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Bigey F, Pasteur E, Połomska X, Thomas S, Crutz-Le Coq AM, Devillers H, Neuvéglise C. Insights into the Genomic and Phenotypic Landscape of the Oleaginous Yeast Yarrowia lipolytica. J Fungi (Basel) 2023; 9:jof9010076. [PMID: 36675897 PMCID: PMC9865632 DOI: 10.3390/jof9010076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/30/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023] Open
Abstract
Although Yarrowia lipolytica is a model yeast for the study of lipid metabolism, its diversity is poorly known, as studies generally consider only a few standard laboratory strains. To extend our knowledge of this biotechnological workhorse, we investigated the genomic and phenotypic diversity of 56 natural isolates. Y. lipolytica is classified into five clades with no correlation between clade membership and geographic or ecological origin. A low genetic diversity (π = 0.0017) and a pan-genome (6528 genes) barely different from the core genome (6315 genes) suggest Y. lipolytica is a recently evolving species. Large segmental duplications were detected, totaling 892 genes. With three new LTR-retrotransposons of the Gypsy family (Tyl4, Tyl9, and Tyl10), the transposable element content of genomes appeared diversified but still low (from 0.36% to 3.62%). We quantified 34 traits with substantial phenotypic diversity, but genome-wide association studies failed to evidence any associations. Instead, we investigated known genes and found four mutational events leading to XPR2 protease inactivation. Regarding lipid metabolism, most high-impact mutations were found in family-belonging genes, such as ALK or LIP, and therefore had a low phenotypic impact, suggesting that the huge diversity of lipid synthesis and accumulation is multifactorial or due to complex regulations.
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Affiliation(s)
- Frédéric Bigey
- INRAE, Institut Agro, SPO, University Montpellier, 34060 Montpellier, France
| | - Emilie Pasteur
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Xymena Połomska
- Department of Biotechnology & Food Microbiology, Wroclaw University of Environmental and Life Sciences (WUELS), 50-375 Wroclaw, Poland
| | - Stéphane Thomas
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Anne-Marie Crutz-Le Coq
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
- IJPB, INRAE, 78000 Versailles, France
| | - Hugo Devillers
- INRAE, Institut Agro, SPO, University Montpellier, 34060 Montpellier, France
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Cécile Neuvéglise
- INRAE, Institut Agro, SPO, University Montpellier, 34060 Montpellier, France
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
- Correspondence:
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Rakicka-Pustułka M, Ziuzia P, Pierwoła J, Szymański K, Wróbel-Kwiatkowska M, Lazar Z. The microbial production of kynurenic acid using Yarrowia lipolytica yeast growing on crude glycerol and soybean molasses. Front Bioeng Biotechnol 2022; 10:936137. [PMID: 36061425 PMCID: PMC9428254 DOI: 10.3389/fbioe.2022.936137] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/18/2022] [Indexed: 12/25/2022] Open
Abstract
Yarrowia lipolytica yeast are able to produce kynurenic acid—a very valuable compound acting as a neuroprotective and antioxidant agent in humans. The recent data proved the existence of the kynurenine biosynthesis pathway in this yeast cells. Due to this fact, the aim of this work was to enhance kynurenic acid production using crude glycerol and soybean molasses as cheap and renewable carbon and nitrogen sources. The obtained results showed that Y. lipolytica GUT1 mutants are able to produce kynurenic acid in higher concentrations (from 4.5 mg dm−3 to 14.1 mg dm−3) than the parental strain (3.6 mg dm−3) in the supernatant in a medium with crude glycerol. Moreover, the addition of soybean molasses increased kynurenic acid production by using wild type and transformant strains. The A-101.1.31 GUT1/1 mutant strain produced 17.7 mg dm−3 of kynurenic acid in the supernatant during 150 h of the process and 576.7 mg kg−1 of kynurenic acid in dry yeast biomass. The presented work proves the great potential of microbial kynurenic acid production using waste feedstock. Yeast biomass obtained in this work is rich in protein, with a low content of lipid, and can be a healthy ingredient of animal and human diet.
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Rong L, Miao L, Wang S, Wang Y, Liu S, Lu Z, Zhao B, Zhang C, Xiao D, Pushpanathan K, Wong A, Yu A. Engineering Yarrowia lipolytica to Produce Itaconic Acid From Waste Cooking Oil. Front Bioeng Biotechnol 2022; 10:888869. [PMID: 35547171 PMCID: PMC9083544 DOI: 10.3389/fbioe.2022.888869] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/04/2022] [Indexed: 11/25/2022] Open
Abstract
Itaconic acid (IA) is a high-value organic acid with a plethora of industrial applications. In this study, we seek to develop a microbial cell factory that could utilize waste cooking oil (WCO) as raw material for circular and cost-effective production of the abovementioned biochemical. Specifically, we expressed cis-aconitic acid decarboxylase (CAD) gene from Aspergillus terreus in either the cytosol or peroxisome of Yarrowia lipolytica and assayed for production of IA on WCO. To further improve production yield, the 10 genes involved in the production pathway of acetyl-CoA, an intermediate metabolite necessary for the synthesis of cis-aconitic acid, were individually overexpressed and investigated for their impact on IA production. To minimize off-target flux channeling, we had also knocked out genes related to competing pathways in the peroxisome. Impressively, IA titer up to 54.55 g/L was achieved in our engineered Y. lipolytica in a 5 L bioreactor using WCO as the sole carbon source.
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Affiliation(s)
- Lanxin Rong
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Lin Miao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Shuhui Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yaping Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Shiqi Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Zhihui Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Baixiang Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Cuiying Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Dongguang Xiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Krithi Pushpanathan
- Food, Chemical and Biotechnology Cluster, Singapore Institute of Technology, Dover, Singapore
| | - Adison Wong
- Food, Chemical and Biotechnology Cluster, Singapore Institute of Technology, Dover, Singapore
- *Correspondence: Adison Wong, ; Aiqun Yu,
| | - Aiqun Yu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- *Correspondence: Adison Wong, ; Aiqun Yu,
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Control of D-lactic acid content in P(LA-3HB) copolymer in the yeast Saccharomyces cerevisiae using a synthetic gene expression system. Metab Eng Commun 2022; 14:e00199. [PMID: 35571351 PMCID: PMC9095885 DOI: 10.1016/j.mec.2022.e00199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/26/2022] [Accepted: 04/22/2022] [Indexed: 11/22/2022] Open
Abstract
The fully biobased polyhydroxyalkanoate (PHA) polymers provide interesting alternatives for petrochemical derived plastic materials. The mechanical properties of some PHAs, including the common poly(3-hydroxybutyrate) (PHB), are limited, but tunable by addition of other monomers into the polymer chain. In this study we present a precise synthetic biology method to adjust lactate monomer fraction of a polymer by controlling the monomer formation in vivo at gene expression level, independent of cultivation conditions. We used the modified doxycycline-based Tet-On approach to adjust the expression of the stereospecific D-lactate dehydrogenase gene (ldhA) from Leuconostoc mesenteroides to control D-lactic acid formation in yeast Saccharomyces cerevisiae. The synthetic Tet-On transcription factor with a VP16 activation domain was continuously expressed and its binding to a synthetic promoter with eight transcription factor specific binding sites upstream of the ldhA gene was controlled with the doxycycline concentration in the media. The increase in doxycycline concentration correlated positively with ldhA expression, D-lactic acid production, poly(D-lactic acid) (PDLA) accumulation in vivo, and D-lactic acid content in the poly(D-lactate-co-3-hydroxybutyrate) P(LA-3HB) copolymer. We demonstrated that the D-lactic acid content of the P(LA-3HB) copolymer can be adjusted linearly from 6 mol% to 93 mol% in vivo in S. cerevisiae. These results highlight the power of controlling gene expression and monomer formation in the tuning of the polymer composition. In addition, we obtained 5.6% PDLA and 19% P(LA-3HB) of the cell dry weight (CDW), which are over two- and five-fold higher accumulation levels, respectively, than reported in the previous studies with yeast. We also compared two engineered PHA synthases and discovered that in S. cerevisiae the PHA synthase PhaC1437Ps6-19 produced P(LA-3HB) copolymers with lower D-lactic acid content, but with higher molecular weight, in comparison to the PHA synthase PhaC1Pre. P(LA-3HB) monomer structure was adjusted with controlled gene expression. Expression of D-lactate dehydrogenase (ldhA) was controlled with Tet-On approach. Lactic acid content in copolymer P(LA-3HB) was adjusted from 6 mol% up to 93 mol%. 5.6% PDLA and 19% P(LA-3HB) of cell dry weight (CDW) were obtained in S. cerevisiae. PhaC1437Ps6-19 P(LA-3HB) had lower D-lactic acid % than PhaC1Pre P(LA-3HB).
