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Zhu Y, Liu J, Sun L, Liu M, Qi Q, Hou J. Development of genetic markers in Yarrowia lipolytica. Appl Microbiol Biotechnol 2024; 108:14. [PMID: 38170308 DOI: 10.1007/s00253-023-12835-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 10/28/2023] [Accepted: 11/04/2023] [Indexed: 01/05/2024]
Abstract
The oleaginous yeast Yarrowia lipolytica represents a potential microbial cell factory for the recombinant production of various valuable products. Currently, the commonly used selection markers for transformation in Y. lipolytica are limited, and successive genetic manipulations are often restricted by the number of available selection markers. In our study, we developed a dominant marker, dsdA, which encodes a D-serine deaminase for genetic manipulation in Y. lipolytica. In Y. lipolytica, this marker confers the ability to use D-serine as a nitrogen source. In addition, the selection conditions of several infrequently used dominant markers including bleoR (zeocin resistance), kanMX (G418 resistance), and guaB (mycophenolic acid resistance) were also analyzed. Our results demonstrated that these selection markers can be used for the genetic manipulation of Y. lipolytica and their selection conditions were different for various strains. Ultimately, the selection markers tested here will be useful to expand the genetic toolbox of Y. lipolytica. KEY POINTS: • The dsdA from Escherichia coli was developed as a dominant marker. • The applicability of several resistance markers in Y. lipolytica was determined. • We introduced the Cre/mutant lox system for marker recycling.
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Affiliation(s)
- Yamin Zhu
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong, 266237, People's Republic of China
| | - Jianhui Liu
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong, 266237, People's Republic of China
| | - Lingxuan Sun
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong, 266237, People's Republic of China
| | - Mengmeng Liu
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong, 266237, People's Republic of China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong, 266237, People's Republic of China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong, 266237, People's Republic of China.
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Guo Q, Peng QQ, Li YW, Yan F, Wang YT, Ye C, Shi TQ. Advances in the metabolic engineering of Saccharomyces cerevisiae and Yarrowia lipolytica for the production of β-carotene. Crit Rev Biotechnol 2024; 44:337-351. [PMID: 36779332 DOI: 10.1080/07388551.2023.2166809] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/20/2022] [Accepted: 12/08/2022] [Indexed: 02/14/2023]
Abstract
β-Carotene is one kind of the most important carotenoids. The major functions of β-carotene include the antioxidant and anti-cardiovascular properties, which make it a growing market. Recently, the use of metabolic engineering to construct microbial cell factories to synthesize β-carotene has become the latest model for its industrial production. Among these cell factories, yeasts including Saccharomyces cerevisiae and Yarrowia lipolytica have attracted the most attention because of the: security, mature genetic manipulation tools, high flux toward carotenoids using the native mevalonate pathway and robustness for large-scale fermentation. In this review, the latest strategies for β-carotene biosynthesis, including protein engineering, promoters engineering and morphological engineering are summarized in detail. Finally, perspectives for future engineering approaches are proposed to improve β-carotene production.
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Affiliation(s)
- Qi Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
| | - Qian-Qian Peng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Ya-Wen Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Fang Yan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Yue-Tong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
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Guo B, Wu Q, Jiang C, Chen Y, Dai Y, Ji C, Zhang S, Dong L, Liang H, Lin X. Inoculation of Yarrowia lipolytica promotes the growth of lactic acid bacteria, Debaryomyces udenii and the formation of ethyl esters in sour meat. Food Microbiol 2024; 119:104447. [PMID: 38225049 DOI: 10.1016/j.fm.2023.104447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/23/2023] [Accepted: 12/01/2023] [Indexed: 01/17/2024]
Abstract
Yarrowia lipolytica N12 and A13 with high lipase activity obtained by mutagenesis were inoculated into sour meat, and their effects on physicochemical properties, microbial community succession, free amino acids, and volatile compounds of sour meat were investigated. Inoculation fermentation increased the contents of free amino acids observably, rapidly reduced pH, promoted the accumulation of total acids, decreased 2-thiobarbituric acid reactive substances (TBARS) values. In addition, the addition of Y. lipolytica might contribute to the growth of lactic acid bacteria, Candida spp., and Debaryomyces udenii, which play an important role in production of volatile compounds. It was shown that inoculation promoted the production of esters, aldehydes, and alcohols, especially ethyl esters, giving sour meat a better meat flavor. Besides, it was found that Y. lipolytica A13 had better fermenting property. Sample of A13 group had higher contents of ethyl esters, free amino acids and dominant microorganisms. The results may help to provide new strains for sour meat fermentation.
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Affiliation(s)
- Bingrui Guo
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, China.
| | - Qi Wu
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, China.
| | - Cuicui Jiang
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, China.
| | - Yingxi Chen
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, China.
| | - Yiwei Dai
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, China.
| | - Chaofan Ji
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, China.
| | - Sufang Zhang
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, China.
| | - Liang Dong
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, China.
| | - Huipeng Liang
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, China; Institute of Technology, China Resources Beer (Holdings) Company Limited, Room 306 China Resources Building No.8 Jianguomen North Avenue, Dongcheng District, Beijing, 100005, China.
| | - Xinping Lin
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, China.
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Wu Y, Li S, Sun B, Guo J, Zheng M, Li A. Enhancing Gastrodin Production in Yarrowia lipolytica by Metabolic Engineering. ACS Synth Biol 2024; 13:1332-1342. [PMID: 38563122 DOI: 10.1021/acssynbio.4c00050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Gastrodin, 4-hydroxybenzyl alcohol-4-O-β-D-glucopyranoside, has been widely used in the treatment of neurogenic and cardiovascular diseases. Currently, gastrodin biosynthesis is being achieved in model microorganisms. However, the production levels are insufficient for industrial applications. In this study, we successfully engineered a Yarrowia lipolytica strain to overproduce gastrodin through metabolic engineering. Initially, the engineered strain expressing the heterologous gastrodin biosynthetic pathway, which comprises chorismate lyase, carboxylic acid reductase, phosphopantetheinyl transferase, endogenous alcohol dehydrogenases, and a UDP-glucosyltransferase, produced 1.05 g/L gastrodin from glucose in a shaking flask. Then, the production was further enhanced to 6.68 g/L with a productivity of 2.23 g/L/day by overexpressing the key node DAHP synthases of the shikimate pathway and alleviating the native tryptophan and phenylalanine biosynthetic pathways. Finally, the best strain, Gd07, produced 13.22 g/L gastrodin in a 5 L fermenter. This represents the highest reported production of gastrodin in an engineered microorganism to date, marking the first successful de novo production of gastrodin using Y. lipolytica.
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Affiliation(s)
- Yuanqing Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, #368 Youyi Road, Wuhan 430062, P. R. China
| | - Shuocheng Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, #368 Youyi Road, Wuhan 430062, P. R. China
| | - Baijian Sun
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, #368 Youyi Road, Wuhan 430062, P. R. China
| | - Jingyi Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, #368 Youyi Road, Wuhan 430062, P. R. China
| | - Meiyi Zheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, #368 Youyi Road, Wuhan 430062, P. R. China
| | - Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, #368 Youyi Road, Wuhan 430062, P. R. China
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Xu M, Yang N, Pan J, Hua Q, Li CX, Xu JH. Remodeling the Homologous Recombination Mechanism of Yarrowia lipolytica for High-Level Biosynthesis of Squalene. J Agric Food Chem 2024. [PMID: 38635942 DOI: 10.1021/acs.jafc.4c01779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Squalene is a high-value antioxidant with many commercial applications. The use of microbial cell factories to produce squalene as an alternative to plant and animal extracts could meet increasing market demand. Yarrowia lipolytica is an excellent host for squalene production due to its high levels of acetyl-CoA and a hydrophobic environment. However, the need for precise and complicated gene editing has hindered the industrialization of this strain. Herein, the rapid construction of a strain with high squalene production was achieved by enhancing the homologous recombination efficiency in Y. lipolytica. First, remodeling of the homologous recombination efficiency resulted in a 10-fold increase in the homologous recombination rate. Next, the whole mevalonate pathway was integrated into the chromosome to enhance squalene production. Then, a higher level of squalene accumulation was achieved by increasing the level of acetyl coenzyme A and regulating the downstream steroid synthesis pathway. Finally, the squalene production reached 35 g/L after optimizing the fermentation conditions and performing a fed-batch culture in a 5 L jar fermenter. This is the highest squalene production ever reported to date by de novo biosynthesis without adding any inhibitors, paving a new path toward the industrial production of squalene and its downstream products.
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Affiliation(s)
- Man Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Nan Yang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jiang Pan
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qiang Hua
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Chun-Xiu Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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Ren X, Liu M, Yue M, Zeng W, Zhou S, Zhou J, Xu S. Metabolic Pathway Coupled with Fermentation Process Optimization for High-Level Production of Retinol in Yarrowia lipolytica. J Agric Food Chem 2024; 72:8664-8673. [PMID: 38564669 DOI: 10.1021/acs.jafc.4c00377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Retinol is a lipid-soluble form of vitamin A that is crucial for human visual and immune functions. The production of retinol through microbial fermentation has been the focus of recent exploration. However, the obtained titer remains limited and the product is often a mixture of retinal, retinol, and retinoic acid, necessitating purification. To achieve efficient biosynthesis of retinol in Yarrowia lipolytica, we improved the metabolic flux of β-carotene to provide sufficient precursors for retinol in this study. Coupled with the optimization of the expression level of β-carotene 15,15'-dioxygenase, de novo production of retinol was achieved. Furthermore, Tween 80 was used as an extractant and butylated hydroxytoluene as an antioxidant to extract intracellular retinol and prevent retinol oxidation, respectively. This strategy significantly increased the level of retinol production. By optimizing the enzymes converting retinal to retinol, the proportion of extracellular retinol in the produced retinoids reached 100%, totaling 1042.3 mg/L. Finally, total retinol production reached 5.4 g/L through fed-batch fermentation in a 5 L bioreactor, comprising 4.2 g/L extracellular retinol and 1.2 g/L intracellular retinol. This achievement represents the highest reported titer so far and advances the industrial production of retinol.
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Affiliation(s)
- Xuefeng Ren
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Mengsu Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Mingyu Yue
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Weizhu Zeng
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Shenghu Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Sha Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
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Wang DN, Yu CX, Feng J, Wei LJ, Chen J, Liu Z, Ouyang L, Zhang L, Liu F, Hua Q. Comparative transcriptome analysis reveals the redirection of metabolic flux from cell growth to astaxanthin biosynthesis in Yarrowia lipolytica. Yeast 2024. [PMID: 38613186 DOI: 10.1002/yea.3938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/09/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
Engineering Yarrowia lipolytica to produce astaxanthin provides a promising route. Here, Y. lipolytica M2 producing a titer of 181 mg/L astaxanthin was isolated by iterative atmospheric and room-temperature plasma mutagenesis and diphenylamine-mediated screening. Interestingly, a negative correlation was observed between cell biomass and astaxanthin production. To reveal the underlying mechanism, RNA-seq analysis of transcriptional changes was performed in high producer M2 and reference strain M1, and a total of 1379 differentially expressed genes were obtained. Data analysis revealed that carbon flux was elevated through lipid metabolism, acetyl-CoA and mevalonate supply, but restrained through central carbon metabolism in strain M2. Moreover, upregulation of other pathways such as ATP-binding cassette transporter and thiamine pyrophosphate possibly provided more cofactors for carotenoid hydroxylase and relieved cell membrane stress caused by astaxanthin insertion. These results suggest that balancing cell growth and astaxanthin production may be important to promote efficient biosynthesis of astaxanthin in Y. lipolytica.
