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Worland AM, Han Z, Maruwan J, Wang Y, Du ZY, Tang YJ, Su WW, Roell GW. Elucidation of triacylglycerol catabolism in Yarrowia lipolytica: How cells balance acetyl-CoA and excess reducing equivalents. Metab Eng 2024; 85:1-13. [PMID: 38942196 DOI: 10.1016/j.ymben.2024.06.010] [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: 03/04/2024] [Revised: 06/06/2024] [Accepted: 06/24/2024] [Indexed: 06/30/2024]
Abstract
Yarrowia lipolytica is an industrial yeast that can convert waste oil to value-added products. However, it is unclear how this yeast metabolizes lipid feedstocks, specifically triacylglycerol (TAG) substrates. This study used 13C-metabolic flux analysis (13C-MFA), genome-scale modeling, and transcriptomics analyses to investigate Y. lipolytica W29 growth with oleic acid, glycerol, and glucose. Transcriptomics data were used to guide 13C-MFA model construction and to validate the 13C-MFA results. The 13C-MFA data were then used to constrain a genome-scale model (GSM), which predicted Y. lipolytica fluxes, cofactor balance, and theoretical yields of terpene products. The three data sources provided new insights into cellular regulation during catabolism of glycerol and fatty acid components of TAG substrates, and how their consumption routes differ from glucose catabolism. We found that (1) over 80% of acetyl-CoA from oleic acid is processed through the glyoxylate shunt, a pathway that generates less CO2 compared to the TCA cycle, (2) the carnitine shuttle is a key regulator of the cytosolic acetyl-CoA pool in oleic acid and glycerol cultures, (3) the oxidative pentose phosphate pathway and mannitol cycle are key routes for NADPH generation, (4) the mannitol cycle and alternative oxidase activity help balance excess NADH generated from β-oxidation of oleic acid, and (5) asymmetrical gene expressions and GSM simulations of enzyme usage suggest an increased metabolic burden for oleic acid catabolism.
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Affiliation(s)
- Alyssa M Worland
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, United States
| | - Zhenlin Han
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i at Mānoa, Honolulu, HI, 96822, United States
| | - Jessica Maruwan
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i at Mānoa, Honolulu, HI, 96822, United States
| | - Yu Wang
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i at Mānoa, Honolulu, HI, 96822, United States
| | - Zhi-Yan Du
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i at Mānoa, Honolulu, HI, 96822, United States
| | - Yinjie J Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, United States
| | - Wei Wen Su
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i at Mānoa, Honolulu, HI, 96822, United States.
| | - Garrett W Roell
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i at Mānoa, Honolulu, HI, 96822, United States.
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2
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Wu Y, Li S, Sun B, Guo J, Zheng M, Li A. Enhancing Gastrodin Production in Yarrowia lipolytica by Metabolic Engineering. ACS Synth Biol 2024; 13:1332-1342. [PMID: 38563122 DOI: 10.1021/acssynbio.4c00050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Gastrodin, 4-hydroxybenzyl alcohol-4-O-β-D-glucopyranoside, has been widely used in the treatment of neurogenic and cardiovascular diseases. Currently, gastrodin biosynthesis is being achieved in model microorganisms. However, the production levels are insufficient for industrial applications. In this study, we successfully engineered a Yarrowia lipolytica strain to overproduce gastrodin through metabolic engineering. Initially, the engineered strain expressing the heterologous gastrodin biosynthetic pathway, which comprises chorismate lyase, carboxylic acid reductase, phosphopantetheinyl transferase, endogenous alcohol dehydrogenases, and a UDP-glucosyltransferase, produced 1.05 g/L gastrodin from glucose in a shaking flask. Then, the production was further enhanced to 6.68 g/L with a productivity of 2.23 g/L/day by overexpressing the key node DAHP synthases of the shikimate pathway and alleviating the native tryptophan and phenylalanine biosynthetic pathways. Finally, the best strain, Gd07, produced 13.22 g/L gastrodin in a 5 L fermenter. This represents the highest reported production of gastrodin in an engineered microorganism to date, marking the first successful de novo production of gastrodin using Y. lipolytica.
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Affiliation(s)
- Yuanqing Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, #368 Youyi Road, Wuhan 430062, P. R. China
| | - Shuocheng Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, #368 Youyi Road, Wuhan 430062, P. R. China
| | - Baijian Sun
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, #368 Youyi Road, Wuhan 430062, P. R. China
| | - Jingyi Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, #368 Youyi Road, Wuhan 430062, P. R. China
| | - Meiyi Zheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, #368 Youyi Road, Wuhan 430062, P. R. China
| | - Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, #368 Youyi Road, Wuhan 430062, P. R. China
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3
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Yue M, Liu M, Gao S, Ren X, Zhou S, Rao Y, Zhou J. High-Level De Novo Production of (2 S)-Eriodictyol in Yarrowia Lipolytica by Metabolic Pathway and NADPH Regeneration Engineering. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4292-4300. [PMID: 38364826 DOI: 10.1021/acs.jafc.3c08861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
(2S)-Eriodictyol, a polyphenolic flavonoid, has found widespread applications in health supplements and food additives. However, the limited availability of plant-derived (2S)-eriodictyol cannot meet the market demand. Microbial production of (2S)-eriodictyol faces challenges, including the low catalytic efficiency of flavone 3'-hydroxylase/cytochrome P450 reductase (F3'H/CPR), insufficient precursor supplementation, and inadequate NADPH regeneration. This study systematically engineered Yarrowia lipolytica for high-level (2S)-eriodictyol production. In doing this, the expression of F3'H/CPR was balanced, and the supply of precursors was enhanced by relieving feedback inhibition of the shikimate pathway, promoting fatty acid β-oxidation, and increasing the copy number of synthetic pathway genes. These strategies, combined with NADPH regeneration, achieved an (2S)-eriodictyol titer of 423.6 mg/L. Finally, in fed-batch fermentation, a remarkable 6.8 g/L (2S)-eriodictyol was obtained, representing the highest de novo microbial titer reported to date and paving the way for industrial production.
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Affiliation(s)
- Mingyu Yue
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Mengsu Liu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Song Gao
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Xuefeng Ren
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shenghu Zhou
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yijian Rao
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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4
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Koh HG, Yook S, Oh H, Rao CV, Jin YS. Toward rapid and efficient utilization of nonconventional substrates by nonconventional yeast strains. Curr Opin Biotechnol 2024; 85:103059. [PMID: 38171048 DOI: 10.1016/j.copbio.2023.103059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024]
Abstract
Economic and sustainable production of biofuels and chemicals necessitates utilizing abundant and inexpensive lignocellulosic biomass. Yet, Saccharomyces cerevisiae, a workhorse strain for industrial biotechnology based on starch and sugarcane-derived sugars, is not suitable for lignocellulosic bioconversion due to a lack of pentose metabolic pathways and severe inhibition by toxic inhibitors in cellulosic hydrolysates. This review underscores the potential of nonconventional yeast strains, specifically Yarrowia lipolytica and Rhodotorula toruloides, for converting underutilized carbon sources, such as xylose and acetate, into high-value products. Multi-omics studies with nonconventional yeast have elucidated the structure and regulation of metabolic pathways for efficient and rapid utilization of xylose and acetate. The review delves into the advantages of using xylose and acetate for producing biofuels and chemicals. Collectively, value-added biotransformation of nonconventional substrates by nonconventional yeast strains is a promising strategy to improve both economics and sustainability of bioproduction.
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Affiliation(s)
- Hyun Gi Koh
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Sangdo Yook
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hyunjoon Oh
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Christopher V Rao
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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5
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Sun ML, Gao X, Lin L, Yang J, Ledesma-Amaro R, Ji XJ. Building Yarrowia lipolytica Cell Factories for Advanced Biomanufacturing: Challenges and Solutions. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:94-107. [PMID: 38126236 DOI: 10.1021/acs.jafc.3c07889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Microbial cell factories have shown great potential for industrial production with the benefit of being environmentally friendly and sustainable. Yarrowia lipolytica is a promising and superior non-model host for biomanufacturing due to its cumulated advantages compared to model microorganisms, such as high fluxes of metabolic precursors (acetyl-CoA and malonyl-CoA) and its naturally hydrophobic microenvironment. However, although diverse compounds have been synthesized in Y. lipolytica cell factories, most of the relevant studies have not reached the level of industrialization and commercialization due to a number of remaining challenges, including unbalanced metabolic flux, conflict between cell growth and product synthesis, and cytotoxic effects. Here, various metabolic engineering strategies for solving the challenges are summarized, which is developing fast and extremely conducive to rational design and reconstruction of robust Y. lipolytica cell factories for advanced biomanufacturing. Finally, future engineering efforts for enhancing the production efficiency of this platform strain are highlighted.
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Affiliation(s)
- Mei-Li Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Xiaoxia Gao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Lu Lin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Jing Yang
- 2011 College, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Xiao-Jun Ji
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
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6
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Walker C, Mortensen M, Poudel B, Cotter C, Myers R, Okekeogbu IO, Ryu S, Khomami B, Giannone RJ, Laursen S, Trinh CT. Proteomes reveal metabolic capabilities of Yarrowia lipolytica for biological upcycling of polyethylene into high-value chemicals. mSystems 2023; 8:e0074123. [PMID: 37882587 PMCID: PMC10734471 DOI: 10.1128/msystems.00741-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/18/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Sustainable processes for biological upcycling of plastic wastes in a circular bioeconomy are needed to promote decarbonization and reduce environmental pollution due to increased plastic consumption, incineration, and landfill storage. Strain characterization and proteomic analysis revealed the robust metabolic capabilities of Yarrowia lipolytica to upcycle polyethylene into high-value chemicals. Significant proteome reallocation toward energy and lipid metabolisms was required for robust growth on hydrocarbons with n-hexadecane as the preferential substrate. However, an apparent over-investment in these same categories to utilize complex depolymerized plastic (DP) oil came at the expense of protein biosynthesis, limiting cell growth. Taken together, this study elucidates how Y. lipolytica activates its metabolism to utilize DP oil and establishes Y. lipolytica as a promising host for the upcycling of plastic wastes.
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Affiliation(s)
- Caleb Walker
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Max Mortensen
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Bindica Poudel
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Christopher Cotter
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Ryan Myers
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Ikenna O. Okekeogbu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Seunghyun Ryu
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Bamin Khomami
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Richard J. Giannone
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Siris Laursen
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Cong T. Trinh
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
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7
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Mei J, Liu X, Liu X, Bao Y, Luo T, Wang J. Metabolomics analysis of the metabolic effects of citric acid on Issatchenkia terricola WJL-G4. J Biosci Bioeng 2023; 136:452-461. [PMID: 37798226 DOI: 10.1016/j.jbiosc.2023.09.006] [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: 03/16/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 10/07/2023]
Abstract
In current research, yeast species Issatchenkia terricola WJL-G4 was shown to be capable of degrading citric acid, especially in the processing of fruit juice and wine. I. terricola WJL-G4 was able to use citric acid as a carbon source, but the metabolic effects of citric acid on yeast remained unclear. In this study, the metabolic effects of citric acid on I. terricola WJL-G4 were studied using liquid chromatography-mass spectrometry metabolomics technology, with glucose treatment as the control. Results showed that organic acid contents related to the extracellular tricarboxylic acid cycle (TCA) varied greatly. The metabolomics results indicated that I. terricola WJL-G4 might metabolize citric acid through the TCA pathway, and the glycolysis pathway might be inhibited; however, gluconeogenesis proceeded normally during citric acid treatment. Some fatty acids and phospholipids, along with the metabolic pathways of amino acids, vitamins, purines and nicotinamide in I. terricola WJL-G4 were also affected by the citric acid treatment. This work provided a theoretical basis for further study of the mechanism of yeast metabolism of citric acid.
