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Nowrouzi B, Torres-Montero P, Kerkhoven EJ, Martínez JL, Rios-Solis L. Rewiring Saccharomyces cerevisiae metabolism for optimised Taxol® precursors production. Metab Eng Commun 2024; 18:e00229. [PMID: 38098801 PMCID: PMC10716015 DOI: 10.1016/j.mec.2023.e00229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/09/2023] [Accepted: 11/04/2023] [Indexed: 12/17/2023] Open
Abstract
Saccharomyces cerevisiae has been conveniently used to produce Taxol® anticancer drug early precursors. However, the harmful impact of oxidative stress by the first cytochrome P450-reductase enzymes (CYP725A4-POR) of Taxol® pathway has hampered sufficient progress in yeast. Here, we evolved an oxidative stress-resistant yeast strain with three-fold higher titre of their substrate, taxadiene. The performance of the evolved and parent strains were then evaluated in galactose-limited chemostats before and under the oxidative stress by an oxidising agent. The interaction of evolution and oxidative stress was comprehensively evaluated through transcriptomics and metabolite profiles integration in yeast enzyme-constrained genome scale model. Overall, the evolved strain showed improved respiration, reduced overflow metabolites production and oxidative stress re-induction tolerance. The cross-protection mechanism also potentially contributed to better heme, flavin and NADPH availability, essential for CYP725A4 and POR optimal activity in yeast. The results imply that the evolved strain is a robust cell factory for future efforts towards Taxol© production.
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Affiliation(s)
- Behnaz Nowrouzi
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
- Centre for Engineering Biology, The University of Edinburgh, Edinburgh, EH9 3BD, United Kingdom
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Pablo Torres-Montero
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Eduard J. Kerkhoven
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- SciLifeLab, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - José L. Martínez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
- Centre for Engineering Biology, The University of Edinburgh, Edinburgh, EH9 3BD, United Kingdom
- School of Natural and Environmental Sciences, Molecular Biology and Biotechnology Division, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
- Department of Biochemical Engineering, The Advanced Centre for Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, United Kingdom
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Galindo-Rodriguez GR, Sarwar MS, Rios-Solis L, Dimartino S. Development, characterization and application of 3D printed adsorbents for in situ recovery of taxadiene from microbial cultivations. J Chromatogr A 2024; 1721:464815. [PMID: 38522406 DOI: 10.1016/j.chroma.2024.464815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/06/2024] [Accepted: 03/11/2024] [Indexed: 03/26/2024]
Abstract
Microbial cell factories are an attractive alternative to produce high-value natural products using sustainable processes. However, product recovery is one of the main challenges to reduce production cost and make these technologies economically interesting. In this work, new resins were formulated to 3D print hydrophobic adsorbents for the recovery of biologics from microbial cultivations. Benzyl methacrylate (BEMA) and butyl methacrylate (BUMA) were selected as functional monomers suitable for the adsorption of hydrophobic compounds. Pore morphology was tailored through the inclusion of pore forming agents (porogens) in the resin. Different porogens and porogen concentrations were evaluated resulting in materials with different porous networks. Sudan 1 and the anticancer drug paclitaxel were employed as model compounds to test the adsorption performance of hydrophobic and terpene molecules onto the developed 3D printed materials. The material with greatest adsorption capacity was obtained using BEMA monomer with 40 % (v/v) porogen (BEMA40). The performance of BEMA40 to recover taxadiene from small-scale (5 mL) Saccharomyces cerevisiae cultivations was tested and compared with commercial Diaion HP-20 beads. Taxadiene titres on BEMA40 (46 ± 2 mg/L) and Diaion HP-20 (54 ± 4 mg/L) were comparable, with no taxadiene detected in the cells and cell-free media, suggesting near 100 % taxadiene partition on the adsorbents. Compared to commercial beads, 3D printed adsorbents can be customized with adjustments in the resin formulation, are well adaptable to diverse bioreactor types, do not clog sampling ports and columns and are easier to handle during post processing. The results of this work demonstrate the potential of 3D printing to fabricate hydrophobic interaction adsorbent materials and their application in the recovery of biological products.
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Affiliation(s)
| | - M Sulaiman Sarwar
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh EH9 3BF, United Kingdom; Centre for Engineering Biology, The University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Simone Dimartino
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh EH9 3BF, United Kingdom.
