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.
Similar content being viewed by others
References
Barth G (2013) Yarrowia lipolytica—biotechnological applications. Microbiology monographs, vol 25. Springer, Heidelberg. https://doi.org/10.1007/978-3-642-38583-4
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):251–262
Blazeck J, Alper HS (2013) Promoter engineering: recent advances in controlling transcription at the most fundamental level. Biotechnol J 8(1):46–58
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):7905–7914
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
Blazeck J, Hill A, Jamoussi M, Pan A, Miller J, Alper HS (2015) Metabolic engineering of Yarrowia lipolytica for itaconic acid production. Metab Eng 32:66–73
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
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
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
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
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
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
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):824–832
Darvishi F (2012) Expression of native and mutant extracellular lipases from Yarrowia lipolytica in Saccharomyces cerevisiae. Microb Biotechnol 5(5):634–641
Darvishi Harzevili F (2014) Biotechnological applications of the yeast Yarrowia lipolytica. Springer, Heidelberg
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
Darvishi F, Fathi Z, Ariana M, Moradi H (2017) Yarrowia lipolytica as a workhorse for biofuel production. Biochem Eng J 127:87–96
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
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–e01016
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
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):e0146773
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):35–44
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):1255–1262
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):1085–1093
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 41:192–201
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
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
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
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):59–72
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
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):238–348
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 18:97–113
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
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
Labuschagne M, Albertyn J (2007) Cloning of an epoxide hydrolase encoding gene from Rhodotorula mucilaginosa and functional expression in Yarrowia lipolytica. Yeast 24:69–78
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
Li M, Borodina I (2015) Application of synthetic biology for production of chemicals in yeast Saccharomyces cerevisiae. FEMS Yeast Res 15(1):1–12
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
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–e00614
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):1124–1127
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
Madzak C, Beckerich J-M (2013) Heterologous protein expression and secretion in Yarrowia lipolytica. Springer, Berlin, pp 1–76
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):207–216
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):337–340
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):1660–1669
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):346–351
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 2:371–379
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):3098–3107
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
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
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):356–359
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):402–409
Shabbir Hussain M, Gambill L, Smith S, Blenner MA (2015) Engineering promoter architecture in oleaginous yeast Yarrowia lipolytica. ACS Synth Biol 5(3):213–223
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 63–112
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
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
Tai M, Stephanopoulos G (2013) Engineering the push and pull of lipid biosynthesis in oleaginous yeast Yarrowia lipolytica for biofuel production. Metab Eng 15:1–9
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
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):163–171
Wagner JM, Alper HS (2016) Synthetic biology and molecular genetics in non-conventional yeasts: current tools and future advances. Fungal Genet Biol 89:126–136
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
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):1
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
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):10848–10853
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):734–740
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
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):116–123
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
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
Acknowledgments
The authors would like to thank Dr. Ali Abghari, Dr. Carina Holkenbrink, and Hamideh Moradi for their valuable comments on this review.
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
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.
Rights and permissions
About this article
Cite this article
Darvishi, F., Ariana, M., Marella, E.R. et al. Advances in synthetic biology of oleaginous yeast Yarrowia lipolytica for producing non-native chemicals. Appl Microbiol Biotechnol 102, 5925–5938 (2018). https://doi.org/10.1007/s00253-018-9099-x
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00253-018-9099-x