1
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Chen Q, Lei J, Li X, Zhang J, Liu D, Cui X, Ge F. Heterologous synthesis of ginsenoside F1 and its precursors in Nicotiana benthamiana. JOURNAL OF PLANT PHYSIOLOGY 2024; 299:154276. [PMID: 38801806 DOI: 10.1016/j.jplph.2024.154276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 05/15/2024] [Accepted: 05/22/2024] [Indexed: 05/29/2024]
Abstract
Ginsenoside F1 has high medicinal values, which is a kind of rare triterpene saponin isolated from Panax plants. The extremely low content of ginsenoside F1 in herbs has limited its research and application in medical field. In this work, we constructed a pathway in tobacco for the biosynthesis of ginsenoside F1 by metabolic engineering. Four enzyme genes (PnDDS, CYP716A47, CYP716S1 and UGT71A56) isolated from Panax notoginseng were introduced into tobacco. Thus, a biosynthetic pathway for ginsenoside F1 synthesis was artificially constructed in tobacco cells; moreover, the four exogenous genes could be expressed in the roots, stems and leaves of transgenic plants. Consequently, ginsenoside F1 and its precursors were successfully synthesized in the transgenic tobacco, compared with Panax plants, the content of ginsenoside F1 in transgenic tobacco was doubled. In addition, accumulation of ginsenoside F1 and its precursors in transgenic tobacco shows organ specificity. Based on these results, a new approach was established to produce rare ginsenoside F1; meanwhile, such strategy could also be employed in plant hosts for the heterologous synthesis of other important or rare natural products.
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Affiliation(s)
- Qin Chen
- Key Laboratory of Sustainable Utilization of Panax Notoginseng Resources of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Jun Lei
- Key Laboratory of Sustainable Utilization of Panax Notoginseng Resources of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Xiaolei Li
- Key Laboratory of Sustainable Utilization of Panax Notoginseng Resources of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China; Analytical & Testing Research Center, Kunming University of Science and Technology, Kunming, 650500, China
| | - Jinyu Zhang
- Institute of Medicinal Plants, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Diqiu Liu
- Key Laboratory of Sustainable Utilization of Panax Notoginseng Resources of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Xiuming Cui
- Key Laboratory of Sustainable Utilization of Panax Notoginseng Resources of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Beijing, 100700, China.
| | - Feng Ge
- Key Laboratory of Sustainable Utilization of Panax Notoginseng Resources of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Beijing, 100700, China.
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2
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Dong G, Zhao Y, Ding W, Xu S, Zhang Q, Zhao H, Shi S. Metabolic engineering of Saccharomyces cerevisiae for de novo production of odd-numbered medium-chain fatty acids. Metab Eng 2024; 82:100-109. [PMID: 38325640 DOI: 10.1016/j.ymben.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 12/18/2023] [Accepted: 01/26/2024] [Indexed: 02/09/2024]
Abstract
Odd-numbered fatty acids (FAs) have been widely used in nutrition, agriculture, and chemical industries. Recently, some studies showed that they could be produced from bacteria or yeast, but the products are almost exclusively odd-numbered long-chain FAs. Here we report the design and construction of two biosynthetic pathways in Saccharomyces cerevisiae for de novo production of odd-numbered medium-chain fatty acids (OMFAs) via ricinoleic acid and 10-hydroxystearic acid, respectively. The production of OMFAs was enabled by introducing a hydroxy fatty acid cleavage pathway, including an alcohol dehydrogenase from Micrococcus luteus, a Baeyer-Villiger monooxygenase from Pseudomonas putida, and a lipase from Pseudomonas fluorescens. These OMFA biosynthetic pathways were optimized by eliminating the rate-limiting step, generating heptanoic acid, 11-hydroxyundec-9-enoic acid, nonanoic acid, and 9-hydroxynonanoic acid at 7.83 mg/L, 9.68 mg/L, 9.43 mg/L and 13.48 mg/L, respectively. This work demonstrates the biological production of OMFAs in a sustainable manner in S. cerevisiae.
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Affiliation(s)
- Genlai Dong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China; Key Laboratory of Natural Products, Henan Academy of Sciences, Zhengzhou, 450002, China
| | - Ying Zhao
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Wentao Ding
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shijie Xu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Qi Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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3
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Arnolds KL, Higgins RC, Crandall J, Li G, Linger JG, Guarnieri MT. Risk Assessment of Industrial Microbes Using a Terrestrial Mesocosm Platform. MICROBIAL ECOLOGY 2023; 87:12. [PMID: 38072911 PMCID: PMC10710964 DOI: 10.1007/s00248-023-02321-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023]
Abstract
Industrial microbes and bio-derived products have emerged as an integral component of the bioeconomy, with an array of agricultural, bioenergy, and biomedical applications. However, the rapid development of microbial biotechnology raises concerns related to environmental escape of laboratory microbes, detection and tracking thereof, and resultant impact upon native ecosystems. Indeed, though wild-type and genetically modified microbes are actively deployed in industrial bioprocesses, an understanding of microbial interactivity and impact upon the environment is severely lacking. In particular, the persistence and sustained ecosystem impact of industrial microbes following laboratory release or unintentional laboratory escape remains largely unexplored. Herein, we investigate the applicability of soil-sorghum mesocosms for the ecological risk assessment of the industrial microbe, Saccharomyces cerevisiae. We developed and applied a suite of diagnostic and bioinformatic analyses, including digital droplet PCR, microscopy, and phylogenomic analyses to assess the impacts of a terrestrial ecosystem perturbation event over a 30-day time course. The platform enables reproducible, high-sensitivity tracking of S. cerevisiae in a complex soil microbiome and analysis of the impact upon abiotic soil characteristics and soil microbiome population dynamics and diversity. The resultant data indicate that even though S. cerevisiae is relatively short-lived in the soil, a single perturbation event can have sustained impact upon mesocosm soil composition and underlying microbial populations in our system, underscoring the necessity for more comprehensive risk assessment and development of mitigation and biocontainment strategies in industrial bioprocesses.
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Affiliation(s)
- Kathleen L Arnolds
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Pkwy, Golden, CO, 80401, USA
| | - Riley C Higgins
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Pkwy, Golden, CO, 80401, USA
| | - Jennifer Crandall
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Pkwy, Golden, CO, 80401, USA
| | - Gabriella Li
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Pkwy, Golden, CO, 80401, USA
| | - Jeffrey G Linger
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Pkwy, Golden, CO, 80401, USA
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Michael T Guarnieri
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Pkwy, Golden, CO, 80401, USA.
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO, 80401, USA.
- Renewable & Sustainable Energy Institute, University of Colorado, Boulder, CO, 80303, USA.
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4
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Pozdniakova TA, Cruz JP, Silva PC, Azevedo F, Parpot P, Domingues MR, Carlquist M, Johansson B. Optimization of a hybrid bacterial/ Arabidopsis thaliana fatty acid synthase system II in Saccharomyces cerevisiae. Metab Eng Commun 2023; 17:e00224. [PMID: 37415783 PMCID: PMC10320613 DOI: 10.1016/j.mec.2023.e00224] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/27/2023] [Accepted: 05/02/2023] [Indexed: 07/08/2023] Open
Abstract
Fatty acids are produced by eukaryotes like baker's yeast Saccharomyces cerevisiae mainly using a large multifunctional type I fatty acid synthase (FASI) where seven catalytic steps and a carrier domain are shared between one or two protein subunits. While this system may offer efficiency in catalysis, only a narrow range of fatty acids are produced. Prokaryotes, chloroplasts and mitochondria rely instead on a FAS type II (FASII) where each catalytic step is carried out by a monofunctional enzyme encoded by a separate gene. FASII is more flexible and capable of producing a wider range of fatty acid structures, such as the direct production of unsaturated fatty acids. An efficient FASII in the preferred industrial organism S. cerevisiae could provide a platform for developing sustainable production of specialized fatty acids. We functionally replaced either yeast FASI genes (FAS1 or FAS2) with a FASII consisting of nine genes from Escherichia coli (acpP, acpS and fab -A, -B, -D, -F, -G, -H, -Z) as well as three from Arabidopsis thaliana (MOD1, FATA1 and FATB). The genes were expressed from an autonomously replicating multicopy vector assembled using the Yeast Pathway Kit for in-vivo assembly in yeast. Two rounds of adaptation led to a strain with a maximum growth rate (μmax) of 0.19 h-1 without exogenous fatty acids, twice the growth rate previously reported for a comparable strain. Additional copies of the MOD1 or fabH genes resulted in cultures with higher final cell densities and three times higher lipid content compared to the control.
