Metabolic engineering of Yarrowia lipolytica for industrial applications

Current Opinion in Biotechnology

Volumn 36, Issue , 2015, Pages 65-72

  Zhu, Quinn ^a   Jackson, Ethel N ^a  

^a DUPONT COMPANY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COST EFFECTIVENESS; METABOLIC ENGINEERING; METABOLISM;

BIO-DIESEL FUEL; COST-EFFECTIVE PRODUCTION; EICOSAPENTAENOIC ACID; INDUSTRIAL SCALE; RECENT PROGRESS; TWO-PRODUCT; Y. LIPOLYTICA; YARROWIA LIPOLYTICA;

FATTY ACIDS;

BIODIESEL; CAROTENOID; FATTY ACID; BIOFUEL;

BIOFUEL PRODUCTION; BIOTECHNOLOGICAL PRODUCTION; FUNGAL STRAIN; HUMAN; LIPOGENESIS; METABOLIC ENGINEERING; METABOLIC REGULATION; NONHUMAN; PRIORITY JOURNAL; REVIEW; YARROWIA LIPOLYTICA; ANIMAL; BIOSYNTHESIS; GENETICS; INDUSTRY; METABOLISM; PROCEDURES; YARROWIA;

YARROWIA LIPOLYTICA;

ANIMALS; BIOFUELS; CAROTENOIDS; FATTY ACIDS; HUMANS; INDUSTRY; METABOLIC ENGINEERING; YARROWIA;

EID: 84940100557     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2015.08.010     Document Type: Review

References (66)

