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Liu J, Li Y, Xu X, Wu Y, Liu Y, Li J, Du G, Chen J, Lv X, Liu L. Multiplexed engineering of cytochrome P450 enzymes for promoting terpenoid synthesis in Saccharomyces cerevisiae cell factories: A review. Biotechnol Adv 2025; 81:108560. [PMID: 40068711 DOI: 10.1016/j.biotechadv.2025.108560] [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: 11/20/2024] [Revised: 01/23/2025] [Accepted: 03/07/2025] [Indexed: 03/15/2025]
Abstract
Terpenoids, also known as isoprenoids, represent the largest and most structurally diverse family of natural products, and their biosynthesis is closely related to cytochrome P450 enzymes (P450s). Given the limitations of direct extraction from natural resources, such as low productivity and environmental concerns, heterologous expression of P450s in microbial cell factories has emerged as a promising, efficient, and sustainable strategy for terpenoid production. The yeast expression system is a preferred selection for terpenoid synthesis because of its inner membrane system, which is required for eukaryotic P450 expression, and the inherent mevalonate pathway providing precursors for terpenoid synthesis. In this review, we discuss the advanced strategies used to enhance the local enzyme concentration and catalytic properties of P450s in Saccharomyces cerevisiae, with a focus on recent developments in metabolic and protein engineering. Expression enhancement and subcellular compartmentalization are specifically employed to increase the local enzyme concentration, whereas cofactor, redox partner, and enzyme engineering are utilized to improve the catalytic efficiency and substrate specificity of P450s. Subsequently, we discuss the application of P450s for the pathway engineering of terpenoid synthesis and whole-cell biotransformation, which are profitable for the industrial application of P450s in S. cerevisiae chassis. Finally, we explore the potential of using computational and artificial intelligence technologies to rationally design and construct high-performance cell factories, which offer promising pathways for future terpenoid biosynthesis.
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Affiliation(s)
- Jiaheng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi 214122, China; Food Laboratory of Zhongyuan, Jiangnan University, Wuxi 214122, China
| | - Yangyang Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Ministry of Education, 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, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yaokang Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Ministry of Education, 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, Ministry of Education, 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, Ministry of Education, 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, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jian Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Ministry of Education, 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, Ministry of Education, 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, Ministry of Education, Jiangnan University, Wuxi 214122, China; Food Laboratory of Zhongyuan, Jiangnan University, Wuxi 214122, China.
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2
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Sun Y, Chen C, Lin C, Zhang H, Lian J, Hong B. Elucidation and de novo reconstitution of glyceollin biosynthesis. MOLECULAR PLANT 2025; 18:820-832. [PMID: 40211535 DOI: 10.1016/j.molp.2025.04.003] [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: 02/07/2025] [Revised: 03/23/2025] [Accepted: 04/07/2025] [Indexed: 05/03/2025]
Abstract
Glyceollins are phytoalexins, soybean-produced compounds that respond to pathogen invasion, injury, and environmental challenges. While these compounds have diverse bioactivities, their limited accessibility hinders further physiological and biochemical studies. Additionally, the incomplete understanding of glyceollin biosynthesis, particularly cyclization steps, remains a major barrier to sustainable production through synthetic biology. In this study, we uncover the complete biosynthetic pathway of glyceollins through a combinatorial approach involving transient expression in Nicotiana benthamiana, in vitro enzyme characterization, and yeast feeding studies. We identified previously uncharacterized genes encoding reductases for 7,2',4'-trihydroxyisoflavanol biosynthesis and five P450 enzymes that mediate the final oxidative cyclization to produce glyceollins I, II, and III. By de novo reconstruction of the pathway through synthetic biology and metabolic engineering, we successfully produced glyceollins from simple carbon sources in baker's yeast. This work advances the understanding of glyceollin biosynthesis in soybeans, enables sustainable production in microbial hosts, and offers new opportunities for their application in agriculture and biology.
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Affiliation(s)
- Yunlong Sun
- Zhejiang Key Laboratory of Precise Synthesis of Functional Molecules, Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou, China
| | - Cong Chen
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Chao Lin
- Zhejiang Key Laboratory of Precise Synthesis of Functional Molecules, Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou, China
| | - Hao Zhang
- Zhejiang Key Laboratory of Precise Synthesis of Functional Molecules, Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China; Zhejiang Key Laboratory of Intelligent Manufacturing for Functional Chemicals, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China.
| | - Benke Hong
- Zhejiang Key Laboratory of Precise Synthesis of Functional Molecules, Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou, China.
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Fan B, Liang X, Li Y, Li M, Yu T, Qin Y, Li B, An T, Wang G. Biosynthesis and metabolic engineering of natural sweeteners. AMB Express 2025; 15:50. [PMID: 40100508 PMCID: PMC11920521 DOI: 10.1186/s13568-025-01864-y] [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: 12/11/2024] [Accepted: 03/10/2025] [Indexed: 03/20/2025] Open
Abstract
Natural sweeteners have attracted widespread attention because they are eco-friendly, healthy, low in calories, and tasty. The demand for natural sweeteners is increasing together with the popularity of green, low-carbon, sustainable development. With the development of synthetic biology, microbial cell factories have emerged as an effective method to produce large amounts of natural sweeteners. This technology has significantly progressed in recent years. This review summarizes the pathways and the enzymes related to the biosynthesis of natural sweeteners, such as mogrosides, steviol glycosides, glycyrrhizin, glycyrrhetinic acid, phlorizin, trilobatin, erythritol, sorbitol, mannitol, thaumatin, monellin, and brazzein. Moreover, it focuses on the research about the microbial production of these natural sweeteners using synthetic biology methods, aiming to provide a reference for future research on the production of natural sweeteners.