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Affiliation(s)
- Jiajia Mei
- College of Life Science, Northeast Forestry University, No. 26 Hexing St., Harbin, Heilongjiang 150040, China
| | - Xiaojie Liu
- Shanghai Urban Construction Vocational College, No. 2080 Nanting St., Shanghai 201415, China
| | - Xinyi Liu
- College of Life Science, Northeast Forestry University, No. 26 Hexing St., Harbin, Heilongjiang 150040, China
| | - Yihong Bao
- College of Life Science, Northeast Forestry University, No. 26 Hexing St., Harbin, Heilongjiang 150040, China; Key Laboratory of Forest Food Resources Utilization of Heilongjiang Province, No. 26 Hexing St., Harbin, Heilongjiang 150040, China
| | - Ting Luo
- State Key Laboratory of Food Science and Technology, Nanchang University, No. 999 Xuefu St., Nanchang, Jiangxi 330047, China
| | - Jinling Wang
- College of Life Science, Northeast Forestry University, No. 26 Hexing St., Harbin, Heilongjiang 150040, China; Key Laboratory of Forest Food Resources Utilization of Heilongjiang Province, No. 26 Hexing St., Harbin, Heilongjiang 150040, China.
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8
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Zhang Y, Li M, Zhu R, Xin Y, Guo Z, Gu Z, Guo Z, Zhang L. Installing xylose assimilation and cellodextrin phosphorolysis pathways in obese Yarrowia lipolytica facilitates cost-effective lipid production from lignocellulosic hydrolysates. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:186. [PMID: 38031183 PMCID: PMC10688077 DOI: 10.1186/s13068-023-02434-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/14/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND Yarrowia lipolytica, one of the most charming chassis cells in synthetic biology, is unable to use xylose and cellodextrins. RESULTS Herein, we present work to tackle for the first time the engineering of Y. lipolytica to produce lipids from cellodextrins and xylose by employing rational and combinatorial strategies. This includes constructing a cellodextrin-phosphorolytic Y. lipolytica by overexpressing Neurospora crassa cellodextrin transporter, Clostridium thermocellum cellobiose/cellodextrin phosphorylase and Saccharomyces cerevisiae phosphoglucomutase. The effect of glucose repression on xylose consumption was relieved by installing a xylose uptake facilitator combined with enhanced PPP pathway and increased cytoplasmic NADPH supply. Further enhancing lipid production and interrupting its consumption conferred the obese phenotype to the engineered yeast. The strain is able to co-ferment glucose, xylose and cellodextrins efficiently, achieving a similar μmax of 0.19 h-1, a qs of 0.34 g-s/g-DCW/h and a YX/S of 0.54 DCW-g/g-s on these substrates, and an accumulation of up to 40% of lipids on the sugar mixture and on wheat straw hydrolysate. CONCLUSIONS Therefore, engineering Y. lipolytica capable of assimilating xylose and cellodextrins is a vital step towards a simultaneous saccharification and fermentation (SSF) process of LC biomass, allowing improved substrate conversion rate and reduced production cost due to low demand of external glucosidase.
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Affiliation(s)
- Yiran Zhang
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, People's Republic of China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, People's Republic of China
| | - Moying Li
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Rui Zhu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Yu Xin
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Zitao Guo
- School of Food and Biological Engineering, Jiangsu University, Xuefu Road 301, Jingkou District, Zhenjiang, Jiangsu, 212013, People's Republic of China
| | - Zhenghua Gu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Zhongpeng Guo
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China.
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, People's Republic of China.
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, People's Republic of China.
| | - Liang Zhang
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, People's Republic of China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, People's Republic of China
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9
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Qin J, Kurt E, LBassi T, Sa L, Xie D. Biotechnological production of omega-3 fatty acids: current status and future perspectives. Front Microbiol 2023; 14:1280296. [PMID: 38029217 PMCID: PMC10662050 DOI: 10.3389/fmicb.2023.1280296] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Omega-3 fatty acids, including alpha-linolenic acids (ALA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA), have shown major health benefits, but the human body's inability to synthesize them has led to the necessity of dietary intake of the products. The omega-3 fatty acid market has grown significantly, with a global market from an estimated USD 2.10 billion in 2020 to a predicted nearly USD 3.61 billion in 2028. However, obtaining a sufficient supply of high-quality and stable omega-3 fatty acids can be challenging. Currently, fish oil serves as the primary source of omega-3 fatty acids in the market, but it has several drawbacks, including high cost, inconsistent product quality, and major uncertainties in its sustainability and ecological impact. Other significant sources of omega-3 fatty acids include plants and microalgae fermentation, but they face similar challenges in reducing manufacturing costs and improving product quality and sustainability. With the advances in synthetic biology, biotechnological production of omega-3 fatty acids via engineered microbial cell factories still offers the best solution to provide a more stable, sustainable, and affordable source of omega-3 fatty acids by overcoming the major issues associated with conventional sources. This review summarizes the current status, key challenges, and future perspectives for the biotechnological production of major omega-3 fatty acids.
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Affiliation(s)
| | | | | | | | - Dongming Xie
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA, United States
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10
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Jovanovic Gasovic S, Dietrich D, Gläser L, Cao P, Kohlstedt M, Wittmann C. Multi-omics view of recombinant Yarrowia lipolytica: Enhanced ketogenic amino acid catabolism increases polyketide-synthase-driven docosahexaenoic production to high selectivity at the gram scale. Metab Eng 2023; 80:45-65. [PMID: 37683719 DOI: 10.1016/j.ymben.2023.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/04/2023] [Accepted: 09/04/2023] [Indexed: 09/10/2023]
Abstract
DHA is a marine PUFA of commercial value, given its multiple health benefits. The worldwide emerging shortage in DHA supply has increased interest in microbial cell factories that can provide the compound de novo. In this regard, the present work aimed to improve DHA production in the oleaginous yeast strain Y. lipolytica Af4, which synthetized the PUFA via a heterologous myxobacterial polyketide synthase (PKS)-like gene cluster. As starting point, we used transcriptomics, metabolomics, and 13C-based metabolic pathway profiling to study the cellular dynamics of Y. lipolytica Af4. The shift from the growth to the stationary DHA-production phase was associated with fundamental changes in carbon core metabolism, including a strong upregulation of the PUFA gene cluster, as well as an increase in citrate and fatty acid degradation. At the same time, the intracellular levels of the two DHA precursors acetyl-CoA and malonyl-CoA dropped by up to 98% into the picomolar range. Interestingly, the degradation pathways for the ketogenic amino acids l-lysine, l-leucine, and l-isoleucine were transcriptionally activated, presumably to provide extra acetyl-CoA. Supplementation with small amounts of these amino acids at the beginning of the DHA production phase beneficially increased the intracellular CoA-ester pools and boosted the DHA titer by almost 40%. Isotopic 13C-tracer studies revealed that the supplements were efficiently directed toward intracellular CoA-esters and DHA. Hereby, l-lysine was found to be most efficient, as it enabled long-term activation, due to storage within the vacuole and continuous breakdown. The novel strategy enabled DHA production in Y. lipolytica at the gram scale for the first time. DHA was produced at a high selectivity (27% of total fatty acids) and free of the structurally similar PUFA DPA, which facilitates purification for high-value medical applications that require API-grade DHA. The assembled multi-omics picture of the central metabolism of Y. lipolytica provides valuable insights into this important yeast. Beyond our work, the enhanced catabolism of ketogenic amino acids seems promising for the overproduction of other compounds in Y. lipolytica, whose synthesis is limited by the availability of CoA ester precursors.
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Affiliation(s)
| | - Demian Dietrich
- Institute of Systems Biotechnology, Saarland University, Germany
| | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Germany
| | - Peng Cao
- Institute of Systems Biotechnology, Saarland University, Germany
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11
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Huang C, Chen Y, Cheng S, Li M, Wang L, Cheng M, Li F, Cao Y, Song H. Enhanced acetate utilization for value-added chemicals production in Yarrowia lipolytica by integration of metabolic engineering and microbial electrosynthesis. Biotechnol Bioeng 2023; 120:3013-3024. [PMID: 37306471 DOI: 10.1002/bit.28465] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/19/2023] [Accepted: 05/31/2023] [Indexed: 06/13/2023]
Abstract
The limited supply of reducing power restricts the efficient utilization of acetate in Yarrowia lipolytica. Here, microbial electrosynthesis (MES) system, enabling direct conversion of inward electrons to NAD(P)H, was used to improve the production of fatty alcohols from acetate based on pathway engineering. First, the conversion efficiency of acetate to acetyl-CoA was reinforced by heterogenous expression of ackA-pta genes. Second, a small amount of glucose was used as cosubstrate to activate the pentose phosphate pathway and promote intracellular reducing cofactors synthesis. Third, through the employment of MES system, the final fatty alcohols production of the engineered strain YLFL-11 reached 83.8 mg/g dry cell weight (DCW), which was 6.17-fold higher than the initial production of YLFL-2 in shake flask. Furthermore, these strategies were also applied for the elevation of lupeol and betulinic acid synthesis from acetate in Y. lipolytica, demonstrating that our work provides a practical solution for cofactor supply and the assimilation of inferior carbon sources.
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Affiliation(s)
- Congcong Huang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Yaru Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Shuai Cheng
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Mengxu Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Luxin Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Meijie Cheng
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Feng Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Yingxiu Cao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Hao Song
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
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12
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Nurwono G, O'Keeffe S, Liu N, Park JO. Sustainable metabolic engineering requires a perfect trifecta. Curr Opin Biotechnol 2023; 83:102983. [PMID: 37573625 PMCID: PMC10960266 DOI: 10.1016/j.copbio.2023.102983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/10/2023] [Accepted: 07/15/2023] [Indexed: 08/15/2023]
Abstract
The versatility of cellular metabolism in converting various substrates to products inspires sustainable alternatives to conventional chemical processes. Metabolism can be engineered to maximize the yield, rate, and titer of product generation. However, the numerous combinations of substrate, product, and organism make metabolic engineering projects difficult to navigate. A perfect trifecta of substrate, product, and organism is prerequisite for an environmentally and economically sustainable metabolic engineering endeavor. As a step toward this endeavor, we propose a reverse engineering strategy that starts with product selection, followed by substrate and organism pairing. While a large bioproduct space has been explored, the top-ten compounds have been synthesized mainly using glucose and model organisms. Unconventional feedstocks (e.g. hemicellulosic sugars and CO2) and non-model organisms are increasingly gaining traction for advanced bioproduct synthesis due to their specialized metabolic modes. Judicious selection of the substrate-organism-product combination will illuminate the untapped territory of sustainable metabolic engineering.
