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Zhang J, Li F, Liu D, Liu Q, Song H. Engineering extracellular electron transfer pathways of electroactive microorganisms by synthetic biology for energy and chemicals production. Chem Soc Rev 2024; 53:1375-1446. [PMID: 38117181 DOI: 10.1039/d3cs00537b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The excessive consumption of fossil fuels causes massive emission of CO2, leading to climate deterioration and environmental pollution. The development of substitutes and sustainable energy sources to replace fossil fuels has become a worldwide priority. Bio-electrochemical systems (BESs), employing redox reactions of electroactive microorganisms (EAMs) on electrodes to achieve a meritorious combination of biocatalysis and electrocatalysis, provide a green and sustainable alternative approach for bioremediation, CO2 fixation, and energy and chemicals production. EAMs, including exoelectrogens and electrotrophs, perform extracellular electron transfer (EET) (i.e., outward and inward EET), respectively, to exchange energy with the environment, whose rate determines the efficiency and performance of BESs. Therefore, we review the synthetic biology strategies developed in the last decade for engineering EAMs to enhance the EET rate in cell-electrode interfaces for facilitating the production of electricity energy and value-added chemicals, which include (1) progress in genetic manipulation and editing tools to achieve the efficient regulation of gene expression, knockout, and knockdown of EAMs; (2) synthetic biological engineering strategies to enhance the outward EET of exoelectrogens to anodes for electricity power production and anodic electro-fermentation (AEF) for chemicals production, including (i) broadening and strengthening substrate utilization, (ii) increasing the intracellular releasable reducing equivalents, (iii) optimizing c-type cytochrome (c-Cyts) expression and maturation, (iv) enhancing conductive nanowire biosynthesis and modification, (v) promoting electron shuttle biosynthesis, secretion, and immobilization, (vi) engineering global regulators to promote EET rate, (vii) facilitating biofilm formation, and (viii) constructing cell-material hybrids; (3) the mechanisms of inward EET, CO2 fixation pathway, and engineering strategies for improving the inward EET of electrotrophic cells for CO2 reduction and chemical production, including (i) programming metabolic pathways of electrotrophs, (ii) rewiring bioelectrical circuits for enhancing inward EET, and (iii) constructing microbial (photo)electrosynthesis by cell-material hybridization; (4) perspectives on future challenges and opportunities for engineering EET to develop highly efficient BESs for sustainable energy and chemical production. We expect that this review will provide a theoretical basis for the future development of BESs in energy harvesting, CO2 fixation, and chemical synthesis.
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Affiliation(s)
- Junqi Zhang
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Feng Li
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Dingyuan Liu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Qijing Liu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Hao Song
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
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2
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Zhu Z, Chen R, Zhang L. Simple phenylpropanoids: recent advances in biological activities, biosynthetic pathways, and microbial production. Nat Prod Rep 2024; 41:6-24. [PMID: 37807808 DOI: 10.1039/d3np00012e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Covering: 2000 to 2023Simple phenylpropanoids are a large group of natural products with primary C6-C3 skeletons. They are not only important biomolecules for plant growth but also crucial chemicals for high-value industries, including fragrances, nutraceuticals, biomaterials, and pharmaceuticals. However, with the growing global demand for simple phenylpropanoids, direct plant extraction or chemical synthesis often struggles to meet current needs in terms of yield, titre, cost, and environmental impact. Benefiting from the rapid development of metabolic engineering and synthetic biology, microbial production of natural products from inexpensive and renewable sources provides a feasible solution for sustainable supply. This review outlines the biological activities of simple phenylpropanoids, compares their biosynthetic pathways in different species (plants, bacteria, and fungi), and summarises key research on the microbial production of simple phenylpropanoids over the last decade, with a focus on engineering strategies that seem to hold most potential for further development. Moreover, constructive solutions to the current challenges and future perspectives for industrial production of phenylpropanoids are presented.
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Affiliation(s)
- Zhanpin Zhu
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China.
| | - Ruibing Chen
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China.
| | - Lei Zhang
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China.
- Institute of Interdisciplinary Integrative Medicine Research, Medical School of Nantong University, Nantong 226001, China
- Innovative Drug R&D Centre, College of Life Sciences, Huaibei Normal University, Huaibei 235000, China
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3
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Gao M, Zhao Y, Yao Z, Su Q, Van Beek P, Shao Z. Xylose and shikimate transporters facilitates microbial consortium as a chassis for benzylisoquinoline alkaloid production. Nat Commun 2023; 14:7797. [PMID: 38016984 PMCID: PMC10684500 DOI: 10.1038/s41467-023-43049-w] [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: 07/30/2022] [Accepted: 10/30/2023] [Indexed: 11/30/2023] Open
Abstract
Plant-sourced aromatic amino acid (AAA) derivatives are a vast group of compounds with broad applications. Here, we present the development of a yeast consortium for efficient production of (S)-norcoclaurine, the key precursor for benzylisoquinoline alkaloid biosynthesis. A xylose transporter enables the concurrent mixed-sugar utilization in Scheffersomyces stipitis, which plays a crucial role in enhancing the flux entering the highly regulated shikimate pathway located upstream of AAA biosynthesis. Two quinate permeases isolated from Aspergillus niger facilitates shikimate translocation to the co-cultured Saccharomyces cerevisiae that converts shikimate to (S)-norcoclaurine, resulting in the maximal titer (11.5 mg/L), nearly 110-fold higher than the titer reported for an S. cerevisiae monoculture. Our findings magnify the potential of microbial consortium platforms for the economical de novo synthesis of complex compounds, where pathway modularization and compartmentalization in distinct specialty strains enable effective fine-tuning of long biosynthetic pathways and diminish intermediate buildup, thereby leading to increases in production.
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Affiliation(s)
- Meirong Gao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
- NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA
| | - Yuxin Zhao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
- NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA
| | - Zhanyi Yao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
- NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA
| | - Qianhe Su
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
| | - Payton Van Beek
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
| | - Zengyi Shao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA.
- NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA.
- Interdepartmental Microbiology Program, Iowa State University, Ames, IA, USA.
- Bioeconomy Institute, Iowa State University, Ames, IA, USA.
- The Ames Laboratory, Ames, IA, USA.
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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4
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Ding Q, Ye C. Microbial engineering for shikimate biosynthesis. Enzyme Microb Technol 2023; 170:110306. [PMID: 37598506 DOI: 10.1016/j.enzmictec.2023.110306] [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: 06/27/2023] [Revised: 08/03/2023] [Accepted: 08/14/2023] [Indexed: 08/22/2023]
Abstract
Shikimate, a precursor to the antiviral drug oseltamivir (Tamiflu®), can influence aromatic metabolites and finds extensive use in antimicrobial, antitumor, and cardiovascular applications. Consequently, various strategies have been developed for chemical synthesis and plant extraction to enhance shikimate biosynthesis, potentially impacting environmental conditions, economic sustainability, and separation and purification processes. Microbial engineering has been developed as an environmentally friendly approach for shikimate biosynthesis. In this review, we provide a comprehensive summary of microbial strategies for shikimate biosynthesis. These strategies primarily include chassis construction, biochemical optimization, pathway remodelling, and global regulation. Furthermore, we discuss future perspectives on shikimate biosynthesis and emphasize the importance of utilizing advanced metabolic engineering tools to regulate microbial networks for constructing robust microbial cell factories.
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Affiliation(s)
- Qiang Ding
- School of Life Sciences, Anhui University, Hefei 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, China; Anhui Key Laboratory of Modern Biomanufacturing, Hefei 230601, Anhui, China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China.
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5
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Wu Z, Liang X, Li M, Ma M, Zheng Q, Li D, An T, Wang G. Advances in the optimization of central carbon metabolism in metabolic engineering. Microb Cell Fact 2023; 22:76. [PMID: 37085866 PMCID: PMC10122336 DOI: 10.1186/s12934-023-02090-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/10/2023] [Indexed: 04/23/2023] Open
Abstract
Central carbon metabolism (CCM), including glycolysis, tricarboxylic acid cycle and the pentose phosphate pathway, is the most fundamental metabolic process in the activities of living organisms that maintains normal cellular growth. CCM has been widely used in microbial metabolic engineering in recent years due to its unique regulatory role in cellular metabolism. Using yeast and Escherichia coli as the representative organisms, we summarized the metabolic engineering strategies on the optimization of CCM in eukaryotic and prokaryotic microbial chassis, such as the introduction of heterologous CCM metabolic pathways and the optimization of key enzymes or regulatory factors, to lay the groundwork for the future use of CCM optimization in metabolic engineering. Furthermore, the bottlenecks in the application of CCM optimization in metabolic engineering and future application prospects are summarized.
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Affiliation(s)
- Zhenke Wu
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Xiqin Liang
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Mingkai Li
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Mengyu Ma
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Qiusheng Zheng
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Defang Li
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
| | - Tianyue An
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
| | - Guoli Wang
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
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6
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Dinh HV, Maranas CD. Evaluating proteome allocation of Saccharomyces cerevisiae phenotypes with resource balance analysis. Metab Eng 2023; 77:242-255. [PMID: 37080482 DOI: 10.1016/j.ymben.2023.04.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/12/2023] [Accepted: 04/16/2023] [Indexed: 04/22/2023]
Abstract
Saccharomyces cerevisiae is an important model organism and a workhorse in bioproduction. Here, we reconstructed a compact and tractable genome-scale resource balance analysis (RBA) model (i.e., named scRBA) to analyze metabolic fluxes and proteome allocation in a computationally efficient manner. Resource capacity models such as scRBA provide the quantitative means to identify bottlenecks in biosynthetic pathways due to enzyme, compartment size, and/or ribosome availability limitations. ATP maintenance rate and in vivo apparent turnover numbers (kapp) were regressed from metabolic flux and protein concentration data to capture observed physiological growth yield and proteome efficiency and allocation, respectively. Estimated parameter values were found to vary with oxygen and nutrient availability. Overall, this work (i) provides condition-specific model parameters to recapitulate phenotypes corresponding to different extracellular environments, (ii) alludes to the enhancing effect of substrate channeling and post-translational activation on in vivo enzyme efficiency in glycolysis and electron transport chain, and (iii) reveals that the Crabtree effect is underpinned by specific limitations in mitochondrial proteome capacity and secondarily ribosome availability rather than overall proteome capacity.
