1
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Sha Y, Ge M, Lu M, Xu Z, Zhai R, Jin M. Advances in metabolic engineering for enhanced acetyl-CoA availability in yeast. Crit Rev Biotechnol 2025; 45:904-922. [PMID: 39266266 DOI: 10.1080/07388551.2024.2399542] [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: 06/23/2024] [Revised: 07/21/2024] [Accepted: 08/21/2024] [Indexed: 09/14/2024]
Abstract
Acetyl-CoA is an intermediate metabolite in cellular central metabolism. It's a precursor for various valuable commercial products, including: terpenoids, fatty acids, and polyketides. With the advancement of metabolic and synthetic biology tools, microbial cell factories have been constructed for the efficient synthesis of acetyl-CoA and derivatives, with the Saccharomyces cerevisiae and Yarrowia lipolytica as two prominent chassis. This review summarized the recent developments in the biosynthetic pathways and metabolic engineering approaches for acetyl-CoA and its derivatives synthesis in these two yeasts. First, the metabolic routes involved in the biosynthesis of acetyl-CoA and derived products were outlined. Then, the advancements in metabolic engineering strategies for channeling acetyl-CoA toward the desired products were summarized, with particular emphasis on: enhancing metabolic flux in different organelles, refining precursor CoA synthesis, optimizing substrate utilization, and modifying protein acetylation level. Finally, future developments in advancing the metabolic engineering strategies for acetyl-CoA and related derivatives synthesis, including: reducing CO2 emissions, dynamically regulating metabolic pathways, and exploring the regulatory functions between acetyl-CoA levels and protein acetylation, are highlighted. This review provided new insights into regulating acetyl-CoA synthesis to create more effective microbial cell factories for bio-manufacturing.
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Affiliation(s)
- Yuanyuan Sha
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
- Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing, China
| | - Mianshen Ge
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
- Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing, China
| | - Minrui Lu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
- Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing, China
| | - Zhaoxian Xu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
- Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing, China
| | - Rui Zhai
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
- Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing, China
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
- Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing, China
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2
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Won JY, Lee HJ, Yoon EB, Chin YW, Kim SK. Compartmentalization of heme biosynthetic pathways into yeast mitochondria enhances heme production. NPJ Sci Food 2025; 9:83. [PMID: 40404692 PMCID: PMC12098746 DOI: 10.1038/s41538-025-00453-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2024] [Accepted: 05/12/2025] [Indexed: 05/24/2025] Open
Abstract
Saccharomyces cerevisiae is a generally recognized as safe (GRAS) workhorse strain widely used in the food industry for the cost-effective production of food ingredients. However, the heme production yield in yeast is significantly lower than in bacteria for two main reasons: (1) the heme biosynthetic pathway is bifurcated into the cytosol and mitochondria, and (2) yeast's heme biosynthetic protoporphyrin-dependent (PPD) pathway is thermodynamically unfavorable compared with bacteria's coproporphyrin-dependent (CPD) pathway. To overcome these limitations, the PPD and CPD pathways were compartmentalized into the mitochondria by attaching mitochondria-targeting sequences (MTSs) to the N-terminus of the enzymes. All the enzyme activities required for the CPD pathway are present in S. cerevisiae, except for copro-heme decarboxylase (HemQ); therefore, bacterial HemQ with the N-terminal MTS was introduced to complete the CPD pathway. The resulting S. cerevisiae H4+MTS9HemQCg strain with mitochondrial PPD and CPD pathways showed 65% higher heme concentration than the engineered strain with only the mitochondrial PPD pathway. Furthermore, the functional expression level of HemQ from Corynebacterium glutamicum was significantly enhanced in vitro and in vivo by the co-expression of Group-I HSP60 chaperonins (GroEL and GroES) derived from Escherichia coli. The engineered S. cerevisiae H4+MTS9HemQCg+GroELS strain containing the mitochondrial PPD and CPD pathways and the Group-I HSP60 chaperonins produced the highest heme concentration (4.6 mg/L), which was 17% higher than that produced by the H4+MTS9HemQCg strain.
