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Xiao Z, Zhao Y, Wang Y, Tan X, Wang L, Mao J, Zhang S, Lu Q, Hu F, Zuo S, Liu J, Shan Y. Sucrose-driven carbon redox rebalancing eliminates the Crabtree effect and boosts energy metabolism in yeast. Nat Commun 2025; 16:5211. [PMID: 40473667 PMCID: PMC12141580 DOI: 10.1038/s41467-025-60578-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2024] [Accepted: 05/28/2025] [Indexed: 06/11/2025] Open
Abstract
Saccharomyces cerevisiae primarily generates energy through glycolysis and respiration. However, the manifestation of the Crabtree effect results in substantial carbon loss and energy inefficiency, which significantly diminishes product yield and escalates substrate costs in microbial cell factories. To address this challenge, we introduce the sucrose phosphorolysis pathway and delete the phosphoglucose isomerase gene PGI1, effectively decoupling glycolysis from respiration and facilitating the metabolic transition of yeast to a Crabtree-negative state. Additionally, a synthetic energy system is engineered to regulate the NADH/NAD+ ratio, ensuring sufficient ATP supply and maintaining redox balance for optimal growth. The reprogrammed yeast strain exhibits significantly higher yields of various non-ethanol compounds, with lactic acid and 3-hydroxypropionic acid production increasing by 8- to 11-fold comparing to the conventional Crabtree-positive strain. This study describes an approach for overcoming the Crabtree effect in yeast, substantially improving energy metabolism, carbon recovery, and product yields.
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Affiliation(s)
- Zhiqiang Xiao
- Longping Agricultural College, Hunan University, Changsha, 410125, China
- Hunan Institute of Agricultural Product Processing and Quality Safety, DongTing Laboratory, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
- Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Agricultural Products Processing Institute, Changsha, 410125, China
| | - Yifei Zhao
- Longping Agricultural College, Hunan University, Changsha, 410125, China
- Hunan Institute of Agricultural Product Processing and Quality Safety, DongTing Laboratory, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
- Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Agricultural Products Processing Institute, Changsha, 410125, China
| | - Yongtong Wang
- Longping Agricultural College, Hunan University, Changsha, 410125, China
- Hunan Institute of Agricultural Product Processing and Quality Safety, DongTing Laboratory, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
- Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Agricultural Products Processing Institute, Changsha, 410125, China
| | - Xinjia Tan
- Longping Agricultural College, Hunan University, Changsha, 410125, China
- Hunan Institute of Agricultural Product Processing and Quality Safety, DongTing Laboratory, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
- Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Agricultural Products Processing Institute, Changsha, 410125, China
| | - Lian Wang
- 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
| | - Jiwei Mao
- Department of Life Sciences, Chalmers University of Technology, SE412 96, Gothenburg, Sweden
| | - Siqi Zhang
- Longping Agricultural College, Hunan University, Changsha, 410125, China
- Hunan Institute of Agricultural Product Processing and Quality Safety, DongTing Laboratory, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
- Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Agricultural Products Processing Institute, Changsha, 410125, China
| | - Qiyuan Lu
- Longping Agricultural College, Hunan University, Changsha, 410125, China
- Hunan Institute of Agricultural Product Processing and Quality Safety, DongTing Laboratory, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
- Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Agricultural Products Processing Institute, Changsha, 410125, China
| | - Fanglin Hu
- Longping Agricultural College, Hunan University, Changsha, 410125, China
- Hunan Institute of Agricultural Product Processing and Quality Safety, DongTing Laboratory, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
- Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Agricultural Products Processing Institute, Changsha, 410125, China
| | - Shasha Zuo
- Longping Agricultural College, Hunan University, Changsha, 410125, China
- Hunan Institute of Agricultural Product Processing and Quality Safety, DongTing Laboratory, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
- Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Agricultural Products Processing Institute, Changsha, 410125, China
| | - Juan Liu
- Hunan Institute of Agricultural Product Processing and Quality Safety, DongTing Laboratory, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
- Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Agricultural Products Processing Institute, Changsha, 410125, China.
| | - Yang Shan
- Longping Agricultural College, Hunan University, Changsha, 410125, China.
- Hunan Institute of Agricultural Product Processing and Quality Safety, DongTing Laboratory, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
- Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Agricultural Products Processing Institute, Changsha, 410125, China.
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Xiong B, Yang T, Zhang Z, Li X, Yu H, Wang L, You Z, Peng W, Jin L, Song H. Metabolic reprogramming and machine learning-guided cofactor engineering to boost nicotinamide mononucleotide production in Escherichia coli. BIORESOURCE TECHNOLOGY 2025; 426:132350. [PMID: 40054751 DOI: 10.1016/j.biortech.2025.132350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2025] [Revised: 03/04/2025] [Accepted: 03/04/2025] [Indexed: 03/14/2025]
Abstract
Nicotinamide mononucleotide (NMN) is a bioactive compound in NAD(P)+ metabolism, which exhibits diverse pharmaceutical interests. However, enhancing NMN biosynthesis faces the challange of competing with cell growth and disturbing intracellular redox homeostasis. Herein, we boosted NMN production in Escherichia coli by reprogramming central carbon metabolism with a machine learning (ML)-guided cofactor engineering strategy. Engnieering NMN biosynthesis-related pathway directed carbon flux toward NMN with the NADPH level increased by 73 %, which, although enhanced NMN titer (2.45 g/L), impaired cell growth. A quorum sensing (QS)-controlled cofactor engineering system was thus contructed and optimized by ML models to address redox imbalance, which led to 3.04 g/L NMN with improved cell growth. The final strain S344 produced 20.13 g/L NMN in fed-batch fermentation. This study showed that perturbation on cofactor level is a crucial limiting factor for NMN biosynthesis, and proposed a novel ML-guided strategy to manipulate intracellular redox state for efficient NMN production.