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Affiliation(s)
- Tatiana A. Pozdniakova
- CBMA - Center of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
| | - João P. Cruz
- CBMA - Center of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
| | - Paulo César Silva
- CBMA - Center of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
| | - Flávio Azevedo
- CBMA - Center of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
| | - Pier Parpot
- CEB - C, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga, Portugal
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Maria Rosario Domingues
- Mass Spectrometry Center & LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
- CESAM–Centre for Environmental and Marine Studies, Aveiro, Portugal
- Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Magnus Carlquist
- Division of Applied Microbiology, Lund University, Box 124, 221 00, Lund, Sweden
| | - Björn Johansson
- CBMA - Center of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
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5
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Su H, Shi P, Shen Z, Meng H, Meng Z, Han X, Chen Y, Fan W, Fa Y, Yang C, Li F, Wang S. High-level production of nervonic acid in the oleaginous yeast Yarrowia lipolytica by systematic metabolic engineering. Commun Biol 2023; 6:1125. [PMID: 37935958 PMCID: PMC10630375 DOI: 10.1038/s42003-023-05502-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023] Open
Abstract
Nervonic acid benefits the treatment of neurological diseases and the health of brain. In this study, we employed the oleaginous yeast Yarrowia lipolytica to overproduce nervonic acid oil by systematic metabolic engineering. First, the production of nervonic acid was dramatically improved by iterative expression of the genes ecoding β-ketoacyl-CoA synthase CgKCS, fatty acid elongase gELOVL6 and desaturase MaOLE2. Second, the biosynthesis of both nervonic acid and lipids were further enhanced by expression of glycerol-3-phosphate acyltransferases and diacylglycerol acyltransferases from Malania oleifera in endoplasmic reticulum (ER). Third, overexpression of a newly identified ER structure regulator gene YlINO2 led to a 39.3% increase in lipid production. Fourth, disruption of the AMP-activated S/T protein kinase gene SNF1 increased the ratio of nervonic acid to lignoceric acid by 61.6%. Next, pilot-scale fermentation using the strain YLNA9 exhibited a lipid titer of 96.7 g/L and a nervonic acid titer of 17.3 g/L (17.9% of total fatty acids), the highest reported titer to date. Finally, a proof-of-concept purification and separation of nervonic acid were performed and the purity of it reached 98.7%. This study suggested that oleaginous yeasts are attractive hosts for the cost-efficient production of nervonic acid and possibly other very long-chain fatty acids (VLCFAs).
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Affiliation(s)
- Hang Su
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Penghui Shi
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
| | - Zhaoshuang Shen
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
| | - Huimin Meng
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Qingdao Institute for Food and Drug Control, Qingdao, 266073, China
| | - Ziyue Meng
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Xingfeng Han
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Yanna Chen
- Zhejiang Zhenyuan Biotech Co., LTD, Shaoxing, 312365, China
| | - Weiming Fan
- Zhejiang Zhenyuan Biotech Co., LTD, Shaoxing, 312365, China
| | - Yun Fa
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Chunyu Yang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Fuli Li
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Shandong Energy Institute, Qingdao, 266101, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China.
| | - Shi'an Wang
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Shandong Energy Institute, Qingdao, 266101, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China.
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6
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Liu F, Lu Z, Lu T, Shi M, Wang H, Wu R, Cao J, Su E, Ma X. Metabolic engineering of oleaginous yeast in the lipogenic phase enhances production of nervonic acid. Metab Eng 2023; 80:193-206. [PMID: 37827446 DOI: 10.1016/j.ymben.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/14/2023] [Accepted: 10/09/2023] [Indexed: 10/14/2023]
Abstract
Insufficient biosynthesis efficiency during the lipogenic phase can be a major obstacle to engineering oleaginous yeasts to overproduce very long-chain fatty acids (VLCFAs). Taking nervonic acid (NA, C24:1) as an example, we overcame the bottleneck to overproduce NA in an engineered Rhodosporidium toruloides by improving the biosynthesis of VLCFAs during the lipogenic phase. First, evaluating the catalytic preferences of three plant-derived ketoacyl-CoA synthases (KCSs) rationally guided reconstructing an efficient NA biosynthetic pathway in R. toruloides. More importantly, a genome-wide transcriptional analysis endowed clues to strengthen the fatty acid elongation (FAE) module and identify/use lipogenic phase-activated promoter, collectively addressing the stagnation of NA accumulation during the lipogenic phase. The best-designed strain exhibited a high NA content (as the major component in total fatty acid [TFA], 46.3%) and produced a titer of 44.2 g/L in a 5 L bioreactor. The strategy developed here provides an engineering framework to establish the microbial process of producing valuable VLCFAs in oleaginous yeasts.
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Affiliation(s)
- Feixiang Liu
- Co-innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China; Department of Food Science and Technology, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037, China; Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China; Department of Biological Science and Food Engineering, Bozhou University, Bozhou, 236800, China
| | - Zewei Lu
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Tingting Lu
- Co-innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China; Department of Food Science and Technology, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Manman Shi
- Co-innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China; Department of Food Science and Technology, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Huimin Wang
- Co-innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China; Department of Food Science and Technology, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Rong Wu
- Co-innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China; Department of Food Science and Technology, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Jun Cao
- Co-innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China; Department of Food Science and Technology, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Erzheng Su
- Co-innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China; Department of Food Science and Technology, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037, China.
| | - Xiaoqiang Ma
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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7
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Wang X, Li Y, Jin Z, Liu X, Gao X, Guo S, Yu T. A novel CRISPR/Cas9 system with high genomic editing efficiency and recyclable auxotrophic selective marker for multiple-step metabolic rewriting in Pichia pastoris. Synth Syst Biotechnol 2023; 8:445-451. [PMID: 37448527 PMCID: PMC10336193 DOI: 10.1016/j.synbio.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/29/2023] [Accepted: 06/08/2023] [Indexed: 07/15/2023] Open
Abstract
The methylotrophic budding yeast Pichia pastoris has been utilized to the production of a variety of heterologous recombinant proteins owing to the strong inducible alcohol oxidase promoter (pAOX1). However, it is difficult to use P. pastoris as the chassis cell factory for high-valuable metabolite biosynthesis due to the low homologous recombination (HR) efficiency and the limitation of handy selective markers, especially in the condition of multistep biosynthetic pathways. Hence, we developed a novel CRISPR/Cas9 system with highly editing efficiencies and recyclable auxotrophic selective marker (HiEE-ReSM) to facilitate cell factory in P. pastoris. Firstly, we improved the HR rates of P. pastoris through knocking out the non-homologous-end-joining gene (Δku70) and overexpressing HR-related proteins (RAD52 and RAD59), resulting in higher positive rate compared to the basal strain, achieved 97%. Then, we used the uracil biosynthetic genes PpURA3 as the reverse screening marker, which can improve the recycling efficiency of marker. Meanwhile, the HR rate is still 100% in uracil auxotrophic yeast. Specially, we improved the growth rate of uracil auxotrophic yeast strains by overexpressing the uracil transporter (scFUR4) to increase the uptake of exogenous uracil from medium. Meanwhile, we explored the optimal concentration of uracil (90 mg/L) for strain growth. In the end, the HiEE-ReSM system has been applied for the inositol production (250 mg/L) derived from methanol in P. pastoris. The systems will contribute to P. pastoris as an attractive cell factory for the complex compound biosynthesis through multistep metabolic pathway engineering and will be a useful tool to improve one carbon (C1) bio-utilization.
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Affiliation(s)
- Xiang Wang
- Center for Synthetic Biochemistry, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, 518055, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi Li
- Center for Synthetic Biochemistry, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, 518055, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhehao Jin
- Center for Synthetic Biochemistry, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, 518055, China
| | - Xiangjian Liu
- Center for Synthetic Biochemistry, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, 518055, China
| | - Xiang Gao
- Center for Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology of CAS, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academic of Science, Shenzhen, 518055, China
| | - Shuyuan Guo
- Center for Synthetic Biochemistry, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, 518055, China
| | - Tao Yu
- Center for Synthetic Biochemistry, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, 518055, China
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8
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Eigenfeld M, Wittmann L, Kerpes R, Schwaminger SP, Becker T. Studying the impact of cell age on the yeast growth behaviour of Saccharomyces pastorianus var. carlsbergensis by magnetic separation. Biotechnol J 2023; 18:e2200610. [PMID: 37014328 DOI: 10.1002/biot.202200610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/22/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023]
Abstract
Despite the fact that yeast is a widely used microorganism in the food, beverage, and pharmaceutical industries, the impact of viability and age distribution on cultivation performance has yet to be fully understood. For a detailed analysis of fermentation performance and physiological state, we introduced a method of magnetic batch separation to isolate daughter and mother cells from a heterogeneous culture. By binding functionalised iron oxide nanoparticles, it is possible to separate the chitin-enriched bud scars by way of a linker protein. This reveals that low viability cultures with a high daughter cell content perform similarly to a high viability culture with a low daughter cell content. Magnetic separation results in the daughter cell fraction (>95%) showing a 21% higher growth rate in aerobic conditions than mother cells and a 52% higher rate under anaerobic conditions. These findings emphasise the importance of viability and age during cultivation and are the first step towards improving the efficiency of yeast-based processes.
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Affiliation(s)
- Marco Eigenfeld
- TUM School of Life Science, Technical University of Munich, Chair of Brewing and Beverage Technology, Freising, Germany
| | - Leonie Wittmann
- TUM School of Engineering and Design, Technical University of Munich, Chair of Bioseparation Engineering, Garching, Germany
| | - Roland Kerpes
- TUM School of Life Science, Technical University of Munich, Chair of Brewing and Beverage Technology, Freising, Germany
| | - Sebastian P Schwaminger
- TUM School of Engineering and Design, Technical University of Munich, Chair of Bioseparation Engineering, Garching, Germany
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Thomas Becker
- TUM School of Life Science, Technical University of Munich, Chair of Brewing and Beverage Technology, Freising, Germany
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9
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Rahman MT, Koski MK, Panecka-Hofman J, Schmitz W, Kastaniotis AJ, Wade RC, Wierenga RK, Hiltunen JK, Autio KJ. An engineered variant of MECR reductase reveals indispensability of long-chain acyl-ACPs for mitochondrial respiration. Nat Commun 2023; 14:619. [PMID: 36739436 PMCID: PMC9899272 DOI: 10.1038/s41467-023-36358-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 01/25/2023] [Indexed: 02/06/2023] Open
Abstract
Mitochondrial fatty acid synthesis (mtFAS) is essential for respiratory function. MtFAS generates the octanoic acid precursor for lipoic acid synthesis, but the role of longer fatty acid products has remained unclear. The structurally well-characterized component of mtFAS, human 2E-enoyl-ACP reductase (MECR) rescues respiratory growth and lipoylation defects of a Saccharomyces cerevisiae Δetr1 strain lacking native mtFAS enoyl reductase. To address the role of longer products of mtFAS, we employed in silico molecular simulations to design a MECR variant with a shortened substrate binding cavity. Our in vitro and in vivo analyses indicate that the MECR G165Q variant allows synthesis of octanoyl groups but not long chain fatty acids, confirming the validity of our computational approach to engineer substrate length specificity. Furthermore, our data imply that restoring lipoylation in mtFAS deficient yeast strains is not sufficient to support respiration and that long chain acyl-ACPs generated by mtFAS are required for mitochondrial function.