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Affiliation(s)
- Dan-Ni Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Chen-Xi Yu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Jie Feng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Liu-Jing Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Jun Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Zhijie Liu
- Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Wuhan, China
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Liming Ouyang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai, China
| | - Feng Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Qiang Hua
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai, China
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Lin L, Ledesma-Amaro R, Ji XJ, Huang H. Harnessing oleaginous yeast to produce omega fatty acids. Trends Biotechnol 2024:S0167-7799(24)00084-2. [PMID: 38594144 DOI: 10.1016/j.tibtech.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/04/2024] [Accepted: 03/15/2024] [Indexed: 04/11/2024]
Abstract
Omega fatty acids are important for human health. They are traditionally extracted from animals or plants but can be alternatively produced using oleaginous yeast. Current efforts are producing yeast strains with similar fatty acid distributions and powerful lipogenesis capacity. The next step is to further make the process more competitive.
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Affiliation(s)
- Lu Lin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing 211816, PRC
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK.
| | - Xiao-Jun Ji
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing 211816, PRC.
| | - He Huang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing 211816, PRC; School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Nanjing 210023, PRC.
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Liu L, Zhao K, Liu Z. Construction and Regulation of the Abscisic Acid Biosynthesis Pathway in Yarrowia lipolytica. J Agric Food Chem 2024; 72:7299-7307. [PMID: 38504621 DOI: 10.1021/acs.jafc.4c00223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Abscisic acid (ABA) is an important plant hormone with a variety of physiological functions such as regulating plant growth and helping plants to resist an adverse growth environment. However, at present, the ABA yield of heterologous biosynthesis by metabolic engineering is still low for industrial production. Therefore, five Botrytis cinerea genes (bcaba1, bcaba2, bcaba3, bcaba4, and bccpr1) related to ABA biosynthesis were expressed in Yarrowia lipolytica PO1h; its ABA production was 24.33 mg/L. By increasing the copy number of IDI and ERG12S, ERG20YMT, and bcaba3, bcaba1 genes, the yield of ABA was increased to 54.51 mg/L. By locating HMG-CoA reductase and HMG-CoA synthase in mitochondria, acetyl-CoA in mitochondria was converted into mevalonate; this increased the ABA yield to 102.12 mg/L. Finally, in the fed-batch fermentation process with the addition of dodecane, the ABA yield was up to 1212.57 mg/L, which is the highest yield of heterologous production of ABA by metabolic engineering.
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Affiliation(s)
- Lilu Liu
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China
- Qingdao Key Laboratory of Food Biotechnology, Qingdao 266404, PR China
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China
| | - Kaiyuan Zhao
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China
- Qingdao Key Laboratory of Food Biotechnology, Qingdao 266404, PR China
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China
| | - Zhen Liu
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China
- Qingdao Key Laboratory of Food Biotechnology, Qingdao 266404, PR China
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China
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Darvishi F, Beiranvand E, Kalhor H, Shahbazi B, Mafakher L. Homology modeling and molecular docking studies to decrease glutamine affinity of Yarrowia lipolytica L-asparaginase. Int J Biol Macromol 2024; 263:130312. [PMID: 38403216 DOI: 10.1016/j.ijbiomac.2024.130312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/10/2024] [Accepted: 02/18/2024] [Indexed: 02/27/2024]
Abstract
L-Asparaginase is a key component in the treatment of leukemias and lymphomas. However, the glutamine affinity of this therapeutic enzyme is an off-target activity that causes several side effects. The modeling and molecular docking study of Yarrowia lipolytica L-asparaginase (YL-ASNase) to reduce its l-glutamine affinity and increase its stability was the aim of this study. Protein-ligand interactions of wild-type and different mutants of YL-ASNase against L-asparagine compared to l-glutamine were assessed using AutoDock Vina tools because the crystal structure of YL-ASNase does not exist in the protein data banks. The results showed that three mutants, T171S, T171S-N60A, and T171A-T223A, caused a considerable increase in L-asparagine affinity and a decrease in l-glutamine affinity as compared to the wild-type and other mutants. Then, molecular dynamics simulation and MM/GBSA free energy were applied to assess the stability of protein structure and its interaction with ligands. The three mutated proteins, especially T171S-N60A, had higher stability and interactions with L-asparagine than l-glutamine in comparison with the wild-type. The YL-ASNase mutants could be introduced as appropriate therapeutic candidates that might cause lower side effects. However, the functional properties of these mutated enzymes need to be confirmed by genetic manipulation and in vitro and in vivo studies.
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Affiliation(s)
- Farshad Darvishi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran; Research Center for Applied Microbiology and Microbial Biotechnology (CAMB), Alzahra University, Tehran, Iran.
| | - Elham Beiranvand
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Hourieh Kalhor
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran
| | - Behzad Shahbazi
- School of Pharmacy, Semnan University of Medical Sciences, Semnan, Iran
| | - Ladan Mafakher
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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11
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Bejenari M, Spedtsberg EML, Mathiesen J, Jeppesen AC, Cernat L, Toussaint A, Apostol C, Stoianov V, Pedersen TB, Nielsen MR, Sørensen JL. First-class - biosynthesis of 6-MSA and bostrycoidin type I polyketides in Yarrowia lipolytica. Front Fungal Biol 2024; 5:1327777. [PMID: 38586602 PMCID: PMC10995274 DOI: 10.3389/ffunb.2024.1327777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/09/2024] [Indexed: 04/09/2024]
Abstract
Fungal polyketides are a large group of secondary metabolites, valuable due to their diverse spectrum of pharmacological activities. Polyketide biosynthesis in filamentous fungi presents some challenges: small yield and low-purity titers. To tackle these issues, we switched to the yeast Yarrowia lipolytica, an easily cultivable heterologous host. As an oleaginous yeast, Y. lipolytica displays a high flux of acetyl- and malonyl-CoA precursors used in lipid synthesis. Likewise, acetyl- and malonyl-CoA are the building blocks of many natural polyketides, and we explored the possibility of redirecting this flux toward polyketide production. Despite its promising prospect, Y. lipolytica has so far only been used for heterologous expression of simple type III polyketide synthases (PKSs) from plants. Therefore, we decided to evaluate the potential of Y. lipolytica by targeting the more complex fungal polyketides synthesized by type I PKSs. We employed a CRISPR-Cas9-mediated genome editing method to achieve markerless gene integration of the genes responsible for bostrycoidin biosynthesis in Fusarium solani (fsr1, fsr2, and fsr3) and 6-methylsalicylic acid (6-MSA) biosynthesis in Aspergillus hancockii (6MSAS). Moreover, we attempted titer optimization through metabolic engineering by overexpressing two enzymes, TGL4 and AOX2, involved in lipid β-oxidation, but we did not observe an effect on polyketide production. With maximum titers of 403 mg/L 6-MSA and 35 mg/L bostrycoidin, the latter being substantially higher than our previous results in Saccharomyces cerevisiae (2.2 mg/L), this work demonstrates the potential of Y. lipolytica as a platform for heterologous production of complex fungal polyketides.
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Affiliation(s)
- Mihaela Bejenari
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | - Eva Mie Lang Spedtsberg
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
- Department of Energy, Aalborg University, Esbjerg, Denmark
| | - Julie Mathiesen
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | | | - Lucia Cernat
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | - Aouregane Toussaint
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire Végétale, CEA, CNRS, INRA, IRIG-LPCV, Grenoble, France
| | - Cristina Apostol
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | - Victor Stoianov
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | | | - Mikkel Rank Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
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12
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Zhu J, Yang S, Cao Q, Li X, Jiao L, Shi Y, Yan Y, Xu L, Yang M, Xie X, Madzak C, Yan J. Engineering Yarrowia lipolytica as a Cellulolytic Cell Factory for Production of p-Coumaric Acid from Cellulose and Hemicellulose. J Agric Food Chem 2024; 72:5867-5877. [PMID: 38446418 DOI: 10.1021/acs.jafc.4c00567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
De novo biosynthesis of high-value added food additive p-coumaric acid (p-CA) direct from cellulose/hemicellulose is a more sustainable route compared to the chemical route, considering the abundant cellulose/hemicellulose resources. In this study, a novel factory was constructed for the production of p-CA in Yarrowia lipolytica using cellulose/hemicellulose as the sole carbon source. Based on multicopy integration of the TAL gene and reprogramming the shikimic acid pathway, the engineered strain produced 1035.5 ± 67.8 mg/L p-CA using glucose as a carbon source. The strains with overexpression of cellulases and hemicellulases produced 84.3 ± 2.4 and 65.3 ± 4.6 mg/L p-CA, using cellulose (carboxymethyl-cellulose) or hemicellulose (xylan from bagasse) as the carbon source, respectively. This research demonstrated the feasibility of conversion of cost-effective cellulose/hemicellulose into a value-added product and provided a sustainable cellulolytic cell factory for the utilization of cellulose/hemicellulose.
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Affiliation(s)
- Jiarui Zhu
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
| | - Shu Yang
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
| | | | - Xiaoyan Li
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
| | - Liangcheng Jiao
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
| | - Yuanxing Shi
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
| | - Yunjun Yan
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
| | - Li Xu
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
| | - Min Yang
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
| | - Xiaoman Xie
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
| | - Catherine Madzak
- UMR 782 SayFood, INRAE, AgroParisTech, Paris-Saclay University, Palaiseau 91400, France
| | - Jinyong Yan
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
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13
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Qin Z, Liu M, Ren X, Zeng W, Luo Z, Zhou J. De Novo Biosynthesis of Lutein in Yarrowia lipolytica. J Agric Food Chem 2024; 72:5348-5357. [PMID: 38412053 DOI: 10.1021/acs.jafc.3c09080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Lutein is a high-value tetraterpenoid carotenoid that is widely used in feed, cosmetics, food, and drugs. Microbial synthesis of lutein is an important method for green and sustainable production, serving as an alternative to plant extraction methods. However, an inadequate precursor supply and low catalytic efficiency of key pathway enzymes are the main reasons for the low efficacy of microbial synthesis of lutein. In this study, some strategies, such as enhancing the MVA pathway and localizing α-carotene synthase OluLCY within the subcellular organelles in Yarrowia lipolytica, were adopted to enhance the synthesis of precursor α-carotene, which resulted in a 10.50-fold increase in α-carotene titer, reaching 38.50 mg/L. Subsequently, by improving hydroxylase activity with truncated N-terminal transport peptide and locating hydroxylases to subcellular organelles, the final strain L9 producing 75.25 mg/L lutein was obtained. Eventually, a lutein titer of 675.40 mg/L (6.13 mg/g DCW) was achieved in a 5 L bioreactor by adding the antioxidant 2,6-ditert-butyl-4-methylphenol. This study realizes de novo synthesis of lutein in Y. lipolytica for the first time and achieves the highest lutein titer reported so far.
