Advertisement

Applied Microbiology and Biotechnology

, Volume 102, Issue 14, pp 5925–5938 | Cite as

Advances in synthetic biology of oleaginous yeast Yarrowia lipolytica for producing non-native chemicals

  • Farshad Darvishi
  • Mehdi Ariana
  • Eko Roy Marella
  • Irina Borodina
Mini-Review

Abstract

Oleaginous yeast Yarrowia lipolytica is an important industrial host for the production of enzymes, oils, fragrances, surfactants, cosmetics, and pharmaceuticals. More recently, improved synthetic biology tools have allowed more extensive engineering of this yeast species, which lead to the production of non-native metabolites. In this review, we summarize the recent advances of genome editing tools for Y. lipolytica, including the application of CRISPR/Cas9 system and discuss case studies, where Y. lipolytica was engineered to produce various non-native chemicals: short-chain fatty alcohols and alkanes as biofuels, polyunsaturated fatty acids for nutritional and pharmaceutical applications, polyhydroxyalkanoates and dicarboxylic acids as precursors for biodegradable plastics, carotenoid-type pigments for food and feed, and campesterol as a precursor for steroid drugs.

Keywords

Yarrowia lipolytica Synthetic biology CRISPR/Cas9 Bio-based chemicals 

Notes

Acknowledgments

The authors would like to thank Dr. Ali Abghari, Dr. Carina Holkenbrink, and Hamideh Moradi for their valuable comments on this review.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical statement

This article does not contain any studies with human participants or animals performed by any of the authors.