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Affiliation(s)
- Bo Xiong
- State Key Laboratory of Synthetic Biology, and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Tianrui Yang
- State Key Laboratory of Synthetic Biology, and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Zixiong Zhang
- State Key Laboratory of Synthetic Biology, and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Xiang Li
- State Key Laboratory of Synthetic Biology, and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Huan Yu
- College of Life and Health Sciences, Northeastern University, Shenyang 110169, China
| | - Lian Wang
- State Key Laboratory of Synthetic Biology, and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Zixuan You
- State Key Laboratory of Synthetic Biology, and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Wenbin Peng
- State Key Laboratory of Synthetic Biology, and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Luyu Jin
- State Key Laboratory of Synthetic Biology, and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Hao Song
- State Key Laboratory of Synthetic Biology, and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; College of Life and Health Sciences, Northeastern University, Shenyang 110169, China.
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Guo B, Yu W, Xu X, Liu Y, Liu Y, Du G, Liu L, Lv X. Adaptively Evolved and Multiplexed Engineered Saccharomyces cerevisiae for Neutralizer-Free Production of l-Lactic Acid. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2025; 73:9009-9018. [PMID: 40191959 DOI: 10.1021/acs.jafc.4c12575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
Abstract
l-Lactic acid is a three-carbon monocarboxylic acid that has extensive applications. However, the bioproduction of l-lactic acid requires the addition of neutralizers, which significantly increases the production costs and can cause environmental pollution. To address this, a Saccharomyces cerevisiae mutant, TMG2, which can tolerate a lactic acid environment (pH 2.60), was obtained through adaptive laboratory evolution. Subsequently, the "push-pull-restrain" strategy was used to improve l-lactic acid production, resulting in a production of 46.8 g/L l-lactic acid. Finally, by overexpressing the transport protein pPfFNT and improving the NADH and acetyl-CoA supply, the l-lactic acid titer of strain TMG27 was improved by 33.8% to 62.6 g/L. Without neutralizers, the l-lactic acid titer reached 76.2 g/L (the fermentation pH was 2.90) with a productivity of 2.1 g/(L h) in a 5-L bioreactor, representing the highest productivity ever reported. Collectively, these results lay the foundation for the environmentally friendly bioproduction of l-lactic acid.
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Affiliation(s)
- Baoyuan Guo
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Yixing Institute of Food Biotechnology Co., Ltd., Yixing 214200, China
| | - Wenwen Yu
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xianhao Xu
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yujie Liu
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Henan Jindan Lactic Acid Technology Co., Ltd., Dancheng 477100, China
| | - Yanfeng Liu
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xueqin Lv
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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Sweetlove LJ, Ratcliffe RG, Fernie AR. Non-canonical plant metabolism. NATURE PLANTS 2025; 11:696-708. [PMID: 40164785 DOI: 10.1038/s41477-025-01965-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2024] [Accepted: 03/01/2025] [Indexed: 04/02/2025]
Abstract
Metabolism is essential for plant growth and has become a major target for crop improvement by enhancing nutrient use efficiency. Metabolic engineering is also the basis for producing high-value plant products such as pharmaceuticals, biofuels and industrial biochemicals. An inherent problem for such engineering endeavours is the tendency to view metabolism as a series of distinct metabolic pathways-glycolysis, the tricarboxylic acid cycle, the Calvin-Benson cycle and so on. While these canonical pathways may represent a dominant or frequently occurring flux mode, systematic analyses of metabolism via computational modelling have emphasized the inherent flexibility of the metabolic network to carry flux distributions that are distinct from the canonical pathways. Recent experimental estimates of metabolic network fluxes using 13C-labelling approaches have revealed numerous instances in which non-canonical pathways occur under different conditions and in different tissues. In this Review, we bring these non-canonical pathways to the fore, summarizing the evidence for their occurrence and the context in which they operate. We also emphasize the importance of non-canonical pathways for metabolic engineering. We argue that the introduction of a high-flux pathway to a desired metabolic product will, by necessity, require non-canonical supporting fluxes in central metabolism to provide the necessary carbon skeletons, energy and reducing power. We illustrate this using the overproduction of isoprenoids and fatty acids as case studies.
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Affiliation(s)
| | | | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
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Chen N, Shen R, He T, Xi J, Zhao R, Du N, Yang Y, Yu L, Yuan Q. A photosynthesis-derived bionic system for sustainable biosynthesis. Angew Chem Int Ed Engl 2025; 64:e202414981. [PMID: 39805801 DOI: 10.1002/anie.202414981] [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: 08/07/2024] [Revised: 12/03/2024] [Accepted: 01/13/2025] [Indexed: 01/16/2025]
Abstract
"Cell factory" strategy based on microbial anabolism pathways offers an intriguing alternative to relieve the dependence on fossil fuels, which are recognized as the main sources of CO2 emission. Typically, anabolism of intracellular substance in cell factory requires the consumption of sufficient reduced nicotinamide adenine dinucleotide /nicotinamide adenine dinucleotide phosphate NAD(P)H and adenosine triphosphate ATP. However, it is of great challenge to modify the natural limited anabolism and to increase the insufficient level of NAD(P)H and ATP to optimum concentrations without causing metabolic disorder. Inspired by the natural photosynthesis process in which NAD(P)H and ATP can both be produced through the coupled electron-proton transfer processes driven by sunlight, herein we designed a light-driven bionic system composed of three modules including photo-induced electron module, electron transfer channel module and proton gradient module. The proposed strategy of light-driven bionic system enables for achieving simultaneous and controllable supplies of NAD(P)H and ATP, thus facilitating both highly efficient CO2 fixation and biomanufacturing. The proposed light-driven bionic system design strategy in this work might pave new sustainable ways for reducing power and energy regeneration to optimize microbial metabolism, offering intriguing alternatives for CO2 emission mitigation and high-value chemical biomanufacturing.