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Affiliation(s)
- Zhilei Qin
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Mengsu Liu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Xuefeng Ren
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Weizhu Zeng
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Zhengshan Luo
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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14
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Liu J, Li J, Chen P, Zeng Y, Yang J, Sun Y. Efficient production of isomaltulose using engineered Yarrowia lipolytica strain facilitated by non-yeast signal peptide-mediated cell surface display. J Sci Food Agric 2024. [PMID: 38436580 DOI: 10.1002/jsfa.13426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/05/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND Isomaltulose is a 'generally recognized as safe' ingredient and is widely used in the food, pharmaceutical and chemical industries. The exploration and development of efficient technologies is essential for enhancing isomaltulose yield. RESULTS In the present study, a simple and efficient surface display platform mediated by a non-yeast signal peptide was developed in Yarrowia lipolytica and utilized to efficiently produce isomaltulose from sucrose. We discovered that the signal peptide SP1 of sucrose isomerase from Pantoea dispersa UQ68J (PdSI) could guide SIs anchoring to the cell surface of Y. lipolytica, demonstrating a novel and simple cell surface display strategy. Furthermore, the PdSI expression level was significantly increased through optimizing the promoters and multi-site integrating genes into chromosome. The final strain gained 451.7 g L-1 isomaltulose with a conversion rate of 90.3% and a space-time yield of 50.2 g L-1 h-1 . CONCLUSION The present study provides an efficient way for manufacturing isomaltulose with a high space-time yield. This heterogenous signal peptide-mediated cell surface display strategy featured with small fusion tag (approximately 2.2 kDa of SP1), absence of enzyme leakage in fermentation broth and ample room for optimization, providing a convenient way to construct whole-cell biocatalysts to synthesize other products and broadening the array of molecular toolboxes accessible for engineering Y. lipolytica. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Juanjuan Liu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jiao Li
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Peng Chen
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yan Zeng
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jiangang Yang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yuanxia Sun
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
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15
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Ning Y, Liu M, Ru Z, Zeng W, Liu S, Zhou J. Efficient synthesis of squalene by cytoplasmic-peroxisomal engineering and regulating lipid metabolism in Yarrowia lipolytica. Bioresour Technol 2024; 395:130379. [PMID: 38281547 DOI: 10.1016/j.biortech.2024.130379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/04/2024] [Accepted: 01/23/2024] [Indexed: 01/30/2024]
Abstract
Squalene, a high-value acyclic triterpenoid compound, is broadly used in the food and medical industries. Although the large acetyl-CoA pool and hydrophobic space of Yarrowia lipolytica are suitable for the accumulation of squalene, the current production level in Y. lipolytica is still not sufficient for industrial production. In this study, two rounds of multicopy integration of genes encoding key enzymes were performed to enhance squalene anabolic flux in the cytoplasm. Furthermore, the mevalonate pathway was imported into peroxisomes through the compartmentalization strategy, and the production of squalene was significantly increased. By augmenting the acetyl-CoA supply in peroxisomes and the cytoplasm, the squalene was boosted to 2549.1 mg/L. Finally, the squalene production reached 51.2 g/L by fed-batch fermentation in a 5-L bioreactor. This is the highest squalene production reported to date for microbial production, and this study lays the foundation for the synthesis of steroids and squalene derivatives.
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Affiliation(s)
- Yang Ning
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Mengsu Liu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Ziyun Ru
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Weizhu Zeng
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Song Liu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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16
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Liu M, Wu J, Yue M, Ning Y, Guan X, Gao S, Zhou J. YaliCMulti and YaliHMulti: Stable, efficient multi-copy integration tools for engineering Yarrowia lipolytica. Metab Eng 2024; 82:29-40. [PMID: 38224832 DOI: 10.1016/j.ymben.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/17/2024]
Abstract
Yarrowia lipolytica is widely used in biotechnology to produce recombinant proteins, food ingredients and diverse natural products. However, unstable expression of plasmids, difficult and time-consuming integration of single and low-copy-number plasmids hampers the construction of efficient production pathways and application to industrial production. Here, by exploiting sequence diversity in the long terminal repeats (LTRs) of retrotransposons and ribosomal DNA (rDNA) sequences, a set of vectors and methods that can recycle multiple and high-copy-number plasmids was developed that can achieve stable integration of long-pathway genes in Y. lipolytica. By combining these sequences, amino acids and antibiotic tags with the Cre-LoxP system, a series of multi-copy site integration recyclable vectors were constructed and assessed using the green fluorescent protein (HrGFP) reporter system. Furthermore, by combining the consensus sequence with the vector backbone of a rapidly degrading selective marker and a weak promoter, multiple integrated high-copy-number vectors were obtained and high levels of stable HrGFP expression were achieved. To validate the universality of the tools, simple integration of essential biosynthesis modules was explored, and 7.3 g/L of L-ergothioneine and 8.3 g/L of (2S)-naringenin were achieved in a 5 L fermenter, the highest titres reported to date for Y. lipolytica. These novel multi-copy genome integration strategies provide convenient and effective tools for further metabolic engineering of Y. lipolytica.
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Affiliation(s)
- Mengsu Liu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Junjun Wu
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Mingyu Yue
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Yang Ning
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Xin Guan
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Song Gao
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
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17
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Taratynova MO, Tikhonova EE, Fedyaeva IM, Dementev DA, Yuzbashev TV, Solovyev AI, Sineoky SP, Yuzbasheva EY. Boosting Geranyl Diphosphate Synthesis for Linalool Production in Engineered Yarrowia lipolytica. Appl Biochem Biotechnol 2024; 196:1304-1315. [PMID: 37392322 DOI: 10.1007/s12010-023-04581-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2023] [Indexed: 07/03/2023]
Abstract
Linalool is a pleasant-smelling monoterpenoid widely found in the essential oils of most flowers. Due to its biologically active properties, linalool has considerable commercial potential, especially in the food and perfume industries. In this study, the oleaginous yeast Yarrowia lipolytica was successfully engineered to produce linalool de novo. The (S)-linalool synthase (LIS) gene from Actinidia argute was overexpressed to convert geranyl diphosphate (GPP) into linalool. Flux was diverted from farnesyl diphosphate (FPP) synthesis to GPP by introducing a mutated copy of the native ERG20F88W-N119W gene, and CrGPPS gene from Catharanthus roseus on its own and as part of a fusion with LIS. Disruption of native diacylglycerol kinase enzyme, DGK1, by oligo-mediated CRISPR-Cas9 inactivation further increased linalool production. The resulting strain accumulated 109.6 mg/L of linalool during cultivation in shake flasks with sucrose as a carbon source. CrGPPS expression in Yarrowia lipolytica increased linalool accumulation more efficiently than the ERG20F88W-N119W expression, suggesting that the increase in linalool production was predominantly influenced by the level of GPP precursor supply.
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Affiliation(s)
- Maria O Taratynova
- NRC "Kurchatov Institute", Kurchatov Genomic Center, sq. Academician Kurchatova, 1, Moscow, 123182, Russia.
| | - Ekaterina E Tikhonova
- NRC "Kurchatov Institute", Kurchatov Genomic Center, sq. Academician Kurchatova, 1, Moscow, 123182, Russia
| | - Iuliia M Fedyaeva
- NRC "Kurchatov Institute", Kurchatov Genomic Center, sq. Academician Kurchatova, 1, Moscow, 123182, Russia
| | - Dmitry A Dementev
- NRC "Kurchatov Institute", Kurchatov Genomic Center, sq. Academician Kurchatova, 1, Moscow, 123182, Russia
| | - Tigran V Yuzbashev
- Plant Sciences and the Bioeconomy, Rothamsted Research, Harpenden, AL5 2JQ, West Common, UK
| | - Andrey I Solovyev
- Gamaleya National Research Center of Epidemiology and Microbiology, Russian Ministry of Health, Gamaleya St. 18, Moscow, 123098, Russia
| | - Sergey P Sineoky
- NRC "Kurchatov Institute", Kurchatov Genomic Center, sq. Academician Kurchatova, 1, Moscow, 123182, Russia
| | - Evgeniya Y Yuzbasheva
- BioMediCan Inc, 40471 Encyclopedia Circle, Fremont, CA, 94538, USA
- BioKai Inc, 40471 Encyclopedia Circle, Fremont, CA, 94538, USA
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18
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Yue M, Liu M, Gao S, Ren X, Zhou S, Rao Y, Zhou J. High-Level De Novo Production of (2 S)-Eriodictyol in Yarrowia Lipolytica by Metabolic Pathway and NADPH Regeneration Engineering. J Agric Food Chem 2024; 72:4292-4300. [PMID: 38364826 DOI: 10.1021/acs.jafc.3c08861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
(2S)-Eriodictyol, a polyphenolic flavonoid, has found widespread applications in health supplements and food additives. However, the limited availability of plant-derived (2S)-eriodictyol cannot meet the market demand. Microbial production of (2S)-eriodictyol faces challenges, including the low catalytic efficiency of flavone 3'-hydroxylase/cytochrome P450 reductase (F3'H/CPR), insufficient precursor supplementation, and inadequate NADPH regeneration. This study systematically engineered Yarrowia lipolytica for high-level (2S)-eriodictyol production. In doing this, the expression of F3'H/CPR was balanced, and the supply of precursors was enhanced by relieving feedback inhibition of the shikimate pathway, promoting fatty acid β-oxidation, and increasing the copy number of synthetic pathway genes. These strategies, combined with NADPH regeneration, achieved an (2S)-eriodictyol titer of 423.6 mg/L. Finally, in fed-batch fermentation, a remarkable 6.8 g/L (2S)-eriodictyol was obtained, representing the highest de novo microbial titer reported to date and paving the way for industrial production.
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Affiliation(s)
- Mingyu Yue
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Mengsu Liu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Song Gao
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Xuefeng Ren
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shenghu Zhou
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yijian Rao
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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19
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Jia YL, Zhang QM, Du F, Yang WQ, Zhang ZX, Xu YS, Ma W, Sun XM, Huang H. Identification of lipid synthesis genes in Schizochytrium sp. and their application in improving eicosapentaenoic acid synthesis in Yarrowia lipolytica. Biotechnol Biofuels Bioprod 2024; 17:32. [PMID: 38402213 PMCID: PMC10894473 DOI: 10.1186/s13068-024-02471-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 02/02/2024] [Indexed: 02/26/2024]
Abstract
BACKGROUND Eicosapentaenoic acid (EPA) is widely used in the functional food and nutraceutical industries due to its important benefits to human health. Oleaginous microorganisms are considered a promising alternative resource for the production of EPA lipids. However, the storage of EPA in triglyceride (TG) becomes a key factor limiting its level. RESULTS This study aimed to incorporate more EPA into TG storage through metabolic engineering. Firstly, key enzymes for TG synthesis, the diacylglycerol acyltransferase (DGAT) and glycerol-3-phosphate acyltransferase (GPAT) genes from Schizochytrium sp. HX-308 were expressed in Yarrowia lipolytica to enhance lipid and EPA accumulation. In addition, engineering the enzyme activity of DGATs through protein engineering was found to be effective in enhancing lipid synthesis by replacing the conserved motifs "HFS" in ScDGAT2A and "FFG" in ScDGAT2B with the motif "YFP". Notably, combined with lipidomic analysis, the expression of ScDGAT2C and GPAT2 enhanced the storage of EPA in TG. Finally, the accumulation of lipid and EPA was further promoted by identifying and continuing to introduce the ScACC, ScACS, ScPDC, and ScG6PD genes from Schizochytrium sp., and the lipid and EPA titer of the final engineered strain reached 2.25 ± 0.03 g/L and 266.44 ± 5.74 mg/L, respectively, which increased by 174.39% (0.82 ± 0.02 g/L) and 282.27% (69.70 ± 0.80 mg/L) compared to the initial strain, respectively. CONCLUSION This study shows that the expression of lipid synthesis genes from Schizochytrium sp. in Y. lipolytica effectively improves the synthesis of lipids and EPA, which provided a promising target for EPA-enriched microbial oil production.
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Affiliation(s)
- Yu-Lei Jia
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210000, China
| | - Qing-Ming Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210000, China
| | - Fei Du
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210000, China
| | - Wen-Qian Yang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210000, China
| | - Zi-Xu Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210000, China
| | - Ying-Shuang Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210000, China
| | - Wang Ma
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210000, China
| | - Xiao-Man Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210000, China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210000, China
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20
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Ovseychik EA, Klein OI, Gessler NN, Deryabina YI, Lukashenko VS, Isakova EP. The Efficacy of Encapsulated Phytase Based on Recombinant Yarrowia lipolytica on Quails' Zootechnic Features and Phosphorus Assimilation. Vet Sci 2024; 11:91. [PMID: 38393109 PMCID: PMC10891838 DOI: 10.3390/vetsci11020091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
In this study, we used the Manchurian golden breed of quails. We assessed the efficacy of the food additives of the phytase from Obesumbacterium proteus encapsulated in the recombinant Yarrowia lipolytica yeast, which was supplied at a concentration of 500 phytase activity units per kg of the feed. One hundred fifty one-day-old quails were distributed into six treatment groups. The results showed that adding the O. proteus encapsulated phytase to the quails' diets improved live weight, body weight gain, and feed conversion compared to those in the control groups and the groups using a commercial phytase from Aspergillus ficuum. The results obtained during the experiments indicate a high degree of assimilation of phytate-containing feeds if the encapsulated phytase was fed by the quails compared to that in the other groups. We can conclude that the class D encapsulated phytase is an expedient additive to the diets possessing better kinetic features compared to the PhyA and PhyC classes phytases when it acts inside the quail's chyme.
