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Song Y, Liu H, Quax WJ, Zhang Z, Chen Y, Yang P, Cui Y, Shi Q, Xie X. Application of valencene and prospects for its production in engineered microorganisms. Front Microbiol 2024; 15:1444099. [PMID: 39171255 PMCID: PMC11335630 DOI: 10.3389/fmicb.2024.1444099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 07/29/2024] [Indexed: 08/23/2024] Open
Abstract
Valencene, a sesquiterpene with the odor of sweet and fresh citrus, is widely used in the food, beverage, flavor and fragrance industry. Valencene is traditionally obtained from citrus fruits, which possess low concentrations of this compound. In the past decades, the great market demand for valencene has attracted considerable attention from researchers to develop novel microbial cell factories for more efficient and sustainable production modes. This review initially discusses the biosynthesis of valencene in plants, and summarizes the current knowledge of the key enzyme valencene synthase in detail. In particular, we highlight the heterologous production of valencene in different hosts including bacteria, fungi, microalgae and plants, and focus on describing the engineering strategies used to improve valencene production. Finally, we propose potential engineering directions aiming to further increase the production of valencene in microorganisms.
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Affiliation(s)
- Yafeng Song
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Detection Center of Microbiology, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Huizhong Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Detection Center of Microbiology, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Wim J. Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Zhiqing Zhang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Detection Center of Microbiology, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yiwen Chen
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Detection Center of Microbiology, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Ping Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Detection Center of Microbiology, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yinhua Cui
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Detection Center of Microbiology, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qingshan Shi
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Detection Center of Microbiology, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiaobao Xie
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Detection Center of Microbiology, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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Lv X, Li Y, Xiu X, Liao C, Xu Y, Liu Y, Li J, Du G, Liu L. CRISPR genetic toolkits of classical food microorganisms: Current state and future prospects. Biotechnol Adv 2023; 69:108261. [PMID: 37741424 DOI: 10.1016/j.biotechadv.2023.108261] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/17/2023] [Accepted: 09/18/2023] [Indexed: 09/25/2023]
Abstract
Production of food-related products using microorganisms in an environmentally friendly manner is a crucial solution to global food safety and environmental pollution issues. Traditional microbial modification methods rely on artificial selection or natural mutations, which require time for repeated screening and reproduction, leading to unstable results. Therefore, it is imperative to develop rapid, efficient, and precise microbial modification technologies. This review summarizes recent advances in the construction of gene editing and metabolic regulation toolkits based on the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (CRISPR-Cas) systems and their applications in reconstructing food microorganism metabolic networks. The development and application of gene editing toolkits from single-site gene editing to multi-site and genome-scale gene editing was also introduced. Moreover, it presented a detailed introduction to CRISPR interference, CRISPR activation, and logic circuit toolkits for metabolic network regulation. Moreover, the current challenges and future prospects for developing CRISPR genetic toolkits were also discussed.
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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
| | - Yang 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
| | - Xiang Xiu
- 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
| | - Chao Liao
- 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
| | - Yameng 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
| | - 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
| | - 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; Food Laboratory of Zhongyuan, Jiangnan University, Wuxi 214122, China.
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Boukid F, Ganeshan S, Wang Y, Tülbek MÇ, Nickerson MT. Bioengineered Enzymes and Precision Fermentation in the Food Industry. Int J Mol Sci 2023; 24:10156. [PMID: 37373305 DOI: 10.3390/ijms241210156] [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: 05/20/2023] [Revised: 06/06/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Enzymes have been used in the food processing industry for many years. However, the use of native enzymes is not conducive to high activity, efficiency, range of substrates, and adaptability to harsh food processing conditions. The advent of enzyme engineering approaches such as rational design, directed evolution, and semi-rational design provided much-needed impetus for tailor-made enzymes with improved or novel catalytic properties. Production of designer enzymes became further refined with the emergence of synthetic biology and gene editing techniques and a plethora of other tools such as artificial intelligence, and computational and bioinformatics analyses which have paved the way for what is referred to as precision fermentation for the production of these designer enzymes more efficiently. With all the technologies available, the bottleneck is now in the scale-up production of these enzymes. There is generally a lack of accessibility thereof of large-scale capabilities and know-how. This review is aimed at highlighting these various enzyme-engineering strategies and the associated scale-up challenges, including safety concerns surrounding genetically modified microorganisms and the use of cell-free systems to circumvent this issue. The use of solid-state fermentation (SSF) is also addressed as a potentially low-cost production system, amenable to customization and employing inexpensive feedstocks as substrate.