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Affiliation(s)
- M Tanvir Rahman
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | | | - Joanna Panecka-Hofman
- Faculty of Physics, University of Warsaw, Warsaw, Poland
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Werner Schmitz
- Faculty of Biochemistry and Molecular Biology, University of Würzburg, Würzburg, Germany
| | | | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
- Zentrum für Molekulare Biologie (ZMBH), DKFZ-ZMBH Alliance and Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany
| | - Rik K Wierenga
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - J Kalervo Hiltunen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Kaija J Autio
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
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10
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Rizzo G, Baroni L, Lombardo M. Promising Sources of Plant-Derived Polyunsaturated Fatty Acids: A Narrative Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:ijerph20031683. [PMID: 36767052 PMCID: PMC9914036 DOI: 10.3390/ijerph20031683] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/11/2023] [Accepted: 01/15/2023] [Indexed: 06/01/2023]
Abstract
(1) Background: Polyunsaturated fatty acids (PUFAs) are known for their ability to protect against numerous metabolic disorders. The consumption of oily fish is the main source of PUFAs in human nutrition and is commonly used for supplement production. However, seafood is an overexploited source that cannot be guaranteed to cover the global demands. Furthermore, it is not consumed by everyone for ecological, economic, ethical, geographical and taste reasons. The growing demand for natural dietary sources of PUFAs suggests that current nutritional sources are insufficient to meet global needs, and less and less will be. Therefore, it is crucial to find sustainable sources that are acceptable to all, meeting the world population's needs. (2) Scope: This review aims to evaluate the recent evidence about alternative plant sources of essential fatty acids, focusing on long-chain omega-3 (n-3) PUFAs. (3) Method: A structured search was performed on the PubMed search engine to select available human data from interventional studies using omega-3 fatty acids of non-animal origin. (4) Results: Several promising sources have emerged from the literature, such as algae, microorganisms, plants rich in stearidonic acid and GM plants. However, the costs, acceptance and adequate formulation deserve further investigation.
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Affiliation(s)
- Gianluca Rizzo
- Independent Researcher, Via Venezuela 66, 98121 Messina, Italy
| | - Luciana Baroni
- Scientific Society for Vegetarian Nutrition, 30171 Venice, Italy
| | - Mauro Lombardo
- Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Open University, 00166 Rome, Italy
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11
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Biosynthesis of alkanes/alkenes from fatty acids or derivatives (triacylglycerols or fatty aldehydes). Biotechnol Adv 2022; 61:108045. [DOI: 10.1016/j.biotechadv.2022.108045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/27/2022]
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12
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Overproducing nervonic acid by synergism of fatty acid elongases in engineered Saccharomyces cerevisiae. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Yu T, Liu Q, Wang X, Liu X, Chen Y, Nielsen J. Metabolic reconfiguration enables synthetic reductive metabolism in yeast. Nat Metab 2022; 4:1551-1559. [PMID: 36302903 PMCID: PMC9684072 DOI: 10.1038/s42255-022-00654-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/06/2022] [Indexed: 02/08/2023]
Abstract
Cell proliferation requires the integration of catabolic processes to provide energy, redox power and biosynthetic precursors. Here we show how the combination of rational design, metabolic rewiring and recombinant expression enables the establishment of a decarboxylation cycle in the yeast cytoplasm. This metabolic cycle can support growth by supplying energy and increased provision of NADPH or NADH in the cytosol, which can support the production of highly reduced chemicals such as glycerol, succinate and free fatty acids. With this approach, free fatty acid yield reached 40% of theoretical yield, which is the highest yield reported for Saccharomyces cerevisiae to our knowledge. This study reports the implementation of a synthetic decarboxylation cycle in the yeast cytosol, and its application in achieving high yields of valuable chemicals in cell factories. Our study also shows that, despite extensive regulation of catabolism in yeast, it is possible to rewire the energy metabolism, illustrating the power of biodesign.
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Affiliation(s)
- Tao Yu
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
- Center for Synthetic Biochemistry, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Quanli Liu
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Xiang Wang
- Center for Synthetic Biochemistry, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiangjian Liu
- Center for Synthetic Biochemistry, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yun Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
- BioInnovation Institute, Copenhagen, Denmark.
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14
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Zhang Y, Zhang S, Chu Y, Zhang Q, Zhou R, Yu D, Wang S, Lyu L, Xu G, Zhao ZK. Genetic manipulation of the interconversion between diacylglycerols and triacylglycerols in Rhodosporidium toruloides. Front Bioeng Biotechnol 2022; 10:1034972. [PMID: 36394004 PMCID: PMC9643831 DOI: 10.3389/fbioe.2022.1034972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/13/2022] [Indexed: 11/29/2022] Open
Abstract
The basidiomycetous yeast Rhodosporidium toruloides (R. toruloides) is an excellent producer for neutral lipids, including triacylglycerols (TAG). Partially because genetic tools for this yeast were less developed, limited efforts were shown to explore its capacity for the production of higher-value lipids such as diacylglycerols (DAG). Here, four genes linked to the interconversion between DAG and TAG were manipulated to promote the production of DAG and free fatty acids (FFA). Among them, three TAG synthesis-related genes, DGA1, LRO1, and ARE1, were down-regulated successively via the RNA interference technology, and an endogenous TAG lipase encoded by TGL5 was fused with LDP1 and over-expressed to convert TAG into DAG and FFA. Results showed that those engineered R. toruloides strains grew normally under nutrient-rich conditions but notably slower than the parental strain NP11 in the lipid production stage. When cultivated in nitrogen-limited media, engineered strains were able to produce total lipids with improved contents of DAG and FFA by up to two-fold and three-fold, respectively. Further correlation analysis between lipid composition and cell density indicated that the formation of TAG correlated positively with cell growth; however, other lipids including DAG did negatively. This study offered valuable information and strains to engineer R. toruloides for advanced production of fatty acid derivatives.
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Affiliation(s)
- Yue Zhang
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Sufang Zhang
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, China
| | - Yadong Chu
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, China
| | - Qi Zhang
- University of Chinese Academy of Sciences, Beijing, China
| | - Renhui Zhou
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, China
| | - Di Yu
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, China
| | - Shuang Wang
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liting Lyu
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Guowang Xu
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, China
| | - Zongbao Kent Zhao
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- *Correspondence: Zongbao Kent Zhao,
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15
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Liu F, Wu R, Ma X, Su E. The Advancements and Prospects of Nervonic Acid Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12772-12783. [PMID: 36166330 DOI: 10.1021/acs.jafc.2c05770] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Nervonic acid (NA) is a monounsaturated very long-chain fatty acid (VLCFA) and has been identified with critical biological functions in medical and health care for brain development and injury repair. Yet, the approaches to producing NA from the sources of plants or animals continue to pose challenges to meet increasing market demand, as they are generally associated with high costs, a lack of natural resources, a long life cycle, and low production efficiency. The recent technological advance in metabolic engineering allows us to precisely engineer oleaginous microbes to develop high-content NA-producing strains, which has the potential to provide a possible solution to produce NA on a commercial fermentation scale. In this Review, the biosynthetic pathway, natural sources, and metabolic engineering of NA are summarized. The strategies of metabolic engineering that could be adopted to modify oleaginous yeast to produce NA are discussed in detail, providing the prospecting views for the microbial cells producing NA.
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Affiliation(s)
- Feixiang Liu
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Department of Food Science and Technology, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, China
- Department of Biological Science and Food Engineering, Bozhou University, Bozhou 236800, China
| | - Rong Wu
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Department of Food Science and Technology, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Xiaoqiang Ma
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Erzheng Su
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Department of Food Science and Technology, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, China
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16
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Comparative Fatty Acid Compositional Profiles of Rhodotorula toruloides Haploid and Diploid Strains under Various Storage Conditions. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8090467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Microbial-based fatty acids (FAs), biofuels and oleochemicals are potential alternatives to fossil fuels and other non-renewable resources. Rhodotorula toruloides (formerly Rhodosporidium toruloides) is a basidiomycetous oleaginous yeast, and cells of the wild-type diploids can accumulate lipids to over 70 wt% on a dry cell weight basis in nutrient-limited conditions. Meanwhile, several haploid strains have been applied as hosts for producing high-value fatty acid derivatives through genetic modification and metabolic engineering. However, the differences in fatty acid compositional profiles and their stability between diploid and haploid strains remain unknown in this oleaginous yeast. Here, we grew a haploid strain R. toruloides NP11 and its parental diploid strain R. toruloides CGMCC 2.1389 (4#) under identical conditions and compared the profiles in terms of cell growth, lipid production, fatty acid compositions of lipids as well as storage stability of fatty acid methyl esters (FAMEs). It was found that lipids from R. toruloides composed of fatty acids in terms of chain length ranged from short-chain FAs (C6–C9) to very long-chain FAs (VLCFAs, C20–C24) and some odd-chain FAs (C15 and C17), while long-chain fatty acids (C14–C18) were the most abundant ones. In addition, NP11 produced a little more (1 wt%) VLCFAs than that of the diploid strain 4#. Moreover, no major changes were found for FAMEs being held under varied storage conditions, suggesting that FAMEs samples were stable and robust for fatty acid compositional analysis of microbial lipids. This work revealed the fatty acid profiles of lipids from R. toruloides haploid and diploid strains, and their stability under various storage conditions. The information is valuable for reliable assessment of fatty acid compositions of lipids from oleaginous yeasts and related microbial cell factories.
