Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

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


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.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

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.

Accession codes


NCBI Reference Sequence


  1. Ma, D.W.L. et al. n-3 PUFA and membrane microdomains: a new frontier in bioactive lipid research. J. Nutr. Biochem. 15, 700–706 (2004).

    Article  CAS  PubMed  Google Scholar 

  2. Funk, C.D. Prostaglandins and leukotrienes: advances in eicosanoid biology. Science 294, 1871–1875 (2001).

    Article  CAS  PubMed  Google Scholar 

  3. Deckelbaum, R.J. & Torrejon, C. The omega-3 fatty acid nutritional landscape: health benefits and sources. J. Nutr. 142, 587S–591S (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Yokoyama, M. et al. Effects of eicosapentaenoic acid on major coronary events in hypercholesterolaemic patients (JELIS): a randomised open-label, blinded endpoint analysis. Lancet 369, 1090–1098 (2007).

    Article  CAS  PubMed  Google Scholar 

  5. Bays, H.E. et al. Eicosapentaenoic acid ethyl ester (AMR101) therapy in patients with very high triglyceride levels (from the multi-center, plAcebo-controlled, randomized, double-blINd, 12-week study with an open-label extension [MARINE] trial). Am. J. Cardiol. 108, 682–690 (2011).

    Article  CAS  PubMed  Google Scholar 

  6. Schaefer, E.J. et al. Effects of eicosapentaenoic acid, docosahexaenoic acid, and olive oil on cardiovascular disease risk factors. Circulation 122, A20007 (2010).

    Google Scholar 

  7. Gillies, P.J., Harris, W.S. & Kris-Etherton, P.M. Omega-3 fatty acids in food and pharma: the enabling role of biotechnology. Curr. Atheroscler. Rep. 13, 467–473 (2011).

    Article  CAS  PubMed  Google Scholar 

  8. Metz, J.G. et al. Production of polyunsaturated fatty acids by polyketide synthases in both prokaryotes and eukaryotes. Science 293, 290–293 (2001).

    Article  CAS  PubMed  Google Scholar 

  9. Meesapyodsuk, D. & Qiu, X. The front-end desaturase: structure, function, evolution and biotechnological use. Lipids 47, 227–237 (2012).

    Article  CAS  PubMed  Google Scholar 

  10. Wallis, J.G. & Browse, J. The Δ8-desaturase of Euglena gracilis: an alternate pathway for synthesis of 20-carbon polyunsaturated fatty acids. Arch. Biochem. Biophys. 365, 307–316 (1999).

    Article  CAS  PubMed  Google Scholar 

  11. Zhu, Q. et al. Metabolic engineering of an oleaginous yeast for the production of omega-3 fatty acids. in Single Cell Oils: Microbial and Algal Oils (eds. Cohen, Z. & Ratledge, C.) 51–73 (AOCS press, Urbana, 2010).

  12. Barclay, W.R., Meager, K.M. & Abril, J.R. Heterotrophic production of long chain omega-3 fatty acids utilizing algae and algae-like microorganisms. J. Appl. Phycol. 6, 123–129 (1994).

    Article  CAS  Google Scholar 

  13. Barclay, W., Weaver, C. & Metz, J. Development of a docosahexaenoic acid production technology using Schizochytrium: a history perspective. in Single Cell Oils (eds. Cohen, Z. & Ratledge, C.) 36–73 (AOCS press, Champaign, Illinois, 2005).

  14. Qi, B. et al. Production of very long chain polysaturated omega-3 and omega-6 fatty acids in plants. Nat. Biotechnol. 22, 739–745 (2004).

    Article  CAS  PubMed  Google Scholar 

  15. Napier, J.A. & Sayanova, O. The production of very-long-chain PUFA biosynthesis in transgenic plants: towards a sustainable source of fish oils. Proc. Nutr. Soc. 64, 387–393 (2005).

    Article  CAS  PubMed  Google Scholar 

  16. Damude, H.G. & Kinney, A.J. Engineering oilseeds to produce nutritional fatty acids. Physiol. Plant. 132, 1–10 (2008).

    CAS  PubMed  Google Scholar 

  17. Cheng, B. et al. Towards the production of high levels of eicosapentaenoic acid in transgenic plants: the effects of different host species, genes and promoters. Transgenic Res. 19, 221–229 (2010).