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Affiliation(s)
| | - Samantha O'Keeffe
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
| | - Nian Liu
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA.
| | - Junyoung O Park
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA.
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13
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Zhang P, Wei W, Shang Y, Ye BC. Metabolic engineering of Yarrowia lipolytica for high-level production of scutellarin. BIORESOURCE TECHNOLOGY 2023:129421. [PMID: 37392967 DOI: 10.1016/j.biortech.2023.129421] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/03/2023]
Abstract
Scutellarin drugs have been recognized as a key item in the national development of essential clinical emergency drugs for treating cardiovascular and cerebrovascular diseases; therefore, the market demand for scutellarin is growing rapidly. Microbial synthesis based on synthetic biology is a promising method for industrial production of scutellarin. In this study, the highest reported scutellarin titer in the shake flask of 703.01 ± 4.83 mg/L was achieved in Yarrowia lipolytica through the systematic metabolic engineering modifications, including screening for the optimal flavone-6-hydroxylase-cytochrome P450 reductase combination SbF6H-ATR2 to enhance P450 enzyme activity, increasing the copy numbers of rate-limiting enzyme genes, overexpressing ZWF1 and GND1 to increase NADPH supply, enhancing the supply of p-coumaric acid and uridine diphosphate glucose, and introducing the heterologous gene VHb to enhance oxygen supply. This study has significant implications for the industrial production of scutellarin and other valuable flavonoids in green economies.
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Affiliation(s)
- Ping Zhang
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wenping Wei
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Yanzhe Shang
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
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14
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Using oils and fats to replace sugars as feedstocks for biomanufacturing: Challenges and opportunities for the yeast Yarrowia lipolytica. Biotechnol Adv 2023; 65:108128. [PMID: 36921878 DOI: 10.1016/j.biotechadv.2023.108128] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/16/2023]
Abstract
More than 200 million tons of plant oils and animal fats are produced annually worldwide from oil, crops, and the rendered animal fat industry. Triacylglycerol, an abundant energy-dense compound, is the major form of lipid in oils and fats. While oils or fats are very important raw materials and functional ingredients for food or related products, a significant portion is currently diverted to or recovered as waste. To significantly increase the value of waste oils or fats and expand their applications with a minimal environmental footprint, microbial biomanufacturing is presented as an effective strategy for adding value. Though both bacteria and yeast can be engineered to use oils or fats as the biomanufacturing feedstocks, the yeast Yarrowia lipolytica is presented as one of the most attractive platforms. Y. lipolytica is oleaginous, generally regarded as safe, demonstrated as a promising industrial producer, and has unique capabilities for efficient catabolism and bioconversion of lipid substrates. This review summarizes the major challenges and opportunities for Y. lipolytica as a new biomanufacturing platform for the production of value-added products from oils and fats. This review also discusses relevant cellular and metabolic engineering strategies such as fatty acid transport, fatty acid catabolism and bioconversion, redox balances and energy yield, cell morphology and stress response, and bioreaction engineering. Finally, this review highlights specific product classes including long-chain diacids, wax esters, terpenes, and carotenoids with unique synthesis opportunities from oils and fats in Y. lipolytica.
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15
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Zhu J, Gu Y, Yan Y, Ma J, Sun X, Xu P. Knocking out central metabolism genes to identify new targets and alternating substrates to improve lipid synthesis in Y. lipolytica. Front Bioeng Biotechnol 2023; 11:1098116. [PMID: 36714010 PMCID: PMC9880266 DOI: 10.3389/fbioe.2023.1098116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023] Open
Abstract
Introduction: Systematic gene knockout studies may offer us novel insights on cell metabolism and physiology. Specifically, the lipid accumulation mechanism at the molecular or cellular level is yet to be determined in the oleaginous yeast Y. lipolytica. Methods: Herein, we established ten engineered strains with the knockout of important genes involving in central carbon metabolism, NADPH generation, and fatty acid biosynthetic pathways. Results: Our result showed that NADPH sources for lipogenesis include the OxPP pathway, POM cycle, and a trans-mitochondrial isocitrate-α-oxoglutarate NADPH shuttle in Y. lipolytica. Moreover, we found that knockout of mitochondrial NAD+ isocitrate dehydrogenase IDH2 and overexpression of cytosolic NADP+ isocitrate dehydrogenase IDP2 could facilitate lipid synthesis. Besides, we also demonstrated that acetate is a more favorable carbon source for lipid synthesis when glycolysis step is impaired, indicating the evolutionary robustness of Y. lipolytica. Discussion: This systematic investigation of gene deletions and overexpression across various lipogenic pathways would help us better understand lipogenesis and engineer yeast factories to upgrade the lipid biomanufacturing platform.
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Affiliation(s)
- Jiang Zhu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Yang Gu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China,Department of Chemical, Biochemical and Environmental Engineering, University of MD, Baltimore County, Baltimore, MD, United States,*Correspondence: Yang Gu, ; Peng Xu,
| | - Yijing Yan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Jingbo Ma
- Department of Chemical, Biochemical and Environmental Engineering, University of MD, Baltimore County, Baltimore, MD, United States,College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, Anhui, China
| | - Xiaoman Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Peng Xu
- Department of Chemical, Biochemical and Environmental Engineering, University of MD, Baltimore County, Baltimore, MD, United States,Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology (GTIIT), Shantou, Guangdong, China,The Wolfson Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, Israel,*Correspondence: Yang Gu, ; Peng Xu,
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16
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Liu Z, Tian J, Miao Z, Liang W, Wang G. Metabolome and Transcriptome Profiling Reveal Carbon Metabolic Flux Changes in Yarrowia lipolytica Cells to Rapamycin. J Fungi (Basel) 2022; 8:jof8090939. [PMID: 36135664 PMCID: PMC9504542 DOI: 10.3390/jof8090939] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/04/2022] [Accepted: 09/04/2022] [Indexed: 11/24/2022] Open
Abstract
Yarrowia lipolytica is an oleaginous yeast for the production of oleochemicals and biofuels. Nitrogen deficiency is beneficial to lipids biosynthesis in Y. lipolytica. Target of rapamycin (TOR) regulates the utilization of nutrients, which is inhibited in nitrogen starvation or by rapamycin treatment. However, under nitrogen-rich conditions, the lipids biosynthesis in Y. lipolytica after inhibition of TOR by rapamycin is elusive. Combining metabolomics and transcriptomics analysis, we found that rapamycin altered multiple metabolic processes of Y. lipolytica grown in nitrogen-rich medium, especially the metabolisms of amino acids and lipids. A total of 176 differentially accumulated metabolites were identified after rapamycin treatment. Rapamycin increased the levels of tryptophan, isoleucine, proline, serine, glutamine, histidine, lysine, arginine and glutamic acid, and decreased the levels of threonine, tyrosine and aspartic acid. Two fatty acids in lipid droplets, stearic acid (down-regulated) and stearidonic acid (up-regulated), were identified. The expression of 2224 genes changed significantly after rapamycin treatment. Further analysis revealed that rapamycin reduced carbon flux through lipids biosynthesis, accompanied by increased carbon flux through fatty acids degradation and amino acid (especially glutamic acid, glutamine, proline and arginine) biosynthesis. The dataset provided here is valuable for understanding the molecular mechanisms of amino acid and lipids metabolisms in oleaginous yeast.
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Affiliation(s)
- Ziyu Liu
- Shandong Province Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Junjie Tian
- Shandong Province Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Zhengang Miao
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Wenxing Liang
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Guangyuan Wang
- Shandong Province Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
- Correspondence:
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17
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Narisetty V, Prabhu AA, Bommareddy RR, Cox R, Agrawal D, Misra A, Haider MA, Bhatnagar A, Pandey A, Kumar V. Development of Hypertolerant Strain of Yarrowia lipolytica Accumulating Succinic Acid Using High Levels of Acetate. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2022; 10:10858-10869. [PMID: 36035440 PMCID: PMC9400109 DOI: 10.1021/acssuschemeng.2c02408] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 07/16/2022] [Indexed: 05/26/2023]
Abstract
Acetate is emerging as a promising feedstock for biorefineries as it can serve as an alternate carbon source for microbial cell factories. In this study, we expressed acetyl-CoA synthase in Yarrowia lipolytica PSA02004PP, and the recombinant strain grew on acetate as the sole carbon source and accumulated succinic acid or succinate (SA). Unlike traditional feedstocks, acetate is a toxic substrate for microorganisms; therefore, the recombinant strain was further subjected to adaptive laboratory evolution to alleviate toxicity and improve tolerance against acetate. At high acetate concentrations, the adapted strain Y. lipolytica ACS 5.0 grew rapidly and accumulated lipids and SA. Bioreactor cultivation of ACS 5.0 with 22.5 g/L acetate in a batch mode resulted in a maximum cell OD600 of 9.2, with lipid and SA accumulation being 0.84 and 5.1 g/L, respectively. However, its fed-batch cultivation yielded a cell OD600 of 23.5, SA titer of 6.5 g/L, and lipid production of 1.5 g/L with an acetate uptake rate of 0.2 g/L h, about 2.86 times higher than the parent strain. Cofermentation of acetate and glucose significantly enhanced the SA titer and lipid accumulation to 12.2 and 1.8 g/L, respectively, with marginal increment in cell growth (OD600: 26.7). Furthermore, metabolic flux analysis has drawn insights into utilizing acetate for the production of metabolites that are downstream to acetyl-CoA. To the best of our knowledge, this is the first report on SA production from acetate by Y. lipolytica and demonstrates a path for direct valorization of sugar-rich biomass hydrolysates with elevated acetate levels to SA.