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Affiliation(s)
- Jae Yoon Won
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi, Republic of Korea
- GreenTech-based Food Safety Research Group, BK21 Four, Chung-Ang University, Anseong, Gyeonggi, Republic of Korea
| | - Hyun-Jae Lee
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi, Republic of Korea
- GreenTech-based Food Safety Research Group, BK21 Four, Chung-Ang University, Anseong, Gyeonggi, Republic of Korea
| | - Eun Bi Yoon
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi, Republic of Korea
- GreenTech-based Food Safety Research Group, BK21 Four, Chung-Ang University, Anseong, Gyeonggi, Republic of Korea
| | - Young-Wook Chin
- Research Group of Traditional Food, Korea Food Research Institute, Wanju, Republic of Korea.
| | - Sun-Ki Kim
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi, Republic of Korea.
- GreenTech-based Food Safety Research Group, BK21 Four, Chung-Ang University, Anseong, Gyeonggi, Republic of Korea.
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3
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Su C, Wang Z, Zhang G, Wang T, Su Y, Liu Y, Wang R, Li P, Wang J, Wang T, Su J. Engineering Compartmentalization and Cofactor Regulation for 10-Hydroxy-2-decenoic Acid Biosynthesis in Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2025; 73:12364-12373. [PMID: 40354551 DOI: 10.1021/acs.jafc.5c02058] [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: 05/14/2025]
Abstract
10-Hydroxy-2-decenoic acid (10-HDA), a bioactive component of royal jelly, exhibits significant pharmacological value in various applications. To date, its biosynthesis has been reported exclusively in endotoxin-prone Escherichia coli, which limits its biomedical utility. In this study, we successfully engineered the Generally Recognized As Safe (GRAS) yeast Saccharomyces cerevisiae as a biosynthetic platform for producing 10-HDA, thereby addressing the limitations associated with E. coli systems. By rewiring the β-oxidation pathway, combining compartmentalization with chaperone-assisted P450 folding in mitochondria, and enhancing NADPH supply, a yield of 40.50 mg/L of 10-HDA was achieved using 100 mg/L decanoic acid as the substrate. Finally, to mitigate substrate toxicity, fed-batch fermentation using ethyl decanoate increased production 7.5-fold, reaching 298.6 mg/L, which is the highest titer reported in yeast to date. This GRAS-compliant platform not only facilitates the safe and efficient production of 10-HDA but also establishes a novel paradigm for the functional expression of prokaryotic P450 enzymes in yeast.
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Affiliation(s)
- ChunLi Su
- State Key Laboratory of Green Papermaking and Resource Recycling, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - ZhaoYun Wang
- State Key Laboratory of Green Papermaking and Resource Recycling, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - GuoBin Zhang
- State Key Laboratory of Green Papermaking and Resource Recycling, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - TaiChang Wang
- State Key Laboratory of Green Papermaking and Resource Recycling, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - YuMing Su
- State Key Laboratory of Green Papermaking and Resource Recycling, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - YiHan Liu
- State Key Laboratory of Green Papermaking and Resource Recycling, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - RuiMing Wang
- State Key Laboratory of Green Papermaking and Resource Recycling, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - PiWu Li
- State Key Laboratory of Green Papermaking and Resource Recycling, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - JunQing Wang
- State Key Laboratory of Green Papermaking and Resource Recycling, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - Ting Wang
- State Key Laboratory of Green Papermaking and Resource Recycling, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - Jing Su
- State Key Laboratory of Green Papermaking and Resource Recycling, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
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4
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Tran PHN, Lee TS. Harnessing organelle engineering to facilitate biofuels and biochemicals production in yeast. J Microbiol 2025; 63:e2501006. [PMID: 40195834 DOI: 10.71150/jm.2501006] [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: 01/06/2025] [Accepted: 02/13/2025] [Indexed: 04/09/2025]
Abstract
Microbial biosynthesis using yeast species offers numerous advantages to produce industrially relevant biofuels and biochemicals. Conventional metabolic engineering approaches in yeast focus on biosynthetic pathways in the cytoplasm, but these approaches are disturbed by various undesired factors including metabolic crosstalk, competing pathways and insufficient precursors. Given that eukaryotic cells contain subcellular organelles with distinct physicochemical properties, an emerging strategy to overcome cytosolic pathway engineering bottlenecks is through repurposing these organelles as specialized microbial cell factories for enhanced production of valuable chemicals. Here, we review recent progress and significant outcomes of harnessing organelle engineering for biofuels and biochemicals production in both conventional and non-conventional yeasts. We highlight key engineering strategies for the compartmentalization of biosynthetic pathways within specific organelles such as mitochondria, peroxisomes, and endoplasmic reticulum; involved in engineering of signal peptide, cofactor and energy enhancement, organelle biogenesis and dual subcellular engineering. Finally, we discuss the potential and challenges of organelle engineering for future studies and propose an automated pipeline to fully exploit this approach.
