1
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Morales-Palomo S, Navarrete C, Martínez JL, González-Fernández C, Tomás-Pejó E. Transcriptomic profiling of an evolved Yarrowia lipolytica strain: tackling hexanoic acid fermentation to increase lipid production from short-chain fatty acids. Microb Cell Fact 2024; 23:101. [PMID: 38566056 PMCID: PMC10988856 DOI: 10.1186/s12934-024-02367-4] [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: 11/23/2023] [Accepted: 03/17/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Short-chain fatty acids (SCFAs) are cost-effective carbon sources for an affordable production of lipids. Hexanoic acid, the acid with the longest carbon chain in the SCFAs pool, is produced in anaerobic fermentation of organic residues and its use is very challenging, even inhibiting oleaginous yeasts growth. RESULTS In this investigation, an adaptive laboratory evolution (ALE) was performed to improve Yarrowia lipolytica ACA DC 50109 tolerance to high hexanoic acid concentrations. Following ALE, the transcriptomic analysis revealed several genetic adaptations that improved the assimilation of this carbon source in the evolved strain compared to the wild type (WT). Indeed, the evolved strain presented a high expression of the up-regulated gene YALI0 E16016g, which codes for FAT1 and is related to lipid droplets formation and responsible for mobilizing long-chain acids within the cell. Strikingly, acetic acid and other carbohydrate transporters were over-expressed in the WT strain. CONCLUSIONS A more tolerant yeast strain able to attain higher lipid content under the presence of high concentrations of hexanoic acid has been obtained. Results provided novel information regarding the assimilation of hexanoic acid in yeasts.
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Affiliation(s)
| | - Clara Navarrete
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - José Luis Martínez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Cristina González-Fernández
- Biotechnological Processes Unit, IMDEA Energy, Móstoles (Madrid), Spain
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, Valladolid University, Valladolid, 47011, Spain
- Institute of Sustainable Processes, Valladolid, 47011, Spain
| | - Elia Tomás-Pejó
- Biotechnological Processes Unit, IMDEA Energy, Móstoles (Madrid), Spain.
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2
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Sofeo N, Toi MG, Ee EQG, Ng JY, Busran CT, Lukito BR, Thong A, Hermansen C, Peterson EC, Glitsos R, Arumugam P. Sustainable production of lipids from cocoa fatty acid distillate fermentation driven by adaptive evolution in Yarrowia lipolytica. BIORESOURCE TECHNOLOGY 2024; 394:130302. [PMID: 38199440 DOI: 10.1016/j.biortech.2024.130302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/20/2023] [Accepted: 01/06/2024] [Indexed: 01/12/2024]
Abstract
Single cell oil production using oleaginous yeasts is a promising alternative to animal and plant-derived lipids. But substrate costs for microbial fermentation are a major bottleneck. Using side streams as alternative to substrates like glucose, for growing yeast, is a potential cost-effective solution. By combining a previously reported process of growing yeasts on a solid cocoa fatty acid distillate side stream with adaptive evolution techniques, the growth of oleaginous yeast Yarrowia lipolytica was improved by 2-fold. The lipid titre was also boosted by more than 3-fold. Using transcriptomics, key genes were identified that are possibly involved in tailoring of lipid composition, side stream utilisation and enhancement of lipid titres. Candidate genes were also identified that might enable efficient growth and utilization of fatty acids and triacylglycerides found in cocoa fatty acid distillate. In summary, this research has improved the understanding of side stream utilisation for lipid production in oleaginous yeast.
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Affiliation(s)
- Naazneen Sofeo
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore.
| | - Min Gin Toi
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - En Qi Grace Ee
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - Jing Yang Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - Coleen Toledo Busran
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - Benedict Ryan Lukito
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - Aaron Thong
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - Christian Hermansen
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - Eric Charles Peterson
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore; Institut National de la Recherche Scientifique - Eau Terre Environnement (INRS-ETE), 490 Rue de la Couronne, Quebec City, QC G1K 9A9, Canada
| | - Renata Glitsos
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - Prakash Arumugam
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
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3
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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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4
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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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5
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Srikant S, Gaudet R, Murray AW. Extending the reach of homology by using successive computational filters to find yeast pheromone genes. Curr Biol 2023; 33:4098-4110.e3. [PMID: 37699395 PMCID: PMC10592104 DOI: 10.1016/j.cub.2023.08.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 07/04/2023] [Accepted: 08/14/2023] [Indexed: 09/14/2023]
Abstract
The mating of fungi depends on pheromones that mediate communication between two mating types. Most species use short peptides as pheromones, which are either unmodified (e.g., α-factor in Saccharomyces cerevisiae) or C-terminally farnesylated (e.g., a-factor in S. cerevisiae). Peptide pheromones have been found by genetics or biochemistry in a small number of fungi, but their short sequences and modest conservation make it impossible to detect homologous sequences in most species. To overcome this problem, we used a four-step computational pipeline to identify candidate a-factor genes in sequenced genomes of the Saccharomycotina, the fungal clade that contains most of the yeasts: we require that candidate genes have a C-terminal prenylation motif, are shorter than 100 amino acids long, and contain a proteolytic-processing motif upstream of the potential mature pheromone sequence and that closely related species contain highly conserved homologs of the potential mature pheromone sequence. Additional manual curation exploits the observation that many species carry more than one a-factor gene, encoding identical or nearly identical pheromones. From 332 Saccharomycotina genomes, we identified strong candidate pheromone genes in 241 genomes, covering 13 clades that are each separated from each other by at least 100 million years, the time required for evolution to remove detectable sequence homology among small pheromone genes. For one small clade, the Yarrowia, we demonstrated that our algorithm found the a-factor genes: deleting all four related genes in the a-mating type of Yarrowia lipolytica prevents mating.
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Affiliation(s)
- Sriram Srikant
- Department of Molecular and Cellular Biology, Harvard University, Oxford Street, Cambridge, MA 02138, USA
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Oxford Street, Cambridge, MA 02138, USA
| | - Andrew W Murray
- Department of Molecular and Cellular Biology, Harvard University, Oxford Street, Cambridge, MA 02138, USA.
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6
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Urbanikova V, Park YK, Krajciova D, Tachekort M, Certik M, Grigoras I, Holic R, Nicaud JM, Gajdos P. Yarrowia lipolytica as a Platform for Punicic Acid Production. Int J Mol Sci 2023; 24:ijms24108823. [PMID: 37240172 DOI: 10.3390/ijms24108823] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/03/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Punicic acid (PuA) is a polyunsaturated fatty acid with significant medical, biological, and nutraceutical properties. The primary source of punicic acid is the pomegranate seed oil obtained from fruits of trees that are mainly cultivated in subtropical and tropical climates. To establish sustainable production of PuA, various recombinant microorganisms and plants have been explored as platforms with limited efficiencies. In this study, the oleaginous yeast Yarrowia lipolytica was employed as a host for PuA production. First, growth and lipid accumulation of Y. lipolytica were evaluated in medium supplemented with pomegranate seed oil, resulting in the accumulation of lipids up to 31.2%, consisting of 22% PuA esterified in the fraction of glycerolipids. In addition, lipid-engineered Y. lipolytica strains, transformed with the bifunctional fatty acid conjugase/desaturase from Punica granatum (PgFADX), showed the ability to accumulate PuA de novo. PuA was detected in both polar and neutral lipid fractions, especially in phosphatidylcholine and triacylglycerols. Promoter optimization for PgFADX expression resulted in improved accumulation of PuA from 0.9 to 1.8 mg/g of dry cell weight. The best-producing strain expressing PgFADX under the control of a strong erythritol-inducible promoter produced 36.6 mg/L PuA. These results demonstrate that the yeast Y. lipolytica is a promising host for PuA production.
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Grants
- APVV-20-0166 INRAE, the French National Research Institute for Agriculture, Food and Environment, Micalis Institute, the Slovak Research and Development Agency
- VEGA 2/0012/20 Ministry of Education, Science, Research, and Sport of the Slovak Republic, and the Slovak Academy of Sciences
- NA Genopole, University of Evry-val-d'Essonne, University of Paris-Saclay, Investissements d'Avenir
- NA New England BioLabs (NEB)
- NA Integrated DNA Technologies Inc. (IDT)
- NA Twist Biosciences
- NA SnapGene
- NA Macherey Nagel
- NA Zymo Research
- NA Promega
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Affiliation(s)
- Veronika Urbanikova
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, 81237 Bratislava, Slovakia
| | - Young-Kyoung Park
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Daniela Krajciova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 84005 Bratislava, Slovakia
| | - Mehdi Tachekort
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
- Université Paris-Saclay, Univ Evry, CNRS, CEA, Génomique métabolique, 91057 Evry-Courcouronnes, France
| | - Milan Certik
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, 81237 Bratislava, Slovakia
| | - Ioana Grigoras
- Université Paris-Saclay, Univ Evry, CNRS, CEA, Génomique métabolique, 91057 Evry-Courcouronnes, France
| | - Roman Holic
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 84005 Bratislava, Slovakia
| | - Jean-Marc Nicaud
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Peter Gajdos
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, 81237 Bratislava, Slovakia
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7
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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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8
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Salvador Lopez JM, Jezierska S, Ekim Kocabey A, Lee J, Schneiter R, Van Bogaert INA. The oleaginous yeast Starmerella bombicola reveals limitations of Saccharomyces cerevisiae as a model for fatty acid transport studies. FEMS Yeast Res 2022; 22:6832774. [PMID: 36398741 DOI: 10.1093/femsyr/foac054] [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: 12/03/2021] [Revised: 10/21/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022] Open
Abstract
Saccharomyces cerevisiae is the model organism to most yeast researchers, and information obtained from its physiology is generally extrapolated to other yeasts. Studies on fatty acid transport in S. cerevisiae are based on the expression of both native fatty acid export genes as well as heterologous proteins. Starmerella bombicola, on the other hand, is an oleaginous yeast of industrial relevance but its fatty acid transport mechanisms are unknown. In this study, we attempt to use existing knowledge from S. cerevisiae to study fatty acid transport in S. bombicola, but the obtained results differ from those observed in S. cerevisiae. First, we observed that deletion of SbPRY1 in S. bombicola leads to higher fatty acid export, the opposite effect to the one previously observed for the Pry homologues in S. cerevisiae. Second, following reports that human FATP1 could export fatty acids and alcohols in S. cerevisiae, we expressed FATP1 in a fatty acid-accumulating S. bombicola strain. However, FATP1 reduced fatty acid export in S. bombicola, most likely due to its acyl-CoA synthetase activity. These results not only advance knowledge on fatty acid physiology of S. bombicola, but also improve our understanding of S. cerevisiae and its limitations as a model organism.