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Affiliation(s)
- Bengui Fan
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Xiqin Liang
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Yichi Li
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Mingkai Li
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Tongle Yu
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Yuan Qin
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Bohan Li
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Tianyue An
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, 264003, China.
| | - Guoli Wang
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, 264003, China.
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4
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Zhang D, Xu F, Wang F, Le L, Pu L. Synthetic biology and artificial intelligence in crop improvement. PLANT COMMUNICATIONS 2025; 6:101220. [PMID: 39668563 PMCID: PMC11897457 DOI: 10.1016/j.xplc.2024.101220] [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: 07/10/2024] [Revised: 10/29/2024] [Accepted: 12/09/2024] [Indexed: 12/14/2024]
Abstract
Synthetic biology plays a pivotal role in improving crop traits and increasing bioproduction through the use of engineering principles that purposefully modify plants through "design, build, test, and learn" cycles, ultimately resulting in improved bioproduction based on an input genetic circuit (DNA, RNA, and proteins). Crop synthetic biology is a new tool that uses circular principles to redesign and create innovative biological components, devices, and systems to enhance yields, nutrient absorption, resilience, and nutritional quality. In the digital age, artificial intelligence (AI) has demonstrated great strengths in design and learning. The application of AI has become an irreversible trend, with particularly remarkable potential for use in crop breeding. However, there has not yet been a systematic review of AI-driven synthetic biology pathways for plant engineering. In this review, we explore the fundamental engineering principles used in crop synthetic biology and their applications for crop improvement. We discuss approaches to genetic circuit design, including gene editing, synthetic nucleic acid and protein technologies, multi-omics analysis, genomic selection, directed protein engineering, and AI. We then outline strategies for the development of crops with higher photosynthetic efficiency, reshaped plant architecture, modified metabolic pathways, and improved environmental adaptability and nutrient absorption; the establishment of trait networks; and the construction of crop factories. We propose the development of SMART (self-monitoring, adapted, and responsive technology) crops through AI-empowered synthetic biotechnology. Finally, we address challenges associated with the development of synthetic biology and offer potential solutions for crop improvement.
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Affiliation(s)
- Daolei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; School of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Fan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Fanhua Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; School of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Liang Le
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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5
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Germann SM, Holtz M, Jensen MK, Acevedo-Rocha CG. Debottlenecking cytochrome P450-dependent metabolic pathways for the biosynthesis of commercial natural products. Nat Prod Rep 2024; 41:1846-1857. [PMID: 39552440 DOI: 10.1039/d4np00027g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
Abstract
Covering: 2016 to the end of 2024This highlight article aims to provide a perspective on the challenges that novel biotechnological processes face in the biomanufacturing of natural products (NPs) whose biosynthesis pathways rely on cytochrome P450 monooxygenases. This enzyme superfamily is one of the most versatile in the biosynthesis of a plethora of NPs finding use across the food, nutrition, medicine, chemical and cosmetics industries. These enzymes often exhibit excellent regio- and stereoselectivity, but they can suffer from low activity and instability, which are serious issues impairing the development of high performing bioprocesses. We start with a brief introduction to industrial biotechnology and the importance of looking for alternative means for producing NPs independently from unsustainable fossil fuels or plant extractions. We then discuss the challenges and implemented solutions during the development of commercial NP processes focusing on the P450-dependent steps primarily in yeast cell factories. Our main focus is to highlight the challenges often encountered when utilizing P450-dependent NP pathways, and how protein engineering can be used for debottlenecking them. Finally, we briefly touch upon the importance of artificial intelligence and machine learning for guiding engineering efforts.
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Affiliation(s)
| | - Maxence Holtz
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | | | - Carlos G Acevedo-Rocha
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
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6
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Wan X, Shahrear S, Chew SW, Vilaplana F, Mäkelä MR. Discovery of alkaline laccases from basidiomycete fungi through machine learning-based approach. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:120. [PMID: 39261970 PMCID: PMC11391777 DOI: 10.1186/s13068-024-02566-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 09/02/2024] [Indexed: 09/13/2024]
Abstract
BACKGROUND Laccases can oxidize a broad spectrum of substrates, offering promising applications in various sectors, such as bioremediation, biomass fractionation in future biorefineries, and synthesis of biochemicals and biopolymers. However, laccase discovery and optimization with a desirable pH optimum remains a challenge due to the labor-intensive and time-consuming nature of the traditional laboratory methods. RESULTS This study presents a machine learning (ML)-integrated approach for predicting pH optima of basidiomycete fungal laccases, utilizing a small, curated dataset against a vast metagenomic data. Comparative computational analyses unveiled the structural and pH-dependent solubility differences between acidic and neutral-alkaline laccases, helping us understand the molecular bases of enzyme pH optimum. The pH profiling of the two ML-predicted alkaline laccase candidates from the basidiomycete fungus Lepista nuda further validated our computational approach, showing the accuracy of this comprehensive method. CONCLUSIONS This study uncovers the efficacy of ML in the prediction of enzyme pH optimum from minimal datasets, marking a significant step towards harnessing computational tools for systematic screening of enzymes for biotechnology applications.