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Affiliation(s)
- Na Chen
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, Wuhan University, Wuhan, 430072, P. R. China
| | - Ruichen Shen
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Tianpei He
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, Wuhan University, Wuhan, 430072, P. R. China
| | - Jing Xi
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, Wuhan University, Wuhan, 430072, P. R. China
| | - Rui Zhao
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, Wuhan University, Wuhan, 430072, P. R. China
| | - Na Du
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, Wuhan University, Wuhan, 430072, P. R. China
| | - Yangbing Yang
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, Wuhan University, Wuhan, 430072, P. R. China
| | - Lilei Yu
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, Wuhan University, Wuhan, 430072, P. R. China
| | - Quan Yuan
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, Wuhan University, Wuhan, 430072, P. R. China
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
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Guo Y, Xiong Z, Zhai H, Wang Y, Qi Q, Hou J. The advances in creating Crabtree-negative Saccharomyces cerevisiae and the application for chemicals biosynthesis. FEMS Yeast Res 2025; 25:foaf014. [PMID: 40121184 PMCID: PMC11974387 DOI: 10.1093/femsyr/foaf014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2024] [Revised: 03/12/2025] [Accepted: 03/21/2025] [Indexed: 03/25/2025] Open
Abstract
Saccharomyces cerevisiae is a promising microbial cell factory. However, the overflow metabolism, known as the Crabtree effect, directs the majority of the carbon source toward ethanol production, in many cases, resulting in low yields of other target chemicals and byproducts accumulation. To construct Crabtree-negative S. cerevisiae, the deletion of pyruvate decarboxylases and/or ethanol dehydrogenases is required. However, these modifications compromises the growth of the strains on glucose. This review discusses the metabolic engineering approaches used to eliminate ethanol production, the efforts to alleviate growth defect of Crabtree-negative strains, and the underlying mechanisms of the growth rescue. In addition, it summarizes the applications of Crabtree-negative S. cerevisiae in the synthesis of various chemicals such as lactic acid, 2,3-butanediol, malic acid, succinic acid, isobutanol, and others.
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Affiliation(s)
- Yalin Guo
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong, 266237, PR China
| | - Zhen Xiong
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong, 266237, PR China
| | - Haotian Zhai
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong, 266237, PR China
| | - Yuqi Wang
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong, 266237, PR China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong, 266237, PR China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong, 266237, PR China
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Guo F, Liu K, Qiao Y, Zheng Y, Liu C, Wu Y, Zhang Z, Jiang W, Jiang Y, Xin F, Jiang M, Zhang W. Evolutionary engineering of Saccharomyces cerevisiae: Crafting a synthetic methylotroph via self-reprogramming. SCIENCE ADVANCES 2024; 10:eadq3484. [PMID: 39705340 DOI: 10.1126/sciadv.adq3484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 11/18/2024] [Indexed: 12/22/2024]
Abstract
Methanol, as a non-edible feedstock, offers a promising sustainable alternative to sugar-based substrates in biochemical production. Despite progress in engineering methanol assimilation in nonmethylotrophs, the full transformation into methanol-dependent synthetic methylotrophs remains a formidable challenge. Here, moving beyond the conventional rational design principle, we engineered a synthetic methylotrophic Saccharomyces cerevisiae through genome rearrangement and adaptive laboratory evolution. This evolutionarily advanced strain unexpectedly shed the heterologous methanol assimilation pathway and demonstrated the robust growth on sole methanol. We discovered that the evolved strain likely realized methanol assimilation through a previously unidentified Adh2-Sfa1-rGly (ASrG) pathway, facilitating the concurrent assimilation of formate and CO2. Furthermore, the incorporation of electron transfer material C3N4 quantum dots obviously enhanced methanol-dependent growth, emphasizing the role of energy availability in the ASrG pathway. This breakthrough introduces a previously unidentified C1 utilization pathway and highlights the exceptional adaptability and self-evolving capacity of the S. cerevisiae metabolic network.
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Affiliation(s)
- Feng Guo
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Kang Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Yangyi Qiao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - YongMin Zheng
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Chenguang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200241, China
| | - Yi Wu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Zhonghai Zhang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200240, China
| | - Wankui Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
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Li B, He J, Zuo K, Xu X, Zou X. Engineering the by-products pathway in Aureobasidium pullulans for highly purified polymalic acid fermentation with concurrent recovery of l-malic acid. BIORESOURCE TECHNOLOGY 2024; 414:131578. [PMID: 39384045 DOI: 10.1016/j.biortech.2024.131578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2024] [Revised: 10/05/2024] [Accepted: 10/05/2024] [Indexed: 10/11/2024]
Abstract
The fermentation of polymalic acid (PMA) by Aureobasidium pullulans, followed by acid hydrolysis to release the monomer l-malic acid (l-MA), has emerged as a promising process for the bio-based production of l-MA. However, the presence of specific by-products significantly affects the quality of the final products. In this study, chassis strains harboring an overexpressed endogenous malate dehydrogenase gene (ApMDH2) were engineered to delete key genes involved in the pullulan, melanin, and liamocin biosynthetic pathways. Furthermore, to enhance PMA synthesis productivity and prevent intracellular NADPH accumulation, an irreversible trans-hydrogenase transformation system was designed to efficiently convert NADPH to NADH. In fed-batch fermentation, the engineered strain produced the highest PMA titer (194.3 ± 1.1 g/L) and l-MA yield (0.89 ± 0.01 g/g) with an increased productivity (1.45 ± 0.06 g/L∙h). Moreover, a total of 86.19 % l-MA, with a purity of 99.7 %, was successfully extracted from fermentation broth.
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Affiliation(s)
- Bingqin Li
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China
| | - Jinzhao He
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China
| | - Kangjia Zuo
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China
| | - Xingran Xu
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China
| | - Xiang Zou
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China.