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Affiliation(s)
- Vivek Narisetty
- School
of Water, Energy and Environment, Cranfield
University, Cranfield MK43 0AL, United Kingdom
| | - Ashish A. Prabhu
- School
of Water, Energy and Environment, Cranfield
University, Cranfield MK43 0AL, United Kingdom
| | - Rajesh Reddy Bommareddy
- Department
of Applied Sciences, Northumbria University, Newcastle Upon Tyne NE1
8ST, United Kingdom
| | - Rylan Cox
- School
of Aerospace, Transport and Manufacturing, Cranfield University, Wharley
End MK43 0AL, United Kingdom
| | - Deepti Agrawal
- Biochemistry
and Biotechnology Area, Material Resource Efficiency Division, CSIR- Indian Institute of Petroleum, Mohkampur, Dehradun 248005, India
| | - Ashish Misra
- Department
of Biochemical Engineering& Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - M. Ali Haider
- Department
of Chemical Engineering, Indian Institute
of Technology Delhi, New Delhi 110016, India
| | - Amit Bhatnagar
- Department
of Separation Science, LUT School of Engineering Science, LUT University, Sammonkatu 12, Mikkeli FI-50130, Finland
| | - Ashok Pandey
- Centre
for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow 226 001, India
- Centre
for Energy and Environmental Sustainability, Lucknow 226 029, India
- Sustainability
Cluster, School of Engineering, University
of Petroleum and Energy Studies, Dehradun 248 007, India
| | - Vinod Kumar
- School
of Water, Energy and Environment, Cranfield
University, Cranfield MK43 0AL, United Kingdom
- Department
of Chemical Engineering, Indian Institute
of Technology Delhi, New Delhi 110016, India
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18
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Luo H, Shen T, Xie X. Stochastic simulation of enzymatic kinetics for 13C isotope labeling at the single-cell scale. REACTION KINETICS MECHANISMS AND CATALYSIS 2022. [DOI: 10.1007/s11144-022-02262-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Liu J, Wang X, Dai G, Zhang Y, Bian X. Microbial chassis engineering drives heterologous production of complex secondary metabolites. Biotechnol Adv 2022; 59:107966. [PMID: 35487394 DOI: 10.1016/j.biotechadv.2022.107966] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 12/27/2022]
Abstract
The cryptic secondary metabolite biosynthetic gene clusters (BGCs) far outnumber currently known secondary metabolites. Heterologous production of secondary metabolite BGCs in suitable chassis facilitates yield improvement and discovery of new-to-nature compounds. The two juxtaposed conventional model microorganisms, Escherichia coli, Saccharomyces cerevisiae, have been harnessed as microbial chassis to produce a bounty of secondary metabolites with the help of certain host engineering. In last decade, engineering non-model microbes to efficiently biosynthesize secondary metabolites has received increasing attention due to their peculiar advantages in metabolic networks and/or biosynthesis. The state-of-the-art synthetic biology tools lead the way in operating genetic manipulation in non-model microorganisms for phenotypic optimization or yields improvement of desired secondary metabolites. In this review, we firstly discuss the pros and cons of several model and non-model microbial chassis, as well as the importance of developing broader non-model microorganisms as alternative programmable heterologous hosts to satisfy the desperate needs of biosynthesis study and industrial production. Then we highlight the lately advances in the synthetic biology tools and engineering strategies for optimization of non-model microbial chassis, in particular, the successful applications for efficient heterologous production of multifarious complex secondary metabolites, e.g., polyketides, nonribosomal peptides, as well as ribosomally synthesized and post-translationally modified peptides. Lastly, emphasis is on the perspectives of chassis cells development to access the ideal cell factory in the artificial intelligence-driven genome era.
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Affiliation(s)
- Jiaqi Liu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China; Present address: Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
| | - Xue Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Guangzhi Dai
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China.
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20
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Modelling of the Citric Acid Production from Crude Glycerol by Wild-Type Yarrowia lipolytica DSM 8218 Using Response Surface Methodology (RSM). Life (Basel) 2022; 12:life12050621. [PMID: 35629288 PMCID: PMC9147156 DOI: 10.3390/life12050621] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 11/17/2022] Open
Abstract
Crude glycerol is the main by-product of the biodiesel manufacturing industry (10% w/w). Its use as a substrate in microbial fermentations is a concrete strategy to efficiently address its market surplus. In this study, the conversion of crude glycerol to citric acid, a key biochemical in the emerging bioeconomy, by a wild-type yeast Yarrowia lipolytica DSM 8218 was modelled using the Response Surface Methodology. The model relates C/N mass ratio and crude glycerol concentration to maximize the citric acid yield in flask scale using two different N sources, yeast extract and ammonium sulphate. Under the optimal conditions (yeast extract, C/N 141, glycerol 33 g/L), the conversion yield was 0.249 g/g. The optimal conditions were used for up-scaling a fed-batch fermentation in a 2 L bioreactor highlighting a metabolic shift from mannitol to citric acid when high stirring rates were applied (800 rpm). In these conditions, a morphic transition from pseudo-mycelial form to round-shaped yeast-like cells was observed too.
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21
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Pereira AS, Lopes M, Miranda SM, Belo I. Bio-oil production for biodiesel industry by Yarrowia lipolytica from volatile fatty acids in two-stage batch culture. Appl Microbiol Biotechnol 2022; 106:2869-2881. [PMID: 35394162 DOI: 10.1007/s00253-022-11900-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/23/2022] [Accepted: 03/26/2022] [Indexed: 11/26/2022]
Abstract
Microbial lipids-derived biodiesel is garnering much attention owing to its potential to substitute diesel fuel. In this study, lipid accumulation by Yarrowia lipolytica from volatile fatty acids (VFAs) was studied in a lab-scale stirred tank bioreactor. In batch cultures, Y. lipolytica NCYC 2904 was able to grow in 18 g·L-1 of VFAs (acetate, propionate, and butyrate), and the addition of a co-substrate (glucose) led to a fivefold improvement in lipid concentration. Furthermore, the two-stage batch culture (growth phase in glucose (1st stage) followed by a lipogenic phase in VFAs (2nd stage)) was the best strategy to obtain the highest lipid content in the cells (37%, w/w), with aeration conditions that kept dissolved oxygen concentration between 40% and 50% of saturation during the lipogenic phase. The estimated fuel properties of biodiesel produced from Y. lipolytica NCYC 2904 lipids are comparable with those of the biodiesel produced from vegetable oils and are in accordance with the international standards (EN 14214 and ASTM D6751). The cultivation strategies herein devised enable a sustainable, eco-friendly, and economical production of microbial lipids, based on feedstocks such as VFAs that can be derived from the acidogenic fermentation of organic wastes. KEY POINTS: • Addition of glucose to VFAs enhances lipids in Y. lipolytica in batch cultures • Two-stage batch culture - growth in glucose followed by VFAs pulse - rises lipids • Dissolved oxygen of 40-50% of saturation is crucial at the lipogenic phase.
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Affiliation(s)
- Ana S Pereira
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Marlene Lopes
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal.
| | - Sílvia M Miranda
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Isabel Belo
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
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22
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Sundaramahalingam MA, Sivashanmugam P, Rajeshbanu J, Ashokkumar M. A review on contemporary approaches in enhancing the innate lipid content of yeast cell. CHEMOSPHERE 2022; 293:133616. [PMID: 35033523 DOI: 10.1016/j.chemosphere.2022.133616] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
For the past few decades, industrialization has made a huge environmental hazard to the world with its waste. The approach of waste to wealth in the recent era has made many Eco-economical suggestions for the industries. The valuable products in biorefinery aspects of the eco-economical suggestions include; energy products, high-value drugs and novel materials. Bio-lipids are found to be the major influencing eco-economical products in the process. Production of bio-lipid from microbial sources has paved the way for future research on lipid-bioproducts. The yeast cell is a unique organism with a large unicellular structure capable of accumulating a high amount of lipids. It constitutes 90% of neutral lipids. Various strategies enhance the lipid profile of yeast cells: usage of oleaginous yeast, usage of low cost (or) alternative substrates, developing stress conditions in the growth medium, using genetically modified yeast, altering metabolic pathways of yeast and by using the symbiotic cultures of yeast with other microbes. The metabolic alterations of lipid pathways such as lipid biosynthesis, lipid elongation, lipid accumulation and lipid degradation have been a striking feature of research in lipid-based microbial work. The lipid-bioproducts have also made a strong footprint in the history of alternative energy products. It includes partial acyl glycerol, oleochemicals, phospholipids and biofuels. This report comprises the recent approaches carried out in the yeast cell for enhancing its lipid content. The limitations, challenges and future scope of individual strategies were also highlighted in this article.
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Affiliation(s)
- M A Sundaramahalingam
- Chemical and Biochemical Process Engineering Laboratory, Department of Chemical Engineering, National Institute of Technology, Tiruchirappalli, Tamil Nadu, India
| | - P Sivashanmugam
- Chemical and Biochemical Process Engineering Laboratory, Department of Chemical Engineering, National Institute of Technology, Tiruchirappalli, Tamil Nadu, India.
| | - J Rajeshbanu
- Department of Life Sciences, Central University of Tamil Nadu, Neelakudi, Thiruvarur, Tamil Nadu, India
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23
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Chi G, Xu Y, Cao X, Li Z, Cao M, Chisti Y, He N. Production of polyunsaturated fatty acids by Schizochytrium (Aurantiochytrium) spp. Biotechnol Adv 2021; 55:107897. [PMID: 34974158 DOI: 10.1016/j.biotechadv.2021.107897] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/05/2021] [Accepted: 12/20/2021] [Indexed: 12/28/2022]
Abstract
Diverse health benefits are associated with dietary consumption of omega-3 long-chain polyunsaturated fatty acids (ω-3 LC-PUFA), particularly docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA). Traditionally, these fatty acids have been obtained from fish oil, but limited supply, variably quality, and an inability to sustainably increase production for a rapidly growing market, are driving the quest for alternative sources. DHA derived from certain marine protists (heterotrophic thraustochytrids) already has an established history of commercial production for high-value dietary use, but is too expensive for use in aquaculture feeds, a much larger potential market for ω-3 LC-PUFA. Sustainable expansion of aquaculture is prevented by its current dependence on wild-caught fish oil as the source of ω-3 LC-PUFA nutrients required in the diet of aquacultured animals. Although several thraustochytrids have been shown to produce DHA and EPA, there is a particular interest in Schizochytrium spp. (now Aurantiochytrium spp.), as some of the better producers. The need for larger scale production has resulted in development of many strategies for improving productivity and production economics of ω-3 PUFA in Schizochytrium spp. Developments in fermentation technology and metabolic engineering for enhancing LC-PUFA production in Schizochytrium spp. are reviewed.
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Affiliation(s)
- Guoxiang Chi
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; The Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen 361005, China
| | - Yiyuan Xu
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; The Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen 361005, China
| | - Xingyu Cao
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; The Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen 361005, China
| | - Zhipeng Li
- College of Food and Biological Engineering, Jimei University, Xiamen 361000, China
| | - Mingfeng Cao
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; The Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen 361005, China.
| | - Yusuf Chisti
- School of Engineering, Massey University, Private Bag 11 222, Palmerston North, New Zealand.
| | - Ning He
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; The Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen 361005, China.
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24
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Jia D, He M, Tian Y, Shen S, Zhu X, Wang Y, Zhuang Y, Jiang W, Gu Y. Metabolic Engineering of Gas-Fermenting Clostridium ljungdahlii for Efficient Co-production of Isopropanol, 3-Hydroxybutyrate, and Ethanol. ACS Synth Biol 2021; 10:2628-2638. [PMID: 34549587 DOI: 10.1021/acssynbio.1c00235] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rational design and modification of autotrophic bacteria to efficiently produce high-value chemicals and biofuels are crucial for establishing a sustainable and economically viable process for one-carbon (C1) source utilization, which, however, remains a challenge in metabolic engineering. In this study, autotrophic Clostridium ljungdahlii was metabolically engineered to efficiently co-produce three important bulk chemicals, isopropanol, 3-hydroxybutyrate (3-HB), and ethanol (together, IHE), using syngas (CO2/CO). An artificial isopropanol-producing pathway was first constructed and optimized in C. ljungdahlii to achieve an efficient production of isopropanol and an unexpected product, 3-HB. Based on this finding, an endogenous active dehydrogenase capable of converting acetoacetate to 3-HB was identified in C. ljungdahlii, thereby revealing an efficient 3-HB-producing pathway. The engineered strain was further optimized to reassimilate acetic acid and synthesize 3-HB by introducing heterologous functional genes. Finally, the best-performing strain was able to produce 13.4, 3.0, and 28.4 g/L of isopropanol, 3-HB, and ethanol, respectively, in continuous gas fermentation. Therefore, this work represents remarkable progress in microbial production of bulk chemicals using C1 gases.