1. Bailey J.E. Toward a science of metabolic engineering. Science 1991, 252:1668-1675.
2. Stephanopoulos G., Vallino J. Network rigidity and metabolic engineering in metabolite overproduction. Science 1991, 252:1675-1681.
3. Chen Y., Nielsen J. Advances in metabolic pathway and strain engineering paving the way for sustainable production of chemical building blocks. Curr Opin Biotechnol 2013, 24:965-972.
4. Woolston B.M., Edgar S., Stephanopoulos G. Metabolic engineering: past and future. Annu Rev Chem Biomol Eng 2013, 4:259-288.
5. Liu Y., Shin H.-D., Li J., Liu L. Towards metabolic engineering in the context of system biology and synthetic biology: advances and prospects. Appl Microbiol Biotechnol 2015, 99:1109-1118.
6. Nakamura C.E., Whited G.M. Metabolic engineering for the microbial production of 1,3-propanediol. Curr Opin Biotechnol 2003, 14:454-459.
7. Yim H., Haselbeck R., Niu W., Pujol-Baxley C., Burgard A., Bold J., Khandurina J., Trawick J.D., Osterhout R.E., Stephen R., Estadilla J., Teisan S., Schreyer H.B., Andrae S., Yang T.H., Lee S.P., Burk M.J., Van Dien S. Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. Nat Chem Biol 2011, 7:445-452.
8. Ro D.K., Paradise E.M., Ouellet M., Fisher K.J., Newman K.L., Ndungu J.M., Ho K.A., Eachus R.A., Ham T.S., Kirby J., Michelle C., Chang M.C.Y., Withers S.T., Shiba Y., Sarpong R., Keasling J.D. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 2006, 440:940-943.
9. Westfall P.J., Pitera D.J., Lenihan J.R., Eng D., Woolard F.X., Regentin R., Horning T., Tsuruta H., Melis D.J., Owens A., Fickes S., Diola D., Benjamin K.R., Keasling J.D., Leavell M.D., McPhee D.J., Renninger N.S., Newman J.D., Paddon C.J. Production of amorphadiene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin. Proc Natl Acad Sci U S A 2012, 109:111-118.
10. Paddon C.J., Keasling J.D. Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development. Nat Rev Microbiol 2014, 12:355-367.
11. Xie D., Jackson E.N., Zhu Q. Sustainable source of omega-3 eicosapentaenoic acid from metabolically engineered Yarrowia lipolytica: from fundamental research to commercial production. Appl Microbiol Biotechnol 2015, 99:1599-1610.
12. Beopoulos A., Chardot T., Nicaud J.-M. Yarrowia lipolytica: a model and a tool to understand the mechanisms implicated in lipid accumulation. Biochimie 2009, 91:692-696.
13. Nicaud J.-M. Yarrowia lipolytica. Yeast 2012, 29:409-418.
14. Fukuda R. Metabolism of hydrophobic carbon sources and regulation of it in n-alkane-assimilating yeast Yarrowia lipolytica. Biosci Biotechnol Biochem 2013, 77:1149-1154.
15. Abghari A., Chen S. Yarrowia lipolytica as an oleaginous cell factory platform for production of fatty acid-based biofuel and bioproducts. Front Energy Res 2014, 2:1-21.
16. Thevenieau F., Gaillardin C., Nicaud J.-M. Applications of the non-conventional yeast Yarrowia lipolytica. Yeast Biotechnology: Diversity and Applications 2009, 589-613. Springer, Netherlands. T. Satyanarayana, G. Kunze (Eds.).
17. Groenewald M., Boekhout T., Neuvéglise C., Gaillardin C., van Dijck P.W., Wyss M. Yarrowia lipolytica: safety assessment of an oleaginous yeast with a great industrial potential. Crit Rev Microbiol 2014, 40:187-206.
18. Tsigie Y.A., Wang C.Y., Truong C.T., Ju Y.H. Lipid production from Yarrowia lipolytica Po1g grown in sugarcane bagasse hydrolysate. Bioresour Technol 2011, 102:9216-9222.
19. Hong S.-Y., Seip J., Walters-Pollak D., Rupert R., Jackson R., Xue Z., Zhu Q. Engineering Yarrowia lipolytica to express secretory invertase with strong FBA1IN promoter. Yeast 2011, 29:59-72.
20. Lazar Z., Rossignol T., Verbeke J., Crutz-Le Coq A.M., Nicaud J.M., Robak M. Optimized invertase expression and secretion cassette for improving Yarrowia lipolytica growth on sucrose for industrial applications. J Ind Microbiol Biotechnol 2013, 40:1273-1283.
21. Lazar Z., Dulermo T., Neuvéglise C., Crutz-Le Coq A.M., Nicaud J.M. Hexokinase-A limiting factor in lipid production from fructose in Yarrowia lipolytica. Metab Eng 2014, 26:89-99.
22. Blank L.M., Lehmbeck F., Sauer U. Metabolic-flux and network analysis in fourteen hemiascomycetous yeasts. FEMS Yeast Res 2005, 5:545-558.
23. 13C flux analysis and metabolomics. FEMS Yeast Res 2011, 11:263-272.