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Galindo-Rodriguez GR, Santoyo-Garcia JH, Rios-Solis L, Dimartino S. In situ recovery of taxadiene using solid adsorption in cultivations with Saccharomyces cerevisiae. Prep Biochem Biotechnol 2024; 54:86-94. [PMID: 37162336 DOI: 10.1080/10826068.2023.2207204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In this study, an engineered strain of Saccharomyces cerevisiae was used to produce taxadiene, a precursor in the biosynthetic pathway of the anticancer drug paclitaxel. Taxadiene was recovered in situ with the polymeric adsorbent Diaion © HP-20. Here we tested two bioreactor configurations and adsorbent concentrations to maximize the production and recovery of taxadiene. An external recovery configuration (ERC) was performed with the integration of an expanded bed adsorption column, whereas the internal recovery configuration (IRC) consisted in dispersed beads inside the bioreactor vessel. Taxadiene titers recovered in IRC were higher to ERC by 3.4 and 3.5 fold by using 3% and 12% (w/v) adsorbent concentration respectively. On the other hand, cell growth kinetics were faster in ERC which represents an advantage in productivity (mg of taxadiene/L*h). High resin bead concentration (12% w/v) improved the partition of taxadiene onto the beads up to 98%. This result represents an advantage over previous studies using a 3% resin concentration where the partition of taxadiene on the beads was around 50%. This work highlights the potential of in situ product recovery to improve product partition, reduce processing steps and promote cell growth. Nevertheless, a careful design of bioreactor configuration and process conditions is critical.
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Affiliation(s)
| | - Jorge H Santoyo-Garcia
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, UK
- Centre for Synthetic and Systems Biology (SynthSys), The University of Edinburgh, Edinburgh, UK
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, UK
- Centre for Synthetic and Systems Biology (SynthSys), The University of Edinburgh, Edinburgh, UK
| | - Simone Dimartino
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, UK
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Malcı K, Santibáñez R, Jonguitud-Borrego N, Santoyo-Garcia JH, Kerkhoven EJ, Rios-Solis L. Improved production of Taxol ® precursors in S. cerevisiae using combinatorial in silico design and metabolic engineering. Microb Cell Fact 2023; 22:243. [PMID: 38031061 PMCID: PMC10687855 DOI: 10.1186/s12934-023-02251-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/14/2023] [Indexed: 12/01/2023] Open
Abstract
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®.
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Affiliation(s)
- Koray Malcı
- Institute for Bioengineering, School of Engineering, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK.
- Centre for Engineering Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK.
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
| | - Rodrigo Santibáñez
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA
| | - Nestor Jonguitud-Borrego
- Institute for Bioengineering, School of Engineering, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK
- Centre for Engineering Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK
| | - Jorge H Santoyo-Garcia
- Institute for Bioengineering, School of Engineering, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK
- Centre for Engineering Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK
| | - Eduard J Kerkhoven
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- SciLifeLab, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs, Lyngby, Denmark
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK.
- Centre for Engineering Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK.
- School of Natural and Environmental Sciences, Molecular Biology and Biotechnology Division, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK.
- Department of Biochemical Engineering, The Advanced Centre for Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, UK.
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Xu M, Xie W, Luo Z, Li CX, Hua Q, Xu J. Improving solubility and copy number of taxadiene synthase to enhance the titer of taxadiene in Yarrowia lipolytica. Synth Syst Biotechnol 2023; 8:331-338. [PMID: 37215159 PMCID: PMC10196790 DOI: 10.1016/j.synbio.2023.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 05/24/2023] Open
Abstract
Taxadiene is an important precursor for the biosynthesis of highly effective anticancer drug paclitaxel, but its microbial biosynthesis yield is very low. In this study, we employed Yarrowia lipolytica as a microbial host to produce taxadiene. First, a "push-pull" strategy was adopted to increase taxadiene production by 234%. Then taxadiene synthase was fused with five solubilizing tags respectively, leading a maximum increase of 62.3% in taxadiene production when fused with SUMO. Subsequently, a multi-copy iterative integration method was used to further increase taxadiene titer, achieving the maximum titer of 23.7 mg/L in shake flask culture after three rounds of integration. Finally, the taxadiene titer was increased to 101.4 mg/L by optimization of the fed-batch fermentation conditions. This is the first report of taxadiene biosynthesis accomplished in Y. lipolytica, serving as a good example for the sustainable production of taxadiene and other terpenoids in this oleaginous yeast.
