Rewiring and application of Yarrowia lipolytica chassis cell

doi:10.12211/2096-8280.2022-060

Abstract

Abstract:

Engineering microbial chassis cells to efficiently synthesize high value-added products has received increasing attention. This biomanufacturing mode based on excellent performance microbial chassis cells has become the research frontier in the field of synthetic biology. Yarrowia lipolytica, an unconventional oleaginous yeast, is emerging as one of the popular microbial chassis cells in the field of advanced and green biomanufacturing. This is due to its unique physiological and biochemical characteristics, such as the inherent mevalonate pathway, adequate acetyl-CoA supply, broad substrate spectrum, and high tolerance to multiple extreme environments. These characteristics make Y. lipolytica a superior chassis candidate for the advanced and green biomanufacturing. In recent years, the researches and applications on the rewiring of Y. lipolytica chassis cell for biomanufacturing have gradually increased, which promoted the further upgrading of Y. lipolytica chassis cells. This review firstly describes the development of the genetic elements for rewiring Y. lipolytica chassis cell, including promoters, terminators, and selecting markers. Then, this review summarizes the expression modes and integration methods for endogenous and heterogenous genes, including gene expression based on episomal plasmid, genomic integration based on homologous recombination (HR) and non-homologous end joining (NHEJ). This review further summarizes the research progress of various synthetic biology tools developed for Y. lipolytica, including various gene overexpression methods, biosensor-based dynamic regulation strategies, CRISPR/Cas-based gene expression regulation methods, and the emerging strategies such as genome-scale metabolic modelling, genome-wide mutational screening, etc. This review also introduces the achievements of rewiring Y. lipolytica chassis cell for the synthesis of different high value-added products, including proteins, organic acids, terpenes, functional sugars and sugar alcohols, fatty acids and their derivatives, flavonoids and polyketides, and amino acid derivatives. In addition, the prospects of Y. lipolytica chassis cell-based biomanufacturing are discussed in light of the current progresses, challenges, and trends in this field. Finally, guidelines for building next-generation Y. lipolytica chassis cell for production of the aforementioned products are also emphasized. {L-End}

Key words: Yarrowia lipolytica, chassis cell, oleaginous yeast, cell factory, synthetic biology, biomanufacturing

摘要：

基于性能卓越的微生物底盘细胞，开发高效的绿色生物制造技术，已经成为合成生物学领域的研究前沿。解脂耶氏酵母作为一种非常规产油酵母，由于其独特的生理生化特征，正迅速成为面向绿色生物制造的合成生物学研究领域的热门底盘细胞之一。近年来，围绕解脂耶氏酵母底盘细胞工程改造的研究与应用日益增多，促进了解脂耶氏酵母底盘细胞的进一步升级。本文总结了针对解脂耶氏酵母底盘细胞的工程改造策略及其在生物制造中的应用，从遗传改造技术及工具开发，基因的表达与调控策略等方面介绍各类合成生物学工具及技术在解脂耶氏酵母中的研究进展，并从底盘细胞合成高附加值产品的研究进展方面介绍了其工程改造效果。最后，对解脂耶氏酵母底盘细胞的应用前景和未来发展方向进行了展望。

关键词: 解脂耶氏酵母, 底盘细胞, 产油酵母, 细胞工厂, 合成生物学, 生物制造

CLC Number:

Q819

Meili SUN, Kaifeng WANG, Ran LU, Xiaojun JI. Rewiring and application of Yarrowia lipolytica chassis cell[J]. Synthetic Biology Journal, 2023, 4(4): 779-807.

孙美莉, 王凯峰, 陆然, 纪晓俊. 解脂耶氏酵母底盘细胞的工程改造及应用[J]. 合成生物学, 2023, 4(4): 779-807.