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Affiliation(s)
- Fatma Boukid
- ClonBio Group Ltd., 6 Fitzwilliam Pl, D02 XE61 Dublin, Ireland
| | | | - Yingxin Wang
- Saskatchewan Food Industry Development Centre, Saskatoon, SK S7M 5V1, Canada
| | | | - Michael T Nickerson
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
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Kolasinliler G, Aagre MM, Akkale C, Kaya HB. The use of CRISPR-Cas-based systems in bacterial cell factories. Biochem Eng J 2023. [DOI: 10.1016/j.bej.2023.108880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
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5
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Metabolism balance regulation for squalene production by disturbing triglyceride (TAG) synthesis in Schizochytrium sp. ALGAL RES 2023. [DOI: 10.1016/j.algal.2022.102946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Park J, Woo HM. Co-production of l-Lysine and Heterologous Squalene in CRISPR/dCas9-Assisted Corynebacterium glutamicum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14755-14760. [PMID: 36374274 DOI: 10.1021/acs.jafc.2c05562] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Corynebacterium glutamicum is widely used for a large-scale industrial producer of feed additive amino acids, such as l-lysine. Moreover, C. glutamicum has been engineered for producing various non-native chemicals, including terpenes. For the first time, C. glutamicum was engineered for co-production of l-lysine and heterologous squalene. To control metabolic fluxes for either the l-lysine biosynthesis pathway or the squalene biosynthesis pathway, pyruvate, an intermediate in the central metabolism, a node was regulated by a clustered regularly interspaced short palindromic repeat (CRISPR) interference system. Repressing pyc encoding for pyruvate carboxylase in the l-lysine producer (DM1919) and its derivatives resulted in 99.24 ± 7.63 mg/L total squalene and 6.25 ± 0.20 g/L extracellular lysine at 120 h. Furthermore, various oil overlays were tested for efficient co-productions. In situ extraction with corn oil (10%, v/v) exhibited a separation of 99.75% (w/v) of total squalene (intra- and extracellular squalene), while l-lysine can be secreted in the medium. This co-production strategy will help a potential bioprocess of amino acid production with various terpenes.
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Affiliation(s)
- Jaehyun Park
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- BioFoundry Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- BioFoundry Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
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Li N, Shan X, Zhou J, Yu S. Identification of key genes through the constructed CRISPR-dcas9 to facilitate the efficient production of O-acetylhomoserine in Corynebacterium glutamicum. Front Bioeng Biotechnol 2022; 10:978686. [PMID: 36185436 PMCID: PMC9515461 DOI: 10.3389/fbioe.2022.978686] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
O-Acetylhomoserine (OAH) is an important platform chemical for the synthesis of L-methamidophos and l-methionine. It has been produced efficiently in Corynebacterium glutamicum. However, a wider range of key factors had not been identified, limiting further increases in OAH production. This study successfully identified some limiting factors and regulated them to improve OAH titer. Firstly, an efficient clustered regularly interspaced short palindromic repeats/dead CRISPR associated protein 9 (CRISPR-dCas9) system was constructed and used to identify the key genes in central metabolism and branch pathways associated with OAH biosynthesis. Then, the gltA gene involved in TCA cycle was identified as the most critical gene. A sequential promoter PNCgl2698, which showed different transcriptional intensity in different strain growth periods, was used to control the expression of gltA gene, resulting in OAH production of 7.0 g/L at 48 h. Finally, the OAH titer of the engineered strain reached 25.9 g/L at 72 h in a 5-L bioreactor. These results show that the identification and regulation of key genes are critical for OAH biosynthesis, which would provide a better research basis for the industrial production of OAH in C. glutamicum.