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Yarrowia lipolytica as an Alternative and Valuable Source of Nutritional and Bioactive Compounds for Humans. Molecules 2022; 27:molecules27072300. [PMID: 35408699 PMCID: PMC9000428 DOI: 10.3390/molecules27072300] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [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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Choi BH, Kang HJ, Kim SC, Lee PC. Organelle Engineering in Yeast: Enhanced Production of Protopanaxadiol through Manipulation of Peroxisome Proliferation in Saccharomyces cerevisiae. Microorganisms 2022; 10:microorganisms10030650. [PMID: 35336225 PMCID: PMC8950469 DOI: 10.3390/microorganisms10030650] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/13/2022] [Accepted: 03/14/2022] [Indexed: 12/15/2022] Open
Abstract
Isoprenoids, which are natural compounds with diverse structures, possess several biological activities that are beneficial to humans. A major consideration in isoprenoid production in microbial hosts is that the accumulation of biosynthesized isoprenoid within intracellular membranes may impede balanced cell growth, which may consequently reduce the desired yield of the target isoprenoid. As a strategy to overcome this suggested limitation, we selected peroxisome membranes as depots for the additional storage of biosynthesized isoprenoids to facilitate increased isoprenoid production in Saccharomyces cerevisiae. To maximize the peroxisome membrane storage capacity of S.cerevisiae, the copy number and size of peroxisomes were increased through genetic engineering of the expression of three peroxisome biogenesis-related peroxins (Pex11p, Pex34p, and Atg36p). The genetically enlarged and high copied peroxisomes in S.cerevisiae were stably maintained under a bioreactor fermentation condition. The peroxisome-engineered S.cerevisiae strains were then utilized as host strains for metabolic engineering of heterologous protopanaxadiol pathway. The yields of protopanaxadiol from the engineered peroxisome strains were ca 78% higher than those of the parent strain, which strongly supports the rationale for harnessing the storage capacity of the peroxisome membrane to accommodate the biosynthesized compounds. Consequently, this study presents in-depth knowledge on peroxisome biogenesis engineering in S.cerevisiae and could serve as basic information for improvement in ginsenosides production and as a potential platform to be utilized for other isoprenoids.
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Affiliation(s)
- Bo Hyun Choi
- Department of Molecular Science and Technology, Ajou University, World Cup-ro, Yeongtong-gu, Suwon 16499, Korea; (B.H.C.); (H.J.K.)
| | - Hyun Joon Kang
- Department of Molecular Science and Technology, Ajou University, World Cup-ro, Yeongtong-gu, Suwon 16499, Korea; (B.H.C.); (H.J.K.)
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea;
| | - Pyung Cheon Lee
- Department of Molecular Science and Technology, Ajou University, World Cup-ro, Yeongtong-gu, Suwon 16499, Korea; (B.H.C.); (H.J.K.)
- Correspondence: ; Tel.: +82-31-219-2461
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Chatterjee S, Venkata Mohan S. Fungal biorefinery for sustainable resource recovery from waste. BIORESOURCE TECHNOLOGY 2022; 345:126443. [PMID: 34852279 DOI: 10.1016/j.biortech.2021.126443] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/21/2021] [Accepted: 11/24/2021] [Indexed: 06/13/2023]
Abstract
Depletion of natural resources and negative impact of fossil fuels on environment are becoming a global concern. The concept of biorefinery is one of the alternative platforms for the production of biofuels and chemicals. Valorisation of biological resources through complete utilization of waste, reusing secondary products and generating energy to power the process are the key principles of biorefinery. Agricultural residues and biogenic municipal solid wastes are getting importance as a potential feedstock for the generation of bioproducts. This communication reviews and highlights the scope of yeast and fungi as a potent candidate for the synthesis of gamut of bioproducts in an integrated approach addressing sustainability and circular bioeconomy. It also provides a close view on importance of microbes in biorefinery, feedstock pretreatment strategies for renewable sugar production, cultivation systems and yeast and fungi based products. Integrated closed loop approach towards multiple product generation with zero waste discharge is also discussed.
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Affiliation(s)
- Sulogna Chatterjee
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, 500007, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - S Venkata Mohan
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, 500007, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India.
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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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Yarrowia lipolytica Strains and Their Biotechnological Applications: How Natural Biodiversity and Metabolic Engineering Could Contribute to Cell Factories Improvement. J Fungi (Basel) 2021; 7:jof7070548. [PMID: 34356927 PMCID: PMC8307478 DOI: 10.3390/jof7070548] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 11/20/2022] Open
Abstract
Among non-conventional yeasts of industrial interest, the dimorphic oleaginous yeast Yarrowia lipolytica appears as one of the most attractive for a large range of white biotechnology applications, from heterologous proteins secretion to cell factories process development. The past, present and potential applications of wild-type, traditionally improved or genetically modified Yarrowia lipolytica strains will be resumed, together with the wide array of molecular tools now available to genetically engineer and metabolically remodel this yeast. The present review will also provide a detailed description of Yarrowia lipolytica strains and highlight the natural biodiversity of this yeast, a subject little touched upon in most previous reviews. This work intends to fill this gap by retracing the genealogy of the main Yarrowia lipolytica strains of industrial interest, by illustrating the search for new genetic backgrounds and by providing data about the main publicly available strains in yeast collections worldwide. At last, it will focus on exemplifying how advances in engineering tools can leverage a better biotechnological exploitation of the natural biodiversity of Yarrowia lipolytica and of other yeasts from the Yarrowia clade.
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Sestric R, Spicer V, V Krokhin O, Sparling R, B Levin D. Analysis of the Yarrowia lipolytica proteome reveals subtle variations in expression levels between lipogenic and non-lipogenic conditions. FEMS Yeast Res 2021; 21:6133473. [PMID: 33571365 DOI: 10.1093/femsyr/foab007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/09/2021] [Indexed: 11/13/2022] Open
Abstract
Oleaginous yeasts have the ability to store greater than 20% of their mass as neutral lipids, in the form of triacylglycerides. The ATP citrate lyase is thought to play a key role in triacylglyceride synthesis, but the relationship between expression levels of this and other related enzymes is not well understood in the role of total lipid accumulation conferring the oleaginous phenotype. We conducted comparative proteomic analyses with the oleaginous yeast, Yarrowia lipolytica, grown in either nitrogen-sufficient rich media or nitrogen-limited minimal media. Total proteins extracted from cells collected during logarithmic and late stationary growth phases were analyzed by 1D liquid chromatography, followed by mass spectroscopy. The ATP citrate lyase enzyme was expressed at similar concentrations in both conditions, in both logarithmic and stationary phase, but many upstream and downstream enzymes showed drastically different expression levels. In non-lipogenic conditions, several pyruvate enzymes were expressed at higher concentration. These enzymes, especially the pyruvate decarboxylase and pyruvate dehydrogenase, may be regulating carbon flux away from central metabolism and reducing the amount of citrate being produced in the mitochondria. While crucial for the oleaginous phenotype, the constitutively expressed ATP citrate lyase appears to cleave citrate in response to carbon flux upstream from other enzymes creating the oleaginous phenotype.