    Article  CAS  PubMed  Google Scholar 

  18. Petrie, J.R. et al. Metabolic engineering of omega-3 long-chain polyunsaturated fatty acids in plants using an acyl-CoA Δ6-desaturase with ω3-preference from the marine microalga Micromonas pusilla. Metab. Eng. 12, 233–240 (2010).

    Article  CAS  PubMed  Google Scholar 

  19. Tavares, S. et al. Metabolic engineering of Saccharomyces cerevisiae for production of eicosapentaenoic acid, using a novel Δ5-desaturase from Paramecium tetraurelia. Appl. Environ. Microbiol. 77, 1854–1861 (2011).

    Article  CAS  PubMed  Google Scholar 

  20. Adarme-Vega, T.C. et al. Microalgal biofactories: a promising approach towards sustainable omega-3 fatty acid production. Microb. Cell Fact. 11, 96 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Xue, Z. et al. Identification and characterization of new Δ-17 fatty acid desaturases. Appl. Microbiol. Biotechnol. 97, 1973–1985 (2013).

    Article  CAS  PubMed  Google Scholar 

  22. Pollak, D.W. et al. Isolation of a Δ5 desaturase gene from Euglena gracilis and functional dissection of its HPGG and HDASH motifs. Lipids 47, 913–926 (2012).

    Article  CAS  PubMed Central  Google Scholar 

  23. Hong, S.-P. et al. Engineering Yarrowia lipolytica to express secretory invertase with strong FBA1IN promoter. Yeast 29, 59–72 (2011).

    Article  PubMed  Google Scholar 

  24. Blazeck, J., Liu, L., Redden, H. & Alper, H. Tuning gene expression in Yarrowia lipolytica by a hybrid promoter approach. Appl. Environ. Microbiol. 77, 7905–7914 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Weterings, E. & Chen, D.J. The endless tale of non-homologous end-joining. Cell Res. 18, 114–124 (2008).

    Article  CAS  PubMed  Google Scholar 

  26. Damude, H.G., He, H., Liao, D.-I. & Zhu, Q.Q. Mutant Δ8 desaturase genes engineered by targeted mutagenesis and their use in making polyunsaturated fatty acids. US patent 7,709,239 (2010).

  27. Prestele, J. et al. Different functions of the C3HC4 zinc RING finger peroxins PEX10, PEX2, and PEX12 in peroxisome formation and matrix protein import. Proc. Natl. Acad. Sci. USA 107, 14915–14920 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Titorenko, V.I., Smith, J.j., Szilard, R.K. & Rachubinski, R.A. Peroxisome biogenesis in the yeast Yarrowia lipolytica. Cell Biochem. Biophys. 32, 21–26 (2000).

    Article  CAS  PubMed  Google Scholar 

  29. Aursand, M., Standal, I.B. & Axelson, D.E. High-resolution 13C nuclear magnetic resonance spectroscopy pattern recognition of fish oil capsules. J. Agric. Food Chem. 55, 38–47 (2007).

    Article  CAS  PubMed  Google Scholar 

  30. Tai, M. & Stephanopoulos, G. Engineering the push and pull of lipid biosynthesis in oleaginous yeast Yarrowia lipolytica for biofuel production. Metab. Eng. 15, 1–9 (2013).

    Article  CAS  PubMed  Google Scholar 

  31. Wen, Z. & Chen, F. Prospects for eicosapentaenoic acid production using microorganisms. in Single Cell Oils (eds. Cohen, Z. & Ratledge, C) 138–160 (AOCS Press, Champaign, Illinois, 2005).

  32. Ratledge, C. Single cell oils for the 21st century. in Single Cell Oils (eds. Cohen, Z. & Ratledge, C.) 1–20 (AOCS Press, Champaign, Illinois, 2005).

  33. Groenewald, M. et al. Yarrowia lipolytica: safety assessment of an oleaginous yeast with a great industrial potential. Crit. Rev. Microbiol. (2013).

  34. Barth, G. et al. Functional genetics of Yarrowia lipolytica. in Functional Genetics of Industrial Yeasts: Topics in Current Genetics (ed. de-Winde, H.) 227–271 (Springer Verlag, Berlin, Germany, 2003).