References

  1. Barth G (2013) Yarrowia lipolytica—biotechnological applications. Microbiology monographs, vol 25. Springer, Heidelberg.  https://doi.org/10.1007/978-3-642-38583-4 CrossRefGoogle Scholar
  2. Béopoulos A, Verbeke J, Bordes F, Guicherd M, Bressy M, Marty A, Nicaud J-M (2014) Metabolic engineering for ricinoleic acid production in the oleaginous yeast Yarrowia lipolytica. Appl Microbiol Biotechnol 98(1):251–262CrossRefPubMedGoogle Scholar
  3. Blazeck J, Alper HS (2013) Promoter engineering: recent advances in controlling transcription at the most fundamental level. Biotechnol J 8(1):46–58CrossRefPubMedGoogle Scholar
  4. Blazeck J, Liu L, Redden H, Alper H (2011) Tuning gene expression in Yarrowia lipolytica by a hybrid promoter approach. Appl Environ Microbiol 77(22):7905–7914CrossRefPubMedPubMedCentralGoogle Scholar
  5. Blazeck J, Liu L, Knight R, Alper HS (2013) Heterologous production of pentane in the oleaginous yeast Yarrowia lipolytica. J Biotechnol 165:184–194.  https://doi.org/10.1016/j.jbiotec.2013.04.003 CrossRefPubMedGoogle Scholar
  6. Blazeck J, Hill A, Jamoussi M, Pan A, Miller J, Alper HS (2015) Metabolic engineering of Yarrowia lipolytica for itaconic acid production. Metab Eng 32:66–73CrossRefPubMedGoogle Scholar
  7. Borodina I, Nielsen J (2014) Advances in metabolic engineering of yeast Saccharomyces cerevisiae for production of chemicals. Biotechnol J 9(5):609–620.  https://doi.org/10.1002/biot.201300445 CrossRefPubMedGoogle Scholar
  8. Braga A, Belo I (2016) Biotechnological production of γ-decalactone, a peach like an aroma, by Yarrowia lipolytica. World J Microbiol Biotechnol 32(10):169.  https://doi.org/10.1007/s11274-016-2116-2 CrossRefPubMedGoogle Scholar
  9. Braga A, Crutz-Le Coq AM, Dulermo R, Nicaud JM, Belo I (2015) Effect of POX genotype and Lip2p overexpression on lactone production and reconsumption by Yarrowia lipolytica using castor oil as substrate. Process Biochem 50:1357–1362.  https://doi.org/10.1016/j.procbio.2015.05.019 CrossRefGoogle Scholar
  10. Bredeweg EL, Pomraning KR, Dai Z, Nielsen J, Kerkhoven EJ, Baker SE (2017) A molecular genetic toolbox for Yarrowia lipolytica. Biotechnol Biofuels 10(1):2.  https://doi.org/10.1186/s13068-016-0687-7 CrossRefPubMedPubMedCentralGoogle Scholar
  11. Cao X, Lv Y-B, Chen J, Imanaka T, Wei L-J, Hua Q (2016) Metabolic engineering of oleaginous yeast Yarrowia lipolytica for limonene overproduction. Biotechnol Biofuels 9:214.  https://doi.org/10.1186/s13068-016-0626-7 CrossRefPubMedPubMedCentralGoogle Scholar
  12. Celińska E, Ledesma-Amaro R, Larroude M, Rossignol T, Pauthenier G, Nicaud J-M (2017) Golden gate assembly system dedicated to complex pathway manipulation in Yarrowia lipolytica. Microb Biotechnol 10(2):450–455.  https://doi.org/10.1111/1751-7915.12605 CrossRefPubMedPubMedCentralGoogle Scholar
  13. Curran KA, Morse NJ, Markham KA, Wagman AM, Gupta A, Alper HS (2015) Short synthetic terminators for improved heterologous gene expression in yeast. ACS Synth Biol 4(7):824–832CrossRefPubMedGoogle Scholar
  14. Darvishi F (2012) Expression of native and mutant extracellular lipases from Yarrowia lipolytica in Saccharomyces cerevisiae. Microb Biotechnol 5(5):634–641CrossRefPubMedPubMedCentralGoogle Scholar
  15. Darvishi Harzevili F (2014) Biotechnological applications of the yeast Yarrowia lipolytica. Springer, HeidelbergCrossRefGoogle Scholar
  16. Darvishi F, Destain J, Nahvi I, Thonart P, Zarkesh-Esfahani H (2012) Effect of additives on freeze-drying and storage of Yarrowia lipolytica lipase. Appl Biochem Biotechnol 168(5):1101–1107.  https://doi.org/10.1007/s12010-012-9844-z CrossRefPubMedGoogle Scholar
  17. Darvishi F, Fathi Z, Ariana M, Moradi H (2017) Yarrowia lipolytica as a workhorse for biofuel production. Biochem Eng J 127:87–96CrossRefGoogle Scholar
  18. De Pourcq K, Tiels P, Van Hecke A, Geysens S, Vervecken W, Callewaert N (2012) Engineering the yeast Yarrowia lipolytica for the production of therapeutic proteins homogeneously glycosylated with Man8GlcNAc2 and Man5GlcNAc2. Microb Cell Factories 11:53.  https://doi.org/10.1186/1475-2859-11-53 CrossRefGoogle Scholar
