1
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Moreno-Paz S, Schmitz J, Suarez-Diez M. In silico analysis of design of experiment methods for metabolic pathway optimization. Comput Struct Biotechnol J 2024; 23:1959-1967. [PMID: 38736694 PMCID: PMC11087228 DOI: 10.1016/j.csbj.2024.04.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/14/2024] Open
Abstract
Microbial cell factories allow the production of chemicals presenting an alternative to traditional fossil fuel-dependent production. However, finding the optimal expression of production pathway genes is crucial for the development of efficient production strains. Unlike sequential experimentation, combinatorial optimization captures the relationships between pathway genes and production, albeit at the cost of conducting multiple experiments. Fractional factorial designs followed by linear modeling and statistical analysis reduce the experimental workload while maximizing the information gained during experimentation. Although tools to perform and analyze these designs are available, guidelines for selecting appropriate factorial designs for pathway optimization are missing. In this study, we leverage a kinetic model of a seven-genes pathway to simulate the performance of a full factorial strain library. We compare this approach to resolution V, IV, III, and Plackett Burman (PB) designs. Additionally, we evaluate the performance of these designs as training sets for a random forest algorithm aimed at identifying best-producing strains. Evaluating the robustness of these designs to noise and missing data, traits inherent to biological datasets, we find that while resolution V designs capture most information present in full factorial data, they necessitate the construction of a large number of strains. On the other hand, resolution III and PB designs fall short in identifying optimal strains and miss relevant information. Besides, given the small number of experiments required for the optimization of a pathway with seven genes, linear models outperform random forest. Consequently, we propose the use of resolution IV designs followed by linear modeling in Design-Build-Test-Learn (DBTL) cycles targeting the screening of multiple factors. These designs enable the identification of optimal strains and provide valuable guidance for subsequent optimization cycles.
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Affiliation(s)
- Sara Moreno-Paz
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708WE Wageningen, the Netherlands
| | - Joep Schmitz
- Department of Science and Research - dsm-firmenich, Science & Research, 2600 MA Delft, the Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708WE Wageningen, the Netherlands
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2
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Yan W, Qi X, Cao Z, Yao M, Ding M, Yuan Y. Biotransformation of ethylene glycol by engineered Escherichia coli. Synth Syst Biotechnol 2024; 9:531-539. [PMID: 38645974 PMCID: PMC11031724 DOI: 10.1016/j.synbio.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/05/2024] [Accepted: 04/08/2024] [Indexed: 04/23/2024] Open
Abstract
There has been extensive research on the biological recycling of PET waste to address the issue of plastic waste pollution, with ethylene glycol (EG) being one of the main components recovered from this process. Therefore, finding ways to convert PET monomer EG into high-value products is crucial for effective PET waste recycling. In this study, we successfully engineered Escherichia coli to utilize EG and produce glycolic acid (GA), expecting to facilitate the biological recycling of PET waste. The engineered E. coli, able to utilize 10 g/L EG to produce 1.38 g/L GA within 96 h, was initially constructed. Subsequently, strategies based on overexpression of key enzymes and knock-out of the competing pathways are employed to enhance EG utilization along with GA biosynthesis. An engineered E. coli, characterized by the highest GA production titer and substrate conversion rate, was obtained. The GA titer increased to 5.1 g/L with a yield of 0.75 g/g EG, which is the highest level in the shake flake experiments. Transcriptional level analysis and metabolomic analysis were then conducted, revealing that overexpression of key enzymes and knock-out of the competing pathways improved the metabolic flow in the EG utilization. The improved metabolic flow also leads to accelerated synthesis and metabolism of amino acids.
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Affiliation(s)
- Wenlong Yan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, 300072, China
| | - Xinhua Qi
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, 300072, China
| | - Zhibei Cao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, 300072, China
| | - Mingdong Yao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, 300072, China
| | - Mingzhu Ding
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, 300072, China
| | - Yingjin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, 300072, China
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3
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Zhou Z, Feng J, Huo J, Qiu S, Zhang P, Wang Y, Li Q, Li Y, Han C, Feng X, Duan Y, Chen R, Xiao Y, He Y, Zhang L, Chen W. Versatile CYP98A enzymes catalyse meta-hydroxylation reveals diversity of salvianolic acids biosynthesis. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1536-1548. [PMID: 38226779 PMCID: PMC11123398 DOI: 10.1111/pbi.14284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/08/2023] [Accepted: 12/18/2023] [Indexed: 01/17/2024]
Abstract
Salvianolic acids (SA), such as rosmarinic acid (RA), danshensu (DSS), and their derivative salvianolic acid B (SAB), etc. widely existed in Lamiaceae and Boraginaceae families, are of interest due to medicinal properties in the pharmaceutical industries. Hundreds of studies in past decades described that 4-coumaroyl-CoA and 4-hydroxyphenyllactic acid (4-HPL) are common substrates to biosynthesize SA with participation of rosmarinic acid synthase (RAS) and cytochrome P450 98A (CYP98A) subfamily enzymes in different plants. However, in our recent study, several acyl donors and acceptors included DSS as well as their ester-forming products all were determined in SA-rich plants, which indicated that previous recognition to SA biosynthesis is insufficient. Here, we used Salvia miltiorrhiza, a representative important medicinal plant rich in SA, to elucidate the diversity of SA biosynthesis. Various acyl donors as well as acceptors are catalysed by SmRAS to form precursors of RA and two SmCYP98A family members, SmCYP98A14 and SmCYP98A75, are responsible for different positions' meta-hydroxylation of these precursors. SmCYP98A75 preferentially catalyses C-3' hydroxylation, and SmCYP98A14 preferentially catalyses C-3 hydroxylation in RA generation. In addition, relative to C-3' hydroxylation of the acyl acceptor moiety in RA biosynthesis, SmCYP98A75 has been verified as the first enzyme that participates in DSS formation. Furthermore, SmCYP98A enzymes knockout resulted in the decrease and overexpression leaded to dramatic increase of SA accumlation. Our study provides new insights into SA biosynthesis diversity in SA-abundant species and versatility of CYP98A enzymes catalytic preference in meta-hydroxylation reactions. Moreover, CYP98A enzymes are ideal metabolic engineering targets to elevate SA content.