Figures/Tables 6

References 224

1	XU X H, LIU Y F, DU G C, et al. Microbial chassis development for natural product biosynthesis[J]. Trends in Biotechnology, 2020, 38(7): 779-796.
2	LIU J Y, WU X, YAO M D, et al. Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms[J]. Current Opinion in Biotechnology, 2020, 66: 105-112.
3	LIU H H, JI X J, HUANG H. Biotechnological applications of Yarrowia lipolytica: past, present and future[J]. Biotechnology Advances, 2015, 33(8): 1522-1546.
4	PARK Y K, LEDESMA AMARO R. What makes Yarrowia lipolytica well suited for industry?[J]. Trends in Biotechnology, 2023, 41(2): 242-254.
5	MADZAK C. Yarrowia lipolytica strains and their biotechnological applications: how natural biodiversity and metabolic engineering could contribute to cell factories improvement[J]. Journal of Fungi, 2021, 7(7): 548.
6	ABDEL-MAWGOUD A M, MARKHAM K A, PALMER C M, et al. Metabolic engineering in the host Yarrowia lipolytica [J]. Metabolic Engineering, 2018, 50: 192-208.
7	MARKHAM K A, ALPER H S. Synthetic biology expands the industrial potential of Yarrowia lipolytica [J]. Trends in Biotechnology, 2018, 36(10): 1085-1095.
8	WANG K F, SHI T Q, LIN L, et al. Advances in synthetic biology tools paving the way for the biomanufacturing of unusual fatty acids using the Yarrowia lipolytica chassis[J]. Biotechnology Advances, 2022, 59: 107984.
9	WANG J P, LEDESMA-AMARO R, WEI Y J, et al. Metabolic engineering for increased lipid accumulation in Yarrowia lipolytica—a review[J]. Bioresource Technology, 2020, 313: 123707.
10	MA Y R, WANG K F, WANG W J, et al. Advances in the metabolic engineering of Yarrowia lipolytica for the production of terpenoids[J]. Bioresource Technology, 2019, 281: 449-456.
11	MUHAMMAD A, FENG X D, RASOOL A, et al. Production of plant natural products through engineered Yarrowia lipolytica [J]. Biotechnology Advances, 2020, 43: 107555.
12	徐鹏. 纪念王义翘教授:解脂耶氏酵母替代植物油脂的技术瓶颈及展望[J]. 合成生物学, 2021, 2(4): 509-527.
	XU P. In memory of Prof. Daniel I.C. Wang: engineering Yarrowia lipolytica for the production of plant-based lipids: technical constraints and perspectives for a sustainable cellular agriculture economy[J]. Synthetic Biology Journal, 2021, 2(4): 509-527.
13	ZINJARDE S, APTE M, MOHITE P, et al. Yarrowia lipolytica and pollutants: interactions and applications[J]. Biotechnology Advances, 2014, 32(5): 920-933.
14	LEDESMA AMARO R, NICAUD J M. Metabolic engineering for expanding the substrate range of Yarrowia lipolytica [J]. Trends in Biotechnology, 2016, 34(10): 798-809.
15	SUN M L, SHI T Q, LIN L, et al. Advancing Yarrowia lipolytica as a superior biomanufacturing platform by tuning gene expression using promoter engineering[J]. Bioresource Technology, 2022, 347: 126717.
16	DAVIDOW L S, O'DONNELL M M, KACZMAREK F S, et al. Cloning and sequencing of the alkaline extracellular protease gene of Yarrowia lipolytica [J]. Journal of Bacteriology, 1987, 169(10): 4621-4629.
17	MÜLLER S, SANDAL T, KAMP-HANSEN P, et al. Comparison of expression systems in the yeasts Saccharomyces cerevisiae, Hansenula polymorpha, Klyveromyces lactis, Schizosaccharomyces pombe and Yarrowia lipolytica. Cloning of two novel promoters from Yarrowia lipolytica [J]. Yeast, 1998, 14(14): 1267-1283.
18	TRASSAERT M, VANDERMIES M, CARLY F, et al. New inducible promoter for gene expression and synthetic biology in Yarrowia lipolytica [J]. Microbial Cell Factories, 2017, 16(1): 141.
19	JURETZEK T, WANG H J, NICAUD J M, et al. Comparison of promoters suitable for regulated overexpression of β-galactosidase in the alkane-utilizing yeast Yarrowia lipolytica [J]. Biotechnology and Bioprocess Engineering, 2000, 5(5): 320-326.