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Affiliation(s)
| | - Sylwia Jezierska
- Centre for Synthetic Biology, Ghent University, Belgium.,Avecom N.V., Industrieweg 122P 9032 Wondelgem, Belgium
| | | | - Jungho Lee
- Centre for Synthetic Biology, Ghent University, Belgium
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9
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Salvador López JM, Vandeputte M, Van Bogaert INA. Oleaginous yeasts: Time to rethink the definition? Yeast 2022; 39:553-606. [PMID: 36366783 DOI: 10.1002/yea.3827] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 10/21/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
Oleaginous yeasts are typically defined as those able to accumulate more than 20% of their cell dry weight as lipids or triacylglycerides. Research on these yeasts has increased lately fuelled by an interest to use biotechnology to produce lipids and oleochemicals that can substitute those coming from fossil fuels or offer sustainable alternatives to traditional extractions (e.g., palm oil). Some oleaginous yeasts are attracting attention both in research and industry, with Yarrowia lipolytica one of the best-known and studied ones. Oleaginous yeasts can be found across several clades and different metabolic adaptations have been found, affecting not only fatty acid and neutral lipid synthesis, but also lipid particle stability and degradation. Recently, many novel oleaginous yeasts are being discovered, including oleaginous strains of the traditionally considered non-oleaginous Saccharomyces cerevisiae. In the face of this boom, a closer analysis of the definition of "oleaginous yeast" reveals that this term has instrumental value for biotechnology, while it does not give information about distinct types of yeasts. Having this perspective in mind, we propose to expand the term "oleaginous yeast" to those able to produce either intracellular or extracellular lipids, not limited to triacylglycerides, in at least one growth condition (including ex novo lipid synthesis). Finally, a critical look at Y. lipolytica as a model for oleaginous yeasts shows that the term "oleaginous" should be reserved only for strains and not species and that in the case of Y. lipolytica, it is necessary to distinguish clearly between the lipophilic and oleaginous phenotype.
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Affiliation(s)
- José Manuel Salvador López
- BioPort Group, Centre for Synthetic Biology (CSB), Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Meriam Vandeputte
- BioPort Group, Centre for Synthetic Biology (CSB), Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Inge N A Van Bogaert
- BioPort Group, Centre for Synthetic Biology (CSB), Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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10
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Liu Y, Zhang J, Li Q, Wang Z, Cui Z, Su T, Lu X, Qi Q, Hou J. Engineering Yarrowia lipolytica for the sustainable production of β-farnesene from waste oil feedstock. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:101. [PMID: 36192797 PMCID: PMC9528160 DOI: 10.1186/s13068-022-02201-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/24/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND β-Farnesene is a sesquiterpene with versatile industrial applications. The production of β-farnesene from waste lipid feedstock is an attractive method for sustainable production and recycling waste oil. Yarrowia lipolytica is an unconventional oleaginous yeast, which can use lipid feedstock and has great potential to synthesize acetyl-CoA-derived chemicals. RESULTS In this study, we engineered Y. lipolytica to produce β-farnesene from lipid feedstock. To direct the flux of acetyl-CoA, which is generated from lipid β-oxidation, to β-farnesene synthesis, the mevalonate synthesis pathway was compartmentalized into peroxisomes. β-Farnesene production was then engineered by the protein engineering of β-farnesene synthase and pathway engineering. The regulation of lipid metabolism by enhancing β-oxidation and eliminating intracellular lipid synthesis was further performed to improve the β-farnesene synthesis. As a result, the final β-farnesene production with bio-engineering reached 35.2 g/L and 31.9 g/L using oleic acid and waste cooking oil, respectively, which are the highest β-farnesene titers reported in Y. lipolytica. CONCLUSIONS This study demonstrates that engineered Y. lipolytica could realize the sustainable production of value-added acetyl-CoA-derived chemicals from waste lipid feedstock.
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Affiliation(s)
- Yinghang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, China
| | - Jin Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, China
| | - Qingbin Li
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, China
| | - Zhaoxuan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, China
| | - Zhiyong Cui
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, China
| | - Tianyuan Su
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, China
| | - Xuemei Lu
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, China.
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, China.
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11
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Onésime D, Vidal L, Thomas S, Henry C, Martin V, André G, Kubiak P, Minard P, Celinska E, Nicaud JM. A unique, newly discovered four-member protein family involved in extracellular fatty acid binding in Yarrowia lipolytica. Microb Cell Fact 2022; 21:200. [PMID: 36182920 PMCID: PMC9526294 DOI: 10.1186/s12934-022-01925-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Yarrowia lipolytica, a nonconventional oleaginous yeast species, has attracted attention due to its high lipid degradation and accumulation capacities. Y. lipolytica is used as a chassis for the production of usual and unusual lipids and lipid derivatives. While the genes involved in the intracellular transport and activation of fatty acids in different cellular compartments have been characterized, no genes involved in fatty acid transport from the extracellular medium into the cell have been identified thus far. In this study, we identified secreted proteins involved in extracellular fatty acid binding. RESULTS Recent analysis of the Y. lipolytica secretome led to the identification of a multigene family that encodes four secreted proteins, preliminarily named UP1 to UP4. These proteins were efficiently overexpressed individually in wild-type and multideletant strain (Q4: Δup1Δup2Δup3Δup4) backgrounds. Phenotypic analysis demonstrated the involvement of these proteins in the binding of extracellular fatty acids. Additionally, gene deletion and overexpression prevented and promoted sensitivity to octanoic acid (C8) toxicity, respectively. The results suggested binding is dependent on aliphatic chain length and fatty acid concentration. 3D structure modeling supports the proteins' role in fatty acid assimilation at the molecular level. CONCLUSIONS We discovered a family of extracellular-fatty-acid-binding proteins in Y. lipolytica and have proposed to name its members eFbp1 to eFbp4. The exact mode of eFbps action remains to be deciphered individually and synergistically; nevertheless, it is expected that the proteins will have applications in lipid biotechnology, such as improving fatty acid production and/or bioconversion.
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Affiliation(s)
- Djamila Onésime
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Léa Vidal
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Stéphane Thomas
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Céline Henry
- Plateforme d'Analyse Protéomique Paris Sud-Ouest (PAPPSO), INRAE, MICALIS Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Véronique Martin
- INRAE, MaIAGE, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Gwenaëlle André
- INRAE, MaIAGE, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Piotr Kubiak
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Philippe Minard
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Ewelina Celinska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Jean-Marc Nicaud
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France. .,INRAE-AgroParisTech, UMR1319, Team BIMLip: Integrative Metabolism of Microbial Lipids, Micalis Institute, Domaine de Vilvert, 78352, Jouy-en-Josas, France.
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12
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Vyas S, Matsakas L, Rova U, Christakopoulos P, Patel A. Insights into hydrophobic waste valorization for the production of value-added oleochemicals. Microb Biotechnol 2022; 16:177-183. [PMID: 35932161 PMCID: PMC9871509 DOI: 10.1111/1751-7915.14122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/11/2022] [Accepted: 07/16/2022] [Indexed: 01/27/2023] Open
Affiliation(s)
- Sachin Vyas
- Biochemical Process EngineeringDivision of Chemical EngineeringDepartment of CivilEnvironmental, and Natural Resources EngineeringLuleå University of TechnologyLuleåSweden
| | - Leonidas Matsakas
- Biochemical Process EngineeringDivision of Chemical EngineeringDepartment of CivilEnvironmental, and Natural Resources EngineeringLuleå University of TechnologyLuleåSweden
| | - Ulrika Rova
- Biochemical Process EngineeringDivision of Chemical EngineeringDepartment of CivilEnvironmental, and Natural Resources EngineeringLuleå University of TechnologyLuleåSweden
| | - Paul Christakopoulos
- Biochemical Process EngineeringDivision of Chemical EngineeringDepartment of CivilEnvironmental, and Natural Resources EngineeringLuleå University of TechnologyLuleåSweden
| | - Alok Patel
- Biochemical Process EngineeringDivision of Chemical EngineeringDepartment of CivilEnvironmental, and Natural Resources EngineeringLuleå University of TechnologyLuleåSweden
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13
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Gajdoš P, Urbaníková V, Vicenová M, Čertík M. Enhancing very long chain fatty acids production in Yarrowia lipolytica. Microb Cell Fact 2022; 21:138. [PMID: 35818073 PMCID: PMC9275168 DOI: 10.1186/s12934-022-01866-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/20/2022] [Indexed: 11/23/2022] Open
Abstract
Background Very long chain fatty acids (VLCFA) and their derivatives are industrially attractive compounds. The most important are behenic acid (C22:0) and erucic acid (C22:1Δ13), which are used as lubricants, and moisturizers. C22:0 and C22:1Δ13 have also potential for biofuel production. These fatty acids are conventionally obtained from plant oils. Yarrowia lipolytica is an oleaginous yeast with a long history of gene manipulations resulting in the production of industrially interesting compounds, such as organic acids, proteins, and various lipophilic molecules. It has been shown previously that it has potential for the production of VLCFA enriched single cell oils. Results The metabolism of Y. lipolytica was redesigned to achieve increased production of VLCFA. The effect of native diacylglycerol acyltransferases of this yeast YlLro1p, YlDga1p, and YlDga2p on the accumulation of VLCFA was examined. It was found that YlDga1p is the only enzyme with a beneficial effect. Further improvement of accumulation was achieved by overexpression of 3-ketoacyl-CoA synthase (TaFAE1) under 8UAS-pTEF promoter and blockage fatty acid degradation pathway by deletion of YlMFE1. The best-producing strain YL53 (Δmfe, pTEF-YlDGA1, 8UAS-pTEF-TaFAE1) produced 120 µg of very long chain fatty acids per g of produced biomass, which accounted for 34% of total fatty acids in biomass. Conclusions Recombinant strains of Y. lipolytica have proved to be good producers of VLCFA. Redesign of lipid metabolism pathways had a positive effect on the accumulation of C22:1Δ13 and C22:0, which are technologically attractive compounds.