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17
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Wang K, Shi TQ, Lin L, Wei P, Ledesma-Amaro R, Ji XJ. Engineering Yarrowia lipolytica to Produce Tailored Chain-Length Fatty Acids and Their Derivatives. ACS Synth Biol 2022; 11:2564-2577. [DOI: 10.1021/acssynbio.2c00305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 1 Wenyuan Road, Nanjing 210046, 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
| | - Ping Wei
- 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, United Kindom
| | - 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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18
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Zhang Y, Pang J, Liu S, Nie K, Deng L, Wang F, Liu J. Harnessing transcription factor Mga2 and fatty acid elongases to overproduce palmitoleic acid in Saccharomyces cerevisiae. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108402] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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19
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Giwa AS, Ali N. Perspectives of nervonic acid production by Yarrowia lipolytica. Biotechnol Lett 2022; 44:193-202. [PMID: 35119573 DOI: 10.1007/s10529-022-03231-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/26/2022] [Indexed: 11/02/2022]
Abstract
Nervonic acid (cis-15-tetracosenoic acid, 24:1Δ15) is a long chain monounsaturated fatty acid, mainly exists in white matt er of the human brains. It plays an important role in the development of nervous system and curing neurological diseases. The limited natural sources and high price are considered limiting factors for the extensive application of nervonic acid. Yarrowia lipolytica is a high lipid producing yeast and engineered strain which can produce nervonic acid. The biosynthesis of nervonic acid has yet to be investigated, although the metabolism has been examined for couple of years. Normally, oleic acid is considered the origin of nervonic acid synthesis through fatty acid prolongation, where malonyl-CoA and acyl-CoA are initially concise by 3-ketoacyl-CoA synthase (KCS). To meet the high requirement of industrial production, the optimization of fermentation and bioreactors configurations are necessary tools to be carried out. This review article summarizes the research literature on advancements and recent trends about the production, synthesis and properties of nervonic acid.
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Affiliation(s)
- Abdulmoseen Segun Giwa
- School of Human Settlements and Environment, Nanchang Institute of Science and Technology, Nanchang, 330108, China.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Nasir Ali
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
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20
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Cui X, Ma X, Prather K, Zhou K. Controlling protein expression by using intron-aided promoters in Saccharomyces cerevisiae. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Zhang X, Miao Q, Xu X, Ji B, Qu L, Wei Y. Developments in Fatty Acid-Derived Insect Pheromone Production Using Engineered Yeasts. Front Microbiol 2021; 12:759975. [PMID: 34858372 PMCID: PMC8632438 DOI: 10.3389/fmicb.2021.759975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/26/2021] [Indexed: 11/13/2022] Open
Abstract
The use of traditional chemical insecticides for pest control often leads to environmental pollution and a decrease in biodiversity. Recently, insect sex pheromones were applied for sustainable biocontrol of pests in fields, due to their limited adverse impacts on biodiversity and food safety compared to that of other conventional insecticides. However, the structures of insect pheromones are complex, and their chemical synthesis is not commercially feasible. As yeasts have been widely used for fatty acid-derived pheromone production in the past few years, using engineered yeasts may be promising and sustainable for the low-cost production of fatty acid-derived pheromones. The primary fatty acids produced by Saccharomyces cerevisiae and other yeasts are C16 and C18, and it is also possible to rewire/reprogram the metabolic flux for other fatty acids or fatty acid derivatives. This review summarizes the fatty acid biosynthetic pathway in S. cerevisiae and recent progress in yeast engineering in terms of metabolic engineering and synthetic biology strategies to produce insect pheromones. In the future, insect pheromones produced by yeasts might provide an eco-friendly pest control method in agricultural fields.
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Affiliation(s)
- Xiaoling Zhang
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, China
| | - Qin Miao
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, China
| | - Xia Xu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Boyang Ji
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Lingbo Qu
- Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, China
- College of Chemistry, Zhengzhou University, Zhengzhou, China
| | - Yongjun Wei
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, China
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22
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Homayoonfar M, Roosta Azad R, Sardari S. Analytical methods in fatty acid analysis for microbial applications: the recent trends. Prep Biochem Biotechnol 2021; 51:937-952. [PMID: 34506247 DOI: 10.1080/10826068.2021.1881910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Fatty acids are among the most important components of many biological systems and have been highlighted in many research fields in recent decades. In the food industry, it is important to check the amount and types of fatty acids in edible oils, beverages and other foods products, and checking the fatty acids parameters are among the quality control parameters for those products. In medical applications, investigation of fatty acids in biological samples and comparing imbalances in them can help to diagnose some diseases. On the other hand, the development of cell factories for the production of biofuels and other valuable chemicals requires the accurate analysis of fatty acids, which serve as precursors in development of those products. As a result, given all these different applications of fatty acids, rapid and accurate methods for characterization and quantification of fatty acids are essential. In recent years, various methods for the analysis of fatty acids have been proposed, which according to the specific purpose of the analysis, some of them can be used with consideration of speed, accuracy and cost. In this article, the available methods for the analysis of fatty acids are reviewed with a special emphasis on the analysis of microbial samples to pave the way for more widespread metabolic engineering research.
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Affiliation(s)
- Mohammad Homayoonfar
- Chemical and Petroleum Engineering Department, Sharif University of Technology, Tahran, Iran.,Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Reza Roosta Azad
- Chemical and Petroleum Engineering Department, Sharif University of Technology, Tahran, Iran
| | - Soroush Sardari
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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23
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Harnessing the yeast Saccharomyces cerevisiae for the production of fungal secondary metabolites. Essays Biochem 2021; 65:277-291. [PMID: 34061167 PMCID: PMC8314005 DOI: 10.1042/ebc20200137] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/09/2021] [Accepted: 04/14/2021] [Indexed: 12/17/2022]
Abstract
Fungal secondary metabolites (FSMs) represent a remarkable array of bioactive compounds, with potential applications as pharmaceuticals, nutraceuticals, and agrochemicals. However, these molecules are typically produced only in limited amounts by their native hosts. The native organisms may also be difficult to cultivate and genetically engineer, and some can produce undesirable toxic side-products. Alternatively, recombinant production of fungal bioactives can be engineered into industrial cell factories, such as aspergilli or yeasts, which are well amenable for large-scale manufacturing in submerged fermentations. In this review, we summarize the development of baker's yeast Saccharomyces cerevisiae to produce compounds derived from filamentous fungi and mushrooms. These compounds mainly include polyketides, terpenoids, and amino acid derivatives. We also describe how native biosynthetic pathways can be combined or expanded to produce novel derivatives and new-to-nature compounds. We describe some new approaches for cell factory engineering, such as genome-scale engineering, biosensor-based high-throughput screening, and machine learning, and how these tools have been applied for S. cerevisiae strain improvement. Finally, we prospect the challenges and solutions in further development of yeast cell factories to more efficiently produce FSMs.
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24
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Cerone M, Smith TK. A Brief Journey into the History of and Future Sources and Uses of Fatty Acids. Front Nutr 2021; 8:570401. [PMID: 34355007 PMCID: PMC8329090 DOI: 10.3389/fnut.2021.570401] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 06/21/2021] [Indexed: 01/04/2023] Open
Abstract
Fats and lipids have always had a primary role in the history of humankind, from ancient civilisations to the modern and contemporary time, going from domestic and cosmetic uses, to the first medical applications and later to the large-scale industrial uses for food, pharmaceutical, cosmetics, and biofuel production. Sources and uses of those have changed during time following the development of chemical sciences and industrial technological advances. Plants, fish, and animal fats have represented the primary source of lipids and fats for century. Nowadays, the use of fatty acid sources has taken a turn: industries are mainly interested in polyunsaturated fatty acids (PUFAs), which have beneficial properties in human health; and also, for high-value fatty acids product for innovative and green production of biofuel and feedstocks. Thus, the constant increase in demand of fatty acids, the fact that marine and vegetable sources are not adequate to meet the high level of fatty acids required worldwide and climate change, have determined the necessity of the search for renewable and sustainable sources for fatty acids. Biotechnological advances and bioengineering have started looking at the genetic modification of algae, bacteria, yeasts, seeds, and plants to develop cell factory able to produce high value fatty acid products in a renewable and sustainable manner. This innovative approach applied to FA industry is a peculiar example of how biotechnology can serve as a powerful mean to drive the production of high value fatty acid derivatives on the concept of circular bioeconomy, based on the reutilisation of organic resources for alternative and sustainable productive patterns that are environmentally friendly.
