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Ramesh A, Lee S, Wheeldon I. Genome Editing, Transcriptional Regulation, and Forward Genetic Screening Using CRISPR-Cas12a Systems in Yarrowia lipolytica. Methods Mol Biol 2024; 2760:169-198. [PMID: 38468089 DOI: 10.1007/978-1-0716-3658-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Class II Type V endonucleases have increasingly been adapted to develop sophisticated and easily accessible synthetic biology tools for genome editing, transcriptional regulation, and functional genomic screening in a wide range of organisms. One such endonuclease, Cas12a, presents itself as an attractive alternative to Cas9-based systems. The ability to mature its own guide RNAs (gRNAs) from a single transcript has been leveraged for easy multiplexing, and its lack of requirement of a tracrRNA element, also allows for short gRNA expression cassettes. To extend these functionalities into the industrially relevant oleaginous yeast Yarrowia lipolytica, we developed a set of CRISPR-Cas12a vectors for easy multiplexed gene knockout, repression, and activation. We further extended the utility of this CRISPR-Cas12a system to functional genomic screening by constructing a genome-wide guide library targeting every gene with an eightfold coverage. Pooled CRISPR screens conducted with this library were used to profile Cas12a guide activities and develop a machine learning algorithm that could accurately predict highly efficient Cas12a gRNA. In this protocols chapter, we first present a method by which protein coding genes may be functionally disrupted via indel formation with CRISPR-Cas12a systems. Further, we describe how Cas12a fused to a transcriptional regulator can be used in conjunction with shortened gRNA to achieve transcriptional repression or activation. Finally, we describe the design, cloning, and validation of a genome-wide library as well as a protocol for the execution of a pooled CRISPR screen, to determine guide activity profiles in a genome-wide context in Y. lipolytica. The tools and strategies discussed here expand the list of available synthetic biology tools for facile genome engineering in this industrially important host.
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Affiliation(s)
- Adithya Ramesh
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - Sangcheon Lee
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
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2
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Abstract
Our current food system relies on unsustainable practices, which often fail to provide healthy diets to a growing population. Therefore, there is an urgent demand for new sustainable nutrition sources and processes. Microorganisms have gained attention as a new food source solution, due to their low carbon footprint, low reliance on land, water and seasonal variations coupled with a favourable nutritional profile. Furthermore, with the emergence and use of new tools, specifically in synthetic biology, the uses of microorganisms have expanded showing great potential to fulfil many of our dietary needs. In this review, we look at the different applications of microorganisms in food, and examine the history, state-of-the-art and potential to disrupt current foods systems. We cover both the use of microbes to produce whole foods out of their biomass and as cell factories to make highly functional and nutritional ingredients. The technical, economical, and societal limitations are also discussed together with the current and future perspectives.
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Affiliation(s)
- Alicia E Graham
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.
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Hambalko J, Gajdoš P, Nicaud JM, Ledesma-Amaro R, Tupec M, Pichová I, Čertík M. Biosynthesis of Fatty Acid Derivatives by Recombinant Yarrowia lipolytica Containing MsexD2 and MsexD3 Desaturase Genes from Manduca sexta. J Fungi (Basel) 2023; 9:jof9010114. [PMID: 36675935 PMCID: PMC9862095 DOI: 10.3390/jof9010114] [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: 12/19/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
One of the most interesting groups of fatty acid derivates is the group of conjugated fatty acids from which the most researched include: conjugated linoleic acid (CLA) and conjugated linolenic acid (CLNA), which are associated with countless health benefits. Sex pheromone mixtures of some insect species, including tobacco horn-worm (Manduca sexta), are typical for the production of uncommon C16 long conjugated fatty acids with two and three conjugated double bonds, as opposed to C18 long CLA and CLNA. In this study, M. sexta desaturases MsexD2 and MsexD3 were expressed in multiple strains of Y. lipolytica with different genotypes. Experiments with the supplementation of fatty acid methyl esters into the medium resulted in the production of novel fatty acids. Using GCxGC-MS, 20 new fatty acids with two or three double bonds were identified. Fatty acids with conjugated or isolated double bonds, or a combination of both, were produced in trace amounts. The results of this study prove that Y. lipolytica is capable of synthesizing C16-conjugated fatty acids. Further genetic optimization of the Y. lipolytica genome and optimization of the fermentation process could lead to increased production of novel fatty acid derivatives with biotechnologically interesting properties.