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Affiliation(s)
- Xing Wan
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Biocenter 1, Viikinkaari 9, 00790, Helsinki, Finland.
| | - Sazzad Shahrear
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Biocenter 1, Viikinkaari 9, 00790, Helsinki, Finland
| | - Shea Wen Chew
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Biocenter 1, Viikinkaari 9, 00790, Helsinki, Finland
| | - Francisco Vilaplana
- Division of Glycoscience, Department of Chemistry, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, Roslagstullbacken 21, 11421, Stockholm, Sweden
| | - Miia R Mäkelä
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Biocenter 1, Viikinkaari 9, 00790, Helsinki, Finland.
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland.
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7
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Lin C, Zhang X, Ji Z, Fan B, Chen Y, Wu Y, Gan Y, Li Z, Shang Y, Duan L, Wang F. Metabolic engineering of Saccharomyces cerevisiae for high-level production of (+)-ambrein from glucose. Biotechnol Lett 2024; 46:615-626. [PMID: 38884886 DOI: 10.1007/s10529-024-03502-2] [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: 04/10/2024] [Revised: 05/12/2024] [Accepted: 05/18/2024] [Indexed: 06/18/2024]
Abstract
(+)-Ambrein is the primary component of ambergris, a rare product found in sperm whales (Physeter microcephalus). Microbial production using sustainable resources is a promising way to replace animal extraction and chemical synthesis. We constructed an engineered yeast strain to produce (+)-ambrein de novo. Squalene is a substrate for the biosynthesis of (+)-ambrein. Firstly, strain LQ2, with a squalene yield of 384.4 mg/L was obtained by optimizing the mevalonate pathway. Then we engineered a method for the de novo production of (+)-ambrein using glucose as a carbon source by overexpressing codon-optimized tetraprenyl-β-curcumene cyclase (BmeTC) and its double mutant enzyme (BmeTCY167A/D373C), evaluating different promoters, knocking out GAL80, and fusing the protein with BmeTC and squalene synthase (AtSQS2). Nevertheless, the synthesis of (+)-ambrein is still limited, causing low catalytic activity in BmeTC. We carried out a protein surface amino acid modification of BmeTC. The dominant mutant BmeTCK6A/Q9E/N454A for the first step was obtained to improve its catalytic activity. The yield of (+)-ambrein increased from 35.2 to 59.0 mg/L in the shake flask and finally reached 457.4 mg/L in the 2 L fermenter, the highest titer currently available for yeast. Efficiently engineered strains and inexpensive fermentation conditions for the industrial production of (+)-ambrein. The metabolic engineering tools provide directions for optimizing the biosynthesis of other high-value triterpenes.
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Affiliation(s)
- Chumin Lin
- Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of TCM, School of Chinese Materia Medica, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Xiaopeng Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518116, China
| | - Zhongju Ji
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, And International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Baolian Fan
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, And International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Yaman Chen
- Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of TCM, School of Chinese Materia Medica, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Yuhong Wu
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, And International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Yuhong Gan
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, And International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Zhengping Li
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, And International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Yi Shang
- Yunnan Key Laboratory of Potato Biology, The CAAS-YNNU-YINMORE Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650500, China
| | - Lixin Duan
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, And International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
| | - Feng Wang
- Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of TCM, School of Chinese Materia Medica, Guangdong Pharmaceutical University, Guangzhou, 510006, China.
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Luo X, Cao L, Yu L, Gao M, Ai J, Gao D, Zhang X, John Lucas W, Huang S, Xu J, Shang Y. Deep learning-based characterization and redesign of major potato tuber storage protein. Food Chem 2024; 443:138556. [PMID: 38290299 DOI: 10.1016/j.foodchem.2024.138556] [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: 08/17/2023] [Revised: 01/20/2024] [Accepted: 01/21/2024] [Indexed: 02/01/2024]
Abstract
Potato is one of the most important crops worldwide, to feed a fast-growing population. In addition to providing energy, fiber, vitamins, and minerals, potato storage proteins are considered as one of the most valuable sources of non-animal proteins due to their high essential amino acid (EAA) index. However, low tuber protein content and limited knowledge about potato storage proteins restrict their widespread utilization in the food industry. Here, we report a proof-of-concept study, using deep learning-based protein design tools, to characterize the biological and chemical characteristics of patatins, the major potato storage proteins. This knowledge was then employed to design multiple cysteines on the patatin surface to build polymers linked by disulfide bonds, which significantly improved viscidity and nutrient of potato flour dough. Our study shows that deep learning-based protein design strategies are efficient to characterize and to create novel proteins for future food sources.