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Affiliation(s)
- Hoang V Dinh
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA; Center for Advanced Bioenergy and Bioproducts Innovation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Costas D Maranas
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA; Center for Advanced Bioenergy and Bioproducts Innovation, The Pennsylvania State University, University Park, PA, 16802, USA.
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7
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Recent Advances In Microbe-Photocatalyst Hybrid Systems for Production of Bulk Chemicals: A Review. Appl Biochem Biotechnol 2023; 195:1574-1588. [PMID: 36346559 DOI: 10.1007/s12010-022-04169-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2022] [Indexed: 11/11/2022]
Abstract
Solar-driven biocatalysis technologies can combine inorganic photocatalytic materials with biological catalysts to convert CO2, light, and water into chemicals, offering the promise of high energy efficiency and a broader product scope than that of natural photosynthesis. Solar energy is the most abundant renewable energy source on earth, but it cannot be directly utilized by current industrial microorganisms. Therefore, the establishment of a solar-driven bio-catalysis platform, a bridge between solar energy and heterotrophic microorganisms, can dramatically increase carbon flux in biomanufacturing systems and consequently may revolutionize the biorefinery. This review first discusses the main applications of microbe-photocatalyst hybrid (MPH) systems in biorefinery processes. Then, various strategies to improve the electron transfer by microorganisms at the inorganic photocatalytic material interface are discussed, especially biohybrid systems based on autotrophic or heterotrophic bacteria and photocatalytic materials. Finally, we discuss the current challenges and offer potential solutions for the development of MPH systems.
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8
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Sheng Q, Yi L, Zhong B, Wu X, Liu L, Zhang B. Shikimic acid biosynthesis in microorganisms: Current status and future direction. Biotechnol Adv 2023; 62:108073. [PMID: 36464143 DOI: 10.1016/j.biotechadv.2022.108073] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/03/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022]
Abstract
Shikimic acid (SA), a hydroaromatic natural product, is used as a chiral precursor for organic synthesis of oseltamivir (Tamiflu®, an antiviral drug). The process of microbial production of SA has recently undergone vigorous development. Particularly, the sustainable construction of recombinant Corynebacterium glutamicum (141.2 g/L) and Escherichia coli (87 g/L) laid a solid foundation for the microbial fermentation production of SA. However, its industrial application is restricted by limitations such as the lack of fermentation tests for industrial-scale and the requirement of growth-limiting factors, antibiotics, and inducers. Therefore, the development of SA biosensors and dynamic molecular switches, as well as genetic modification strategies and optimization of the fermentation process based on omics technology could improve the performance of SA-producing strains. In this review, recent advances in the development of SA-producing strains, including genetic modification strategies, metabolic pathway construction, and biosensor-assisted evolution, are discussed and critically reviewed. Finally, future challenges and perspectives for further reinforcing the development of robust SA-producing strains are predicted, providing theoretical guidance for the industrial production of SA.
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Affiliation(s)
- Qi Sheng
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Lingxin Yi
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Bin Zhong
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xiaoyu Wu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Bin Zhang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China.
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9
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Ahn YJ, Lee JA, Choi KR, Bang J, Lee SY. Can microbes be harnessed to reduce atmospheric loads of greenhouse gases? Environ Microbiol 2023; 25:17-25. [PMID: 36655716 DOI: 10.1111/1462-2920.16161] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/06/2022] [Indexed: 01/21/2023]
Abstract
Reducing atmospheric loads of greenhouse gases (GHGs), especially CO2 and CH4 , has been considered the key to alleviating global crises we are facing, such as climate change, sea level elevation and ocean acidification. To this end, development of strategies and technologies for carbon capture, sequestration and utilization (CCSU) is urgently needed. Although physicochemical methods have been the most actively studied in the early stages of developing CCSU technologies, there have recently been growing interests in developing microbe-based CCSU processes. In this article, we discuss advantages of microbe-based CCSU technologies over physicochemical approaches and even plant-based approaches. Next, various parts of the global carbon cycle where microorganisms can contribute, such as sequestering atmospheric GHGs, facilitating the carbon cycle, and slowing down the depletion of carbon reservoirs are described, emphasizing the impacts of microbes on the carbon cycle. Strategies to upgrade microbes and increase their performance in assimilating GHGs or converting GHGs to value-added chemicals are also provided. Moreover, several examples of exploiting microbes to address environmental crises are discussed. Finally, we discuss things to overcome in microbe-based CCSU technologies and provide future perspectives.
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Affiliation(s)
- Yeah-Ji Ahn
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Jong An Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Kyeong Rok Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,BioProcess Engineering Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Junho Bang
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,BioProcess Engineering Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,BioInformatics Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
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10
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Zomorrodi AR, Hemez C, Arranz-Gibert P, Wu T, Isaacs FJ, Segrè D. Computational design and engineering of an Escherichia coli strain producing the nonstandard amino acid para-aminophenylalanine. iScience 2022; 25:104562. [PMID: 35789833 PMCID: PMC9249619 DOI: 10.1016/j.isci.2022.104562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/16/2022] [Accepted: 06/02/2022] [Indexed: 11/16/2022] Open
Abstract
Introducing heterologous pathways into host cells constitutes a promising strategy for synthesizing nonstandard amino acids (nsAAs) to enable the production of proteins with expanded chemistries. However, this strategy has proven challenging, as the expression of heterologous pathways can disrupt cellular homeostasis of the host cell. Here, we sought to optimize the heterologous production of the nsAA para-aminophenylalanine (pAF) in Escherichia coli. First, we incorporated a heterologous pAF biosynthesis pathway into a genome-scale model of E. coli metabolism and computationally identified metabolic interventions in the host’s native metabolism to improve pAF production. Next, we explored different approaches of imposing these flux interventions experimentally and found that the upregulation of flux in the chorismate biosynthesis pathway through the elimination of feedback inhibition mechanisms could significantly raise pAF titers (∼20-fold) while maintaining a reasonable pAF production-growth rate trade-off. Overall, this study provides a promising strategy for the biosynthesis of nsAAs in engineered cells. Sought to optimize para-aminophenylalanine (pAF) production and growth in E. coli Identified interventions in the host native metabolism using genome-scale models Constructed multiple mutant strains involving gene knockouts and/or overexpressions Flux modification in chorismate biosynthesis pathway significantly raised pAF titer
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Affiliation(s)
- Ali R. Zomorrodi
- Mucosal Immunology and Biology Research Center, Pediatrics Department, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Bioinformatics Graduate Program, Boston University, Boston, MA, USA
| | - Colin Hemez
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Systems Biology Institute, Yale University, West Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Pol Arranz-Gibert
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Systems Biology Institute, Yale University, West Haven, CT, USA
| | - Terrence Wu
- Yale West Campus Analytical Core, 600 West Campus Drive, West Haven, USA
| | - Farren J. Isaacs
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Systems Biology Institute, Yale University, West Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Corresponding author
| | - Daniel Segrè
- Bioinformatics Graduate Program, Boston University, Boston, MA, USA
- Department of Biology, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
- Corresponding author
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11
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Liu Y, Liu H, Hu H, Ng KR, Yang R, Lyu X. De Novo Production of Hydroxytyrosol by Metabolic Engineering of Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:7490-7499. [PMID: 35649155 DOI: 10.1021/acs.jafc.2c02137] [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: 06/15/2023]
Abstract
Hydroxytyrosol is an olive-derived phenolic compound of increasing commercial interest due to its health-promoting properties. In this study, a high-yield hydroxytyrosol-producing Saccharomyces cerevisiae cell factory was established via a comprehensive metabolic engineering scheme. First, de novo biosynthetic pathway of hydroxytyrosol was constructed in yeast by gene screening and overexpression of different phenol hydroxylases, among which paHD (from Pseudomonas aeruginosa) displayed the best catalytic performance. Next, hydroxytyrosol precursor supply was enhanced via a multimodular engineering approach: elimination of tyrosine feedback inhibition through genomic integration of aro4K229L and aro7G141S, construction of an aromatic aldehyde synthase (AAS)-based tyrosine metabolic pathway, and redistribution of metabolic flux between glycolytic pathway and pentose phosphate pathway (PPP) by introducing the exogenous gene Bbxfpkopt. As a result, the titer of hydroxytyrosol was improved by 6.88-fold. Finally, a glucose-responsive dynamic regulation system based on GAL80 deletion was implemented, resulting in the final hydroxytyrosol yields of 308.65 mg/L and 167.98 mg/g cell mass, the highest known from de novo production in S. cerevisiae to date.
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Affiliation(s)
- Yingjie Liu
- School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
| | - Han Liu
- School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
| | - Haitao Hu
- School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
| | - Kuan Rei Ng
- Food Science and Technology Programme, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
| | - Ruijin Yang
- School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
| | - Xiaomei Lyu
- School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
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12
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Xiao F, Lian J, Tu S, Xie L, Li J, Zhang F, Linhardt RJ, Huang H, Zhong W. Metabolic Engineering of Saccharomyces cerevisiae for High-Level Production of Chlorogenic Acid from Glucose. ACS Synth Biol 2022; 11:800-811. [PMID: 35107250 DOI: 10.1021/acssynbio.1c00487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chlorogenic acid (CGA), a major dietary phenolic compound, has been increasingly used in the food and pharmaceutical industries because of its ready availability and extensive biological and pharmacological activities. Traditionally, extraction from plants has been the main approach for the commercial production of CGA. This study reports the first efficient microbial production of CGA by engineering the yeast, Saccharomyces cerevisiae, on a simple mineral medium. First, an optimized de novo biosynthetic pathway for CGA was reconstructed in S. cerevisiae from glucose with a CGA titer of 36.6 ± 2.4 mg/L. Then, a multimodule engineering strategy was employed to improve CGA production: (1) unlocking the shikimate pathway and optimizing carbon distribution; (2) optimizing the l-Phe branch and pathway balancing; and (3) increasing the copy number of CGA pathway genes. The combination of these interventions resulted in an about 6.4-fold improvement of CGA titer up to 234.8 ± 11.1 mg/L in shake flask cultures. CGA titers of 806.8 ± 1.7 mg/L were achieved in a 1 L fed-batch fermenter. This study opens a route to effectively produce CGA from glucose in S. cerevisiae and establishes a platform for the biosynthesis of CGA-derived value-added metabolites.