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Affiliation(s)
- Jaroslav Hambalko
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia
| | - Peter Gajdoš
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia
| | - Jean-Marc Nicaud
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Domaine de Vilvert, 78352 Jouy-en-Josas, France
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Faculty of Engineering, Imperial College, London SW7 2AZ, UK
| | - Michal Tupec
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 542/2, 160 00 Prague 6, Czech Republic
| | - Iva Pichová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 542/2, 160 00 Prague 6, Czech Republic
| | - Milan Čertík
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia
- Correspondence:
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Mouren A, Avérous L. Sustainable cycloaliphatic polyurethanes: from synthesis to applications. Chem Soc Rev 2023; 52:277-317. [PMID: 36520183 DOI: 10.1039/d2cs00509c] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Polyurethanes (PUs) are a versatile and major polymer family, mainly produced via polyaddition between polyols and polyisocyanates. A large variety of fossil-based building blocks is commonly used to develop a wide range of macromolecular architectures with specific properties. Due to environmental concerns, legislation, rarefaction of some petrol fractions and price fluctuation, sustainable feedstocks are attracting significant attention, e.g., plastic waste and biobased resources from biomass. Consequently, various sustainable building blocks are available to develop new renewable macromolecular architectures such as aromatics, linear aliphatics and cycloaliphatics. Meanwhile, the relationship between the chemical structures of these building blocks and properties of the final PUs can be determined. For instance, aromatic building blocks are remarkable to endow materials with rigidity, hydrophobicity, fire resistance, chemical and thermal stability, whereas acyclic aliphatics endow them with oxidation and UV light resistance, flexibility and transparency. Cycloaliphatics are very interesting as they combine most of the advantages of linear aliphatic and aromatic compounds. This original and unique review presents a comprehensive overview of the synthesis of sustainable cycloaliphatic PUs using various renewable products such as biobased terpenes, carbohydrates, fatty acids and cholesterol and/or plastic waste. Herein, we summarize the chemical modification of the main sustainable cycloaliphatic feedstocks, synthesis of PUs using these building blocks and their corresponding properties and subsequently present their major applications in hot-topic fields, including building, transportation, packaging and biomedicine.
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Affiliation(s)
- Agathe Mouren
- BioTeam/ICPEES-ECPM, UMR CNRS 7515, Université de Strasbourg, 25 rue Becquerel, 67087 Strasbourg Cedex 2, France.
| | - Luc Avérous
- BioTeam/ICPEES-ECPM, UMR CNRS 7515, Université de Strasbourg, 25 rue Becquerel, 67087 Strasbourg Cedex 2, France.
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Wang K, Shi TQ, Lin L, Wei P, Ledesma-Amaro R, Ji XJ. Engineering Yarrowia lipolytica to Produce Tailored Chain-Length Fatty Acids and Their Derivatives. ACS Synth Biol 2022; 11:2564-2577. [DOI: 10.1021/acssynbio.2c00305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Kaifeng Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People’s Republic of China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 1 Wenyuan Road, Nanjing 210046, People’s Republic of China
| | - Lu Lin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People’s Republic of China
| | - Ping Wei
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People’s Republic of China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kindom
| | - Xiao-Jun Ji
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People’s Republic of China
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Wang K, Shi TQ, Lin L, Wei P, Ledesma-Amaro R, Ji XJ, Huang H. Advances in synthetic biology tools paving the way for the biomanufacturing of unusual fatty acids using the Yarrowia lipolytica chassis. Biotechnol Adv 2022; 59:107984. [DOI: 10.1016/j.biotechadv.2022.107984] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 12/18/2022]
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Controlling the Formation of Foams in Broth to Promote the Co-Production of Microbial Oil and Exopolysaccharide in Fed-Batch Fermentation. FERMENTATION 2022. [DOI: 10.3390/fermentation8020068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A large amount of foam is generated in the production of microbial oil and exopolysaccharide (EPS) by Sporidiobolus pararoseus JD-2, which causes low efficiency in fermentation. In this study, we aimed to reduce the negative effects of foams on the co-production of oil and EPS by controlling the formation of foams in broth. As we have found, the formation of foams is positively associated with cell growth state, air entrapment, and properties of broth. The efficient foam-control method of adding 0.03% (v/v) of the emulsified polyoxyethylene polyoxypropylene pentaerythritol ether (PPE) and feeding corn steep liquor (CSL) at 8–24 h with speed of 0.02 L/h considerably improved the fermentation performance of S. pararoseus JD-2, and significantly increased the oil and EPS concentrations by 8.7% and 12.9%, respectively. The biomass, oil, and EPS concentrations were further increased using a foam backflow device combined with adding 0.03% (v/v) of the emulsified PPE and feeding CSL at 8–24 h, which reached to 62.3 ± 1.8 g/L, 31.2 ± 0.8 g/L, and 10.9 ± 0.4 g/L, respectively. The effective strategy for controlling the formation of foams in fermentation broth reported here could be used as a technical reference for producing frothing products in fed-batch fermentation.