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Affiliation(s)
- Dechen Jia
- Key Laboratory of Synthetic Biology, The State Key Laboratory of Plant Carbon-Nitrogen Assimilation, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meiyu He
- Key Laboratory of Synthetic Biology, The State Key Laboratory of Plant Carbon-Nitrogen Assimilation, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yi Tian
- Key Laboratory of Synthetic Biology, The State Key Laboratory of Plant Carbon-Nitrogen Assimilation, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Shaohuang Shen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xianfeng Zhu
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yonghong Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Weihong Jiang
- Key Laboratory of Synthetic Biology, The State Key Laboratory of Plant Carbon-Nitrogen Assimilation, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yang Gu
- Key Laboratory of Synthetic Biology, The State Key Laboratory of Plant Carbon-Nitrogen Assimilation, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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25
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Zhou K, Stephanopoulos G. Harness
Yarrowia lipolytica
to Make Small Molecule Products. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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26
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Lopes M, Miranda SM, Costa AR, Pereira AS, Belo I. Yarrowia lipolytica as a biorefinery platform for effluents and solid wastes valorization - challenges and opportunities. Crit Rev Biotechnol 2021; 42:163-183. [PMID: 34157916 DOI: 10.1080/07388551.2021.1931016] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Due to its physiological and enzymatic features, Yarrowia lipolytica produces several valuable compounds from a wide range of substrates. Appointed by some authors as an industrial workhorse, Y. lipolytica has an extraordinary ability to use unrefined and complex low-cost substrates as carbon and nitrogen sources, aiding to reduce the waste surplus and to produce added-value compounds in a cost-effective way. Dozens of review papers regarding Y. lipolytica have been published till now, proving the interest that this yeast arouses in the scientific community. However, most of them are focused on metabolic pathways involved in substrates assimilation and product formation, or the development of synthetic biology tools in order to obtain engineered strains for biotechnological applications. This paper provides an exhaustive and up-to-date revision on the application of Y. lipolytica to valorize liquid effluents and solid wastes and its role in developing cleaner biotechnological approaches, aiming to boost the circular economy. Firstly, a general overview about Y. lipolytica is introduced, describing its intrinsic features and biotechnological applications. Then, an extensive survey of the literature regarding the assimilation of oily wastes (waste cooking oils, oil cakes and olive mill wastewaters), animal fat wastes, hydrocarbons-rich effluents, crude glycerol and agro-food wastes by Y. lipolytica strains will be discussed. This is the first article that brings together the environmental issue of all such residues and their valorization as feedstock for valuable compounds production by Y. lipolytica. Finally, it will demonstrate the potential of this non-conventional yeast to be used as a biorefinery platform.
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Affiliation(s)
- Marlene Lopes
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Sílvia M Miranda
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Ana R Costa
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Ana S Pereira
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Isabel Belo
- Centre of Biological Engineering, University of Minho, Braga, Portugal
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27
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Poorinmohammad N, Kerkhoven EJ. Systems-level approaches for understanding and engineering of the oleaginous cell factory Yarrowia lipolytica. Biotechnol Bioeng 2021; 118:3640-3654. [PMID: 34129240 DOI: 10.1002/bit.27859] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 03/07/2021] [Accepted: 06/10/2021] [Indexed: 12/12/2022]
Abstract
Concerns about climate change and the search for renewable energy sources together with the goal of attaining sustainable product manufacturing have boosted the use of microbial platforms to produce fuels and high-value chemicals. In this regard, Yarrowia lipolytica has been known as a promising yeast with potentials in diverse array of biotechnological applications such as being a host for different oleochemicals, organic acid, and recombinant protein production. Having a rapidly increasing number of molecular and genetic tools available, Y. lipolytica has been well studied amongst oleaginous yeasts and metabolic engineering has been used to explore its potentials. More recently, with the advancement in systems biotechnology and the implementation of mathematical modeling and high throughput omics data-driven approaches, in-depth understanding of cellular mechanisms of cell factories have been made possible resulting in enhanced rational strain design. In case of Y. lipolytica, these systems-level studies and the related cutting-edge technologies have recently been initiated which is expected to result in enabling the biotechnology sector to rationally engineer Y. lipolytica-based cell factories with favorable production metrics. In this regard, here, we highlight the current status of systems metabolic engineering research and assess the potential of this yeast for future cell factory design development.
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Affiliation(s)
- Naghmeh Poorinmohammad
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Eduard J Kerkhoven
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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28
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Mesquita I, Ferreira C, Moreira D, Kluck GEG, Barbosa AM, Torrado E, Dinis-Oliveira RJ, Gonçalves LG, Beauparlant CJ, Droit A, Berod L, Sparwasser T, Bodhale N, Saha B, Rodrigues F, Cunha C, Carvalho A, Castro AG, Estaquier J, Silvestre R. The Absence of HIF-1α Increases Susceptibility to Leishmania donovani Infection via Activation of BNIP3/mTOR/SREBP-1c Axis. Cell Rep 2021; 30:4052-4064.e7. [PMID: 32209468 DOI: 10.1016/j.celrep.2020.02.098] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 01/14/2020] [Accepted: 02/26/2020] [Indexed: 12/13/2022] Open
Abstract
Hypoxia-inducible factor-1 alpha (HIF-1α) is considered a global regulator of cellular metabolism and innate immune cell functions. Intracellular pathogens such as Leishmania have been reported to manipulate host cell metabolism. Herein, we demonstrate that myeloid cells from myeloid-restricted HIF-1α-deficient mice and individuals with loss-of-function HIF1A gene polymorphisms are more susceptible to L. donovani infection through increased lipogenesis. Absence of HIF-1α leads to a defect in BNIP3 expression, resulting in the activation of mTOR and nuclear translocation of SREBP-1c. We observed the induction of lipogenic gene transcripts, such as FASN, and lipid accumulation in infected HIF-1α-/- macrophages. L. donovani-infected HIF-1α-deficient mice develop hypertriglyceridemia and lipid accumulation in splenic and hepatic myeloid cells. Most importantly, our data demonstrate that manipulating FASN or SREBP-1c using pharmacological inhibitors significantly reduced parasite burden. As such, genetic deficiency of HIF-1α is associated with increased lipid accumulation, which results in impaired host-protective anti-leishmanial functions of myeloid cells.
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Affiliation(s)
- Inês Mesquita
- Microbiology and Infection Research Domain (MIRD), Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Carolina Ferreira
- Microbiology and Infection Research Domain (MIRD), Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Diana Moreira
- Microbiology and Infection Research Domain (MIRD), Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - George Eduardo Gabriel Kluck
- Microbiology and Infection Research Domain (MIRD), Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal; Laboratory of Lipid and Lipoprotein Biochemistry, Medical Biochemistry Institute, Federal University of Rio de Janeiro, 21941-901 Rio de Janeiro, Brazil
| | - Ana Margarida Barbosa
- Microbiology and Infection Research Domain (MIRD), Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Egídio Torrado
- Microbiology and Infection Research Domain (MIRD), Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Ricardo Jorge Dinis-Oliveira
- Department of Public Health and Forensic Sciences, and Medical Education, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; Department of Sciences, IINFACTS-Institute of Research and Advanced Training in Health Sciences and Technologies, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal; UCIBIO-REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Luís Gafeira Gonçalves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Charles-Joly Beauparlant
- Département de Médecine Moléculaire-Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada; Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada
| | - Arnaud Droit
- Département de Médecine Moléculaire-Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada; Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada
| | - Luciana Berod
- Institute of Infection Immunology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Niedersachsen 30625, Germany
| | - Tim Sparwasser
- Department of Medical Microbiology and Hygiene, Medical Center of the Johannes Gutenberg-University of Mainz, Obere Zahlbacherstrasse, 6755131 Mainz, Germany
| | | | - Bhaskar Saha
- National Centre for Cell Science, 411007 Pune, India; Case Western Reserve University, Cleveland, OH 44106, USA; Trident Academy of Creative Technology, 751024 Bhubaneswar, Odisha, India
| | - Fernando Rodrigues
- Microbiology and Infection Research Domain (MIRD), Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Cristina Cunha
- Microbiology and Infection Research Domain (MIRD), Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Agostinho Carvalho
- Microbiology and Infection Research Domain (MIRD), Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - António Gil Castro
- Microbiology and Infection Research Domain (MIRD), Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Jérôme Estaquier
- Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada; INSERM U1124, Université de Paris, 75006 Paris, France.
| | - Ricardo Silvestre
- Microbiology and Infection Research Domain (MIRD), Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal.
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29
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Oleaginous Yeasts as Cell Factories for the Sustainable Production of Microbial Lipids by the Valorization of Agri-Food Wastes. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation7020050] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The agri-food industry annually produces huge amounts of crops residues and wastes, the suitable management of these products is important to increase the sustainability of agro-industrial production by optimizing the entire value chain. This is also in line with the driving principles of the circular economy, according to which residues can become feedstocks for novel processes. Oleaginous yeasts represent a versatile tool to produce biobased chemicals and intermediates. They are flexible microbial factories able to grow on different side-stream carbon sources such as those deriving from agri-food wastes, and this characteristic makes them excellent candidates for integrated biorefinery processes through the production of microbial lipids, known as single cell oils (SCOs), for different applications. This review aims to present an extensive overview of research progress on the production and use of oleaginous yeasts and present discussions on the current bottlenecks and perspectives of their exploitation in different sectors, such as foods, biofuels and fine chemicals.
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30
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Park BG, Kim J, Kim EJ, Kim Y, Kim J, Kim JY, Kim BG. Application of Random Mutagenesis and Synthetic FadR Promoter for de novo Production of ω-Hydroxy Fatty Acid in Yarrowia lipolytica. Front Bioeng Biotechnol 2021; 9:624838. [PMID: 33692989 PMCID: PMC7937803 DOI: 10.3389/fbioe.2021.624838] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 01/12/2021] [Indexed: 11/19/2022] Open
Abstract
As a means to develop oleaginous biorefinery, Yarrowia lipolytica was utilized to produce ω-hydroxy palmitic acid from glucose using evolutionary metabolic engineering and synthetic FadR promoters for cytochrome P450 (CYP) expression. First, a base strain was constructed to produce free fatty acids (FFAs) from glucose using metabolic engineering strategies. Subsequently, through ethyl methanesulfonate (EMS)-induced random mutagenesis and fluorescence-activated cell sorting (FACS) screening, improved FFA overproducers were screened. Additionally, synthetic promoters containing bacterial FadR binding sequences for CYP expression were designed to respond to the surge of the concentration of FFAs to activate the ω-hydroxylating pathway, resulting in increased transcriptional activity by 14 times from the third day of culture compared to the first day. Then, endogenous alk5 was screened and expressed using the synthetic FadR promoter in the developed strain for the production of ω-hydroxy palmitic acid. By implementing the synthetic FadR promoter, cell growth and production phases could be efficiently decoupled. Finally, in batch fermentation, we demonstrated de novo production of 160 mg/L of ω-hydroxy palmitic acid using FmeN3-TR1-alk5 in nitrogen-limited media. This study presents an excellent example of the production of ω-hydroxy fatty acids using synthetic promoters with bacterial transcriptional regulator (i.e., FadR) binding sequences in oleaginous yeasts.