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Affiliation(s)
- Feng Xiao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Shuai Tu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Linlin Xie
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jun Li
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Fuming Zhang
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Robert J. Linhardt
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Haichan Huang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Weihong Zhong
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
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13
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Kawaguchi H, Takada K, Elkasaby T, Pangestu R, Toyoshima M, Kahar P, Ogino C, Kaneko T, Kondo A. Recent advances in lignocellulosic biomass white biotechnology for bioplastics. BIORESOURCE TECHNOLOGY 2022; 344:126165. [PMID: 34695585 DOI: 10.1016/j.biortech.2021.126165] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/14/2021] [Accepted: 10/16/2021] [Indexed: 06/13/2023]
Abstract
Lignocellulosic biomass has great potential as an inedible feedstock for bioplastic synthesis, although its use is still limited compared to current edible feedstocks of glucose and starch. This review focuses on recent advances in the production of biopolymers and biomonomers from lignocellulosic feedstocks with downstream processing and chemical polymer syntheses. In microbial production, four routes composed of existing poly (lactic acid) and polyhydroxyalkanoates (PHAs) and the emerging biomonomers of itaconic acid and aromatic compounds were presented to review present challenges and future perspectives, focusing on the use of lignocellulosic feedstocks. Recently, advances in purification technologies decreased the number of processes and their environmental burden. Additionally, the unique structures and high-performance of emerging lignocellulose-based bioplastics have expanded the possibilities for the use of bioplastics. The sequence of processes provides insight into the emerging technologies that are needed for the practical use of bioplastics made from lignocellulosic biomass.
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Affiliation(s)
- Hideo Kawaguchi
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Kenji Takada
- Energy and Environmental Area, Graduate School of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Taghreed Elkasaby
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Botany Department, Faculty of Science, Mansoura University, 60 Elgomhoria st, Mansoura 35516, Egypt
| | - Radityo Pangestu
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Research Center for Biotechnology, Indonesian Institute of Sciences, Cibinong, West Java 16911, Indonesia
| | - Masakazu Toyoshima
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Prihardi Kahar
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Tatsuo Kaneko
- Energy and Environmental Area, Graduate School of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Biomass Engineering Research Division, RIKEN, 1-7-22 Suehiro, Turumi, Yokohama, Kanagawa 230-0045, Japan.
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14
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Tan Y, Agustin RVC, Stein LY, Sauvageau D. Transcriptomic analysis of synchrony and productivity in self-cycling fermentation of engineered yeast producing shikimic acid. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 32:e00691. [PMID: 34934640 PMCID: PMC8660916 DOI: 10.1016/j.btre.2021.e00691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/09/2021] [Accepted: 11/23/2021] [Indexed: 05/25/2023]
Abstract
Industrial fermentation provides a wide variety of bioproducts, such as food, biofuels and pharmaceuticals. Self-cycling fermentation (SCF), an advanced automated semi-continuous fermentation approach, has shown significant advantages over batch reactors (BR); including cell synchrony and improved production. Here, Saccharomyces cerevisiae engineered to overproduce shikimic acid was grown under SCF operation. This led to four-fold increases in product yield and volumetric productivity compared to BR. Transcriptomic analyses were performed to understand the cellular mechanisms leading to these increases. Results indicate an up-regulation of a large number of genes related to the cell cycle and DNA replication in the early stages of SCF cycles, inferring substantial synchronization. Moreover, numerous genes related to gluconeogenesis, the citrate cycle and oxidative phosphorylation were significantly up-regulated in the late stages of SCF cycles, consistent with significant increases in shikimic acid yield and productivity.
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Key Words
- BR, Batch reactor
- CER, Carbon dioxide evolution rate
- DDT, Dithiothreitol
- DNA, Deoxyribonucleic acid
- EDTA, Ethylenediaminetetraacetic acid
- FC, Fold change
- OD600, Optical density at 600 nm
- RNA, Ribonucleic acid
- SCF, Self-cycling fermentation
- STP, Standard temperature and pressure
- Saccharomyces cerevisiae
- Self-cycling fermentation (SCF)
- Shikimic acid
- Synchrony
- Transcriptomics
- cDNA, Complementary deoxyribonucleic acid
- mRNA, Messenger ribonucleic acid
- qPCR, Quantitative polymerase chain reaction
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Affiliation(s)
- Yusheng Tan
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - Roman Vincent C. Agustin
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - Lisa Y. Stein
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Dominic Sauvageau
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta, Canada
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15
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Wang G, Tavares A, Schmitz S, França L, Almeida H, Cavalheiro J, Carolas A, Øzmerih S, Blank LM, Ferreira BS, Borodina I. An integrated yeast-based process for cis,cis-muconic acid production. Biotechnol Bioeng 2021; 119:376-387. [PMID: 34786710 PMCID: PMC9299173 DOI: 10.1002/bit.27992] [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: 07/12/2021] [Revised: 10/07/2021] [Accepted: 11/11/2021] [Indexed: 11/25/2022]
Abstract
Cis,cis‐muconic acid (CCM) is a promising polymer building block. CCM can be made by whole‐cell bioconversion of lignin hydrolysates or de novo biosynthesis from sugar feedstocks using engineered microorganisms. At present, however, there is no established process for large‐scale CCM production. In this study, we developed an integrated process for manufacturing CCM from glucose by yeast fermentation. We systematically engineered the CCM‐producing Saccharomyces cerevisiae strain by rewiring the shikimate pathway flux and enhancing phosphoenolpyruvate supply. The engineered strain ST10209 accumulated less biomass but produced 1.4 g/L CCM (70 mg CCM per g glucose) in microplate assay, 71% more than the previously engineered strain ST8943. The strain ST10209 produced 22.5 g/L CCM in a 2 L fermenter with a productivity of 0.19 g/L/h, compared to 0.14 g/L/h achieved by ST8943 in our previous report under the same fermentation conditions. The fermentation process was demonstrated at pilot scale in 10 and 50 L steel tanks. In 10 L fermenter, ST10209 produced 20.8 g/L CCM with a CCM yield of 0.1 g/g glucose and a productivity of 0.21 g/L/h, representing the highest to‐date CCM yield and productivity. We developed a CCM recovery and purification process by treating the fermentation broth with activated carbon at low pH and low temperature, achieving an overall CCM recovery yield of 66.3% and 95.4% purity. In summary, we report an integrated CCM production process employing engineered S. cerevisiae yeast.
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Affiliation(s)
- Guokun Wang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Aline Tavares
- Biotrend - Inovação e Engenharia em Biotecnologia SA, Cantanhede, Portugal
| | - Simone Schmitz
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Aachen, Germany
| | - Lucas França
- Biotrend - Inovação e Engenharia em Biotecnologia SA, Cantanhede, Portugal
| | - Hugo Almeida
- Biotrend - Inovação e Engenharia em Biotecnologia SA, Cantanhede, Portugal
| | - João Cavalheiro
- Biotrend - Inovação e Engenharia em Biotecnologia SA, Cantanhede, Portugal
| | - Ana Carolas
- Biotrend - Inovação e Engenharia em Biotecnologia SA, Cantanhede, Portugal
| | - Süleyman Øzmerih
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lars M Blank
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Aachen, Germany
| | - Bruno S Ferreira
- Biotrend - Inovação e Engenharia em Biotecnologia SA, Cantanhede, Portugal
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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16
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Liu H, Tian Y, Zhou Y, Kan Y, Wu T, Xiao W, Luo Y. Multi-modular engineering of Saccharomyces cerevisiae for high-titre production of tyrosol and salidroside. Microb Biotechnol 2021; 14:2605-2616. [PMID: 32990403 PMCID: PMC8601180 DOI: 10.1111/1751-7915.13667] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 08/27/2020] [Indexed: 02/06/2023] Open
Abstract
Tyrosol and its glycosylated product salidroside are important ingredients in pharmaceuticals, nutraceuticals and cosmetics. Despite the ability of Saccharomyces cerevisiae to naturally synthesize tyrosol, high yield from de novo synthesis remains a challenge. Here, we used metabolic engineering strategies to construct S. cerevisiae strains for high-level production of tyrosol and salidroside from glucose. First, tyrosol production was unlocked from feedback inhibition. Then, transketolase and ribose-5-phosphate ketol-isomerase were overexpressed to balance the supply of precursors. Next, chorismate synthase and chorismate mutase were overexpressed to maximize the aromatic amino acid flux towards tyrosol synthesis. Finally, the competing pathway was knocked out to further direct the carbon flux into tyrosol synthesis. Through a combination of these interventions, tyrosol titres reached 702.30 ± 0.41 mg l-1 in shake flasks, which were approximately 26-fold greater than that of the WT strain. RrU8GT33 from Rhodiola rosea was also applied to cells and maximized salidroside production from tyrosol in S. cerevisiae. Salidroside titres of 1575.45 ± 19.35 mg l-1 were accomplished in shake flasks. Furthermore, titres of 9.90 ± 0.06 g l-1 of tyrosol and 26.55 ± 0.43 g l-1 of salidroside were achieved in 5 l bioreactors, both are the highest titres reported to date. The synergistic engineering strategies presented in this study could be further applied to increase the production of high value-added aromatic compounds derived from the aromatic amino acid biosynthesis pathway in S. cerevisiae.