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Affiliation(s)
- Zheng Zhou
- Navy Special Medical CentreSecond Military Medical UniversityShanghaiChina
- Department of Pharmacy, Changzheng HospitalSecond Military Medical UniversityShanghaiChina
| | - Jingxian Feng
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SHTCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, The MOE Innovation Centre for Basic Medicine Research on Qi‐Blood TCM TheoriesInstitute of Chinese Materia Medica, Shanghai University of Traditional Chinese MedicineShanghaiChina
| | - Juncheng Huo
- Department of Pharmacy, Changzheng HospitalSecond Military Medical UniversityShanghaiChina
| | - Shi Qiu
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SHTCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, The MOE Innovation Centre for Basic Medicine Research on Qi‐Blood TCM TheoriesInstitute of Chinese Materia Medica, Shanghai University of Traditional Chinese MedicineShanghaiChina
| | - Pan Zhang
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SHTCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, The MOE Innovation Centre for Basic Medicine Research on Qi‐Blood TCM TheoriesInstitute of Chinese Materia Medica, Shanghai University of Traditional Chinese MedicineShanghaiChina
| | - Yun Wang
- Biomedical Innovation R&D Center, School of MedicineShanghai UniversityShanghaiChina
| | - Qing Li
- Department of Pharmacy, Changzheng HospitalSecond Military Medical UniversityShanghaiChina
| | - Yajing Li
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SHTCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, The MOE Innovation Centre for Basic Medicine Research on Qi‐Blood TCM TheoriesInstitute of Chinese Materia Medica, Shanghai University of Traditional Chinese MedicineShanghaiChina
| | - Cuicui Han
- Navy Special Medical CentreSecond Military Medical UniversityShanghaiChina
| | - Xiaobing Feng
- Navy Special Medical CentreSecond Military Medical UniversityShanghaiChina
| | - Yonghao Duan
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SHTCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, The MOE Innovation Centre for Basic Medicine Research on Qi‐Blood TCM TheoriesInstitute of Chinese Materia Medica, Shanghai University of Traditional Chinese MedicineShanghaiChina
| | - Ruibin Chen
- School of PharmacySecond Military Medical UniversityShanghaiChina
| | - Ying Xiao
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SHTCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, The MOE Innovation Centre for Basic Medicine Research on Qi‐Blood TCM TheoriesInstitute of Chinese Materia Medica, Shanghai University of Traditional Chinese MedicineShanghaiChina
| | - Ying He
- Navy Special Medical CentreSecond Military Medical UniversityShanghaiChina
| | - Lei Zhang
- Biomedical Innovation R&D Center, School of MedicineShanghai UniversityShanghaiChina
- School of PharmacySecond Military Medical UniversityShanghaiChina
| | - Wansheng Chen
- Department of Pharmacy, Changzheng HospitalSecond Military Medical UniversityShanghaiChina
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SHTCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, The MOE Innovation Centre for Basic Medicine Research on Qi‐Blood TCM TheoriesInstitute of Chinese Materia Medica, Shanghai University of Traditional Chinese MedicineShanghaiChina
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4
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Wang S, Zhao F, Yang M, Lin Y, Han S. Metabolic engineering of Saccharomyces cerevisiae for the synthesis of valuable chemicals. Crit Rev Biotechnol 2024; 44:163-190. [PMID: 36596577 DOI: 10.1080/07388551.2022.2153008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/11/2022] [Accepted: 10/29/2022] [Indexed: 01/05/2023]
Abstract
In the twenty first century, biotechnology offers great opportunities and solutions to climate change mitigation, energy and food security and resource efficiency. The use of metabolic engineering to modify microorganisms for producing industrially significant chemicals is developing and becoming a trend. As a famous, generally recognized as a safe (GRAS) model microorganism, Saccharomyces cerevisiae is widely used due to its excellent operational convenience and high fermentation efficiency. This review summarizes recent advancements in the field of using metabolic engineering strategies to construct engineered S. cerevisiae over the past ten years. Five different types of compounds are classified by their metabolites, and the modified metabolic pathways and strategies are summarized and discussed independently. This review may provide guidance for future metabolic engineering efforts toward such compounds and analogues. Additionally, the limitations of S. cerevisiae as a cell factory and its future trends are comprehensively discussed.
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Affiliation(s)
- Shuai Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Fengguang Zhao
- School of Light Industry and Engineering, South China University of Technology, Guangzhou, China
| | - Manli Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ying Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Shuangyan Han
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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5
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Boob AG, Chen J, Zhao H. Enabling pathway design by multiplex experimentation and machine learning. Metab Eng 2024; 81:70-87. [PMID: 38040110 DOI: 10.1016/j.ymben.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/01/2023] [Accepted: 11/25/2023] [Indexed: 12/03/2023]
Abstract
The remarkable metabolic diversity observed in nature has provided a foundation for sustainable production of a wide array of valuable molecules. However, transferring the biosynthetic pathway to the desired host often runs into inherent failures that arise from intermediate accumulation and reduced flux resulting from competing pathways within the host cell. Moreover, the conventional trial and error methods utilized in pathway optimization struggle to fully grasp the intricacies of installed pathways, leading to time-consuming and labor-intensive experiments, ultimately resulting in suboptimal yields. Considering these obstacles, there is a pressing need to explore the enzyme expression landscape and identify the optimal pathway configuration for enhanced production of molecules. This review delves into recent advancements in pathway engineering, with a focus on multiplex experimentation and machine learning techniques. These approaches play a pivotal role in overcoming the limitations of traditional methods, enabling exploration of a broader design space and increasing the likelihood of discovering optimal pathway configurations for enhanced production of molecules. We discuss several tools and strategies for pathway design, construction, and optimization for sustainable and cost-effective microbial production of molecules ranging from bulk to fine chemicals. We also highlight major successes in academia and industry through compelling case studies.