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Affiliation(s)
- Michela Cerone
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
| | - Terry K Smith
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
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25
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Xiao M, Chen N, He C, Shi S, Lu Q, Lv S. Generation of Yeast Protoplasts by Lytic Actions of Iron Oxide Magnetic Nanoparticles. Ind Eng Chem Res 2021. [DOI: 10.1021/acs.iecr.1c01816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Menglin Xiao
- State Key Laboratory of Organic-Inorganic Composite Materials, Beijing University of Chemical Technology, 15 Beisanhuan Dong Road, Chaoyang District, Beijing 100029, China
| | - Niuniu Chen
- State Key Laboratory of Organic-Inorganic Composite Materials, Beijing University of Chemical Technology, 15 Beisanhuan Dong Road, Chaoyang District, Beijing 100029, China
| | - Chengzhi He
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, 15 Beisanhuan Dong Road, Chaoyang District, Beijing 100029, China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, 15 Beisanhuan Dong Road, Chaoyang District, Beijing 100029, China
| | - Qinfu Lu
- State Key Laboratory of Organic-Inorganic Composite Materials, Beijing University of Chemical Technology, 15 Beisanhuan Dong Road, Chaoyang District, Beijing 100029, China
| | - Shanshan Lv
- State Key Laboratory of Organic-Inorganic Composite Materials, Beijing University of Chemical Technology, 15 Beisanhuan Dong Road, Chaoyang District, Beijing 100029, China
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26
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Wernig F, Baumann L, Boles E, Oreb M. Production of octanoic acid in Saccharomyces cerevisiae: Investigation of new precursor supply engineering strategies and intrinsic limitations. Biotechnol Bioeng 2021; 118:3046-3057. [PMID: 34003487 DOI: 10.1002/bit.27814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/08/2021] [Accepted: 04/30/2021] [Indexed: 11/12/2022]
Abstract
The eight-carbon fatty acid octanoic acid (OA) is an important platform chemical and precursor of many industrially relevant products. Its microbial biosynthesis is regarded as a promising alternative to current unsustainable production methods. In Saccharomyces cerevisiae, the production of OA had been previously achieved by rational engineering of the fatty acid synthase. For the supply of the precursor molecule acetyl-CoA and of the redox cofactor NADPH, the native pyruvate dehydrogenase bypass had been harnessed, or the cells had been additionally provided with a pathway involving a heterologous ATP-citrate lyase. Here, we redirected the flux of glucose towards the oxidative branch of the pentose phosphate pathway and overexpressed a heterologous phosphoketolase/phosphotransacetylase shunt to improve the supply of NADPH and acetyl-CoA in a strain background with abolished OA degradation. We show that these modifications lead to an increased yield of OA during the consumption of glucose by more than 60% compared to the parental strain. Furthermore, we investigated different genetic engineering targets to identify potential factors that limit the OA production in yeast. Toxicity assays performed with the engineered strains suggest that the inhibitory effects of OA on cell growth likely impose an upper limit to attainable OA yields.
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Affiliation(s)
- Florian Wernig
- Department of Biological Sciences, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Leonie Baumann
- Department of Biological Sciences, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Eckhard Boles
- Department of Biological Sciences, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Mislav Oreb
- Department of Biological Sciences, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
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27
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Liu F, Wang P, Xiong X, Zeng X, Zhang X, Wu G. A Review of Nervonic Acid Production in Plants: Prospects for the Genetic Engineering of High Nervonic Acid Cultivars Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:626625. [PMID: 33747006 PMCID: PMC7973461 DOI: 10.3389/fpls.2021.626625] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/29/2021] [Indexed: 05/15/2023]
Abstract
Nervonic acid (NA) is a very-long-chain monounsaturated fatty acid that plays crucial roles in brain development and has attracted widespread research interest. The markets encouraged the development of a refined, NA-enriched plant oil as feedstocks for the needed further studies of NA biological functions to the end commercial application. Plant seed oils offer a renewable and environmentally friendly source of NA, but their industrial production is presently hindered by various factors. This review focuses on the NA biosynthesis and assembly, NA resources from plants, and the genetic engineering of NA biosynthesis in oil crops, discusses the factors that affect NA production in genetically engineered oil crops, and provides prospects for the application of NA and prospective trends in the engineering of NA. This review emphasizes the progress made toward various NA-related topics and explores the limitations and trends, thereby providing integrated and comprehensive insight into the nature of NA production mechanisms during genetic engineering. Furthermore, this report supports further work involving the manipulation of NA production through transgenic technologies and molecular breeding for the enhancement of crop nutritional quality or creation of plant biochemical factories to produce NA for use in nutraceutical, pharmaceutical, and chemical industries.
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Affiliation(s)
- Fang Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Pandi Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaojuan Xiong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xinhua Zeng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaobo Zhang
- Life Science and Technology Center, China National Seed Group Co. Ltd., Wuhan, China
| | - Gang Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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28
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Slagman S, Fessner WD. Biocatalytic routes to anti-viral agents and their synthetic intermediates. Chem Soc Rev 2021; 50:1968-2009. [DOI: 10.1039/d0cs00763c] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
An assessment of biocatalytic strategies for the synthesis of anti-viral agents, offering guidelines for the development of sustainable production methods for a future COVID-19 remedy.
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Affiliation(s)
- Sjoerd Slagman
- Institut für Organische Chemie und Biochemie
- Technische Universität Darmstadt
- Germany
| | - Wolf-Dieter Fessner
- Institut für Organische Chemie und Biochemie
- Technische Universität Darmstadt
- Germany
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29
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Chawla K, Kaur S, Kaur R, Bhunia RK. Metabolic engineering of oleaginous yeasts to enhance single cell oil production. J FOOD PROCESS ENG 2020. [DOI: 10.1111/jfpe.13634] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kirti Chawla
- Plant Tissue Culture and Genetic Engineering National Agri‐Food Biotechnology Institute (NABI) Mohali Punjab India
| | - Sumandeep Kaur
- Department of Biotechnology, Sector‐25 Panjab University Chandigarh India
| | - Ranjeet Kaur
- Department of Genetics University of Delhi South Campus New Delhi India
| | - Rupam Kumar Bhunia
- Plant Tissue Culture and Genetic Engineering National Agri‐Food Biotechnology Institute (NABI) Mohali Punjab India
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30
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Krishnan A, McNeil BA, Stuart DT. Biosynthesis of Fatty Alcohols in Engineered Microbial Cell Factories: Advances and Limitations. Front Bioeng Biotechnol 2020; 8:610936. [PMID: 33344437 PMCID: PMC7744569 DOI: 10.3389/fbioe.2020.610936] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/10/2020] [Indexed: 11/19/2022] Open
Abstract
Concerns about climate change and environmental destruction have led to interest in technologies that can replace fossil fuels and petrochemicals with compounds derived from sustainable sources that have lower environmental impact. Fatty alcohols produced by chemical synthesis from ethylene or by chemical conversion of plant oils have a large range of industrial applications. These chemicals can be synthesized through biological routes but their free forms are produced in trace amounts naturally. This review focuses on how genetic engineering of endogenous fatty acid metabolism and heterologous expression of fatty alcohol producing enzymes have come together resulting in the current state of the field for production of fatty alcohols by microbial cell factories. We provide an overview of endogenous fatty acid synthesis, enzymatic methods of conversion to fatty alcohols and review the research to date on microbial fatty alcohol production. The primary focus is on work performed in the model microorganisms, Escherichia coli and Saccharomyces cerevisiae but advances made with cyanobacteria and oleaginous yeasts are also considered. The limitations to production of fatty alcohols by microbial cell factories are detailed along with consideration to potential research directions that may aid in achieving viable commercial scale production of fatty alcohols from renewable feedstock.
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Affiliation(s)
- Anagha Krishnan
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Bonnie A McNeil
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - David T Stuart
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
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31
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Zhang Y, Nielsen J, Liu Z. Yeast based biorefineries for oleochemical production. Curr Opin Biotechnol 2020; 67:26-34. [PMID: 33360103 DOI: 10.1016/j.copbio.2020.11.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/04/2020] [Accepted: 11/22/2020] [Indexed: 12/17/2022]
Abstract
Biosynthesis of oleochemicals enables sustainable production of natural and unnatural alternatives from renewable feedstocks. Yeast cell factories have been extensively studied and engineered to produce a variety of oleochemicals, focusing on both central carbon metabolism and lipid metabolism. Here, we review recent progress towards oleochemical synthesis in yeast based biorefineries, as well as utilization of alternative renewable feedstocks, such as xylose and l-arabinose. We also review recent studies of C1 compound utilization or co-utilization and discuss how these studies can lead to third generation yeast based biorefineries for oleochemical production.
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Affiliation(s)
- Yiming Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jens Nielsen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China; Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; BioInnovation Institute, Ole Maaløes Vej 3, DK2200 Copenhagen N, Denmark.
| | - Zihe Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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32
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Meng J, Qiu Y, Shi S. CRISPR/Cas9 Systems for the Development of Saccharomyces cerevisiae Cell Factories. Front Bioeng Biotechnol 2020; 8:594347. [PMID: 33330425 PMCID: PMC7710542 DOI: 10.3389/fbioe.2020.594347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/19/2020] [Indexed: 01/09/2023] Open
Abstract
Synthetic yeast cell factories provide a remarkable solution for the sustainable supply of a range of products, ranging from large-scale industrial chemicals to high-value pharmaceutical compounds. Synthetic biology is a field in which metabolic pathways are intensively studied and engineered. The clustered, regularly interspaced, short, palindromic repeat-associated (CRISPR)/CRISPR-associated protein 9 (Cas9) technology has emerged as the state-of-the-art gene editing technique for synthetic biology. Recently, the use of different CRISPR/Cas9 systems has been extended to the field of yeast engineering for single-nucleotide resolution editing, multiple-gene editing, transcriptional regulation, and genome-scale modifications. Such advancing systems have led to accelerated microbial engineering involving less labor and time and also enhanced the understanding of cellular genetics and physiology. This review provides a brief overview of the latest research progress and the use of CRISPR/Cas9 systems in genetic manipulation, with a focus on the applications of Saccharomyces cerevisiae cell factory engineering.