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Affiliation(s)
- Phuong Hoang Nguyen Tran
- Joint BioEnergy Institute, Emeryville 94608, CA, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley 94720, CA, USA
| | - Taek Soon Lee
- Joint BioEnergy Institute, Emeryville 94608, CA, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley 94720, CA, USA
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5
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Ge W, Pai H, Zhang J, Zhang C, Lu W. Construction of isopentenol utilization pathway and artificial multifunctional enzyme for miltiradiene synthesis in Saccharomyces cerevisiae. BIORESOURCE TECHNOLOGY 2025; 419:132065. [PMID: 39809383 DOI: 10.1016/j.biortech.2025.132065] [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: 06/27/2024] [Revised: 11/26/2024] [Accepted: 01/10/2025] [Indexed: 01/16/2025]
Abstract
Miltiradiene serves as a pivotal precursor for the synthesis of numerous abietane-type diterpenes with important pharmacological activities. The endogenous mevalonate (MVA) pathway is tightly regulated in Saccharomyces cerevisiae, which limits the availability of precursors for the heterologous production of miltiradiene. In this study, the orthogonal isopentenol utilization pathway (IUP) was constructed and investigated for its adaptability with mitochondria and peroxisomes in S. cerevisiae for the synthesis of miltiradiene. Compartments combinatorial engineering was used to enhance precursor supply and miltiradiene synthesis, thereby elevating the production of miltiradiene to 146.1 mg/L in S. cerevisiae. Furthermore, an artificial multifunctional enzyme, tSmCPS-tSmKSL-PvPT, was constructed by mimicking the natural multifunctional enzyme to enhance the biosynthesis of miltiradiene in S. cerevisiae strain PCM-MT1, which is capable of producing 414.4 mg/L miltiradiene. Finally, the titer of miltiradiene was increased to 1.02 g/L by fed-batch fermentation in a 5 L bioreactor. This study broadens the application of the IUP in S. cerevisiae by integrating compartmentalization and artificial multifunctional enzymes for the synthesis of diterpenes.
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Affiliation(s)
- Weiwei Ge
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China
| | - Huihui Pai
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China
| | - Jiale Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China
| | - Chuanbo Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China; Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, PR China; Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, PR China.
| | - Wenyu Lu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China; Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, PR China; Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, PR China.
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6
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Yu W, Jin K, Xu X, Liu Y, Li J, Du G, Chen J, Lv X, Liu L. Engineering microbial cell factories by multiplexed spatiotemporal control of cellular metabolism: Advances, challenges, and future perspectives. Biotechnol Adv 2025; 79:108497. [PMID: 39645209 DOI: 10.1016/j.biotechadv.2024.108497] [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: 09/25/2024] [Revised: 12/01/2024] [Accepted: 12/02/2024] [Indexed: 12/09/2024]
Abstract
Generally, the metabolism in microbial organism is an intricate, spatiotemporal process that emerges from gene regulatory networks, which affects the efficiency of product biosynthesis. With the coming age of synthetic biology, spatiotemporal control systems have been explored as versatile strategies to promote product biosynthesis at both spatial and temporal levels. Meanwhile, the designer synthetic compartments provide new and promising approaches to engineerable spatiotemporal control systems to construct high-performance microbial cell factories. In this article, we comprehensively summarize recent developments in spatiotemporal control systems for tailoring advanced cell factories, and illustrate how to apply spatiotemporal control systems in different microbial species with desired applications. Future challenges of spatiotemporal control systems and perspectives are also discussed.
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Affiliation(s)
- Wenwen Yu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Ke Jin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Xianhao Xu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Jiangsu Province Basic Research Center for Synthetic Biology, Jiangnan University, Wuxi 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Jiangsu Province Basic Research Center for Synthetic Biology, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Jiangsu Province Basic Research Center for Synthetic Biology, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Jiangsu Province Basic Research Center for Synthetic Biology, Jiangnan University, Wuxi 214122, China
| | - Jian Chen
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Jiangsu Province Basic Research Center for Synthetic Biology, Jiangnan University, Wuxi 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Jiangsu Province Basic Research Center for Synthetic Biology, Jiangnan University, Wuxi 214122, China.