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Affiliation(s)
- Peter Gajdoš
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 81237, Bratislava, Slovak Republic.
| | - Veronika Urbaníková
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 81237, Bratislava, Slovak Republic
| | - Mária Vicenová
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 81237, Bratislava, Slovak Republic
| | - Milan Čertík
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 81237, Bratislava, Slovak Republic
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14
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Zhang XY, Li B, Huang BC, Wang FB, Zhang YQ, Zhao SG, Li M, Wang HY, Yu XJ, Liu XY, Jiang J, Wang ZP. Production, Biosynthesis, and Commercial Applications of Fatty Acids From Oleaginous Fungi. Front Nutr 2022; 9:873657. [PMID: 35694158 PMCID: PMC9176664 DOI: 10.3389/fnut.2022.873657] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/31/2022] [Indexed: 12/18/2022] Open
Abstract
Oleaginous fungi (including fungus-like protists) are attractive in lipid production due to their short growth cycle, large biomass and high yield of lipids. Some typical oleaginous fungi including Galactomyces geotrichum, Thraustochytrids, Mortierella isabellina, and Mucor circinelloides, have been well studied for the ability to accumulate fatty acids with commercial application. Here, we review recent progress toward fermentation, extraction, of fungal fatty acids. To reduce cost of the fatty acids, fatty acid productions from raw materials were also summarized. Then, the synthesis mechanism of fatty acids was introduced. We also review recent studies of the metabolic engineering strategies have been developed as efficient tools in oleaginous fungi to overcome the biochemical limit and to improve production efficiency of the special fatty acids. It also can be predictable that metabolic engineering can further enhance biosynthesis of fatty acids and change the storage mode of fatty acids.
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Affiliation(s)
- Xin-Yue Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Bing Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Bei-Chen Huang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Feng-Biao Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Yue-Qi Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Shao-Geng Zhao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Min Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Hai-Ying Wang
- Key Laboratory of Sustainable Development of Polar Fishery, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xin-Jun Yu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Xiao-Yan Liu
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, Huaian, China
| | - Jing Jiang
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Zhi-Peng Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
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15
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Syed N, Singh S, Chaturvedi S, Nannaware AD, Khare SK, Rout PK. Production of lactones for flavoring and pharmacological purposes from unsaturated lipids: an industrial perspective. Crit Rev Food Sci Nutr 2022; 63:10047-10078. [PMID: 35531939 DOI: 10.1080/10408398.2022.2068124] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The enantiomeric pure and natural (+)-Lactones (C ≤ 14) with aromas obtained from fruits and milk are considered flavoring compounds. The flavoring value is related to the lactones' ring size and chain length, which blend in varying concentrations to produce different stone-fruit flavors. The nature-identical and enantiomeric pure (+)-lactones are only produced through whole-cell biotransformation of yeast. The industrially important γ-decalactone and δ-decalactone are produced by a four-step aerobic-oxidation of ricinoleic acid (RA) following the lactonization mechanism. Recently, metabolic engineering strategies have opened up new possibilities for increasing productivity. Another strategy for increasing yield is to immobilize the RA and remove lactones from the broth regularly. Besides flavor impact, γ-, δ-, ε-, ω-lactones of the carbon chain (C8-C12), the macro-lactones and their derivatives are vital in pharmaceuticals and healthcare. These analogues are isolated from natural sources or commercially produced via biotransformation and chemical synthesis processes for medicinal use or as active pharmaceutical ingredients. The various approaches to biotransformation have been discussed in this review to generate more prospects from a commercial point of view. Finally, this work will be regarded as a magical brick capable of containing both traditional and genetic engineering technology while contributing to a wide range of commercial applications.
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Affiliation(s)
- Naziya Syed
- Phytochemistry Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
| | - Suman Singh
- Phytochemistry Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
| | - Shivani Chaturvedi
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology, New Delhi, India
| | - Ashween Deepak Nannaware
- Phytochemistry Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Gaziabad, Uttar Pradesh, India
| | - Sunil Kumar Khare
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology, New Delhi, India
| | - Prasant Kumar Rout
- Phytochemistry Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Gaziabad, Uttar Pradesh, India
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16
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Jach ME, Malm A. Yarrowia lipolytica as an Alternative and Valuable Source of Nutritional and Bioactive Compounds for Humans. Molecules 2022; 27:2300. [PMID: 35408699 PMCID: PMC9000428 DOI: 10.3390/molecules27072300] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 12/04/2022] Open
Abstract
Yarrowia lipolytica, an oleagineous species of yeast, is a carrier of various important nutrients. The biomass of this yeast is an extensive source of protein, exogenous amino acids, bioavailable essenctial trace minerals, and lipid compounds as mainly unsaturated fatty acids. The biomass also contains B vitamins, including vitamin B12, and many other bioactive components. Therefore, Y. lipolytica biomass can be used in food supplements for humans as safe and nutritional additives for maintaining the homeostasis of the organism, including for vegans and vegetarians, athletes, people after recovery, and people at risk of B vitamin deficiencies.
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Affiliation(s)
- Monika Elżbieta Jach
- Department of Molecular Biology, The John Paul II Catholic University of Lublin, Konstantynów Street 1I, 20-708 Lublin, Poland
| | - Anna Malm
- Department of Pharmaceutical Microbiology, Medical University of Lublin, Chodźki Street 1, 20-093 Lublin, Poland;
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17
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Expression Profile of Selected Genes Involved in Storage Lipid Synthesis in a Model Oleaginous Yeast Species Yarrowia lipolytica. Int J Mol Sci 2022; 23:ijms23031041. [PMID: 35162970 PMCID: PMC8834811 DOI: 10.3390/ijms23031041] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 02/04/2023] Open
Abstract
Yarrowia lipolytica yeast is a model species of the group of oleaginous microorganisms capable of intracellular lipids accumulation in an amount exceeding 20% of the dry mass. Single cell oil biosynthesis can follow one of two biochemical pathways—de novo accumulation of cellular lipids in medium containing non-lipid carbon sources (including saccharides, glycerol) and ex novo microbial oil synthesis which involves fatty acids uptake from the environment. The mRNA expression of selected genes of de novo and ex novo lipid synthesis pathways was analyzed and correlated with the phenotypically observed features. It was proved that the accumulation yield of storage lipids via ex novo pathway was to some extent dependent on the limitation of the nitrogen source in the medium. It was also proposed that the synthesis of intracellular lipids in lipid-rich medium proceeded mainly via ex novo pathway, although the activity of genes encoding the enzymes of the de novo pathway were not completely inhibited at the stage of transcription by fatty acids present in the medium (e.g., ATP-citrate lyase). Molecular markers of two biosynthesis routes has been outlined and a hypothetical connection point between de novo and ex novo route were indicated.
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18
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Deragon E, Schuler M, Aiese Cigliano R, Dellero Y, Si Larbi G, Falconet D, Jouhet J, Maréchal E, Michaud M, Amato A, Rébeillé F. An Oil Hyper-Accumulator Mutant Highlights Peroxisomal ATP Import as a Regulatory Step for Fatty Acid Metabolism in Aurantiochytrium limacinum. Cells 2021; 10:2680. [PMID: 34685660 PMCID: PMC8534400 DOI: 10.3390/cells10102680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/24/2021] [Accepted: 09/24/2021] [Indexed: 11/17/2022] Open
Abstract
Thraustochytrids are marine protists that naturally accumulate triacylglycerol with long chains of polyunsaturated fatty acids, such as ω3-docosahexaenoic acid (DHA). They represent a sustainable response to the increasing demand for these "essential" fatty acids (FAs). Following an attempt to transform a strain of Aurantiochytrium limacinum, we serendipitously isolated a clone that did not incorporate any recombinant DNA but contained two to three times more DHA than the original strain. Metabolic analyses indicated a deficit in FA catabolism. However, whole transcriptome analysis did not show down-regulation of genes involved in FA catabolism. Genome sequencing revealed extensive DNA deletion in one allele encoding a putative peroxisomal adenylate transporter. Phylogenetic analyses and yeast complementation experiments confirmed the gene as a peroxisomal adenylate nucleotide transporter (AlANT1), homologous to yeast ScANT1 and plant peroxisomal adenylate nucleotide carrier AtPNC genes. In yeast and plants, a deletion of the peroxisomal adenylate transporter inhibits FA breakdown and induces FA accumulation, a phenotype similar to that described here. In response to this metabolic event, several compensatory mechanisms were observed. In particular, genes involved in FA biosynthesis were upregulated, also contributing to the high FA accumulation. These results support AlANT1 as a promising target for enhancing DHA production in Thraustochytrids.
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Affiliation(s)
- Etienne Deragon
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, CEDEX 9, 38054 Grenoble, France; (E.D.); (M.S.); (Y.D.); (G.S.L.); (D.F.); (J.J.); (E.M.); (M.M.)
| | - Martin Schuler
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, CEDEX 9, 38054 Grenoble, France; (E.D.); (M.S.); (Y.D.); (G.S.L.); (D.F.); (J.J.); (E.M.); (M.M.)
| | | | - Younès Dellero
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, CEDEX 9, 38054 Grenoble, France; (E.D.); (M.S.); (Y.D.); (G.S.L.); (D.F.); (J.J.); (E.M.); (M.M.)