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Affiliation(s)
- Ning Li
- Science Center for Future Foods, Jiangnan University, Wuxi, China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiaoyu Shan
- Science Center for Future Foods, Jiangnan University, Wuxi, China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, Wuxi, China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
| | - Shiqin Yu
- Science Center for Future Foods, Jiangnan University, Wuxi, China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, China
- *Correspondence: Shiqin Yu,
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Li W, Huang C, Chen J. The application of CRISPR /Cas mediated gene editing in synthetic biology: Challenges and optimizations. Front Bioeng Biotechnol 2022; 10:890155. [PMID: 36091445 PMCID: PMC9452635 DOI: 10.3389/fbioe.2022.890155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and its associated enzymes (Cas) is a simple and convenient genome editing tool that has been used in various cell factories and emerging synthetic biology in the recent past. However, several problems, including off-target effects, cytotoxicity, and low efficiency of multi-gene editing, are associated with the CRISPR/Cas system, which have limited its application in new species. In this review, we briefly describe the mechanisms of CRISPR/Cas engineering and propose strategies to optimize the system based on its defects, including, but not limited to, enhancing targeted specificity, reducing toxicity related to Cas protein, and improving multi-point editing efficiency. In addition, some examples of improvements in synthetic biology are also highlighted. Finally, future perspectives of system optimization are discussed, providing a reference for developing safe genome-editing tools for new species.
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Affiliation(s)
- Wenqian Li
- MOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing,China
| | - Can Huang
- MOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing,China
| | - Jingyu Chen
- MOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing,China
- *Correspondence: Jingyu Chen,
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Call SN, Andrews LB. CRISPR-Based Approaches for Gene Regulation in Non-Model Bacteria. Front Genome Ed 2022; 4:892304. [PMID: 35813973 PMCID: PMC9260158 DOI: 10.3389/fgeed.2022.892304] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/11/2022] [Indexed: 01/08/2023] Open
Abstract
CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) have become ubiquitous approaches to control gene expression in bacteria due to their simple design and effectiveness. By regulating transcription of a target gene(s), CRISPRi/a can dynamically engineer cellular metabolism, implement transcriptional regulation circuitry, or elucidate genotype-phenotype relationships from smaller targeted libraries up to whole genome-wide libraries. While CRISPRi/a has been primarily established in the model bacteria Escherichia coli and Bacillus subtilis, a growing numbering of studies have demonstrated the extension of these tools to other species of bacteria (here broadly referred to as non-model bacteria). In this mini-review, we discuss the challenges that contribute to the slower creation of CRISPRi/a tools in diverse, non-model bacteria and summarize the current state of these approaches across bacterial phyla. We find that despite the potential difficulties in establishing novel CRISPRi/a in non-model microbes, over 190 recent examples across eight bacterial phyla have been reported in the literature. Most studies have focused on tool development or used these CRISPRi/a approaches to interrogate gene function, with fewer examples applying CRISPRi/a gene regulation for metabolic engineering or high-throughput screens and selections. To date, most CRISPRi/a reports have been developed for common strains of non-model bacterial species, suggesting barriers remain to establish these genetic tools in undomesticated bacteria. More efficient and generalizable methods will help realize the immense potential of programmable CRISPR-based transcriptional control in diverse bacteria.
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Affiliation(s)
- Stephanie N. Call
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, United States
| | - Lauren B. Andrews
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, United States
- Biotechnology Training Program, University of Massachusetts Amherst, Amherst, MA, United States
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, United States
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Recent advances in the microbial production of squalene. World J Microbiol Biotechnol 2022; 38:91. [PMID: 35426523 PMCID: PMC9010451 DOI: 10.1007/s11274-022-03273-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/30/2022] [Indexed: 11/06/2022]
Abstract
Squalene is a triterpene hydrocarbon, a biochemical precursor for all steroids in plants and animals. It is a principal component of human surface lipids, in particular of sebum. Squalene has several applications in the food, pharmaceutical, and medical sectors. It is essentially used as a dietary supplement, vaccine adjuvant, moisturizer, cardio-protective agent, anti-tumor agent and natural antioxidant. With the increased demand for squalene along with regulations on shark-derived squalene, there is a need to find alternatives for squalene production which are low-cost as well as sustainable. Microbial platforms are being considered as a potential option to meet such challenges. Considerable progress has been made using both wild-type and engineered microbial strains for improved productivity and yields of squalene. Native strains for squalene production are usually limited by low growth rates and lesser titers. Metabolic engineering, which is a rational strain engineering tool, has enabled the development of microbial strains such as Saccharomyces cerevisiae and Yarrowia lipolytica, to overproduce the squalene in high titers. This review focuses on key strain engineering strategies involving both in-silico and in-vitro techniques. Emphasis is made on gene manipulations for improved precursor pool, enzyme modifications, cofactor regeneration, up-regulation of limiting reactions, and downregulation of competing reactions during squalene production. Process strategies and challenges related to both upstream and downstream during mass cultivation are detailed.