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Jiangsu Province Basic Research Center for Synthetic Biology, Jiangnan University, Wuxi 214122, China.
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7
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Zhang F, Hao X, Liu J, Hou H, Chen S, Wang C. Herbal Multiomics Provide Insights into Gene Discovery and Bioproduction of Triterpenoids by Engineered Microbes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2025; 73:47-65. [PMID: 39666531 DOI: 10.1021/acs.jafc.4c08372] [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: 12/14/2024]
Abstract
Triterpenoids are natural products found in plants that exhibit industrial and agricultural importance. Triterpenoids are typically synthesized through two main pathways: the mevalonate (MVA) and methylerythritol 4-phosphate (MEP) pathways. They then undergo structural diversification with the help of squalene cyclases (OSCs), cytochrome P450 monooxygenases (P450s), UDP glycosyltransferases (UGTs), and acyltransferases (ATs). Advances in multiomics technologies for herbal plants have led to the identification of novel triterpenoid biosynthetic pathways. The application of various analytical techniques facilitates the qualitative and quantitative analysis of triterpenoids. Progress in synthetic biology and metabolic engineering has also facilitated the heterologous production of triterpenoids in microorganisms, such as Escherichia coli and Saccharomyces cerevisiae. This review summarizes recent advances in biotechnological approaches aimed at elucidating the complex pathway of triterpenoid biosynthesis. It also discusses the metabolic engineering strategies employed to increase the level of triterpenoid production in chassis cells.
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Affiliation(s)
- Feng Zhang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xuemi Hao
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jia Liu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Hongping Hou
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Shilin Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137 Chengdu, Sichuan China
| | - Caixia Wang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
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8
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Guo Q, Yang YX, Li DX, Ji XJ, Wu N, Wang YT, Ye C, Shi TQ. Advances in multi-enzyme co-localization strategies for the construction of microbial cell factory. Biotechnol Adv 2024; 77:108453. [PMID: 39278372 DOI: 10.1016/j.biotechadv.2024.108453] [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: 07/03/2024] [Revised: 09/05/2024] [Accepted: 09/10/2024] [Indexed: 09/18/2024]
Abstract
Biomanufacturing, driven by technologies such as synthetic biology, offers significant potential to advance the bioeconomy and promote sustainable development. It is anticipated to transform traditional manufacturing and become a key industry in future strategies. Cell factories are the core of biomanufacturing. The advancement of synthetic biology and growing market demand have led to the production of a greater variety of natural products and increasingly complex metabolic pathways. However, this progress also presents challenges, notably the conflict between natural product production and chassis cell growth. This conflict results in low productivity and yield, adverse side effects, metabolic imbalances, and growth retardation. Enzyme co-localization strategies have emerged as a promising solution. This article reviews recent progress and applications of these strategies in constructing cell factories for efficient natural product production. It comprehensively describes the applications of enzyme-based compartmentalization, metabolic pathway-based compartmentalization, and synthetic organelle-based compartmentalization in improving product titers. The article also explores future research directions and the prospects of combining multiple strategies with advanced technologies.
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Affiliation(s)
- Qi Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Yu-Xin Yang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Dong-Xun Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Xiao-Jun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Na Wu
- College of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng, China
| | - Yue-Tong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China.
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China.
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China.
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9
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Bi K, Wang W, Tang D, Shi Z, Tian S, Huang L, Lian J, Xu Z. Engineering sub-organelles of a diploid Saccharomyces cerevisiae to enhance the production of 7-dehydrocholesterol. Metab Eng 2024; 84:169-179. [PMID: 38936763 DOI: 10.1016/j.ymben.2024.06.011] [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: 04/08/2024] [Revised: 06/09/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
7-Dehydrocholesterol (7-DHC) is widely present in various organisms and is an important precursor of vitamin D3. Despite significant improvements in the biosynthesis of 7-DHC, it remains insufficient to meet the industrial demands. In this study, we reported high-level production of 7-DHC in an industrial Saccharomyces cerevisiae leveraging subcellular organelles. Initially, the copy numbers of DHCR24 were increased in combination with sterol transcriptional factor engineering and rebalanced the redox power of the strain. Subsequently, the effects of compartmentalizing the post-squalene pathway in peroxisomes were validated by assembling various pathway modules in this organelle. Furthermore, several peroxisomes engineering was conducted to enhance the production of 7-DHC. Utilizing the peroxisome as a vessel for partial post-squalene pathways, the potential of yeast for 7-dehydrocholesterol production was demonstrated by achieving a 26-fold increase over the initial production level. 7-DHC titer reached 640.77 mg/L in shake flasks and 4.28 g/L in a 10 L bench-top fermentor, the highest titer ever reported. The present work lays solid foundation for large-scale and cost-effective production of 7-DHC for practical applications.