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Affiliation(s)
- Ekanerina A. Ovseychik
- Federal State Budget Scientific Institution Federal Scientific Center “Russian Research and Technological Poultry Institute” of Russian Academy of Sciences, Sergiev Posad 141311, Russia; (E.A.O.); (V.S.L.)
| | - Olga I. Klein
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (O.I.K.); (N.N.G.); (Y.I.D.)
| | - Natalia N. Gessler
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (O.I.K.); (N.N.G.); (Y.I.D.)
| | - Yulia I. Deryabina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (O.I.K.); (N.N.G.); (Y.I.D.)
| | - Valery S. Lukashenko
- Federal State Budget Scientific Institution Federal Scientific Center “Russian Research and Technological Poultry Institute” of Russian Academy of Sciences, Sergiev Posad 141311, Russia; (E.A.O.); (V.S.L.)
| | - Elena P. Isakova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (O.I.K.); (N.N.G.); (Y.I.D.)
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21
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Liu X, Deng J, Zhang J, Cui Z, Qi Q, Hou J. Genome-scale transcriptional activation by non-homologous end joining-mediated integration in Yarrowia lipolytica. Biotechnol Biofuels Bioprod 2024; 17:24. [PMID: 38360689 PMCID: PMC10870441 DOI: 10.1186/s13068-024-02472-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 02/05/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND Genome-scale screening can be applied to efficiently mine for unknown genes with phenotypes of interest or special functions. It is also useful to identify new targets for engineering desirable properties of cell factories. RESULTS Here, we designed a new approach for genome-scale transcription activation using non-homologous end joining (NHEJ)-mediated integration in Yarrowia lipolytica. We utilized this approach to screen for genes that, upon activation, confer phenotypes including improved acetic acid tolerance and xylose metabolism. The candidates were validated using gene overexpression, and functional changes including improved growth performance under multiple stressors and activated pentose metabolism were identified. CONCLUSIONS This study provides a simple and effective approach to randomly activate endogenous genes and mine for key targets associated with phenotypes of interest. The specific gene targets identified here will be useful for cell factory construction and biorefining lignocellulose.
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Affiliation(s)
- Xiaoqin Liu
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, People's Republic of China
| | - Jingyu Deng
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, People's Republic of China
| | - Jinhong Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, People's Republic of China
| | - Zhiyong Cui
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, People's Republic of China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, People's Republic of China.
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, People's Republic of China.
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22
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Zipori D, Hollmann J, Rigling M, Zhang Y, Weiss A, Schmidt H. Rapid Acidification and Off-Flavor Reduction of Pea Protein by Fermentation with Lactic Acid Bacteria and Yeasts. Foods 2024; 13:588. [PMID: 38397565 PMCID: PMC10888418 DOI: 10.3390/foods13040588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/05/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
Pea protein is widely used as an alternative protein source in plant-based products. In the current study, we fermented pea protein to reduce off-flavor compounds, such as hexanal, and to produce a suitable fermentate for further processing. Laboratory fermentations using 5% (w/v) pea protein suspension were carried out using four selected lactic acid bacteria (LAB) strains, investigating their growth and acidification capabilities in pea protein. Rapid acidification of pea protein was achieved with Lactococcus lactis subsp. lactis strain LTH 7123. Next, this strain was co-inoculated together with either the yeasts Kluyveromyces lactis LTH 7165, Yarrowia lipolytica LTH 6056, or Kluyveromyces marxianus LTH 6039. Fermentation products of the mixed starter cultures and of the single strains were further analyzed by gas chromatography coupled with mass spectrometry to quantify selected volatile flavor compounds. Fermentation with L. lactis LTH 7123 led to an increase in compounds associated with the "beany" off-flavors of peas, including hexanal. However, significant reduction in those compounds was achieved after fermentation with Y. lipolytica LTH 6056 with or without L. lactis LTH 7123. Thus, fermentation using co-cultures of LAB and yeasts strains could prove to be a valuable method for enhancing quality attributes of pea protein-based products.
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Affiliation(s)
- Dor Zipori
- Department of Food Microbiology and Hygiene, Institute of Food Science and Biotechnology, University of Hohenheim, Garbenstrasse 28, 70599 Stuttgart, Germany; (D.Z.); (J.H.)
| | - Jana Hollmann
- Department of Food Microbiology and Hygiene, Institute of Food Science and Biotechnology, University of Hohenheim, Garbenstrasse 28, 70599 Stuttgart, Germany; (D.Z.); (J.H.)
| | - Marina Rigling
- Department of Flavor Chemistry, Institute of Food Science and Biotechnology, University of Hohenheim, Fruwirthstrasse 12, 70599 Stuttgart, Germany; (M.R.); (Y.Z.)
| | - Yanyan Zhang
- Department of Flavor Chemistry, Institute of Food Science and Biotechnology, University of Hohenheim, Fruwirthstrasse 12, 70599 Stuttgart, Germany; (M.R.); (Y.Z.)
| | - Agnes Weiss
- Food Microbiology, Hamburg School of Food Science, University of Hamburg, Ohnhorstsrasse 18, 22609 Hamburg, Germany;
| | - Herbert Schmidt
- Department of Food Microbiology and Hygiene, Institute of Food Science and Biotechnology, University of Hohenheim, Garbenstrasse 28, 70599 Stuttgart, Germany; (D.Z.); (J.H.)
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23
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Wang K, Zhou Y, Cao L, Lin L, Ledesma-Amaro R, Ji XJ. Engineering Yarrowia lipolytica for Sustainable Production of the Pomegranate Seed Oil-Derived Punicic Acid. J Agric Food Chem 2024; 72:3088-3098. [PMID: 38282297 DOI: 10.1021/acs.jafc.3c08718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Punicic acid is a conjugated linolenic acid with various biological activities including antiobesity, antioxidant, anticancer, and anti-inflammatory effects. It is often used as a nutraceutical, dietary additive, and animal feed. Currently, punicic acid is primarily extracted from pomegranate seed oil, but it is restricted due to the extended growth cycle, climatic limitations, and low recovery level. There have also been reports on the chemical synthesis of punicic acid, but it resulted in a mixture of structurally similar isomers, requiring additional purification/separation steps. In this study, a comprehensive strategy for the production of punicic acid in Yarrowia lipolytica was implemented by pushing the supply of linoleic acid precursors in a high-oleic oil strain, expressing multiple copies of the fatty acid conjugase gene from Punica granatum, engineering the acyl-editing pathway to improve the phosphatidylcholine pool, and promoting the assembly of punicic acid in the form of triglycerides. The optimal strain with high oil production capacity and a significantly increased punicic acid ratio accumulated 3072.72 mg/L punicic acid, accounting for 6.19% of total fatty acids in fed-batch fermentation, providing a viable, sustainable, and green approach for punicic acid production to substitute plant extraction and chemical synthesis production.
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Affiliation(s)
- Kaifeng Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Yueyue Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Lizhen Cao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Lu Lin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
| | - Xiao-Jun Ji
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
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24
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Chang Y, Wang Z, Li H, Dang W, Song Y, Kang X, Zhang H. Morphological Changes and Strong Cytotoxicity in Yarrowia lipolytica by Overexpressing Delta-12-Desaturase. J Fungi (Basel) 2024; 10:126. [PMID: 38392798 PMCID: PMC10890566 DOI: 10.3390/jof10020126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/24/2024] Open
Abstract
In this study, delta-12 desaturase was overexpressed in Yarrowia lipolytica using the single-copy integrative vector pINA1312 and multicopy integrative vector pINA1292, resulting in the engineered yeast strains 1312-12 and 1292-12, respectively. The content of intracellular linoleic acid (LA) in the 1292-12 strain was much higher than in the 1312-12 strain and the control group. One interesting finding was that the 1292-12 strain showed obvious changes in surface morphology. The 1292-12 colonies were much smaller and smoother, whereas their single cells became much larger compared to the control strain. In addition, the dry cell weight (DCW) of the 1292-12 strain was obviously increased from 8.5 to 12.7 g/L, but the viable cell number sharply decreased from 107 to 105/mL. These results indicated that increased LA content in Yarrowia lipolytica could induce morphological changes or even oxidative stress-dependent cell death. The reactive oxygen species (ROS) and malondialdehyde (MDA) were accumulated in the 1292-12 strain, while the antioxidant activities of intracellular catalase (CAT) and superoxide dismutase (SOD) were significantly decreased by 27.6 and 32.0%, respectively. Furthermore, it was also revealed that these issues could be ameliorated by the exogenous supplementation of vitamin C, fish and colza oil.
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Affiliation(s)
- Yufei Chang
- Colin Ratledge Center for Microbial Lipids, School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255049, China
| | - Zhen Wang
- School of Public Health, Qilu Medical University, Zibo 255300, China
| | - Hequn Li
- Colin Ratledge Center for Microbial Lipids, School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255049, China
| | - Wenrui Dang
- Colin Ratledge Center for Microbial Lipids, School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255049, China
| | - Yuanda Song
- Colin Ratledge Center for Microbial Lipids, School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255049, China
| | - Xinxin Kang
- Colin Ratledge Center for Microbial Lipids, School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255049, China
| | - Huaiyuan Zhang
- Colin Ratledge Center for Microbial Lipids, School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255049, China
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25
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Liu Z, Huang M, Chen H, Lu X, Tian Y, Hu P, Zhao Q, Li P, Li C, Ji X, Liu H. Metabolic engineering of Yarrowia lipolytica for high-level production of squalene. Bioresour Technol 2024; 394:130233. [PMID: 38141883 DOI: 10.1016/j.biortech.2023.130233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 12/25/2023]
Abstract
Squalene is an important triterpene with a wide range of applications. Given the growing market demand for squalene, the development of microbial cell factories capable of squalene production is considered a sustainable method. This study aimed to investigate the squalene production potential of Yarrowia lipolytica. First, HMG-CoA reductase from Saccharomyces cerevisiae and squalene synthase from Y. lipolytica was co-overexpressed in Y. lipolytica. Second, by enhancing the supply of NADPH in the squalene synthesis pathway, the production of squalene in Y. lipolytica was effectively increased. Furthermore, by constructing an isoprenol utilization pathway and overexpressing YlDGA1, the strain YLSQ9, capable of producing 868.1 mg/L squalene, was obtained. Finally, by optimizing the fermentation conditions, the highest squalene concentration of 1628.2 mg/L (81.0 mg/g DCW) in Y. lipolytica to date was achieved. This study demonstrated the potential for achieving high squalene production using Y. lipolytica.
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Affiliation(s)
- Ziying Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Mingkang Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Hong Chen
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Xiangyang Lu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Yun Tian
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan 410128, China; State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, Hunan 410004, China
| | - Pengcheng Hu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Qiaoqin Zhao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Peiwang Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, Hunan 410004, China
| | - Changzhu Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, Hunan 410004, China
| | - Xiaojun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Huhu Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan 410128, China.
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26
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Shen Q, Yan F, Li YW, Wang J, Ji J, Yan WX, He DC, Song P, Shi TQ. Expansion of YALIcloneHR toolkit for Yarrowia lipolytica combined with Golden Gate and CRISPR technology. Biotechnol Lett 2024; 46:37-46. [PMID: 38064043 DOI: 10.1007/s10529-023-03444-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/29/2023] [Accepted: 10/17/2023] [Indexed: 01/14/2024]
Abstract
Metabolic Engineering of yeast is a critical approach to improving the production capacity of cell factories. To obtain genetically stable recombinant strains, the exogenous DNA is preferred to be integrated into the genome. Previously, we developed a Golden Gate toolkit YALIcloneNHEJ, which could be used as an efficient modular cloning toolkit for the random integration of multigene pathways through the innate non-homologous end-joining repair mechanisms of Yarrowia lipolytica. We expanded the toolkit by designing additional building blocks of homologous arms and using CRISPR technology. The reconstructed toolkit was thus entitled YALIcloneHR and designed for gene-specific knockout and integration. To verify the effectiveness of the system, the gene PEX10 was selected as the target for the knockout. This system was subsequently applied for the arachidonic acid production, and the reconstructed strain can accumulate 4.8% of arachidonic acid. The toolkit will expand gene editing technology in Y. lipolytica, which would help produce other chemicals derived from acetyl-CoA in the future.