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Affiliation(s)
- Jie Meng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yue Qiu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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33
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Park YK, Nicaud JM. Metabolic Engineering for Unusual Lipid Production in Yarrowia lipolytica. Microorganisms 2020; 8:E1937. [PMID: 33291339 PMCID: PMC7762315 DOI: 10.3390/microorganisms8121937] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 12/15/2022] Open
Abstract
Using microorganisms as lipid-production factories holds promise as an alternative method for generating petroleum-based chemicals. The non-conventional yeast Yarrowia lipolytica is an excellent microbial chassis; for example, it can accumulate high levels of lipids and use a broad range of substrates. Furthermore, it is a species for which an array of efficient genetic engineering tools is available. To date, extensive work has been done to metabolically engineer Y. lipolytica to produce usual and unusual lipids. Unusual lipids are scarce in nature but have several useful applications. As a result, they are increasingly becoming the targets of metabolic engineering. Unusual lipids have distinct structures; they can be generated by engineering endogenous lipid synthesis or by introducing heterologous enzymes to alter the functional groups of fatty acids. In this review, we describe current metabolic engineering strategies for improving lipid production and highlight recent researches on unusual lipid production in Y. lipolytica.
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Affiliation(s)
- Young-Kyoung Park
- Micalis Institute, AgroParisTech, INRAE, Université Paris-Saclay, 78352 Jouy-en-Josas, France;
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34
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Li S, Zhang Q, Wang J, Liu Y, Zhao Y, Deng Y. Recent progress in metabolic engineering of Saccharomyces cerevisiae for the production of malonyl-CoA derivatives. J Biotechnol 2020; 325:83-90. [PMID: 33278463 DOI: 10.1016/j.jbiotec.2020.11.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/10/2020] [Accepted: 11/10/2020] [Indexed: 02/08/2023]
Abstract
To reduce dependence on petroleum, the biosynthesis of important chemicals from simple substrates using industrial microorganisms has attracted increased attention. Metabolic engineering of Saccharomyces cerevisiae offers a sustainable and flexible alternative for the production of various chemicals. As a key metabolic intermediate, malonyl-CoA is a precursor for many useful compounds. However, the productivity of malonyl-CoA derivatives is restricted by the low cellular level of malonyl-CoA and enzymatic performance. In this review, we focused on how to increase the intracellular malonyl-CoA level and summarize the recent advances in different metabolic engineering strategies for directing intracellular malonyl-CoA to the desired malonyl-CoA derivatives, including strengthening the malonyl-CoA supply, reducing malonyl-CoA consumption, and precisely controlling the intracellular malonyl-CoA level. These strategies provided new insights for further improving the synthesis of malonyl-CoA derivatives in microorganisms.
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Affiliation(s)
- Shiyun Li
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Qiyue Zhang
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jing Wang
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing 100048, China
| | - Yingli Liu
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing 100048, China
| | - Yunying Zhao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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35
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Cho IJ, Choi KR, Lee SY. Microbial production of fatty acids and derivative chemicals. Curr Opin Biotechnol 2020; 65:129-141. [DOI: 10.1016/j.copbio.2020.02.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 12/11/2022]
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36
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Srivastava RK, Akhtar N, Verma M, Imandi SB. Primary metabolites from overproducing microbial system using sustainable substrates. Biotechnol Appl Biochem 2020; 67:852-874. [PMID: 32294277 DOI: 10.1002/bab.1927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 04/12/2020] [Indexed: 02/06/2023]
Abstract
Primary (or secondary) metabolites are produced by animals, plants, or microbial cell systems either intracellularly or extracellularly. Production capabilities of microbial cell systems for many types of primary metabolites have been exploited at a commercial scale. But the high production cost of metabolites is a big challenge for most of the bioprocess industries and commercial production needs to be achieved. This issue can be solved to some extent by screening and developing the engineered microbial systems via reconstruction of the genome-scale metabolic model. The predicted genetic modification is applied for an increased flux in biosynthesis pathways toward the desired product. Wherein the resulting microbial strain is capable of converting a large amount of carbon substrate to the expected product with minimum by-product formation in the optimal operating conditions. Metabolic engineering efforts have also resulted in significant improvement of metabolite yields, depending on the nature of the products, microbial cell factory modification, and the types of substrate used. The objective of this review is to comprehend the state of art for the production of various primary metabolites by microbial strains system, focusing on the selection of efficient strain and genetic or pathway modifications, applied during strain engineering.
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Affiliation(s)
- Rajesh K Srivastava
- Department of Biotechnology, GIT, GITAM (Deemed to be University), Gandhi Nagar Campus, Rushikonda, Visakhapatnam, India
| | - Nasim Akhtar
- Department of Biotechnology, GIT, GITAM (Deemed to be University), Gandhi Nagar Campus, Rushikonda, Visakhapatnam, India
| | - Malkhey Verma
- Departments of Biochemistry and Microbial Sciences, Central University of Punjab, Bathinda, India
| | - Sarat Babu Imandi
- Department of Biotechnology, GIT, GITAM (Deemed to be University), Gandhi Nagar Campus, Rushikonda, Visakhapatnam, India
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37
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Zafar S, Tang MQ, Liu SY, Tan XL. Candidate genes association study to identify allele-specific SNP marker of ω-3 fatty acid in Brassica napus. JOURNAL OF PLANT PHYSIOLOGY 2020; 248:153159. [PMID: 32276152 DOI: 10.1016/j.jplph.2020.153159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 03/13/2020] [Accepted: 03/13/2020] [Indexed: 06/11/2023]
Abstract
Due to the rapid decline in oceanic fish stock, ω-3 fatty acid (C18:3) has attracted serious attention and, hence, the identification of genotypes with high ω-3 content has become the main objective of Brassica napus (rapeseed) breeding. A candidate genes association study permitted us to delineate a genomic region linked to ω-3 content, offering a detailed understanding of the complex genetic mechanism of fatty acid biosynthesis in B. napus. Herein, the candidate genes association study, conducted on 324 genetically diverse rapeseed accessions, detected 114 single nucleotide polymorphisms (SNPs) associated with ω-3 fatty acid. Furthermore, these loci were functionally characterized in Saccharomyces cerevisiae. These associated loci were selected based on their contribution to a high C18:3 ratio, and the selected candidate loci were validated using allele-specific SNPs markers in an inbred population through polymerase chain reaction (PCR). These findings may contribute to improving the fatty acid composition by marker-based breeding and will facilitate the development of rapeseed varieties with high ω-3 content.
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Affiliation(s)
- Sundus Zafar
- School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, China; Institute of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Min-Qiang Tang
- The Oil Crops Research Institute (OCRI) of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Sheng-Yi Liu
- The Oil Crops Research Institute (OCRI) of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Xiao-Li Tan
- Institute of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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38
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Hu Y, Zhu Z, Nielsen J, Siewers V. Engineering Saccharomyces cerevisiae cells for production of fatty acid-derived biofuels and chemicals. Open Biol 2020; 9:190049. [PMID: 31088249 PMCID: PMC6544985 DOI: 10.1098/rsob.190049] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The yeast Saccharomyces cerevisiae is a widely used cell factory for the production of fuels and chemicals, in particular ethanol, a biofuel produced in large quantities. With a need for high-energy-density fuels for jets and heavy trucks, there is, however, much interest in the biobased production of hydrocarbons that can be derived from fatty acids. Fatty acids also serve as precursors to a number of oleochemicals and hence provide interesting platform chemicals. Here, we review the recent strategies applied to metabolic engineering of S. cerevisiae for the production of fatty acid-derived biofuels and for improvement of the titre, rate and yield (TRY). This includes, for instance, redirection of the flux towards fatty acids through engineering of the central carbon metabolism, balancing the redox power and varying the chain length of fatty acids by enzyme engineering. We also discuss the challenges that currently hinder further TRY improvements and the potential solutions in order to meet the requirements for commercial application.
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Affiliation(s)
- Yating Hu
- 1 Department of Biology and Biological Engineering, Chalmers University of Technology , 41296 Gothenburg , Sweden.,2 Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology , 41296 Gothenburg , Sweden
| | - Zhiwei Zhu
- 1 Department of Biology and Biological Engineering, Chalmers University of Technology , 41296 Gothenburg , Sweden.,2 Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology , 41296 Gothenburg , Sweden
| | - Jens Nielsen
- 1 Department of Biology and Biological Engineering, Chalmers University of Technology , 41296 Gothenburg , Sweden.,2 Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology , 41296 Gothenburg , Sweden.,3 Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , 2800 Kgs Lyngby , Denmark.,4 BioInnovation Institute , Ole Måløes Vej, 2200 Copenhagen N , Denmark
| | - Verena Siewers
- 1 Department of Biology and Biological Engineering, Chalmers University of Technology , 41296 Gothenburg , Sweden.,2 Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology , 41296 Gothenburg , Sweden
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39
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Zhang X, Zhao Y, Liu Y, Wang J, Deng Y. Recent progress on bio-based production of dicarboxylic acids in yeast. Appl Microbiol Biotechnol 2020; 104:4259-4272. [PMID: 32215709 DOI: 10.1007/s00253-020-10537-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/06/2020] [Accepted: 03/09/2020] [Indexed: 12/25/2022]
Abstract
Dicarboxylic acids are widely used in fine chemical and food industries as well as the monomer for polymerisation of high molecular material. Given the problems of environmental contamination and sustainable development faced by traditional production of dicarboxylic acids based on petrol, new approaches such as bio-based production of dicarboxylic acids drew more attentions. The yeast, Saccharomyces cerevisiae, was regarded as an ideal organism for bio-based production of dicarboxylic acids with high tolerance to acidic and hyperosmotic environments, robust growth using a broad range of substrates, great convenience for genetic manipulation, stable inheritance via sub-cultivation, and food compatibility. In this review, the production of major dicarboxylates via S. cerevisiae was concluded and the challenges and opportunities facing were discussed.Key Points• Summary of current production of major dicarboxylic acids by Saccharomyces cerevisiae.• Discussion of influence factors on four-carbon dicarboxylic acids production by Saccharomyces cerevisiae.• Outlook of potential production of five- and six-carbon dicarboxylic acids by Saccharomyces cerevisiae.