  19. Devillers H, Brunel F, Połomska X, Sarilar V, Lazar Z, Robak M, Neuvéglise C (2016) Draft genome sequence of Yarrowia lipolytica strain A-101 isolated from polluted soil in Poland. Genome Announc 4(5):e01094–e01016CrossRefPubMedPubMedCentralGoogle Scholar
  20. DiCarlo JE, Norville JE, Mali P, Rios X, Aach J, Church GM (2013) Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res 41(7):4336–4343.  https://doi.org/10.1093/nar/gkt135 CrossRefPubMedPubMedCentralGoogle Scholar
  21. Du H-X, Xiao W-H, Wang Y, Zhou X, Zhang Y, Liu D, Yuan Y-J (2016) Engineering Yarrowia lipolytica for campesterol overproduction. PLoS One 11(1):e0146773CrossRefPubMedPubMedCentralGoogle Scholar
  22. Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuvéglise C, Talla E (2004) Genome evolution in yeasts. Nature 430(6995):35–44CrossRefPubMedGoogle Scholar
  23. Gao C, Qi Q, Madzak C, Lin CSK (2015) Exploring medium-chain-length polyhydroxyalkanoates production in the engineered yeast Yarrowia lipolytica. J Ind Microbiol Biotechnol 42(9):1255–1262CrossRefPubMedGoogle Scholar
  24. Gao S, Tong Y, Wen Z, Zhu L, Ge M, Chen D, Jiang Y, Yang S (2016) Multiplex gene editing of the Yarrowia lipolytica. J Ind Microbiol Biotechnol 43(8):1085–1093CrossRefPubMedGoogle Scholar
  25. Gao S, Tong Y, Zhu L, Ge M, Zhang Y, Chen D, Jiang Y, Yang S (2017) Iterative integration of multiple-copy pathway genes in Yarrowia lipolytica for heterologous β-carotene production. Metab Eng 41:192–201CrossRefPubMedGoogle Scholar
  26. Gatter M, Förster A, Bär K, Winter M, Otto C, Petzsch P, Ježková M, Bahr K, Pfeiffer M, Matthäus F, Barth G (2014) A newly identified fatty alcohol oxidase gene is mainly responsible for the oxidation of long-chain ω-hydroxy fatty acids in Yarrowia lipolytica. FEMS Yeast Res 14:858–872.  https://doi.org/10.1111/1567-1364.12176 CrossRefPubMedGoogle Scholar
  27. Groenewald M, Boekhout T, Neuvéglise C, Gaillardin C, van Dijck PW, Wyss M (2014) Yarrowia lipolytica: safety assessment of an oleaginous yeast with a great industrial potential. Crit Rev Microbiol 40(3):187–206.  https://doi.org/10.3109/1040841X.2013.770386 CrossRefPubMedGoogle Scholar
  28. Holkenbrink C, Dam MI, Kildegaard KR, Beder J, Dahlin J, Doménech D, Borodina I (2018) EasyCloneYALI: CRISPR/Cas9-based synthetic toolbox for engineering of the yeast Yarrowia lipolytica. Biotechnol J.  https://doi.org/10.1002/biot.201700543
  29. Hong SP, Seip J, Walters-Pollak D, Rupert R, Jackson R, Xue Z, Zhu Q (2012) Engineering Yarrowia lipolytica to express secretory invertase with the strong FBA1IN promoter. Yeast 29(2):59–72CrossRefPubMedGoogle Scholar
  30. Imatoukene N, Verbeke J, Beopoulos A, Taghki AI, Thomasset B, Sarde C-O, Nonus M, Nicaud J-M (2017) A metabolic engineering strategy for producing conjugated linoleic acids using the oleaginous yeast Yarrowia lipolytica. Appl Microbiol Biotechnol:1–12.  https://doi.org/10.1007/s00253-017-8240-6
  31. Jensen NB, Strucko T, Kildegaard KR, David F, Maury J, Mortensen UH, Forster J, Nielsen J, Borodina I (2014) EasyClone: method for iterative chromosomal integration of multiple genes in Saccharomyces cerevisiae. FEMS Yeast Res 14(2):238–348CrossRefPubMedGoogle Scholar
  32. Juretzek T, Le Dall M, Mauersberger S, Gaillardin C, Barth G, Nicaud JM (2001) Vectors for gene expression and amplification in the yeast Yarrowia lipolytica. Yeast 18:97–113CrossRefPubMedGoogle Scholar
  33. Kildegaard KR, Adiego-Pérez B, Belda DD, Khangura JK, Holkenbrink C, Borodina I (2017) Engineering of Yarrowia lipolytica for production of astaxanthin. Synth Syst Biotechnol 2(4):287–294.  https://doi.org/10.1016/j.synbio.2017.10.002 CrossRefPubMedPubMedCentralGoogle Scholar
  34. Kretzschmar A, Otto C, Holz M, Werner S, Hübner L, Barth G (2013) Increased homologous integration frequency in Yarrowia lipolytica strains defective in non-homologous end-joining. Curr Genet 59:63–72.  https://doi.org/10.1007/s00294-013-0389-7 CrossRefPubMedGoogle Scholar
  35. Labuschagne M, Albertyn J (2007) Cloning of an epoxide hydrolase encoding gene from Rhodotorula mucilaginosa and functional expression in Yarrowia lipolytica. Yeast 24:69–78CrossRefPubMedGoogle Scholar