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Affiliation(s)
- Aashutosh Girish Boob
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Junyu Chen
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.
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6
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Zhang X, Chen S, Lin Y, Li W, Wang D, Ruan S, Yang Y, Liang S. Metabolic Engineering of Pichia pastoris for High-Level Production of Lycopene. ACS Synth Biol 2023; 12:2961-2972. [PMID: 37782893 DOI: 10.1021/acssynbio.3c00294] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Lycopene is widely used in cosmetics, food, and nutritional supplements. Microbial production of lycopene has been intensively studied. However, few metabolic engineering studies on Pichia pastoris have been aimed at achieving high-yield lycopene production. In this study, the CRISPR/Cpf1-based gene repression system was developed and the gene editing system was optimized, which were applied to improve lycopene production successfully. In addition, the sterol regulatory element-binding protein SREBP (Sre) was used for the regulation of lipid metabolic pathways to promote lycopene overproduction in P. pastoris for the first time. The final engineered strain produced lycopene at 7.24 g/L and 75.48 mg/g DCW in fed-batch fermentation, representing the highest lycopene yield in P. pastoris reported to date. These findings provide effective strategies for extended metabolic engineering assisted by the CRISPR/Cpf1 system and new insights into metabolic engineering through transcriptional regulation of related metabolic pathways to enhance carotenoid production in P. pastoris.
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Affiliation(s)
- Xinying Zhang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Shuting Chen
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Wenjie Li
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Denggang Wang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Shupeng Ruan
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Yuxin Yang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Shuli Liang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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7
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van Lent P, Schmitz J, Abeel T. Simulated Design-Build-Test-Learn Cycles for Consistent Comparison of Machine Learning Methods in Metabolic Engineering. ACS Synth Biol 2023; 12:2588-2599. [PMID: 37616156 PMCID: PMC10510747 DOI: 10.1021/acssynbio.3c00186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Indexed: 08/25/2023]
Abstract
Combinatorial pathway optimization is an important tool in metabolic flux optimization. Simultaneous optimization of a large number of pathway genes often leads to combinatorial explosions. Strain optimization is therefore often performed using iterative design-build-test-learn (DBTL) cycles. The aim of these cycles is to develop a product strain iteratively, every time incorporating learning from the previous cycle. Machine learning methods provide a potentially powerful tool to learn from data and propose new designs for the next DBTL cycle. However, due to the lack of a framework for consistently testing the performance of machine learning methods over multiple DBTL cycles, evaluating the effectiveness of these methods remains a challenge. In this work, we propose a mechanistic kinetic model-based framework to test and optimize machine learning for iterative combinatorial pathway optimization. Using this framework, we show that gradient boosting and random forest models outperform the other tested methods in the low-data regime. We demonstrate that these methods are robust for training set biases and experimental noise. Finally, we introduce an algorithm for recommending new designs using machine learning model predictions. We show that when the number of strains to be built is limited, starting with a large initial DBTL cycle is favorable over building the same number of strains for every cycle.
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Affiliation(s)
- Paul van Lent
- Delft
Bioinformatics Lab, Delft University of
Technology Van Mourik, Delft 2628 XE, The Netherlands
| | - Joep Schmitz
- Department
of Science and Research, Joep Schmitz -
dsm-firmenich, Science & Research, P.O. Box 1, 2600
MA Delft, The Netherlands
| | - Thomas Abeel
- Delft
Bioinformatics Lab, Delft University of
Technology Van Mourik, Delft 2628 XE, The Netherlands
- Infectious
Disease and Microbiome Program, Broad Institute
of MIT and Harvard, Cambridge, Massachusetts 02142, United States
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8
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Zhang M, Zhang J, Hou M, Zhao S. Comparative metabolomic and transcriptomic analysis of Saccharomyces cerevisiae W303a and CEN.PK2-1C. World J Microbiol Biotechnol 2023; 39:298. [PMID: 37661201 DOI: 10.1007/s11274-023-03736-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/20/2023] [Indexed: 09/05/2023]
Abstract
Saccharomyces cerevisiae is a health microorganism closely related to human life, especially in food and pharmaceutical industries. S. cerevisiae W303a and CEN.PK2-1C are two commonly used strains for synthetic biology-based natural product production. Yet, the metabolomic and transcriptomic differences between these two strains have not been compared. In this study, metabolomics and transcriptomics were applied to analyze the differential metabolites and differential expression genes (DEGs) between W303a and CEN.PK2-1C cultured in YPD and SD media. The growth rate of W303a in YPD medium was the lowest compared with other groups. When cultured in YPD medium, CEN.PK2-1C produced more phenylalanine than W303a; when cultured in SD medium, W303a produced more phospholipids than CEN.PK2-1C. Transcriptomic analysis revealed that 19 out of 22 genes in glycolysis pathway were expressed at higher levels in CEN.PK2-1C than that in W303a no matter which media were used, and three key genes related to phenylalanine biosynthesis including ARO9, ARO7 and PHA2 were up-regulated in CEN.PK2-1C compared with W303a when cultured in YPD medium, whereas seven DEGs associated with phospholipid biosynthesis were up-regulated in W303a compared with CEN.PK2-1C when cultured in SD medium. The high phenylalanine produced by CEN.PK2-1C and high phospholipids produced by W303a indicated that CEN.PK2-1C may be more suitable for synthesis of natural products with phenylalanine as precursor, whereas W303a may be more appropriate for synthesis of phospholipid metabolites. This finding provides primary information for strain selection between W303a and CEN.PK2-1C for synthetic biology-based natural product production.