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Chen L, Yan W, Qian X, Chen M, Zhang X, Xin F, Zhang W, Jiang M, Ochsenreither K. Increased Lipid Production in Yarrowia lipolytica from Acetate through Metabolic Engineering and Cosubstrate Fermentation. ACS Synth Biol 2021; 10:3129-3138. [PMID: 34714052 DOI: 10.1021/acssynbio.1c00405] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bioconversion of acetate, a byproduct generated in industrial processes, into microbial lipids using oleaginous yeasts offers a promising alternative for the economic utilization of acetate-containing waste streams. However, high acetate concentrations will inhibit microbial growth and metabolism. In this study, the acetate utilization capability of Yarrowia lipolytica PO1f was successively improved by overexpressing the key enzyme of acetyl-CoA synthetase (ACS), which resulted in an accumulation of 9.2% microbial lipids from acetate in shake flask fermentation. By further overexpressing the second key enzymes of acetyl-CoA carboxylase (ACC1) and fatty acid synthase (FAS) in Y. lipolytica, the lipid content was increased to 25.7% from acetate. Finally, the maximum OD600 of 29.2 and a lipid content of 41.7% were obtained with the engineered strain by the adoption of cosubstrate (glycerol and acetate) fed-batch fermentation, which corresponded to an increase of 68 and 95%, respectively. These results presented a promising strategy for economic and efficient microbial lipid production from the waste acetate.
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Affiliation(s)
- Lin Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu Road South, Nanjing 211816, China
| | - Wei Yan
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu Road South, Nanjing 211816, China
| | - Xiujuan Qian
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu Road South, Nanjing 211816, China
| | - Minjiao Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu Road South, Nanjing 211816, China
| | - Xiaoyu Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu Road South, Nanjing 211816, China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu Road South, Nanjing 211816, China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, No. 30, Puzhu Road South, Nanjing 211816, China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu Road South, Nanjing 211816, China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, No. 30, Puzhu Road South, Nanjing 211816, China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu Road South, Nanjing 211816, China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, No. 30, Puzhu Road South, Nanjing 211816, China
| | - Katrin Ochsenreither
- Institute of Process Engineering in Life Sciences, Section II: Technical Biology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131 Karlsruhe, Germany
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9
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Sun T, Yu Y, Wang K, Ledesma-Amaro R, Ji XJ. Engineering Yarrowia lipolytica to produce fuels and chemicals from xylose: A review. BIORESOURCE TECHNOLOGY 2021; 337:125484. [PMID: 34320765 DOI: 10.1016/j.biortech.2021.125484] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/26/2021] [Accepted: 06/28/2021] [Indexed: 06/13/2023]
Abstract
The production of chemicals and fuels from lignocellulosic biomass has great potential industrial applications due to its economic feasibility and environmental attractiveness. However, the utilized microorganisms must be able to use all the sugars present in lignocellulosic hydrolysates, especially xylose, the second most plentiful monosaccharide on earth. Yarrowia lipolytica is a good candidate for producing various valuable products from biomass, but this yeast is unable to catabolize xylose efficiently. The development of metabolic engineering facilitated the application of Y. lipolytica as a platform for the bioconversion of xylose into various value-added products. Here, we reviewed the research progress on natural xylose-utilization pathways and their reconstruction in Y. lipolytica. The progress and emerging trends in metabolic engineering of Y. lipolytica for producing chemicals and fuels are further introduced. Finally, challenges and future perspectives of using lignocellulosic hydrolysate as substrate for Y. lipolytica are discussed.