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Affiliation(s)
- Ryan Sestric
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - Vic Spicer
- Manitoba Centre for Proteomics and Systems Biology, Department of Internal Medicine, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Oleg V Krokhin
- Manitoba Centre for Proteomics and Systems Biology, Department of Internal Medicine, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Richard Sparling
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - David B Levin
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
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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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Borsenberger V, Croux C, Daboussi F, Neuvéglise C, Bordes F. Developing Methods to Circumvent the Conundrum of Chromosomal Rearrangements Occurring in Multiplex Gene Edition. ACS Synth Biol 2020; 9:2562-2575. [PMID: 32786349 DOI: 10.1021/acssynbio.0c00325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR/Cas9 is a powerful tool to edit the genome of the yeast Yarrowia lipolytica. Here, we design a simple and robust method to knockout multiple gene families based on the construction of plasmids enabling the simultaneous expression of several sgRNAs. We exemplify the potency of this approach by targeting the well-characterized acyl-CoA oxidase family (POX) and the uncharacterized SPS19 family. We establish a correlation between the high lethality observed upon editing multiple loci and chromosomal translocations resulting from the simultaneous generation of several double-strand breaks (DSBs) and develop multiplex gene editing strategies. Using homologous directed recombination to reduce chromosomal translocations, we demonstrated that simultaneous editing of four genes can be achieved and constructed a strain carrying a sextuple deletion of POX genes. We explore an "excision approach" by simultaneously performing two DSBs in genes and reached 73 to 100% editing efficiency in double disruptions and 41.7% in a triple disruption. This work led to identifying SPS193 as a gene encoding a 2-4 dienoyl-CoA reductase, demonstrating the potential of this method to accelerate knowledge on gene function in expanded gene families.
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Affiliation(s)
- Vinciane Borsenberger
- Toulouse Biotechnology Institute, Université de Toulouse, INSA, INRAE, CNRS, Toulouse, 31077, France
| | - Christian Croux
- Toulouse Biotechnology Institute, Université de Toulouse, INSA, INRAE, CNRS, Toulouse, 31077, France
| | - Fayza Daboussi
- Toulouse Biotechnology Institute, Université de Toulouse, INSA, INRAE, CNRS, Toulouse, 31077, France
- Toulouse White Biotechnology, Ramonville-Saint-Agne, 31520, France
| | - Cécile Neuvéglise
- AgroParisTech, Micalis Institute, Université Paris-Saclay, INRAE, Paris, 78350, France
| | - Florence Bordes
- Toulouse Biotechnology Institute, Université de Toulouse, INSA, INRAE, CNRS, Toulouse, 31077, France
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Ju JH, Oh BR, Heo SY, Lee YU, Shon JH, Kim CH, Kim YM, Seo JW, Hong WK. Production of adipic acid by short- and long-chain fatty acid acyl-CoA oxidase engineered in yeast Candida tropicalis. Bioprocess Biosyst Eng 2019; 43:33-43. [PMID: 31549308 DOI: 10.1007/s00449-019-02202-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 07/10/2019] [Accepted: 08/08/2019] [Indexed: 01/11/2023]
Abstract
In this study, to produce adipic acid, mutant strains of Candida tropicalis KCTC 7212 deficient of AOX genes encoding acyl-CoA oxidases which are important in the β-oxidation pathway were constructed. Production of adipic acid in the mutants from the most favorable substrate C12 methyl laurate was significantly increased. The highest level of production of adipic acid was obtained in the C. tropicalis ΔAOX4::AOX5 mutant of 339.8 mg L-1 which was about 5.4-fold higher level compared to the parent strain. The C. tropicalis ΔAOX4::AOX5 mutant was subjected to fed-batch fermentation at optimized conditions of agitation rate of 1000 rpm, pH 5.0 and methyl laurate of 3% (w/v), giving the maximum level of adipic acid of 12.1 g L-1 and production rate of 0.1 g L-1 h-1.
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Affiliation(s)
- Jung-Hyun Ju
- Applied Microbial Research Center, Jeonbuk Branch Institute, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Jeonbuk, Korea
- Department of Food Science and Technology and Functional Food Research Center, Chonnam National University, Gwangju, 61186, Korea
| | - Baek-Rock Oh
- Applied Microbial Research Center, Jeonbuk Branch Institute, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Jeonbuk, Korea
| | - Sun-Yeon Heo
- Applied Microbial Research Center, Jeonbuk Branch Institute, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Jeonbuk, Korea
| | - Young-Uk Lee
- Applied Microbial Research Center, Jeonbuk Branch Institute, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Jeonbuk, Korea
| | - Jung-Hoon Shon
- Bioenergy and Biochemical Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Chul-Ho Kim
- Applied Microbial Research Center, Jeonbuk Branch Institute, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Jeonbuk, Korea
| | - Young-Min Kim
- Department of Food Science and Technology and Functional Food Research Center, Chonnam National University, Gwangju, 61186, Korea
| | - Jeong-Woo Seo
- Applied Microbial Research Center, Jeonbuk Branch Institute, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Jeonbuk, Korea.
| | - Won-Kyung Hong
- Division of Biotechnology, College of Environmental and Bioresource Science, Chonbuk National University, Iksan, 54596, Jeonbuk, Korea.
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Do DTH, Theron CW, Fickers P. Organic Wastes as Feedstocks for Non-Conventional Yeast-Based Bioprocesses. Microorganisms 2019; 7:E229. [PMID: 31370226 PMCID: PMC6722544 DOI: 10.3390/microorganisms7080229] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 12/22/2022] Open
Abstract
Non-conventional yeasts are efficient cell factories for the synthesis of value-added compounds such as recombinant proteins, intracellular metabolites, and/or metabolic by-products. Most bioprocess, however, are still designed to use pure, ideal sugars, especially glucose. In the quest for the development of more sustainable processes amid concerns over the future availability of resources for the ever-growing global population, the utilization of organic wastes or industrial by-products as feedstocks to support cell growth is a crucial approach. Indeed, vast amounts of industrial and commercial waste simultaneously represent an environmental burden and an important reservoir for recyclable or reusable material. These alternative feedstocks can provide microbial cell factories with the required metabolic building blocks and energy to synthesize value-added compounds, further representing a potential means of reduction of process costs as well. This review highlights recent strategies in this regard, encompassing knowledge on catabolic pathways and metabolic engineering solutions developed to endow cells with the required metabolic capabilities, and the connection of these to the synthesis of value-added compounds. This review focuses primarily, but not exclusively, on Yarrowia lipolytica as a yeast cell factory, owing to its broad range of naturally metabolizable carbon sources, together with its popularity as a non-conventional yeast.
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Affiliation(s)
- Diem T Hoang Do
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, University of Liège - Gembloux AgroBio Tech, Av. de la Faculté, 2B. B-5030 Gembloux, Belgium
| | - Chrispian W Theron
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, University of Liège - Gembloux AgroBio Tech, Av. de la Faculté, 2B. B-5030 Gembloux, Belgium
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, University of Liège - Gembloux AgroBio Tech, Av. de la Faculté, 2B. B-5030 Gembloux, Belgium.