- Institute of Genetic, Environment and Plant Protection, UMR 1349 IGEPP INRA, Agrocampus Ouest Rennes, Université Rennes 1, Domaine de la Motte BP35327, CEDEX, 35653 Le Rheu, France
| | - Gregory Si Larbi
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, CEDEX 9, 38054 Grenoble, France; (E.D.); (M.S.); (Y.D.); (G.S.L.); (D.F.); (J.J.); (E.M.); (M.M.)
| | - Denis Falconet
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, CEDEX 9, 38054 Grenoble, France; (E.D.); (M.S.); (Y.D.); (G.S.L.); (D.F.); (J.J.); (E.M.); (M.M.)
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, CEDEX 9, 38054 Grenoble, France; (E.D.); (M.S.); (Y.D.); (G.S.L.); (D.F.); (J.J.); (E.M.); (M.M.)
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, CEDEX 9, 38054 Grenoble, France; (E.D.); (M.S.); (Y.D.); (G.S.L.); (D.F.); (J.J.); (E.M.); (M.M.)
| | - Morgane Michaud
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, CEDEX 9, 38054 Grenoble, France; (E.D.); (M.S.); (Y.D.); (G.S.L.); (D.F.); (J.J.); (E.M.); (M.M.)
| | - Alberto Amato
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, CEDEX 9, 38054 Grenoble, France; (E.D.); (M.S.); (Y.D.); (G.S.L.); (D.F.); (J.J.); (E.M.); (M.M.)
| | - Fabrice Rébeillé
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, CEDEX 9, 38054 Grenoble, France; (E.D.); (M.S.); (Y.D.); (G.S.L.); (D.F.); (J.J.); (E.M.); (M.M.)
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Park YK, González-Fernández C, Robles-Iglesias R, Vidal L, Fontanille P, Kennes C, Tomás Pejó E, Nicaud JM, Fickers P. Bioproducts generation from carboxylate platforms by the non-conventional yeast Yarrowia lipolytica. FEMS Yeast Res 2021; 21:6359137. [PMID: 34453534 DOI: 10.1093/femsyr/foab047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/26/2021] [Indexed: 12/27/2022] Open
Abstract
In recent years, there has been a growing interest in the use of renewable sources for bio-based production aiming at developing sustainable and feasible approaches towards a circular economy. Among these renewable sources, organic wastes (OWs) can be anaerobically digested to generate carboxylates like volatile fatty acids (VFAs), lactic acid, and longer-chain fatty acids that are regarded as novel building blocks for the synthesis of value-added compounds by yeasts. This review discusses on the processes that can be used to create valuable molecules from OW-derived VFAs; the pathways employed by the oleaginous yeast Yarrowia lipolytica to directly metabolize such molecules; and the relationship between OW composition, anaerobic digestion, and VFA profiles. The review also summarizes the current knowledge about VFA toxicity, the pathways by which VFAs are metabolized and the metabolic engineering strategies that can be employed in Y. lipolytica to produce value-added biobased compounds from VFAs.
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Affiliation(s)
- Young-Kyoung Park
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
| | | | - Raúl Robles-Iglesias
- Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research (CICA), BIOENGIN group, University of La Coruña, Rúa da Fraga 10, E-15008 La Coruña, Spain
| | - Lea Vidal
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
| | - Pierre Fontanille
- Institut Pascal UMR CNRS 6602, Polytech Clermont-Ferrand, Université Clermont Auvergne (UCA), F-63178 Aubière, France
| | - Christian Kennes
- Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research (CICA), BIOENGIN group, University of La Coruña, Rúa da Fraga 10, E-15008 La Coruña, Spain
| | - Elia Tomás Pejó
- Biotechnological Processes Unit, IMDEA Energy, Avenida Ramón De La Sagra, 3. 28935, Móstoles, Madrid, Spain
| | - Jean-Marc Nicaud
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, University of Liège - Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
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Subcellular Localizations of Catalase and Exogenously Added Fatty Acid in Chlamydomonas reinhardtii. Cells 2021; 10:cells10081940. [PMID: 34440712 PMCID: PMC8391285 DOI: 10.3390/cells10081940] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 02/01/2023] Open
Abstract
Fatty acids are important biological components, yet the metabolism of fatty acids in microalgae is not clearly understood. Previous studies found that Chlamydomonas reinhardtii, the model microalga, incorporates exogenously added fatty acids but metabolizes them differently from animals and yeast. Furthermore, a recent metabolic flux analysis found that the majority of lipid turnover in C. reinhardtii is the recycling of acyl chains from and to membranes, rather than β -oxidation. This indicates that for the alga, the maintenance of existing acyl chains may be more valuable than their breakdown for energy. To gain cell-biological knowledge of fatty acid metabolism in C. reinhardtii, we conducted microscopy analysis with fluorescent probes. First, we found that CAT1 (catalase isoform 1) is in the peroxisomes while CAT2 (catalase isoform 2) is localized in the endoplasmic reticulum, indicating the alga is capable of detoxifying hydrogen peroxide that would be produced during β-oxidation in the peroxisomes. Second, we compared the localization of exogenously added FL-C16 (fluorescently labelled palmitic acid) with fluorescently marked endosomes, mitochondria, peroxisomes, lysosomes, and lipid droplets. We found that exogenously added FL-C16 are incorporated and compartmentalized via a non-endocytic route within 10 min. However, the fluorescence signals from FL-C16 did not colocalize with any marked organelles, including peroxisomes. During triacylglycerol accumulation, the fluorescence signals from FL-C16 were localized in lipid droplets. These results support the idea that membrane turnover is favored over β-oxidation in C. reinhardtii. The knowledge gained in these analyses would aid further studies of the fatty acid metabolism.
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Kell DB. A protet-based, protonic charge transfer model of energy coupling in oxidative and photosynthetic phosphorylation. Adv Microb Physiol 2021; 78:1-177. [PMID: 34147184 DOI: 10.1016/bs.ampbs.2021.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Textbooks of biochemistry will explain that the otherwise endergonic reactions of ATP synthesis can be driven by the exergonic reactions of respiratory electron transport, and that these two half-reactions are catalyzed by protein complexes embedded in the same, closed membrane. These views are correct. The textbooks also state that, according to the chemiosmotic coupling hypothesis, a (or the) kinetically and thermodynamically competent intermediate linking the two half-reactions is the electrochemical difference of protons that is in equilibrium with that between the two bulk phases that the coupling membrane serves to separate. This gradient consists of a membrane potential term Δψ and a pH gradient term ΔpH, and is known colloquially as the protonmotive force or pmf. Artificial imposition of a pmf can drive phosphorylation, but only if the pmf exceeds some 150-170mV; to achieve in vivo rates the imposed pmf must reach 200mV. The key question then is 'does the pmf generated by electron transport exceed 200mV, or even 170mV?' The possibly surprising answer, from a great many kinds of experiment and sources of evidence, including direct measurements with microelectrodes, indicates it that it does not. Observable pH changes driven by electron transport are real, and they control various processes; however, compensating ion movements restrict the Δψ component to low values. A protet-based model, that I outline here, can account for all the necessary observations, including all of those inconsistent with chemiosmotic coupling, and provides for a variety of testable hypotheses by which it might be refined.
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Affiliation(s)
- Douglas B Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative, Biology, University of Liverpool, Liverpool, United Kingdom; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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22
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Salvador López JM, Van Bogaert INA. Microbial fatty acid transport proteins and their biotechnological potential. Biotechnol Bioeng 2021; 118:2184-2201. [PMID: 33638355 DOI: 10.1002/bit.27735] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 01/08/2021] [Accepted: 02/24/2021] [Indexed: 12/11/2022]
Abstract
Fatty acid metabolism has been widely studied in various organisms. However, fatty acid transport has received less attention, even though it plays vital physiological roles, such as export of toxic free fatty acids or uptake of exogenous fatty acids. Hence, there are important knowledge gaps in how fatty acids cross biological membranes, and many mechanisms and proteins involved in these processes still need to be determined. The lack of information is more predominant in microorganisms, even though the identification of fatty acids transporters in these cells could lead to establishing new drug targets or improvements in microbial cell factories. This review provides a thorough analysis of the current information on fatty acid transporters in microorganisms, including bacteria, yeasts and microalgae species. Most available information relates to the model organisms Escherichia coli and Saccharomyces cerevisiae, but transport systems of other species are also discussed. Intracellular trafficking of fatty acids and their transport through organelle membranes in eukaryotic organisms is described as well. Finally, applied studies and engineering efforts using fatty acids transporters are presented to show the applied potential of these transporters and to stress the need for further identification of new transporters and their engineering.
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Affiliation(s)
- José M Salvador López
- BioPort Group, Faculty of Bioscience Engineering, Centre for Synthetic Biology (CSB), Ghent University, Ghent, Belgium
| | - Inge N A Van Bogaert
- BioPort Group, Faculty of Bioscience Engineering, Centre for Synthetic Biology (CSB), Ghent University, Ghent, Belgium
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23
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Patel A, Sarkar O, Rova U, Christakopoulos P, Matsakas L. Valorization of volatile fatty acids derived from low-cost organic waste for lipogenesis in oleaginous microorganisms-A review. BIORESOURCE TECHNOLOGY 2021; 321:124457. [PMID: 33316701 DOI: 10.1016/j.biortech.2020.124457] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/21/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
To meet environmental sustainability goals, microbial oils have been suggested as an alternative to petroleum-based products. At present, microbial fermentation for oil production relies on pure sugar-based feedstocks. However, these feedstocks are expensive and are in limited supply. Volatile fatty acids, which are generated as intermediates during anaerobic digestion of organic waste have emerged as a renewable feedstock that has the potential to replace conventional sugar sources for microbial oil production. They comprise short-chain (C2 to C6) organic acids and are employed as building blocks in the chemical industry. The present review discusses the use of oleaginous microorganisms for the production of biofuels and added-value products starting from volatile fatty acids as feedstocks. The review describes the metabolic pathways enabling lipogenesis from volatile fatty acids, and focuses on strategies to enhance lipid accumulation in oleaginous microorganisms by tuning the ratios of volatile fatty acids generated via anaerobic fermentation.
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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
| | - Omprakash Sarkar
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-971 87 Luleå, Sweden
| | - 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
| | - 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
| | - 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.