20	WONG L, ENGEL J, JIN E Q, et al. YaliBricks, a versatile genetic toolkit for streamlined and rapid pathway engineering in Yarrowia lipolytica [J]. Metabolic Engineering Communications, 2017, 5: 68-77.
21	KAMINENI A, CHEN S Y, CHIFAMBA G, et al. Promoters for lipogenesis-specific downregulation in Yarrowia lipolytica [J]. FEMS Yeast Research, 2020, 20(5): foaa035.
22	XIONG X C, CHEN S L. Expanding toolbox for genes expression of Yarrowia lipolytica to include novel inducible, repressible, and hybrid promoters[J]. ACS Synthetic Biology, 2020, 9(8): 2208-2213.
23	HONG S P, SEIP J, WALTERS-POLLAK D, et al. Engineering Yarrowia lipolytica to express secretory invertase with strong FBA1IN promoter[J]. Yeast, 2012, 29(2): 59-72.
24	XUE Z X, ZHU Q Q. Ammonium transporter promoter for gene expression in oleaginous yeast: US08323960B2[P]. 2012-12-04.
25	BLAZECK J, LIU L Q, REDDEN H, et al. Tuning gene expression in Yarrowia lipolytica by a hybrid promoter approach[J]. Applied and Environmental Microbiology, 2011, 77(22): 7905-7914.
26	TAI M, STEPHANOPOULOS G. Engineering the push and pull of lipid biosynthesis in oleaginous yeast Yarrowia lipolytica for biofuel production[J]. Metabolic Engineering, 2013, 15: 1-9.
27	GEISBERG J V, MOQTADERI Z, FAN X C, et al. Global analysis of mRNA isoform half-lives reveals stabilizing and destabilizing elements in yeast[J]. Cell, 2014, 156(4): 812-824.
28	WAGNER J M, ALPER H S. Synthetic biology and molecular genetics in non-conventional yeasts: current tools and future advances[J]. Fungal Genetics and Biology, 2016, 89: 126-136.
29	CURRAN K A, MORSE N J, MARKHAM K A, et al. Short synthetic terminators for improved heterologous gene expression in yeast[J]. ACS Synthetic Biology, 2015, 4(7): 824-832.
30	BARTH G, GAILLARDIN C. Yarrowia lipolytica[M/OL]//Nonconventional Yeasts in Biotechnology: a handbook. Berlin, Heidelberg: Springer Berlin Heidelberg, 1996: 313-388 [2022-11-01]. .
31	LE DALL M T, NICAUD J M, GAILLARDIN C. Multiple-copy integration in the yeast Yarrowia lipolytica [J]. Current Genetics, 1994, 26(1): 38-44.
32	BLAZECK J, HILL A, LIU L Q, et al. Harnessing Yarrowia lipolytica lipogenesis to create a platform for lipid and biofuel production[J]. Nature Communications, 2014, 5: 3131.
33	KERKHOVEN E J, KIM Y M, WEI S W, et al. Leucine biosynthesis is involved in regulating high lipid accumulation in Yarrowia lipolytica [J]. mBio, 2017, 8(3): e00857-e00817.
34	BOEKE J D, TRUEHEART J, NATSOULIS G, et al. 5-Fluoroorotic acid as a selective agent in yeast molecular genetics[M/OL]//Methods in enzymology. New York: Academic Press, 1987: 164-175 [2022-11-01]. .
35	FICKERS P, LE DALL M T, GAILLARDIN C, et al. New disruption cassettes for rapid gene disruption and marker rescue in the yeast Yarrowia lipolytica [J]. Journal of Microbiological Methods, 2003, 55(3): 727-737.
36	CELIŃSKA E, BORKOWSKA M, KORPYS-WOŹNIAK P, et al. Optimization of Yarrowia lipolytica-based consolidated biocatalyst through synthetic biology approach: transcription units and signal peptides shuffling[J]. Applied Microbiology and Biotechnology, 2020, 104(13): 5845-5859.
37	LARROUDE M, TRABELSI H, NICAUD J M, et al. A set of Yarrowia lipolytica CRISPR/Cas9 vectors for exploiting wild-type strain diversity[J]. Biotechnology Letters, 2020, 42(5): 773-785.
38	HESLOT H. Genetics and genetic engineering of the industrial yeast Yarrowia lipolytica [M/OL]//Applied molecular genetics. Berlin: Springer, 1990: 43-73 [2022-11-01]. .
39	FOURNIER P, ABBAS A, CHASLES M, et al. Colocalization of centromeric and replicative functions on autonomously replicating sequences isolated from the yeast Yarrowia lipolytica [J]. Proceedings of the National Academy of Sciences of the United States of America, 1993, 90(11): 4912-4916.