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Hao H, Yao M, Wang Y, Zhang C, Liu Z, Nielsen J, Shi S, Xiao W, Yuan Y. Extending the G1 phase improves the production of lipophilic compounds in yeast by boosting enzyme expression and increasing cell size. Proc Natl Acad Sci U S A 2024; 121:e2413486121. [PMID: 39536088 PMCID: PMC11588078 DOI: 10.1073/pnas.2413486121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Accepted: 10/12/2024] [Indexed: 11/16/2024] Open
Abstract
Cell phase engineering can significantly impact protein synthesis and cell size, potentially enhancing the production of lipophilic products. This study investigated the impact of G1 phase extension on resource allocation, metabolic functions, and the unfolded protein response (UPR) in yeast, along with the potential for enhancing the production of lipophilic compounds. In brief, the regulation of the G1 phase was achieved by deleting CLN3 (G1 cyclin) in various yeast strains. This modification resulted in a 83% increase in cell volume, a 76.9% increase in dry cell weight, a 82% increase in total protein content, a 41% increase in carotenoid production, and a 159% increase in fatty alcohol production. Transcriptomic analysis revealed significant upregulation of multiple metabolic pathways involved in acetyl-CoA (acetyl coenzyme A) synthesis, ensuring an ample supply of precursors for the synthesis of lipophilic products. Furthermore, we observed improved protein synthesis, attributed to UPR activation during the prolonged G1 phase. These findings not only enhanced our understanding and application of yeast's capacity to synthesize lipophilic compounds in applied biotechnology but also offered unique insights into cellular behavior during the modified G1 phase, particularly regarding the UPR response, for basic research. This study demonstrates the potential of G1 phase intervention to increase the yield of hydrophobic compounds in yeast, providing a promising direction for further research.
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Affiliation(s)
- He Hao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin300072, China
| | - Mingdong Yao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin300072, China
| | - Ying Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin300072, China
| | - Chenglong Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin300072, China
| | - Zihe Liu
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing100029, China
| | - Jens Nielsen
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing100029, China
- Department of Life Sciences, Chalmers University of Technology, GothenburgSE41296, Sweden
- BioInnovation Institute, CopenhagenDK2200, Denmark
| | - Shuobo Shi
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing100029, China
| | - Wenhai Xiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin300072, China
- School of Life Sciences, Faculty of Medicine, Tianjin University, Tianjin300072, China
- Georgia Tech Shenzhen Institute, Tianjin University, Shenzhen518071, China
| | - Yingjin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin300072, China
- Frontier Research Institute for Synthetic Biology, Tianjin University, Tianjin300072, China
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10
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Li G, Liang H, Gao R, Qin L, Xu P, Huang M, Zong MH, Cao Y, Lou WY. Yeast metabolism adaptation for efficient terpenoids synthesis via isopentenol utilization. Nat Commun 2024; 15:9844. [PMID: 39537637 PMCID: PMC11561230 DOI: 10.1038/s41467-024-54298-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 11/06/2024] [Indexed: 11/16/2024] Open
Abstract
Microbial biosynthesis has become the leading commercial approach for large-scale production of terpenoids, a valuable class of natural products. Enhancing terpenoid production, however, requires complex modifications on the host organism. Recently, a two-step isopentenol utilization (IU) pathway relying solely on ATP as the cofactor has been proposed as an alternative to the mevalonate (MVA) pathway, streamlining the synthesis of the common terpenoid precursors. Herein, we find that isopentenol inhibits energy metabolism, leading to reduced efficiency of the IU pathway in Saccharomyces cerevisiae. To overcome this, we engineer an IU pathway-dependent (IUPD) strain, designed for growth-coupled production. The IUPD strain is compelled to enhance the ATP supply, essential for the IU pathway, and incorporates a high-throughput screening method for enzyme evolution. The refined IU pathway surpasses the MVA pathway in synthesizing complex terpenoids. Our work offers valuable insights into developing growth-coupled strains adapted to efficient natural product synthesis.
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Affiliation(s)
- Guangjian Li
- Lab of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou, Guangdong, China
| | - Hui Liang
- Lab of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou, Guangdong, China
| | - Ruichen Gao
- Lab of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou, Guangdong, China
| | - Ling Qin
- Lab of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou, Guangdong, China
| | - Pei Xu
- Lab of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou, Guangdong, China
| | - Mingtao Huang
- Lab of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou, Guangdong, China
| | - Min-Hua Zong
- Lab of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou, Guangdong, China
| | - Yufei Cao
- Lab of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou, Guangdong, China.
- Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, No. 381 Wushan Road, Guangzhou, Guangdong, China.
| | - Wen-Yong Lou
- Lab of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou, Guangdong, China.
- Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, No. 381 Wushan Road, Guangzhou, Guangdong, China.
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11
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Chen Q, Chen Y, Hou Z, Ma Y, Huang J, Zhang Z, Chen Y, Yang X, Zhang Y, Zhao G. Unlocking the formate utilization of wild-type Yarrowia lipolytica through adaptive laboratory evolution. Biotechnol J 2024; 19:e2400290. [PMID: 38900053 DOI: 10.1002/biot.202400290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024]
Abstract
Synthetic biology is contributing to the advancement of the global net-negative carbon economy, with emphasis on formate as a member of the one-carbon substrate garnering substantial attention. In this study, we employed base editing tools to facilitate adaptive evolution, achieving a formate tolerance of Yarrowia lipolytica to 1 M within 2 months. This effort resulted in two mutant strains, designated as M25-70 and M25-14, both exhibiting significantly enhanced formate utilization capabilities. Transcriptomic analysis revealed the upregulation of nine endogenous genes encoding formate dehydrogenases when cultivated utilizing formate as the sole carbon source. Furthermore, we uncovered the pivotal role of the glyoxylate and threonine-based serine pathway in enhancing glycine supply to promote formate assimilation. The full potential of Y. lipolytica to tolerate and utilize formate establishing the foundation for pyruvate carboxylase-based carbon sequestration pathways. Importantly, this study highlights the existence of a natural formate metabolic pathway in Y. lipolytica.