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Affiliation(s)
- Tao Sun
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Yizi Yu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Kaifeng Wang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Xiao-Jun Ji
- 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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Chaturvedi S, Sadaf A, Bhattacharya A, Rout PK, Nain L, Khare SK. Environment‐Friendly Synergistic Abiotic Stress for Enhancing the Yield of Lipids from Oleaginous Yeasts. EUR J LIPID SCI TECH 2021. [DOI: 10.1002/ejlt.202000376] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Shivani Chaturvedi
- Enzyme and Microbial Biochemistry Laboratory Department of Chemistry Indian Institute of Technology New Delhi 110016 India
| | - Ayesha Sadaf
- Enzyme and Microbial Biochemistry Laboratory Department of Chemistry Indian Institute of Technology New Delhi 110016 India
| | - Amrik Bhattacharya
- Enzyme and Microbial Biochemistry Laboratory Department of Chemistry Indian Institute of Technology New Delhi 110016 India
| | - Prasant Kumar Rout
- Phytochemistry Division CSIR‐Central Institute of medicinal and Aromatic Plants Lucknow Uttar Pradesh 226015 India
| | - Lata Nain
- Division of Microbiology ICAR‐Indian Agricultural Research Institute New Delhi 110014 India
| | - Sunil Kumar Khare
- Enzyme and Microbial Biochemistry Laboratory Department of Chemistry Indian Institute of Technology New Delhi 110016 India
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Szczepańska P, Hapeta P, Lazar Z. Advances in production of high-value lipids by oleaginous yeasts. Crit Rev Biotechnol 2021; 42:1-22. [PMID: 34000935 DOI: 10.1080/07388551.2021.1922353] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The global market for high-value fatty acids production, mainly omega-3/6, hydroxy fatty-acids, waxes and their derivatives, has seen strong development in the last decade. The reason for this growth was the increasing utilization of these lipids as significant ingredients for cosmetics, food and the oleochemical industries. The large demand for these compounds resulted in a greater scientific interest in research focused on alternative sources of oil production - among which microorganisms attracted the most attention. Microbial oil production offers the possibility to engineer the pathways and store lipids enriched with the desired fatty acids. Moreover, costly chemical steps are avoided and direct commercial use of these fatty acids is available. Among all microorganisms, the oleaginous yeasts have become the most promising hosts for lipid production - their efficient lipogenesis, ability to use various (often highly affordable) carbon sources, feasible large-scale cultivations and wide range of available genetic engineering tools turns them into powerful micro-factories. This review is an in-depth description of the recent developments in the engineering of the lipid biosynthetic pathway with oleaginous yeasts. The different classes of valuable lipid compounds with their derivatives are described and their importance for human health and industry is presented. The emphasis is also placed on the optimization of culture conditions in order to improve the yield and titer of these valuable compounds. Furthermore, the important economic aspects of the current microbial oil production are discussed.
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Affiliation(s)
- Patrycja Szczepańska
- Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Piotr Hapeta
- Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Zbigniew Lazar
- Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
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12
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Wang J, Ledesma-Amaro R, Wei Y, Ji B, Ji XJ. Metabolic engineering for increased lipid accumulation in Yarrowia lipolytica - A Review. BIORESOURCE TECHNOLOGY 2020; 313:123707. [PMID: 32595069 DOI: 10.1016/j.biortech.2020.123707] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 06/11/2023]
Abstract
Current energy security and climate change policies encourage the development and utilization of bioenergy. Oleaginous yeasts provide a particularly attractive platform for the sustainable production of biofuels and industrial chemicals due to their ability to accumulate high amounts of lipids. In particular, microbial lipids in the form of triacylglycerides (TAGs) produced from renewable feedstocks have attracted considerable attention because they can be directly used in the production of biodiesel and oleochemicals analogous to petrochemicals. As an oleaginous yeast that is generally regarded as safe, Yarrowia lipolytica has been extensively studied, with large amounts of data on its lipid metabolism, genetic tools, and genome sequencing and annotation. In this review, we highlight the newest strategies for increasing lipid accumulation using metabolic engineering and summarize the research advances on the overaccumulation of lipids in Y. lipolytica. Finally, perspectives for future engineering approaches are proposed.