24. Dujon B., Sherman D., Fischer G., Durrens P., Casaregola S., Lafontaine I., Montigny J., Marck C., Neuvéglise C., Talla E., Goffard N., Frangeul L., Aigle M., Anthouard V., Babour A., Barbe V., Barnay S., Blanchin S., Beckerich J.M., Beyne E., Bleykasten C., Boisramé A., Boyer J., Cattolico L., Confanioleri F., Daruvar A., Despons L., Fabre E., Fairhead C., Ferry-Dumazet H., Groppi A., Hantraye F., Hennequin C., Jauniaux N., Joyet P., Kachouri R., Kerrest A., Koszul R., Lemaire M., Lesur I., Ma L., Muller H., Nicaud J.M., Nikolsk M., Oztas S., Ozier-Kalogeropoulos O., Pellenz S., Potier S., Richard G.F., Straub M.L., Suleau A., Swennen D., Tekaia F., Wésolowski-Louvel M., Westhof E., Wirth B., Zeniou-Meyer M., Zivanovic I., Bolotin-Fukuhara M., Thierry A., Bouchier C., Caudron B., Scarpelli C., Gaillardin C., Weissenbach J., Wincker P., Souciet J.L. Genome evolution in yeasts. Nature 2004, 430:35-44.
25. Liu L., Alper H.S. Draft genome sequence of the oleaginous yeast Yarrowia lipolytica PO1f, a commonly used metabolic engineering host. Genome 2014, 2:1-2.
26. Blazeck J., Liu L., Redden H., Alper H. Tuning gene expression in Yarrowia lipolytica by a hybrid promoter approach. Appl Environ Microbiol 2011, 77:7905-7914.
27. Lennen R.M., Pfleger B.F. Microbial production of fatty acid-derived fuels and chemicals. Curr Opin Biotechnol 2013, 24:1044-1053.
28. Koutinas A.A., Chatzifragkou A., Kopsahelis N., Papanikolaou S., Kookos I.K. Design and tech-economic evaluation of microbial oil production as a renewable resource for biodiesel and oleochemical production. Fuel 2014, 116:566-577.
29. Hong S-P, Xue Z, Zhu Q: Pentose phosphate pathway upregulation to increase production of non-native products of interest in transgenic microorganisms. US Patent 2011, US20,110,244,512.
30. Zhang H., Zhang L., Chen H., Chen Y.Q., Ratledge C., Song Y., Chen W. Regulatory properties of malic enzyme in the oleaginous yeast, Yarrowia lipolytica, and its non-involvement in lipid accumulation. Biotechnol Lett 2013, 35:2091-2098.
31. Wang G.Y., Zhang Y., Chi Z., Liu G.L., Wang Z.P., Chi Z.M. Role of pyruvate carboxylase in accumulation of intracellular lipid of the oleaginous yeast Yarrowia lipolytica ACA-DC 50109. Appl Microbiol Biotechnol 2015, 99:1637-1645.
32. Hedbacker K., Carlson M. SNF1/AMPK pathways in yeast. Front Biosci 2008, 13:2408-2420.
33. Seip J., Jackson R., He H., Zhu Q., Hong S.P. Snf1 is a regulator of lipid accumulation in Yarrowia lipolytica. Appl Environ Microbiol 2013, 79:7360-7370.
34. Wang Z.P., Xu H.M., Wang G.Y., Chi Z., Chi Z.M. Disruption of the MIG1 gene enhances lipid biosynthesis in the oleaginous yeast Yarrowia lipolytica ACA-DC 50109. Biochim Biophys Acta 2013, 1831:675-682.
35. Zhang H., Damude H.G., Yadav N.S. Three diacylglycerol acyltransferases contribute to oil biosynthesis and normal growth in Yarrowia lipolytica. Yeast 2012, 29:25-38.
36. Beopoulos A., Haddouche R., Kabran P., Dulermo T., Chardot T., Nicaud J.M. Identification and characterization of DGA2, an acyltransferase of the DGAT1 acyl-CoA:diacylglycerol acyltransferase family in the oleaginous yeast Yarrowia lipolytica. New insights into the storage lipid metabolism of oleaginous yeasts. Appl Microbiol Biotechnol 2012, 93:1523-1537.
37. Xue Z., Sharpe P.L., Hong S.P., Yadav N.S., Xie D., Short D.R., Damude H.G., Rupert R.A., Seip J.E., Wang J., Pollak D.W., Bostick M.W., Bosak M.D., Macool D.J., Hollerbach D.H., Zhang H., Arcilla D.M., Bledsoe S.A., Croker K., McCord E.F., Tyreus B.D., Jackson E.N., Zhu Q. Production of omega-3 eicosapentaenoic acid by metabolic engineering of Yarrowia lipolytica. Nat Biotechnol 2013, 31:734-740.
38. Tai M., Stephanopoulos G. Engineering the push and pull of lipid biosynthesis in oleaginous yeast Yarrowia lipolytica for biofuel production. Metab Eng 2013, 15:1-9.
39. Blazeck J., Hill A., Liu L., Knight R., Miller J., Pan A., Otoupal P., Alper H. Harnessing Yarrowia lipolytica lipogenesis to create a platform for lipid and biofuel production. Nat Commun 2014, 5:3131.
40. Wei H., Wang W., Alahuhta M., Vander Wall T., Baker J.O., Taylor L.E., Decker S.R., Himmel M.E., Zhang M. Engineering towards a complete heterologous cellulase secretome in Yarrowia lipolytica reveals its potential for consolidated bioprocessing. Biotechnol Biofuels 2014, 7:148.
41. Wang W., Wei H., Alahuhta M., Chen X., Hyman D., Johnson D.K., Zhang M., Himmel M.E. Heterologous expression of xylanase enzymes in lipogenic yeast Yarrowia lipolytica. PLoS One 2014, 9:e111443.
42. Mlícková K1, Roux E., Athenstaedt K., d'Andrea S., Daum G., Chardot T., Nicaud J.M. Lipid accumulation, lipid body formation, and acyl coenzyme A oxidases of the yeast Yarrowia lipolytica. Appl Environ Microbiol 2004, 70:3918-3924.