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Affiliation(s)
- Qian Chen
- Tianjin University of Science & Technology, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Haihe Laboratory of Synthetic Biology, Tianjin, China
| | - Yunhong Chen
- Tianjin University of Science & Technology, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Haihe Laboratory of Synthetic Biology, Tianjin, China
| | - Zeming Hou
- Tianjin University of Science & Technology, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Haihe Laboratory of Synthetic Biology, Tianjin, China
| | - Yuyue Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Jianfeng Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Zhidan Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yefu Chen
- Tianjin University of Science & Technology, Tianjin, China
| | - Xue Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Yanfei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Guoping Zhao
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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12
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Pan X, Heacock ML, Abdulaziz EN, Violante S, Zuckerman AL, Shrestha N, Yao C, Goodman RP, Cross JR, Cracan V. A genetically encoded tool to increase cellular NADH/NAD + ratio in living cells. Nat Chem Biol 2024; 20:594-604. [PMID: 37884806 PMCID: PMC11045668 DOI: 10.1038/s41589-023-01460-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 09/25/2023] [Indexed: 10/28/2023]
Abstract
Impaired redox metabolism is a key contributor to the etiology of many diseases, including primary mitochondrial disorders, cancer, neurodegeneration and aging. However, mechanistic studies of redox imbalance remain challenging due to limited strategies that can perturb redox metabolism in various cellular or organismal backgrounds. Most studies involving impaired redox metabolism have focused on oxidative stress; consequently, less is known about the settings where there is an overabundance of NADH reducing equivalents, termed reductive stress. Here we introduce a soluble transhydrogenase from Escherichia coli (EcSTH) as a novel genetically encoded tool to promote reductive stress in living cells. When expressed in mammalian cells, EcSTH, and a mitochondrially targeted version (mitoEcSTH), robustly elevated the NADH/NAD+ ratio in a compartment-specific manner. Using this tool, we determined that metabolic and transcriptomic signatures of the NADH reductive stress are cellular background specific. Collectively, our novel genetically encoded tool represents an orthogonal strategy to promote reductive stress.
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Affiliation(s)
- Xingxiu Pan
- Laboratory of Redox Biology and Metabolism, Scintillon Institute, San Diego, CA, USA
| | - Mina L Heacock
- Laboratory of Redox Biology and Metabolism, Scintillon Institute, San Diego, CA, USA
- Calibr, The Scripps Research Institute, La Jolla, CA, USA
| | - Evana N Abdulaziz
- Laboratory of Redox Biology and Metabolism, Scintillon Institute, San Diego, CA, USA
- Process Development Associate, Amgen, Thousand Oaks, CA, USA
| | - Sara Violante
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Austin L Zuckerman
- Laboratory of Redox Biology and Metabolism, Scintillon Institute, San Diego, CA, USA
- Program in Mathematics and Science Education, University of California San Diego, San Diego, CA, USA
- Program in Mathematics and Science Education, San Diego State University, San Diego, USA
| | - Nirajan Shrestha
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Canglin Yao
- Laboratory of Redox Biology and Metabolism, Scintillon Institute, San Diego, CA, USA
| | - Russell P Goodman
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Justin R Cross
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Valentin Cracan
- Laboratory of Redox Biology and Metabolism, Scintillon Institute, San Diego, CA, USA.
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
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13
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Murphy AC, McReynolds MR. Toying with reductive stress. Nat Chem Biol 2024; 20:542-543. [PMID: 37884808 DOI: 10.1038/s41589-023-01461-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Affiliation(s)
- Alexandria C Murphy
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Melanie R McReynolds
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
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14
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Ma X, Sun C, Xian M, Guo J, Zhang R. Progress in research on the biosynthesis of 1,2,4-butanetriol by engineered microbes. World J Microbiol Biotechnol 2024; 40:68. [PMID: 38200399 DOI: 10.1007/s11274-024-03885-4] [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: 11/25/2023] [Accepted: 01/05/2024] [Indexed: 01/12/2024]
Abstract
1,2,4-butanetriol (BT) is a polyol with unique chemical properties, which has a stereocenter and can be divided into D-BT (the S-enantiomer) and L-BT (the R-enantiomer). BT can be used for the synthesis of 1,2,4-butanetriol trinitrate, 3-hydroxytetrahydrofuran, polyurethane, and other chemicals. It is widely used in the military industry, medicine, tobacco, polymer. At present, the BT is mainly synthesized by chemical methods, which are accompanied by harsh reaction conditions, poor selectivity, many by-products, and environmental pollution. Therefore, BT biosynthesis methods with the advantages of mild reaction conditions and green sustainability have become a current research hotspot. In this paper, the research status of microbial synthesis of BT was summarized from the following three aspects: (1) the biosynthetic pathway establishment for BT from xylose; (2) metabolic engineering strategies employed for improving BT production from xylose; (3) other substrates for BT production. Finally, the challenges and prospects of biosynthetic BT were discussed for future methods to improve competitiveness for industrial production.
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Affiliation(s)
- Xiangyu Ma
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Sun
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Mo Xian
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Jing Guo
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Shandong Energy Institute, Qingdao, 266101, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China.
| | - Rubing Zhang
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Shandong Energy Institute, Qingdao, 266101, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China.