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Affiliation(s)
- Jinpeng Wang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Yongjun Wei
- School of Pharmaceutical Sciences, Key Laboratory of State Ministry of Education, Key Laboratory of Henan Province for Drug Quality Control and Evaluation, Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, 100 Kexue Avenue, Zhengzhou 450001, People's Republic of China
| | - Boyang Ji
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Xiao-Jun Ji
- 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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Patel A, Karageorgou D, Rova E, Katapodis P, Rova U, Christakopoulos P, Matsakas L. An Overview of Potential Oleaginous Microorganisms and Their Role in Biodiesel and Omega-3 Fatty Acid-Based Industries. Microorganisms 2020; 8:E434. [PMID: 32204542 PMCID: PMC7143722 DOI: 10.3390/microorganisms8030434] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 12/17/2022] Open
Abstract
Microorganisms are known to be natural oil producers in their cellular compartments. Microorganisms that accumulate more than 20% w/w of lipids on a cell dry weight basis are considered as oleaginous microorganisms. These are capable of synthesizing vast majority of fatty acids from short hydrocarbonated chain (C6) to long hydrocarbonated chain (C36), which may be saturated (SFA), monounsaturated (MUFA), or polyunsaturated fatty acids (PUFA), depending on the presence and number of double bonds in hydrocarbonated chains. Depending on the fatty acid profile, the oils obtained from oleaginous microorganisms are utilized as feedstock for either biodiesel production or as nutraceuticals. Mainly microalgae, bacteria, and yeasts are involved in the production of biodiesel, whereas thraustochytrids, fungi, and some of the microalgae are well known to be producers of very long-chain PUFA (omega-3 fatty acids). In this review article, the type of oleaginous microorganisms and their expertise in the field of biodiesel or omega-3 fatty acids, advances in metabolic engineering tools for enhanced lipid accumulation, upstream and downstream processing of lipids, including purification of biodiesel and concentration of omega-3 fatty acids are reviewed.
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Affiliation(s)
- Alok Patel
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, SE-971 87 Luleå, Sweden; (A.P.); (E.R.); (U.R.); (P.C.)
| | - Dimitra Karageorgou
- Laboratory of Biotechnology, Department of Biological Applications and Technologies, University of Ioannina, Ioannina 45110, Greece; (D.K.); (P.K.)
| | - Emma Rova
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, SE-971 87 Luleå, Sweden; (A.P.); (E.R.); (U.R.); (P.C.)
| | - Petros Katapodis
- Laboratory of Biotechnology, Department of Biological Applications and Technologies, University of Ioannina, Ioannina 45110, Greece; (D.K.); (P.K.)
| | - Ulrika Rova
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, SE-971 87 Luleå, Sweden; (A.P.); (E.R.); (U.R.); (P.C.)
| | - Paul Christakopoulos
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, SE-971 87 Luleå, Sweden; (A.P.); (E.R.); (U.R.); (P.C.)
| | - Leonidas Matsakas
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, SE-971 87 Luleå, Sweden; (A.P.); (E.R.); (U.R.); (P.C.)
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Abstract
Oleaginous microbes, which contain over 20% intracellular lipid, predominantly triacylglycerols (TG), by dry weight, have been discovered to have high oil content by many different protocols, ranging from simple staining to more complex chromatographic methods. In our laboratory, a methodical process was implemented to identify high oil yeasts, designed to minimize labor while optimizing success in identifying high oil strains among thousands of candidates. First, criteria were developed to select candidate yeast strains for analysis. These included observation of buoyancy of the yeast cell mass in 20% glycerol, and phylogenetic placement near known oleaginous species. A low-labor, semiquantitative Nile red staining protocol was implemented to screen numerous yeast cultures for high oil content in 96-well plates. Then, promising candidates were selected for more quantitative analysis. A more labor-intensive and quantitative gravimetric assay was implemented that gave consistent values for intracellular oil content for a broad range of yeast species. Finally, an LC-MS protocol was utilized to quantify and identify yeast triacylglycerols. This progressive approach was successful in identifying 30 new oleaginous yeast species, out of over 1000 species represented in the Phaff Yeast Culture Collection.