40	VERNIS L, ABBAS A, CHASLES M, et al. An origin of replication and a centromere are both needed to establish a replicative plasmid in the yeast Yarrowia lipolytica [J]. Molecular and Cellular Biology, 1997, 17(4): 1995-2004.
41	LIU L Q, OTOUPAL P, PAN A, et al. Increasing expression level and copy number of a Yarrowia lipolytica plasmid through regulated centromere function[J]. FEMS Yeast Research, 2014, 14(7): 1124-1127.
42	LOPEZ C, CAO M F, YAO Z Y, et al. Revisiting the unique structure of autonomously replicating sequences in Yarrowia lipolytica and its role in pathway engineering[J]. Applied Microbiology and Biotechnology, 2021, 105(14): 5959-5972.
43	CUI Z Y, ZHENG H H, JIANG Z N, et al. Identification and characterization of the mitochondrial replication origin for stable and episomal expression in Yarrowia lipolytica [J]. ACS Synthetic Biology, 2021, 10(4): 826-835.
44	GUO Z P, BORSENBERGER V, CROUX C, et al. An artificial chromosome ylAC enables efficient assembly of multiple genes in Yarrowia lipolytica for biomanufacturing[J]. Communications Biology, 2020, 3(1): 199.
45	MADZAK C, TRÉTON B, BLANCHIN-ROLAND S. Strong hybrid promoters and integrative expression/secretion vectors for quasi-constitutive expression of heterologous proteins in the yeast Yarrowia lipolytica [J]. Journal of Molecular Microbiology and Biotechnology, 2000, 2(2): 207-216.
46	NICAUD J M. Yarrowia lipolytica[J]. Yeast, 2012, 29(10): 409-418.
47	LARROUDE M, ROSSIGNOL T, NICAUD J M, et al. Synthetic biology tools for engineering Yarrowia lipolytica [J]. Biotechnology Advances, 2018, 36(8): 2150-2164.
48	DING Y, WANG K F, WANG W J, et al. Increasing the homologous recombination efficiency of eukaryotic microorganisms for enhanced genome engineering[J]. Applied Microbiology and Biotechnology, 2019, 103(11): 4313-4324.
49	JI Q C, MAI J, DING Y, et al. Improving the homologous recombination efficiency of Yarrowia lipolytica by grafting heterologous component from Saccharomyces cerevisiae [J]. Metabolic Engineering Communications, 2020, 11: e00152.
50	BARTH G. Yarrowia lipolytica: biotechnological Applications[M/OL]. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013[2022-11-01]. .
51	PIGNÈDE G, WANG H J, FUDALEJ F, et al. Autocloning and amplification of LIP2 in Yarrowia lipolytica [J]. Applied and Environmental Microbiology, 2000, 66(8): 3283-3289.
52	BORDES F, FUDALEJ F, DOSSAT V, et al. A new recombinant protein expression system for high-throughput screening in the yeast Yarrowia lipolytica [J]. Journal of Microbiological Methods, 2007, 70(3): 493-502.
53	CUI Z Y, ZHENG H H, ZHANG J H, et al. A CRISPR/Cas9-mediated, homology-independent tool developed for targeted genome integration in Yarrowia lipolytica [J]. Applied and Environmental Microbiology, 2021, 87(6): e02666-20.
54	BAI Q Y, CHENG S, ZHANG J L, et al. Establishment of genomic library technology mediated by non-homologous end joining mechanism in Yarrowia lipolytica [J]. Science China Life Sciences, 2021, 64(12): 2114-2128.
55	CUI Z Y, JIANG X, ZHENG H H, et al. Homology-independent genome integration enables rapid library construction for enzyme expression and pathway optimization in Yarrowia lipolytica [J]. Biotechnology and Bioengineering, 2019, 116(2): 354-363.
56	LIU Y H, JIANG X, CUI Z Y, et al. Engineering the oleaginous yeast Yarrowia lipolytica for production of α-farnesene[J].Biotechnology for Biofuels, 2019, 12(1): 296.
57	LI Y W, YANG C L, SHEN Q, et al. YALIcloneNHEJ: an efficient modular cloning toolkit for NHEJ integration of multigene pathway and terpenoid production in Yarrowia lipolytica [J]. Frontiers in Bioengineering and Biotechnology, 2022, 9: 816980.