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Affiliation(s)
- Meihong Zhang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jinjia Zhang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Maoqi Hou
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Shujuan Zhao
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
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9
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Tiwari P, Dufossé L. Focus and Insights into the Synthetic Biology-Mediated Chassis of Economically Important Fungi for the Production of High-Value Metabolites. Microorganisms 2023; 11:1141. [PMID: 37317115 DOI: 10.3390/microorganisms11051141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 06/16/2023] Open
Abstract
Substantial progress has been achieved and knowledge gaps addressed in synthetic biology-mediated engineering of biological organisms to produce high-value metabolites. Bio-based products from fungi are extensively explored in the present era, attributed to their emerging importance in the industrial sector, healthcare, and food applications. The edible group of fungi and multiple fungal strains defines attractive biological resources for high-value metabolites comprising food additives, pigments, dyes, industrial chemicals, and antibiotics, including other compounds. In this direction, synthetic biology-mediated genetic chassis of fungal strains to enhance/add value to novel chemical entities of biological origin is opening new avenues in fungal biotechnology. While substantial success has been achieved in the genetic manipulation of economically viable fungi (including Saccharomyces cerevisiae) in the production of metabolites of socio-economic relevance, knowledge gaps/obstacles in fungal biology and engineering need to be remedied for complete exploitation of valuable fungal strains. Herein, the thematic article discusses the novel attributes of bio-based products from fungi and the creation of high-value engineered fungal strains to promote yield, bio-functionality, and value-addition of the metabolites of socio-economic value. Efforts have been made to discuss the existing limitations in fungal chassis and how the advances in synthetic biology provide a plausible solution.
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Affiliation(s)
- Pragya Tiwari
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Laurent Dufossé
- Chemistry and Biotechnology of Natural Products, CHEMBIOPRO, Université de La Réunion, ESIROI Agroalimentaire, 15 Avenue René Cassin, F-97490 Saint-Denis, France
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10
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System network analysis of Rosmarinus officinalis transcriptome and metabolome-Key genes in biosynthesis of secondary metabolites. PLoS One 2023; 18:e0282316. [PMID: 36862714 PMCID: PMC9980811 DOI: 10.1371/journal.pone.0282316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 02/13/2023] [Indexed: 03/03/2023] Open
Abstract
Medicinal plants contain valuable compounds that have attracted worldwide interest for their use in the production of natural drugs. The presence of compounds such as rosmarinic acid, carnosic acid, and carnosol in Rosmarinus officinalis has made it a plant with unique therapeutic effects. The identification and regulation of the biosynthetic pathways and genes will enable the large-scale production of these compounds. Hence, we studied the correlation between the genes involved in biosynthesis of the secondary metabolites in R. officinalis using proteomics and metabolomics data by WGCNA. We identified three modules as having the highest potential for the metabolite engineering. Moreover, the hub genes highly connected to particular modules, TFs, PKs, and transporters were identified. The TFs of MYB, C3H, HB, and C2H2 were the most likely candidates associated with the target metabolic pathways. The results indicated that the hub genes including Copalyl diphosphate synthase (CDS), Phenylalanine ammonia lyase (PAL), Cineole synthase (CIN), Rosmarinic acid synthase (RAS), Tyrosine aminotransferase (TAT), Cinnamate 4-hydroxylase (C4H), and MYB58 are responsible for biosynthesis of important secondary metabolites. Thus, we confirmed these results using qRT-PCR after treating R. officinalis seedlings with methyl jasmonate. These candidate genes may be employed for genetic and metabolic engineering research to increase R. officinalis metabolite production.
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11
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Virklund A, Jensen SI, Nielsen AT, Woodley JM. Combining genetic engineering and bioprocess concepts for improved phenylpropanoid production. Biotechnol Bioeng 2023; 120:613-628. [PMID: 36418654 DOI: 10.1002/bit.28292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 11/02/2022] [Accepted: 11/22/2022] [Indexed: 11/26/2022]
Abstract
The group of natural aromatic compounds known as phenylpropanoids has diverse applications, but current methods of production which are largely based on synthesis from petrochemicals or extraction from agricultural biomass are unsustainable. Bioprocessing is a promising alternative, but improvements in production titers and rates are required to make this method profitable. Here the recent advances in genetic engineering and bioprocess concepts for the production of phenylpropanoids are presented for the purpose of identifying successful strategies, including adaptive laboratory evolution, enzyme engineering, in-situ product removal, and biocatalysis. The pros and cons of bacterial and yeast hosts for phenylpropanoid production are discussed, also in the context of different phenylpropanoid targets and bioprocess concepts. Finally, some broad recommendations are made regarding targets for continued improvement and areas requiring specific attention from researchers to further improve production titers and rates.
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Affiliation(s)
- Alexander Virklund
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark
| | - Sheila I Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Alex T Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - John M Woodley
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark
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12
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Wang L, Wang H, Chen J, Qin Z, Yu S, Zhou J. Coordinating caffeic acid and salvianic acid A pathways for efficient production of rosmarinic acid in Escherichia coli. Metab Eng 2023; 76:29-38. [PMID: 36623792 DOI: 10.1016/j.ymben.2023.01.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 12/17/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
Rosmarinic acid is a natural hydroxycinnamic acid ester used widely in the food and pharmaceutical industries. Although many attempts have been made to screen rate-limiting enzymes and optimize modules through co-culture fermentation, the titer of rosmarinic acid remains at the microgram level by microorganisms. A de novo biosynthetic pathway for rosmarinic acid was constructed based on caffeic acid synthesis modules in Escherichia coli. Knockout of competing pathways increased the titer of rosmarinic acid and reduced the synthesis of rosmarinic acid analogues. An L-amino acid deaminase was introduced to balance metabolic flux between the synthesis of caffeic acid and salvianic acid A. The ratio of FADH2/FAD was maintained via the coordination of deaminase and HpaBC, which is responsible for caffeic acid synthesis. Knockout of menI, encoding an endogenous thioesterase, increased the stability of caffeoyl-CoA. The final strain produced 5780.6 mg/L rosmarinic acid in fed-batch fermentation, the highest yet reported for microbial production. The strategies applied in this study lay a foundation for the synthesis of other caffeic acid and rosmarinic acid derivatives.