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Abstract
Terpenoids represent the largest group of secondary metabolites with variable structures and functions. Terpenoids are well known for their beneficial application in human life, such as pharmaceutical products, vitamins, hormones, anticancer drugs, cosmetics, flavors and fragrances, foods, agriculture, and biofuels. Recently, engineering microbial cells have been provided with a sustainable approach to produce terpenoids with high yields. Noticeably, the clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) system has emerged as one of the most efficient genome-editing technologies to engineer microorganisms for improving terpenoid production. In this review, we summarize the application of the CRISPR-Cas system for the production of terpenoids in microbial hosts such as Escherichia coli, Saccharomyces cerevisiae, Corynebacterium glutamicum, and Pseudomonas putida. CRISPR-Cas9 deactivated Cas9 (dCas9)-based CRISPR (CRISPRi), and the dCas9-based activator (CRISPRa) have been used in either individual or combinatorial systems to control the metabolic flux for enhancing the production of terpenoids. Finally, the prospects of using the CRISPR-Cas system in terpenoid production are also discussed.
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Affiliation(s)
- Luan Luong Chu
- Faculty of Biotechnology, Chemistry and Environmental Engineering, Phenikaa University, Hanoi, Viet Nam.,Bioresource Research Center, Phenikaa University, Hanoi, Viet Nam
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Fordjour E, Mensah EO, Hao Y, Yang Y, Liu X, Li Y, Liu CL, Bai Z. Toward improved terpenoids biosynthesis: strategies to enhance the capabilities of cell factories. BIORESOUR BIOPROCESS 2022; 9:6. [PMID: 38647812 PMCID: PMC10992668 DOI: 10.1186/s40643-022-00493-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/04/2022] [Indexed: 02/22/2023] Open
Abstract
Terpenoids form the most diversified class of natural products, which have gained application in the pharmaceutical, food, transportation, and fine and bulk chemical industries. Extraction from naturally occurring sources does not meet industrial demands, whereas chemical synthesis is often associated with poor enantio-selectivity, harsh working conditions, and environmental pollutions. Microbial cell factories come as a suitable replacement. However, designing efficient microbial platforms for isoprenoid synthesis is often a challenging task. This has to do with the cytotoxic effects of pathway intermediates and some end products, instability of expressed pathways, as well as high enzyme promiscuity. Also, the low enzymatic activity of some terpene synthases and prenyltransferases, and the lack of an efficient throughput system to screen improved high-performing strains are bottlenecks in strain development. Metabolic engineering and synthetic biology seek to overcome these issues through the provision of effective synthetic tools. This review sought to provide an in-depth description of novel strategies for improving cell factory performance. We focused on improving transcriptional and translational efficiencies through static and dynamic regulatory elements, enzyme engineering and high-throughput screening strategies, cellular function enhancement through chromosomal integration, metabolite tolerance, and modularization of pathways.
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Affiliation(s)
- Eric Fordjour
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Emmanuel Osei Mensah
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Yunpeng Hao
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Yankun Yang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Xiuxia Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Ye Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Chun-Li Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China.
| | - Zhonghu Bai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China.
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Tang R, Wen Q, Li M, Zhang W, Wang Z, Yang J. Recent Advances in the Biosynthesis of Farnesene Using Metabolic Engineering. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:15468-15483. [PMID: 34905684 DOI: 10.1021/acs.jafc.1c06022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Farnesene, as an important sesquiterpene isoprenoid polymer of acetyl-CoA, is a renewable feedstock for diesel fuel, polymers, and cosmetics. It has been widely applied in agriculture, medicine, energy, and other fields. In recent years, farnesene biosynthesis is considered a green and economical approach because of its mild reaction conditions, low environmental pollution, and sustainability. Metabolic engineering has been widely applied to construct cell factories for farnesene biosynthesis. In this paper, the research progress, common problems, and strategies of farnesene biosynthesis are reviewed. They are mainly described from the perspectives of the current status of farnesene biosynthesis in different host cells, optimization of the metabolic pathway for farnesene biosynthesis, and key enzymes for farnesene biosynthesis. Furthermore, the challenges and prospects for future farnesene biosynthesis are discussed.