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Rigouin C, Lajus S, Ocando C, Borsenberger V, Nicaud JM, Marty A, Avérous L, Bordes F. Production and characterization of two medium-chain-length polydroxyalkanoates by engineered strains of Yarrowia lipolytica. Microb Cell Fact 2019; 18:99. [PMID: 31151440 PMCID: PMC6545009 DOI: 10.1186/s12934-019-1140-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/17/2019] [Indexed: 11/24/2022] Open
Abstract
Background The oleaginous yeast Yarrowia lipolytica is an organism of choice for the tailored production of various compounds such as biofuels or biopolymers. When properly engineered, it is capable of producing medium-chain-length polyhydroxyalkanoate (mcl-PHA), a biobased and biodegradable polymer that can be used as bioplastics or biopolymers for environmental and biomedical applications. Results This study describes the bioproduction and the main properties of two different mcl-PHA polymers. We generated by metabolic engineering, strains of Y. lipolytica capable of accumulating more than 25% (g/g) of mcl-PHA polymers. Depending of the strain genetic background and the culture conditions, we produced (i) a mcl-PHA homopolymer of 3-hydroxydodecanoic acids, with a mass-average molar mass (Mw) of 316,000 g/mol, showing soft thermoplastic properties with potential applications in packaging and (ii) a mcl-PHA copolymer made of 3-hydroxyoctanoic (3HO), decanoic (3HD), dodecanoic (3HDD) and tetradecanoic (3TD) acids with a Mw of 128,000 g/mol, behaving like a thermoplastic elastomer with potential applications in biomedical material. Conclusion The ability to engineer Y. lipolytica to produce tailored PHAs together with the range of possible applications regarding their biophysical and mechanical properties opens new perspectives in the field of PHA bioproduction. Electronic supplementary material The online version of this article (10.1186/s12934-019-1140-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Coraline Rigouin
- LISBP, CNRS, INRA, INSA, Université de Toulouse, Toulouse, France
| | - Sophie Lajus
- LISBP, CNRS, INRA, INSA, Université de Toulouse, Toulouse, France
| | - Connie Ocando
- BioTeam/ICPEES-ECPM, UMR CNRS 7515, Université de Strasbourg, 25 rue Becquerel, 67087, Strasbourg Cedex 2, France
| | | | - Jean Marc Nicaud
- Micalis Institute, INRA-AgroParisTech, UMR1319, Team BIMLip: Integrative Metabolism of Microbial Lipids, Domaine de Vilvert, 78352, Jouy-en-Josas, France
| | - Alain Marty
- Carbios - Biopôle Clermont-Limagne, 3 rue Emile Duclaux, 63360, Saint-Beauzire, France
| | - Luc Avérous
- BioTeam/ICPEES-ECPM, UMR CNRS 7515, Université de Strasbourg, 25 rue Becquerel, 67087, Strasbourg Cedex 2, France
| | - Florence Bordes
- LISBP, CNRS, INRA, INSA, Université de Toulouse, Toulouse, France.
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Chang J, Rachubinski RA. Pex20p functions as the receptor for non‐PTS1/non‐PTS2 acyl‐CoA oxidase import into peroxisomes of the yeast
Yarrowia lipolytica. Traffic 2019; 20:504-515. [DOI: 10.1111/tra.12652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 04/29/2019] [Accepted: 04/29/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Jinlan Chang
- Department of Cell BiologyUniversity of Alberta Edmonton Alberta Canada
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17
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Understanding lipogenesis by dynamically profiling transcriptional activity of lipogenic promoters in Yarrowia lipolytica. Appl Microbiol Biotechnol 2019; 103:3167-3179. [PMID: 30734122 DOI: 10.1007/s00253-019-09664-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/07/2019] [Accepted: 01/22/2019] [Indexed: 10/27/2022]
Abstract
Lipogenesis is a complicated process involving global transcriptional reprogramming of lipogenic pathways. It is commonly believed that nitrogen starvation triggers a metabolic shift that reroutes carbon flux from Krebs cycles to lipogenesis. In this study, we systematically surveyed and dynamically profiled the transcriptional activity of 22 lipogenic promoters aiming to delineate a picture how nitrogen starvation regulates lipogenesis in Y. lipolytica. These lipogenic promoters drive the expression of critical pathways that are responsible for the generation of reducing equivalents (NADPH), carbon backbones (acetyl-CoA, malonyl-CoA, DHAP, etc.), synthesis and degradation of fatty acids. Specifically, our investigated promoters span across an array of metabolic pathways, including glycolysis, Krebs cycle, pentose phosphate pathway, mannitol cycle, glutamine-GABA cycle, fatty acid and lipid synthesis, glyoxylate, β-oxidation, and POM (pyruvate-oxaloacetate-malate) cycle. Our work provides evidences that mannitol cycle, glutamine-GABA cycle and amino acid degradation, pyruvate oxidation, and acetate assimilation pathways are lipogenesis-related steps involved in generating cytosolic NADPH and acetyl-CoA precursors. This systematic investigation and dynamic profiling of lipogenic promoters may help us better understand lipogenesis, facilitate the formulation of structure-based kinetic models, as well as develop efficient cell factories for fuels and chemical production in oleaginous species.
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Larroude M, Rossignol T, Nicaud JM, Ledesma-Amaro R. Synthetic biology tools for engineering Yarrowia lipolytica. Biotechnol Adv 2018; 36:2150-2164. [PMID: 30315870 PMCID: PMC6261845 DOI: 10.1016/j.biotechadv.2018.10.004] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 09/11/2018] [Accepted: 10/07/2018] [Indexed: 12/15/2022]
Abstract
The non-conventional oleaginous yeast Yarrowia lipolytica shows great industrial promise. It naturally produces certain compounds of interest but can also artificially generate non-native metabolites, thanks to an engineering process made possible by the significant expansion of a dedicated genetic toolbox. In this review, we present recently developed synthetic biology tools that facilitate the manipulation of Y. lipolytica, including 1) DNA assembly techniques, 2) DNA parts for constructing expression cassettes, 3) genome-editing techniques, and 4) computational tools.
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Affiliation(s)
- M Larroude
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - T Rossignol
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - J-M Nicaud
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - R Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom.
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19
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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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20
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Brabender M, Hussain MS, Rodriguez G, Blenner MA. Urea and urine are a viable and cost-effective nitrogen source for Yarrowia lipolytica biomass and lipid accumulation. Appl Microbiol Biotechnol 2018; 102:2313-2322. [DOI: 10.1007/s00253-018-8769-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 12/26/2017] [Accepted: 01/05/2018] [Indexed: 12/31/2022]
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21
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Trassaert M, Vandermies M, Carly F, Denies O, Thomas S, Fickers P, Nicaud JM. New inducible promoter for gene expression and synthetic biology in Yarrowia lipolytica. Microb Cell Fact 2017; 16:141. [PMID: 28810867 PMCID: PMC5557077 DOI: 10.1186/s12934-017-0755-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 08/05/2017] [Indexed: 12/02/2022] Open
Abstract
Background The oleaginous yeast Yarrowia lipolytica is increasingly used as alternative cell factory for the production of recombinant proteins. At present, several promoters with different strengths have been developed based either on the constitutive pTEF promoter or on oleic acid inducible promoters such as pPOX2 and pLIP2. Although these promoters are highly efficient, there is still a lack of versatile inducible promoters for gene expression in Y. lipolytica. Results We have isolated and characterized the promoter of the EYK1 gene coding for an erythrulose kinase. pEYK1 induction was found to be impaired in media supplemented with glucose and glycerol, while the presence of erythritol and erythrulose strongly increased the promoter induction level. Promoter characterization and mutagenesis allowed the identification of the upstream activating sequence UAS1EYK1. New hybrid promoters containing tandem repeats of either UAS1XPR2 or UAS1EYK1 were developed showing higher expression levels than the native pEYK1 promoter. Furthermore, promoter strength was improved in a strain carrying a deletion in the EYK1 gene, allowing thus the utilization of erythritol and erythrulose as free inducer. Conclusions Novel tunable and regulated promoters with applications in the field of heterologous protein production, metabolic engineering, and synthetic biology have been developed, thus filling the gap of the absence of versatile inducible promoter in the yeast Y. lipolytica. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0755-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marion Trassaert
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Marie Vandermies
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, University of Liège - Gembloux Agro-Bio Tech, Gembloux, Belgium
| | - Fréderic Carly
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Unité de Biotechnologies et Bioprocédés, Université Libre de Bruxelles, Brussels, Belgium
| | - Olivia Denies
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, University of Liège - Gembloux Agro-Bio Tech, Gembloux, Belgium
| | - Stéphane Thomas
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, University of Liège - Gembloux Agro-Bio Tech, Gembloux, Belgium
| | - Jean-Marc Nicaud
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France. .,Micalis Institute, INRA-AgroParisTech, UMR1319, Team BIMLip: Integrative Metabolism of Microbial Lipids, Bâtiment 526, domaine de Vilvert, 78352, Jouy-en-Josas, France.