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Chu M, Zhang L, Lou W, Zong M, Tang Y, Yang J. Preparation and Characterization of Oil Rich in Odd Chain Fatty Acids from Rhodococcus opacusPD630. J AM OIL CHEM SOC 2020. [DOI: 10.1002/aocs.12304] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Mei‐Yun Chu
- School of Food Science and EngineeringSouth China University of Technology, Wushan Road Guangzhou 510641 China
| | - Lin‐Shang Zhang
- School of Food Science and EngineeringSouth China University of Technology, Wushan Road Guangzhou 510641 China
| | - Wen‐Yong Lou
- School of Food Science and EngineeringSouth China University of Technology, Wushan Road Guangzhou 510641 China
| | - Min‐Hua Zong
- School of Food Science and EngineeringSouth China University of Technology, Wushan Road Guangzhou 510641 China
| | - Yu‐Qian Tang
- School of Food Science and EngineeringSouth China University of Technology, Wushan Road Guangzhou 510641 China
- South China Institute of Collaborative Innovation, Xincheng Road Dongguan 523808 China
| | - Ji‐Guo Yang
- School of Food Science and EngineeringSouth China University of Technology, Wushan Road Guangzhou 510641 China
- South China Institute of Collaborative Innovation, Xincheng Road Dongguan 523808 China
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Jezierska S, Claus S, Ledesma-Amaro R, Van Bogaert I. Redirecting the lipid metabolism of the yeast Starmerella bombicola from glycolipid to fatty acid production. ACTA ACUST UNITED AC 2019; 46:1697-1706. [DOI: 10.1007/s10295-019-02234-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 09/04/2019] [Indexed: 01/06/2023]
Abstract
Abstract
Free fatty acids are basic oleochemicals implemented in a range of applications including surfactants, lubricants, paints, plastics, and cosmetics. Microbial fatty acid biosynthesis has gained much attention as it provides a sustainable alternative for petrol- and plant oil-derived chemicals. The yeast Starmerella bombicola is a microbial cell factory that naturally employs its powerful lipid metabolism for the production of the biodetergents sophorolipids (> 300 g/L). However, in this study we exploit the lipidic potential of S. bombicola and convert it from the glycolipid production platform into a free fatty acid cell factory. We used several metabolic engineering strategies to promote extracellular fatty acid accumulation which include blocking competing pathways (sophorolipid biosynthesis and β-oxidation) and preventing free fatty acid activation. The best producing mutant (Δcyp52m1Δfaa1Δmfe2) secreted 0.933 g/L (± 0.04) free fatty acids with a majority of C18:1 (43.8%) followed by C18:0 and C16:0 (40.0 and 13.2%, respectively). Interestingly, deletion of SbFaa1 in a strain still producing sophorolipids also resulted in 25% increased de novo sophorolipid synthesis (P = 0.0089) and when oil was supplemented to the same strain, a 50% increase in sophorolipid production was observed compared to the wild type (P = 0.03). We believe that our work is pivotal for the further development and exploration of S. bombicola as a platform for synthesis of environmentally friendly oleochemicals.
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Affiliation(s)
- Sylwia Jezierska
- grid.5342.0 0000 0001 2069 7798 Centre for Synthetic Biology, Department of Biotechnology Ghent University Coupure Links 653 9000 Ghent Belgium
| | - Silke Claus
- grid.5342.0 0000 0001 2069 7798 Centre for Synthetic Biology, Department of Biotechnology Ghent University Coupure Links 653 9000 Ghent Belgium
| | - Rodrigo Ledesma-Amaro
- grid.7445.2 0000 0001 2113 8111 Imperial College Centre for Synthetic Biology and Department of Bioengineering Imperial College London South Kensington Campus SW7 2AZ London UK
| | - Inge Van Bogaert
- grid.5342.0 0000 0001 2069 7798 Centre for Synthetic Biology, Department of Biotechnology Ghent University Coupure Links 653 9000 Ghent Belgium
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Yao Q, Chen H, Wang S, Tang X, Gu Z, Zhang H, Chen W, Chen YQ. An efficient strategy for screening polyunsaturated fatty acid-producing oleaginous filamentous fungi from soil. J Microbiol Methods 2019; 158:80-85. [DOI: 10.1016/j.mimet.2018.12.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/26/2018] [Accepted: 12/29/2018] [Indexed: 02/05/2023]
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Bioactivity and biotechnological production of punicic acid. Appl Microbiol Biotechnol 2018; 102:3537-3549. [DOI: 10.1007/s00253-018-8883-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 02/18/2018] [Accepted: 02/19/2018] [Indexed: 02/01/2023]
