Improved production of Taxol® precursors in S. cerevisiae using combinatorial in silico design and metabolic engineering
Journal article, 2023

Background: Integrated metabolic engineering approaches that combine system and synthetic biology tools enable the efficient design of microbial cell factories for synthesizing high-value products. In this study, we utilized in silico design algorithms on the yeast genome-scale model to predict genomic modifications that could enhance the production of early-step Taxol® in engineered Saccharomyces cerevisiae cells. Results: Using constraint-based reconstruction and analysis (COBRA) methods, we narrowed down the solution set of genomic modification candidates. We screened 17 genomic modifications, including nine gene deletions and eight gene overexpressions, through wet-lab studies to determine their impact on taxadiene production, the first metabolite in the Taxol® biosynthetic pathway. Under different cultivation conditions, most single genomic modifications resulted in increased taxadiene production. The strain named KM32, which contained four overexpressed genes (ILV2, TRR1, ADE13, and ECM31) involved in branched-chain amino acid biosynthesis, the thioredoxin system, de novo purine synthesis, and the pantothenate pathway, respectively, exhibited the best performance. KM32 achieved a 50% increase in taxadiene production, reaching 215 mg/L. Furthermore, KM32 produced the highest reported yields of taxa-4(20),11-dien-5α-ol (T5α-ol) at 43.65 mg/L and taxa-4(20),11-dien-5-α-yl acetate (T5αAc) at 26.2 mg/L among early-step Taxol® metabolites in S. cerevisiae. Conclusions: This study highlights the effectiveness of computational and integrated approaches in identifying promising genomic modifications that can enhance the performance of yeast cell factories. By employing in silico design algorithms and wet-lab screening, we successfully improved taxadiene production in engineered S. cerevisiae strains. The best-performing strain, KM32, achieved substantial increases in taxadiene as well as production of T5α-ol and T5αAc. These findings emphasize the importance of using systematic and integrated strategies to develop efficient yeast cell factories, providing potential implications for the industrial production of high-value isoprenoids like Taxol®.

Taxol

Synthetic biology

Computational metabolic engineering

Saccharomyces cerevisiae

in silico design

Genome-scale modelling

Systems biology

Mevalonate pathway

Taxadiene

Author

Koray Malcı

University of Edinburgh

Imperial College London

Rodrigo Santibáñez

University of California

Nestor Jonguitud-Borrego

University of Edinburgh

Jorge H. Santoyo-Garcia

University of Edinburgh

Eduard Kerkhoven

Novo Nordisk Foundation

Chalmers, Life Sciences, Systems and Synthetic Biology

Leonardo Rios-Solis

Newcastle University

University of Edinburgh

University College London (UCL)

Microbial Cell Factories

14752859 (eISSN)

Vol. 22 1 243

Subject Categories

Microbiology

Bioinformatics and Systems Biology

DOI

10.1186/s12934-023-02251-7

More information

Latest update

12/20/2023