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Affiliation(s)
- Huayi Liu
- Department of GastroenterologyState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041China
| | - Yujuan Tian
- Department of GastroenterologyState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041China
| | - Yi Zhou
- Department of GastroenterologyState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041China
| | - Yeyi Kan
- Department of GastroenterologyState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041China
| | - Tingting Wu
- Department of GastroenterologyState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041China
| | - Wenhai Xiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education)Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)School of Chemical Engineering and TechnologyTianjin UniversityTianjin300072China
| | - Yunzi Luo
- Department of GastroenterologyState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education)Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)School of Chemical Engineering and TechnologyTianjin UniversityTianjin300072China
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17
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Gao C, Guo L, Hu G, Liu J, Chen X, Xia X, Liu L. Engineering a CRISPRi Circuit for Autonomous Control of Metabolic Flux in Escherichia coli. ACS Synth Biol 2021; 10:2661-2671. [PMID: 34609846 DOI: 10.1021/acssynbio.1c00294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Building autonomous switches is an effective approach for rewiring metabolic flux during microbial synthesis of chemicals. However, current autonomous switches largely rely on metabolite-responsive biosensors or quorum-sensing circuits. In this study, a stationary phase promoter (SPP) and a protein degradation tag (PDT) were combined with the CRISPR interference (CRISPRi) system to construct an autonomous repression system that could shut down multiple-gene expression depending on the cellular physiological state. With this autonomous CRISPRi system to regulate one target gene, a fermenter-scale titer of shikimic acid reached 21 g/L, which was the highest titer ever reported by Escherichia coli in a minimal medium without any chemical inducers. With three target genes repressed, 26 g/L glutaric acid could be achieved with decreased byproduct accumulation. These results highlight the applicability of the autonomous CRISPRi system for microbial production of value-added chemicals.
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Affiliation(s)
- Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Guipeng Hu
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Xiaoxia Xia
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
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18
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Abdolmohammadi S, Gansebom D, Goyal S, Lee TH, Kuehl B, Forrester MJ, Lin FY, Hernández N, Shanks BH, Tessonnier JP, Cochran EW. Analysis of the Amorphous and Interphase Influence of Comononomer Loading on Polymer Properties toward Forwarding Bioadvantaged Copolyamides. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00651] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Sanaz Abdolmohammadi
- Department of Chemical and Biological Engineering, Iowa State University, 618 Bissell Road, Ames, Iowa 50011, United States
- Center for Biorenewable Chemicals (CBiRC), 617 Bissell Road, Ames, Iowa 50011, United States
| | - Dustin Gansebom
- Department of Chemical and Biological Engineering, Iowa State University, 618 Bissell Road, Ames, Iowa 50011, United States
- Center for Biorenewable Chemicals (CBiRC), 617 Bissell Road, Ames, Iowa 50011, United States
| | - Shailja Goyal
- Department of Chemical and Biological Engineering, Iowa State University, 618 Bissell Road, Ames, Iowa 50011, United States
| | - Ting-Han Lee
- Department of Chemical and Biological Engineering, Iowa State University, 618 Bissell Road, Ames, Iowa 50011, United States
| | - Baker Kuehl
- Department of Chemical and Biological Engineering, Iowa State University, 618 Bissell Road, Ames, Iowa 50011, United States
| | - Michael J. Forrester
- Department of Chemical and Biological Engineering, Iowa State University, 618 Bissell Road, Ames, Iowa 50011, United States
| | - Fang-Yi Lin
- Department of Chemical and Biological Engineering, Iowa State University, 618 Bissell Road, Ames, Iowa 50011, United States
| | - Nacú Hernández
- Department of Chemical and Biological Engineering, Iowa State University, 618 Bissell Road, Ames, Iowa 50011, United States
| | - Brent H. Shanks
- Department of Chemical and Biological Engineering, Iowa State University, 618 Bissell Road, Ames, Iowa 50011, United States
- Center for Biorenewable Chemicals (CBiRC), 617 Bissell Road, Ames, Iowa 50011, United States
| | - Jean-Philippe Tessonnier
- Department of Chemical and Biological Engineering, Iowa State University, 618 Bissell Road, Ames, Iowa 50011, United States
- Center for Biorenewable Chemicals (CBiRC), 617 Bissell Road, Ames, Iowa 50011, United States
| | - Eric W. Cochran
- Department of Chemical and Biological Engineering, Iowa State University, 618 Bissell Road, Ames, Iowa 50011, United States
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19
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Nicolaï T, Deparis Q, Foulquié-Moreno MR, Thevelein JM. In-situ muconic acid extraction reveals sugar consumption bottleneck in a xylose-utilizing Saccharomyces cerevisiae strain. Microb Cell Fact 2021; 20:114. [PMID: 34098954 PMCID: PMC8182918 DOI: 10.1186/s12934-021-01594-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/11/2021] [Indexed: 11/17/2022] Open
Abstract
Background The current shift from a fossil-resource based economy to a more sustainable, bio-based economy requires development of alternative production routes based on utilization of biomass for the many chemicals that are currently produced from petroleum. Muconic acid is an attractive platform chemical for the bio-based economy because it can be converted in chemicals with wide industrial applicability, such as adipic and terephthalic acid, and because its two double bonds offer great versatility for chemical modification. Results We have constructed a yeast cell factory converting glucose and xylose into muconic acid without formation of ethanol. We consecutively eliminated feedback inhibition in the shikimate pathway, inserted the heterologous pathway for muconic acid biosynthesis from 3-dehydroshikimate (DHS) by co-expression of DHS dehydratase from P. anserina, protocatechuic acid (PCA) decarboxylase (PCAD) from K. pneumoniae and oxygen-consuming catechol 1,2-dioxygenase (CDO) from C. albicans, eliminated ethanol production by deletion of the three PDC genes and minimized PCA production by enhancing PCAD overexpression and production of its co-factor. The yeast pitching rate was increased to lower high biomass formation caused by the compulsory aerobic conditions. Maximal titers of 4 g/L, 4.5 g/L and 3.8 g/L muconic acid were reached with glucose, xylose, and a mixture, respectively. The use of an elevated initial sugar level, resulting in muconic acid titers above 2.5 g/L, caused stuck fermentations with incomplete utilization of the sugar. Application of polypropylene glycol 4000 (PPG) as solvent for in situ product removal during the fermentation shows that this is not due to toxicity by the muconic acid produced. Conclusions This work has developed an industrial yeast strain able to produce muconic acid from glucose and also with great efficiency from xylose, without any ethanol production, minimal production of PCA and reaching the highest titers in batch fermentation reported up to now. Utilization of higher sugar levels remained conspicuously incomplete. Since this was not due to product inhibition by muconic acid or to loss of viability, an unknown, possibly metabolic bottleneck apparently arises during muconic acid fermentation with high sugar levels and blocks further sugar utilization. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01594-3.
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Affiliation(s)
- Thomas Nicolaï
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, 3001, Leuven-Heverlee, Flanders, Belgium
| | - Quinten Deparis
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, 3001, Leuven-Heverlee, Flanders, Belgium
| | - María R Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium. .,Center for Microbiology, VIB, Kasteelpark Arenberg 31, 3001, Leuven-Heverlee, Flanders, Belgium.
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium. .,Center for Microbiology, VIB, Kasteelpark Arenberg 31, 3001, Leuven-Heverlee, Flanders, Belgium. .,NovelYeast Bv, Open Bio-Incubator, Erasmus High School, Laarbeeklaan 121, 1090, Brussels (Jette), Belgium.
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20
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Zhao EM, Lalwani MA, Chen JM, Orillac P, Toettcher JE, Avalos JL. Optogenetic Amplification Circuits for Light-Induced Metabolic Control. ACS Synth Biol 2021; 10:1143-1154. [PMID: 33835777 DOI: 10.1021/acssynbio.0c00642] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Dynamic control of microbial metabolism is an effective strategy to improve chemical production in fermentations. While dynamic control is most often implemented using chemical inducers, optogenetics offers an attractive alternative due to the high tunability and reversibility afforded by light. However, a major concern of applying optogenetics in metabolic engineering is the risk of insufficient light penetration at high cell densities, especially in large bioreactors. Here, we present a new series of optogenetic circuits we call OptoAMP, which amplify the transcriptional response to blue light by as much as 23-fold compared to the basal circuit (OptoEXP). These circuits show as much as a 41-fold induction between dark and light conditions, efficient activation at light duty cycles as low as ∼1%, and strong homogeneous light-induction in bioreactors of at least 5 L, with limited illumination at cell densities above 40 OD600. We demonstrate the ability of OptoAMP circuits to control engineered metabolic pathways in novel three-phase fermentations using different light schedules to control enzyme expression and improve production of lactic acid, isobutanol, and naringenin. These circuits expand the applicability of optogenetics to metabolic engineering.
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Affiliation(s)
- Evan M. Zhao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Makoto A. Lalwani
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Jhong-Min Chen
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Paulina Orillac
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Jared E. Toettcher
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - José L. Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- The Andlinger Center for Energy and the Environment, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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21
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The Pentose Phosphate Pathway in Yeasts-More Than a Poor Cousin of Glycolysis. Biomolecules 2021; 11:biom11050725. [PMID: 34065948 PMCID: PMC8151747 DOI: 10.3390/biom11050725] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/04/2021] [Accepted: 05/10/2021] [Indexed: 01/14/2023] Open
Abstract
The pentose phosphate pathway (PPP) is a route that can work in parallel to glycolysis in glucose degradation in most living cells. It has a unidirectional oxidative part with glucose-6-phosphate dehydrogenase as a key enzyme generating NADPH, and a non-oxidative part involving the reversible transketolase and transaldolase reactions, which interchange PPP metabolites with glycolysis. While the oxidative branch is vital to cope with oxidative stress, the non-oxidative branch provides precursors for the synthesis of nucleic, fatty and aromatic amino acids. For glucose catabolism in the baker’s yeast Saccharomyces cerevisiae, where its components were first discovered and extensively studied, the PPP plays only a minor role. In contrast, PPP and glycolysis contribute almost equally to glucose degradation in other yeasts. We here summarize the data available for the PPP enzymes focusing on S. cerevisiae and Kluyveromyces lactis, and describe the phenotypes of gene deletions and the benefits of their overproduction and modification. Reference to other yeasts and to the importance of the PPP in their biotechnological and medical applications is briefly being included. We propose future studies on the PPP in K. lactis to be of special interest for basic science and as a host for the expression of human disease genes.