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19
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Koster D, Gutkowski R, Masa J, Schuhmann W. H2 quantification based on selective pre-concentration and oxidative stripping at Pd modified microelectrodes. J Electroanal Chem (Lausanne) 2018. [DOI: 10.1016/j.jelechem.2017.12.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ledesma-Amaro R, Nicaud JM. Metabolic Engineering for Expanding the Substrate Range of Yarrowia lipolytica. Trends Biotechnol 2016; 34:798-809. [DOI: 10.1016/j.tibtech.2016.04.010] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/19/2016] [Accepted: 04/21/2016] [Indexed: 11/16/2022]
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Ledesma-Amaro R, Lazar Z, Rakicka M, Guo Z, Fouchard F, Coq AMCL, Nicaud JM. Metabolic engineering of Yarrowia lipolytica to produce chemicals and fuels from xylose. Metab Eng 2016; 38:115-124. [PMID: 27396355 DOI: 10.1016/j.ymben.2016.07.001] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 06/17/2016] [Accepted: 07/05/2016] [Indexed: 11/29/2022]
Abstract
Yarrowia lipolytica is a biotechnological chassis for the production of a range of products, such as microbial oils and organic acids. However, it is unable to consume xylose, the major pentose in lignocellulosic hydrolysates, which are considered a preferred carbon source for bioprocesses due to their low cost, wide abundance and high sugar content. Here, we engineered Y. lipolytica to metabolize xylose to produce lipids or citric acid. The overexpression of xylose reductase and xylitol dehydrogenase from Scheffersomyces stipitis were necessary but not sufficient to permit growth. The additional overexpression of the endogenous xylulokinase enabled identical growth as the wild type strain in glucose. This mutant was able to produce up to 80g/L of citric acid from xylose. Transferring these modifications to a lipid-overproducing strain boosted the production of lipids from xylose. This is the first step towards a consolidated bioprocess to produce chemicals and fuels from lignocellulosic materials.
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Affiliation(s)
- Rodrigo Ledesma-Amaro
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Zbigniew Lazar
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; Department of Biotechnology and Food Microbiology, Wrocław University of Environmental and Life Sciences, Chełmońskiego Str. 37/41, 51-630 Wrocław, Poland
| | - Magdalena Rakicka
- Department of Biotechnology and Food Microbiology, Wrocław University of Environmental and Life Sciences, Chełmońskiego Str. 37/41, 51-630 Wrocław, Poland
| | - Zhongpeng Guo
- LISBP-Biocatalysis Group, INSA/INRA, Université de Toulouse, 135 Avenue de Rangueil, 31077 Toulouse, France; INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, 31400 Toulouse, France; CNRS, UMR5504, 31400 Toulouse, France
| | - Florian Fouchard
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Anne-Marie Crutz-Le Coq
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Jean-Marc Nicaud
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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Ledesma-Amaro R, Dulermo R, Niehus X, Nicaud JM. Combining metabolic engineering and process optimization to improve production and secretion of fatty acids. Metab Eng 2016; 38:38-46. [PMID: 27301328 DOI: 10.1016/j.ymben.2016.06.004] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 04/10/2016] [Accepted: 06/10/2016] [Indexed: 12/16/2022]
Abstract
Microbial oils are sustainable alternatives to petroleum for the production of chemicals and fuels. Oleaginous yeasts are promising source of oils and Yarrowia lipolytica is the most studied and engineered one. Nonetheless the commercial production of biolipids is so far limited to high value products due to the elevated production and extraction costs. In order to contribute to overcoming these limitations we exploited the possibility of secreting lipids to the culture broth, uncoupling production and biomass formation and facilitating the extraction. We therefore considered two synthetic approaches, Strategy I where fatty acids are produced by enhancing the flux through neutral lipid formation, as typically occurs in eukaryotic systems and Strategy II where the bacterial system to produce free fatty acids is mimicked. The engineered strains, in a coupled fermentation and extraction process using alkanes, secreted the highest titer of lipids described so far, with a content of 120% of DCW.