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Affiliation(s)
- Ke Bi
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Wenguang Wang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dandan Tang
- School of Pharmaceutical Science, Nanjing Tech University, Nanjing, 211816, China
| | - Zhuwei Shi
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Shuyu Tian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; Institute of Bioengineering, College of Chemical and Biological Engineering, 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; Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
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10
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Ye C, Hong H, Gao J, Li M, Gou Y, Gao D, Dong C, Huang L, Xu Z, Lian J. Characterization and engineering of peroxisome targeting sequences for compartmentalization engineering in Pichia pastoris. Biotechnol Bioeng 2024; 121:2091-2105. [PMID: 38568751 DOI: 10.1002/bit.28706] [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: 12/27/2023] [Revised: 03/03/2024] [Accepted: 03/19/2024] [Indexed: 04/05/2024]
Abstract
Peroxisomal compartmentalization has emerged as a highly promising strategy for reconstituting intricate metabolic pathways. In recent years, significant progress has been made in the peroxisomes through harnessing precursor pools, circumventing metabolic crosstalk, and minimizing the cytotoxicity of exogenous pathways. However, it is important to note that in methylotrophic yeasts (e.g. Pichia pastoris), the abundance and protein composition of peroxisomes are highly variable, particularly when peroxisome proliferation is induced by specific carbon sources. The intricate subcellular localization of native proteins, the variability of peroxisomal metabolic pathways, and the lack of systematic characterization of peroxisome targeting signals have limited the applications of peroxisomal compartmentalization in P. pastoris. Accordingly, this study established a high-throughput screening method based on β-carotene biosynthetic pathway to evaluate the targeting efficiency of PTS1s (Peroxisome Targeting Signal Type 1) in P. pastoris. First, 25 putative endogenous PTS1s were characterized and 3 PTS1s with high targeting efficiency were identified. Then, directed evolution of PTS1s was performed by constructing two PTS1 mutant libraries, and a total of 51 PTS1s (29 classical and 22 noncanonical PTS1s) with presumably higher peroxisomal targeting efficiency were identified, part of which were further characterized via confocal microscope. Finally, the newly identified PTS1s were employed for peroxisomal compartmentalization of the geraniol biosynthetic pathway, resulting in more than 30% increase in the titer of monoterpene compared with when the pathway was localized to the cytosol. The present study expands the synthetic biology toolkit and lays a solid foundation for peroxisomal compartmentalization in P. pastoris.
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Affiliation(s)
- Cuifang Ye
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Haosen Hong
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Jucan Gao
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Mengxin Li
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Yuanwei Gou
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Di Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Chang Dong
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
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11
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An T, Lin G, Liu Y, Qin L, Xu Y, Feng X, Li C. De novo biosynthesis of anticarcinogenic icariin in engineered yeast. Metab Eng 2023; 80:207-215. [PMID: 37852432 DOI: 10.1016/j.ymben.2023.10.003] [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: 07/18/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/20/2023]
Abstract
Icariin (ICA) has wide applications in nutraceuticals and medicine with strong anticancer activities. However, the structural complexity and low abundance in plants of ICA lead to the unsustainable and high-cost supply from chemical synthesis and plant extraction. Here, the whole biosynthesis pathway of ICA was elucidated, then was constructed in Saccharomyces cerevisiae, including a 13-step heterologous ICA pathway from eleven kinds of plants as well as deletions or overexpression of ten yeast endogenous genes. Spatial regulation of 8-C-prenyltransferase to mitochondria and three-stage sequential control of 4'-O-methyltransferase, 3-OH rhamnosyltransferase, and 7-OH glycosyltransferase expression successfully achieved the de novo synthesis of ICA with a titer of 130 μg/L under shake-flask culture. The ICA synthesis from glucose represents the longest reconstructed pathway of flavonoid in microbe so far. This study provides a potential choice for the sustainable microbial production of number of complex flavonoids.
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Affiliation(s)
- Ting An
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China
| | - Guangyuan Lin
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Yang Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lei Qin
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Yuquan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xudong Feng
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China.
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China; Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China; Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China.