58	PLAGENS A, TJADEN B, HAGEMANN A, et al. Characterization of the CRISPR/cas subtype I-A system of the hyperthermophilic crenarchaeon thermoproteus tenax[J]. Journal of Bacteriology, 2012, 194(10): 2491-2500.
59	SHI T Q, HUANG H, KERKHOVEN E J, et al. Advancing metabolic engineering of Yarrowia lipolytica using the CRISPR/Cas system[J]. Applied Microbiology and Biotechnology, 2018, 102(22): 9541-9548.
60	DARVISHI F, ARIANA M, MARELLA E R, et al. Advances in synthetic biology of oleaginous yeast Yarrowia lipolytica for producing non-native chemicals[J]. Applied Microbiology and Biotechnology, 2018, 102(14): 5925-5938.
61	SCHWARTZ C M, HUSSAIN M S, BLENNER M, et al. Synthetic RNA polymeraseⅢpromoters facilitate high-efficiency CRISPR-Cas9-mediated genome editing in Yarrowia lipolytica [J]. ACS Synthetic Biology, 2016, 5(4): 356-359.
62	HOLKENBRINK C, DAM M I, KILDEGAARD K R, et al. EasyCloneYALI: CRISPR/Cas9-based synthetic toolbox for engineering of the yeast Yarrowia lipolytica [J]. Biotechnology Journal, 2018, 13(9): e1700543.
63	GAO S L, TONG Y Y, WEN Z Q, et al. Multiplex gene editing of the Yarrowia lipolytica genome using the CRISPR-Cas9 system[J]. Journal of Industrial Microbiology & Biotechnology, 2016, 43(8): 1085-1093.
64	GAO D F, SMITH S, SPAGNUOLO M, et al. Dual CRISPR-Cas9 cleavage mediated gene excision and targeted integration in Yarrowia lipolytica [J]. Biotechnology Journal, 2018, 13(9): e1700590.
65	MA J B, GU Y, MARSAFARI M, et al. Synthetic biology, systems biology, and metabolic engineering of Yarrowia lipolytica toward a sustainable biorefinery platform[J]. Journal of Industrial Microbiology & Biotechnology, 2020, 47(9/10): 845-862.
66	YANG Z L, EDWARDS H, XU P. CRISPR-Cas12a/Cpf1-assisted precise, efficient and multiplexed genome-editing in Yarrowia lipolytica [J]. Metabolic Engineering Communications, 2020, 10: e00112.
67	MA H H, TU L C, NASERI A, et al. Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow[J]. Nature Biotechnology, 2016, 34(5): 528-530.
68	SCHWARTZ C, FROGUE K, RAMESH A, et al. CRISPRi repression of nonhomologous end-joining for enhanced genome engineering via homologous recombination in Yarrowia lipolytica [J]. Biotechnology and Bioengineering, 2017, 114(12): 2896-2906.
69	ZHANG J L, PENG Y Z, LIU D, et al. Gene repression via multiplex gRNA strategy in Y. lipolytica [J]. Microbial Cell Factories, 2018, 17(1): 62.
70	SCHWARTZ C, WHEELDON I. CRISPR-Cas9-mediated genome editing and transcriptional control in Yarrowia lipolytica [M]//Synthetic Biology. New York, NY: Springer New York, 2018: 327-345.
71	RAMESH A, ONG T, GARCIA J A, et al. Guide RNA engineering enables dual purpose CRISPR-Cpf1 for simultaneous gene editing and gene regulation in Yarrowia lipolytica [J]. ACS Synthetic Biology, 2020, 9(4): 967-971.
72	SHIMATANI Z, KASHOJIYA S, TAKAYAMA M, et al. Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion[J]. Nature Biotechnology, 2017, 35(5): 441-443.
73	BAE S J, PARK B G, KIM B G, et al. Multiplex gene disruption by targeted base editing of Yarrowia lipolytica genome using cytidine deaminase combined with the CRISPR/Cas9 system[J]. Biotechnology Journal, 2020, 15(1): e1900238.
74	SCHWARTZ C, CHENG J F, EVANS R, et al. Validating genome-wide CRISPR-Cas9 function improves screening in the oleaginous yeast Yarrowia lipolytica [J]. Metabolic Engineering, 2019, 55: 102-110.
75	LUPISH B, HALL J, SCHWARTZ C, et al. Genome-wide CRISPR-Cas9 screen reveals a persistent null-hyphal phenotype that maintains high carotenoid production in Yarrowia lipolytica [J]. Biotechnology and Bioengineering, 2022, 119(12): 3623-3631.
76	BAISYA D, RAMESH A, SCHWARTZ C, et al. Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and-Cas12a guides in Yarrowia lipolytica [J]. Nature Communications, 2022, 13(1): 922.