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Affiliation(s)
- Lian Wang
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
| | - Huijing Wang
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Jianbin Chen
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Zhijie Qin
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Shiqin Yu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, 214122, China.
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13
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Rosmarinic Acid Attenuates Rotenone-Induced Neurotoxicity in SH-SY5Y Parkinson’s Disease Cell Model through Abl Inhibition. Nutrients 2022; 14:nu14173508. [PMID: 36079767 PMCID: PMC9460683 DOI: 10.3390/nu14173508] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
Rosmarinic acid (RA) is a natural polyphenolic compound with antioxidative property. With the present study, we aimed to evaluate the neuroprotective role of RA on Parkinson’s disease using rotenone induced SH-SY5Y cell model of Parkinson’s disease, the underlying mechanism of action of RA was also investigated. Cell viability, cell morphology, apoptosis, signaling protein phosphorylation and expression, cellular reactive oxygen species (ROS) production, ATP content, and mitochondrial membrane potential were tested in SH-SY5Y cells. RA showed a neuroprotective effect in a rotenone-induced SH-SY5Y cell model of Parkinson’s disease with dose-dependent manner, it reduced cell apoptosis and restored normal cell morphology. RA not only decreased levels of α-synuclein and Tau phosphorylation but also elevated the contents of AMPK phosphorylation, Akt phosphorylation, and PGC-1α. RA restored the reduced mitochondrial membrane potential and ATP content as well as inhibited rotenone-induced ROS overproduction. Further findings demonstrated that the neuroprotective role of RA was partially due to the inhibition of Abl tyrosine kinase. RA treatment suppressed the hyperphosphorylation of Abl Y412 and CrkII Y221 induced by rotenone. Nilotinib, a specific inhibitor of Abl, elicited a similar neuroprotective effect as that of RA. The present study indicates that RA has a property of neuroprotection against rotenone, and the neuroprotective effect is partially attributed to the inhibition of Abl.
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Mansinhos I, Gonçalves S, Rodríguez-Solana R, Duarte H, Ordóñez-Díaz JL, Moreno-Rojas JM, Romano A. Response of Thymus lotocephalus In Vitro Cultures to Drought Stress and Role of Green Extracts in Cosmetics. Antioxidants (Basel) 2022; 11:antiox11081475. [PMID: 36009194 PMCID: PMC9404771 DOI: 10.3390/antiox11081475] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
The impact of drought stress induced by polyethylene glycol (PEG) on morphological, physiological, (bio)chemical, and biological characteristics of Thymus lotocephalus López and Morales shoot cultures have been investigated, as well as the potential of iron oxide nanoparticles, salicylic acid, and methyl jasmonate (MeJA) as alleviating drought stress agents. Results showed that PEG caused oxidative stress in a dose-dependent manner, raising H2O2 levels and reducing shoots’ growth, photosynthetic pigment contents, and phenolic compounds production, especially phenolic acids, including the major compound rosmarinic acid. Moreover, Fourier Transform Infrared Spectra analysis revealed that PEG treatment caused changes in shoots’ composition, enhancing terpenoids biosynthesis. PEG also decreased the biological activities (antioxidant, anti-tyrosinase, and photoprotective) of the eco-friendly extracts obtained with a Natural Deep Eutectic Solvent. MeJA was the most efficient agent in protecting cells from oxidative damage caused by drought, by improving the biosynthesis of phenolics, like methyl 6-O-galloyl-β-D-glucopyranoside and salvianolic acids, as well as improving the extracts’ antioxidant activity. Altogether, the obtained results demonstrated a negative impact of PEG on T. lotocephalus shoots and an effective role of MeJA as a mitigating agent of drought stress. Additionally, extracts showed a good potential to be used in the cosmetics industry as skincare products.
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Affiliation(s)
- Inês Mansinhos
- MED–Mediterranean Institute for Agriculture, Environment and Development & CHANGE–Global Change and Sustainability Institute, Faculdade de Ciências e Tecnologia, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; (I.M.); (R.R.-S.); (H.D.)
| | - Sandra Gonçalves
- MED–Mediterranean Institute for Agriculture, Environment and Development & CHANGE–Global Change and Sustainability Institute, Faculdade de Ciências e Tecnologia, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; (I.M.); (R.R.-S.); (H.D.)
- Correspondence: (S.G.); (A.R.); Tel.: +351-289800900 (S.G.); +351-289800910 (A.R.)
| | - Raquel Rodríguez-Solana
- MED–Mediterranean Institute for Agriculture, Environment and Development & CHANGE–Global Change and Sustainability Institute, Faculdade de Ciências e Tecnologia, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; (I.M.); (R.R.-S.); (H.D.)
- Department of Agroindustry and Food Quality, Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Avenida Menendez-Pidal, SN, 14004 Córdoba, Spain; (J.L.O.-D.); (J.M.M.-R.)
| | - Hugo Duarte
- MED–Mediterranean Institute for Agriculture, Environment and Development & CHANGE–Global Change and Sustainability Institute, Faculdade de Ciências e Tecnologia, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; (I.M.); (R.R.-S.); (H.D.)
| | - José Luis Ordóñez-Díaz
- Department of Agroindustry and Food Quality, Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Avenida Menendez-Pidal, SN, 14004 Córdoba, Spain; (J.L.O.-D.); (J.M.M.-R.)
| | - José Manuel Moreno-Rojas
- Department of Agroindustry and Food Quality, Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Avenida Menendez-Pidal, SN, 14004 Córdoba, Spain; (J.L.O.-D.); (J.M.M.-R.)
| | - Anabela Romano
- MED–Mediterranean Institute for Agriculture, Environment and Development & CHANGE–Global Change and Sustainability Institute, Faculdade de Ciências e Tecnologia, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; (I.M.); (R.R.-S.); (H.D.)