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Zhang L, Nie MY, Liu F, Chen J, Wei LJ, Hua Q. Multiple gene integration to promote erythritol production on glycerol in Yarrowia lipolytica. Biotechnol Lett 2021; 43:1277-1287. [PMID: 33797654 DOI: 10.1007/s10529-021-03113-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 02/28/2021] [Indexed: 11/24/2022]
Abstract
OBJECTIVE Erythritol (1,2,3,4-butanetetrol) is a 4-carbon sugar alcohol that occurs in nature as a metabolite or storage compound. In this study, a multiple gene integration strategy was employed to enhance erythritol production in Y. lipolytica. RESULTS The effects on the production of erythritol in Y. lipolytica of seven key genes involved in the erythritol synthesis pathway were evaluated individually, among which transketolase (TKL1) and transaldolase (TAL1) showed important roles in enhancing erythritol production. The combined overexpression of four genes (GUT1, TPI1, TKL1, TAL1) and disruption of the EYD1 gene (encoding erythritol dehydrogenase), resulted in produce approximately 40 g/L erythritol production from glycerol. Further enhanced erythritol synthesis was obtained by overexpressing the RKI1 gene (encoding ribose 5-phosphate isomerase) and the AMPD gene (encoding AMP deaminase), indicating for the first time that these two genes are also related to the enhancement of erythritol production in Y. lipolytica. CONCLUSIONS A combined gene overexpression strategy was developed to efficiently improve the production of erythritol in Y. lipolytica, suggesting a great capacity and promising potential of this non-conventional yeast in converting glycerol into erythritol.
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Affiliation(s)
- Ling Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Ming-Yue Nie
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Feng Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Jun Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Liu-Jing Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China.
| | - Qiang Hua
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China. .,Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China.
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Zhu L, Wang J, Xu S, Shi G. Improved aromatic alcohol production by strengthening the shikimate pathway in Saccharomyces cerevisiae. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.01.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Kuivanen J, Kannisto M, Mojzita D, Rischer H, Toivari M, Jäntti J. Engineering of Saccharomyces cerevisiae for anthranilate and methyl anthranilate production. Microb Cell Fact 2021; 20:34. [PMID: 33536025 PMCID: PMC7860014 DOI: 10.1186/s12934-021-01532-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/27/2021] [Indexed: 11/10/2022] Open
Abstract
Background Anthranilate is a platform chemical used by the industry in the synthesis of a broad range of high-value products, such as dyes, perfumes and pharmaceutical compounds. Currently anthranilate is produced via chemical synthesis from non-renewable resources. Biological synthesis would allow the use of renewable carbon sources and avoid accumulation of toxic by-products. Microorganisms produce anthranilate as an intermediate in the tryptophan biosynthetic pathway. Several prokaryotic microorganisms have been engineered to overproduce anthranilate but attempts to engineer eukaryotic microorganisms for anthranilate production are scarce. Results We subjected Saccharomyces cerevisiae, a widely used eukaryotic production host organism, to metabolic engineering for anthranilate production. A single gene knockout was sufficient to trigger anthranilate accumulation both in minimal and SCD media and the titer could be further improved by subsequent genomic alterations. The effects of the modifications on anthranilate production depended heavily on the growth medium used. By growing an engineered strain in SCD medium an anthranilate titer of 567.9 mg l−1 was obtained, which is the highest reported with an eukaryotic microorganism. Furthermore, the anthranilate biosynthetic pathway was extended by expression of anthranilic acid methyltransferase 1 from Medicago truncatula. When cultivated in YPD medium, this pathway extension enabled production of the grape flavor compound methyl anthranilate in S. cerevisiae at 414 mg l−1. Conclusions In this study we have engineered metabolism of S. cerevisiae for improved anthranilate production. The resulting strains may serve as a basis for development of efficient production host organisms for anthranilate-derived compounds. In order to demonstrate suitability of the engineered S. cerevisiae strains for production of such compounds, we successfully extended the anthranilate biosynthesis pathway to synthesis of methyl anthranilate.
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Affiliation(s)
- Joosu Kuivanen
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland.,eniferBio Oy, Espoo, Finland
| | - Matti Kannisto
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland.
| | - Dominik Mojzita
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Heiko Rischer
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Mervi Toivari
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Jussi Jäntti
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
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Zhang Y, Yu J, Wu Y, Li M, Zhao Y, Zhu H, Chen C, Wang M, Chen B, Tan T. Efficient production of chemicals from microorganism by metabolic engineering and synthetic biology. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.12.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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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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Kogure T, Suda M, Hiraga K, Inui M. Protocatechuate overproduction by Corynebacterium glutamicum via simultaneous engineering of native and heterologous biosynthetic pathways. Metab Eng 2020; 65:232-242. [PMID: 33238211 DOI: 10.1016/j.ymben.2020.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/28/2020] [Accepted: 11/12/2020] [Indexed: 10/22/2022]
Abstract
Protocatechuic acid (3, 4-dihydroxybenzoic acid, PCA) is a natural bioactive phenolic acid potentially valuable as a pharmaceutical raw material owing to its diverse pharmacological activities. Corynebacterium glutamicum forms PCA as a key intermediate in a native pathway to assimilate shikimate/quinate through direct conversion of the shikimate pathway intermediate 3-dehydroshikimate (DHS), which is catalyzed by qsuB-encoded DHS dehydratase (the DHS pathway). PCA can also be formed via an alternate pathway extending from chorismate by introducing heterologous chorismate pyruvate lyase that converts chorismate into 4-hydroxybenzoate (4-HBA), which is then converted into PCA catalyzed by endogenous 4-HBA 3-hydroxylase (the 4-HBA pathway). In this study, we generated three plasmid-free C. glutamicum strains overproducing PCA based on the markerless chromosomal recombination by engineering each or both of the above mentioned two PCA-biosynthetic pathways combined with engineering of the host metabolism to enhance the shikimate pathway flux and to block PCA consumption. Aerobic growth-arrested cell reactions were performed using the resulting engineered strains, which revealed that strains dependent on either the DHS or 4-HBA pathway as the sole PCA-biosynthetic route produced 43.8 and 26.2 g/L of PCA from glucose with a yield of 35.3% and 10.0% (mol/mol), respectively, indicating that PCA production through the DHS pathway is significantly efficient compared to that produced through the 4-HBA pathway. Remarkably, a strain simultaneously using both DHS and 4-HBA pathways achieved the highest reported PCA productivity of 82.7 g/L with a yield of 32.8% (mol/mol) from glucose in growth-arrested cell reaction. These results indicated that simultaneous engineering of both DHS and 4-HBA pathways is an efficient method for PCA production. The generated PCA-overproducing strain is plasmid-free and does not require supplementation of aromatic amino acids and vitamins due to the intact shikimate pathway, thereby representing a promising platform for the industrial bioproduction of PCA and derived chemicals from renewable sugars.
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Affiliation(s)
- Takahisa Kogure
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan.
| | - Masako Suda
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan.
| | - Kazumi Hiraga
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan.
| | - Masayuki Inui
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan; Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan.
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Reifenrath M, Oreb M, Boles E, Tripp J. Artificial ER-Derived Vesicles as Synthetic Organelles for in Vivo Compartmentalization of Biochemical Pathways. ACS Synth Biol 2020; 9:2909-2916. [PMID: 33074655 DOI: 10.1021/acssynbio.0c00241] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Compartmentalization in membrane-surrounded organelles has the potential to overcome obstacles associated with the engineering of metabolic pathways, such as unwanted side reactions, accumulation of toxic intermediates, drain of intermediates out of the cell, and long diffusion distances. Strategies utilizing natural organelles suffer from the presence of endogenous pathways. In our approach, we make use of endoplasmic reticulum-derived vesicles loaded with enzymes of a metabolic pathway ("metabolic vesicles"). They are generated by fusion of synthetic peptides containing the N-terminal proline-rich and self-assembling region of the maize storage protein gamma-Zein ("Zera") to the pathway enzymes. We have applied a strategy to integrate three enzymes of a cis,cis-muconic acid production pathway into those vesicles in yeast. Using fluorescence microscopy and cell fractionation techniques, we have proven the formation of metabolic vesicles and the incorporation of enzymes. Activities of the enzymes and functionality of the compartmentalized pathway were demonstrated in fermentation experiments.
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Affiliation(s)
- Mara Reifenrath
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Mislav Oreb
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Eckhard Boles
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Joanna Tripp
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
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Rajkumar AS, Morrissey JP. Rational engineering of Kluyveromyces marxianus to create a chassis for the production of aromatic products. Microb Cell Fact 2020; 19:207. [PMID: 33176787 PMCID: PMC7659061 DOI: 10.1186/s12934-020-01461-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/27/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The yeast Kluyveromyces marxianus offers unique potential for industrial biotechnology because of useful features like rapid growth, thermotolerance and a wide substrate range. As an emerging alternative platform, K. marxianus requires the development and validation of metabolic engineering strategies to best utilise its metabolism as a basis for bio-based production. RESULTS To illustrate the synthetic biology strategies to be followed and showcase its potential, we describe a comprehensive approach to rationally engineer a metabolic pathway in K. marxianus. We use the phenylalanine biosynthetic pathway both as a prototype and because phenylalanine is a precursor for commercially valuable secondary metabolites. First, we modify and overexpress the pathway to be resistant to feedback inhibition so as to overproduce phenylalanine de novo from synthetic minimal medium. Second, we assess native and heterologous means to increase precursor supply to the biosynthetic pathway. Finally, we eliminate branch points and competing reactions in the pathway and rebalance precursors to redirect metabolic flux to a specific product, 2-phenylethanol (2-PE). As a result, we are able to construct robust strains capable of producing over 800 mg L-1 2-PE from minimal medium. CONCLUSIONS The strains we constructed are a promising platform for the production of aromatic amino acid-based biochemicals, and our results illustrate challenges with attempting to combine individually beneficial modifications in an integrated platform.