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24
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Liu H, Song Y, Fan X, Wang C, Lu X, Tian Y. Yarrowia lipolytica as an Oleaginous Platform for the Production of Value-Added Fatty Acid-Based Bioproducts. Front Microbiol 2021; 11:608662. [PMID: 33469452 PMCID: PMC7813756 DOI: 10.3389/fmicb.2020.608662] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/26/2020] [Indexed: 01/14/2023] Open
Abstract
The microbial fermentation process has been used as an alternative pathway to the production of value-added natural products. Of the microorganisms, Yarrowia lipolytica, as an oleaginous platform, is able to produce fatty acid-derived biofuels and biochemicals. Nowadays, there are growing progresses on the production of value-added fatty acid-based bioproducts in Y. lipolytica. However, there are fewer reviews performing the metabolic engineering strategies and summarizing the current production of fatty acid-based bioproducts in Y. lipolytica. To this end, we briefly provide the fatty acid metabolism, including fatty acid biosynthesis, transportation, and degradation. Then, we introduce the various metabolic engineering strategies for increasing bioproduct accumulation in Y. lipolytica. Further, the advanced progress in the production of fatty acid-based bioproducts by Y. lipolytica, including nutraceuticals, biofuels, and biochemicals, is summarized. This review will provide attractive thoughts for researchers working in the field of Y. lipolytica.
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Affiliation(s)
- Huhu Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Yulan Song
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Xiao Fan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Chong Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Xiangyang Lu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Yun Tian
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
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25
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Park YK, Nicaud JM. Metabolic Engineering for Unusual Lipid Production in Yarrowia lipolytica. Microorganisms 2020; 8:E1937. [PMID: 33291339 PMCID: PMC7762315 DOI: 10.3390/microorganisms8121937] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 12/15/2022] Open
Abstract
Using microorganisms as lipid-production factories holds promise as an alternative method for generating petroleum-based chemicals. The non-conventional yeast Yarrowia lipolytica is an excellent microbial chassis; for example, it can accumulate high levels of lipids and use a broad range of substrates. Furthermore, it is a species for which an array of efficient genetic engineering tools is available. To date, extensive work has been done to metabolically engineer Y. lipolytica to produce usual and unusual lipids. Unusual lipids are scarce in nature but have several useful applications. As a result, they are increasingly becoming the targets of metabolic engineering. Unusual lipids have distinct structures; they can be generated by engineering endogenous lipid synthesis or by introducing heterologous enzymes to alter the functional groups of fatty acids. In this review, we describe current metabolic engineering strategies for improving lipid production and highlight recent researches on unusual lipid production in Y. lipolytica.
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Affiliation(s)
- Young-Kyoung Park
- Micalis Institute, AgroParisTech, INRAE, Université Paris-Saclay, 78352 Jouy-en-Josas, France;
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26
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Lajus S, Dusséaux S, Verbeke J, Rigouin C, Guo Z, Fatarova M, Bellvert F, Borsenberger V, Bressy M, Nicaud JM, Marty A, Bordes F. Engineering the Yeast Yarrowia lipolytica for Production of Polylactic Acid Homopolymer. Front Bioeng Biotechnol 2020; 8:954. [PMID: 33195110 PMCID: PMC7609957 DOI: 10.3389/fbioe.2020.00954] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/23/2020] [Indexed: 12/17/2022] Open
Abstract
Polylactic acid is a plastic polymer widely used in different applications from printing filaments for 3D printer to mulching films in agriculture, packaging materials, etc. Here, we report the production of poly-D-lactic acid (PDLA) in an engineered yeast strain of Yarrowia lipolytica. Firstly, the pathway for lactic acid consumption in this yeast was identified and interrupted. Then, the heterologous pathway for PDLA production, which contains a propionyl-CoA transferase (PCT) converting lactic acid into lactyl-CoA, and an evolved polyhydroxyalkanoic acid (PHA) synthase polymerizing lactyl-CoA, was introduced into the engineered strain. Among the different PCT proteins that were expressed in Y. lipolytica, the Clostridium propionicum PCT exhibited the highest efficiency in conversion of D-lactic acid to D-lactyl-CoA. We further evaluated the lactyl-CoA and PDLA productions by expressing this PCT and a variant of Pseudomonas aeruginosa PHA synthase at different subcellular localizations. The best PDLA production was obtained by expressing the PCT in the cytosol and the variant of PHA synthase in peroxisome. PDLA homopolymer accumulation in the cell reached 26 mg/g-DCW, and the molecular weights of the polymer (Mw = 50.5 × 103 g/mol and Mn = 12.5 × 103 g/mol) were among the highest reported for an in vivo production.
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Affiliation(s)
- Sophie Lajus
- TBI, CNRS, INRAE, INSA, Université de Toulouse, Toulouse, France
| | - Simon Dusséaux
- TBI, CNRS, INRAE, INSA, Université de Toulouse, Toulouse, France
| | - Jonathan Verbeke
- INRAE, AgroParisTech, Université Paris-Saclay, Micalis Institute, Jouy-en-Josas, France
| | - Coraline Rigouin
- TBI, CNRS, INRAE, INSA, Université de Toulouse, Toulouse, France
| | - Zhongpeng Guo
- TBI, CNRS, INRAE, INSA, Université de Toulouse, Toulouse, France
| | - Maria Fatarova
- TBI, CNRS, INRAE, INSA, Université de Toulouse, Toulouse, France
| | | | | | - Mélusine Bressy
- TBI, CNRS, INRAE, INSA, Université de Toulouse, Toulouse, France
| | - Jean-Marc Nicaud
- INRAE, AgroParisTech, Université Paris-Saclay, Micalis Institute, Jouy-en-Josas, France
| | - Alain Marty
- TBI, CNRS, INRAE, INSA, Université de Toulouse, Toulouse, France
- Carbios, Biopôle Clermont Limagne, Saint-Beauzire, France
| | - Florence Bordes
- TBI, CNRS, INRAE, INSA, Université de Toulouse, Toulouse, France
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27
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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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28
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Ghogare R, Chen S, Xiong X. Metabolic Engineering of Oleaginous Yeast Yarrowia lipolytica for Overproduction of Fatty Acids. Front Microbiol 2020; 11:1717. [PMID: 32849364 PMCID: PMC7418586 DOI: 10.3389/fmicb.2020.01717] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 06/30/2020] [Indexed: 01/24/2023] Open
Abstract
The oleaginous yeast Yarrowia lipolytica has attracted much attention due to its ability to utilize a wide range of substrates to accumulate high lipid content and its flexibility for genetic manipulation. In this study, intracellular lipid metabolism in Y. lipolytica was tailored to produce fatty acid, a renewable oleochemical and precursor for production of advanced biofuels. Two main strategies, including blocking activation and peroxisomal uptake of fatty acids and elimination of biosynthesis of lipids, were employed to reduce fatty acid consumption by the native pathways in Y. lipolytica. Both genetic modifications improved fatty acid production. However, disruption of the genes responsible for assembly of nonpolar lipid molecules including triacylglycerols (TAGs) and steryl esters resulted in the deleterious effects on the cell growth. The gene tesA encoding thioesterase from Escherichia coli was expressed in the strain with disrupted faa genes encoding fatty acyl-CoA synthetases and pxa1 encoding peroxisomal acyl-CoA transporter, and the titer of fatty acids resulted in 2.3 g/L in shake flask culture, representing 11-fold improvement compared with the parent strain. Expressing the native genes encoding acetyl-CoA carboxylase (ACC) and hexokinase also increased fatty acid production, although the improvement was not as significant as that with tesA expression. Saturated fatty acids including palmitic acid (C16:0) and stearic acid (C18:0) increased remarkably in the fatty acid composition of the recombinant bearing tesA compared with the parent strain. The recombinant expressing tesA gene resulted in high lipid content, indicating the great fatty acid producing potential of Y. lipolytica. The results highlight the achievement of fatty acid overproduction without adverse effect on growth of the strain. Results of this study provided insight into the relationship between fatty acid and lipid metabolism in Y. lipolytica, confirming the avenue to reprogram lipid metabolism of this host for overproduction of renewable fatty acids.
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Affiliation(s)
- Rishikesh Ghogare
- Department of Biological Systems Engineering, Washington State University, Pullman, WA, United States
| | - Shulin Chen
- Department of Biological Systems Engineering, Washington State University, Pullman, WA, United States
| | - Xiaochao Xiong
- Department of Biological Systems Engineering, Washington State University, Pullman, WA, United States
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29
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Comparison and Analysis of Published Genome-scale Metabolic Models of Yarrowia lipolytica. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0208-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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30
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Llamas M, Magdalena JA, González-Fernández C, Tomás-Pejó E. Volatile fatty acids as novel building blocks for oil-based chemistry via oleaginous yeast fermentation. Biotechnol Bioeng 2019; 117:238-250. [PMID: 31544974 DOI: 10.1002/bit.27180] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/20/2019] [Accepted: 09/16/2019] [Indexed: 02/06/2023]
Abstract
Microbial oils are proposed as a suitable alternative to petroleum-based chemistry in terms of environmental preservation. These oils have traditionally been studied using sugar-based feedstock, which implies high costs, substrate limitation, and high contamination risks. In this sense, low-cost carbon sources such as volatile fatty acids (VFAs) are envisaged as promising building blocks for lipid biosynthesis to produce oil-based bioproducts. VFAs can be generated from a wide variety of organic wastes through anaerobic digestion and further converted into lipids by oleaginous yeasts (OYs) in a fermentation process. These microorganisms can accumulate in the form of lipid bodies, lipids of up to 60% wt/wt of their biomass. In this context, OY is a promising biotechnological tool for biofuel and bioproduct generation using low-cost VFA media as substrates. This review covers recent advances in microbial oil production from VFAs. Production of VFAs via anaerobic digestion processes and the involved metabolic pathways are reviewed. The main challenges as well as recent approaches for lipid overproduction are also discussed.