- Correspondence: (S.G.); (A.R.); Tel.: +351-289800900 (S.G.); +351-289800910 (A.R.)
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Zhou P, Yue C, Zhang Y, Li Y, Da X, Zhou X, Ye L. Alleviation of the Byproducts Formation Enables Highly Efficient Biosynthesis of Rosmarinic Acid in Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:5077-5087. [PMID: 35416041 DOI: 10.1021/acs.jafc.2c01179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Rosmarinic acid as a polyphenolic compound has great values in the pharmaceutical, cosmetic, and food industries. To achieve efficient biosynthesis of rosmarinic acid, the major obstacles such as imbalanced metabolic flux among branching pathways and substrate promiscuity of pathway enzymes should be eliminated. Here, a rosmarinic acid producing Saccharomyces cerevisiae strain was constructed by introducing codon optimized d-lactate dehydrogenase gene mutant (OD-LDHY52A), 4-coumarate CoA ligase gene (OPc4CL2), and rosmarinic acid synthase gene (OMoRAS) into a previously constructed caffeic acid hyper-producer. To identify the metabolic bottleneck, the substrate specificity of OPc4CL2 and OMoRAS was figured out by bioconversion experiments and HPLC-MS/MS analysis. Subsequently, the byproducts formation was alleviated by removing prephenate dehydratase and tuning down the expression level of OPc4CL2. The final strain YRA113-15B produced 208 mg/L rosmarinic acid in a shake-flask culture (a 63-fold improvement over the initial strain), which was the highest rosmarinic acid titer by engineered microbial cells reported to date. This work provides a promising platform for fermentative production of rosmarinic acid and offers a strategy to overcome the intrapathway competition.
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Affiliation(s)
- Pingping Zhou
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, P. R. China
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, P. R. China
| | - Chunlei Yue
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, P. R. China
| | - Yuchen Zhang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, P. R. China
| | - Yan Li
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, P. R. China
| | - Xinyi Da
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, P. R. China
| | - Xiuqi Zhou
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, P. R. China
| | - Lidan Ye
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, P. R. China
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16
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Zhou L, Huang Y, Han Z, Wang J, Sun N, Zhang R, Dong W, Deng C, Zhuang G. Effects of rosmarinic acid on the inflammatory response in allergic rhinitis rat models after PM2.5 exposure. J Clin Lab Anal 2022; 36:e24316. [PMID: 35285093 PMCID: PMC8993598 DOI: 10.1002/jcla.24316] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 02/07/2022] [Accepted: 02/16/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Studies have shown the promising prospects of rosmarinic acid (RosA) for the prevention and treatment of allergic diseases. OBJECTIVE The aim of this study was to investigate the effects of RosA on inflammatory reaction in rat models of allergic rhinitis (AR) after PM2.5 exposure. METHODS Allergic rhinitis rat models were established by ovalbumin sensitization, and PM2.5 was applied at a concentration of 1000 μg/m3 , 3 h a day for 30 consecutive days. RosA was administered via intraperitoneal injection (20 mg/kg/d) for seven consecutive days. Allergic nasal symptoms were recorded. The expressions of interleukin (IL)-4, IL-13, interferon (INF)-γ, and OVA-sIgE were determined by ELISA. Histopathological changes in nasal mucosa were observed by HE staining. mRNA expressions of T-bet and GATA-3 in nasal mucosa were detected by RT-PCR. NF-κBp65 in cell nuclei and IκBα in cytoplasm were analyzed by Western blot. RESULTS PM2.5 exposure worsened allergic nasal symptoms in AR rats, while RosA ameliorated these symptoms. Histopathologically, AR rats exhibited disorganized nasal mucosal epithelium, cell exfoliation, eosinophilic infiltration of lamina propria, gland swelling, and submucosal vascular congestion, which were aggravated by PM2.5 exposure and alleviated by RosA. RosA decreased the expressions of IL-4, IL-13, and increased the level of IFN-γ in PM2.5-exposed AR rats. After RosA intervention, the expressions of GATA-3 mRNA and NF-κBp65 in PM2.5-exposed AR rats were significantly reduced, while those of T-bet mRNA and IκBα were markedly increased. CONCLUSION Rosmarinic acid may alleviate symptoms of AR rat models exposed to PM2.5 through the modulation of the NF-κB pathway and Th1/Th2 balance.