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Affiliation(s)
- Xuming Luo
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Lijuan Cao
- Yunnan Key Laboratory of Potato Biology, The CAAS-YNNU-YINMORE Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
| | - Langhua Yu
- Yunnan Key Laboratory of Potato Biology, The CAAS-YNNU-YINMORE Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
| | - Meng Gao
- Yunnan Key Laboratory of Potato Biology, The CAAS-YNNU-YINMORE Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
| | - Ju Ai
- Yunnan Key Laboratory of Potato Biology, The CAAS-YNNU-YINMORE Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
| | - Dongli Gao
- Yunnan Key Laboratory of Potato Biology, The CAAS-YNNU-YINMORE Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
| | - Xiaopeng Zhang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - William John Lucas
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Sanwen Huang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.
| | - Jianfei Xu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Yi Shang
- Yunnan Key Laboratory of Potato Biology, The CAAS-YNNU-YINMORE Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China.
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Lu Y, Liu Y, Zhang Y, Gao H, Chen X, Tu L, Luo Y, Jiang Z, Yin Y, Zhou J, Hu T, Wu X, Wang J, Gao W, Huang L. Characterization of the Cytochrome P450 CYP716C52 in Celastrol Biosynthesis and Its Applications in Engineered Saccharomyces cerevisiae. JOURNAL OF NATURAL PRODUCTS 2024; 87:176-185. [PMID: 38277488 DOI: 10.1021/acs.jnatprod.3c00674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
Celastrol is a bioactive pentacyclic triterpenoid with promising therapeutic effects that is mainly distributed in Celastraceae plants. Although some enzymes involved in the celastrol biosynthesis pathway have been reported, many biosynthetic steps remain unknown. Herein, transcriptomics and metabolic profiles of multiple species in Celastraceae were integrated to screen for cytochrome P450s (CYPs) that are closely related to celastrol biosynthesis. The CYP716 enzyme, TwCYP716C52, was found to be able to oxidize the C-2 position of polpunonic acid, a precursor of celastrol, to form the wilforic acid C. RNAi-mediated repression of TwCYP716C52 in Tripterygium wilfordii suspension cells further confirmed its involvement in celastrol biosynthesis. The C-2 catalytic mechanisms of TwCYP716C52 were further explored by using molecular docking and site-directed mutagenesis experiments. Moreover, a modular optimization strategy was used to construct an engineered yeast to produce wilforic acid C at a titer of 5.8 mg·L-1. This study elucidates the celastrol biosynthetic pathway and provides important functional genes and sufficient precursors for further enzyme discovery.
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Affiliation(s)
- Yun Lu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China
- Chengdu Second People's Hospital, Chengdu 610017, China
| | - Yuan Liu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China
| | - Yifeng Zhang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100050, China
| | - Haiyun Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China
| | - Xiaochao Chen
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China
| | - Lichan Tu
- School of Medicine, Zhejiang University City College, Hangzhou 310027, China
| | - Yunfeng Luo
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China
| | - Zhouqian Jiang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China
| | - Yan Yin
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Jiawei Zhou
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310027, China
| | - Tianyuan Hu
- School of Pharmacy, College of Medicine, Hangzhou Normal University, Hangzhou 310027, China
| | - Xiaoyi Wu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China
| | - Jiadian Wang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China
| | - Wei Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100050, China
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10
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Qu G, Liu Y, Ma Q, Li J, Du G, Liu L, Lv X. Progress and Prospects of Natural Glycoside Sweetener Biosynthesis: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:15926-15941. [PMID: 37856872 DOI: 10.1021/acs.jafc.3c05074] [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: 10/21/2023]
Abstract
To achieve an adequate sense of sweetness with a healthy low-sugar diet, it is necessary to explore and produce sugar alternatives. Recently, glycoside sweeteners and their biosynthetic approaches have attracted the attention of researchers. In this review, we first outlined the synthetic pathways of glycoside sweeteners, including the key enzymes and rate-limiting steps. Next, we reviewed the progress in engineered microorganisms producing glycoside sweeteners, including de novo synthesis, whole-cell catalysis synthesis, and in vitro synthesis. The applications of metabolic engineering strategies, such as cofactor engineering and enzyme modification, in the optimization of glycoside sweetener biosynthesis were summarized. Finally, the prospects of combining enzyme engineering and machine learning strategies to enhance the production of glycoside sweeteners were discussed. This review provides a perspective on synthesizing glycoside sweeteners in microbial cells, theoretically guiding the bioproduction of glycoside sweeteners.