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Affiliation(s)
- Arun S Rajkumar
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork, T12 K8AF, Ireland
| | - John P Morrissey
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork, T12 K8AF, Ireland.
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Zhang X, Liu Y, Wang J, Zhao Y, Deng Y. Biosynthesis of adipic acid in metabolically engineered Saccharomyces cerevisiae. J Microbiol 2020; 58:1065-1075. [PMID: 33095385 DOI: 10.1007/s12275-020-0261-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/27/2020] [Accepted: 08/12/2020] [Indexed: 11/26/2022]
Abstract
Adipic Acid (AA) is a valued platform chemical compound, which can be used as a precursor of nylon-6,6. Due to the generation of an enormous amount of nitric oxide metabolites and the growing depletion of oil resources as a result of AA production from a mixture of cyclohexanol and cyclohexanone, the microbial methods for synthesizing AA have attracted significant attention. Of the several AA-producing pathways, the reverse adipate degradation pathway in Thermobifida fusca (Tfu RADP) is reported to be the most efficient, which has been confirmed in Escherichia coli. In this study, the heterologous Tfu RADP was constructed for producing AA in S. cerevisiae by co-expressing genes of Tfu_0875, Tfu_2399, Tfu_0067, Tfu_1647, Tfu_2576, and Tfu_2576. The AA titer combined with biomass, cofactors and other by-products was all determined after fermentation. During batch fermentation in a shake flask, the maximum AA titer was 3.83 mg/L, while the titer increased to 10.09 mg/L during fed-batch fermentation in a 5-L bioreactor after fermentation modification.
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Affiliation(s)
- Xi Zhang
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, P. R. China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, P. R. China
| | - Yingli Liu
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing, 100048, P. R. China
| | - Jing Wang
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing, 100048, P. R. China
| | - Yunying Zhao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, P. R. China.
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, P. R. China.
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, P. R. China.
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, P. R. China.
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, P. R. China.
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Antonakoudis A, Barbosa R, Kotidis P, Kontoravdi C. The era of big data: Genome-scale modelling meets machine learning. Comput Struct Biotechnol J 2020; 18:3287-3300. [PMID: 33240470 PMCID: PMC7663219 DOI: 10.1016/j.csbj.2020.10.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 12/15/2022] Open
Abstract
With omics data being generated at an unprecedented rate, genome-scale modelling has become pivotal in its organisation and analysis. However, machine learning methods have been gaining ground in cases where knowledge is insufficient to represent the mechanisms underlying such data or as a means for data curation prior to attempting mechanistic modelling. We discuss the latest advances in genome-scale modelling and the development of optimisation algorithms for network and error reduction, intracellular constraining and applications to strain design. We further review applications of supervised and unsupervised machine learning methods to omics datasets from microbial and mammalian cell systems and present efforts to harness the potential of both modelling approaches through hybrid modelling.
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Affiliation(s)
| | | | | | - Cleo Kontoravdi
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
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32
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Current state of aromatics production using yeast: achievements and challenges. Curr Opin Biotechnol 2020; 65:65-74. [DOI: 10.1016/j.copbio.2020.01.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/21/2020] [Accepted: 01/24/2020] [Indexed: 12/14/2022]
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Choi S, Lee HN, Park E, Lee SJ, Kim ES. Recent Advances in Microbial Production of cis,cis-Muconic Acid. Biomolecules 2020; 10:biom10091238. [PMID: 32854378 PMCID: PMC7564838 DOI: 10.3390/biom10091238] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/20/2020] [Accepted: 08/20/2020] [Indexed: 02/06/2023] Open
Abstract
cis,cis-Muconic acid (MA) is a valuable C6 dicarboxylic acid platform chemical that is used as a starting material for the production of various valuable polymers and drugs, including adipic acid and terephthalic acid. As an alternative to traditional chemical processes, bio-based MA production has progressed to the establishment of de novo MA pathways in several microorganisms, such as Escherichia coli, Corynebacterium glutamicum, Pseudomonas putida, and Saccharomyces cerevisiae. Redesign of the metabolic pathway, intermediate flux control, and culture process optimization were all pursued to maximize the microbial MA production yield. Recently, MA production from biomass, such as the aromatic polymer lignin, has also attracted attention from researchers focusing on microbes that are tolerant to aromatic compounds. This paper summarizes recent microbial MA production strategies that involve engineering the metabolic pathway genes as well as the heterologous expression of some foreign genes involved in MA biosynthesis. Microbial MA production will continue to play a vital role in the field of bio-refineries and a feasible way to complement various petrochemical-based chemical processes.
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Affiliation(s)
- Sisun Choi
- Department of Biological Engineering, Inha University, Incheon 22212, Korea; (S.C.); (H.-N.L.); (E.P.)
| | - Han-Na Lee
- Department of Biological Engineering, Inha University, Incheon 22212, Korea; (S.C.); (H.-N.L.); (E.P.)
- STR Biotech Co., Ltd., Chuncheon-si, Gangwon-do 24232, Korea;
| | - Eunhwi Park
- Department of Biological Engineering, Inha University, Incheon 22212, Korea; (S.C.); (H.-N.L.); (E.P.)
| | - Sang-Jong Lee
- STR Biotech Co., Ltd., Chuncheon-si, Gangwon-do 24232, Korea;
| | - Eung-Soo Kim
- Department of Biological Engineering, Inha University, Incheon 22212, Korea; (S.C.); (H.-N.L.); (E.P.)
- Correspondence: ; Tel.: +82-32-860-8318; Fax: +82-32-872-4046
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Hydrogenation of Trans,Trans-Muconic Acid to Bio-Adipic Acid: Mechanism Identification and Kinetic Modelling. Processes (Basel) 2020. [DOI: 10.3390/pr8080929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The hydrogenation of trans,trans-muconic acid was investigated on a Pt/C 5% (wt) catalyst in a batch slurry reactor at constant hydrogen pressure (4 bar) and temperature (323, 333 and 343 K), with the purpose of developing a kinetic model able to predict conversions and product distributions. A dual-site Langmuir–Hinshelwood–Hougen–Watson (LHHW) model with hydrogen dissociation provided good fitting of the experimental data. The model parameters were regressed by robust numerical methods to overcome the computational challenges of the model parameters’ collinearity. Different reaction mechanisms were tested; the best model involved two subsequent hydrogenation steps. The first step yielded from trans,trans-muconic acid a monounsaturated intermediate (trans-2-hexenedioic acid), which was further hydrogenated to adipic acid in the second step. The intermediate was subjected to an equilibrium isomerization with cis-2-hexenedioic acid. The activation energy values and the rate constants were calculated for the reactions, providing the first reference for trans,trans-muconic acid hydrogenation.
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Zhao Y, Yao Z, Ploessl D, Ghosh S, Monti M, Schindler D, Gao M, Cai Y, Qiao M, Yang C, Cao M, Shao Z. Leveraging the Hermes Transposon to Accelerate the Development of Nonconventional Yeast-based Microbial Cell Factories. ACS Synth Biol 2020; 9:1736-1752. [PMID: 32396718 DOI: 10.1021/acssynbio.0c00123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We broadened the usage of DNA transposon technology by demonstrating its capacity for the rapid creation of expression libraries for long biochemical pathways, which is beyond the classical application of building genome-scale knockout libraries in yeasts. This strategy efficiently leverages the readily available fine-tuning impact provided by the diverse transcriptional environment surrounding each random integration locus. We benchmark the transposon-mediated integration against the nonhomologous end joining-mediated strategy. The latter strategy was demonstrated for achieving pathway random integration in other yeasts but is associated with a high false-positive rate in the absence of a high-throughput screening method. Our key innovation of a nonreplicable circular DNA platform increased the possibility of identifying top-producing variants to 97%. Compared to the classical DNA transposition protocol, the design of a nonreplicable circular DNA skipped the step of counter-selection for plasmid removal and thus not only reduced the time required for the step of library creation from 10 to 5 d but also efficiently removed the "transposition escapers", which undesirably represented almost 80% of the entire population as false positives. Using one endogenous product (i.e., shikimate) and one heterologous product (i.e., (S)-norcoclaurine) as examples, we presented a streamlined procedure to rapidly identify high-producing variants with titers significantly higher than the reported data in the literature. We selected Scheffersomyces stipitis, a representative nonconventional yeast, as a demo, but the strategy can be generalized to other nonconventional yeasts. This new exploration of transposon technology, therefore, adds a highly versatile tool to accelerate the development of novel species as microbial cell factories for producing value-added chemicals.
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Affiliation(s)
- Yuxin Zhao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Zhanyi Yao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Deon Ploessl
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Saptarshi Ghosh
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Marco Monti
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, U.K
| | - Daniel Schindler
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, U.K
| | - Meirong Gao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Yizhi Cai
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, U.K
| | - Mingqiang Qiao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Chao Yang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Mingfeng Cao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Zengyi Shao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
- NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa, United States
- Bioeconomy Institute, Iowa State University, Ames, Iowa, United States
- Interdepartmental Microbiology Program, Iowa State University, Ames, Iowa, United States
- The Ames Laboratory, Ames, Iowa, United States
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36
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Aminian-Dehkordi J, Mousavi SM, Marashi SA, Jafari A, Mijakovic I. A Systems-Based Approach for Cyanide Overproduction by Bacillus megaterium for Gold Bioleaching Enhancement. Front Bioeng Biotechnol 2020; 8:528. [PMID: 32582661 PMCID: PMC7283520 DOI: 10.3389/fbioe.2020.00528] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/04/2020] [Indexed: 12/15/2022] Open
Abstract
With the constant accumulation of electronic waste, extracting precious metals contained therein is becoming a major challenge for sustainable development. Bacillus megaterium is currently one of the microbes used for the production of cyanide, which is the main leaching agent for gold recovery. The present study aimed to propose a strategy for metabolic engineering of B. megaterium to overproduce cyanide, and thus ameliorate the bioleaching process. For this, we employed constraint-based modeling, running in silico simulations on iJA1121, the genome-scale metabolic model of B. megaterium DSM319. Flux balance analysis (FBA) was initially used to identify amino acids to be added to the culture medium. Considering cyanide as the desired product, we used growth-coupled methods, constrained minimal cut sets (cMCSs) and OptKnock to identify gene inactivation targets. To identify gene overexpression targets, flux scanning based on enforced objective flux (FSEOF) was performed. Further analysis was carried out on the identified targets to determine compounds with beneficial regulatory effects. We have proposed a chemical-defined medium for accelerating cyanide production on the basis of microplate assays to evaluate the components with the greatest improving effects. Accordingly, the cultivation of B. megaterium DSM319 in a chemically-defined medium with 5.56 mM glucose as the carbon source, and supplemented with 413 μM cysteine, led to the production of considerably increased amounts of cyanide. Bioleaching experiments were successfully performed in this medium to recover gold and copper from telecommunication printed circuit boards. The results of inductively coupled plasma (ICP) analysis confirmed that gold recovery peaked out at around 55% after 4 days, whereas copper recovery continued to increase for several more days, peaking out at around 85%. To further validate the bioleaching results, FESEM, XRD, FTIR, and EDAX mapping analyses were performed. We concluded that the proposed strategy represents a viable route for improving the performance of the bioleaching processes.