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15
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Yang X, Zhang Y, Zhao G. Artificial carbon assimilation: From unnatural reactions and pathways to synthetic autotrophic systems. Biotechnol Adv 2024; 70:108294. [PMID: 38013126 DOI: 10.1016/j.biotechadv.2023.108294] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/26/2023] [Accepted: 11/18/2023] [Indexed: 11/29/2023]
Abstract
Synthetic biology is being increasingly used to establish novel carbon assimilation pathways and artificial autotrophic strains that can be used in low-carbon biomanufacturing. Currently, artificial pathway design has made significant progress from advocacy to practice within a relatively short span of just over ten years. However, there is still huge scope for exploration of pathway diversity, operational efficiency, and host suitability. The accelerated research process will bring greater opportunities and challenges. In this paper, we provide a comprehensive summary and interpretation of representative one-carbon assimilation pathway designs and artificial autotrophic strain construction work. In addition, we propose some feasible design solutions based on existing research results and patterns to promote the development and application of artificial autotrophy.
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Affiliation(s)
- Xue Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China; Haihe Laboratory of Synthetic Biology, Tianjin 300308, China
| | - Yanfei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.
| | - Guoping Zhao
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China; CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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16
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Wang L, Luo H, Yao B, Yao J, Zhang J. Optimizing Hexose Utilization Pathways of Cupriavidus necator for Improving Growth and L-Alanine Production under Heterotrophic and Autotrophic Conditions. Int J Mol Sci 2023; 25:548. [PMID: 38203719 PMCID: PMC10778655 DOI: 10.3390/ijms25010548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Cupriavidus necator is a versatile microbial chassis to produce high-value products. Blocking the poly-β-hydroxybutyrate synthesis pathway (encoded by the phaC1AB1 operon) can effectively enhance the production of C. necator, but usually decreases cell density in the stationary phase. To address this problem, we modified the hexose utilization pathways of C. necator in this study by implementing strategies such as blocking the Entner-Doudoroff pathway, completing the phosphopentose pathway by expressing the gnd gene (encoding 6-phosphogluconate dehydrogenase), and completing the Embden-Meyerhof-Parnas pathway by expressing the pfkA gene (encoding 6-phosphofructokinase). During heterotrophic fermentation, the OD600 of the phaC1AB1-knockout strain increased by 44.8% with pfkA gene expression alone, and by 93.1% with gnd and pfkA genes expressing simultaneously. During autotrophic fermentation, gnd and pfkA genes raised the OD600 of phaC1AB1-knockout strains by 19.4% and 12.0%, respectively. To explore the effect of the pfkA gene on the production of C. necator, an alanine-producing C. necator was constructed by expressing the NADPH-dependent L-alanine dehydrogenase, alanine exporter, and knocking out the phaC1AB1 operon. The alanine-producing strain had maximum alanine titer and yield of 784 mg/L and 11.0%, respectively. And these values were significantly improved to 998 mg/L and 13.4% by expressing the pfkA gene. The results indicate that completing the Embden-Meyerhof-Parnas pathway by expressing the pfkA gene is an effective method to improve the growth and production of C. necator.
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Affiliation(s)
- Lei Wang
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (L.W.); (B.Y.)
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Bin Yao
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (L.W.); (B.Y.)
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (L.W.); (B.Y.)
| | - Jie Zhang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
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17
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Vásquez Castro E, Memari G, Ata Ö, Mattanovich D. Carbon efficient production of chemicals with yeasts. Yeast 2023; 40:583-593. [PMID: 37997485 PMCID: PMC10946752 DOI: 10.1002/yea.3909] [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: 07/04/2023] [Revised: 10/16/2023] [Accepted: 10/29/2023] [Indexed: 11/25/2023] Open
Abstract
Microbial metabolism offers a wide variety of opportunities to produce chemicals from renewable resources. Employing such processes of industrial biotechnology provides valuable means to fight climate change by replacing fossil feedstocks by renewable substrate to reduce or even revert carbon emission. Several yeast species are well suited chassis organisms for this purpose, illustrated by the fact that the still largest microbial production of a chemical, namely bioethanol is based on yeast. Although production of ethanol and some other chemicals is highly efficient, this is not the case for many desired bulk chemicals. One reason for low efficiency is carbon loss, which decreases the product yield and increases the share of total production costs that is taken by substrate costs. Here we discuss the causes for carbon loss in metabolic processes, approaches to avoid carbon loss, as well as opportunities to incorporate carbon from CO2 , based on the electron balance of pathways. These aspects of carbon efficiency are illustrated for the production of succinic acid from a diversity of substrates using different pathways.
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Affiliation(s)
- Evelyn Vásquez Castro
- Austrian Centre of Industrial Biotechnology (ACIB)ViennaAustria
- University of Natural Resources and Life Sciences, Department of BiotechnologyInstitute of Microbiology and Microbial BiotechnologyViennaAustria
| | - Golnaz Memari
- Austrian Centre of Industrial Biotechnology (ACIB)ViennaAustria
- University of Natural Resources and Life Sciences, Department of BiotechnologyInstitute of Microbiology and Microbial BiotechnologyViennaAustria
| | - Özge Ata
- Austrian Centre of Industrial Biotechnology (ACIB)ViennaAustria
- University of Natural Resources and Life Sciences, Department of BiotechnologyInstitute of Microbiology and Microbial BiotechnologyViennaAustria
| | - Diethard Mattanovich
- Austrian Centre of Industrial Biotechnology (ACIB)ViennaAustria
- University of Natural Resources and Life Sciences, Department of BiotechnologyInstitute of Microbiology and Microbial BiotechnologyViennaAustria
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18
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Kulakowski S, Banerjee D, Scown CD, Mukhopadhyay A. Improving microbial bioproduction under low-oxygen conditions. Curr Opin Biotechnol 2023; 84:103016. [PMID: 37924688 DOI: 10.1016/j.copbio.2023.103016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/17/2023] [Accepted: 10/07/2023] [Indexed: 11/06/2023]
Abstract
Microbial bioconversion provides access to a wide range of sustainably produced chemicals and commodities. However, industrial-scale bioproduction process operations are preferred to be anaerobic due to the cost associated with oxygen transfer. Anaerobic bioconversion generally offers limited substrate utilization profiles, lower product yields, and reduced final product diversity compared with aerobic processes. Bioproduction under conditions of reduced oxygen can overcome the limitations of fully aerobic and anaerobic bioprocesses, but many microbial hosts are not developed for low-oxygen bioproduction. Here, we describe advances in microbial strain engineering involving the use of redox cofactor engineering, genome-scale metabolic modeling, and functional genomics to enable improved bioproduction processes under low oxygen and provide a viable path for scaling these bioproduction systems to industrial scales.