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Affiliation(s)
- Xi Zhang
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Yunying Zhao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Yingli Liu
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing, 100048, China
| | - Jing Wang
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing, 100048, China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China. .,School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
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40
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Ye C, Xu N, Gao C, Liu G, Xu J, Zhang W, Chen X, Nielsen J, Liu L. Comprehensive understanding of Saccharomyces cerevisiae phenotypes with whole-cell model WM_S288C. Biotechnol Bioeng 2020; 117:1562-1574. [PMID: 32022245 DOI: 10.1002/bit.27298] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 01/28/2020] [Accepted: 02/03/2020] [Indexed: 02/01/2023]
Abstract
Biological network construction for Saccharomyces cerevisiae is a widely used approach for simulating phenotypes and designing cell factories. However, due to a complicated regulatory mechanism governing the translation of genotype to phenotype, precise prediction of phenotypes remains challenging. Here, we present WM_S288C, a computational whole-cell model that includes 15 cellular states and 26 cellular processes and which enables integrated analyses of physiological functions of Saccharomyces cerevisiae. Using WM_S288C to predict phenotypes of S. cerevisiae, the functions of 1140 essential genes were characterized and linked to phenotypes at five levels. During the cell cycle, the dynamic allocation of intracellular molecules could be tracked in real-time to simulate cell activities. Additionally, one-third of non-essential genes were identified to affect cell growth via regulating nucleotide concentrations. These results demonstrated the value of WM_S288C as a tool for understanding and investigating the phenotypes of S. cerevisiae.
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Affiliation(s)
- Chao Ye
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,Key Laboratory of Industrial Biotechnology, Jiangnan University, Ministry of Education, Wuxi, Jiangsu, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Nan Xu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,Key Laboratory of Industrial Biotechnology, Jiangnan University, Ministry of Education, Wuxi, Jiangsu, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Gaoqiang Liu
- Hunan Provincial Key Laboratory for Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Jianzhong Xu
- Key Laboratory of Industrial Biotechnology, Jiangnan University, Ministry of Education, Wuxi, Jiangsu, China
| | - Weiguo Zhang
- Key Laboratory of Industrial Biotechnology, Jiangnan University, Ministry of Education, Wuxi, Jiangsu, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,Key Laboratory of Industrial Biotechnology, Jiangnan University, Ministry of Education, Wuxi, Jiangsu, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,Key Laboratory of Industrial Biotechnology, Jiangnan University, Ministry of Education, Wuxi, Jiangsu, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, China
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41
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Zafar S, Tang MQ, Wang YK, Sarwar R, Liu SY, Tan XL. Candidate genes-association study to identify loci related to oleic acid in Brassica napus using SNP markers and their heterologous expression in yeast. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 146:294-302. [PMID: 31783205 DOI: 10.1016/j.plaphy.2019.11.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 11/14/2019] [Accepted: 11/16/2019] [Indexed: 06/10/2023]
Abstract
Brassica napus (rapeseed) serves as a main source of edible oil, and the oil's quality is mainly determined by the relative proportions of fatty acids. A high oleic acid concentration in B. napus oil increases its shelf life and oxidative stability. Therefore, attaining a high oleic acid concentration is necessary to enhance the nutritional quality of rapeseed oil. Here, an association study of candidate genes was conducted using a population of 324 genetically diverse rapeseed accessions, and several loci related to oleic acid content were identified. Furthermore, these loci were functionally characterized in Saccharomyces cerevisiae to assess their functions, and the promising candidate loci were validated using single nucleotide polymorphic markers in an independent inbred population. The results increased our understanding of fatty acid metabolism in B. napus. Moreover, these findings may assist in marker-based breeding efforts to improve the fatty acid composition and quality of B. napus oil.
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Affiliation(s)
- Sundus Zafar
- School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, China; Institute of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Min-Qiang Tang
- The Oil Crops Research Institute (OCRI) of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Yu-Kang Wang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Rehman Sarwar
- Institute of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Sheng-Yi Liu
- The Oil Crops Research Institute (OCRI) of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Xiao-Li Tan
- Institute of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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Liu Y, Liu Q, Krivoruchko A, Khoomrung S, Nielsen J. Engineering yeast phospholipid metabolism for de novo oleoylethanolamide production. Nat Chem Biol 2019; 16:197-205. [PMID: 31844304 DOI: 10.1038/s41589-019-0431-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 11/08/2019] [Indexed: 11/09/2022]
Abstract
Phospholipids, the most abundant membrane lipid components, are crucial in maintaining membrane structures and homeostasis for biofunctions. As a structurally diverse and tightly regulated system involved in multiple organelles, phospholipid metabolism is complicated to manipulate. Thus, repurposing phospholipids for lipid-derived chemical production remains unexplored. Herein, we develop a Saccharomyces cerevisiae platform for de novo production of oleoylethanolamide, a phospholipid derivative with promising pharmacological applications in ameliorating lipid dysfunction and neurobehavioral symptoms. Through deregulation of phospholipid metabolism, screening of biosynthetic enzymes, engineering of subcellular trafficking and process optimization, we could produce oleoylethanolamide at a titer of 8,115.7 µg l-1 and a yield on glucose of 405.8 µg g-1. Our work provides a proof-of-concept study for systemically repurposing phospholipid metabolism for conversion towards value-added biological chemicals, and this multi-faceted framework may shed light on tailoring phospholipid metabolism in other microbial hosts.
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Affiliation(s)
- Yi Liu
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Quanli Liu
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Anastasia Krivoruchko
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden.,Biopetrolia AB, Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden
| | - Sakda Khoomrung
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Department of Biochemistry, Siriraj Metabolomics and Phonemics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden. .,Biopetrolia AB, Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark. .,BioInnovation Institute, Copenhagen, Denmark.
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43
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Recent trends in metabolic engineering of microbial chemical factories. Curr Opin Biotechnol 2019; 60:188-197. [DOI: 10.1016/j.copbio.2019.05.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 05/09/2019] [Indexed: 11/24/2022]
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44
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Su WC, Lin YH, Pagac M, Wang CW. Seipin negatively regulates sphingolipid production at the ER-LD contact site. J Cell Biol 2019; 218:3663-3680. [PMID: 31594806 PMCID: PMC6829658 DOI: 10.1083/jcb.201902072] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 06/23/2019] [Accepted: 08/08/2019] [Indexed: 01/06/2023] Open
Abstract
Su et al. show that seipin negatively regulates the production of sphingoid intermediates by binding the enzymes serine palmitoyltransferase and fatty acid elongase at discrete regions of the ER in close vicinity to lipid droplets, thereby mediating the synthesis of two major building blocks for sphingolipids. Seipin is known for its critical role in controlling lipid droplet (LD) assembly at the LD-forming subdomain of the endoplasmic reticulum (ER). Here, we identified a new function of seipin as a negative regulator for sphingolipid production. We show that yeast cells lacking seipin displayed altered sensitivity to sphingolipid inhibitors, accumulated sphingoid precursors and intermediates, and increased serine palmitoyltransferase (SPT) and fatty acid (FA) elongase activities. Seipin associated with SPT and FA elongase, and the interaction was reduced by inhibitors for sphingolipid synthesis in a concentration-dependent manner. We further show that the interactions of seipin with SPT and FA elongase occurred at ER–LD contacts and were likely regulated differentially. Further evidence indicated that LD biogenesis was intact when SPT activity was blocked, whereas excess sphingoid intermediates may affect LD morphology. Expression of human seipin rescued the altered sphingolipids in yeast seipin mutants, suggesting that the negative regulation of sphingolipid synthesis by seipin is likely an evolutionarily conserved process.
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Affiliation(s)
- Wei-Cheng Su
- Institute of Plant and Microbial Biology, Academia Sinica, Nangang, Taipei, Taiwan
| | - Yi-Hsiu Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Nangang, Taipei, Taiwan
| | - Martin Pagac
- Institute of Plant and Microbial Biology, Academia Sinica, Nangang, Taipei, Taiwan
| | - Chao-Wen Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Nangang, Taipei, Taiwan
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Arhar S, Natter K. Common aspects in the engineering of yeasts for fatty acid- and isoprene-based products. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:158513. [PMID: 31465888 DOI: 10.1016/j.bbalip.2019.08.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 06/26/2019] [Accepted: 08/20/2019] [Indexed: 11/18/2022]
Abstract
The biosynthetic pathways for most lipophilic metabolites share several common principles. These substances are built almost exclusively from acetyl-CoA as the donor for the carbon scaffold and NADPH is required for the reductive steps during biosynthesis. Due to their hydrophobicity, the end products are sequestered into the same cellular compartment, the lipid droplet. In this review, we will summarize the efforts in the metabolic engineering of yeasts for the production of two major hydrophobic substance classes, fatty acid-based lipids and isoprenoids, with regard to these common aspects. We will compare and discuss the results of genetic engineering strategies to construct strains with enhanced synthesis of the precursor acetyl-CoA and with modified redox metabolism for improved NADPH supply. We will also discuss the role of the lipid droplet in the storage of the hydrophobic product and review the strategies to either optimize this organelle for higher capacity or to achieve excretion of the product into the medium.
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Affiliation(s)
- Simon Arhar
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria
| | - Klaus Natter
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria.