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Affiliation(s)
| | | | | | | | | | - Jianhe Xu
- Corresponding author. State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
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Fu J, Xu W, Huang W, Wang B, Li S, Zhang J, Chang L. Importation of taxadiene synthase into chloroplast improves taxadiene production in tobacco. Planta 2021; 253:107. [PMID: 33866441 DOI: 10.1007/s00425-021-03626-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 04/09/2021] [Indexed: 06/12/2023]
Abstract
MAIN CONCLUSION Importation of taxadiene synthase into chloroplasts is important for the efficient heterologous production of taxadiene. Taxadiene, the first committed precursor to taxol, is synthesized from geranylgeranyl pyrophosphate (GGPP) by action of taxadiene synthase (TS). Heterologous production of taxadiene could potentially rely on both cytosolic mevalonic acid (MVA) pathway and the plastidic methylerythritol phosphate (MEP) pathway. We suggest the compartmentalized engineering in chloroplast as an efficient approach for taxadiene production. In this study, we directly introduced the TS gene from Taxus brevifolia into the tobacco chloroplast genome and found that the transplastomic plants accumulated a low content of taxadiene, ~ 5.6 μg/g dry weight (DW). Moreover, we tried a combination of MEP and MVA pathways for taxadiene synthesis by nuclear transformation with a truncated version of TS (without encoding a transit peptide) into the transplastomic plants. However, this did not further improve the taxadiene production. In contrast, we found that taxadiene could be produced up to 87.8 μg/g DW in leaves of transgenic plants expressing TS with a chloroplast transit peptide, which was significantly higher than that in leaves of transplastomic plants. Thus, this study highlights the importance of TS importation into chloroplast for production of taxadiene.
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Affiliation(s)
- Jinqiu Fu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Wenbo Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Wei Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Bipeng Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Shengchun Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Jiang Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Ling Chang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China.
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Rouck JE, Biggs BW, Kambalyal A, Arnold WR, De Mey M, Ajikumar PK, Das A. Heterologous expression and characterization of plant Taxadiene-5α-Hydroxylase (CYP725A4) in Escherichia coli. Protein Expr Purif 2017; 132:60-67. [PMID: 28109855 DOI: 10.1016/j.pep.2017.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 10/11/2016] [Accepted: 01/17/2017] [Indexed: 01/05/2023]
Abstract
Taxadiene-5α-Hydroxylase (CYP725A4) is a membrane-bound plant cytochrome P450 that catalyzes the oxidation of taxadiene to taxadiene-5α-ol. This oxidation is a key step in the production of the valuable cancer therapeutic and natural plant product, taxol. In this work, we report the bacterial expression and purification of six different constructs of CYP725A4. All six of these constructs are N-terminally modified and three of them are fused to cytochrome P450 reductase to form a chimera construct. The construct with the highest yield of CYP725A4 protein was then selected for substrate binding and kinetic analysis. Taxadiene binding followed type-1 substrate patterns with an observed KD of 2.1 ± 0.4 μM. CYP725A4 was further incorporated into nanoscale lipid bilayers (nanodiscs) and taxadiene metabolism was measured. Taxadiene metabolism followed Michaelis-Menten kinetics with an observed Vmax of 30 ± 8 pmol/min/nmolCYP725A4 and a KM of 123 ± 52 μM. Additionally, molecular operating environment (MOE) modeling was performed in order to gain insight into the interactions of taxadiene with CYP725A4 active site. Taken together, we demonstrate the successful expression and purification of the functional membrane-bound plant CYP, CYP725A4, in E. coli.
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Affiliation(s)
- John Edward Rouck
- Department of Comparative Biosciences, Department of Biochemistry, Department of Bioengineering, Division of Nutritional Science, Center for Biophysics and Quantitative Biology, Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Bradley Walters Biggs
- Manus Biosynthesis, 1030 Massachusetts Avenue, Suite 300, Cambridge, MA 02138, USA; Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Amogh Kambalyal
- Department of Comparative Biosciences, Department of Biochemistry, Department of Bioengineering, Division of Nutritional Science, Center for Biophysics and Quantitative Biology, Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - William R Arnold
- Department of Comparative Biosciences, Department of Biochemistry, Department of Bioengineering, Division of Nutritional Science, Center for Biophysics and Quantitative Biology, Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Marjan De Mey
- Centre for Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000, Belgium
| | | | - Aditi Das
- Department of Comparative Biosciences, Department of Biochemistry, Department of Bioengineering, Division of Nutritional Science, Center for Biophysics and Quantitative Biology, Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA.
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Abstract
A full account of synthetic efforts toward a lowly oxidized taxane framework is presented. A non-natural taxane, dubbed "taxadienone", was synthesized as our first entry into the taxane family of diterpenes. The final synthetic sequence illustrates a seven-step, gram-scale and enantioselective route to this tricyclic compound in 18% overall yield. This product was then modified further to give (+)-taxadiene, the lowest oxidized member of the taxane family of natural products.
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Affiliation(s)
- Yoshihiro Ishihara
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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