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Affiliation(s)
- Guanyi Qu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, P. R. China
- Shandong Jincheng Biological Pharmaceutical Company, Limited, Zibo 255000, P. R. China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, P. R. China
| | - Qinyuan Ma
- Shandong Jincheng Biological Pharmaceutical Company, Limited, Zibo 255000, P. R. China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, P. R. China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, P. R. China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, P. R. China
- Yixing Institute of Food Biotechnology Company, Limited, Yixing 214200, P. R. China
- Food Laboratory of Zhongyuan, Jiangnan University, Wuxi 214122, P. R. China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, P. R. China
- Yixing Institute of Food Biotechnology Company, Limited, Yixing 214200, P. R. China
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11
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Huang X, Sun Y, Osawa Y, Chen YE, Zhang H. Computational redesign of cytochrome P450 CYP102A1 for highly stereoselective omeprazole hydroxylation by UniDesign. J Biol Chem 2023; 299:105050. [PMID: 37451479 PMCID: PMC10413352 DOI: 10.1016/j.jbc.2023.105050] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/03/2023] [Accepted: 07/09/2023] [Indexed: 07/18/2023] Open
Abstract
Cytochrome P450 CYP102A1 is a prototypic biocatalyst that has great potential in chemical synthesis, drug discovery, and biotechnology. CYP102A1 variants engineered by directed evolution and/or rational design are capable of catalyzing the oxidation of a wide range of organic compounds. However, it is difficult to foresee the outcome of engineering CYP102A1 for a compound of interest. Here, we introduce UniDesign as a computational framework for enzyme design and engineering. We tested UniDesign by redesigning CYP102A1 for stereoselective metabolism of omeprazole (OMP), a proton pump inhibitor, starting from an active but nonstereoselective triple mutant (TM: A82F/F87V/L188Q). To shift stereoselectivity toward (R)-OMP, we computationally scanned three active site positions (75, 264, and 328) for mutations that would stabilize the binding of the transition state of (R)-OMP while destabilizing that of (S)-OMP and picked three variants, namely UD1 (TM/L75I), UD2 (TM/A264G), and UD3 (TM/A328V), for experimentation, based on computed energy scores and models. UD1, UD2, and UD3 exhibit high turnover rates of 55 ± 4.7, 84 ± 4.8, and 79 ± 5.7 min-1, respectively, for (R)-OMP hydroxylation, whereas the corresponding rates for (S)-OMP are only 2.2 ± 0.19, 6.0 ± 0.68, and 14 ± 2.8 min-1, yielding an enantiomeric excess value of 92, 87, and 70%, respectively. These results suggest the critical roles of L75I, A264G, and A328V in steering OMP in the optimal orientation for stereoselective oxidation and demonstrate the utility of UniDesign for engineering CYP102A1 to produce drug metabolites of interest. The results are discussed in the context of protein structures.
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Affiliation(s)
- Xiaoqiang Huang
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.
| | - Yudong Sun
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan, USA
| | - Yoichi Osawa
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan, USA
| | - Y Eugene Chen
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Haoming Zhang
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan, USA.
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12
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Zhang Z, Wu QY, Ge Y, Huang ZY, Hong R, Li A, Xu JH, Yu HL. Hydroxylases involved in terpenoid biosynthesis: a review. BIORESOUR BIOPROCESS 2023; 10:39. [PMID: 38647640 PMCID: PMC10992849 DOI: 10.1186/s40643-023-00656-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/10/2023] [Indexed: 04/25/2024] Open
Abstract
Terpenoids are pervasive in nature and display an immense structural diversity. As the largest category of plant secondary metabolites, terpenoids have important socioeconomic value in the fields of pharmaceuticals, spices, and food manufacturing. The biosynthesis of terpenoid skeletons has made great progress, but the subsequent modifications of the terpenoid framework are poorly understood, especially for the functionalization of inert carbon skeleton usually catalyzed by hydroxylases. Hydroxylase is a class of enzymes that plays an important role in the modification of terpenoid backbone. This review article outlines the research progress in the identification, molecular modification, and functional expression of this class of enzymes in the past decade, which are profitable for the discovery, engineering, and application of more hydroxylases involved in the plant secondary metabolism.
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Affiliation(s)
- Zihan Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Qing-Yang Wu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Yue Ge
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Zheng-Yu Huang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Ran Hong
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Aitao Li
- School of Life Sciences, State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, 430062, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China.
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13
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Sun Y, Huang X, Osawa Y, Chen YE, Zhang H. The Versatile Biocatalyst of Cytochrome P450 CYP102A1: Structure, Function, and Engineering. Molecules 2023; 28:5353. [PMID: 37513226 PMCID: PMC10383305 DOI: 10.3390/molecules28145353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Wild-type cytochrome P450 CYP102A1 from Bacillus megaterium is a highly efficient monooxygenase for the oxidation of long-chain fatty acids. The unique features of CYP102A1, such as high catalytic activity, expression yield, regio- and stereoselectivity, and self-sufficiency in electron transfer as a fusion protein, afford the requirements for an ideal biocatalyst. In the past three decades, remarkable progress has been made in engineering CYP102A1 for applications in drug discovery, biosynthesis, and biotechnology. The repertoire of engineered CYP102A1 variants has grown tremendously, whereas the substrate repertoire is avalanched to encompass alkanes, alkenes, aromatics, organic solvents, pharmaceuticals, drugs, and many more. In this article, we highlight the major advances in the past five years in our understanding of the structure and function of CYP102A1 and the methodologies used to engineer CYP102A1 for novel applications. The objective is to provide a succinct review of the latest developments with reference to the body of CYP102A1-related literature.
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Affiliation(s)
- Yudong Sun
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA; (Y.S.); (Y.O.)
| | - Xiaoqiang Huang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Yoichi Osawa
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA; (Y.S.); (Y.O.)
| | - Yuqing Eugene Chen
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Haoming Zhang
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA; (Y.S.); (Y.O.)