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Affiliation(s)
- Ruohao Tang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center of Qingdao Agricultural University. Qingdao, Shandong 266109, People's Republic of China
- Shandong Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong 266109, People's Republic of China
| | - Qifeng Wen
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center of Qingdao Agricultural University. Qingdao, Shandong 266109, People's Republic of China
- Shandong Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong 266109, People's Republic of China
| | - Meijie Li
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center of Qingdao Agricultural University. Qingdao, Shandong 266109, People's Republic of China
- Shandong Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong 266109, People's Republic of China
| | - Wei Zhang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center of Qingdao Agricultural University. Qingdao, Shandong 266109, People's Republic of China
- Shandong Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong 266109, People's Republic of China
| | - Zhaobao Wang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center of Qingdao Agricultural University. Qingdao, Shandong 266109, People's Republic of China
- Shandong Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong 266109, People's Republic of China
| | - Jianming Yang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center of Qingdao Agricultural University. Qingdao, Shandong 266109, People's Republic of China
- Shandong Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong 266109, People's Republic of China
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Recent progress in metabolic engineering of Corynebacterium glutamicum for the production of C4, C5, and C6 chemicals. KOREAN J CHEM ENG 2021. [DOI: 10.1007/s11814-021-0788-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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15
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Young R, Haines M, Storch M, Freemont PS. Combinatorial metabolic pathway assembly approaches and toolkits for modular assembly. Metab Eng 2020; 63:81-101. [PMID: 33301873 DOI: 10.1016/j.ymben.2020.12.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 11/16/2020] [Accepted: 12/03/2020] [Indexed: 12/18/2022]
Abstract
Synthetic Biology is a rapidly growing interdisciplinary field that is primarily built upon foundational advances in molecular biology combined with engineering design principles such as modularity and interoperability. The field considers living systems as programmable at the genetic level and has been defined by the development of new platform technologies and methodological advances. A key concept driving the field is the Design-Build-Test-Learn cycle which provides a systematic framework for building new biological systems. One major application area for synthetic biology is biosynthetic pathway engineering that requires the modular assembly of different genetic regulatory elements and biosynthetic enzymes. In this review we provide an overview of modular DNA assembly and describe and compare the plethora of in vitro and in vivo assembly methods for combinatorial pathway engineering. Considerations for part design and methods for enzyme balancing are also presented, and we briefly discuss alternatives to intracellular pathway assembly including microbial consortia and cell-free systems for biosynthesis. Finally, we describe computational tools and automation for pathway design and assembly and argue that a deeper understanding of the many different variables of genetic design, pathway regulation and cellular metabolism will allow more predictive pathway design and engineering.
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Affiliation(s)
- Rosanna Young
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK
| | - Matthew Haines
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK
| | - Marko Storch
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK; London Biofoundry, Imperial College Translation & Innovation Hub, London, W12 0BZ, UK
| | - Paul S Freemont
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK; London Biofoundry, Imperial College Translation & Innovation Hub, London, W12 0BZ, UK; UK DRI Care Research and Technology Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK.
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16
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Lim H, Park J, Woo HM. Overexpression of the Key Enzymes in the Methylerythritol 4-phosphate Pathway in Corynebacterium glutamicum for Improving Farnesyl Diphosphate-Derived Terpene Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:10780-10786. [PMID: 32854502 DOI: 10.1021/acs.jafc.0c04307] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
A systematic and combinatorial optimization has been employed to metabolically engineer microbes for identifying key gene targets for overexpression to increase the intermediate pools for terpenoid production. Herein, the methylerythritol 4-phosphate (MEP) pathway in Corynebacterium glutamicum, an industrial host, was investigated to identify the key genes whose overexpression would improve the production of farnesyl diphosphate (FPP)-derived terpenoids (squalene and α-farnesene). Using a combinatorial approach with the single, double, and triple expression of genes in the MEP pathway in a high-throughput fermentation, overexpression of the ispDF genes, along with the known dxs and idi genes, was most effective at increasing the squalene contents, i.e., by 14-fold. The dxr gene was identified as the key target enzyme for α-farnesene production. This result could provide fundamental information for improving the metabolic engineering of C. glutamicum for terpene production via an optimized MEP pathway.