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Affiliation(s)
- Mercedes Llamas
- Biotechnological Processes Unit, IMDEA Energy, Móstoles, Spain
| | | | | | - Elia Tomás-Pejó
- Biotechnological Processes Unit, IMDEA Energy, Móstoles, Spain
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31
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Marella ER, Dahlin J, Dam MI, Ter Horst J, Christensen HB, Sudarsan S, Wang G, Holkenbrink C, Borodina I. A single-host fermentation process for the production of flavor lactones from non-hydroxylated fatty acids. Metab Eng 2019; 61:427-436. [PMID: 31404648 DOI: 10.1016/j.ymben.2019.08.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/28/2019] [Accepted: 08/08/2019] [Indexed: 01/17/2023]
Abstract
Lactone flavors with fruity, milky, coconut, and other aromas are widely used in the food and fragrance industries. Lactones are produced by chemical synthesis or by biotransformation of plant-sourced hydroxy fatty acids. We established a novel method to produce flavor lactones from abundant non-hydroxylated fatty acids using yeast cell factories. Oleaginous yeast Yarrowia lipolytica was engineered to perform hydroxylation of fatty acids and chain-shortening via β-oxidation to preferentially twelve or ten carbons. The strains could produce γ-dodecalactone from oleic acid and δ-decalactone from linoleic acid. Through metabolic engineering, the titer was improved 4-fold, and the final strain produced 282 mg/L γ-dodecalactone in a fed-batch bioreactor. The study paves the way for the production of lactones by fermentation of abundant fatty feedstocks.
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Affiliation(s)
- Eko Roy Marella
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs, Lyngby, Denmark
| | - Jonathan Dahlin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs, Lyngby, Denmark
| | - Marie Inger Dam
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs, Lyngby, Denmark
| | - Jolanda Ter Horst
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs, Lyngby, Denmark
| | - Hanne Bjerre Christensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs, Lyngby, Denmark
| | - Suresh Sudarsan
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs, Lyngby, Denmark
| | - Guokun Wang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs, Lyngby, Denmark
| | - Carina Holkenbrink
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs, Lyngby, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs, Lyngby, Denmark.
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32
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Claus S, Jezierska S, Van Bogaert INA. Protein‐facilitated transport of hydrophobic molecules across the yeast plasma membrane. FEBS Lett 2019; 593:1508-1527. [DOI: 10.1002/1873-3468.13469] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 05/31/2019] [Accepted: 06/03/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Silke Claus
- Biochemical and Microbial Technology Universiteit Gent Belgium
| | | | - Inge N. A. Van Bogaert
- Lab. of Industrial Microbiology and Biocatalysis Faculty of Bioscience Engineering Ghent University Belgium
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33
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High production of fatty alcohols in Yarrowia lipolytica by coordination with glycolysis. Sci China Chem 2019. [DOI: 10.1007/s11426-019-9456-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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34
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Soong YHV, Liu N, Yoon S, Lawton C, Xie D. Cellular and metabolic engineering of oleaginous yeast Yarrowia lipolytica for bioconversion of hydrophobic substrates into high-value products. Eng Life Sci 2019; 19:423-443. [PMID: 32625020 DOI: 10.1002/elsc.201800147] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 12/12/2018] [Accepted: 02/07/2019] [Indexed: 12/17/2022] Open
Abstract
The non-conventional oleaginous yeast Yarrowia lipolytica is able to utilize both hydrophilic and hydrophobic carbon sources as substrates and convert them into value-added bioproducts such as organic acids, extracellular proteins, wax esters, long-chain diacids, fatty acid ethyl esters, carotenoids and omega-3 fatty acids. Metabolic pathway analysis and previous research results show that hydrophobic substrates are potentially more preferred by Y. lipolytica than hydrophilic substrates to make high-value products at higher productivity, titer, rate, and yield. Hence, Y. lipolytica is becoming an efficient and promising biomanufacturing platform due to its capabilities in biosynthesis of extracellular lipases and directly converting the extracellular triacylglycerol oils and fats into high-value products. It is believed that the cell size and morphology of the Y. lipolytica is related to the cell growth, nutrient uptake, and product formation. Dimorphic Y. lipolytica demonstrates the yeast-to-hypha transition in response to the extracellular environments and genetic background. Yeast-to-hyphal transition regulating genes, such as YlBEM1, YlMHY1 and YlZNC1 and so forth, have been identified to involve as major transcriptional factors that control morphology transition in Y. lipolytica. The connection of the cell polarization including cell cycle and the dimorphic transition with the cell size and morphology in Y. lipolytica adapting to new growth are reviewed and discussed. This review also summarizes the general and advanced genetic tools that are used to build a Y. lipolytica biomanufacturing platform.
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Affiliation(s)
- Ya-Hue Valerie Soong
- Massachusetts Biomanufacturing Center Department of Chemical Engineering University of Massachusetts Lowell Lowell MA USA
| | - Na Liu
- Massachusetts Biomanufacturing Center Department of Chemical Engineering University of Massachusetts Lowell Lowell MA USA
| | - Seongkyu Yoon
- Massachusetts Biomanufacturing Center Department of Chemical Engineering University of Massachusetts Lowell Lowell MA USA
| | - Carl Lawton
- Massachusetts Biomanufacturing Center Department of Chemical Engineering University of Massachusetts Lowell Lowell MA USA
| | - Dongming Xie
- Massachusetts Biomanufacturing Center Department of Chemical Engineering University of Massachusetts Lowell Lowell MA USA
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Wei H, Wang W, Alper HS, Xu Q, Knoshaug EP, Van Wychen S, Lin CY, Luo Y, Decker SR, Himmel ME, Zhang M. Ameliorating the Metabolic Burden of the Co-expression of Secreted Fungal Cellulases in a High Lipid-Accumulating Yarrowia lipolytica Strain by Medium C/N Ratio and a Chemical Chaperone. Front Microbiol 2019; 9:3276. [PMID: 30687267 PMCID: PMC6333634 DOI: 10.3389/fmicb.2018.03276] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/17/2018] [Indexed: 12/19/2022] Open
Abstract
Yarrowia lipolytica, known to accumulate lipids intracellularly, lacks the cellulolytic enzymes needed to break down solid biomass directly. This study aimed to evaluate the potential metabolic burden of expressing core cellulolytic enzymes in an engineered high lipid-accumulating strain of Y. lipolytica. Three fungal cellulases, Talaromyces emersonii-Trichoderma reesei chimeric cellobiohydrolase I (chimeric-CBH I), T. reesei cellobiohydrolase II (CBH II), and T. reesei endoglucanase II (EG II) were expressed using three constitutive strong promoters as a single integrative expression block in a recently engineered lipid hyper-accumulating strain of Y. lipolytica (HA1). In yeast extract-peptone-dextrose (YPD) medium, the resulting cellulase co-expressing transformant YL165-1 had the chimeric-CBH I, CBH II, and EG II secretion titers being 26, 17, and 132 mg L-1, respectively. Cellulase co-expression in YL165-1 in culture media with a moderate C/N ratio of ∼4.5 unexpectedly resulted in a nearly two-fold reduction in cellular lipid accumulation compared to the parental control strain, a sign of cellular metabolic drain. Such metabolic drain was ameliorated when grown in media with a high C/N ratio of 59 having a higher glucose utilization rate that led to approximately twofold more cell mass and threefold more lipid production per liter culture compared to parental control strain, suggesting cross-talk between cellulase and lipid production, both of which involve the endoplasmic reticulum (ER). Most importantly, we found that the chemical chaperone, trimethylamine N-oxide dihydride increased glucose utilization, cell mass and total lipid titer in the transformants, suggesting further amelioration of the metabolic drain. This is the first study examining lipid production in cellulase-expressing Y. lipolytica strains under various C/N ratio media and with a chemical chaperone highlighting the metabolic complexity for developing robust, cellulolytic and lipogenic yeast strains.
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Affiliation(s)
- Hui Wei
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Wei Wang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Hal S Alper
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Qi Xu
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Eric P Knoshaug
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Stefanie Van Wychen
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States.,National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Chien-Yuan Lin
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Yonghua Luo
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Stephen R Decker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Min Zhang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States.,National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
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van Nieuwenhuijzen EJ, Sailer MF, van den Heuvel ER, Rensink S, Adan OCG, Samson RA. Vegetable oils as carbon and energy source for Aureobasidium melanogenum in batch cultivation. Microbiologyopen 2018; 8:e00764. [PMID: 30515994 PMCID: PMC6562153 DOI: 10.1002/mbo3.764] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/10/2018] [Accepted: 10/12/2018] [Indexed: 11/22/2022] Open
Abstract
Dark homogenous fungal‐based layers called biofinishes and vegetable oils are key ingredients of an innovative wood protecting system. The aim of this study was to determine which of the vegetable oils that have been used to generate biofinishes on wood will provide carbon and energy for the biofinish‐inhabiting fungus Aureobasidium melanogenum, and to determine the effect of the oil type and the amount of oil on the cell yield. Aureobasidium melanogenum was cultivated in shake flasks with different types and amounts of carbon‐based nutrients. Oil‐related total cell and colony‐forming unit growth were demonstrated in suspensions with initially 1% raw linseed, stand linseed, and olive oil. Oil‐related cell growth was also demonstrated with raw linseed oil, using an initial amount of 0.02% and an oil addition during cultivation. Nile red staining showed the accumulation of fatty acids inside cells grown in the presence of oil. In conclusion, each tested vegetable oil was used as carbon and energy source by A. melanogenum. The results indicated that stand linseed oil provides less carbon and energy than olive and raw linseed oil. This research is a fundamental step in unraveling the effects of vegetable oils on biofinish formation.