  36. Larroude M, Celinska E, Back A, Thomas S, Nicaud J-M, Ledesma-Amaro R (2018) A synthetic biology approach to transform Yarrowia lipolytica into a competitive biotechnological producer of β-carotene. Biotechnol Bioeng 115(2):464–472.  https://doi.org/10.1002/bit.26473 CrossRefPubMedGoogle Scholar
  37. Li M, Borodina I (2015) Application of synthetic biology for production of chemicals in yeast Saccharomyces cerevisiae. FEMS Yeast Res 15(1):1–12CrossRefPubMedGoogle Scholar
  38. Li Z-J, Qiao K, Liu N, Stephanopoulos G (2017) Engineering Yarrowia lipolytica for poly-3-hydroxybutyrate production. J Ind Microbiol Biotechnol 44(4):605–612.  https://doi.org/10.1007/s10295-016-1864-1 CrossRefPubMedGoogle Scholar
  39. Liu L, Alper HS (2014) Draft genome sequence of the oleaginous yeast Yarrowia lipolytica PO1f, a commonly used metabolic engineering host. Genome Announc 2(4):e00652–e00614PubMedPubMedCentralGoogle Scholar
  40. Liu L, Otoupal P, Pan A, Alper HS (2014) Increasing expression level and copy number of a Yarrowia lipolytica plasmid through regulated centromere function. FEMS Yeast Res 14(7):1124–1127PubMedGoogle Scholar
  41. Madzak C (2015) Yarrowia lipolytica: recent achievements in heterologous protein expression and pathway engineering. Appl Microbiol Biotechnol 99(11):4559–4577.  https://doi.org/10.1007/s00253-015-6624-z CrossRefPubMedGoogle Scholar
  42. Madzak C, Beckerich J-M (2013) Heterologous protein expression and secretion in Yarrowia lipolytica. Springer, Berlin, pp 1–76Google Scholar
  43. Madzak C, Treton B, Blanchin-Roland S (2000) Strong hybrid promoters and integrative expression/secretion vectors for quasi-constitutive expression of heterologous proteins in the yeast Yarrowia lipolytica. J Mol Microbiol Biotechnol 2(2):207–216PubMedGoogle Scholar
  44. Mafakher L, Mirbagheri M, Darvishi F, Nahvi I, Zarkesh-Esfahani H, Emtiazi G (2010) Isolation of lipase and citric acid producing yeasts from agro-industrial wastewater. New Biotechnol 27(4):337–340CrossRefGoogle Scholar
  45. Matthäus F, Ketelhot M, Gatter M, Barth G (2014) Production of lycopene in the non-carotenoid-producing yeast Yarrowia lipolytica. Appl Environ Microbiol 80(5):1660–1669CrossRefPubMedPubMedCentralGoogle Scholar
  46. Mirbagheri M, Nahvi I, Emtiazi G, Mafakher L, Darvishi F (2012) Taxonomic characterization and potential biotechnological applications of Yarrowia lipolytica isolated from meat and meat products. Jundishapur J Microbiol 5(1):346–351Google Scholar
  47. Nicaud JM, Madzak C, van den Broek P, Gysler C, Duboc P, Niederberger P, Gaillardin C (2002) Protein expression and secretion in the yeast Yarrowia lipolytica. FEMS Yeast Res 2:371–379PubMedGoogle Scholar
  48. Richard M, Quijano RR, Bezzate S, Bordon-Pallier F, Gaillardin C (2001) Tagging morphogenetic genes by insertional mutagenesis in the yeast Yarrowia lipolytica. J Bacteriol 183(10):3098–3107CrossRefPubMedPubMedCentralGoogle Scholar
  49. Rutter CD, Rao CV (2016) Production of 1-decanol by metabolically engineered Yarrowia lipolytica. Metab Eng 38:139–147.  https://doi.org/10.1016/j.ymben.2016.07.011 CrossRefPubMedGoogle Scholar
  50. Santiago-Gómez MP, Thanh HT, De Coninck J, Cachon R, Kermasha S, Belin J-M, Gervais P, Husson F (2009) Modeling hexanal production in oxido-reducing conditions by the yeast Yarrowia lipolytica. Process Biochem 44:1013–1018.  https://doi.org/10.1016/j.procbio.2009.04.028 CrossRefGoogle Scholar
  51. Schwartz CM, Hussain MS, Blenner M, Wheeldon I (2016) Synthetic RNA polymerase III promoters facilitate high-efficiency CRISPR–Cas9-mediated genome editing in Yarrowia lipolytica. ACS Synth Biol 5(4):356–359CrossRefPubMedGoogle Scholar
  52. Schwartz CM, Hussain MS, Frogue K, Blenner M, Wheeldon I (2017) Standardized markerless gene integration for pathway engineering in Yarrowia lipolytica. ACS Synth Biol 6(3):402–409CrossRefPubMedGoogle Scholar
  53. Shabbir Hussain M, Gambill L, Smith S, Blenner MA (2015) Engineering promoter architecture in oleaginous yeast Yarrowia lipolytica. ACS Synth Biol 5(3):213–223CrossRefPubMedGoogle Scholar