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22
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Harnessing yeast organelles for metabolic engineering. Nat Chem Biol 2017; 13:823-832. [DOI: 10.1038/nchembio.2429] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 05/23/2016] [Indexed: 11/08/2022]
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23
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Kong F, Liang Y, Légeret B, Beyly-Adriano A, Blangy S, Haslam RP, Napier JA, Beisson F, Peltier G, Li-Beisson Y. Chlamydomonas carries out fatty acid β-oxidation in ancestral peroxisomes using a bona fide acyl-CoA oxidase. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:358-371. [PMID: 28142200 DOI: 10.1111/tpj.13498] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/25/2017] [Accepted: 01/27/2017] [Indexed: 05/03/2023]
Abstract
Peroxisomes are thought to have played a key role in the evolution of metabolic networks of photosynthetic organisms by connecting oxidative and biosynthetic routes operating in different compartments. While the various oxidative pathways operating in the peroxisomes of higher plants are fairly well characterized, the reactions present in the primitive peroxisomes (microbodies) of algae are poorly understood. Screening of a Chlamydomonas insertional mutant library identified a strain strongly impaired in oil remobilization and defective in Cre05.g232002 (CrACX2), a gene encoding a member of the acyl-CoA oxidase/dehydrogenase superfamily. The purified recombinant CrACX2 expressed in Escherichia coli catalyzed the oxidation of fatty acyl-CoAs into trans-2-enoyl-CoA and produced H2 O2 . This result demonstrated that CrACX2 is a genuine acyl-CoA oxidase, which is responsible for the first step of the peroxisomal fatty acid (FA) β-oxidation spiral. A fluorescent protein-tagging study pointed to a peroxisomal location of CrACX2. The importance of peroxisomal FA β-oxidation in algal physiology was shown by the impact of the mutation on FA turnover during day/night cycles. Moreover, under nitrogen depletion the mutant accumulated 20% more oil than the wild type, illustrating the potential of β-oxidation mutants for algal biotechnology. This study provides experimental evidence that a plant-type FA β-oxidation involving H2 O2 -producing acyl-CoA oxidation activity has already evolved in the microbodies of the unicellular green alga Chlamydomonas reinhardtii.
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Affiliation(s)
- Fantao Kong
- Commissariat à l'Energie Atomique et aux Energies Alternatives, CNRS, Aix Marseille Université, UMR7265, Institut de Biosciences et Biotechnologies Aix Marseille, 13108, Cadarache, France
| | - Yuanxue Liang
- Commissariat à l'Energie Atomique et aux Energies Alternatives, CNRS, Aix Marseille Université, UMR7265, Institut de Biosciences et Biotechnologies Aix Marseille, 13108, Cadarache, France
| | - Bertrand Légeret
- Commissariat à l'Energie Atomique et aux Energies Alternatives, CNRS, Aix Marseille Université, UMR7265, Institut de Biosciences et Biotechnologies Aix Marseille, 13108, Cadarache, France
| | - Audrey Beyly-Adriano
- Commissariat à l'Energie Atomique et aux Energies Alternatives, CNRS, Aix Marseille Université, UMR7265, Institut de Biosciences et Biotechnologies Aix Marseille, 13108, Cadarache, France
| | - Stéphanie Blangy
- Commissariat à l'Energie Atomique et aux Energies Alternatives, CNRS, Aix Marseille Université, UMR7265, Institut de Biosciences et Biotechnologies Aix Marseille, 13108, Cadarache, France
| | - Richard P Haslam
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Johnathan A Napier
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Fred Beisson
- Commissariat à l'Energie Atomique et aux Energies Alternatives, CNRS, Aix Marseille Université, UMR7265, Institut de Biosciences et Biotechnologies Aix Marseille, 13108, Cadarache, France
| | - Gilles Peltier
- Commissariat à l'Energie Atomique et aux Energies Alternatives, CNRS, Aix Marseille Université, UMR7265, Institut de Biosciences et Biotechnologies Aix Marseille, 13108, Cadarache, France
| | - Yonghua Li-Beisson
- Commissariat à l'Energie Atomique et aux Energies Alternatives, CNRS, Aix Marseille Université, UMR7265, Institut de Biosciences et Biotechnologies Aix Marseille, 13108, Cadarache, France
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Rong S, Yang S, Li Q, Cai B, Guan S, Wang J, Zhou Y, Chen Y. Improvement of γ-decalactone production by stimulating the import of ricinoleic acid and suppressing the degradation of γ-decalactone in Saccharomyces cerevisiae. BIOCATAL BIOTRANSFOR 2017. [DOI: 10.1080/10242422.2017.1289182] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Shaofeng Rong
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, P.R. China
| | - Shulin Yang
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, P.R. China
| | - Qianqian Li
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, P.R. China
| | - Baoguo Cai
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, P.R. China
| | - Shimin Guan
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, P.R. China
| | - Jingwen Wang
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, P.R. China
| | - Yue Zhou
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, P.R. China
| | - Yifei Chen
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, P.R. China
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Gajdoš P, Nicaud JM, Čertík M. Glycerol conversion into a single cell oil by engineered Yarrowia lipolytica. Eng Life Sci 2016; 17:325-332. [PMID: 32624778 DOI: 10.1002/elsc.201600065] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 07/08/2016] [Accepted: 07/28/2016] [Indexed: 01/02/2023] Open
Abstract
Oleaginous yeasts are considered as natural single cell oil producers. Engineering the lipid biosynthetic pathway has the potential to increase lipid accumulation by these yeasts. In Yarrowia lipolytica, three diacylglycerol acyltransferases encoded by LRO1, DGA1, and DGA2 genes are involved in lipid formation. Strain JMY3580 was constructed by overexpressing DGA2 gene in Q4 strain (dga1Δ dga2Δ lro1Δ are1Δ). Reconstruction of triacylglycerol synthesis pathway led to significant improvement in lipid accumulation. Strain JMY3580 accumulated over 40% of lipids in biomass, while lipid accumulation in wild-type strain was not able to exceed 20% when grown on a glycerol-based medium with carbon to nitrogen ratio of 90. Higher lipid accumulation (over 50%) was achieved in fed-batch grown cells when glycerol was added during cultivation. The best biomass yield was 18.5 g/L after 144 h with total fatty acid yield 9.9 g/L. Fatty acid composition was altered when Dga2p was the only diacylglycerol acyltransferase present in yeast cells, especially lower percentage of linoleic acid was present in lipids of JMY3580. Microbial oil prepared by conversion of glycerol by genetically engineered Y. lipolytica could be applied for various value-added products based on single cell oils.