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12
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Wang R, Liu X, Lv B, Sun W, Li C. Designing Intracellular Compartments for Efficient Engineered Microbial Cell Factories. ACS Synth Biol 2023; 12:1378-1395. [PMID: 37083286 DOI: 10.1021/acssynbio.2c00671] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
With the rapid development of synthetic biology, various kinds of microbial cell factories (MCFs) have been successfully constructed to produce high-value-added compounds. However, the complexity of metabolic regulation and pathway crosstalk always cause issues such as intermediate metabolite accumulation, byproduct generation, and metabolic burden in MCFs, resulting in low efficiencies and low yields of industrial biomanufacturing. Such issues could be solved by spatially rearranging the pathways using intracellular compartments. In this review, design strategies are summarized and discussed based on the types and characteristics of natural and artificial subcellular compartments. This review systematically presents information for the construction of efficient MCFs with intracellular compartments in terms of four aspects of design strategy goals: (1) improving local reactant concentration; (2) intercepting and isolating competing pathways; (3) providing specific reaction substances and environments; and (4) storing and accumulating products.
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Affiliation(s)
- Ruwen Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Xin Liu
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, PR China
| | - Bo Lv
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Wentao Sun
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, PR China
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, PR China
- Center for Synthetic and System Biology, Tsinghua University, Beijing, 100084, PR China
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13
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Zhang Y, Su M, Chen Y, Wang Z, Nielsen J, Liu Z. Engineering yeast mitochondrial metabolism for 3-hydroxypropionate production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:64. [PMID: 37031180 PMCID: PMC10082987 DOI: 10.1186/s13068-023-02309-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/24/2023] [Indexed: 04/10/2023]
Abstract
BACKGROUND With unique physiochemical environments in subcellular organelles, there has been growing interest in harnessing yeast organelles for bioproduct synthesis. Among these organelles, the yeast mitochondrion has been found to be an attractive compartment for production of terpenoids and branched-chain alcohols, which could be credited to the abundant supply of acetyl-CoA, ATP and cofactors. In this study we explored the mitochondrial potential for production of 3-hydroxypropionate (3-HP) and performed the cofactor engineering and flux control at the acetyl-CoA node to maximize 3-HP synthesis. RESULTS Metabolic modeling suggested that the mitochondrion serves as a more suitable compartment for 3-HP synthesis via the malonyl-CoA pathway than the cytosol, due to the opportunity to obtain a higher maximum yield and a lower oxygen consumption. With the malonyl-CoA reductase (MCR) targeted into the mitochondria, the 3-HP production increased to 0.27 g/L compared with 0.09 g/L with MCR expressed in the cytosol. With enhanced expression of dissected MCR enzymes, the titer reached to 4.42 g/L, comparable to the highest titer achieved in the cytosol so far. Then, the mitochondrial NADPH supply was optimized by overexpressing POS5 and IDP1, which resulted in an increase in the 3-HP titer to 5.11 g/L. Furthermore, with induced expression of an ACC1 mutant in the mitochondria, the final 3-HP production reached 6.16 g/L in shake flask fermentations. The constructed strain was then evaluated in fed-batch fermentations, and produced 71.09 g/L 3-HP with a productivity of 0.71 g/L/h and a yield on glucose of 0.23 g/g. CONCLUSIONS In this study, the yeast mitochondrion is reported as an attractive compartment for 3-HP production. The final 3-HP titer of 71.09 g/L with a productivity of 0.71 g/L/h was achieved in fed-batch fermentations, representing the highest titer reported for Saccharomyces cerevisiae so far, that demonstrated the potential of recruiting the yeast mitochondria for further development of cell factories.
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Affiliation(s)
- Yiming Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Mo Su
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yu Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Zheng Wang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jens Nielsen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- BioInnovation Institute, Ole Maaløes Vej 3, DK2200, Copenhagen, Denmark
| | - Zihe Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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14
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He S, Zhang Z, Lu W. Natural promoters and promoter engineering strategies for metabolic regulation in Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2023; 50:6986260. [PMID: 36633543 PMCID: PMC9936215 DOI: 10.1093/jimb/kuac029] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023]
Abstract
Sharomyces cerevisiae is currently one of the most important foreign gene expression systems. S. cerevisiae is an excellent host for high-value metabolite cell factories due to its advantages of simplicity, safety, and nontoxicity. A promoter, as one of the basic elements of gene transcription, plays an important role in regulating gene expression and optimizing metabolic pathways. Promoters control the direction and intensity of transcription, and the application of promoters with different intensities and performances will largely determine the effect of gene expression and ultimately affect the experimental results. Due to its significant role, there have been many studies on promoters for decades. While some studies have explored and analyzed new promoters with different functions, more studies have focused on artificially modifying promoters to meet their own scientific needs. Thus, this article reviews current research on promoter engineering techniques and related natural promoters in S. cerevisiae. First, we introduce the basic structure of promoters and the classification of natural promoters. Then, the classification of various promoter strategies is reviewed. Finally, by grouping related articles together using various strategies, this review anticipates the future development direction of promoter engineering.