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Affiliation(s)
- Hyeonbae Lim
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Jaehyun Park
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- BioFoundry Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
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17
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Choi SY, Sim SJ, Ko SC, Son J, Lee JS, Lee HJ, Chang WS, Woo HM. Scalable Cultivation of Engineered Cyanobacteria for Squalene Production from Industrial Flue Gas in a Closed Photobioreactor. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:10050-10055. [PMID: 32851842 DOI: 10.1021/acs.jafc.0c03133] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Economically feasible photosynthetic cultivation of microalgal and cyanobacterial strains is crucial for the biological conversion of CO2 and potential CO2 mitigation to challenge global warming. To overcome the economic barriers, the production of value-added chemicals was desired by compensating for the overall processing cost. Here, we engineered cyanobacteria for photosynthetic squalene production and cultivated them in a scalable photobioreactor using industrial flue gas. First, an inducer-free gene expression system was developed for the cyanobacteria to lower production const. Then, the recombinant cyanobacteria were cultivated in a closed photobioreactor (100 L) using flue gas (5% CO2) as the sole carbon source under natural sunlight as the only energy source. Seasonal light intensities and temperatures were analyzed along with cyanobacterial cell growth and squalene production in August and October 2019. As a result, the effective irradiation hours were the most critical factor for the large-scale cultivation of cyanobacteria. Thus, an automated photobioprocess system will be developed based on the regional light sources.
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Affiliation(s)
- Sun Young Choi
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- BioFoundry Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Sang Jun Sim
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, South Korea
| | - Sung Cheon Ko
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Jigyeong Son
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Jeong Seop Lee
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, South Korea
| | - Hyun Jeong Lee
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- BioFoundry Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Won Seok Chang
- Research Institute, Korea District Heating Corporation, 186 Bundang-dong, Bundang-gu, Seongnam-si 13585, Gyeonggi-do, South Korea
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- BioFoundry Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
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18
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Li N, Zeng W, Xu S, Zhou J. Obtaining a series of native gradient promoter-5'-UTR sequences in Corynebacterium glutamicum ATCC 13032. Microb Cell Fact 2020; 19:120. [PMID: 32493332 PMCID: PMC7268698 DOI: 10.1186/s12934-020-01376-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/25/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Corynebacterium glutamicum is an important industrial microorganism used for the production of many valuable compounds, especially amino acids and their derivatives. For fine-tuning of metabolic pathways, synthetic biological tools are largely based on the rational application of promoters. However, the limited number of promoters make it difficult. RESULTS In this study, according to the analysis of RNA-Seq data, 90 DNA fragments with lengths of 200-500 bp that may contain promoter-5'-UTR (PUTR) sequences were amplified and linked to a fluorescent protein gene. When compared with the common strong PUTR PsodUTR, 17 strong PUTRs were obtained, which maintained stable expression strengths from the early to post stationary phase. Among them, PNCgl1676UTR was the strongest and its fluorescent protein expression level was more than five times higher than that of PsodUTR. Furthermore, nine typical chemicals related to the biosynthesis of sulfur-containing amino acids (such as L-methionine, L-cysteine) were selected as stress substances to preliminarily explore the stress on these PUTRs. The results showed that the expression of PbrnFUTR was activated by L-methionine, while that of PNCgl1202UTR was severely inhibited by L-lysine. CONCLUSIONS These findings demonstrated that the selected PUTRs can stably express different genes, such as the red fluorescence protein gene, and can be useful for fine-tuning regulation of metabolic networks in C. glutamicum or for establishing high-throughput screening strategies through biosensor for the production of useful compounds.