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Affiliation(s)
| | - Michael F Sailer
- Saxion University of Applied Sciences, Enschede, The Netherlands.,Xylotrade BV, Goor, The Netherlands
| | - Edwin R van den Heuvel
- Department of Mathematics and Computer Science, University of Technology Eindhoven, Eindhoven, The Netherlands
| | | | - Olaf C G Adan
- Department of Applied Physics, University of Technology Eindhoven, Eindhoven, The Netherlands
| | - Robert A Samson
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
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Hanko EK, Denby CM, Sànchez i Nogué V, Lin W, Ramirez KJ, Singer CA, Beckham GT, Keasling JD. Engineering β-oxidation in Yarrowia lipolytica for methyl ketone production. Metab Eng 2018; 48:52-62. [DOI: 10.1016/j.ymben.2018.05.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 05/14/2018] [Accepted: 05/27/2018] [Indexed: 11/17/2022]
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Gao D, Smith S, Spagnuolo M, Rodriguez G, Blenner M. Dual CRISPR-Cas9 Cleavage Mediated Gene Excision and Targeted Integration in Yarrowia lipolytica. Biotechnol J 2018; 13:e1700590. [PMID: 29809313 DOI: 10.1002/biot.201700590] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/23/2018] [Indexed: 12/12/2022]
Abstract
CRISPR-Cas9 technology has been successfully applied in Yarrowia lipolytica for targeted genomic editing including gene disruption and integration; however, disruptions by existing methods typically result from small frameshift mutations caused by indels within the coding region, which usually resulted in unnatural protein. In this study, a dual cleavage strategy directed by paired sgRNAs is developed for gene knockout. This method allows fast and robust gene excision, demonstrated on six genes of interest. The targeted regions for excision vary in length from 0.3 kb up to 3.5 kb and contain both non-coding and coding regions. The majority of the gene excisions are repaired by perfect nonhomologous end-joining without indel. Based on this dual cleavage system, two targeted markerless integration methods are developed by providing repair templates. While both strategies are effective, homology mediated end joining (HMEJ) based method are twice as efficient as homology recombination (HR) based method. In both cases, dual cleavage leads to similar or improved gene integration efficiencies compared to gene excision without integration. This dual cleavage strategy will be useful for not only generating more predictable and robust gene knockout, but also for efficient targeted markerless integration, and simultaneous knockout and integration in Y. lipolytica.
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Affiliation(s)
- Difeng Gao
- Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, USA
| | - Spencer Smith
- Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, USA
| | - Michael Spagnuolo
- Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, USA
| | - Gabriel Rodriguez
- Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, USA
| | - Mark Blenner
- Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, USA
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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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40
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Niehus X, Crutz-Le Coq AM, Sandoval G, Nicaud JM, Ledesma-Amaro R. Engineering Yarrowia lipolytica to enhance lipid production from lignocellulosic materials. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:11. [PMID: 29387172 PMCID: PMC5776775 DOI: 10.1186/s13068-018-1010-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 01/08/2018] [Indexed: 05/11/2023]
Abstract
BACKGROUND Yarrowia lipolytica is a common biotechnological chassis for the production of lipids, which are the preferred feedstock for the production of fuels and chemicals. To reduce the cost of microbial lipid production, inexpensive carbon sources must be used, such as lignocellulosic hydrolysates. Unfortunately, lignocellulosic materials often contain toxic compounds and a large amount of xylose, which cannot be used by Y. lipolytica. RESULTS In this work, we engineered this yeast to efficiently use xylose as a carbon source for the production of lipids by overexpressing native genes. We further increased the lipid content by overexpressing heterologous genes to facilitate the conversion of xylose-derived metabolites into lipid precursors. Finally, we showed that these engineered strains were able to grow and produce lipids in a very high yield (lipid content = 67%, titer = 16.5 g/L, yield = 3.44 g/g sugars, productivity 1.85 g/L/h) on a xylose-rich agave bagasse hydrolysate in spite of toxic compounds. CONCLUSIONS This work demonstrates the potential of metabolic engineering to reduce the costs of lipid production from inexpensive substrates as source of fuels and chemicals.
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Affiliation(s)
- Xochitl Niehus
- Industrial Biotechnology, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ) A.C., 44270 Guadalajara, Jalisco Mexico
| | - Anne-Marie Crutz-Le Coq
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Georgina Sandoval
- 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
| | - Rodrigo Ledesma-Amaro
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
- Department of Bioengineering, Imperial College London, London, SW7 2AZ UK
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Larroude M, Celinska E, Back A, Thomas S, Nicaud JM, Ledesma-Amaro R. A synthetic biology approach to transform Yarrowia lipolytica into a competitive biotechnological producer of β-carotene. Biotechnol Bioeng 2017; 115:464-472. [PMID: 28986998 DOI: 10.1002/bit.26473] [Citation(s) in RCA: 193] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/11/2017] [Accepted: 10/05/2017] [Indexed: 12/17/2022]
Abstract
The increasing market demands of β-carotene as colorant, antioxidant and vitamin precursor, requires novel biotechnological production platforms. Yarrowia lipolytica, is an industrial organism unable to naturally synthesize carotenoids but with the ability to produce high amounts of the precursor Acetyl-CoA. We first found that a lipid overproducer strain was capable of producing more β-carotene than a wild type after expressing the heterologous pathway. Thereafter, we developed a combinatorial synthetic biology approach base on Golden Gate DNA assembly to screen the optimum promoter-gene pairs for each transcriptional unit expressed. The best strain reached a production titer of 1.5 g/L and a maximum yield of 0.048 g/g of glucose in flask. β-carotene production was further increased in controlled conditions using a fed-batch fermentation. A total production of β-carotene of 6.5 g/L and 90 mg/g DCW with a concomitant production of 42.6 g/L of lipids was achieved. Such high titers suggest that engineered Y. lipolytica is a competitive producer organism of β-carotene.
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Affiliation(s)
- Macarena Larroude
- BIMLip, Biologie Intégrative du Métabolisme Lipidique Team, Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Ewelina Celinska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Poznan, Poland
| | - Alexandre Back
- BIMLip, Biologie Intégrative du Métabolisme Lipidique Team, Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Stephan Thomas
- BIMLip, Biologie Intégrative du Métabolisme Lipidique Team, Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Jean-Marc Nicaud
- BIMLip, Biologie Intégrative du Métabolisme Lipidique Team, Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Rodrigo Ledesma-Amaro
- BIMLip, Biologie Intégrative du Métabolisme Lipidique Team, Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,Department of Bioengineering, Imperial College London, London, UK
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42
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Effects of glucose concentration on 1,18-cis-octadec-9-enedioic acid biotransformation efficiency and lipid body formation in Candida tropicalis. Sci Rep 2017; 7:13842. [PMID: 29062119 PMCID: PMC5653835 DOI: 10.1038/s41598-017-14173-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 10/06/2017] [Indexed: 11/08/2022] Open
Abstract
The unsaturated long-chain α,ω-dicarboxylic acid 1,18-cis-octadec-9-enedioic acid (cis-ODA) is a versatile precursor of various valuable compounds, such as polymers, and can be obtained from renewable resources. This makes cis-ODA highly attractive for the chemical industry where there is a growing interest in sustainable processes. However, chemical synthesis of the cis isomers is currently not feasible. In contrast, biotechnological production allows for highly specific and selective reactions. Therefore, we developed an efficient production strategy for cis-ODA using Candida tropicalis as a whole-cell biocatalyst for the biotransformation of oleic acid, which naturally occurs in various fats and oils. Applying a bench-top system comprising eight parallel bioreactors, the production process was characterised and optimised for high productivity. Glucose feed rate was identified as the most crucial process parameter influencing product yield, with high rates inducing oleic acid incorporation into triacylglycerols and storage in lipid bodies. Conversely, application of medium-chain length fatty acid as a substrate did not show any occurrence of lipid bodies. Applying the lowest possible molar ratio of glucose to oleic acid (1.5) resulted in marginal lipid body formation, but led to a peak volumetric productivity of 0.56 g/L/h and a final titre of approximately 45 g/L with a corresponding yield of 70%.
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43
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Xie D. Integrating Cellular and Bioprocess Engineering in the Non-Conventional Yeast Yarrowia lipolytica for Biodiesel Production: A Review. Front Bioeng Biotechnol 2017; 5:65. [PMID: 29090211 PMCID: PMC5650997 DOI: 10.3389/fbioe.2017.00065] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/02/2017] [Indexed: 12/14/2022] Open
Abstract
As one of the major biofuels to replace fossil fuel, biodiesel has now attracted more and more attention due to its advantages in higher energy density and overall less greenhouse gas generation. Biodiesel (fatty acid alkyl esters) is produced by chemically or enzymatically catalyzed transesterification of lipids from microbial cells, microalgae, oil crops, or animal fats. Currently, plant oils or waste cooking oils/fats remain the major source for biodiesel production via enzymatic route, but the production capacity is limited either by the uncertain supplement of plant oils or by the low or inconsistent quality of waste oils/fats. In the past decades, significant progresses have been made on synthesis of microalgae oils directly from CO2via a photosynthesis process, but the production cost from any current technologies is still too high to be commercialized due to microalgae’s slow growth rate on CO2, inefficiency in photo-bioreactors, lack of efficient contamination control methods, and high cost in downstream recovery. At the same time, many oleaginous microorganisms have been studied to produce lipids via the fatty acid synthesis pathway under aerobic fermentation conditions, among them one of the most studied is the non-conventional yeast, Yarrowia lipolytica, which is able to produce fatty acids at very high titer, rate, and yield from various economical substrates. This review summarizes the recent research progresses in both cellular and bioprocess engineering in Y. lipolytica to produce lipids at a low cost that may lead to commercial-scale biodiesel production. Specific technologies include the strain engineering for using various substrates, metabolic engineering in high-yield lipid synthesis, cell morphology study for efficient substrate uptake and product formation, free fatty acid formation and secretion for improved downstream recovery, and fermentation engineering for higher productivities and less operating cost. To further improve the economics of the microbial oil-based biodiesel, production of lipid-related or -derived high-value products are also discussed.
