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Production of omega-3 eicosapentaenoic acid by metabolic engineering of Yarrowia lipolytica

Nature Biotechnology volume 31, pages 734–740 (2013)Cite this article

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Abstract

The availability of the omega-3 fatty acids eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) is currently limited because they are produced mainly by marine fisheries that cannot keep pace with the demands of the growing market for these products. A sustainable non-animal source of EPA and DHA is needed. Metabolic engineering of the oleaginous yeast Yarrowia lipolytica resulted in a strain that produced EPA at 15% of dry cell weight. The engineered yeast lipid comprises EPA at 56.6% and saturated fatty acids at less than 5% by weight, which are the highest and the lowest percentages, respectively, among known EPA sources. Inactivation of the peroxisome biogenesis gene PEX10 was crucial in obtaining high EPA yields and may increase the yields of other commercially desirable lipid-related products. This technology platform enables the production of lipids with tailored fatty acid compositions and provides a sustainable source of EPA.

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Figure 1: Fatty acid profiles of Y. lipolytica strains and EPA biosynthetic pathways.
Figure 2: Schematic showing the construction of the EPA-producing strain Y4305.
Figure 3: Fatty acid profiles and lipid content of strains with PEX10 mutations.
Figure 4: Peroxisome morphology and protein import in strains with PEX10 mutations.
Figure 5: EPA and lipid production in strain Y4305.
Figure 6: Fatty acid distribution of lipid species from strain Y4305.

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Acknowledgements

We are grateful to H. Bryndza and J. Pierce for their strong support. We thank A. Kinney and S. Picataggio for their suggestions, K. Czymmek and J. Li for their technical help and D. Chesire for critical reading of this manuscript.

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Authors and Affiliations

  1. Industrial Biosciences, E.I. du Pont de Nemours and Company, Wilmington, Delaware, USA

    Zhixiong Xue, Narendra S Yadav, David R Short, Daniel J Macool, Hongxiang Zhang & Sidney A Bledsoe

  2. Biochemical Sciences and Engineering, Central Research and Development, E.I. du Pont de Nemours and Company, Wilmington, Delaware, USA

    Pamela L Sharpe, Seung-Pyo Hong, Dongming Xie, Ross A Rupert, John E Seip, Jamie Wang, Dana W Pollak, Michael W Bostick, Melissa D Bosak, Dieter H Hollerbach, Dennis M Arcilla, Kevin Croker, Bjorn D Tyreus, Ethel N Jackson & Quinn Zhu

  3. Crop Genetics, E.I. du Pont de Nemours and Company, Wilmington, Delaware, USA

    Howard G Damude

  4. Corporate Center for Analytical Science, E.I. du Pont de Nemours and Company, Wilmington, Delaware, USA

    Elizabeth F McCord

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Contributions

Q.Z. was responsible for strain-construction strategy, codon optimization of synthetic genes and design and construction of integration plasmids, and served as the lead for the strain-development team; Z.X., N.S.Y., H.G.D., E.N.J. and Q.Z. jointly conceived the concepts for gene isolation, selection and pathway engineering; Z.X., P.L.S., S.-P.H. and Q.Z. determined integration sites; R.A.R., J.E.S., J.W., D.W.P., M.D.B., D.J.M. and H.Z. performed molecular biology experiments, transformation, primary screening, flask assays and gas chromatography analyses; D.H.H. performed the analyses of fatty acid profiles, lipid content and different lipid classes; P.L.S. and M.D.B. designed and performed homologous recombination experiments for targeted PEX10 gene disruption; Z.X., D.J.M. and K.C. performed cell biology experiments; D.X., D.R.S., D.M.A., S.A.B. and B.D.T. designed and performed fermentation experiments; D.X. and B.D.T. developed models for fermentation experiments; E.F.M. performed the NMR analysis; Z.X., M.W.B., S.-P.H., N.S.Y., E.N.J. and Q.Z. prepared the manuscript; M.W.B. prepared the figures.

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Correspondence to Quinn Zhu.

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Xue, Z., Sharpe, P., Hong, SP. et al. Production of omega-3 eicosapentaenoic acid by metabolic engineering of Yarrowia lipolytica. Nat Biotechnol 31, 734–740 (2013). https://doi.org/10.1038/nbt.2622

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