  35. Dujon, B. et al. Genome evolution in yeasts. Nature 430, 35–44 (2004).

    Article  PubMed  Google Scholar 

  36. Beopoulos, A., Nicaud, J.-M. & Gaillardin, C. An overview of lipid metabolism in yeasts and its impact on biotechnological processes. Appl. Microbiol. Biotechnol. 90, 1193–1206 (2011).

    Article  CAS  PubMed  Google Scholar 

  37. Nicaud, J.-M. Yarrowia lipolytica. Yeast 29, 409–418 (2012).

    Article  CAS  PubMed  Google Scholar 

  38. Domergue, F. et al. Acyl carriers used as substrates by the desaturases and elongases involved in very long-chain polyunsaturated fatty acids biosynthesis reconstituted in yeast. J. Biol. Chem. 278, 35115–35126 (2003).

    Article  CAS  PubMed  Google Scholar 

  39. Damude, H.G. et al. Identification of bifunctional Δ12/ω3 fatty acid desaturases for improving the ratio of ω3 to ω6 fatty acids in microbes and plants. Proc. Natl. Acad. Sci. USA 103, 9446–9451 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Sumita, T. et al. Peroxisome deficiency represses the expression of n-alkane–inducible YlALK1 encoding cytochrome P450ALK1 in Yarrowia lipolytica. FEMS Microbiol. Lett. 214, 31–38 (2002).

    Article  CAS  PubMed  Google Scholar 

  41. Flores, C.-L. & Gancedo, C. Yarrowia lipolytica mutants devoid of pyruvate carboxylase activity show an unusual growth phenotype. Eukaryot. Cell 4, 356–364 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Griffiths, G., Stobart, A.K. & Stymne, S. Δ6- and Δ12-desaturase activities and phosphatidic acid formation in microsomal preparations from the developing cotyledons of common borage (Borago officinalis). Biochem. J. 252, 641–647 (1988).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Sherman, F. Getting started with yeast. in Methods Enzymology (eds. Guthrie, C. & Fink, G.R.) 194, 3–20 (Academic Press, New York, 1991).

    Article  CAS  Google Scholar 

  44. Ausubel, F.M. et al. Current Protocols in Molecular Biology (John Wiley, New York, 2010).

  45. Chen, D.C., Beckerich, J.M. & Gaillardin, C. One-step transformation of the dimorphic yeast Yarrowia lipolytica. Appl. Microbiol. Biotechnol. 48, 232–235 (1997).

    Article  CAS  PubMed  Google Scholar 

  46. Fickers, P. et al. New disruption cassettes for rapid gene disruption and marker rescue in the yeast Yarrowia lipolytica. J. Microbiol. Methods 55, 727–737 (2003).

    Article  CAS  PubMed  Google Scholar 

  47. Cahoon, E.B., Ripp, K.G., Hall, S.E. & Kinney, A.L. Formation of conjugated Δ8, Δ10-double bonds by Δ12-oleic acid desaturase-related enzymes: biosynthetic origin of calendic acid. J. Biol. Chem. 276, 2637–2643 (2001).

    Article  CAS  PubMed  Google Scholar 

  48. Zhang, H., Damude, H.G. & Yadav, N.S. Three diacylglycerol acyltransferases contribute to oil biosynthesis and normal growth in Yarrowia lipolytica. Yeast 29, 25–38 (2012).

    Article  PubMed  Google Scholar 

  49. Christie, W.W. Lipid Analysis, 3rd ed. (The Oily Press, Bridgwater, UK, 2003).

  50. Walther, P. & Ziegler, A. Freeze substitution of high-pressure frozen samples: the visibility of biological membranes is improved when the substitution medium contains water. J. Microsc. 208, 3–10 (2002).

    Article  CAS  PubMed  Google Scholar 

  51. Troëng, S. Oil determination of oilseed. Gravimetric routine method. J. Am. Oil Chem. Soc. 32, 124–126 (1955).

    Article  Google Scholar 

Download references


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.

Author information

Authors and Affiliations



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.

Corresponding author

Correspondence to Quinn Zhu.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Tables 1–3 (PDF 319 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

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).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing