRODUCTION OF POLYAMIDES FROM SUGAR ......................................................................................................... 45 Abstract ......................................................................................................... 45 1. Introduction .................................................................................................... 46 2. Materials and Methods ................................................................................... 48 2.1. Strains and media .................................................................................... 48 2.2. Plasmid and strain construction .............................................................. 48 2.3. Flux Balance Analysis ............................................................................ 49 2.4. ARO1 variants construction ................................................................... 49 2.5. In vivo PCA decarboxylase activity assay .............................................. 52 2.6. Small scale and bioreactor fermentation ................................................. 52 2.7. Metabolite detection ............................................................................... 52 3. Results ......................................................................................................... 53 3.1. Establishing muconic acid production in S. cerevisiae .......................... 54 3.2. Improving the synthetic flux towards DHS via a novel mutant ............. 55 3.3. Controlling oxygen to alleviate PCA bottleneck .................................... 56 3.4. Electrochemical hydrogenation .............................................................. 61 3.5. Polymerization of HDA .......................................................................... 62 4. Discussion ...................................................................................................... 66 5. Bibliography .................................................................................................. 70 6. Supplementary Information ........................................................................... 75 6.1. Supplementary Methods ......................................................................... 75 6.1.1.Electrocatalytic hydrogenation ....................................................... 75 6.1.2.Separations ...................................................................................... 77 6.1.3.Polymerization ................................................................................ 77 6.2. Supplementary Tables ............................................................................ 78 6.3. Supplementary Figures ........................................................................... 80 CHAPTER 4 INVESTIGATING STRAIN DEPENDENCY IN THE PRODUCTION OF AROMATIC COMPOUNDS IN SACCHAROMYCES CEREVISIAE ......................................................................................................... 82 Abstract ......................................................................................................... 82 1. Introduction .................................................................................................... 83 2. Materials and Methods ................................................................................... 85 2.1. Strains and media .................................................................................... 85 2.2. Plasmid construction ............................................................................... 86 2.3. Biomass and metabolite analysis ............................................................ 88 2.4. Isotopomer analysis of proteinogenic amino acids and SA .................... 88 2.5. Metabolic Flux Analysis ......................................................................... 89 2.6. Plasmid copy number assay .................................................................... 89 3. Results and Discussion .................................................................................. 90 3.1. Building the first yeast platform for SA production ............................... 90 3.2. Comparison of fermentation profiles ...................................................... 97 iv 3.3. Inspection of 13C isotopic “finger prints” of aromatic amino acids ........ 99 3.4. Comparison
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