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Affiliation(s)
- Ning Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Weizhu Zeng
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Sha Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China. .,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China. .,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
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19
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Li M, Chen J, Wang Y, Liu J, Huang J, Chen N, Zheng P, Sun J. Efficient Multiplex Gene Repression by CRISPR-dCpf1 in Corynebacterium glutamicum. Front Bioeng Biotechnol 2020; 8:357. [PMID: 32391351 PMCID: PMC7193084 DOI: 10.3389/fbioe.2020.00357] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 03/31/2020] [Indexed: 01/14/2023] Open
Abstract
Corynebacterium glutamicum is an important workhorse for industrial production of diversiform bioproducts. Multiplex control of metabolic pathway genes is crucial for maximizing biosynthesis of desired products. However, few tools for simultaneously regulating multiple genes in C. glutamicum have been reported. Here, a CRISPR-dCpf1-based multiplex gene repression system was developed for C. glutamicum. This system successfully repressed two fluorescent reporter genes simultaneously by expressing a dCpf1 (E1006A, D917A) and a designed single crRNA array. To demonstrate applications of this CRISPR-dCpf1 system in metabolic engineering, we applied this system to repress four genes involved in lysine biosynthesis (gltA, pck, pgi, and hom) with a single array, which increased the lysine titer and yield for over 4.0-fold. Quantitative PCR demonstrated that transcription of all the four endogenous target genes were repressed by over 90%. Thus, the CRISPR-dCpf1 system is a simple and effective technique for multiplex gene repression in C. glutamicum and holds promise for metabolic engineering of C. glutamicum to produce valuable chemicals and fuels.
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Affiliation(s)
- Mingyue Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jiuzhou Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yu Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jiao Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jingwen Huang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ning Chen
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Ping Zheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jibin Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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20
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Zhang S, Guo F, Yan W, Dai Z, Dong W, Zhou J, Zhang W, Xin F, Jiang M. Recent Advances of CRISPR/Cas9-Based Genetic Engineering and Transcriptional Regulation in Industrial Biology. Front Bioeng Biotechnol 2020; 7:459. [PMID: 32047743 PMCID: PMC6997136 DOI: 10.3389/fbioe.2019.00459] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 12/19/2019] [Indexed: 12/17/2022] Open
Abstract
Industrial biology plays a crucial role in the fields of medicine, health, food, energy, and so on. However, the lack of efficient genetic engineering tools has restricted the rapid development of industrial biology. Recently, the emergence of clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system brought a breakthrough in genome editing technologies due to its high orthogonality, versatility, and efficiency. In this review, we summarized the barriers of CRISPR/Cas9 and corresponding solutions for efficient genetic engineering in industrial microorganisms. In addition, the advances of industrial biology employing the CRISPR/Cas9 system were compared in terms of its application in bacteria, yeast, and filamentous fungi. Furthermore, the cooperation between CRISPR/Cas9 and synthetic biology was discussed to help build complex and programmable gene circuits, which can be used in industrial biotechnology.
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Affiliation(s)
- Shangjie Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Feng Guo
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Wei Yan
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Zhongxue Dai
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, China
| | - Jie Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, China
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21
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Wu XY, Guo XY, Zhang B, Jiang Y, Ye BC. Recent Advances of L-ornithine Biosynthesis in Metabolically Engineered Corynebacterium glutamicum. Front Bioeng Biotechnol 2020; 7:440. [PMID: 31998705 PMCID: PMC6962107 DOI: 10.3389/fbioe.2019.00440] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 12/11/2019] [Indexed: 12/31/2022] Open
Abstract
L-ornithine, a valuable non-protein amino acid, has a wide range of applications in the pharmaceutical and food industries. Currently, microbial fermentation is a promising, sustainable, and environment-friendly method to produce L-ornithine. However, the industrial production capacity of L-ornithine by microbial fermentation is low and rarely meets the market demands. Various strategies have been employed to improve the L-ornithine production titers in the model strain, Corynebacterium glutamicum, which serves as a major indicator for improving the cost-effectiveness of L-ornithine production by microbial fermentation. This review focuses on the development of high L-ornithine-producing strains by metabolic engineering and reviews the recent advances in breeding strategies, such as reducing by-product formation, improving the supplementation of precursor glutamate, releasing negative regulation and negative feedback inhibition, increasing the supply of intracellular cofactors, modulating the central metabolic pathway, enhancing the transport system, and adaptive evolution for improving L-ornithine production.