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Affiliation(s)
- Qi Shen
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, 210023, People's Republic of China
| | - Fang Yan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, 210023, People's Republic of China
| | - Ya-Wen Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, 210023, People's Republic of China
| | - Jian Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, 210023, People's Republic of China
| | - Jia Ji
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, 210023, People's Republic of China
| | - Wen-Xin Yan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, 210023, People's Republic of China
| | - Dan-Chen He
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, 210023, People's Republic of China
| | - Ping Song
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, 210023, People's Republic of China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, 210023, People's Republic of China.
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27
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Robles-Iglesias R, Fernández-Blanco C, Nicaud JM, Veiga MC, Kennes C. Unlocking the potential of one-carbon gases (CO 2, CO) for concomitant bioproduction of β-carotene and lipids. Ecotoxicol Environ Saf 2024; 271:115950. [PMID: 38211510 DOI: 10.1016/j.ecoenv.2024.115950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
This study investigates the use of a Yarrowia lipolytica strain for the bioconversion of syngas-derived acetic acid into β-carotene and lipids. A two-stage process was employed, starting with the acetogenic fermentation of syngas by Clostridium aceticum, metabolising CO, CO2, H2, to produce acetic acid, which is then utilized by Y. lipolytica for simultaneous lipid and β-carotene synthesis. The research demonstrates that acetic acid concentration plays a pivotal role in modulating lipid profiles and enhancing β-carotene production, with increased acetic acid consumption leading to higher yields of these compounds. This approach showcases the potential of using one-carbon gases as substrates in bioprocesses for generating valuable bioproducts, providing a sustainable and cost-effective alternative to more conventional feedstocks and substrates, such as sugars.
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Affiliation(s)
- Raúl Robles-Iglesias
- Chemical Engineering Laboratory, Faculty of Sciences and Interdisciplinary Centre of Chemistry and Biology - Centro Interdisciplinar de Química y Biología (CICA), BIOENGIN group, University of La Coruña, Rúa da Fraga 10, La Coruña 15008, Spain
| | - Carla Fernández-Blanco
- Chemical Engineering Laboratory, Faculty of Sciences and Interdisciplinary Centre of Chemistry and Biology - Centro Interdisciplinar de Química y Biología (CICA), BIOENGIN group, University of La Coruña, Rúa da Fraga 10, La Coruña 15008, Spain
| | - Jean-Marc Nicaud
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - María C Veiga
- Chemical Engineering Laboratory, Faculty of Sciences and Interdisciplinary Centre of Chemistry and Biology - Centro Interdisciplinar de Química y Biología (CICA), BIOENGIN group, University of La Coruña, Rúa da Fraga 10, La Coruña 15008, Spain
| | - Christian Kennes
- Chemical Engineering Laboratory, Faculty of Sciences and Interdisciplinary Centre of Chemistry and Biology - Centro Interdisciplinar de Química y Biología (CICA), BIOENGIN group, University of La Coruña, Rúa da Fraga 10, La Coruña 15008, Spain.
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28
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Do D, Guruk M, Kus-Liśkiewicz M, Damblon C, Arguelles-Arias A, Erten H, Fickers P. Biosynthesis of the antioxidant γ-glutamyl-cysteine with engineered Yarrowia lipolytica. Biotechnol J 2024; 19:e2300564. [PMID: 38403441 DOI: 10.1002/biot.202300564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/10/2023] [Accepted: 12/22/2023] [Indexed: 02/27/2024]
Abstract
The dipeptide γ-glutamylcysteine (γ-GC), the first intermediate of glutathione (GSH) synthesis, is considered as a promising drug to reduce or prevent plethora of age-related disorders such as Alzheimer and Parkinson diseases. The unusual γ-linkage between the two constitutive amino acids, namely cysteine and glutamate, renders its chemical synthesis particularly challenging. Herein, we report on the metabolic engineering of the non-conventional yeast Yarrowia lipolytica for efficient γ-GC synthesis. The yeast was first converted into a γ-GC producer by disruption of gene GSH2 encoding GSH synthase and by constitutive expression of GSH1 encoding glutamylcysteine ligase. Subsequently genes involved in cysteine and glutamate anabolism, namely MET4, CYSE, CYSF, and GDH1 were overexpressed with the aim to increase their intracellular availability. With such a strategy, a γ-GC titer of 464 nmol mg-1 protein (93 mg gDCW-1 ) was obtained within 24 h of cell growth.
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Affiliation(s)
- Diem Do
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium
- Dong Thap Medical College, Cao Lanh City, Dong Thap Province, Vietnam
| | - Mümine Guruk
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium
- Department of Food Engineering, Faculty of Engineering, Cukurova University, Adana, Turkey
| | | | - Christian Damblon
- Laboratoire de Chimie Biologique Structurale, Département de Chimie, Université de Liège, Liège, Belgium
| | - Anthony Arguelles-Arias
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium
| | - Huseyin Erten
- Department of Food Engineering, Faculty of Engineering, Cukurova University, Adana, Turkey
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium
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Rywińska A, Tomaszewska-Hetman L, Lazar Z, Juszczyk P, Sałata P, Malek K, Kawecki A, Rymowicz W. Application of New Yarrowia lipolytica Transformants in Production of Citrates and Erythritol from Glycerol. Int J Mol Sci 2024; 25:1475. [PMID: 38338753 PMCID: PMC10855631 DOI: 10.3390/ijms25031475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Citric acid and erythritol are obtained on an industrial scale using biotechnological methods. Due to the growing market demand for these products, research is underway to improve the process economics by introducing new microorganisms, in particular of the species Yarrowia lipolytica. The aim of this study was to evaluate transformants of Y. lipolytica for growth and ability to overproduce citric acids and erythritol from glycerol. The transformants were constructed by overexpressing glycerol kinase, methylcitrate synthase and mitochondrial succinate-fumarate transporter in the mutant Wratislavia 1.31. Next, strains were assessed for biosynthesis of citrate (pH 5.5; nitrogen limitation) and erythritol (pH 3.0; high osmotic pressure) from glycerol. Regardless of culture conditions strains, 1.31.GUT1/6 and 1.31.GUT1/6.CIT1/3 exhibited high rates of substrate utilization. Under conditions favoring citrate biosynthesis, both strains produced several percent more citrates, accompanied by higher erythritol production compared to the parental strain. During erythritol biosynthesis, the strain 1.31.GUT1/6.CIT1/3.E34672g obtained as a result of co-expression of all three genes stood out, producing 84.0 g/L of erythritol with yield and productivity of 0.54 g/g and 0.72 g/Lh, respectively, which places it in the group of the highest-ranked producers of erythritol among Y. lipolytica species.
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Affiliation(s)
| | - Ludwika Tomaszewska-Hetman
- Department of Biotechnology and Food Microbiology, The Faculty of Biotechnology and Food Science, Wroclaw University of Environmental and Life Sciences, Chełmońskiego Str. 37, 51-630 Wrocław, Poland; (A.R.); (Z.L.); (P.J.); (P.S.); (A.K.); (W.R.)
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30
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Miranda SM, Lopes M, Belo I. Exploring the use of hexadecane by Yarrowia lipolytica: Effect of dissolved oxygen and medium supplementation. J Biotechnol 2024; 380:29-37. [PMID: 38128617 DOI: 10.1016/j.jbiotec.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/30/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023]
Abstract
This work aimed to evaluate the effect of medium composition and volumetric oxygen transfer coefficient (kLa) on Y. lipolytica growth and production of microbial lipids and enzymes from hexadecane. In the stirred tank bioreactor, increasing kLa from 11 h-1 to 132 h-1 improved the hexadecane assimilation rate, biomass concentration, and lipids synthesis (0.90 g·L-1). A cost-effective hexadecane-based medium supplemented with corn steep liquor and a low amount of ammonium sulfate boosted lipids production up to 2.1 g·L-1, composed of palmitic, palmitoleic, oleic, and linoleic acids. The unsaturated/saturated fraction was dependent on the C/N ratio. Lipids of Y. lipolytica CBS 2075 are promising feedstock for animal feed, food additives, or the biodiesel industry. Simultaneous synthesis of extracellular lipase and protease from hexadecane was observed, which is a new feature that was not previously reported. The highest enzyme activity was obtained at the highest C/N ratio conditions. These results open new perspectives on the application of Y. lipolytica-based cultures for the biotransformation of hexadecane-polluted streams into valuable compounds, fulfilling an interesting strategy towards the circular economy concept.
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Affiliation(s)
- Sílvia M Miranda
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - Marlene Lopes
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal; LABBELS - Associate Laboratory, Braga/Guimarães, Portugal.
| | - Isabel Belo
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal; LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
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31
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Zhang B, Cao J. Improving and Streamlining Gene Editing in Yarrowia lipolytica via Integration of Engineered Cas9 Protein. J Fungi (Basel) 2024; 10:63. [PMID: 38248972 PMCID: PMC10817246 DOI: 10.3390/jof10010063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/06/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
The oleaginous yeast Yarrowia lipolytica is a prominent subject of biorefinery research due to its exceptional performance in oil production, exogenous protein secretion, and utilization of various inexpensive carbon sources. Many CRISPR/Cas9 genome-editing systems have been developed for Y. lipolytica to meet the high demand for metabolic engineering studies. However, these systems often necessitate an additional outgrowth step to achieve high gene editing efficiency. In this study, we introduced the eSpCas9 protein, derived from the Streptococcus pyogenes Cas9(SpCas9) protein, into the Y. lipolytica genome to enhance gene editing efficiency and fidelity, and subsequently explored the optimal expression level of eSpCas9 gene by utilizing different promoters and selecting various growth periods for yeast transformation. The results demonstrated that the integrated eSpCas9 gene editing system significantly enhanced gene editing efficiency, increasing from 16.61% to 86.09% on TRP1 and from 33.61% to 95.19% on LIP2, all without the need for a time-consuming outgrowth step. Furthermore, growth curves and dilution assays indicated that the consistent expression of eSpCas9 protein slightly suppressed the growth of Y. lipolytica, revealing that strong inducible promoters may be a potential avenue for future research. This work simplifies the gene editing process in Y. lipolytica, thus advancing its potential as a natural product synthesis chassis and providing valuable insights for other comparable microorganisms.
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Affiliation(s)
- Baixi Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China;
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Jiacan Cao
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China;
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32
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Yu J, Liu X, Guo D, Yang W, Chen X, Zou G, Wang T, Pang S, Zhang G, Dong J, Xu Y, Zhao Y. Antifungal susceptibility profile and local epidemiological cut-off values of Yarrowia ( Candida) lipolytica: an emergent and rare opportunistic yeast. Microbiol Spectr 2024; 12:e0320323. [PMID: 38084981 PMCID: PMC10783140 DOI: 10.1128/spectrum.03203-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/15/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Yarrowia lipolytica, also known as Candida lipolytica, is an emerging opportunistic "rare pathogenic yeast". Due to the limited data on its antifungal susceptibility, the clinical treatments become challenging. Based on the China Hospital Invasive Fungal Surveillance Network (2009-2022), we conducted a comprehensive multi-method study on clinical isolates from various central hospitals. This study is currently the largest study carried out to assess the antifungal susceptibility of Y. lipolytica. It is also the first to establish local epidemiological cut-off values (L-ECOFFs), identify its ERG11 mutations, and assess the consistency between the three prevalent commercial antifungal susceptibility testing methods and the broth microdilution method. We recommend the Sensititre YeastOne as the best option for antifungal susceptibility testing for Y. lipolytica, followed by the ATB FUNGUS 3. Nevertheless, practitioners should use the MIC test strip with discretion.