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Affiliation(s)
- Beom Gi Park
- School of Chemical and Biological Engineering, Seoul National University, Seoul, South Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Junyeob Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul, South Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Eun-Jung Kim
- Bio-MAX/N-Bio, Seoul National University, Seoul, South Korea
| | - Yechan Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul, South Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Joonwon Kim
- Department of Chemical Engineering, Soongsil University, Seoul, South Korea
| | - Jin Young Kim
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea.,Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul, South Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea.,Bio-MAX/N-Bio, Seoul National University, Seoul, South Korea.,Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea
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31
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Konzock O, Zaghen S, Norbeck J. Tolerance of Yarrowia lipolytica to inhibitors commonly found in lignocellulosic hydrolysates. BMC Microbiol 2021; 21:77. [PMID: 33685391 PMCID: PMC7938539 DOI: 10.1186/s12866-021-02126-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/15/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Lignocellulosic material is a suitable renewable carbon and energy source for microbial cell factories, such as Yarrowia lipolytica. To be accessible for microorganisms, the constituent sugars need to be released in a hydrolysis step, which as a side effect leads to the formation of various inhibitory compounds. However, the effects of these inhibitory compounds on the growth of Y. lipolytica have not been thoroughly investigated. RESULTS Here we show the individual and combined effect of six inhibitors from three major inhibitor groups on the growth of Y. lipolytica. We engineered a xylose consuming strain by overexpressing the three native genes XR, XDH, and XK and found that the inhibitor tolerance of Y. lipolytica is similar in glucose and in xylose. Aromatic compounds could be tolerated at high concentrations, while furfural linearly increased the lag phase of the cultivation, and hydroxymethylfurfural only inhibited growth partially. The furfural induced increase in lag phase can be overcome by an increased volume of inoculum. Formic acid only affected growth at concentrations above 25 mM. In a synthetic hydrolysate, formic acid, furfural, and coniferyl aldehyde were identified as the major growth inhibitors. CONCLUSION We showed the individual and combined effect of inhibitors found in hydrolysate on the growth of Y. lipolytica. Our study improves understanding of the growth limiting inhibitors found in hydrolysate and enables a more targeted engineering approach to increase the inhibitor tolerance of Y. lipolytica. This will help to improve the usage of Y. lipolytica as a sustainable microbial cell factory.
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Affiliation(s)
- Oliver Konzock
- Department of Biology and Biological Engineering, division of Systems and Synthetic Biology, Chalmers University of Technology, Göteborg, Sweden
| | - Simone Zaghen
- Department of Biology and Biological Engineering, division of Systems and Synthetic Biology, Chalmers University of Technology, Göteborg, Sweden
| | - Joakim Norbeck
- Department of Biology and Biological Engineering, division of Systems and Synthetic Biology, Chalmers University of Technology, Göteborg, Sweden.
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Factors affecting microbial lipids production by Yarrowia lipolytica strains from volatile fatty acids: Effect of co-substrates, operation mode and oxygen. J Biotechnol 2021; 331:37-47. [PMID: 33652072 DOI: 10.1016/j.jbiotec.2021.02.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/05/2021] [Accepted: 02/22/2021] [Indexed: 11/23/2022]
Abstract
Volatile fatty acids (VFAs), which can be generated by acidogenesis of organic wastes, are important building blocks for chemicals production, and are intermediates in many bioprocesses such as microbial lipids production. Important factors affecting the bioconversion of VFAs (acetate, propionate and butyrate) by Yarrowia lipolytica W29 and NCYC 2904 for growth and lipids accumulation were studied. Yarrowia lipolytica grew efficiently in VFAs-based media, but lipids production was enhanced by the addition of co-substrates (glucose or glycerol) in batch cultures. A two-stage batch culture - growth phase on glucose, followed by VFAs addition, improved lipids accumulation. Lipids concentrations of 2.3 g·L-1 and 3.5 g·L-1 were obtained with this mode of operation, with addition of 18 g·L-1 VFAs, for Y. lipolytica W29 and NCYC 2904, respectively. For the first time, it was demonstrated that oxygen mass transfer is a crucial factor for lipids production by Y. lipolytica from VFAs. Intracellular lipids produced by Y. lipolytica strains were mainly composed by oleic and linoleic acids, similar to common vegetable oils, making these lipids suitable for biodiesel production. Moreover, margaric acid, which may improve biodiesel properties, was only detected in propionate medium. The strategies studied herein will contribute to the feasibility of using VFAs as low-cost feedstock for microbial lipids production by Y. lipolytica strains.
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Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus. mSystems 2021; 6:6/1/e00002-21. [PMID: 33594000 PMCID: PMC8561657 DOI: 10.1128/msystems.00002-21] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Anaerobic gut fungi in the phylum Neocallimastigomycota typically inhabit the digestive tracts of large mammalian herbivores, where they play an integral role in the decomposition of raw lignocellulose into its constitutive sugar monomers. However, quantitative tools to study their physiology are lacking, partially due to their complex and unresolved metabolism that includes the largely uncharacterized fungal hydrogenosome. Modern omics approaches combined with metabolic modeling can be used to establish an understanding of gut fungal metabolism and develop targeted engineering strategies to harness their degradation capabilities for lignocellulosic bioprocessing. Here, we introduce a high-quality genome of the anaerobic fungus Neocallimastix lanati from which we constructed the first genome-scale metabolic model of an anaerobic fungus. Relative to its size (200 Mbp, sequenced at 62× depth), it is the least fragmented publicly available gut fungal genome to date. Of the 1,788 lignocellulolytic enzymes annotated in the genome, 585 are associated with the fungal cellulosome, underscoring the powerful lignocellulolytic potential of N. lanati. The genome-scale metabolic model captures the primary metabolism of N. lanati and accurately predicts experimentally validated substrate utilization requirements. Additionally, metabolic flux predictions are verified by 13C metabolic flux analysis, demonstrating that the model faithfully describes the underlying fungal metabolism. Furthermore, the model clarifies key aspects of the hydrogenosomal metabolism and can be used as a platform to quantitatively study these biotechnologically important yet poorly understood early-branching fungi. IMPORTANCE Recent genomic analyses have revealed that anaerobic gut fungi possess both the largest number and highest diversity of lignocellulolytic enzymes of all sequenced fungi, explaining their ability to decompose lignocellulosic substrates, e.g., agricultural waste, into fermentable sugars. Despite their potential, the development of engineering methods for these organisms has been slow due to their complex life cycle, understudied metabolism, and challenging anaerobic culture requirements. Currently, there is no framework that can be used to combine multi-omic data sets to understand their physiology. Here, we introduce a high-quality PacBio-sequenced genome of the anaerobic gut fungus Neocallimastix lanati. Beyond identifying a trove of lignocellulolytic enzymes, we use this genome to construct the first genome-scale metabolic model of an anaerobic gut fungus. The model is experimentally validated and sheds light on unresolved metabolic features common to gut fungi. Model-guided analysis will pave the way for deepening our understanding of anaerobic gut fungi and provides a systematic framework to guide strain engineering efforts of these organisms for biotechnological use.
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Patra P, Das M, Kundu P, Ghosh A. Recent advances in systems and synthetic biology approaches for developing novel cell-factories in non-conventional yeasts. Biotechnol Adv 2021; 47:107695. [PMID: 33465474 DOI: 10.1016/j.biotechadv.2021.107695] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 12/14/2020] [Accepted: 01/09/2021] [Indexed: 12/14/2022]
Abstract
Microbial bioproduction of chemicals, proteins, and primary metabolites from cheap carbon sources is currently an advancing area in industrial research. The model yeast, Saccharomyces cerevisiae, is a well-established biorefinery host that has been used extensively for commercial manufacturing of bioethanol from myriad carbon sources. However, its Crabtree-positive nature often limits the use of this organism for the biosynthesis of commercial molecules that do not belong in the fermentative pathway. To avoid extensive strain engineering of S. cerevisiae for the production of metabolites other than ethanol, non-conventional yeasts can be selected as hosts based on their natural capacity to produce desired commodity chemicals. Non-conventional yeasts like Kluyveromyces marxianus, K. lactis, Yarrowia lipolytica, Pichia pastoris, Scheffersomyces stipitis, Hansenula polymorpha, and Rhodotorula toruloides have been considered as potential industrial eukaryotic hosts owing to their desirable phenotypes such as thermotolerance, assimilation of a wide range of carbon sources, as well as ability to secrete high titers of protein and lipid. However, the advanced metabolic engineering efforts in these organisms are still lacking due to the limited availability of systems and synthetic biology methods like in silico models, well-characterised genetic parts, and optimized genome engineering tools. This review provides an insight into the recent advances and challenges of systems and synthetic biology as well as metabolic engineering endeavours towards the commercial usage of non-conventional yeasts. Particularly, the approaches in emerging non-conventional yeasts for the production of enzymes, therapeutic proteins, lipids, and metabolites for commercial applications are extensively discussed here. Various attempts to address current limitations in designing novel cell factories have been highlighted that include the advances in the fields of genome-scale metabolic model reconstruction, flux balance analysis, 'omics'-data integration into models, genome-editing toolkit development, and rewiring of cellular metabolisms for desired chemical production. Additionally, the understanding of metabolic networks using 13C-labelling experiments as well as the utilization of metabolomics in deciphering intracellular fluxes and reactions have also been discussed here. Application of cutting-edge nuclease-based genome editing platforms like CRISPR/Cas9, and its optimization towards efficient strain engineering in non-conventional yeasts have also been described. Additionally, the impact of the advances in promising non-conventional yeasts for efficient commercial molecule synthesis has been meticulously reviewed. In the future, a cohesive approach involving systems and synthetic biology will help in widening the horizon of the use of unexplored non-conventional yeast species towards industrial biotechnology.
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Affiliation(s)
- Pradipta Patra
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Manali Das
- School of Bioscience, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Pritam Kundu
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Amit Ghosh
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India; P.K. Sinha Centre for Bioenergy and Renewables, Indian Institute of Technology Kharagpur, West Bengal 721302, India.