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Affiliation(s)
- Peter Gajdoš
- Department of Biochemical Technology, Faculty of Chemical and Food Technology Slovak University of Technology Bratislava Slovakia
| | - Jean-Marc Nicaud
- Micalis Institute, INRA, AgroParisTech Université Paris-Saclay Jouy-en-Josas France
| | - Milan Čertík
- Department of Biochemical Technology, Faculty of Chemical and Food Technology Slovak University of Technology Bratislava Slovakia
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Gajdoš P, Ledesma-Amaro R, Nicaud JM, Čertík M, Rossignol T. Overexpression of diacylglycerol acyltransferase in Yarrowia lipolytica affects lipid body size, number and distribution. FEMS Yeast Res 2016; 16:fow062. [PMID: 27506614 DOI: 10.1093/femsyr/fow062] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2016] [Indexed: 01/20/2023] Open
Abstract
In the oleaginous yeast Yarrowia lipolytica, the diacylglycerol acyltransferases (DGATs) are major factors for triacylglycerol (TAG) synthesis. The Q4 strain, in which the four acyltransferases have been deleted, is unable to accumulate lipids and to form lipid bodies (LBs). However, the expression of a single acyltransferase in this strain restores TAG accumulation and LB formation. Using this system, it becomes possible to characterize the activity and specificity of an individual DGAT. Here, we examined the effects of DGAT overexpression on lipid accumulation and LB formation in Y. lipolytica Specifically, we evaluated the consequences of introducing one or two copies of the Y. lipolytica DGAT genes YlDGA1 and YlDGA2 Overall, multi-copy DGAT overexpression increased the lipid content of yeast cells. However, the size and distribution of LBs depended on the specific DGAT overexpressed. YlDGA2 overexpression caused the formation of large LBs, while YlDGA1 overexpression generated smaller but more numerous LBs. This phenotype was accentuated through the addition of a second copy of the overexpressed gene and might be linked to the distinct subcellular localization of each DGAT, i.e. YlDga1 being localized in LBs, while YlDga2 being localized in a structure strongly resembling the endoplasmic reticulum.
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Affiliation(s)
- Peter Gajdoš
- Department of Biochemical Technology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia
| | - Rodrigo Ledesma-Amaro
- Micalis Institute, INRA UMR1319, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Jean-Marc Nicaud
- Micalis Institute, INRA UMR1319, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Milan Čertík
- Department of Biochemical Technology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia
| | - Tristan Rossignol
- Micalis Institute, INRA UMR1319, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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Dulermo R, Gamboa-Meléndez H, Ledesma-Amaro R, Thevenieau F, Nicaud JM. Yarrowia lipolytica AAL genes are involved in peroxisomal fatty acid activation. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:555-65. [PMID: 27067366 DOI: 10.1016/j.bbalip.2016.04.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 03/15/2016] [Accepted: 04/06/2016] [Indexed: 01/07/2023]
Abstract
In yeast, β-oxidation of fatty acids (FAs) essentially takes place in peroxisomes, and FA activation must precede FA oxidation. In Saccharomyces cerevisiae, a single fatty-acyl–CoA-synthetase, ScFaa2p, mediates peroxisomal FA activation. We have previously shown that this reaction also exists in the oleaginous yeast Yarrowia lipolytica; however, the protein involved in this process remains unknown. Here, we found that proteins, named Aal proteins (Acyl/Aryl-CoA-ligases), resembling the 4-coumarate–CoA-ligase-like enzymes found in plants are involved in peroxisomal FA activation in Y. lipolytica; Y. lipolytica has 10 AAL genes, eight of which are upregulated by oleate. All the Aal proteins contain a PTS1-type peroxisomal targeting sequence (A/SKL), suggesting a peroxisomal localization. The function of the Aal proteins was analyzed using the faa1Δant1Δ mutant strain, which demonstrates neither cytoplasmic FA activation (direct result of FAA1 deletion) nor peroxisomal FA activation (indirect result of ANT1 deletion, a gene coding an ATP transporter). This strain is thus highly sensitive to external FA levels and unable to store external FAs in lipid bodies (LBs). Whereas the overexpression of (cytoplasmic) AAL1ΔPTS1 was able to partially complement the growth defect observed in the faa1Δant1Δ mutant on short-, medium- and long-chain FA media, the presence of Aal2p to Aal10p only allowed growth on the short-chain FA medium. Additionally, partial LB formation was observed in the oleate medium for strains overexpressing Aal1ΔPTS1p, Aal4ΔPTS1p, Aal7ΔPTS1p, and Aal8ΔPTS1p. Finally, an analysis of the FA content of cells grown in the oleate medium suggested that Aal4p and Aal6p present substrate specificity for C16:1 and/or C18:0.
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Affiliation(s)
- Rémi Dulermo
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
| | - Heber Gamboa-Meléndez
- 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
| | - France Thevenieau
- SOFIPROTEOL, Direction Innovation, 11 rue de Monceau, Paris F-75378, France
| | - Jean-Marc Nicaud
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
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Shabbir Hussain M, M Rodriguez G, Gao D, Spagnuolo M, Gambill L, Blenner M. Recent advances in bioengineering of the oleaginous yeast Yarrowia lipolytica. AIMS BIOENGINEERING 2016. [DOI: 10.3934/bioeng.2016.4.493] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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Liu HH, Ji XJ, Huang H. Biotechnological applications of Yarrowia lipolytica: Past, present and future. Biotechnol Adv 2015; 33:1522-46. [DOI: 10.1016/j.biotechadv.2015.07.010] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 07/13/2015] [Accepted: 07/29/2015] [Indexed: 01/01/2023]
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Advances and needs for endotoxin-free production strains. Appl Microbiol Biotechnol 2015; 99:9349-60. [PMID: 26362682 DOI: 10.1007/s00253-015-6947-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 08/16/2015] [Accepted: 08/20/2015] [Indexed: 10/23/2022]
Abstract
The choice of an appropriate microbial host cell and suitable production conditions is crucial for the downstream processing of pharmaceutical- and food-grade products. Although Escherichia coli serves as a highly valuable leading platform for the production of value-added products, like most Gram-negative bacteria, this bacterium contains a potent immunostimulatory lipopolysaccharide (LPS), referred to as an endotoxin. In contrast, Gram-positive bacteria, notably Bacillus, lactic acid bacteria (LAB), Corynebacterium, and yeasts have been extensively used as generally recognized as safe (GRAS) endotoxin-free platforms for the production of a variety of products. This review summarizes the currently available knowledge on the utilization of these representative Gram-positive bacteria for the production of eco- and bio-friendly products, particularly natural polyesters, polyhydroxyalkanoates, bacteriocins, and membrane proteins. The successful case studies presented here serve to inspire the use of these microorganisms as a main-player or by-player depending on their individual properties for the industrial production of these desirable targets.
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31
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Dulermo R, Gamboa-Meléndez H, Ledesma-Amaro R, Thévenieau F, Nicaud JM. Unraveling fatty acid transport and activation mechanisms in Yarrowia lipolytica. Biochim Biophys Acta Mol Cell Biol Lipids 2015; 1851:1202-17. [DOI: 10.1016/j.bbalip.2015.04.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 04/02/2015] [Accepted: 04/07/2015] [Indexed: 11/25/2022]
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Gao C, Qi Q, Madzak C, Lin CSK. Exploring medium-chain-length polyhydroxyalkanoates production in the engineered yeast Yarrowia lipolytica. J Ind Microbiol Biotechnol 2015; 42:1255-62. [PMID: 26153503 DOI: 10.1007/s10295-015-1649-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 06/23/2015] [Indexed: 11/29/2022]
Abstract
Medium-chain-length polyhydroxyalkanoates (mcl-PHAs) are a large class of biopolymers that have attracted extensive attention as renewable and biodegradable bio-plastics. They are naturally synthesized via fatty acid de novo biosynthesis pathway or β-oxidation pathway from Pseudomonads. The unconventional yeast Yarrowia lipolytica has excellent lipid/fatty acid catabolism and anabolism capacity depending of the mode of culture. Nevertheless, it cannot naturally synthesize PHA, as it does not express an intrinsic PHA synthase. Here, we constructed a genetically modified strain of Y. lipolytica by heterologously expressing PhaC1 gene from P. aeruginosa PAO1 with a PTS1 peroxisomal signal. When in single copy, the codon optimized PhaC1 allowed the synthesis of 0.205 % DCW of PHA after 72 h cultivation in YNBD medium containing 0.1 % oleic acid. By using a multi-copy integration strategy, PHA content increased to 2.84 % DCW when the concentration of oleic acid in YNBD was 1.0 %. Furthermore, when the recombinant yeast was grown in the medium containing triolein, PHA accumulated up to 5.0 % DCW with as high as 21.9 g/L DCW, which represented 1.11 g/L in the culture. Our results demonstrated the potential use of Y. lipolytica as a promising microbial cell factory for PHA production using food waste, which contains lipids and other essential nutrients.