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Affiliation(s)
- Jinhan Yu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xueqing Liu
- Department of Clinical Laboratory, Yongzhou Central Hospital, Yongzhou, China
| | - Dawen Guo
- Department of Microbiology, the First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Wenhang Yang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Xinfei Chen
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Guiling Zou
- Department of Microbiology, the Fourth Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Tong Wang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Shichao Pang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Luohe Medical College, Luohe, China
| | - Ge Zhang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Jingjing Dong
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Yingchun Xu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Ying Zhao
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - on behalf of the National China Hospital Invasive Fungal Surveillance Network (CHIF-NET)
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Department of Clinical Laboratory, Yongzhou Central Hospital, Yongzhou, China
- Department of Microbiology, the First Affiliated Hospital, Harbin Medical University, Harbin, China
- Department of Microbiology, the Fourth Affiliated Hospital, Harbin Medical University, Harbin, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Luohe Medical College, Luohe, China
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33
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Sun ML, Gao X, Lin L, Yang J, Ledesma-Amaro R, Ji XJ. Building Yarrowia lipolytica Cell Factories for Advanced Biomanufacturing: Challenges and Solutions. J Agric Food Chem 2024; 72:94-107. [PMID: 38126236 DOI: 10.1021/acs.jafc.3c07889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Microbial cell factories have shown great potential for industrial production with the benefit of being environmentally friendly and sustainable. Yarrowia lipolytica is a promising and superior non-model host for biomanufacturing due to its cumulated advantages compared to model microorganisms, such as high fluxes of metabolic precursors (acetyl-CoA and malonyl-CoA) and its naturally hydrophobic microenvironment. However, although diverse compounds have been synthesized in Y. lipolytica cell factories, most of the relevant studies have not reached the level of industrialization and commercialization due to a number of remaining challenges, including unbalanced metabolic flux, conflict between cell growth and product synthesis, and cytotoxic effects. Here, various metabolic engineering strategies for solving the challenges are summarized, which is developing fast and extremely conducive to rational design and reconstruction of robust Y. lipolytica cell factories for advanced biomanufacturing. Finally, future engineering efforts for enhancing the production efficiency of this platform strain are highlighted.
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Affiliation(s)
- Mei-Li Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Xiaoxia Gao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Lu Lin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Jing Yang
- 2011 College, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Xiao-Jun Ji
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
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Min Lee S, Young Lee J, Hahn JS, Baek SH. Engineering of Yarrowia lipolytica as a platform strain for producing adipic acid from renewable resource. Bioresour Technol 2024; 391:129920. [PMID: 37931767 DOI: 10.1016/j.biortech.2023.129920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 11/08/2023]
Abstract
There is an increasing demand for bio-based dicarboxylic acids (DCA) as an eco-friendly alternatives to chemically synthesized DCA. Adipic acid, which is not naturally produced by microorganisms, is an essential DCA with significant industrial importance. This study aimed to develop a platform strain using Yarrowia lipolytica for efficient bioconversion of renewable resources into adipic acid. To prevent the complete oxidation of adipic acid, peroxisomal β-oxidation was engineered by selectively disrupting acyl-CoA oxidases. Furthermore, ω-oxidation activity was improved via introducing an additional copy of cytochrome P450 monooxygenase (ALK5) and reductase (CPR1) with fatty alcohol oxidase (FAO1). The production phase used SP92D medium in a two-stage bioconversion process, during which the engineered strain exhibited the highest production level, achieving a remarkable 9.7-fold increase compared to that of the parental strain. To our knowledge, this is the first report demonstrating that engineered Y. lipolytica can produce adipic acid from fatty acid methyl esters.
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Affiliation(s)
- Sang Min Lee
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan 44429, Republic of Korea; Interdisciplinary Program for Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Ju Young Lee
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan 44429, Republic of Korea
| | - Ji-Sook Hahn
- Interdisciplinary Program for Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Seung-Ho Baek
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan 44429, Republic of Korea.
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35
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Ramesh A, Lee S, Wheeldon I. Genome Editing, Transcriptional Regulation, and Forward Genetic Screening Using CRISPR-Cas12a Systems in Yarrowia lipolytica. Methods Mol Biol 2024; 2760:169-198. [PMID: 38468089 DOI: 10.1007/978-1-0716-3658-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Class II Type V endonucleases have increasingly been adapted to develop sophisticated and easily accessible synthetic biology tools for genome editing, transcriptional regulation, and functional genomic screening in a wide range of organisms. One such endonuclease, Cas12a, presents itself as an attractive alternative to Cas9-based systems. The ability to mature its own guide RNAs (gRNAs) from a single transcript has been leveraged for easy multiplexing, and its lack of requirement of a tracrRNA element, also allows for short gRNA expression cassettes. To extend these functionalities into the industrially relevant oleaginous yeast Yarrowia lipolytica, we developed a set of CRISPR-Cas12a vectors for easy multiplexed gene knockout, repression, and activation. We further extended the utility of this CRISPR-Cas12a system to functional genomic screening by constructing a genome-wide guide library targeting every gene with an eightfold coverage. Pooled CRISPR screens conducted with this library were used to profile Cas12a guide activities and develop a machine learning algorithm that could accurately predict highly efficient Cas12a gRNA. In this protocols chapter, we first present a method by which protein coding genes may be functionally disrupted via indel formation with CRISPR-Cas12a systems. Further, we describe how Cas12a fused to a transcriptional regulator can be used in conjunction with shortened gRNA to achieve transcriptional repression or activation. Finally, we describe the design, cloning, and validation of a genome-wide library as well as a protocol for the execution of a pooled CRISPR screen, to determine guide activity profiles in a genome-wide context in Y. lipolytica. The tools and strategies discussed here expand the list of available synthetic biology tools for facile genome engineering in this industrially important host.
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Affiliation(s)
- Adithya Ramesh
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - Sangcheon Lee
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
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36
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Yang S, Pan X, You J, Guo B, Liu Z, Cao Y, Li G, Shao M, Zhang X, Rao Z. Systematic metabolic engineering of Yarrowia lipolytica for the enhanced production of erythritol. Bioresour Technol 2024; 391:129918. [PMID: 37884093 DOI: 10.1016/j.biortech.2023.129918] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/23/2023] [Accepted: 10/23/2023] [Indexed: 10/28/2023]
Abstract
In recent times, there has been a growing interest in exploring microbial strains that exhibit enhanced erythritol productivity. Nonetheless, the lack of advanced synthetic biology tools has limited rapid strain development. In this study, the CRISPR/Cas9 system was employed to genetically modify Yarrowia lipolytica at the chromosomal level, which could improve the production of erythritol while saving the time required to markers recovery, and realizing the rapid construction of high-erythritol strains. Firstly, the basic strain E004 was generated by increasing the efficiency of homologous recombination and regulating the erythritol degradation pathway. Secondly, eleven key gene targets and a strong promoter 8UAS1BXPR2-PTEFin was obtained by target screening and promoter engineering. Finally, based on modular pathway engineering and morphological engineering, the high production of erythritol was achieved successfully. The best-engineered strain E326 produced 256 g/L erythritol in a 5-L bioreactor, which is the highest production level reported so far in Y. lipolytica.
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Affiliation(s)
- Shuling Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Xuewei Pan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Jiajia You
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Baomin Guo
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zuyi Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Ying Cao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Guomin Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Minglong Shao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China.
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37
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Godana EA, Zhang X, Yang Q, Hu W, Zhao L, Wang K, Zhang H. Yarrowia lipolytica increased the activities of disease defense related enzymes and anti-fungal compounds in asparagus (Asparagus officinalis). Pestic Biochem Physiol 2024; 198:105748. [PMID: 38225091 DOI: 10.1016/j.pestbp.2023.105748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/08/2023] [Accepted: 12/10/2023] [Indexed: 01/17/2024]
Abstract
Fungal diseases pose significant threats to the production of asparagus, resulting in economic losses and decreased crop quality. The potential of the yeast Yarrowia lipolytica as a biocontrol agent against Fusarium proliferatum, a common pathogen of asparagus, was investigated in this study. The effects of Y. lipolytica treatment on decay incidence, disease index, and activities of major disease defense-related enzymes were investigated. In addition, we examined the levels of antifungal compounds such as total phenols, flavonoids, and lignin in asparagus plants exposed to Y. lipolytica. The results showed that Y. lipolytica treatment significantly reduced decay incidence and disease index caused by F. proliferatum when compared to the control group. Furthermore, Y. lipolytica-treated plants showed increased activity of disease defense-related enzymes, indicating that defense responses were activated. The activities of all evaluated enzymes were significantly higher in Y. lipolytica-treated asparagus, indicating an improved ability to combat fungal pathogens. Furthermore, Y. lipolytica treatment increased the content of antifungal compounds such as total phenols, flavonoids, and lignin, which are known to possess antimicrobial properties. These findings highlight the potential of Y. lipolytica as a biocontrol agent for fungal diseases in asparagus crops. The ability of Y. lipolytica to reduce disease incidence, boost disease defense-related enzymes, and increase antifungal compound content provides valuable insights into its efficacy as a natural and sustainable approach to disease management. However, further investigations are needed to optimize application methods and determine its efficacy under field conditions.
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Affiliation(s)
- Esa Abiso Godana
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Xiaoyun Zhang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Qiya Yang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Wanying Hu
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Lina Zhao
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Kaili Wang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Hongyin Zhang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China.
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Walker C, Mortensen M, Poudel B, Cotter C, Myers R, Okekeogbu IO, Ryu S, Khomami B, Giannone RJ, Laursen S, Trinh CT. Proteomes reveal metabolic capabilities of Yarrowia lipolytica for biological upcycling of polyethylene into high-value chemicals. mSystems 2023; 8:e0074123. [PMID: 37882587 PMCID: PMC10734471 DOI: 10.1128/msystems.00741-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/18/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Sustainable processes for biological upcycling of plastic wastes in a circular bioeconomy are needed to promote decarbonization and reduce environmental pollution due to increased plastic consumption, incineration, and landfill storage. Strain characterization and proteomic analysis revealed the robust metabolic capabilities of Yarrowia lipolytica to upcycle polyethylene into high-value chemicals. Significant proteome reallocation toward energy and lipid metabolisms was required for robust growth on hydrocarbons with n-hexadecane as the preferential substrate. However, an apparent over-investment in these same categories to utilize complex depolymerized plastic (DP) oil came at the expense of protein biosynthesis, limiting cell growth. Taken together, this study elucidates how Y. lipolytica activates its metabolism to utilize DP oil and establishes Y. lipolytica as a promising host for the upcycling of plastic wastes.
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Affiliation(s)
- Caleb Walker
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Max Mortensen
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Bindica Poudel
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Christopher Cotter
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Ryan Myers
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Ikenna O. Okekeogbu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Seunghyun Ryu
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Bamin Khomami
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Richard J. Giannone
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Siris Laursen
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Cong T. Trinh
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
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Jagtap SS, Liu JJ, Walukiewicz HE, Riley R, Ahrendt S, Koriabine M, Cobaugh K, Salamov A, Yoshinaga Y, Ng V, Daum C, Grigoriev IV, Slininger PJ, Dien BS, Jin YS, Rao CV. Draft genome sequence of Yarrowia lipolytica NRRL Y-64008, an oleaginous yeast capable of growing on lignocellulosic hydrolysates. Microbiol Resour Announc 2023; 12:e0043523. [PMID: 37982613 PMCID: PMC10720525 DOI: 10.1128/mra.00435-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/10/2023] [Indexed: 11/21/2023] Open
Abstract
Yarrowia lipolytica is an oleaginous yeast that produces high titers of fatty acid-derived biofuels and biochemicals. It can grow on hydrophobic carbon sources and lignocellulosic hydrolysates. The genome sequence of Y. lipolytica NRRL Y-64008 is reported to aid in its development as a biotechnological chassis for producing biofuels and bioproducts.