43. Beopoulos A., Mrozova Z., Thevenieau F., Dall M.T., Hapala I., Papanikolaou S., Chardot T., Nicaud J.M. Control of lipid accumulation in the yeast Yarrowia lipolytica. Appl Environ Microbiol 2008, 74:7779-7789.
44. Thierry D., Nicaud J.M. Involvement of the G3P shuttle and β-oxidation pathway in the control of TAG synthesis and lipid accumulation in Yarrowia lipolytica. Metab Eng 2011, 13:482-491.
45. Dulermo R., Gamboa-Meléndez H., Dulermo T., Thevenieau F., Nicaud J.M. The fatty acid transport protein Fat1p is involved in the export of fatty acids from lipid bodies in Yarrowia lipolytica. FEMS Yeast Res 2014, 14:883-896.
46. Dulermo T., Tréton B., Beopoulos A., Kabran Gnankon A.P., Haddouche R., Nicaud J.M. Characterization of the two intracellular lipases of Y. lipolytica encoded by TGL3 and TGL4 genes: new insights into the role of intracellular lipases and lipid body organization. Biochim Biophys Acta 2013, 183:1486-1495.
47. Zhu Q., Xue Z., Yadav N., Damude H., Pollak D., Rupert R., Seip J., Hollerbach D., Macool D., Zhang H. Metabolic engineering of an oleaginous yeast for the production of omega-3 fatty acids. Single Cell Oils 2010, 51-73. AOCS Press, Urbana, IL. edn 2. Z. Cohen, C. Ratledge (Eds.).
48. Chuang L.T., Chen D.C., Nicaud J.M., Madzak C., Chen Y.H., Huang Y.S. Co-expression of heterologous desaturase genes in Yarrowia lipolytica. Nat Biotechnol 2010, 27:277-282.
49. Zhu Q, Walters-Pollak DM: Delta 12 and Delta 6 desaturases able to catalyze the conversion of oleic acid to GLA have been introduced into the genome of Yarrowia, using zeta-directed integration. US Patent 2008, US7,465,564.
50. Macool, DJ, Xue Z, Zhu Q: A Mortierella alpina C16/18 fatty acid elongase. US Patent 2008, US7,470,532.
51. Hong S-Y, Seip J, Sharpe PL, Xue Z, Yadav NS, Zhang H, Zhu Q: Recombinant microbial host cells for high eicosapentaenoic acid production. US Patent 2014, US8,703,473.
52. Yadav NS, Zhu Q, Zhang H: Nucleotide sequences coding oxidoreductase for use in transfer, expression and production of omega-3 and omega-6 fatty acids in Yarrowia. US Patent 2009, US7,504,259.
53. Xue Z., He H., Hollerbach D., Macool D.J., Yadav N.S., Zhang H., Szostek B., Zhu Q. Identification and characterization of new δ-17 fatty acid desaturases. Appl Microbiol Biotechnol 2013, 97:1973-1985.
54. Hong SP, Sharpe PL, Xue Z, Yadav NS, Zhu Q: Peroxisome biogenesis factor protein (pex) disruptions for altering polyunsaturated fatty acids and total lipid content in oleaginous eukaryotic organisms. US Patent Application 2009, US20,090,117,253.
55. Damude HG, Macool DJ, Picataggio SK, Ragghianti JJ, Seip JE, Xue Z, Yadav NS, Zhang H, Zhu Q: Docosahexaenoic acid producing strains of Yarrowia lipolytica. US Patent 2009, US7,550,286.
56. Damude HG, Kinney AJ, Ripp KG, Zhu Q: Multizymes and their use in making polyunsaturated fatty acids. US Patent Application 2008, US20,080,254,191.
57. Shahidi F., Wanasundara P.K.J., Wanasundara U.N. Seal blubber oil: a novel source of ω3 fatty acids. J Food Lipids 1996, 3:293-306.
58. Kaur G., Cameron-Smith D., Garg M., Sinclair A.J. Docosapentaenoic acid (22:5n-3): a review of its biological effects. Prog Lipid Res 2011, 50:28-34.
59. Ye V.M., Bhatia S.K. Pathway engineering strategies for production of beneficial carotenoids in microbial hosts. Biotechnol Lett 2012, 34:1405-1414.
60. Lin Y., Jain R., Yan Y. Microbial production of antioxidant food ingredients via metabolic engineering. Curr Opin Biotechnol 2014, 26:71-78.
61. Sharpe PL, Ye RW, Zhu Q: Carotenoid production in a recombinant oleaginous yeast. US Patent 2014, US8,846,374.
62. Bailey R, Madden KT, Trueheart J: Production of carotenoids in oleaginous yeast and fungi. US patent 2012, US8,288,149.
63. Ye R.W., Sharpe P.L., Zhu Q. Bioengineering of oleaginous yeast Yarrowia lipolytica for lycopene production. Methods Mol Biol 2012, 898:153-159.
64. Matthäus F., Ketelhot M., Gatter M., Barth G. Production of lycopene in the non-carotenoid-producing yeast Yarrowia lipolytica. Appl Environ Microbiol 2014, 80:1660-1669.
65. Donald K.A., Hampton R.Y., Fritz I.B. Effects of overproduction of the catalytic domain of 3-hydroxy-3-methylglutaryl coenzyme A reductase on squalene synthesis in Saccharomyces cerevisiae. Appl Environ Microbiol 1997, 63:3341-3344.
66. Grenfell-Lee D., Zeller S., Cardoso R., Pucaj K. The safety of β-carotene from Yarrowia lipolytica. Food Chem Toxicol 2014, 65:1-11.