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Affiliation(s)
- Cuijuan Gao
- School of Life Science, Linyi University, Linyi, 276005, People's Republic of China
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Yarrowia lipolytica: recent achievements in heterologous protein expression and pathway engineering. Appl Microbiol Biotechnol 2015; 99:4559-77. [PMID: 25947247 DOI: 10.1007/s00253-015-6624-z] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/17/2015] [Accepted: 04/18/2015] [Indexed: 12/13/2022]
Abstract
The oleaginous yeast Yarrowia lipolytica has become a recognized system for expression/secretion of heterologous proteins. This non-conventional yeast is currently being developed as a workhorse for biotechnology by several research groups throughout the world, especially for single-cell oil production, whole cell bioconversion and upgrading of industrial wastes. This mini-review presents established tools for protein expression in Y. lipolytica and highlights novel developments in the areas of promoter design, surface display, and host strain or metabolic pathway engineering. An overview of the industrial and commercial biotechnological applications of Y. lipolytica is also presented.
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Role of Pex11p in Lipid Homeostasis in Yarrowia lipolytica. EUKARYOTIC CELL 2015; 14:511-25. [PMID: 25820522 DOI: 10.1128/ec.00051-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 03/25/2015] [Indexed: 01/17/2023]
Abstract
Peroxisomes are essential organelles in the cells of most eukaryotes, from yeasts to mammals. Their role in β-oxidation is particularly essential in yeasts; for example, in Saccharomyces cerevisiae, fatty acid oxidation takes place solely in peroxisomes. In this species, peroxisome biogenesis occurs when lipids are present in the culture medium, and it involves the Pex11p protein family: ScPex11p, ScPex25p, ScPex27p, and ScPex34p. Yarrowia lipolytica has three Pex11p homologues, which are YALI0C04092p (YlPex11p), YALI0C04565p (YlPex11C), and YALI0D25498p (Pex11/25p). We found that these genes are regulated by oleic acid, and as has been observed in other organisms, YlPEX11 deletion generated giant peroxisomes when mutant yeast were grown in oleic acid medium. Moreover, ΔYlpex11 was unable to grow on fatty acid medium and showed extreme dose-dependent sensitivity to oleic acid. Indeed, when the strain was grown in minimum medium with 0.5% glucose and 3% oleic acid, lipid body lysis and cell death were observed. Cell death and lipid body lysis may be partially explained by an imbalance in the expression of the genes involved in lipid storage, namely, DGA1, DGA2, and LRO1, as well as that of TGL4, which is involved in lipid remobilization. TGL4 deletion and DGA2 overexpression resulted in decreased oleic acid sensitivity and delayed cell death of ΔYlpex11, which probably stemmed from the release of free fatty acids into the cytoplasm. All these results show that YlPex11p plays an important role in lipid homeostasis in Y. lipolytica.
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35
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Sibirny A, Madzak C, Fickers P. Genetic engineering of nonconventional yeasts for the production of valuable compounds. Microb Biotechnol 2014. [DOI: 10.1201/b17587-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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36
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Dulermo R, Gamboa-Meléndez H, Dulermo T, Thevenieau F, Nicaud JM. The fatty acid transport protein Fat1p is involved in the export of fatty acids from lipid bodies inYarrowia lipolytica. FEMS Yeast Res 2014; 14:883-96. [DOI: 10.1111/1567-1364.12177] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 06/09/2014] [Accepted: 06/12/2014] [Indexed: 12/01/2022] Open
Affiliation(s)
- Rémi Dulermo
- UMR1319 Micalis; INRA; Jouy-en-Josas France
- UMR Micalis; AgroParisTech; Jouy-en-Josas France
| | - Heber Gamboa-Meléndez
- UMR1319 Micalis; INRA; Jouy-en-Josas France
- UMR Micalis; AgroParisTech; Jouy-en-Josas France
| | - Thierry Dulermo
- UMR1319 Micalis; INRA; Jouy-en-Josas France
- UMR Micalis; AgroParisTech; Jouy-en-Josas France
| | | | - Jean-Marc Nicaud
- UMR1319 Micalis; INRA; Jouy-en-Josas France
- UMR Micalis; AgroParisTech; Jouy-en-Josas France
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37
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Chen L, Zhang J, Chen WN. Engineering the Saccharomyces cerevisiae β-oxidation pathway to increase medium chain fatty acid production as potential biofuel. PLoS One 2014; 9:e84853. [PMID: 24465440 PMCID: PMC3897402 DOI: 10.1371/journal.pone.0084853] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 11/19/2013] [Indexed: 12/16/2022] Open
Abstract
Fatty acid-derived biofuels and biochemicals can be produced in microbes using β-oxidation pathway engineering. In this study, the β-oxidation pathway of Saccharomyces cerevisiae was engineered to accumulate a higher ratio of medium chain fatty acids (MCFAs) when cells were grown on fatty acid-rich feedstock. For this purpose, the haploid deletion strain Δpox1 was obtained, in which the sole acyl-CoA oxidase encoded by POX1 was deleted. Next, the POX2 gene from Yarrowia lipolytica, which encodes an acyl-CoA oxidase with a preference for long chain acyl-CoAs, was expressed in the Δpox1 strain. The resulting Δpox1 [pox2+] strain exhibited a growth defect because the β-oxidation pathway was blocked in peroxisomes. To unblock the β-oxidation pathway, the gene CROT, which encodes carnitine O-octanoyltransferase, was expressed in the Δpox1 [pox2+] strain to transport the accumulated medium chain acyl-coAs out of the peroxisomes. The obtained Δpox1 [pox2+, crot+] strain grew at a normal rate. The effect of these genetic modifications on fatty acid accumulation and profile was investigated when the strains were grown on oleic acids-containing medium. It was determined that the engineered strains Δpox1 [pox2+] and Δpox1 [pox2+, crot+] had increased fatty acid accumulation and an increased ratio of MCFAs. Compared to the wild-type (WT) strain, the total fatty acid production of the strains Δpox1 [pox2+] and Δpox1 [pox2+, crot+] were increased 29.5% and 15.6%, respectively. The intracellular level of MCFAs in Δpox1 [pox2+] and Δpox1 [pox2+, crot+] increased 2.26- and 1.87-fold compared to the WT strain, respectively. In addition, MCFAs in the culture medium increased 3.29-fold and 3.34-fold compared to the WT strain. These results suggested that fatty acids with an increased MCFAs ratio accumulate in the engineered strains with a modified β-oxidation pathway. Our approach exhibits great potential for transforming low value fatty acid-rich feedstock into high value fatty acid-derived products.