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Affiliation(s)
- Sujit Sadashiv Jagtap
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana–Champaign, Urbana, Illinois, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana–Champaign, Urbana, Illinois, USA
| | - Jing-Jing Liu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana–Champaign, Urbana, Illinois, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana–Champaign, Urbana, Illinois, USA
| | - Hanna E. Walukiewicz
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana–Champaign, Urbana, Illinois, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana–Champaign, Urbana, Illinois, USA
| | - Robert Riley
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Steven Ahrendt
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Maxim Koriabine
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Kelly Cobaugh
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Asaf Salamov
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Yuko Yoshinaga
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Vivian Ng
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Chris Daum
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Igor V. Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Patricia J. Slininger
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois, USA
| | - Bruce S. Dien
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois, USA
| | - Yong-Su Jin
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana–Champaign, Urbana, Illinois, USA
- Department of Food Science and Nutrition, University of Illinois at Urbana–Champaign, Urbana, Illinois, USA
| | - Christopher V. Rao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana–Champaign, Urbana, Illinois, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana–Champaign, Urbana, Illinois, USA
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40
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Liu Q, Bi H, Wang K, Zhang Y, Chen B, Zhang H, Wang M, Fang Y. Revealing the Mechanisms of Enhanced β-Farnesene Production in Yarrowia lipolytica through Metabolomics Analysis. Int J Mol Sci 2023; 24:17366. [PMID: 38139198 PMCID: PMC10743872 DOI: 10.3390/ijms242417366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/05/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
β-Farnesene is an advanced molecule with promising applications in agriculture, the cosmetics industry, pharmaceuticals, and bioenergy. To supplement the shortcomings of rational design in the development of high-producing β-farnesene strains, a Metabolic Pathway Design-Fermentation Test-Metabolomic Analysis-Target Mining experimental cycle was designed. In this study, by over-adding 20 different amino acids/nucleobases to induce fluctuations in the production of β-farnesene, the changes in intracellular metabolites in the β-farnesene titer-increased group were analyzed using non-targeted metabolomics. Differential metabolites that were detected in each experimental group were selected, and their metabolic pathways were located. Based on these differential metabolites, targeted strain gene editing and culture medium optimization were performed. The overexpression of the coenzyme A synthesis-related gene pantothenate kinase (PanK) and the addition of four mixed water-soluble vitamins in the culture medium increased the β-farnesene titer in the shake flask to 1054.8 mg/L, a 48.5% increase from the initial strain. In the subsequent fed-batch fermentation, the β-farnesene titer further reached 24.6 g/L. This work demonstrates the tremendous application value of metabolomics analysis for the development of industrial recombinant strains and the optimization of fermentation conditions.
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Affiliation(s)
| | - Haoran Bi
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; (Q.L.); (K.W.); (Y.Z.); (B.C.); (H.Z.); (Y.F.)
| | | | | | | | | | - Meng Wang
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; (Q.L.); (K.W.); (Y.Z.); (B.C.); (H.Z.); (Y.F.)
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41
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Liu H, Huang X, Liu Y, Jing X, Ning Y, Xu P, Deng L, Wang F. Efficient Production of Triacetic Acid Lactone from Lignocellulose Hydrolysate by Metabolically Engineered Yarrowia lipolytica. J Agric Food Chem 2023; 71:18909-18918. [PMID: 37999448 DOI: 10.1021/acs.jafc.3c06528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Lignocellulose is a promising renewable feedstock for the bioproduction of high-value biochemicals. The poorly expressed xylose catabolic pathway was the bottleneck in the efficient utilization of the lignocellulose feedstock in yeast. Herein, multiple genetic and process engineering strategies were explored to debottleneck the conversion of xylose to the platform chemical triacetic acid lactone (TAL) in Yarrowia lipolytica. We identified that xylose assimilation generating more cofactor NADPH was favorable for the TAL synthesis. pH control improved the expression of acetyl-CoA carboxylase and generated more precursor malonyl-CoA. Combined with the suppression of the lipid synthesis pathway, 5.03 and 4.18 g/L TAL were produced from pure xylose and xylose-rich wheat straw hydrolysate, respectively. Our work removed the bottleneck of the xylose assimilation pathway and effectively upgraded wheat straw hydrolysate to TAL, which enabled us to build a sustainable oleaginous yeast cell factory to cost-efficiently produce green chemicals from low-cost lignocellulose by Y. lipolytica.
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Affiliation(s)
- Huan Liu
- Beijing Bioprocess Key Laboratory, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaolan Huang
- Beijing Bioprocess Key Laboratory, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yangming Liu
- Beijing Bioprocess Key Laboratory, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xinyun Jing
- Beijing Bioprocess Key Laboratory, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yuchen Ning
- Beijing Bioprocess Key Laboratory, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Peng Xu
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology, Shantou, Guangdong 515063, China
- Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion-Israel Institute of Technology, Shantou, Guangdong 515063, China
| | - Li Deng
- Beijing Bioprocess Key Laboratory, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Fang Wang
- Beijing Bioprocess Key Laboratory, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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42
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Agrawal A, Yang Z, Blenner M. Engineering Yarrowia lipolytica for the biosynthesis of geraniol. Metab Eng Commun 2023; 17:e00228. [PMID: 38029016 PMCID: PMC10652127 DOI: 10.1016/j.mec.2023.e00228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 10/27/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023] Open
Abstract
Geraniol is a monoterpene with wide applications in the food, cosmetics, and pharmaceutical industries. Microbial production has largely used model organisms lacking favorable properties for monoterpene production. In this work, we produced geraniol in metabolically engineered Yarrowia lipolytica. First, two plant-derived geraniol synthases (GES) from Catharanthus roseus (Cr) and Valeriana officinalis (Vo) were tested based on previous reports of activity. Both wild type and truncated mutants of GES (without signal peptide targeting chloroplast) were examined by co-expressing with MVA pathway enzymes tHMG1 and IDI1. Truncated CrGES (tCrGES) produced the most geraniol and thus was used for further experimentation. The initial strain was obtained by overexpression of the truncated HMG1, IDI and tCrGES. The acetyl-CoA precursor pool was enhanced by overexpressing mevalonate pathway genes such as ERG10, HMGS or MVK, PMK. The final strain overexpressing 3 copies of tCrGES and single copies of ERG10, HMGS, tHMG1, IDI produced approximately 1 g/L in shake-flask fermentation. This is the first demonstration of geraniol production in Yarrowia lipolytica and the highest de novo titer reported to date in yeast.
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Affiliation(s)
- Ayushi Agrawal
- Department of Chemical and Biomolecular Engineering, 590 Avenue 1743, University of Delaware, Newark, DE, 19713, USA
| | - Zhiliang Yang
- Department of Chemical and Biomolecular Engineering, Clemson University, 206 S. Palmetto Blvd., Clemson, SC, 29634, USA
| | - Mark Blenner
- Department of Chemical and Biomolecular Engineering, 590 Avenue 1743, University of Delaware, Newark, DE, 19713, USA
- Department of Chemical and Biomolecular Engineering, Clemson University, 206 S. Palmetto Blvd., Clemson, SC, 29634, USA
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43
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Tomás-Pejó E, Morales-Palomo S, González-Fernández C. Cutaneotrichosporon curvatum and Yarrowia lipolytica as key players for green chemistry: efficient oil producers from food waste via the carboxylate platform. Bioengineered 2023; 14:2286723. [PMID: 38010763 PMCID: PMC10761111 DOI: 10.1080/21655979.2023.2286723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023] Open
Abstract
Cutaneotrichosporon curvatum and Yarrowia lipolytica can accumulate microbial oils using short-chain fatty acids (SCFA) as carbon sources. SCFAs-rich media often contain significant amounts of nitrogen that prevent high carbon:nitrogen (C:N) ratios necessary to boost lipid production. This work assessed the intrinsic ability of C. curvatum and Y. lipolytica to produce high amounts of microbial oils from these unusual carbon sources. Results demonstrated that minor differences in SCFA concentration (only 2 g/L) had a significant effect on yeast growth and lipid production. A C:N of 80 promoted yeast growth at all SCFA concentrations and favored SCFA consumption at 19 g/L SCFAs. The different SCFA uptake preferences in C. curvatum and Y. lipolytica highlighted the importance of considering the SCFA profile to select a suitable yeast strain for microbial oils production. At the most challenging SCFA concentration (19 g/L), 57.2% ±1.6% (w/w) and 78.4 ± 0.6% (w/w) lipid content were obtained in C. curvatum and Y. lipolytica, respectively. These values are among the highest reported for wild-type strains. To circumvent the challenges associated with media with high nitrogen content, this report also proved struvite precipitation as an effective method for increasing lipid production (from 17.9 ± 3.9% (w/w) to 41.9 ± 2.6% (w/w)) after nitrogen removal in food waste-derived media.
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Affiliation(s)
| | | | - Cristina González-Fernández
- Biotechnological Processes Unit, Móstoles (Madrid), Spain
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, Valladolid University, Valladolid, Spain
- Institute of Sustainable Processes, Valladolid, Spain
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44
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Knopp FM, da Rocha Olivieri de Barros R, Drummond BS, Siani AC, Ferrara MA, Bon EPS. Production of perillic acid from orange essential oil by Yarrowia lipolytica using a top-aerated bioreactor. Braz J Microbiol 2023; 54:2663-2670. [PMID: 37684539 PMCID: PMC10689591 DOI: 10.1007/s42770-023-01108-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
R-(+)-Perillic acid, a promising anticancer and immunomodulatory agent, is the major product from the biotransformation of R-(+)-limonene-rich orange essential oil by the yeast Yarrowia lipolytica. Due to the abundance and low cost of orange essential oil, which is a byproduct of the citrus industry, we attempted to improve the biotransformation process by optimizing yeast cell mass production. Then, the whole process was transposed and adapted to a 2-L instrumented bioreactor. Cell mass production was optimized in shaker flasks using a statistical experimental design. The optimized medium (g·L-1: 22.9 glucose, 7.7 peptone, 4.1 yeast extract and 1.0 malt extract) resulted in a 13.0 g·L-1 final cell concentration and 0.18 g cell·L-1·h-1 productivity. A further increase to 18.0 g·L-1 was achieved in a 2-L bioreactor upon fed-batch culture. High-purity limonene bioconversion was performed in the same bioreactor utilizing top aeration to diminish terpene volatilization; as a result, 839.6 mg·L-1 perillic acid accumulated after 48 h. Under the same conditions, industrial orange essential oil afforded 806.4 mg·L-1 perillic acid. The yeast growth medium optimization resulted in a twofold increase in biomass accumulation and a reduction in growth medium nitrogen sources, which lowered the catalytic biomass production cost. Compared with conventional bottom aeration, the bioreactor top aeration strategy resulted in higher bioconversion rates. The conditions developed for high-purity limonene bioconversion were successfully applied to low-cost orange essential oil, showing the robustness of Y. lipolytica yeast.