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Affiliation(s)
- Javad Aminian-Dehkordi
- Biotechnology Group, Department of Chemical Engineering, Tarbiat Modares University, Tehran, Iran
| | - Seyyed Mohammad Mousavi
- Biotechnology Group, Department of Chemical Engineering, Tarbiat Modares University, Tehran, Iran
| | - Sayed-Amir Marashi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Arezou Jafari
- Department of Chemical Engineering, Tarbiat Modares University, Tehran, Iran
| | - Ivan Mijakovic
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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37
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Fatma Z, Schultz JC, Zhao H. Recent advances in domesticating non‐model microorganisms. Biotechnol Prog 2020; 36:e3008. [DOI: 10.1002/btpr.3008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 04/14/2020] [Accepted: 04/18/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Zia Fatma
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
| | - J. Carl Schultz
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
- Departments of Chemistry, Biochemistry, and Bioengineering University of Illinois at Urbana‐Champaign Urbana Illinois USA
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38
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Shi J, Clayton C, Tian B. Nano-enabled cellular engineering for bioelectric studies. NANO RESEARCH 2020; 13:1214-1227. [PMID: 34295455 PMCID: PMC8294124 DOI: 10.1007/s12274-019-2580-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 11/24/2019] [Indexed: 06/13/2023]
Abstract
Engineered cells have opened up a new avenue for scientists and engineers to achieve specialized biological functions. Nanomaterials, such as silicon nanowires and quantum dots, can establish tight interfaces with cells either extra- or intracellularly, and they have already been widely used to control cellular functions. The future exploration of nanomaterials in cellular engineering may reveal numerous opportunities in both fundamental bioelectric studies and clinic applications. In this review, we highlight several nanomaterials-enabled non-genetic approaches to fabricating engineered cells. First, we briefly review the latest progress in engineered or synthetic cells, such as protocells that create cell-like behaviors from nonliving building blocks, and cells made by genetic or chemical modifications. Next, we illustrate the need for non-genetic cellular engineering with semiconductors and present some examples where chemical synthesis yields complex morphology or functions needed for biointerfaces. We then provide discussions in detail about the semiconductor nanostructure-enabled neural, cardiac, and microbial modulations. We also suggest the need to integrate tissue engineering with semiconductor devices to carry out more complex functions. We end this review by providing our perspectives for future development in non-genetic cellular engineering.
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Affiliation(s)
- Jiuyun Shi
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | | | - Bozhi Tian
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
- The James Franck Institute, University of Chicago, Chicago, IL 60637, USA
- The Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
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39
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Zhang X, Zhao Y, Liu Y, Wang J, Deng Y. Recent progress on bio-based production of dicarboxylic acids in yeast. Appl Microbiol Biotechnol 2020; 104:4259-4272. [PMID: 32215709 DOI: 10.1007/s00253-020-10537-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/06/2020] [Accepted: 03/09/2020] [Indexed: 12/25/2022]
Abstract
Dicarboxylic acids are widely used in fine chemical and food industries as well as the monomer for polymerisation of high molecular material. Given the problems of environmental contamination and sustainable development faced by traditional production of dicarboxylic acids based on petrol, new approaches such as bio-based production of dicarboxylic acids drew more attentions. The yeast, Saccharomyces cerevisiae, was regarded as an ideal organism for bio-based production of dicarboxylic acids with high tolerance to acidic and hyperosmotic environments, robust growth using a broad range of substrates, great convenience for genetic manipulation, stable inheritance via sub-cultivation, and food compatibility. In this review, the production of major dicarboxylates via S. cerevisiae was concluded and the challenges and opportunities facing were discussed.Key Points• Summary of current production of major dicarboxylic acids by Saccharomyces cerevisiae.• Discussion of influence factors on four-carbon dicarboxylic acids production by Saccharomyces cerevisiae.• Outlook of potential production of five- and six-carbon dicarboxylic acids by Saccharomyces cerevisiae.
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Affiliation(s)
- Xi Zhang
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Yunying Zhao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Yingli Liu
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing, 100048, China
| | - Jing Wang
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing, 100048, China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China. .,School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
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40
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Milne N, Thomsen P, Mølgaard Knudsen N, Rubaszka P, Kristensen M, Borodina I. Metabolic engineering of Saccharomyces cerevisiae for the de novo production of psilocybin and related tryptamine derivatives. Metab Eng 2020; 60:25-36. [PMID: 32224264 PMCID: PMC7232020 DOI: 10.1016/j.ymben.2019.12.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/12/2019] [Accepted: 12/26/2019] [Indexed: 12/28/2022]
Abstract
Psilocybin is a tryptamine-derived psychoactive alkaloid found mainly in the fungal genus Psilocybe, among others, and is the active ingredient in so-called “magic mushrooms”. Although its notoriety originates from its psychotropic properties and popular use as a recreational drug, clinical trials have recently recognized psilocybin as a promising candidate for the treatment of various psychological and neurological afflictions. In this work, we demonstrate the de novo biosynthetic production of psilocybin and related tryptamine derivatives in Saccharomyces cerevisiae by expression of a heterologous biosynthesis pathway sourced from Psilocybe cubensis. Additionally, we achieve improved product titers by supplementing the pathway with a novel cytochrome P450 reductase from P. cubensis. Further rational engineering resulted in a final production strain producing 627 ± 140 mg/L of psilocybin and 580 ± 276 mg/L of the dephosphorylated degradation product psilocin in triplicate controlled fed-batch fermentations in minimal synthetic media. Pathway intermediates baeocystin, nor norbaeocystin as well the dephosphorylated baeocystin degradation product norpsilocin were also detected in strains engineered for psilocybin production. We also demonstrate the biosynthetic production of natural tryptamine derivative aeruginascin as well as the production of a new-to-nature tryptamine derivative N-acetyl-4-hydroxytryptamine. These results lay the foundation for the biotechnological production of psilocybin in a controlled environment for pharmaceutical applications, and provide a starting point for the biosynthetic production of other tryptamine derivatives of therapeutic relevance. De novo production of psilocybin in S. cerevisiae. Expression of a novel cytochrome P450 reductase from P. cubensis significantly boosts production. Rational metabolic engineering results in 627 mg/L psilocybin production. Production of natural and new-to-nature tryptamine derivatives demonstrated including norbaeocystin, baeocystin, and aeruginascin.
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Affiliation(s)
- N Milne
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark
| | - P Thomsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark
| | - N Mølgaard Knudsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark
| | - P Rubaszka
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark
| | - M Kristensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark
| | - I Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark.
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41
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Wang G, Øzmerih S, Guerreiro R, Meireles AC, Carolas A, Milne N, Jensen MK, Ferreira BS, Borodina I. Improvement of cis, cis-Muconic Acid Production in Saccharomyces cerevisiae through Biosensor-Aided Genome Engineering. ACS Synth Biol 2020; 9:634-646. [PMID: 32058699 PMCID: PMC8457548 DOI: 10.1021/acssynbio.9b00477] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Muconic acid is a potential platform chemical for the production of nylon, polyurethanes, and terephthalic acid. It is also an attractive functional copolymer in plastics due to its two double bonds. At this time, no economically viable process for the production of muconic acid exists. To harness novel genetic targets for improved production of cis,cis-muconic acid (CCM) in the yeast Saccharomyces cerevisiae, we employed a CCM-biosensor coupled to GFP expression with a broad dynamic response to screen UV-mutagenesis libraries of CCM-producing yeast. Via fluorescence activated cell sorting we identified a clone Mut131 with a 49.7% higher CCM titer and 164% higher titer of biosynthetic intermediate-protocatechuic acid (PCA). Genome resequencing of the Mut131 and reverse engineering identified seven causal missense mutations of the native genes (PWP2, EST2, ATG1, DIT1, CDC15, CTS2, and MNE1) and a duplication of two CCM biosynthetic genes, encoding dehydroshikimate dehydratase and catechol 1,2-dioxygenase, which were not recognized as flux controlling before. The Mut131 strain was further rationally engineered by overexpression of the genes encoding for PCA decarboxylase and AROM protein without shikimate dehydrogenase domain (Aro1pΔE), and by restoring URA3 prototrophy. The resulting engineered strain produced 20.8 g/L CCM in controlled fed-batch fermentation, with a yield of 66.2 mg/g glucose and a productivity of 139 mg/L/h, representing the highest reported performance metrics in a yeast for de novo CCM production to date and the highest production of an aromatic compound in yeast. The study illustrates the benefit of biosensor-based selection and brings closer the prospect of biobased muconic acid.