  54. Sibirny A, Madzak C, Fickers P (2014) Genetic engineering of nonconventional yeasts for the production of valuable compounds. In: Darvishi Harzevili F, Chen H (eds) Microbial biotechnology: progress and trends. CRC Press, Florida, pp 63–112CrossRefGoogle Scholar
  55. Stovicek V, Holkenbrink C, Borodina I (2017) CRISPR/Cas system for yeast genome engineering: advances and applications. FEMS Yeast Res 17(5):1–16.  https://doi.org/10.1093/femsyr/fox030 CrossRefGoogle Scholar
  56. Sun M-L, Madzak C, Liu H-H, Song P, Ren L-J, Huang H, Ji X-J (2017) Engineering Yarrowia lipolytica for efficient γ-linolenic acid production. Biochem Eng J 117:172–180.  https://doi.org/10.1016/j.bej.2016.10.014 CrossRefGoogle Scholar
  57. Tai M, Stephanopoulos G (2013) Engineering the push and pull of lipid biosynthesis in oleaginous yeast Yarrowia lipolytica for biofuel production. Metab Eng 15:1–9CrossRefPubMedGoogle Scholar
  58. Trassaert M, Vandermies M, Carly F, Denies O, Thomas S, Fickers P, Nicaud J-M (2017) New inducible promoter for gene expression and synthetic biology in Yarrowia lipolytica. Microb Cell Factories 16(1):141.  https://doi.org/10.1186/s12934-017-0755-0 CrossRefGoogle Scholar
  59. Vorachek-Warren MK, McCusker JH (2004) DsdA (D-serine deaminase): a new heterologous MX cassette for gene disruption and selection in Saccharomyces cerevisiae. Yeast 21(2):163–171CrossRefPubMedGoogle Scholar
  60. Wagner JM, Alper HS (2016) Synthetic biology and molecular genetics in non-conventional yeasts: current tools and future advances. Fungal Genet Biol 89:126–136CrossRefPubMedGoogle Scholar
  61. Wagner JM, Williams EV, Alper HS (2018) Developing a piggyBac transposon system and compatible selection markers for insertional mutagenesis and genome engineering in Yarrowia lipolytica. Biotechnol J 13.  https://doi.org/10.1002/biot.201800022
  62. Wang G, Xiong X, Ghogare R, Wang P, Meng Y, Chen S (2016) Exploring fatty alcohol-producing capability of Yarrowia lipolytica. Biotechnol Biofuels 9(1):1CrossRefGoogle Scholar
  63. Wong L, Engel J, Jin E, Holdridge B, Xu P (2017) YaliBricks, a versatile genetic toolkit for streamlined and rapid pathway engineering in Yarrowia lipolytica. Metab Eng Commun 1(5):68–77.  https://doi.org/10.1016/j.meteno.2017.09.001 CrossRefGoogle Scholar
  64. Xu P, Qiao K, Ahn WS, Stephanopoulos G (2016) Engineering Yarrowia lipolytica as a platform for synthesis of drop-in transportation fuels and oleochemicals. PNAS 113(39):10848–10853CrossRefPubMedPubMedCentralGoogle Scholar
  65. Xue Z, Sharpe PL, Hong S-P, Yadav NS, Xie D, Short DR, Damude HG, Rupert RA, Seip JE, Wang J (2013) Production of omega-3 eicosapentaenoic acid by metabolic engineering of Yarrowia lipolytica. Nat Biotechnol 31(8):734–740CrossRefPubMedGoogle Scholar
  66. Yang X, Nambou K, Wei L, Hua Q (2016) Heterologous production of α-farnesene in metabolically engineered strains of Yarrowia lipolytica. Bioresour Technol 216:1040–1048.  https://doi.org/10.1016/j.biortech.2016.06.028 CrossRefPubMedGoogle Scholar
  67. Yue L, Chi Z, Wang L, Liu J, Madzak C, Li J, Wang X (2008) Construction of a new plasmid for surface display on cells of Yarrowia lipolytica. J Microbiol Methods 72(2):116–123CrossRefPubMedGoogle Scholar
  68. Zhang B, Chen H, Li M, Gu Z, Song Y, Ratledge C, Chen YQ, Zhang H, Chen W (2013) Genetic engineering of Yarrowia lipolytica for enhanced production of trans-10, cis-12 conjugated linoleic acid. Microb Cell Factories 12:70.  https://doi.org/10.1186/1475-2859-12-70 CrossRefGoogle Scholar
  69. Zhang Y, Wang Y, Yao M, Liu H, Zhou X, Xiao W, Yuan Y (2017) Improved campesterol production in engineered Yarrowia lipolytica strains. Biotechnol Lett 39(7):1033–1039.  https://doi.org/10.1007/s10529-017-2331-4 CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Microbial Biotechnology and Bioprocess Engineering (MBBE) Group, Department of Microbiology, Faculty of ScienceUniversity of MaraghehMaraghehIran
  2. 2.The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKgs. LyngbyDenmark

Personalised recommendations