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Affiliation(s)
- Shawn Kulakowski
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Deepanwita Banerjee
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Corinne D Scown
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Energy Analysis and Environmental Impacts Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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19
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Yan Q, Han L, Liu Z, Zhou S, Zhou Z. Stepwise genetic modification for efficient expression of heterologous proteins in Aspergillus nidulans. Appl Microbiol Biotechnol 2023; 107:6923-6935. [PMID: 37698610 DOI: 10.1007/s00253-023-12755-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 08/09/2023] [Accepted: 08/26/2023] [Indexed: 09/13/2023]
Abstract
Filamentous fungi are widely used in food fermentation and therapeutic protein production due to their prominent protein secretion and post-translational modification system. Aspergillus nidulans is an important model strain of filamentous fungi, but not a fully developed cell factory for heterologous protein expression. One of the limitations is its relatively low capacity of protein secretion. To alleviate this limitation, in this study, the protein secretory pathway and mycelium morphology were stepwise modified. With eGFP as a reporter protein, protein secretion was significantly enhanced through reducing the degradation of heterologous proteins by endoplasmic reticulum-associated protein degradation (ERAD) and vacuoles in the secretory pathway. Elimination of mycelial aggregation resulted in a 1.5-fold and 1.3-fold increase in secretory expression of eGFP in typical constitutive and inducible expression systems, respectively. Combined with these modifications, high secretory expression of human interleukin-6 (HuIL-6) was achieved. Consequently, a higher yield of secretory HuIL-6 was realized by further disruption of extracellular proteases. Overall, a superior chassis cell of A. nidulans suitable for efficient secretory expression of heterologous proteins was successfully obtained, providing a promising platform for biosynthesis using filamentous fungi as hosts. KEY POINTS: • Elimination of mycelial aggregation and decreasing the degradation of heterologous protein are effective strategies for improving the heterologous protein expression. • The work provides a high-performance chassis host △agsB-derA for heterologous protein secretory expression. • Human interleukin-6 (HuIL-6) was expressed efficiently in the high-performance chassis host △agsB-derA.
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Affiliation(s)
- Qin Yan
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Laichuang Han
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Zhongmei Liu
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Shengmin Zhou
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai, China.
| | - Zhemin Zhou
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, 214122, China.
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20
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Qiao S, Bai F, Cai P, Zhou YJ, Yao L. An improved CRISPRi system in Pichia pastoris. Synth Syst Biotechnol 2023; 8:479-485. [PMID: 37692202 PMCID: PMC10485788 DOI: 10.1016/j.synbio.2023.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/09/2023] [Accepted: 06/25/2023] [Indexed: 09/12/2023] Open
Abstract
CRISPR interference (CRISPRi) has been developed and widely used for gene repression in various hosts. Here we report an improved CRISPRi system in Pichia pastoris by fusing dCas9 with endogenous transcriptional repressor domains. The CRISPRi system shows strong repression of eGFP, with the highest efficiency of 85%. Repression of native genes is demonstrated by targeting AOX1 promoter. AOX1 is efficiently repressed and the mutant strains show much slower growth in methanol medium. Effects of gRNA expression and processing on CRISPRi efficiency is also investigated. It is found that gRNA processing by HH/HDV ribozymes or Csy4 endoribonuclease generating clean gRNA is critical to achieve strong repression, and Csy4 cleavage shows higher repression efficiency. However, gRNA expression using native tRNA transcription and processing systems results in relatively weaker repression of eGFP. By expression of two gRNAs targeting promoters of eGFP and AOX1 in an array together with Cys4 recognition sites, both genes can be repressed simultaneously. Cys4-mediated gRNA array processing is further applied to repress fatty acyl-CoA synthetase genes (FAA1 and FAA2). Both genes are efficiently repressed, demonstrating that Cys4 endoribonuclease has the ability to cleave gRNAs array and can be can be used for multiplexed gene repression in P. pastoris.
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Affiliation(s)
- Shujing Qiao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fan Bai
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Peng Cai
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Yongjin J. Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, PR China
| | - Lun Yao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, PR China
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21
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Ma W, Li X, Zhang F, Zhang ZY, Yang WQ, Huang PW, Gu Y, Sun XM. Enhancing the biomass and docosahexaenoic acid-rich lipid accumulation of Schizochytrium sp. in propionate wastewater. Biotechnol J 2023; 18:e2300052. [PMID: 37128672 DOI: 10.1002/biot.202300052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/15/2023] [Accepted: 04/26/2023] [Indexed: 05/03/2023]
Abstract
In order to find a more effective way to obtain docosahexaenoic acid (DHA) rich lipid from Schizochytrium sp., a widespread propionate wastewater (PW) is used. PW is a common industrial and domestic wastewater, and transforming it into valuable products is a potential treatment method. Schizochytrium sp. is a rapidly growing oleaginous organism, which has been used commercially for DHA production. Herein, PW is completely used for DHA production by Schizochytrium sp. by genetic engineering and fermentation optimization, which can alleviate the increasingly tense demand for water resources and environmental pollution caused by industrial wastewater. Firstly, the methylmalonyl-CoA mutase (MCM) was overexpressed in Schizochytrium sp. to enhance the metabolism of propionate, then the engineered strain of overexpressed MCM (OMCM) can effectively use propionate. Then, the effects of PW with different concentration of propionate were investigated, and results showed that OMCM can completely replace clean water with PW containing 5 g L-1 propionate. Furthermore, in the fed-batch fermentation, the OMCM obtained the highest biomass of 113.4 g L-1 and lipid yield of 64.4 g L-1 in PW condition, which is 26.8% and 51.7% higher than that of wild type (WT) in PW condition. Moreover, to verify why overexpression of MCM can promote DHA and lipid accumulation, the comparative metabolomics, ATP production level, the antioxidant system, and the transcription of key genes were investigated. Results showed that ATP induced by PW condition could drive the synthesis of DHA, and remarkably improve the antioxidant capacity of cells by enhancing the carotenoids production. Therefore, PW can be used as an effective and economical substrate and water source for Schizochytrium sp. to accumulate biomass and DHA.