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14
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Liu T, Li W, Chen H, Wu T, Zhu C, Zhuo M, Li S. Systematic Optimization of HPO-CPR to Boost (+)-Nootkatone Synthesis in Engineered Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:15548-15559. [PMID: 36468547 DOI: 10.1021/acs.jafc.2c07068] [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: 06/17/2023]
Abstract
As an important and expensive natural sesquiterpene compound in grapefruit, the interest in (+)-nootkatone is stimulated by its strong grapefruit-like odor and physiological activities, which induce efforts for its microbial production. However, the low catalytic efficiency of the cytochrome P450-P450 reductase (HPO-CPR) system is the main challenge. We developed a high-throughput screening (HTS) method using the principle of the color reaction between carbonyl compounds and 2,4-dinitrophenylhydrazine (DNPH), which could rapidly screen the activity of candidate HPO mutants. After optimizing the pairing of HPO and CPR and through semirational design, the optimal mutant HPO_M18 with catalytic performance 2.54 times that of the initial was obtained. An encouraging (+)-nootkatone titer of 2.39 g/L was achieved through two-stage fed-batch fermentation after metabolic engineering and endoplasmic reticulum engineering, representing the highest titer reported to date. Our findings lay the foundation for the development of an economically viable bioprocess for (+)-nootkatone.
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Affiliation(s)
- Tong Liu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Wen Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Hefeng Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Tao Wu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Chaoyi Zhu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Min Zhuo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Shuang Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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15
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Sethi A, Bhandawat A, Pati PK. Engineering medicinal plant-derived CYPs: a promising strategy for production of high-valued secondary metabolites. PLANTA 2022; 256:119. [PMID: 36378350 PMCID: PMC9664027 DOI: 10.1007/s00425-022-04024-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
Cytochorme P450s (CYPs) play a critical role in the catalysis of secondary metabolite biosynthetic pathways. For their commercial use, various strategies for metabolic pathway engineering using CYP as a potential target have been explored. Plants produce a vast diversity of secondary metabolites which are being used to treat various ailments and diseases. Some of these metabolites are difficult to obtain in large quantities limiting their industrial use. Cytochrome P450 enzymes (CYPs) are important catalysts in the biosynthesis of highly valued secondary metabolites, and are found in all domains of life. With the development of high-throughput sequencing and high-resolution mass spectrometry, new biosynthetic pathways and associated CYPs are being identified. In this review, we present CYPs identified from medicinal plants as a potential game changer in the metabolic engineering of secondary metabolic pathways. We present the achievements made so far in enhancing the production of important bioactivities through pathway engineering, giving some popular examples. At last, current challenges and possible strategies to overcome the limitations associated with CYP engineering to enhance the biosynthesis of target secondary metabolites are also highlighted.
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Affiliation(s)
- Anshika Sethi
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, 143 005, India
| | - Abhishek Bhandawat
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, 143 005, India
| | - Pratap Kumar Pati
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, 143 005, India.
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16
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Luo Y, Jiang Y, Chen L, Li C, Wang Y. Applications of protein engineering in the microbial synthesis of plant triterpenoids. Synth Syst Biotechnol 2022; 8:20-32. [PMID: 36381964 PMCID: PMC9634032 DOI: 10.1016/j.synbio.2022.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 11/26/2022] Open
Abstract
Triterpenoids are a class of natural products widely used in fields related to medicine and health due to their biological activities such as hepatoprotection, anti-inflammation, anti-viral, and anti-tumor. With the advancement in biotechnology, microorganisms have been used as cell factories to produce diverse natural products. Despite the significant progress that has been made in the construction of microbial cell factories for the heterogeneous biosynthesis of triterpenoids, the industrial production of triterpenoids employing microorganisms has been stymied due to the shortage of efficient enzymes as well as the low expression and low catalytic activity of heterologous proteins in microbes. Protein engineering has been demonstrated as an effective way for improving the specificity, catalytic activity, and stability of the enzyme, which can be employed to overcome these challenges. This review summarizes the current progress in the studies of Oxidosqualene cyclases (OSCs), cytochrome P450s (P450s), and UDP-glycosyltransferases (UGTs), the key enzymes in the triterpenoids synthetic pathway. The main obstacles restricting the efficient catalysis of these key enzymes are analyzed, the applications of protein engineering for the three key enzymes in the microbial synthesis of triterpenoids are systematically reviewed, and the challenges and prospects of protein engineering are also discussed.
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Affiliation(s)
- Yan Luo
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Yaozhu Jiang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Linhao Chen
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China,Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Ying Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China,Corresponding author.
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17
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Zhou S, Ma Y, Shang Y, Qi X, Huang S, Li J. Functional diversity and metabolic engineering of plant-specialized metabolites. LIFE METABOLISM 2022; 1:109-121. [PMID: 39872355 PMCID: PMC11749740 DOI: 10.1093/lifemeta/loac019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 08/17/2022] [Accepted: 08/22/2022] [Indexed: 01/30/2025]
Abstract
Plants are talented biochemists that produce a broad diversity of small molecules. These so-called specialized metabolites (SMs) play critical roles in the adaptive evolution of plants to defend against biotic and abiotic stresses, attract pollinators, and modulate soil microbiota for their own benefits. Many plant SMs have been used as nutrition and flavor compounds in our daily food, as well as drugs for treatment of human diseases. Current multi-omics tools have significantly accelerated the process of biosynthetic pathway elucidation in plants through correlation analyses, genetic mapping, and de novo biosynthetic gene cluster predictions. Understanding the biosynthesis of plant SMs has enabled reconstitution of naturally occurring specialized metabolic pathways in microbial hosts, providing a sustainable supply of these high-value molecules. In this review, we illustrate the general functions of several typical plant SMs in natural ecosystems and for human societies. We then provide an overview of current methods elucidating the biosynthetic pathways of plant SMs, and synthetic biology strategies that optimize the efficiency of heterologous biosynthetic pathways in microbial hosts. Moving forward, dissection of the functions and application of plant SMs by using current multidiscipline approaches would be greatly benefit to the scientific community and human societies.