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Affiliation(s)
- Lingling Zhou
- Department of OtolaryngologyHuadong Hospital Affiliated to Fudan UniversityShanghaiChina
| | - Yu Huang
- Department of OtolaryngologyHuadong Hospital Affiliated to Fudan UniversityShanghaiChina
| | - Zhijin Han
- Department of OtolaryngologyHuadong Hospital Affiliated to Fudan UniversityShanghaiChina
| | - Jinchao Wang
- Department of OtolaryngologyHuadong Hospital Affiliated to Fudan UniversityShanghaiChina
| | - Na Sun
- Department of OtolaryngologyHuadong Hospital Affiliated to Fudan UniversityShanghaiChina
| | - Ruxin Zhang
- Department of OtolaryngologyHuadong Hospital Affiliated to Fudan UniversityShanghaiChina
| | - Weiyang Dong
- Department of Environmental Science and Engineering, Center for Atmospheric Chemistry StudyFudan UniversityShanghaiChina
| | - Congrui Deng
- Department of Environmental Science and Engineering, Center for Atmospheric Chemistry StudyFudan UniversityShanghaiChina
| | - Guoshun Zhuang
- Department of Environmental Science and Engineering, Center for Atmospheric Chemistry StudyFudan UniversityShanghaiChina
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17
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Xu Y, Geng L, Zhang Y, Jones JA, Zhang M, Chen Y, Tan R, Koffas MAG, Wang Z, Zhao S. De novo Biosynthesis of Salvianolic Acid B in Saccharomyces cerevisiae Engineered with the Rosmarinic Acid Biosynthetic Pathway. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:2290-2302. [PMID: 35157428 DOI: 10.1021/acs.jafc.1c06329] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Salvianolic acid B (SAB), also named lithospermic acid B, belongs to a class of water-soluble phenolic acids, originating from plants such as Salvia miltiorrhiza. SAB exhibits a variety of biological activities and has been clinically used to treat cardio- and cerebrovascular diseases and also has great potential as a health care product and medicine for other disorders. However, its biosynthetic pathway has not been completely elucidated. Here, we report the de novo biosynthesis of SAB in Saccharomyces cerevisiae engineered with the heterologous rosmarinic acid (RA) biosynthetic pathway. The created pathway contains seven genes divided into three modules on separate plasmids, pRS424-FjTAL-Sm4CL2, pRS425-SmTAT-SmHPPR or pRS425-SmTAT-CbHPPR, and pRS426-SmRAS-CbCYP-CbCPR. These three modules were cotransformed into S. cerevisiae, resulting in the recombinant strains YW-44 and YW-45. Incubation of the recombinant strains in a basic medium without supplementing any substrates yielded 34 and 30 μg/L of SAB. The findings in this study indicate that the created heterologous RA pathway cooperates with the native metabolism of S. cerevisiae to enable the de novo biosynthesis of SAB. This provides a novel insight into a biosynthesis mechanism of SAB and also lays the foundation for the production of SAB using microbial cell factories.
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Affiliation(s)
- Yingpeng Xu
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Lijun Geng
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yiwen Zhang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - J Andrew Jones
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Meihong Zhang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yuan Chen
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Ronghui Tan
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Mattheos A G Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Department of Biological Sciences, Rensselaer Polytechnic Institutes, Troy, New York 12180, United States
| | - Zhengtao Wang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Shujuan Zhao
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
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18
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Zheng XY, Zhao SJ, Zhang YW, Nie F. L-tyrosine metabolic pathway in microorganisms and its application in the biosynthesis of plant-derived natural products. WORLD JOURNAL OF TRADITIONAL CHINESE MEDICINE 2022. [DOI: 10.4103/wjtcm.wjtcm_16_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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19
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An M, Oh M, Park KT, Seon KH, Jo JE, Lee SK, Kim JK, Shin KS, Koh JH, Lim YH. Anti-asthma and antitussive effects of a fermented extract of a mixture of Ramulus mori, Anthriscus sylvestris, and Salvia plebeian. Food Sci Biotechnol 2021; 30:1257-1268. [PMID: 34393544 PMCID: PMC8352748 DOI: 10.1007/s10068-021-00955-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/14/2021] [Accepted: 07/22/2021] [Indexed: 01/06/2023] Open
Abstract
Respiratory immunity is getting more important recently due to outbreak of respiratory diseases and increasing the concentration of fine dust. The aim of this study was to investigate respiratory protection effect of a fermented extract of medicinal plants (FEMP) containing Ramulus mori, Salvia plebeia, and Anthriscus sylvestris. The expression levels of IL-8 and IL-17 in LPS/poly-L-arginine (PLA) and FEMP-cotreated A549 cells were lower than those in LPS/PLA only-treated cells. The levels of IgE, IL-17, and IL-4 in the bronchoalveolar lavage fluid (BALF) and serum of FEMP-treated mice with ovalbumin/LPS-induced asthma were lower than the control levels. The lung inflammation score and the number of inflammatory cells in the BALF decreased by FEMP treatment. In the citric acid-induced coughing guinea pig, the FEMP treatment decreased the number of coughs. Therefore, FEMP shows anti-asthmatic and antitussive activities without hepatotoxicity and can be used as a compound aiming to improve respiratory health. Supplementary Information The online version contains supplementary material available at 10.1007/s10068-021-00955-3.
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Affiliation(s)
- Mirae An
- Department of Public Health Science, Graduate School, Korea University, Seoul, 02841 Republic of Korea
| | - Miae Oh
- Department of Integrated Biomedical and Life Sciences, Graduate School, Korea University, Seoul, 02841 Republic of Korea
| | - Keun-Tae Park
- Department of Integrated Biomedical and Life Sciences, Graduate School, Korea University, Seoul, 02841 Republic of Korea
| | - Ki Hwan Seon
- R & D Center, Biocean CO. LTD, Seoul, 08591 Republic of Korea
| | - Jeong Eun Jo
- R & D Center, Biocean CO. LTD, Seoul, 08591 Republic of Korea
| | - Seong Kweon Lee
- R & D Center, Biocean CO. LTD, Seoul, 08591 Republic of Korea
| | - Jeong-Keun Kim
- Department of Chemical Engineering and Biotechnology, Korea Polytechnic University, Shihung-si, Gyeonggi-do 15073 Republic of Korea
| | - Kwang Soon Shin
- Department of Food Science and Biotechnology, Kyonggi University, Suwon, 16227 Republic of Korea
| | - Jong-Ho Koh
- Department of Bio-Food Analysis and Processing, Bio-Campus Korea Polytechnic College, Nonsan, 32943 Republic of Korea
| | - Young-Hee Lim
- Department of Integrated Biomedical and Life Sciences, Graduate School, Korea University, Seoul, 02841 Republic of Korea.,School of Biosystems and Biomedical Sciences, College of Health Science, Korea University, Seoul, 02841 Republic of Korea.,Department of Laboratory Medicine, Korea University Guro Hospital, Seoul, 08308 Republic of Korea
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20
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Babaei M, Sartori L, Karpukhin A, Abashkin D, Matrosova E, Borodina I. Expansion of EasyClone-MarkerFree toolkit for Saccharomyces cerevisiae genome with new integration sites. FEMS Yeast Res 2021; 21:foab027. [PMID: 33893795 PMCID: PMC8112480 DOI: 10.1093/femsyr/foab027] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/22/2021] [Indexed: 11/13/2022] Open
Abstract
Biotechnological production requires genetically stable recombinant strains. To ensure genomic stability, recombinant DNA is commonly integrated into the genome of the host strain. Multiple genetic tools have been developed for genomic integration into baker's yeast Saccharomyces cerevisiae. Previously, we had developed a vector toolkit EasyClone-MarkerFree for stable integration into eleven sites on chromosomes X, XI, and XII of S. cerevisiae. The markerless integration was enabled by CRISPR-Cas9 system. In this study, we have expanded the kit with eight additional intergenic integration sites located on different chromosomes. The integration efficiency into the new sites was above 80%. The expression level of green fluorescence protein (gfp) for all eight sites was similar or above XI-2 site from the original EasyClone-MarkerFree toolkit. The cellular growth was not affected by the integration into any of the new eight locations. The eight-vector expansion kit is available from AddGene.