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Affiliation(s)
- Rodrigo Ledesma-Amaro
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Remi Dulermo
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Xochitl Niehus
- Industrial Biotechnology, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), A.C. 44270 Guadalajara, Jalisco, Mexico
| | - Jean-Marc Nicaud
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
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Ledesma-Amaro R, Revuelta JL. Synthetic biology and metabolic engineering to produce microbial oils: towards a sustainable source of fuels, chemicals and nutraceuticals. N Biotechnol 2016. [DOI: 10.1016/j.nbt.2015.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ledesma-Amaro R, Nicaud JM. Yarrowia lipolytica as a biotechnological chassis to produce usual and unusual fatty acids. Prog Lipid Res 2016; 61:40-50. [DOI: 10.1016/j.plipres.2015.12.001] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 12/02/2015] [Accepted: 12/08/2015] [Indexed: 10/22/2022]
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Ledesma-Amaro R, Dulermo T, Nicaud JM. Engineering Yarrowia lipolytica to produce biodiesel from raw starch. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:148. [PMID: 26379779 PMCID: PMC4571081 DOI: 10.1186/s13068-015-0335-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 09/03/2015] [Indexed: 05/24/2023]
Abstract
BACKGROUND In the last year, the worldwide concern about the abuse of fossil fuels and the seeking for alternatives sources to produce energy have found microbial oils has potential candidates for diesel substitutes. Yarrowia lipolytica has emerged as a paradigm organism for the production of bio-lipids in white biotechnology. It accumulates high amounts of lipids from glucose as sole carbon sources. Nonetheless, to lower the cost of microbial oil production and rival plant-based fuels, the use of raw and waste materials as fermentation substrate is required. Starch is one of the most abundant carbohydrates in nature and it is constituted by glucose monomers. Y. lipolytica lacks the capacity to breakdown this polymer and thus expensive enzymatic and/or physical pre-treatments are needed. RESULTS In this work, we express heterologous alpha-amylase and glucoamylase enzymes in Y. lipolytica. The modified strains were able to produce and secrete high amounts of active form of both proteins in the culture media. These strains were able to grow on starch as sole carbon source and produce certain amount of lipids. Thereafter, we expressed both enzymes in an engineered strain able to overaccumulate lipids. This strain was able to produce up to 21 % of DCW as fatty acids from soluble starch, 5.7 times more than the modified strain in the wild-type background. Media optimization to increase the C/N ratio to 90 increased total lipid content up to 27 % of DCW. We also tested these strains in industrial raw starch as a proof of concept of the feasibility of the consolidated bioprocess. Lipid production from raw starch was further enhanced by the expression of a second copy of each enzyme. Finally, we determined in silico that the properties of a biodiesel produced by this strain from raw starch would fit the established standards. CONCLUSIONS In this work, we performed a strain engineering approach to obtain a consolidated bioprocess to directly produce biolipids from raw starch. Additionally, we proved that lipid production from starch can be enhanced by both metabolic engineering and culture condition optimization, setting up the basis for further studies.
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Affiliation(s)
- Rodrigo Ledesma-Amaro
- />INRA, UMR1319 Micalis, 78350 Jouy-en-Josas, France
- />AgroParisTech, UMR Micalis, Jouy-en-Josas, France
- />Institut Micalis, INRA-AgroParisTech, UMR1319, Team BIMLip, Biologie Intégrative du Métabolisme Lipidique, CBAI, 78850 Thiverval-Grignon, France
| | - Thierry Dulermo
- />INRA, UMR1319 Micalis, 78350 Jouy-en-Josas, France
- />AgroParisTech, UMR Micalis, Jouy-en-Josas, France
| | - Jean Marc Nicaud
- />INRA, UMR1319 Micalis, 78350 Jouy-en-Josas, France
- />AgroParisTech, UMR Micalis, Jouy-en-Josas, France
- />Institut Micalis, INRA-AgroParisTech, UMR1319, Team BIMLip, Biologie Intégrative du Métabolisme Lipidique, CBAI, 78850 Thiverval-Grignon, France
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Metzger JO, Meier MAR. Fats and oils as renewable feedstock for the chemical industry. EUR J LIPID SCI TECH 2015. [DOI: 10.1002/ejlt.201400638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jürgen O. Metzger
- Carl von Ossietzky Universität Oldenburg & Abiosus e.V.OldenburgGermany
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