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Affiliation(s)
- Dongming Xie
- Massachusetts Biomanufacturing Center, Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA, United States
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44
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Yuzbasheva EY, Mostova EB, Andreeva NI, Yuzbashev TV, Laptev IA, Sobolevskaya TI, Sineoky SP. Co-expression of glucose-6-phosphate dehydrogenase and acyl-CoA binding protein enhances lipid accumulation in the yeast Yarrowia lipolytica. N Biotechnol 2017; 39:18-21. [DOI: 10.1016/j.nbt.2017.05.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 02/08/2017] [Accepted: 03/28/2017] [Indexed: 10/19/2022]
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Combinatorial Engineering of Yarrowia lipolytica as a Promising Cell Biorefinery Platform for the de novo Production of Multi-Purpose Long Chain Dicarboxylic Acids. FERMENTATION-BASEL 2017. [DOI: 10.3390/fermentation3030040] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Abstract
Increasing demand for plant oil for food, feed, and fuel production has led to food-fuel competition, higher plant lipid cost, and more need for agricultural land. On the other hand, the growing global production of biodiesel has increased the production of glycerol as a by-product. Efficient utilization of this by-product can reduce biodiesel production costs. We engineered Yarrowia lipolytica (Y. lipolytica) at various metabolic levels of lipid biosynthesis, degradation, and regulation for enhanced lipid and citric acid production. We used a one-step double gene knock-in and site-specific gene knock-out strategy. The resulting final strain combines the overexpression of homologous DGA1 and DGA2 in a POX-deleted background, and deletion of the SNF1 lipid regulator. This increased lipid and citric acid production in the strain under nitrogen-limiting conditions (C/N molar ratio of 60). The engineered strain constitutively accumulated lipid at a titer of more than 4.8 g/L with a lipid content of 53% of dry cell weight (DCW). The secreted citric acid reached a yield of 0.75 g/g (up to ~45 g/L) from pure glycerol in 3 days of batch fermentation using a 1-L bioreactor. This yeast cell factory was capable of simultaneous lipid accumulation and citric acid secretion. It can be used in fed-batch or continuous bioprocessing for citric acid recovery from the supernatant, along with lipid extraction from the harvested biomass.
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A metabolic engineering strategy for producing conjugated linoleic acids using the oleaginous yeast Yarrowia lipolytica. Appl Microbiol Biotechnol 2017; 101:4605-4616. [PMID: 28357546 PMCID: PMC5442254 DOI: 10.1007/s00253-017-8240-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/06/2017] [Accepted: 03/09/2017] [Indexed: 12/13/2022]
Abstract
Conjugated linoleic acids (CLAs) have been found to have beneficial effects on human health when used as dietary supplements. However, their availability is limited because pure, chemistry-based production is expensive, and biology-based fermentation methods can only create small quantities. In an effort to enhance microbial production of CLAs, four genetically modified strains of the oleaginous yeast Yarrowia lipolytica were generated. These mutants presented various genetic modifications, including the elimination of β-oxidation (pox1-6∆), the inability to store lipids as triglycerides (dga1∆ dga2∆ are1∆ lro1∆), and the overexpression of the Y. lipolytica ∆12-desaturase gene (YlFAD2) under the control of the constitutive pTEF promoter. All strains received two copies of the pTEF-oPAI or pPOX-oPAI expression cassettes; PAI encodes linoleic acid isomerase in Propionibacterium acnes. The strains were cultured in neosynthesis or bioconversion medium in flasks or a bioreactor. The strain combining the three modifications mentioned above showed the best results: when it was grown in neosynthesis medium in a flask, CLAs represented 6.5% of total fatty acids and in bioconversion medium in a bioreactor, and CLA content reached 302 mg/L. In a previous study, a CLA degradation rate of 117 mg/L/h was observed in bioconversion medium. Here, by eliminating β-oxidation, we achieved a much lower rate of 1.8 mg/L/h.
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Dulermo R, Brunel F, Dulermo T, Ledesma-Amaro R, Vion J, Trassaert M, Thomas S, Nicaud JM, Leplat C. Using a vector pool containing variable-strength promoters to optimize protein production in Yarrowia lipolytica. Microb Cell Fact 2017; 16:31. [PMID: 28212656 PMCID: PMC5316184 DOI: 10.1186/s12934-017-0647-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 02/10/2017] [Indexed: 11/10/2022] Open
Abstract
Background The yeast Yarrowia lipolytica is an increasingly common biofactory. To enhance protein expression, several promoters have been developed, including the constitutive TEF promoter, the inducible POX2 promotor, and the hybrid hp4d promoter. Recently, new hp4d-inspired promoters have been created that couple various numbers of UAS1 tandem elements with the minimal LEU2 promoter or the TEF promoter. Three different protein-secretion signaling sequences can be used: preLip2, preXpr2, and preSuc2. Results To our knowledge, our study is the first to use a set of vectors with promoters of variable strength to produce proteins of industrial interest. We used the more conventional TEF and hp4d promoters along with five new hybrid promoters: 2UAS1-pTEF, 3UAS1-pTEF, 4UAS1-pTEF, 8UAS1-pTEF, and hp8d. We compared the production of RedStar2, glucoamylase, and xylanase C when strains were grown on three media. As expected, levels of RedStar2 and glucoamylase were greatest in the strain with the 8UAS1-pTEF promoter, which was stronger. However, surprisingly, the 2UAS1-pTEF promoter was associated with the greatest xylanase C production and activity. This finding underscored that stronger promoters are not always better when it comes to protein production. We therefore developed a method for easily identifying the best promoter for a given protein of interest. In this gateway method, genes for YFP and α-amylase were transferred into a pool of vectors containing different promoters and gene expression was then analyzed. We observed that, in most cases, protein production and activity were correlated with promoter strength, although this pattern was protein dependent. Conclusions Protein expression depends on more than just promoter strength. Indeed, promoter suitability appears to be protein dependent; in some cases, optimal expression and activity was obtained using a weaker promoter. We showed that using a vector pool containing promoters of variable strength can be a powerful tool for rapidly identifying the best producer for a given protein of interest. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0647-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rémi Dulermo
- Micalis Institute, INRA-AgroParisTech, UMR1319, Team BIMLip: Integrative Metabolism of Microbial Lipids, Université Paris-Saclay, domaine de Vilvert, 78350, Jouy-en-Josas, France.
| | - François Brunel
- Micalis Institute, INRA-AgroParisTech, UMR1319, Team BIMLip: Integrative Metabolism of Microbial Lipids, Université Paris-Saclay, domaine de Vilvert, 78350, Jouy-en-Josas, France
| | - Thierry Dulermo
- Micalis Institute, INRA-AgroParisTech, UMR1319, Team BIMLip: Integrative Metabolism of Microbial Lipids, Université Paris-Saclay, domaine de Vilvert, 78350, Jouy-en-Josas, France
| | - Rodrigo Ledesma-Amaro
- Micalis Institute, INRA-AgroParisTech, UMR1319, Team BIMLip: Integrative Metabolism of Microbial Lipids, Université Paris-Saclay, domaine de Vilvert, 78350, Jouy-en-Josas, France
| | - Jérémy Vion
- Micalis Institute, INRA-AgroParisTech, UMR1319, Team BIMLip: Integrative Metabolism of Microbial Lipids, Université Paris-Saclay, domaine de Vilvert, 78350, Jouy-en-Josas, France
| | - Marion Trassaert
- Micalis Institute, INRA-AgroParisTech, UMR1319, Team BIMLip: Integrative Metabolism of Microbial Lipids, Université Paris-Saclay, domaine de Vilvert, 78350, Jouy-en-Josas, France
| | - Stéphane Thomas
- Micalis Institute, INRA-AgroParisTech, UMR1319, Team BIMLip: Integrative Metabolism of Microbial Lipids, Université Paris-Saclay, domaine de Vilvert, 78350, Jouy-en-Josas, France
| | - Jean-Marc Nicaud
- Micalis Institute, INRA-AgroParisTech, UMR1319, Team BIMLip: Integrative Metabolism of Microbial Lipids, Université Paris-Saclay, domaine de Vilvert, 78350, Jouy-en-Josas, France.
| | - Christophe Leplat
- Micalis Institute, INRA-AgroParisTech, UMR1319, Team BIMLip: Integrative Metabolism of Microbial Lipids, Université Paris-Saclay, domaine de Vilvert, 78350, Jouy-en-Josas, France.
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Qiao K, Wasylenko TM, Zhou K, Xu P, Stephanopoulos G. Lipid production in Yarrowia lipolytica is maximized by engineering cytosolic redox metabolism. Nat Biotechnol 2017; 35:173-177. [DOI: 10.1038/nbt.3763] [Citation(s) in RCA: 280] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 12/08/2016] [Indexed: 01/12/2023]
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Lozano-Martínez P, Buey RM, Ledesma-Amaro R, Jiménez A, Revuelta JL. Engineering Ashbya gossypii strains for de novo lipid production using industrial by-products. Microb Biotechnol 2016; 10:425-433. [PMID: 28008713 PMCID: PMC5328814 DOI: 10.1111/1751-7915.12487] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/14/2016] [Accepted: 11/16/2016] [Indexed: 11/27/2022] Open
Abstract
Ashbya gossypii is a filamentous fungus that naturally overproduces riboflavin, and it is currently exploited for the industrial production of this vitamin. The utilization of A. gossypii for biotechnological applications presents important advantages such as the utilization of low-cost culture media, inexpensive downstream processing and a wide range of molecular tools for genetic manipulation, thus making A. gossypii a valuable biotechnological chassis for metabolic engineering. A. gossypii has been shown to accumulate high levels of lipids in oil-based culture media; however, the lipid biosynthesis capacity is rather limited when grown in sugar-based culture media. In this study, by altering the fatty acyl-CoA pool and manipulating the regulation of the main ∆9 desaturase gene, we have obtained A. gossypii strains with significantly increased (up to fourfold) de novo lipid biosynthesis using glucose as the only carbon source in the fermentation broth. Moreover, these strains were efficient biocatalysts for the conversion of carbohydrates from sugarcane molasses to biolipids, able to accumulate lipids up to 25% of its cell dry weight. Our results represent a proof of principle showing the promising potential of A. gossypii as a competitive microorganism for industrial biolipid production using cost-effective feed stocks.
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Affiliation(s)
- Patricia Lozano-Martínez
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Rubén M Buey
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Rodrigo Ledesma-Amaro
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Alberto Jiménez
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - José Luis Revuelta
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007, Salamanca, Spain
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