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Affiliation(s)
- Liwei Chen
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, Singapore, Singapore
| | - Jianhua Zhang
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, Singapore, Singapore
| | - Wei Ning Chen
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, Singapore, Singapore
- * E-mail:
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Wriessnegger T, Pichler H. Yeast metabolic engineering – Targeting sterol metabolism and terpenoid formation. Prog Lipid Res 2013; 52:277-93. [DOI: 10.1016/j.plipres.2013.03.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Revised: 03/26/2013] [Accepted: 03/27/2013] [Indexed: 12/28/2022]
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Roelants SL, Saerens KM, Derycke T, Li B, Lin Y, Van de Peer Y, De Maeseneire SL, Van Bogaert IN, Soetaert W. Candida bombicola
as a platform organism for the production of tailor‐made biomolecules. Biotechnol Bioeng 2013; 110:2494-503. [DOI: 10.1002/bit.24895] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 02/17/2013] [Accepted: 02/20/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Sophie L.K.W. Roelants
- Faculty of Bioscience Engineering, Centre for Industrial Biotechnology and Biocatalysis (InBio.be)Ghent UniversityCoupure Links 6539000 Ghent, Belgium
| | - Karen M.J. Saerens
- Faculty of Bioscience Engineering, Centre for Industrial Biotechnology and Biocatalysis (InBio.be)Ghent UniversityCoupure Links 6539000 Ghent, Belgium
| | - Thibaut Derycke
- Faculty of Bioscience Engineering, Centre for Industrial Biotechnology and Biocatalysis (InBio.be)Ghent UniversityCoupure Links 6539000 Ghent, Belgium
| | - Bing Li
- Department of Plant Biotechnology and BioinformaticsGhent UniversityTechnologiepark 927, 9052Zwijnaarde
| | - Yao‐Cheng Lin
- Department of Plant Systems BiologyVIBTechnologiepark 927, 9052Zwijnaarde
| | - Yves Van de Peer
- Department of Plant Biotechnology and BioinformaticsGhent UniversityTechnologiepark 927, 9052Zwijnaarde
- Department of Plant Systems BiologyVIBTechnologiepark 927, 9052Zwijnaarde
| | - Sofie L. De Maeseneire
- Faculty of Bioscience Engineering, Centre for Industrial Biotechnology and Biocatalysis (InBio.be)Ghent UniversityCoupure Links 6539000 Ghent, Belgium
| | - Inge N.A. Van Bogaert
- Faculty of Bioscience Engineering, Centre for Industrial Biotechnology and Biocatalysis (InBio.be)Ghent UniversityCoupure Links 6539000 Ghent, Belgium
| | - Wim Soetaert
- Faculty of Bioscience Engineering, Centre for Industrial Biotechnology and Biocatalysis (InBio.be)Ghent UniversityCoupure Links 6539000 Ghent, Belgium
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40
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Madzak C, Beckerich JM. Heterologous Protein Expression and Secretion in Yarrowia lipolytica. YARROWIA LIPOLYTICA 2013. [DOI: 10.1007/978-3-642-38583-4_1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Abstract
The yeast Yarrowia lipolytica presents specific physiological, metabolic and genomic characteristics, which differentiate it from the model yeast Saccharomyces cerevisiae. These properties have led several research groups to use this yeast as a model for basic knowledge. Thanks to the development of advanced genetic tools and -omic approaches, significant progress has been achieved in the understanding of specific biological processes. This review, after a short presentation of this model yeast, will briefly highlight the different use of Y. lipolytica for basic knowledge and the advantages gained by exploiting this non-conventional yeast. Future perspectives in employing this yeast for basic knowledge in the field of RNA splicing and genome evolution, and for the study of lipid metabolism, are also discussed.
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42
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Kabran P, Rossignol T, Gaillardin C, Nicaud JM, Neuvéglise C. Alternative splicing regulates targeting of malate dehydrogenase in Yarrowia lipolytica. DNA Res 2012; 19:231-44. [PMID: 22368181 PMCID: PMC3372373 DOI: 10.1093/dnares/dss007] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Alternative pre-mRNA splicing is a major mechanism contributing to the proteome complexity of most eukaryotes, especially mammals. In less complex organisms, such as yeasts, the numbers of genes that contain introns are low and cases of alternative splicing (AS) with functional implications are rare. We report the first case of AS with functional consequences in the yeast Yarrowia lipolytica. The splicing pattern was found to govern the cellular localization of malate dehydrogenase, an enzyme of the central carbon metabolism. This ubiquitous enzyme is involved in the tricarboxylic acid cycle in mitochondria and in the glyoxylate cycle, which takes place in peroxisomes and the cytosol. In Saccharomyces cerevisiae, three genes encode three compartment-specific enzymes. In contrast, only two genes exist in Y. lipolytica. One gene (YlMDH1, YALI0D16753g) encodes a predicted mitochondrial protein, whereas the second gene (YlMDH2, YALI0E14190g) generates the cytosolic and peroxisomal forms through the alternative use of two 3'-splice sites in the second intron. Both splicing variants were detected in cDNA libraries obtained from cells grown under different conditions. Mutants expressing the individual YlMdh2p isoforms tagged with fluorescent proteins confirmed that they localized to either the cytosolic or the peroxisomal compartment.
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Haddouche R, Poirier Y, Delessert S, Sabirova J, Pagot Y, Neuvéglise C, Nicaud JM. Engineering polyhydroxyalkanoate content and monomer composition in the oleaginous yeast Yarrowia lipolytica by modifying the ß-oxidation multifunctional protein. Appl Microbiol Biotechnol 2011; 91:1327-40. [PMID: 21603933 DOI: 10.1007/s00253-011-3331-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 04/08/2011] [Accepted: 04/09/2011] [Indexed: 11/30/2022]
Abstract
Recombinant strains of the oleaginous yeast Yarrowia lipolytica expressing the PHA synthase gene (PhaC) from Pseudomonas aeruginosa in the peroxisome were found able to produce polyhydroxyalkanoates (PHA). PHA production yield, but not the monomer composition, was dependent on POX genotype (POX genes encoding acyl-CoA oxidases) (Haddouche et al. FEMS Yeast Res 10:917-927, 2010). In this study of variants of the Y. lipolytica β-oxidation multifunctional enzyme, with deletions or inactivations of the R-3-hydroxyacyl-CoA dehydrogenase domain, we were able to produce hetero-polymers (functional MFE enzyme) or homo-polymers (with no 3-hydroxyacyl-CoA dehydrogenase activity) of PHA consisting principally of 3-hydroxyacid monomers (>80%) of the same length as the external fatty acid used for growth. The redirection of fatty acid flux towards β-oxidation, by deletion of the neutral lipid synthesis pathway (mutant strain Q4 devoid of the acyltransferases encoded by the LRO1, DGA1, DGA2 and ARE1 genes), in combination with variant expressing only the enoyl-CoA hydratase 2 domain, led to a significant increase in PHA levels, to 7.3% of cell dry weight. Finally, the presence of shorter monomers (up to 20% of the monomers) in a mutant strain lacking the peroxisomal 3-hydroxyacyl-CoA dehydrogenase domain provided evidence for the occurrence of partial mitochondrial β-oxidation in Y. lipolytica.
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Beopoulos A, Nicaud JM, Gaillardin C. An overview of lipid metabolism in yeasts and its impact on biotechnological processes. Appl Microbiol Biotechnol 2011; 90:1193-206. [PMID: 21452033 DOI: 10.1007/s00253-011-3212-8] [Citation(s) in RCA: 227] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 01/25/2011] [Indexed: 11/24/2022]
Abstract
High energy prices, depletion of crude oil supplies, and price imbalance created by the increasing demand of plant oils or animal fat for biodiesel and specific lipid derivatives such as lubricants, adhesives, and plastics have given rise to heated debates on land-use practices and to environmental concerns about oil production strategies. However, commercialization of microbial oils with similar composition and energy value to plant and animal oils could have many advantages, such as being non-competitive with food, having shorter process cycle and being independent of season and climate factors. This review focuses on the ongoing research on different oleaginous yeasts producing high added value lipids and on the prospects of such microbial oils to be used in different biotechnological processes and applications. It covers the basic biochemical mechanisms of lipid synthesis and accumulation in these organisms, along with the latest insights on the metabolic processes involved. The key elements of lipid accumulation, the mechanisms suspected to confer the oleaginous character of the cell, and the potential metabolic routes enhancing lipid production are also extensively discussed.
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Affiliation(s)
- Athanasios Beopoulos
- AgroParisTech, UMR1319, Micalis, Centre de Biotechnologie Agro-Industrielle, Thiverval-Grignon, France
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