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Affiliation(s)
- Guokun Wang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DK-2800 Kgs, Denmark
| | - Süleyman Øzmerih
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DK-2800 Kgs, Denmark
| | - Rogério Guerreiro
- Biotrend-Inovação e Engenharia em Biotecnologia SA, Cantanhede, 3060-197, Portugal
| | - Ana C. Meireles
- Biotrend-Inovação e Engenharia em Biotecnologia SA, Cantanhede, 3060-197, Portugal
| | - Ana Carolas
- Biotrend-Inovação e Engenharia em Biotecnologia SA, Cantanhede, 3060-197, Portugal
| | - Nicholas Milne
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DK-2800 Kgs, Denmark
| | - Michael K. Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DK-2800 Kgs, Denmark
| | - Bruno S. Ferreira
- Biotrend-Inovação e Engenharia em Biotecnologia SA, Cantanhede, 3060-197, Portugal
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DK-2800 Kgs, Denmark
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42
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Cao M, Gao M, Suástegui M, Mei Y, Shao Z. Building microbial factories for the production of aromatic amino acid pathway derivatives: From commodity chemicals to plant-sourced natural products. Metab Eng 2020; 58:94-132. [DOI: 10.1016/j.ymben.2019.08.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/03/2019] [Accepted: 08/07/2019] [Indexed: 01/23/2023]
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43
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Wu Y, Cai M, Song X, Li Y, Wang H, Mao J, Liu Q, Xu H, Qiao M. Comparative transcriptome analysis of genomic region deletion strain with enhanced L-tyrosine production in Saccharomyces cerevisiae. Biotechnol Lett 2019; 42:453-460. [PMID: 31863218 DOI: 10.1007/s10529-019-02784-1] [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: 09/24/2019] [Accepted: 12/13/2019] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To determine the effect of large genomic region deletion in a Saccharomyces cerevisiae strain on tyrosine yield and to identify new genetic modification targets through transcriptome analysis. RESULTS TAL was used to produce p-coumaric acid (p-CA) from tyrosine to quantity tyrosine yield. S. cerevisiae mutant strain NK14 with deletion of a 23.8 kb genomic region was identified to have p-CA production of 10.3 mg L- 1, while the wild-type strain BY4741 had p-CA production of 1.06 mg L- 1. Analysis of growth patterns and stress tolerance showed that the deletion did not affect the growth phenotype of NK14. Transcriptome analysis suggested that, compared to BY4741, genes related to glycolysis (ENO2, TKL1) and the tyrosine pathway (ARO1, ARO2, ARO4, ARO7, TYR1) were upregulated in NK14 at different levels. Besides genes related to the tyrosine biosynthetic pathway, amino acid transporters (AVT6, VBA5, THI72) and transcription factor (ARO80) also showed changes in transcription levels. CONCLUSIONS We developed a strain with improved tyrosine yield and identified new genetic modification candidates for tyrosine production.
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Affiliation(s)
- Yuzhen Wu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Miao Cai
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xiaofei Song
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yuanzi Li
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Hesuiyuan Wang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Jiwei Mao
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Quanli Liu
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Haijin Xu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Mingqiang Qiao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China.
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Abstract
Abstract
Living organisms in analogy with chemical factories use simple molecules such as sugars to produce a variety of compounds which are necessary for sustaining life and some of which are also commercially valuable. The metabolisms of simple (such as bacteria) and higher organisms (such as plants) alike can be exploited to convert low value inputs into high value outputs. Unlike conventional chemical factories, microbial production chassis are not necessarily tuned for a single product overproduction. Despite the same end goal, metabolic and industrial engineers rely on different techniques for achieving productivity goals. Metabolic engineers cannot affect reaction rates by manipulating pressure and temperature, instead they have at their disposal a range of enzymes and transcriptional and translational processes to optimize accordingly. In this review, we first highlight how various analytical approaches used in metabolic engineering and synthetic biology are related to concepts developed in systems and control engineering. Specifically, how algorithmic concepts derived in operations research can help explain the structure and organization of metabolic networks. Finally, we consider the future directions and challenges faced by the field of metabolic network modeling and the possible contributions of concepts drawn from the classical fields of chemical and control engineering. The aim of the review is to offer a current perspective of metabolic engineering and all that it entails without requiring specialized knowledge of bioinformatics or systems biology.
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45
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Liu Q, Yu T, Li X, Chen Y, Campbell K, Nielsen J, Chen Y. Rewiring carbon metabolism in yeast for high level production of aromatic chemicals. Nat Commun 2019; 10:4976. [PMID: 31672987 PMCID: PMC6823513 DOI: 10.1038/s41467-019-12961-5] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 10/11/2019] [Indexed: 12/22/2022] Open
Abstract
The production of bioactive plant compounds using microbial hosts is considered a safe, cost-competitive and scalable approach to their production. However, microbial production of some compounds like aromatic amino acid (AAA)-derived chemicals, remains an outstanding metabolic engineering challenge. Here we present the construction of a Saccharomyces cerevisiae platform strain able to produce high levels of p-coumaric acid, an AAA-derived precursor for many commercially valuable chemicals. This is achieved through engineering the AAA biosynthesis pathway, introducing a phosphoketalose-based pathway to divert glycolytic flux towards erythrose 4-phosphate formation, and optimizing carbon distribution between glycolysis and the AAA biosynthesis pathway by replacing the promoters of several important genes at key nodes between these two pathways. This results in a maximum p-coumaric acid titer of 12.5 g L−1 and a maximum yield on glucose of 154.9 mg g−1. Microbial production of aromatic amino acid (AAA)-derived chemicals remains an outstanding metabolic engineering challenge. Here, the authors engineer baker’s yeast for high levels p-coumaric acid production by rewiring the central carbon metabolism and channeling more flux to the AAA biosynthetic pathway.
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Affiliation(s)
- Quanli Liu
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE41296, Gothenburg, Sweden
| | - Tao Yu
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE41296, Gothenburg, Sweden
| | - Xiaowei Li
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE41296, Gothenburg, Sweden
| | - Yu Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE41296, Gothenburg, Sweden
| | - Kate Campbell
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE41296, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800, Kongens Lyngby, Denmark
| | - Yun Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE41296, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE41296, Gothenburg, Sweden.
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46
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Wang C, Wang J, Yuan J, Jiang L, Jiang X, Yang B, Zhao G, Liu B, Huang D. Generation of
Streptomyces hygroscopicus
cell factories with enhanced ascomycin production by combined elicitation and pathway‐engineering strategies. Biotechnol Bioeng 2019; 116:3382-3395. [DOI: 10.1002/bit.27158] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/26/2019] [Accepted: 08/28/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Cheng Wang
- Department of Forestry Engineering, College of ForestryNorthwest A&F UniversityYangling Shaanxi China
| | - Junhua Wang
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin China
| | - Jian Yuan
- Key Laboratory of Molecular Microbiology and TechnologyMinistry of EducationTianjin China
- TEDA Institute of Biological Sciences and BiotechnologyNankai UniversityTianjin China
| | - Lingyan Jiang
- Key Laboratory of Molecular Microbiology and TechnologyMinistry of EducationTianjin China
- TEDA Institute of Biological Sciences and BiotechnologyNankai UniversityTianjin China
| | - Xiaolong Jiang
- Key Laboratory of Molecular Microbiology and TechnologyMinistry of EducationTianjin China
- TEDA Institute of Biological Sciences and BiotechnologyNankai UniversityTianjin China
| | - Bin Yang
- Key Laboratory of Molecular Microbiology and TechnologyMinistry of EducationTianjin China
- TEDA Institute of Biological Sciences and BiotechnologyNankai UniversityTianjin China
| | - Guang Zhao
- Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao Shandong China
| | - Bin Liu
- Key Laboratory of Molecular Microbiology and TechnologyMinistry of EducationTianjin China
- TEDA Institute of Biological Sciences and BiotechnologyNankai UniversityTianjin China
- Tianjin Key Laboratory of Microbial Functional GenomicsNankai UniversityTianjin China
| | - Di Huang
- Key Laboratory of Molecular Microbiology and TechnologyMinistry of EducationTianjin China
- TEDA Institute of Biological Sciences and BiotechnologyNankai UniversityTianjin China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and EngineeringNankai UniversityTianjin China
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Recent advancements in fungal-derived fuel and chemical production and commercialization. Curr Opin Biotechnol 2019; 57:1-9. [DOI: 10.1016/j.copbio.2018.08.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/15/2018] [Accepted: 08/29/2018] [Indexed: 12/11/2022]
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Guo J, Suástegui M, Sakimoto KK, Moody VM, Xiao G, Nocera DG, Joshi NS. Light-driven fine chemical production in yeast biohybrids. Science 2019; 362:813-816. [PMID: 30442806 DOI: 10.1126/science.aat9777] [Citation(s) in RCA: 192] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 10/01/2018] [Indexed: 12/21/2022]
Abstract
Inorganic-biological hybrid systems have potential to be sustainable, efficient, and versatile chemical synthesis platforms by integrating the light-harvesting properties of semiconductors with the synthetic potential of biological cells. We have developed a modular bioinorganic hybrid platform that consists of highly efficient light-harvesting indium phosphide nanoparticles and genetically engineered Saccharomyces cerevisiae, a workhorse microorganism in biomanufacturing. The yeast harvests photogenerated electrons from the illuminated nanoparticles and uses them for the cytosolic regeneration of redox cofactors. This process enables the decoupling of biosynthesis and cofactor regeneration, facilitating a carbon- and energy-efficient production of the metabolite shikimic acid, a common precursor for several drugs and fine chemicals. Our work provides a platform for the rational design of biohybrids for efficient biomanufacturing processes with higher complexity and functionality.
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Affiliation(s)
- Junling Guo
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
| | - Miguel Suástegui
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
| | - Kelsey K Sakimoto
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Vanessa M Moody
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, PA 19104, USA
| | - Gao Xiao
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.,John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Neel S Joshi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA. .,John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
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Modular Metabolic Engineering for Biobased Chemical Production. Trends Biotechnol 2019; 37:152-166. [DOI: 10.1016/j.tibtech.2018.07.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/03/2018] [Accepted: 07/05/2018] [Indexed: 11/21/2022]
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