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Synthesis of high-titer alka(e)nes in Yarrowia lipolytica is enabled by a discovered mechanism. Nat Commun 2020; 11:6198. [PMID: 33273473 PMCID: PMC7713262 DOI: 10.1038/s41467-020-19995-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/08/2020] [Indexed: 12/12/2022] Open
Abstract
Alka(e)nes are ideal fuel components for aviation, long-distance transport, and shipping. They are typically derived from fossil fuels and accounting for 24% of difficult-to-eliminate greenhouse gas emissions. The synthesis of alka(e)nes in Yarrowia lipolytica from CO2-neutral feedstocks represents an attractive alternative. Here we report that the high-titer synthesis of alka(e)nes in Yarrowia lipolytica harboring a fatty acid photodecarboxylase (CvFAP) is enabled by a discovered pathway. We find that acyl-CoAs, rather than free fatty acids (FFAs), are the preferred substrate for CvFAP. This finding allows us to debottleneck the pathway and optimize fermentation conditions so that we are able to redirect 89% of acyl-CoAs from the synthesis of neutral lipids to alka(e)nes and reach titers of 1.47 g/L from glucose. Two other CO2-derived substrates, wheat straw and acetate, are also demonstrated to be effective in producing alka(e)nes. Overall, our technology could advance net-zero emissions by providing CO2-neutral and energy-dense liquid biofuels. Alka(e)nes with chain lengths in C5-C23 range are ideal fuel components. Here, the authors report that high-titer production of alak(e)nes in pathway engineered Yarrowia lipolytica, which is enabled by the finding that acyl-CoA is another substrate of fatty acid photodecarboxylase (FAP).
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Kutscha R, Pflügl S. Microbial Upgrading of Acetate into Value-Added Products-Examining Microbial Diversity, Bioenergetic Constraints and Metabolic Engineering Approaches. Int J Mol Sci 2020; 21:ijms21228777. [PMID: 33233586 PMCID: PMC7699770 DOI: 10.3390/ijms21228777] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 10/29/2020] [Accepted: 11/18/2020] [Indexed: 01/20/2023] Open
Abstract
Ecological concerns have recently led to the increasing trend to upgrade carbon contained in waste streams into valuable chemicals. One of these components is acetate. Its microbial upgrading is possible in various species, with Escherichia coli being the best-studied. Several chemicals derived from acetate have already been successfully produced in E. coli on a laboratory scale, including acetone, itaconic acid, mevalonate, and tyrosine. As acetate is a carbon source with a low energy content compared to glucose or glycerol, energy- and redox-balancing plays an important role in acetate-based growth and production. In addition to the energetic challenges, acetate has an inhibitory effect on microorganisms, reducing growth rates, and limiting product concentrations. Moreover, extensive metabolic engineering is necessary to obtain a broad range of acetate-based products. In this review, we illustrate some of the necessary energetic considerations to establish robust production processes by presenting calculations of maximum theoretical product and carbon yields. Moreover, different strategies to deal with energetic and metabolic challenges are presented. Finally, we summarize ways to alleviate acetate toxicity and give an overview of process engineering measures that enable sustainable acetate-based production of value-added chemicals.
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Antoniewicz MR. A guide to metabolic flux analysis in metabolic engineering: Methods, tools and applications. Metab Eng 2020; 63:2-12. [PMID: 33157225 DOI: 10.1016/j.ymben.2020.11.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 10/28/2020] [Accepted: 11/01/2020] [Indexed: 12/22/2022]
Abstract
The field of metabolic engineering is primarily concerned with improving the biological production of value-added chemicals, fuels and pharmaceuticals through the design, construction and optimization of metabolic pathways, redirection of intracellular fluxes, and refinement of cellular properties relevant for industrial bioprocess implementation. Metabolic network models and metabolic fluxes are central concepts in metabolic engineering, as was emphasized in the first paper published in this journal, "Metabolic fluxes and metabolic engineering" (Metabolic Engineering, 1: 1-11, 1999). In the past two decades, a wide range of computational, analytical and experimental approaches have been developed to interrogate the capabilities of biological systems through analysis of metabolic network models using techniques such as flux balance analysis (FBA), and quantify metabolic fluxes using constrained-based modeling approaches such as metabolic flux analysis (MFA) and more advanced experimental techniques based on the use of stable-isotope tracers, i.e. 13C-metabolic flux analysis (13C-MFA). In this review, we describe the basic principles of metabolic flux analysis, discuss current best practices in flux quantification, highlight potential pitfalls and alternative approaches in the application of these tools, and give a broad overview of pragmatic applications of flux analysis in metabolic engineering practice.
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Affiliation(s)
- Maciek R Antoniewicz
- Department of Chemical Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Michigan, Ann Arbor, MI, 48109, USA.
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Luo Z, Liu N, Lazar Z, Chatzivasileiou A, Ward V, Chen J, Zhou J, Stephanopoulos G. Enhancing isoprenoid synthesis in Yarrowia lipolytica by expressing the isopentenol utilization pathway and modulating intracellular hydrophobicity. Metab Eng 2020; 61:344-351. [DOI: 10.1016/j.ymben.2020.07.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/17/2020] [Accepted: 07/28/2020] [Indexed: 10/23/2022]
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Qian X, Xu N, Jing Y, Song M, Zhou J, Dong W, Xin F, Zhang W, Jiang M, Ochsenreither K. Valorization of Crude Glycerol into Citric Acid and Malic Acid by Yarrowia lipolytica. Ind Eng Chem Res 2020. [DOI: 10.1021/acs.iecr.0c01723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Xiujuan Qian
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P. R. China
| | - Ning Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P. R. China
| | - Yiwen Jing
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P. R. China
| | - Meng Song
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P. R. China
| | - Jie Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P. R. China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P. R. China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, P. R. China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P. R. China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, P. R. China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P. R. China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, P. R. China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P. R. China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, P. R. China
| | - Katrin Ochsenreither
- Institute of Process Engineering in Life Sciences, Section II: Technical Biology, Karlsruhe Institute of Technology, Fritz-Haber-Weg4, Karlsruhe 76131, Germany
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40
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Biological insights into non-model microbial hosts through stable-isotope metabolic flux analysis. Curr Opin Biotechnol 2020; 64:32-38. [DOI: 10.1016/j.copbio.2019.09.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 12/16/2022]
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Synthetic biology, systems biology, and metabolic engineering of Yarrowia lipolytica toward a sustainable biorefinery platform. J Ind Microbiol Biotechnol 2020; 47:845-862. [PMID: 32623653 DOI: 10.1007/s10295-020-02290-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/25/2020] [Indexed: 01/24/2023]
Abstract
Yarrowia lipolytica is an oleaginous yeast that has been substantially engineered for production of oleochemicals and drop-in transportation fuels. The unique acetyl-CoA/malonyl-CoA supply mode along with the versatile carbon-utilization pathways makes this yeast a superior host to upgrade low-value carbons into high-value secondary metabolites and fatty acid-based chemicals. The expanded synthetic biology toolkits enabled us to explore a large portfolio of specialized metabolism beyond fatty acids and lipid-based chemicals. In this review, we will summarize the recent advances in genetic, omics, and computational tool development that enables us to streamline the genetic or genomic modification for Y. lipolytica. We will also summarize various metabolic engineering strategies to harness the endogenous acetyl-CoA/malonyl-CoA/HMG-CoA pathway for production of complex oleochemicals, polyols, terpenes, polyketides, and commodity chemicals. We envision that Y. lipolytica will be an excellent microbial chassis to expand nature's biosynthetic capacity to produce plant secondary metabolites, industrially relevant oleochemicals, agrochemicals, commodity, and specialty chemicals and empower us to build a sustainable biorefinery platform that contributes to the prosperity of a bio-based economy in the future.
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Zhang Z, Liu Z, Meng Y, Chen Z, Han J, Wei Y, Shen T, Yi Y, Xie X. Parallel isotope differential modeling for instationary 13C fluxomics at the genome scale. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:103. [PMID: 32523616 PMCID: PMC7278083 DOI: 10.1186/s13068-020-01737-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 05/22/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND A precise map of the metabolic fluxome, the closest surrogate to the physiological phenotype, is becoming progressively more important in the metabolic engineering of photosynthetic organisms for biofuel and biomass production. For photosynthetic organisms, the state-of-the-art method for this purpose is instationary 13C fluxomics, which has arisen as a sibling of transcriptomics or proteomics. Instationary 13C data processing requires solving high-dimensional nonlinear differential equations and leads to large computational and time costs when its scope is expanded to a genome-scale metabolic network. RESULT Here, we present a parallelized method to model instationary 13C labeling data. The elementary metabolite unit (EMU) framework is reorganized to allow treating individual mass isotopomers and breaking up of their networks into strongly connected components (SCCs). A variable domain parallel algorithm is introduced to process ordinary differential equations in a parallel way. 15-fold acceleration is achieved for constant-step-size modeling and ~ fivefold acceleration for adaptive-step-size modeling. CONCLUSION This algorithm is universally applicable to isotope granules such as EMUs and cumomers and can substantially accelerate instationary 13C fluxomics modeling. It thus has great potential to be widely adopted in any instationary 13C fluxomics modeling.
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Affiliation(s)
- Zhengdong Zhang
- College of Mathematics and Information Science, Guiyang University, Guiyang, Guizhou China
- Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou China
| | - Zhentao Liu
- College of Computer Science and Technology, Guizhou University, Guiyang, Guizhou China
| | - Yafei Meng
- College of Mathematics and Information Science, Guiyang University, Guiyang, Guizhou China
| | - Zhen Chen
- School of Mathematics and Sciences, Guizhou Normal University, Guiyang, Guizhou China
| | - Jiayu Han
- School of Mathematics and Sciences, Guizhou Normal University, Guiyang, Guizhou China
| | - Yimin Wei
- School of Mathematics Sciences and Key Laboratory of Mathematics for Nonlinear Sciences, Fudan University, Shanghai, China
| | - Tie Shen
- Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou China
| | - Yin Yi
- College of Life Science, Guizhou Normal University, Guiyang, Guizhou China
| | - Xiaoyao Xie
- Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou China
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Wada K, Koike H, Fujii T, Morita T. Targeted transcriptomic study of the implication of central metabolic pathways in mannosylerythritol lipids biosynthesis in Pseudozyma antarctica T-34. PLoS One 2020; 15:e0227295. [PMID: 31923270 PMCID: PMC6953796 DOI: 10.1371/journal.pone.0227295] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 12/16/2019] [Indexed: 11/19/2022] Open
Abstract
Pseudozyma antarctica is a nonpathogenic phyllosphere yeast known as an excellent producer of industrial lipases and mannosylerythritol lipids (MELs), which are multi-functional glycolipids. The fungus produces a much higher amount of MELs from vegetable oil than from glucose, whereas its close relative, Ustilago maydis UM521, produces a lower amount of MELs from vegetable oil. In the present study, we used previous gene expression profiles measured by DNA microarray analyses after culturing on two carbon sources, glucose and soybean oil, to further characterize MEL biosynthesis in P. antarctica T-34. A total of 264 genes were found with induction ratios and expression intensities under oily conditions with similar tendencies to those of MEL cluster genes. Of these, 93 were categorized as metabolic genes using the Eukaryotic Orthologous Groups classification. Within this metabolic category, amino acids, carbohydrates, inorganic ions, and secondary metabolite metabolism, as well as energy production and conversion, but not lipid metabolism, were enriched. Furthermore, genes involved in central metabolic pathways, such as glycolysis and the tricarboxylic acid cycle, were highly induced in P. antarctica T-34 under oily conditions, whereas they were suppressed in U. maydis UM521. These results suggest that the central metabolism of P. antarctica T-34 under oily conditions contributes to its excellent oil utilization and extracellular glycolipid production.