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Affiliation(s)
- Felipe M Knopp
- Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | - Bruna S Drummond
- Institute of Drug Technology, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
| | - Antonio Carlos Siani
- Institute of Drug Technology, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
| | | | - Elba P S Bon
- Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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45
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Zhang Y, Zhang X, Liu H, Hou J, Liu M, Qi Q. Efficient production of 2'-fucosyllactose in unconventional yeast Yarrowia lipolytica. Synth Syst Biotechnol 2023; 8:716-723. [PMID: 38053583 PMCID: PMC10694633 DOI: 10.1016/j.synbio.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 12/07/2023] Open
Abstract
2'-Fucosyllactose (2'-FL) has great application value as a nutritional component and the whole cell biosynthesis of 2'-FL has become the focus of current research. Yarrowia lipolytica has great potential in oligosaccharide synthesis and large-scale fermentation. In this study, systematic engineering of Y. lipolytica for efficient 2'-FL production was performed. By fusing different protein tags, the synthesis of 2'-FL was optimized and the ubiquitin tag was demonstrated to be the best choice to increase the 2'-FL production. By iterative integration of the related genes, increasing the precursor supply, and promoting NADPH regeneration, the 2'-FL synthesis was further improved. The final 2'-FL titer, 41.10 g/L, was obtained in the strain F5-1. Our work reports the highest 2'-FL production in Y. lipolytica, and demonstrates that Y. lipolytica is an efficient microbial chassis for the synthesis of oligosaccharides.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xuejing Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Haiyan Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Mengmeng Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
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46
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Ouellet B, Morneau Z, Abdel-Mawgoud AM. Nile red-based lipid fluorometry protocol and its use for statistical optimization of lipids in oleaginous yeasts. Appl Microbiol Biotechnol 2023; 107:7313-7330. [PMID: 37741936 DOI: 10.1007/s00253-023-12786-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/25/2023]
Abstract
As lipogenic yeasts are becoming increasingly harnessed as biofactories of oleochemicals, the availability of efficient protocols for the determination and optimization of lipid titers in these organisms is necessary. In this study, we optimized a quick, reliable, and high-throughput Nile red-based lipid fluorometry protocol adapted for oleaginous yeasts and validated it using different approaches, the most important of which is using gas chromatography coupled to flame ionization detection and mass spectrometry. This protocol was applied in the optimization of the concentrations of ammonium chloride and glycerol for attaining highest lipid titers in Rhodotorula toruloides NRRL Y-6987 and Yarrowia lipolytica W29 using response surface central composite design (CCD). Results of this optimization showed that the optimal concentration of ammonium chloride and glycerol is 4 and 123 g/L achieving a C/N ratio of 57 for R. toruloides, whereas for Y. lipolytica, concentrations are 4 and 139 g/L with a C/N ratio of 61 for Y. lipolytica. Outside the C/N of 33 to 74 and 45 to 75, respectively, for R. toruloides and Y. lipolytica, lipid productions decrease by more than 10%. The developed regression models and response surface plots show the importance of the careful selection of C/N ratio to attain maximal lipid production. KEY POINTS: • Nile red (NR)-based lipid fluorometry is efficient, rapid, cheap, high-throughput. • NR-based lipid fluorometry can be well used for large-scale experiments like DoE. • Optimal molar C/N ratio for maximum lipid production in lipogenic yeasts is ~60.
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Affiliation(s)
- Benjamin Ouellet
- Institute of Integrative Biology and Systems, Laval University, Pavillon Charles-Eugène-Marchand, 1030 Ave. de la Médecine,, QC, QC, G1V 0A6, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Faculty of Science and Engineering, Laval University, 1045 Ave. de la Médecine, QC, Quebec, G1V 0A6, Canada
| | - Zacharie Morneau
- Institute of Integrative Biology and Systems, Laval University, Pavillon Charles-Eugène-Marchand, 1030 Ave. de la Médecine,, QC, QC, G1V 0A6, Canada
| | - Ahmad M Abdel-Mawgoud
- Institute of Integrative Biology and Systems, Laval University, Pavillon Charles-Eugène-Marchand, 1030 Ave. de la Médecine,, QC, QC, G1V 0A6, Canada.
- Department of Biochemistry, Microbiology and Bioinformatics, Faculty of Science and Engineering, Laval University, 1045 Ave. de la Médecine, QC, Quebec, G1V 0A6, Canada.
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Li W, Mai J, Lin L, Zhang ZG, Ledesma-Amaro R, Dong W, Ji XJ. Combination of microbial and chemical synthesis for the sustainable production of β-elemene, a promising plant-extracted anticancer compound. Biotechnol Bioeng 2023; 120:3612-3621. [PMID: 37661795 DOI: 10.1002/bit.28544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 09/05/2023]
Abstract
Beta-elemene, a class of sesquiterpene derived from the Chinese medicinal herb Curcuma wenyujin, is widely used in clinical medicine due to its broad-spectrum antitumor activity. However, the unsustainable plant extraction prompted the search for environmentally friendly strategies for β-elemene production. In this study, we designed a Yarrowia lipolytica cell factory that can continuously produce germacrene A, which is further converted into β-elemene with 100% yield through a Cope rearrangement reaction by shifting the temperature to 250°C. First, the productivity of four plant-derived germacrene A synthases was evaluated. After that, the metabolic flux of the precursor to germacrene A was maximized by optimizing the endogenous mevalonate pathway, inhibiting the competing squalene pathway, and expressing germacrene A synthase gene in multiple copies. Finally, the most promising strain achieved the highest β-elemene titer reported to date with 5.08 g/L. This sustainable and green method has the potential for industrial β-elemene production.
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Affiliation(s)
- Wenjuan Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
| | - Jie Mai
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
| | - Lu Lin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
| | - Zhi-Gang Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering, Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
| | - Xiao-Jun Ji
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
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48
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Zhu X, Li M, Zhu R, Xin Y, Guo Z, Gu Z, Zhang L, Guo Z. Up Front Unfolded Protein Response Combined with Early Protein Secretion Pathway Engineering in Yarrowia lipolytica to Attenuate ER Stress Caused by Enzyme Overproduction. Int J Mol Sci 2023; 24:16426. [PMID: 38003616 PMCID: PMC10670989 DOI: 10.3390/ijms242216426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 10/28/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
Engineering the yeast Yarrowia lipolytica as an efficient host to produce recombinant proteins remains a longstanding goal for applied biocatalysis. During the protein overproduction, the accumulation of unfolded and misfolded proteins causes ER stress and cell dysfunction in Y. lipolytica. In this study, we evaluated the effects of several potential ER chaperones and translocation components on relieving ER stress by debottlenecking the protein synthetic machinery during the production of the endogenous lipase 2 and the E. coli β-galactosidase. Our results showed that improving the activities of the non-dominant translocation pathway (SRP-independent) boosted the production of the two proteins. While the impact of ER chaperones is protein dependent, the nucleotide exchange factor Sls1p for protein folding catalyst Kar2p is recognized as a common contributor enhancing the secretion of the two enzymes. With the identified protein translocation components and ER chaperones, we then exemplified how these components can act synergistically with Hac1p to enhance recombinant protein production and relieve the ER stress on cell growth. Specifically, the yeast overexpressing Sls1p and cytosolic heat shock protein Ssa8p and Ssb1p yielded a two-fold increase in Lip2p secretion compared with the control, while co-overexpressing Ssa6p, Ssb1p, Sls1p and Hac1p resulted in a 90% increase in extracellular β-galp activity. More importantly, the cells sustained a maximum specific growth rate (μmax) of 0.38 h-1 and a biomass yield of 0.95 g-DCW/g-glucose, only slightly lower than that was obtained by the wild type strain. This work demonstrated engineering ER chaperones and translocation as useful strategies to facilitate the development of Y. lipolytica as an efficient protein-manufacturing platform.
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Affiliation(s)
- Xingyu Zhu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; (X.Z.); (M.L.); (R.Z.); (Y.X.); (Z.G.); (L.Z.)
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Moying Li
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; (X.Z.); (M.L.); (R.Z.); (Y.X.); (Z.G.); (L.Z.)
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Rui Zhu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; (X.Z.); (M.L.); (R.Z.); (Y.X.); (Z.G.); (L.Z.)
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Yu Xin
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; (X.Z.); (M.L.); (R.Z.); (Y.X.); (Z.G.); (L.Z.)
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Zitao Guo
- School of Food and Biological Engineering, Jiangsu University, Xuefu Road 301, Jingkou District, Zhenjiang 212013, China;
| | - Zhenghua Gu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; (X.Z.); (M.L.); (R.Z.); (Y.X.); (Z.G.); (L.Z.)
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Liang Zhang
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; (X.Z.); (M.L.); (R.Z.); (Y.X.); (Z.G.); (L.Z.)
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Zhongpeng Guo
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; (X.Z.); (M.L.); (R.Z.); (Y.X.); (Z.G.); (L.Z.)
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
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49
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Jovanovic Gasovic S, Dietrich D, Gläser L, Cao P, Kohlstedt M, Wittmann C. Multi-omics view of recombinant Yarrowia lipolytica: Enhanced ketogenic amino acid catabolism increases polyketide-synthase-driven docosahexaenoic production to high selectivity at the gram scale. Metab Eng 2023; 80:45-65. [PMID: 37683719 DOI: 10.1016/j.ymben.2023.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/04/2023] [Accepted: 09/04/2023] [Indexed: 09/10/2023]
Abstract
DHA is a marine PUFA of commercial value, given its multiple health benefits. The worldwide emerging shortage in DHA supply has increased interest in microbial cell factories that can provide the compound de novo. In this regard, the present work aimed to improve DHA production in the oleaginous yeast strain Y. lipolytica Af4, which synthetized the PUFA via a heterologous myxobacterial polyketide synthase (PKS)-like gene cluster. As starting point, we used transcriptomics, metabolomics, and 13C-based metabolic pathway profiling to study the cellular dynamics of Y. lipolytica Af4. The shift from the growth to the stationary DHA-production phase was associated with fundamental changes in carbon core metabolism, including a strong upregulation of the PUFA gene cluster, as well as an increase in citrate and fatty acid degradation. At the same time, the intracellular levels of the two DHA precursors acetyl-CoA and malonyl-CoA dropped by up to 98% into the picomolar range. Interestingly, the degradation pathways for the ketogenic amino acids l-lysine, l-leucine, and l-isoleucine were transcriptionally activated, presumably to provide extra acetyl-CoA. Supplementation with small amounts of these amino acids at the beginning of the DHA production phase beneficially increased the intracellular CoA-ester pools and boosted the DHA titer by almost 40%. Isotopic 13C-tracer studies revealed that the supplements were efficiently directed toward intracellular CoA-esters and DHA. Hereby, l-lysine was found to be most efficient, as it enabled long-term activation, due to storage within the vacuole and continuous breakdown. The novel strategy enabled DHA production in Y. lipolytica at the gram scale for the first time. DHA was produced at a high selectivity (27% of total fatty acids) and free of the structurally similar PUFA DPA, which facilitates purification for high-value medical applications that require API-grade DHA. The assembled multi-omics picture of the central metabolism of Y. lipolytica provides valuable insights into this important yeast. Beyond our work, the enhanced catabolism of ketogenic amino acids seems promising for the overproduction of other compounds in Y. lipolytica, whose synthesis is limited by the availability of CoA ester precursors.
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Affiliation(s)
| | - Demian Dietrich
- Institute of Systems Biotechnology, Saarland University, Germany
| | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Germany
| | - Peng Cao
- Institute of Systems Biotechnology, Saarland University, Germany
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50
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Turck D, Bohn T, Castenmiller J, De Henauw S, Hirsch‐Ernst KI, Maciuk A, Mangelsdorf I, McArdle HJ, Naska A, Pentieva K, Siani A, Thies F, Tsabouri S, Vinceti M, Aguilera‐Gómez M, Cubadda F, Frenzel T, Heinonen M, Prieto Maradona M, Marchelli R, Neuhäuser‐Berthold M, Poulsen M, Schlatter JR, Siskos A, van Loveren H, Ackerl R, Knutsen HK. Safety of an extension of use of Yarrowia lipolytica yeast biomass as a novel food pursuant to Regulation (EU) 2015/2283. EFSA J 2023; 21:e8416. [PMID: 38035143 PMCID: PMC10685999 DOI: 10.2903/j.efsa.2023.8416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023] Open
Abstract
Following a request from the European Commission, the EFSA Panel on Nutrition, Novel Foods and Food Allergens (NDA) was asked to deliver an opinion on the safety of an extension of use of Yarrowia (Y.) lipolytica yeast biomass as a novel food (NF) pursuant to Regulation (EU) 2015/2283. The extension of use pertains to the use of the NF as a food ingredient in a number of food categories, in foods for special medical purposes and in foods for total diet replacement for weight control. In 2018, Y. lipolytica was attributed the qualified presumption of safety (QPS) status for production purposes, including food and feed products based on biomass. The Panel considers that the data provided sufficient information with respect to the stability of the NF, also when used as a food ingredient. The concentrations of the analysed processing contaminants do not raise safety concerns. The Panel also considers that consumption of the NF is not nutritionally disadvantageous under the proposed conditions of use. The Panel concludes that the NF, Y. lipolytica yeast biomass, is safe under the proposed conditions of use.
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