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Affiliation(s)
- Shaoqun Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Yongshuo Ma
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Yi Shang
- Yunnan Key Laboratory of Potato Biology, The CAAS-YNNU-YINMORE Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, Yunan 650500, China
| | - Xiaoquan Qi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
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18
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Ghanbari Moheb Seraj R, Tohidfar M, Azimzadeh Irani M, Esmaeilzadeh-Salestani K, Moradian T, Ahmadikhah A, Behnamian M. Metabolomics analysis of milk thistle lipids to identify drought-tolerant genes. Sci Rep 2022; 12:12827. [PMID: 35896570 PMCID: PMC9329356 DOI: 10.1038/s41598-022-16887-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 07/18/2022] [Indexed: 11/09/2022] Open
Abstract
Milk thistle is an oil and medicinal crop known as an alternative oil crop with a high level of unsaturated fatty acids, which makes it a favorable edible oil for use in food production. To evaluate the importance of Milk thistle lipids in drought tolerance, an experiment was performed in field conditions under three different water deficit levels (Field capacity (FC), 70% FC and 40% FC). After harvesting seeds of the plant, their oily and methanolic extracts were isolated, and subsequently, types and amounts of lipids were measured using GC-MS. Genes and enzymes engaged in biosynthesizing of these lipids were identified and their expression in Arabidopsis was investigated under similar conditions. The results showed that content of almost all measured lipids of milk thistle decreased under severe drought stress, but genes (belonged to Arabidopsis), which were involved in their biosynthetic pathway showed different expression patterns. Genes biosynthesizing lipids, which had significant amounts were selected and their gene and metabolic network were established. Two networks were correlated, and for each pathway, their lipids and respective biosynthesizing genes were grouped together. Four up-regulated genes including PXG3, LOX2, CYP710A1, PAL and 4 down-regulated genes including FATA2, CYP86A1, LACS3, PLA2-ALPHA were selected. The expression of these eight genes in milk thistle was similar to Arabidopsis under drought stress. Thus, PXG3, PAL, LOX2 and CYP86A1 genes that increased expression were selected for protein analysis. Due to the lack of protein structure of these genes in the milk thistle, modeling homology was performed for them. The results of molecular docking showed that the four proteins CYP86A1, LOX2, PAL and PXG3 bind to ligands HEM, 11O, ACT and LIG, respectively. HEM ligand was involved in production of secondary metabolites and dehydration tolerance, and HEM binding site remained conserved in various plants. CA ligands were involved in synthesis of cuticles and waxes. Overall, this study confirmed the importance of lipids in drought stress tolerance in milk thistle.
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Affiliation(s)
- Rahele Ghanbari Moheb Seraj
- Department of Horticultural Sciences, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Masoud Tohidfar
- Department of Plant Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.
| | | | - Keyvan Esmaeilzadeh-Salestani
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Fr. R. Kreutzwaldi 1, 51014, Tartu, Estonia
| | - Toktam Moradian
- Department of Horticultural Sciences, Islamic Azad University, Shirvan Branch, Shirvan, Iran
| | - Asadollah Ahmadikhah
- Department of Plant Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Mahdi Behnamian
- Department of Horticultural Sciences, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
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19
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Wang S, Xu X, Lv X, Liu Y, Li J, Du G, Liu L. Construction and Optimization of the de novo Biosynthesis Pathway of Mogrol in Saccharomyces Cerevisiae. Front Bioeng Biotechnol 2022; 10:919526. [PMID: 35711645 PMCID: PMC9197265 DOI: 10.3389/fbioe.2022.919526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
Mogrol plays important roles in antihyperglycemic and antilipidemic through activating the AMP-activated protein kinase pathway. Although the synthesis pathway of mogrol in Siraitia grosvenorii has been clarified, few studies have focused on improving mogrol production. This study employed a modular engineerin g strategy to improve mogrol production in a yeast chassis cell. First, a de novo synthesis pathway of mogrol in Saccharomyces cerevisiae was constructed. Then, the metabolic flux of each synthetic module in mogrol metabolism was systematically optimized, including the enhancement of the precursor supply, inhibition of the sterol synthesis pathway using the Clustered Regularly Interspaced Short Palindromic Repeats Interference system (CRISPRi), and optimization of the expression and reduction system of P450 enzymes. Finally, the mogrol titer was increased to 9.1 μg/L, which was 455-fold higher than that of the original strain. The yeast strains engineered in this work can serve as the basis for creating an alternative way for mogrol production in place of extraction from S. grosvenorii.