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Affiliation(s)
- Keisuke Wada
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
| | - Hideaki Koike
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Higashi, Tsukuba, Ibaraki, Japan
| | - Tatsuya Fujii
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
| | - Tomotake Morita
- Research Institute for Innovation in Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Higashi, Tsukuba, Ibaraki, Japan
- * E-mail:
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Park JO, Liu N, Holinski KM, Emerson DF, Qiao K, Woolston BM, Xu J, Lazar Z, Islam MA, Vidoudez C, Girguis PR, Stephanopoulos G. Synergistic substrate cofeeding stimulates reductive metabolism. Nat Metab 2019; 1:643-651. [PMID: 32694804 DOI: 10.1038/s42255-019-0077-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 05/13/2019] [Indexed: 11/09/2022]
Abstract
Advanced bioproduct synthesis via reductive metabolism requires coordinating carbons, ATP and reducing agents, which are generated with varying efficiencies depending on metabolic pathways. Substrate mixtures with direct access to multiple pathways may optimally satisfy these biosynthetic requirements. However, native regulation favouring preferential use precludes cells from co-metabolizing multiple substrates. Here we explore mixed substrate metabolism and tailor pathway usage to synergistically stimulate carbon reduction. By controlled cofeeding of superior ATP and NADPH generators as 'dopant' substrates to cells primarily using inferior substrates, we circumvent catabolite repression and drive synergy in two divergent organisms. Glucose doping in Moorella thermoacetica stimulates CO2 reduction (2.3 g gCDW-1 h-1) into acetate by augmenting ATP synthesis via pyruvate kinase. Gluconate doping in Yarrowia lipolytica accelerates acetate-driven lipogenesis (0.046 g gCDW-1 h-1) by obligatory NADPH synthesis through the pentose cycle. Together, synergistic cofeeding produces CO2-derived lipids with 38% energy yield and demonstrates the potential to convert CO2 into advanced bioproducts. This work advances the systems-level control of metabolic networks and CO2 use, the most pressing and difficult reduction challenge.
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Affiliation(s)
- Junyoung O Park
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Nian Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kara M Holinski
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David F Emerson
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kangjian Qiao
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Benjamin M Woolston
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jingyang Xu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, Zhejiang Police College, Hangzhou, China
| | - Zbigniew Lazar
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, Monskiego, Wroclaw, Poland
| | - M Ahsanul Islam
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Loughborough University, Loughborough, UK
| | - Charles Vidoudez
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Oleaginous yeast for biofuel and oleochemical production. Curr Opin Biotechnol 2019; 57:73-81. [DOI: 10.1016/j.copbio.2019.02.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/27/2019] [Accepted: 02/05/2019] [Indexed: 01/01/2023]
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46
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Understanding lipogenesis by dynamically profiling transcriptional activity of lipogenic promoters in Yarrowia lipolytica. Appl Microbiol Biotechnol 2019; 103:3167-3179. [PMID: 30734122 DOI: 10.1007/s00253-019-09664-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/07/2019] [Accepted: 01/22/2019] [Indexed: 10/27/2022]
Abstract
Lipogenesis is a complicated process involving global transcriptional reprogramming of lipogenic pathways. It is commonly believed that nitrogen starvation triggers a metabolic shift that reroutes carbon flux from Krebs cycles to lipogenesis. In this study, we systematically surveyed and dynamically profiled the transcriptional activity of 22 lipogenic promoters aiming to delineate a picture how nitrogen starvation regulates lipogenesis in Y. lipolytica. These lipogenic promoters drive the expression of critical pathways that are responsible for the generation of reducing equivalents (NADPH), carbon backbones (acetyl-CoA, malonyl-CoA, DHAP, etc.), synthesis and degradation of fatty acids. Specifically, our investigated promoters span across an array of metabolic pathways, including glycolysis, Krebs cycle, pentose phosphate pathway, mannitol cycle, glutamine-GABA cycle, fatty acid and lipid synthesis, glyoxylate, β-oxidation, and POM (pyruvate-oxaloacetate-malate) cycle. Our work provides evidences that mannitol cycle, glutamine-GABA cycle and amino acid degradation, pyruvate oxidation, and acetate assimilation pathways are lipogenesis-related steps involved in generating cytosolic NADPH and acetyl-CoA precursors. This systematic investigation and dynamic profiling of lipogenic promoters may help us better understand lipogenesis, facilitate the formulation of structure-based kinetic models, as well as develop efficient cell factories for fuels and chemical production in oleaginous species.
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Yao R, Li J, Feng L, Zhang X, Hu H. 13C metabolic flux analysis-guided metabolic engineering of Escherichia coli for improved acetol production from glycerol. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:29. [PMID: 30805028 PMCID: PMC6373095 DOI: 10.1186/s13068-019-1372-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 02/06/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND Bioprocessing offers a sustainable and green approach to manufacture various chemicals and materials. Development of bioprocesses requires transforming common producer strains to cell factories. 13C metabolic flux analysis (13C-MFA) can be applied to identify relevant targets to accomplish the desired phenotype, which has become one of the major tools to support systems metabolic engineering. In this research, we applied 13C-MFA to identify bottlenecks in the bioconversion of glycerol into acetol by Escherichia coli. Valorization of glycerol, the main by-product of biodiesel, has contributed to the viability of biofuel economy. RESULTS We performed 13C-MFA and measured intracellular pyridine nucleotide pools in a first-generation acetol producer strain (HJ06) and a non-producer strain (HJ06C), and identified that engineering the NADPH regeneration is a promising target. Based on this finding, we overexpressed nadK encoding NAD kinase or pntAB encoding membrane-bound transhydrogenase either individually or in combination with HJ06, obtaining HJ06N, HJ06P and HJ06PN. The step-wise approach resulted in increasing the acetol titer from 0.91 g/L (HJ06) to 2.81 g/L (HJ06PN). To systematically characterize and the effect of mutation(s) on the metabolism, we also examined the metabolomics and transcriptional levels of key genes in four strains. The pool sizes of NADPH, NADP+ and the NADPH/NADP+ ratio were progressively increased from HJ06 to HJ06PN, demonstrating that the sufficient NADPH supply is critical for acetol production. Flux distribution was optimized towards acetol formation from HJ06 to HJ06PN: (1) The carbon partitioning at the DHAP node directed gradually more carbon from the lower glycolytic pathway through the acetol biosynthetic pathway; (2) The transhydrogenation flux was constantly increased. In addition, 13C-MFA showed the rigidity of upper glycolytic pathway, PP pathway and the TCA cycle to support growth. The flux patterns were supported by most metabolomics data and gene expression profiles. CONCLUSIONS This research demonstrated how 13C-MFA can be applied to drive the cycles of design, build, test and learn implementation for strain development. This succeeding engineering strategy can also be applicable for rational design of other microbial cell factories.
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Affiliation(s)
- Ruilian Yao
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China
| | - Jiawei Li
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China
| | - Lei Feng
- Instrumental Analysis Center, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China
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Abdel-Mawgoud AM, Markham KA, Palmer CM, Liu N, Stephanopoulos G, Alper HS. Metabolic engineering in the host Yarrowia lipolytica. Metab Eng 2018; 50:192-208. [PMID: 30056205 DOI: 10.1016/j.ymben.2018.07.016] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 12/21/2022]
Abstract
The nonconventional, oleaginous yeast, Yarrowia lipolytica is rapidly emerging as a valuable host for the production of a variety of both lipid and nonlipid chemical products. While the unique genetics of this organism pose some challenges, many new metabolic engineering tools have emerged to facilitate improved genetic manipulation in this host. This review establishes a case for Y. lipolytica as a premier metabolic engineering host based on innate metabolic capacity, emerging synthetic tools, and engineering examples. The metabolism underlying the lipid accumulation phenotype of this yeast as well as high flux through acyl-CoA precursors and the TCA cycle provide a favorable metabolic environment for expression of relevant heterologous pathways. These properties allow Y. lipolytica to be successfully engineered for the production of both native and nonnative lipid, organic acid, sugar and acetyl-CoA derived products. Finally, this host has unique metabolic pathways enabling growth on a wide range of carbon sources, including waste products. The expansion of carbon sources, together with the improvement of tools as highlighted here, have allowed this nonconventional organism to act as a cellular factory for valuable chemicals and fuels.
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Affiliation(s)
- Ahmad M Abdel-Mawgoud
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Kelly A Markham
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, United States
| | - Claire M Palmer
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, United States
| | - Nian Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States.
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, United States; Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, United States.
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Holistic Approaches in Lipid Production by Yarrowia lipolytica. Trends Biotechnol 2018; 36:1157-1170. [PMID: 30006239 DOI: 10.1016/j.tibtech.2018.06.007] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/11/2018] [Accepted: 06/18/2018] [Indexed: 01/01/2023]
Abstract
Concerns about climate change have driven research on the production of lipid-derived biofuels as an alternative and renewable liquid fuel source. Using oleaginous yeasts for lipid synthesis creates the potential for cost-effective industrial-scale operations due to their ability to reach high lipid titer, yield, and productivity resulting from their unique metabolism. Yarrowia lipolytica is the model oleaginous yeast, with the best-studied lipid metabolism, the greatest number of genetic tools, and a fully sequenced genome. In this review we highlight multiomics studies that elucidate the mechanisms allowing this yeast to achieve lipid overaccumulation and then present several major metabolic engineering efforts that enhanced the production metrics in Y. lipolytica. Recent achievements that applied novel engineering strategies are emphasized.
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Spagnuolo M, Shabbir Hussain M, Gambill L, Blenner M. Alternative Substrate Metabolism in Yarrowia lipolytica. Front Microbiol 2018; 9:1077. [PMID: 29887845 PMCID: PMC5980982 DOI: 10.3389/fmicb.2018.01077] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 05/07/2018] [Indexed: 11/13/2022] Open
Abstract
Recent advances in genetic engineering capabilities have enabled the development of oleochemical producing strains of Yarrowia lipolytica. Much of the metabolic engineering effort has focused on pathway engineering of the product using glucose as the feedstock; however, alternative substrates, including various other hexose and pentose sugars, glycerol, lipids, acetate, and less-refined carbon feedstocks, have not received the same attention. In this review, we discuss recent work leading to better utilization of alternative substrates. This review aims to provide a comprehensive understanding of the current state of knowledge for alternative substrate utilization, suggest potential pathways identified through homology in the absence of prior characterization, discuss recent work that either identifies, endogenous or cryptic metabolism, and describe metabolic engineering to improve alternative substrate utilization. Finally, we describe the critical questions and challenges that remain for engineering Y. lipolytica for better alternative substrate utilization.
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Affiliation(s)
- Michael Spagnuolo
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, United States
| | - Murtaza Shabbir Hussain
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, United States
| | - Lauren Gambill
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, United States
- Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, United States
| | - Mark Blenner
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, United States
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