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Affiliation(s)
| | - Zhanwei Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China
| | - Wenyu Lu
- Correspondence should be addressed to: W. Y. Lu, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China. Phone: +86-22-853-56523. Fax: +86-22-274-00973. E-mail:
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15
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Chen L, Xiao W, Yao M, Wang Y, Yuan Y. Compartmentalization engineering of yeasts to overcome precursor limitations and cytotoxicity in terpenoid production. Front Bioeng Biotechnol 2023; 11:1132244. [PMID: 36911190 PMCID: PMC9997727 DOI: 10.3389/fbioe.2023.1132244] [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: 12/27/2022] [Accepted: 02/13/2023] [Indexed: 02/25/2023] Open
Abstract
Metabolic engineering strategies for terpenoid production have mainly focused on bottlenecks in the supply of precursor molecules and cytotoxicity to terpenoids. In recent years, the strategies involving compartmentalization in eukaryotic cells has rapidly developed and have provided several advantages in the supply of precursors, cofactors and a suitable physiochemical environment for product storage. In this review, we provide a comprehensive analysis of organelle compartmentalization for terpenoid production, which can guide the rewiring of subcellular metabolism to make full use of precursors, reduce metabolite toxicity, as well as provide suitable storage capacity and environment. Additionally, the strategies that can enhance the efficiency of a relocated pathway by increasing the number and size of organelles, expanding the cell membrane and targeting metabolic pathways in several organelles are also discussed. Finally, the challenges and future perspectives of this approach for the terpenoid biosynthesis are also discussed.
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Affiliation(s)
- Lifei Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 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, Tianjin, China.,Georgia Tech Shenzhen Institute, Tianjin University, Shenzhen, 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, Tianjin, 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, Tianjin, 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, Tianjin, China
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16
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Arceo XG, Koslover EF, Zid BM, Brown AI. Mitochondrial mRNA localization is governed by translation kinetics and spatial transport. PLoS Comput Biol 2022; 18:e1010413. [PMID: 35984860 PMCID: PMC9432724 DOI: 10.1371/journal.pcbi.1010413] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/31/2022] [Accepted: 07/19/2022] [Indexed: 11/24/2022] Open
Abstract
For many nuclear-encoded mitochondrial genes, mRNA localizes to the mitochondrial surface co-translationally, aided by the association of a mitochondrial targeting sequence (MTS) on the nascent peptide with the mitochondrial import complex. For a subset of these co-translationally localized mRNAs, their localization is dependent on the metabolic state of the cell, while others are constitutively localized. To explore the differences between these two mRNA types we developed a stochastic, quantitative model for MTS-mediated mRNA localization to mitochondria in yeast cells. This model includes translation, applying gene-specific kinetics derived from experimental data; and diffusion in the cytosol. Even though both mRNA types are co-translationally localized we found that the steady state number, or density, of ribosomes along an mRNA was insufficient to differentiate the two mRNA types. Instead, conditionally-localized mRNAs have faster translation kinetics which modulate localization in combination with changes to diffusive search kinetics across metabolic states. Our model also suggests that the MTS requires a maturation time to become competent to bind mitochondria. Our work indicates that yeast cells can regulate mRNA localization to mitochondria by controlling mitochondrial volume fraction (influencing diffusive search times) and gene translation kinetics (adjusting mRNA binding competence) without the need for mRNA-specific binding proteins. These results shed light on both global and gene-specific mechanisms that enable cells to alter mRNA localization in response to changing metabolic conditions.