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46
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Programmable biomolecular switches for rewiring flux in Escherichia coli. Nat Commun 2019; 10:3751. [PMID: 31434894 PMCID: PMC6704175 DOI: 10.1038/s41467-019-11793-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 08/01/2019] [Indexed: 12/15/2022] Open
Abstract
Synthetic biology aims to develop programmable tools to perform complex functions such as redistributing metabolic flux in industrial microorganisms. However, development of protein-level circuits is limited by availability of designable, orthogonal, and composable tools. Here, with the aid of engineered viral proteases and proteolytic signals, we build two sets of controllable protein units, which can be rationally configured to three tools. Using a protease-based dynamic regulation circuit to fine-tune metabolic flow, we achieve 12.63 g L−1 shikimate titer in minimal medium without inducer. In addition, the carbon catabolite repression is alleviated by protease-based inverter-mediated flux redistribution under multiple carbon sources. By coordinating reaction rate using a protease-based oscillator in E. coli, we achieve d-xylonate productivity of 7.12 g L−1 h−1 with a titer of 199.44 g L−1. These results highlight the applicability of programmable protein switches to metabolic engineering for valuable chemicals production. Current flux rewiring technologies in metabolic engineering are mainly transcriptional regulation. Here, the authors build two sets of controllable protein units using engineered viral proteases and proteolytic signals, and utilize for increasing titers of shikimate and D-xylonate in E. coli.
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47
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Yan Q, Pfleger BF. Revisiting metabolic engineering strategies for microbial synthesis of oleochemicals. Metab Eng 2019; 58:35-46. [PMID: 31022535 DOI: 10.1016/j.ymben.2019.04.009] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/20/2019] [Accepted: 04/21/2019] [Indexed: 02/06/2023]
Abstract
Microbial production of oleochemicals from renewable feedstocks remains an attractive route to produce high-energy density, liquid transportation fuels and high-value chemical products. Metabolic engineering strategies have been applied to demonstrate production of a wide range of oleochemicals, including free fatty acids, fatty alcohols, esters, olefins, alkanes, ketones, and polyesters in both bacteria and yeast. The majority of these demonstrations synthesized products containing long-chain fatty acids. These successes motivated additional effort to produce analogous molecules comprised of medium-chain fatty acids, molecules that are less common in natural oils and therefore of higher commercial value. Substantial progress has been made towards producing a subset of these chemicals, but significant work remains for most. The other primary challenge to producing oleochemicals in microbes is improving the performance, in terms of yield, rate, and titer, of biocatalysts such that economic large-scale processes are feasible. Common metabolic engineering strategies include blocking pathways that compete with synthesis of oleochemical building blocks and/or consume products, pulling flux through pathways by removing regulatory signals, pushing flux into biosynthesis by overexpressing rate-limiting enzymes, and engineering cells to tolerate the presence of oleochemical products. In this review, we describe the basic fundamentals of oleochemical synthesis and summarize advances since 2013 towards improving performance of heterotrophic microbial cell factories.
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Affiliation(s)
- Qiang Yan
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Wisconsin-Madison, Madison, WI 53706, United States; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706, United States.
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48
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Wenning L, Ejsing CS, David F, Sprenger RR, Nielsen J, Siewers V. Increasing jojoba-like wax ester production in Saccharomyces cerevisiae by enhancing very long-chain, monounsaturated fatty acid synthesis. Microb Cell Fact 2019; 18:49. [PMID: 30857535 PMCID: PMC6410506 DOI: 10.1186/s12934-019-1098-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 02/28/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Fatty acids (FAs) with a chain length of more than 18 carbon atoms (> C18) are interesting for the production of specialty compounds derived from these FAs. These compounds include free FAs, like erucic acid (C22:1-Δ13), primary fatty alcohols (FOHs), like docosanol (C22:0-FOH), as well as jojoba-like wax esters (WEs) (C38-WE to C44-WE), which are esters of (very) long-chain FAs and (very) long-chain FOHs. In particular, FAs, FOHs and WEs are used in the production of chemicals, pharmaceuticals and cosmetic products. Jojoba seed oil is highly enriched in diunsaturated WEs with over 70 mol% being composed of C18:1-C24:1 monounsaturated FOH and monounsaturated FA moieties. In this study, we aim for the production of jojoba-like WEs in the yeast Saccharomyces cerevisiae by increasing the amount of very long-chain, monounsaturated FAs and simultaneously expressing enzymes required for WE synthesis. RESULTS We show that the combined expression of a plant-derived fatty acid elongase (FAE/KCS) from Crambe abyssinica (CaKCS) together with the yeast intrinsic fatty acid desaturase (FAD) Ole1p leads to an increase in C20:1 and C22:1 FAs in S. cerevisiae. We also demonstrate that the best enzyme candidate for C24:1 FA production in S. cerevisiae is a FAE derived from Lunaria annua (LaKCS). The combined overexpression of CaKCS and Ole1p together with a fatty acyl reductase (FAR/FAldhR) from Marinobacter aquaeolei VT8 (MaFAldhR) and a wax synthase (WS) from Simmondsia chinensis (SciWS) in a S. cerevisiae strain, overexpressing a range of other enzymes involved in FA synthesis and elongation, leads to a yeast strain capable of producing high amounts of monounsaturated FOHs (up to C22:1-FOH) as well as diunsaturated WEs (up to C46:2-WE). CONCLUSIONS Changing the FA profile of the yeast S. cerevisiae towards very long-chain monounsaturated FAs is possible by combined overexpression of endogenous and heterologous enzymes derived from various sources (e.g. a marine copepod or plants). This strategy was used to produce jojoba-like WEs in S. cerevisiae and can potentially be extended towards other commercially interesting products derived from very long-chain FAs.
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Affiliation(s)
- Leonie Wenning
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230, Odense, Denmark
| | - Florian David
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden.,Biopetrolia AB, Kemivägen 10, 412 96, Gothenburg, Sweden
| | - Richard R Sprenger
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230, Odense, Denmark
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Verena Siewers
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden.
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49
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Construction of artificial micro-aerobic metabolism for energy- and carbon-efficient synthesis of medium chain fatty acids in Escherichia coli. Metab Eng 2019; 53:1-13. [PMID: 30684584 DOI: 10.1016/j.ymben.2019.01.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 01/18/2019] [Accepted: 01/23/2019] [Indexed: 02/06/2023]
Abstract
Medium-chain (C6-C10) chemicals are important components of fuels, commodities and fine chemicals. Numerous exciting achievements have proven reversed β-oxidation cycle as a promising platform to synthesize these chemicals. However, under native central carbon metabolism, energetic and redox constraints limit the efficient operation of reversed β-oxidation cycle. Current fermentative platform has to use different chemically and energetically inefficient ways for acetyl-CoA and NADH biosynthesis, respectively. The characteristics such as supplementation of additional acetate and formate or high ATP requirement makes this platform incompatible with large-scale production. Here, an artificial micro-aerobic metabolism for energy and carbon-efficient conversion of glycerol to MCFAs was constructed to present solutions towards these barriers. After evaluating numerous bacteria pathways under micro-aerobic conditions, one synthetic metabolic step enabling biosynthesis of acetyl-CoA and NADH simultaneously, without any energy cost and additional carbon requirement, and reducing loss of carbon to carbon dioxide-emitting reactions, was conceived and successfully constructed. The pyruvate dehydrogenase from Enterococcus faecalis was identified and biochemically characterized, demonstrating the most suitable characteristics. Furthermore, the carbon and energy metabolism in Escherichia coli was rewired by the clustered regularly interspaced short palindromic repeats interference system, inhibiting native fermentation pathways outcompeting this synthetic step. The present engineered strain exhibited a 15.7-fold increase in MCFA titer compared with that of the initial strain, and produced 15.67 g/L MCFAs from the biodiesel byproduct glycerol in 3-L bioreactor without exogenous feed of acetate or formate, representing the highest MCFA titer reported to date. This work demonstrates this artificial micro-aerobic metabolism has the potential to enable the cost-effective, large-scale production of fatty acids and other value-added reduced chemicals.
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50
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Wehrs M, Prahl JP, Moon J, Li Y, Tanjore D, Keasling JD, Pray T, Mukhopadhyay A. Production efficiency of the bacterial non-ribosomal peptide indigoidine relies on the respiratory metabolic state in S. cerevisiae. Microb Cell Fact 2018; 17:193. [PMID: 30545355 PMCID: PMC6293659 DOI: 10.1186/s12934-018-1045-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 12/11/2018] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Beyond pathway engineering, the metabolic state of the production host is critical in maintaining the efficiency of cellular production. The biotechnologically important yeast Saccharomyces cerevisiae adjusts its energy metabolism based on the availability of oxygen and carbon sources. This transition between respiratory and non-respiratory metabolic state is accompanied by substantial modifications of central carbon metabolism, which impact the efficiency of metabolic pathways and the corresponding final product titers. Non-ribosomal peptide synthetases (NRPS) are an important class of biocatalysts that provide access to a wide array of secondary metabolites. Indigoidine, a blue pigment, is a representative NRP that is valuable by itself as a renewably produced pigment. RESULTS Saccharomyces cerevisiae was engineered to express a bacterial NRPS that converts glutamine to indigoidine. We characterize carbon source use and production dynamics, and demonstrate that indigoidine is solely produced during respiratory cell growth. Production of indigoidine is abolished during non-respiratory growth even under aerobic conditions. By promoting respiratory conditions via controlled feeding, we scaled the production to a 2 L bioreactor scale, reaching a maximum titer of 980 mg/L. CONCLUSIONS This study represents the first use of the Streptomyces lavendulae NRPS (BpsA) in a fungal host and its scale-up. The final product indigoidine is linked to the activity of the TCA cycle and serves as a reporter for the respiratory state of S. cerevisiae. Our approach can be broadly applied to investigate diversion of flux from central carbon metabolism for NRPS and other heterologous pathway engineering, or to follow a population switch between respiratory and non-respiratory modes.
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Affiliation(s)
- Maren Wehrs
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Institut für Genetik, Technische Universität Braunschweig, Brunswick, Germany
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Jan-Philip Prahl
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Jadie Moon
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Yuchen Li
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
- Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Todd Pray
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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