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Affiliation(s)
- Wang Ma
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Qixia District, Nanjing, China
- College of Life Sciences, Nanjing Normal University, Qixia District, Nanjing, China
| | - Xin Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Qixia District, Nanjing, China
| | - Feng Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Qixia District, Nanjing, China
| | - Zi-Yi Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Qixia District, Nanjing, China
| | - Wen-Qian Yang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Qixia District, Nanjing, China
| | - Peng-Wei Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Qixia District, Nanjing, China
- College of Life Sciences, Nanjing Normal University, Qixia District, Nanjing, China
| | - Yang Gu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Qixia District, Nanjing, China
| | - Xiao-Man Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Qixia District, Nanjing, China
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22
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Guo F, Qiao Y, Xin F, Zhang W, Jiang M. Bioconversion of C1 feedstocks for chemical production using Pichia pastoris. Trends Biotechnol 2023; 41:1066-1079. [PMID: 36967258 DOI: 10.1016/j.tibtech.2023.03.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/14/2023] [Accepted: 03/06/2023] [Indexed: 04/03/2023]
Abstract
Bioconversion of C1 feedstocks for chemical production offers a promising solution to global challenges such as the energy and food crises and climate change. The methylotroph Pichia pastoris is an attractive host system for the production of both recombinant proteins and chemicals from methanol. Recent studies have also demonstrated its potential for utilizing CO2 through metabolic engineering or coupling with electrocatalysis. This review focuses on the bioconversion of C1 feedstocks for chemical production using P. pastoris. Herein the challenges and feasible strategies for chemical production in P. pastoris are discussed. The potential of P. pastoris to utilize other C1 feedstocks - including CO2 and formate - is highlighted, and new insights from the perspectives of synthetic biology and material science are proposed.
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Affiliation(s)
- Feng Guo
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P.R. China
| | - Yangyi Qiao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P.R. China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P.R. China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, P.R. China.
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P.R. China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, P.R. China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P.R. China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, P.R. China
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23
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Cool L, Hanon S, Verstrepen KJ. Metabolism: How a eukaryote adapted to life without respiration. Curr Biol 2023; 33:R444-R447. [PMID: 37279666 DOI: 10.1016/j.cub.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A new study finds that Schizosaccharomyces japonicus, a eukaryote that lost the ability to respire, modified its central carbon metabolism to maintain efficient ATP production, cofactor regeneration, and amino-acid production. This remarkable metabolic flexibility opens new avenues towards applications.
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Affiliation(s)
- Lloyd Cool
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium; CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Samuel Hanon
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium; CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Kevin J Verstrepen
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium; CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium.
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24
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Shang Y, Zhang P, Wei W, Li J, Ye BC. Metabolic engineering for the high-yield production of polydatin in Yarrowia lipolytica. BIORESOURCE TECHNOLOGY 2023; 381:129129. [PMID: 37146696 DOI: 10.1016/j.biortech.2023.129129] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/27/2023] [Accepted: 05/01/2023] [Indexed: 05/07/2023]
Abstract
Polydatin, a glycosylated derivative of resveratrol, has better structural stability and biological activity than resveratrol. Polydatin is the extract of Polygonum cuspidatum, which has various pharmacological effects. Owing to its Crabtree-negative characteristics and high supply of malonyl-CoA, Yarrowia lipolytica was selected to produce polydatin. Initially, the resveratrol synthetic pathway was established in Y. lipolytica. By enhancing the shikimate pathway flow, redirecting carbon metabolism, and increasing the copies of key genes, a resveratrol yield of 487.77 mg/L was obtained. In addition, by blocking the degradation of polydatin, its accumulation was successfully achieved. Finally, by optimizing the glucose concentration and supplementing with two nutritional marker genes, a high polydatin yield of 6.88 g/L was obtained in Y. lipolytica, which is the highest titer of polydatin produced in a microbial host to date. Overall, this study demonstrates that Y. lipolytica has great potential for glycoside synthesis.
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Affiliation(s)
- Yanzhe Shang
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ping Zhang
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wenping Wei
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Jin Li
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
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25
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Kim GB, Choi SY, Cho IJ, Ahn DH, Lee SY. Metabolic engineering for sustainability and health. Trends Biotechnol 2023; 41:425-451. [PMID: 36635195 DOI: 10.1016/j.tibtech.2022.12.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/17/2022] [Accepted: 12/21/2022] [Indexed: 01/12/2023]
Abstract
Bio-based production of chemicals and materials has attracted much attention due to the urgent need to establish sustainability and enhance human health. Metabolic engineering (ME) allows purposeful modification of cellular metabolic, regulatory, and signaling networks to achieve enhanced production of desired chemicals and degradation of environmentally harmful chemicals. ME has significantly progressed over the past 30 years through further integration of the strategies of synthetic biology, systems biology, evolutionary engineering, and data science aided by artificial intelligence. Here we review the field of ME from its emergence to the current state-of-the-art, highlighting its contribution to sustainable production of chemicals, health, and the environment through representative examples. Future challenges of ME and perspectives are also discussed.
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Affiliation(s)
- Gi Bae Kim
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - So Young Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - In Jin Cho
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Da-Hee Ahn
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
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26
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Affiliation(s)
- Steffen N Lindner
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Markus Ralser
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany.
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