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Affiliation(s)
- Siyu Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, China
| | - Xianhao Xu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, China
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20
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Zhang X, Luo W, Yao Y, Luo X, Han C, Zhong Y, Zhang B, Li D, Han L, Huang S, Greisen P, Shang Y. Enhanced chemoselectivity of a plant cytochrome P450 through protein engineering of surface and catalytic residues. ABIOTECH 2021; 2:215-225. [PMID: 36303887 PMCID: PMC9590459 DOI: 10.1007/s42994-021-00056-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/07/2021] [Indexed: 10/31/2022]
Abstract
Cytochrome P450s (P450s) are the most versatile catalysts utilized by plants to produce structurally and functionally diverse metabolites. Given the high degree of gene redundancy and challenge to functionally characterize plant P450s, protein engineering is used as a complementary strategy to study the mechanisms of P450-mediated reactions, or to alter their functions. We previously proposed an approach of engineering plant P450s based on combining high-accuracy homology models generated by Rosetta combined with data-driven design using evolutionary information of these enzymes. With this strategy, we repurposed a multi-functional P450 (CYP87D20) into a monooxygenase after redesigning its active site. Since most plant P450s are membrane-anchored proteins that are adapted to the micro-environments of plant cells, expressing them in heterologous hosts usually results in problems of expression or activity. Here, we applied computational design to tackle these issues by simultaneous optimization of the protein surface and active site. After screening 17 variants, effective substitutions of surface residues were observed to improve both expression and activity of CYP87D20. In addition, the identified substitutions were additive and by combining them a highly efficient C11 hydroxylase of cucurbitadienol was created to participate in the mogrol biosynthesis. This study shows the importance of considering the interplay between surface and active site residues for P450 engineering. Our integrated strategy also opens an avenue to create more tailoring enzymes with desired functions for the metabolic engineering of high-valued compounds like mogrol, the precursor of natural sweetener mogrosides. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-021-00056-z.
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Affiliation(s)
- Xiaopeng Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518116 China
| | - Wei Luo
- Yunnan Key Laboratory of Potato Biology, The CAAS-YNNU-YINMORE Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650500 China
| | - Yinying Yao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518116 China
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xuming Luo
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518116 China
| | - Chao Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yang Zhong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518116 China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Bo Zhang
- Yunnan Key Laboratory of Potato Biology, The CAAS-YNNU-YINMORE Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650500 China
| | - Dawei Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518116 China
| | - Lida Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518116 China
| | - Per Greisen
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518116 China
- Novo Nordisk Research Center Seattle Inc, Seattle, WA 98109 USA
| | - Yi Shang
- Yunnan Key Laboratory of Potato Biology, The CAAS-YNNU-YINMORE Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650500 China
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21
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Jiang L, Huang L, Cai J, Xu Z, Lian J. Functional expression of eukaryotic cytochrome P450s in yeast. Biotechnol Bioeng 2020; 118:1050-1065. [PMID: 33205834 DOI: 10.1002/bit.27630] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 09/28/2020] [Accepted: 11/11/2020] [Indexed: 12/22/2022]
Abstract
Cytochrome P450 enzymes (P450s) are a superfamily of heme-thiolate proteins widely existing in various organisms. Due to their key roles in secondary metabolism, degradation of xenobiotics, and carcinogenesis, there is a great demand to heterologously express and obtain a sufficient amount of active eukaryotic P450s. However, most eukaryotic P450s are endoplasmic reticulum-localized membrane proteins, which is the biggest challenge for functional expression to high levels. Furthermore, the functions of P450s require the cooperation of cytochrome P450 reductases for electron transfer. Great efforts have been devoted to the heterologous expression of eukaryotic P450s, and yeasts, particularly Saccharomyces cerevisiae are frequently considered as the first expression systems to be tested for this challenging purpose. This review discusses the strategies for improving the expression and activity of eukaryotic P450s in yeasts, followed by examples of P450s involved in biosynthetic pathway engineering.
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Affiliation(s)
- Lihong Jiang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Jin Cai
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
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22
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Shang Y, Huang S. Engineering Plant Cytochrome P450s for Enhanced Synthesis of Natural Products: Past Achievements and Future Perspectives. PLANT COMMUNICATIONS 2020; 1:100012. [PMID: 33404545 PMCID: PMC7747987 DOI: 10.1016/j.xplc.2019.100012] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Cytochrome P450s (P450s) are the most versatile catalysts and are widely used by plants to synthesize a vast array of structurally diverse specialized metabolites that not only play essential ecological roles but also constitute a valuable resource for the development of new drugs. To accelerate the metabolic engineering of these high-value metabolites, it is imperative to identify and characterize pathway P450s, and to further improve their activities through protein engineering. In this review, we focus on P450 engineering and summarize the major strategies for enhancing the stability and activity of P450s and successful cases of P450 engineering. Studies in which the functions of P450s were altered to create de novo metabolic pathways or novel compounds are discussed as well. We also overview emerging tools, specifically DNA synthesis, machine learning, and de novo protein design, as well as the evolutionary patterns of P450s unveiled from a massive number of DNA sequences that could be integrated to accelerate the engineering of these enzymes. These approaches would greatly aid in the exploitation of plant-specialized metabolites or derivatives for various uses including medical applications.
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Affiliation(s)
- Yi Shang
- Key Laboratory for Potato Biology of Yunnan Province, The CAAS-YNNU-YINMORE Joint Academy of Potato Science, Yunnan Normal University, Kunming, China
| | - Sanwen Huang
- Lingnan Guangdong Laboratory of Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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23
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Siedhoff NE, Schwaneberg U, Davari MD. Machine learning-assisted enzyme engineering. Methods Enzymol 2020; 643:281-315. [DOI: 10.1016/bs.mie.2020.05.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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