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Affiliation(s)
- Ximena G. Arceo
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California, United States of America
| | - Elena F. Koslover
- Department of Physics, University of California, San Diego, La Jolla, California, United States of America
| | - Brian M. Zid
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California, United States of America
| | - Aidan I. Brown
- Department of Physics, Ryerson University, Toronto, Canada
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17
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Zuo Y, Xiao F, Gao J, Ye C, Jiang L, Dong C, Lian J. Establishing Komagataella phaffii as a Cell Factory for Efficient Production of Sesquiterpenoid α-Santalene. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:8024-8031. [PMID: 35729733 DOI: 10.1021/acs.jafc.2c02353] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Santalene, a major component of the sandalwood essential oil, is a typical representative of sesquiterpenes and has important applications in medicine, food, flavors, and other fields. Due to the limited supply of natural sandalwood resources, there is a growing interest in engineering microbial cell factories for the mass production of santalene. In the present study, Komagataella phaffii (also known as Pichia pastoris) was established as a cell factory for high-level production of α-santalene for the first time. The metabolic fluxes were rewired toward α-santalene biosynthesis through the optimization of promoters to drive the expression of the α-santalene synthase (SAS) gene, overexpression of the key mevalonate pathway genes (i.e., tHMG1, IDI1, and ERG20), and multi-copy integration of the SAS expression cassette. In combination with medium optimization and bioprocess engineering, the optimal strain (STE-9) was able to produce α-santalene with a titer as high as 829.8 ± 70.6 mg/L, 4.4 ± 0.3 g/L, and 21.5 ± 1.6 g/L in a shake flask, batch fermenter, and fed-batch fermenter, respectively. These represented the highest production of α-santalene ever reported, highlighting the advantages of K. phaffii cell factories for the production of terpenoids and other natural products.
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Affiliation(s)
- Yimeng Zuo
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Feng Xiao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Jucan Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Cuifang Ye
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Lihong Jiang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Chang Dong
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-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
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
- Zhejiang Key Laboratory of Smart Biomaterials, Zhejiang University, Hangzhou 310027, China
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18
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Jin K, Xia H, Liu Y, Li J, Du G, Lv X, Liu L. Compartmentalization and transporter engineering strategies for terpenoid synthesis. Microb Cell Fact 2022; 21:92. [PMID: 35599322 PMCID: PMC9125818 DOI: 10.1186/s12934-022-01819-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/12/2022] [Indexed: 12/18/2022] Open
Abstract
Microbial cell factories for terpenoid synthesis form a less expensive and more environment-friendly approach than chemical synthesis and extraction, and are thus being regarded as mainstream research recently. Organelle compartmentalization for terpenoid synthesis has received much attention from researchers owing to the diverse physiochemical characteristics of organelles. In this review, we first systematically summarized various compartmentalization strategies utilized in terpenoid production, mainly plant terpenoids, which can provide catalytic reactions with sufficient intermediates and a suitable environment, while bypassing competing metabolic pathways. In addition, because of the limited storage capacity of cells, strategies used for the expansion of specific organelle membranes were discussed. Next, transporter engineering strategies to overcome the cytotoxic effects of terpenoid accumulation were analyzed. Finally, we discussed the future perspectives of compartmentalization and transporter engineering strategies, with the hope of providing theoretical guidance for designing and constructing cell factories for the purpose of terpenoid production.
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Affiliation(s)
- Ke Jin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Hongzhi Xia
- Richen Bioengineering Co., Ltd, Nantong, 226000, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China.
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China.
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19
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Lv X, Jin K, Sun G, Ledesma-Amaro R, Liu L. Microscopy imaging of living cells in metabolic engineering. Trends Biotechnol 2021; 40:752-765. [PMID: 34799183 DOI: 10.1016/j.tibtech.2021.10.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 01/23/2023]
Abstract
Microscopy imaging of living cells is becoming a pivotal, noninvasive, and highly specific tool in metabolic engineering to visualize molecular dynamics in industrial microorganisms. This review describes the different microscopy methods, from fluorescence to super resolution, with application in microbial bioengineering. Firstly, the role and importance of microscopy imaging is analyzed in the context of strain design. Then, the advantages and disadvantages of different microscopy technologies are discussed, including confocal laser scanning microscopy (CLSM), spatial light interference microscopy (SLIM), and super-resolution microscopy, followed by their applications in synthetic biology. Finally, the future perspectives of live-cell imaging and their potential to transform microbial systems are analyzed. This review provides theoretical guidance and highlights the importance of microscopy in understanding and engineering microbial metabolism.
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Affiliation(s)
- Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Ke Jin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Guoyun Sun
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW72AZ, UK
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.
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