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Affiliation(s)
- Mahsa Babaei
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, DK-2800 Kgs. Lyngby, Denmark
| | - Luisa Sartori
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, DK-2800 Kgs. Lyngby, Denmark
| | - Alexey Karpukhin
- Ajinomoto-Genetika Research Institute, Moscow, Russian Federation
| | - Dmitrii Abashkin
- Ajinomoto-Genetika Research Institute, Moscow, Russian Federation
| | - Elena Matrosova
- Ajinomoto-Genetika Research Institute, Moscow, Russian Federation
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, DK-2800 Kgs. Lyngby, Denmark
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21
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Liu M, Lin YC, Guo JJ, Du MM, Tao X, Gao B, Zhao M, Ma Y, Wang FQ, Wei DZ. High-Level Production of Sesquiterpene Patchoulol in Saccharomyces cerevisiae. ACS Synth Biol 2021; 10:158-172. [PMID: 33395273 DOI: 10.1021/acssynbio.0c00521] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Patchoulol is a tricyclic sesquiterpene widely used in perfumes and cosmetics. Herein, comprehensive engineering strategies were employed to construct an efficient yeast strain for patchoulol production. First, a platform strain was constructed via pathway modification. Second, three off-pathway genes were deleted, which led to significant physiological changes in yeast. Further, strengthening of the ergosterol pathway, enhancement of the energy supply, and a decrease in intracellular reactive oxygen species were implemented to improve the physiological status of yeast, demonstrating a new promotive relationship between ergosterol biosynthesis and synthesis of patchoulol. Moreover, patchoulol synthase was improved through protein modification and Mg2+ addition, reaching a final titer of 141.5 mg/L in a shake flask. Finally, a two-stage fermentation with dodecane addition was employed to achieve the highest production (1632.0 mg/L, 87.0 mg/g dry cell weight, 233.1 mg/L/d) ever reported for patchoulol in a 5 L bioreactor. This work lays a foundation for green and efficient patchoulol production.
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Affiliation(s)
- Min Liu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Yang-Chen Lin
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Jiao-Jiao Guo
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Meng-Meng Du
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Xinyi Tao
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Bei Gao
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Ming Zhao
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Yushu Ma
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Feng-Qing Wang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Dong-Zhi Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
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22
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Li M, Lang X, Moran Cabrera M, De Keyser S, Sun X, Da Silva N, Wheeldon I. CRISPR-mediated multigene integration enables Shikimate pathway refactoring for enhanced 2-phenylethanol biosynthesis in Kluyveromyces marxianus. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:3. [PMID: 33407831 PMCID: PMC7788952 DOI: 10.1186/s13068-020-01852-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/09/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND 2-phenylethanol (2-PE) is a rose-scented flavor and fragrance compound that is used in food, beverages, and personal care products. Compatibility with gasoline also makes it a potential biofuel or fuel additive. A biochemical process converting glucose or other fermentable sugars to 2-PE can potentially provide a more sustainable and economical production route than current methods that use chemical synthesis and/or isolation from plant material. RESULTS We work toward this goal by engineering the Shikimate and Ehrlich pathways in the stress-tolerant yeast Kluyveromyces marxianus. First, we develop a multigene integration tool that uses CRISPR-Cas9 induced breaks on the genome as a selection for the one-step integration of an insert that encodes one, two, or three gene expression cassettes. Integration of a 5-kbp insert containing three overexpression cassettes successfully occurs with an efficiency of 51 ± 9% at the ABZ1 locus and was used to create a library of K. marxianus CBS 6556 strains with refactored Shikimate pathway genes. The 33-factorial library includes all combinations of KmARO4, KmARO7, and KmPHA2, each driven by three different promoters that span a wide expression range. Analysis of the refactored pathway library reveals that high expression of the tyrosine-deregulated KmARO4K221L and native KmPHA2, with the medium expression of feedback insensitive KmARO7G141S, results in the highest increase in 2-PE biosynthesis, producing 684 ± 73 mg/L. Ehrlich pathway engineering by overexpression of KmARO10 and disruption of KmEAT1 further increases 2-PE production to 766 ± 6 mg/L. The best strain achieves 1943 ± 63 mg/L 2-PE after 120 h fed-batch operation in shake flask cultures. CONCLUSIONS The CRISPR-mediated multigene integration system expands the genome-editing toolset for K. marxianus, a promising multi-stress tolerant host for the biosynthesis of 2-PE and other aromatic compounds derived from the Shikimate pathway.
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Affiliation(s)
- Mengwan Li
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Xuye Lang
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Marcos Moran Cabrera
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Sawyer De Keyser
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Xiyan Sun
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Nancy Da Silva
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, CA, 92697, USA
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA.
- Center for Industrial Biotechnology, University of California Riverside, Riverside, CA, 92527, USA.
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