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Affiliation(s)
- Xiao-Yu Wu
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Xiao-Yan Guo
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Bin Zhang
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Yan Jiang
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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22
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Liu W, Tang D, Wang H, Lian J, Huang L, Xu Z. Combined genome editing and transcriptional repression for metabolic pathway engineering in Corynebacterium glutamicum using a catalytically active Cas12a. Appl Microbiol Biotechnol 2019; 103:8911-8922. [PMID: 31583448 DOI: 10.1007/s00253-019-10118-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 08/20/2019] [Accepted: 09/03/2019] [Indexed: 10/25/2022]
Abstract
Corynebacterium glutamicum is a versatile workhorse for producing industrially important commodities. The design of an optimal strain often requires the manipulation of metabolic and regulatory genes to different levels, such as overexpression, downregulation, and deletion. Unfortunately, few tools to achieve multiple functions simultaneously have been reported. Here, a dual-functional clustered regularly interspaced short palindromic repeats (CRISPR) (RE-CRISPR) system that combined genome editing and transcriptional repression was designed using a catalytically active Cas12a (a.k.a. Cpf1) in C. glutamicum. Firstly, gene deletion was achieved using Cas12a under a constitutive promoter. Then, via engineering of the guide RNA sequences, transcriptional repression was successfully achieved using a catalytically active Cas12a with crRNAs containing 15 or 16 bp spacer sequences, whose gene repression efficiency was comparable to that of the canonical system (deactivated Cas12a with full-length crRNAs). Finally, RE-CRISPR was developed to achieve genome editing and transcriptional repression simultaneously by transforming a single crRNA plasmid and Cas12a plasmid. The application of RE-CRISPR was demonstrated to increase the production of cysteine and serine for ~ 3.7-fold and 2.5-fold, respectively, in a single step. This study expands the application of CRISPR/Cas12a-based genome engineering and provides a powerful synthetic biology tool for multiplex metabolic engineering of C. glutamicum.
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Affiliation(s)
- Wei Liu
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Dandan Tang
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- State Key Laboratory of Clean Energy Utilization, College of Energy Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Haijiao Wang
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
- Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
| | - Lei Huang
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
- Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
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23
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Baschieri A, Pizzol R, Guo Y, Amorati R, Valgimigli L. Calibration of Squalene, p-Cymene, and Sunflower Oil as Standard Oxidizable Substrates for Quantitative Antioxidant Testing. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:6902-6910. [PMID: 31132263 DOI: 10.1021/acs.jafc.9b01400] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The autoxidation kinetics of stripped sunflower oil (SSO), squalene (SQ), and p-cymene ( p-C) initiated by 2,2'-azobis(isobutyronitrile) at 303 K were investigated under controlled conditions by differential oximetry in order to build reference model systems that are representative of the natural variability of oxidizable materials, for quantitative antioxidant testing. Rate constants for oxidative chain propagation ( kp) and chain termination (2 kt) and the oxidizability ( kp/√2 kt) were measured using 2,6-di- tert-butyl-4-methoxyphenol, 2,2,5,7,8-pentamethyl-6-chromanol, BHT, and 4-methoxyphenol as reference antioxidants. Measured values of kp (M-1 s-1)/2 kt (M-1 s-1)/oxidizability (M-1/2 s-1/2) at 303 K in chlorobenzene were 66.9/3.45 × 106/3.6 × 10-2, 68.0/7.40 × 106/2.5 × 10-2, and 0.83/2.87 × 106/4.9 × 10-4, respectively, for SSO, SQ, and p-C. Quercetin, magnolol, caffeic acid phenethyl ester, and 2,4,6-trimethylphenol were investigated to validate calibrations. The distinctive usefulness of the three substrates in testing antioxidants is discussed.
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Affiliation(s)
- Andrea Baschieri
- Department of Chemistry "G. Ciamician" , University of Bologna , Via S. Giacomo 11 , 40126 Bologna , Italy
| | - Romeo Pizzol
- Department of Chemistry "G. Ciamician" , University of Bologna , Via S. Giacomo 11 , 40126 Bologna , Italy
| | - Yafang Guo
- Department of Chemistry "G. Ciamician" , University of Bologna , Via S. Giacomo 11 , 40126 Bologna , Italy
| | - Riccardo Amorati
- Department of Chemistry "G. Ciamician" , University of Bologna , Via S. Giacomo 11 , 40126 Bologna , Italy
| | - Luca Valgimigli
- Department of Chemistry "G. Ciamician" , University of Bologna , Via S. Giacomo 11 , 40126 Bologna , Italy
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24
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Establishment and application of CRISPR interference to affect sporulation, hydrogen peroxide detoxification, and mannitol catabolism in the methylotrophic thermophile Bacillus methanolicus. Appl Microbiol Biotechnol 2019; 103:5879-5889. [DOI: 10.1007/s00253-019-09907-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 11/30/2022]
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