77	JURETZEK T, LE DALL M T, MAUERSBERGER S, et al. Vectors for gene expression and amplification in the yeast Yarrowia lipolytica [J]. Yeast, 2001, 18(2): 97-113.
78	WANG K F, SHI T Q, WANG J P, et al. Engineering the lipid and fatty acid metabolism in Yarrowia lipolytica for sustainable production of high oleic oils[J]. ACS Synthetic Biology, 2022, 11(4): 1542-1554.
79	LV Y K, EDWARDS H, ZHOU J W, et al. Combining 26S rDNA and the Cre-loxP system for iterative gene integration and efficient marker curation in Yarrowia lipolytica [J]. ACS Synthetic Biology, 2019, 8(3): 568-576.
80	ZHOU Q H, JIAO L C, LI W J, et al. A novel cre/lox-based genetic tool for repeated, targeted and markerless gene integration in Yarrowia lipolytica [J]. International Journal of Molecular Sciences, 2021, 22(19): 10739.
81	SCHMID-BERGER N, SCHMID B, BARTH G. Ylt1, a highly repetitive retrotransposon in the genome of the dimorphic fungus Yarrowia lipolytica [J]. Journal of Bacteriology, 1994, 176(9): 2477-2482.
82	BULANI S I, MOLELEKI L, ALBERTYN J, et al. Development of a novel rDNA based plasmid for enhanced cell surface display on Yarrowia lipolytica [J]. AMB Express, 2012, 2(1): 27.
83	NICAUD J M, MADZAK C, VAN DEN BROEK P, et al. Protein expression and secretion in the yeast Yarrowia lipolytica [J]. FEMS Yeast Research, 2002, 2(3): 371-379.
84	MADZAK C, GAILLARDIN C, BECKERICH J M. Heterologous protein expression and secretion in the non-conventional yeast Yarrowia lipolytica: a review[J]. Journal of Biotechnology, 2004, 109(1/2): 63-81.
85	ZHAO Y, LIU S Q, LU Z H, et al. Hybrid promoter engineering strategies in Yarrowia lipolytica: isoamyl alcohol production as a test study[J]. Biotechnology for Biofuels, 2021, 14(1): 149.
86	BARTH G, GAILLARDIN C. Physiology and genetics of the dimorphic fungus Yarrowia lipolytica [J]. FEMS Microbiology Reviews, 1997, 19(4): 219-237.
87	JUNEAU K, MIRANDA M, HILLENMEYER M E, et al. Introns regulate RNA and protein abundance in yeast[J]. Genetics, 2006, 174(1): 511-518.
88	MEKOUAR M, BLANC-LENFLE I, OZANNE C, et al. Detection and analysis of alternative splicing in Yarrowia lipolytica reveal structural constraints facilitating nonsense-mediated decay of intron-retaining transcripts[J]. Genome Biology, 2010, 11(6): R65.
89	PELLIZZA L, SMAL C, RODRIGO G, et al. Codon usage clusters correlation: towards protein solubility prediction in heterologous expression systems in E. coli [J]. Scientific Reports, 2018, 8: 10618.
90	GASMI N, FUDALEJ F, KALLEL H, et al. A molecular approach to optimize hIFN α2b expression and secretion in Yarrowia lipolytica [J]. Applied Microbiology and Biotechnology, 2011, 89(1): 109-119.
91	DE POURCQ K, VERVECKEN W, DEWERTE I, et al. Engineering the yeast Yarrowia lipolytica for the production of therapeutic proteins homogeneously glycosylated with Man₈GlcNAc₂ and Man₅GlcNAc₂ [J]. Microbial Cell Factories, 2012, 11: 53.
92	于政, 申晓林, 孙新晓, 等. 动态调控策略在代谢工程中的应用研究进展[J]. 合成生物学, 2020, 1(4): 440-453.
	YU Z, SHEN X L, SUN X X, et al. Application of dynamic regulation strategies in metabolic engineering[J]. Synthetic Biology Journal, 2020, 1(4): 440-453.
93	QIU C X, ZHAI H T, HOU J. Biosensors design in yeast and applications in metabolic engineering[J]. FEMS Yeast Research, 2019, 19(8): foz082.
94	WAN X, MARSAFARI M, XU P. Engineering metabolite-responsive transcriptional factors to sense small molecules in eukaryotes: current state and perspectives[J]. Microbial Cell Factories, 2019, 18(1): 61.
95	PARK B G, KIM J, KIM E J, et al. Application of random mutagenesis and synthetic FadR promoter for de novo production of ω-hydroxy fatty acid in Yarrowia lipolytica [J]. Frontiers in Bioengineering and Biotechnology, 2021, 9: 624838.
96	LV Y K, GU Y, XU J L, et al. Coupling metabolic addiction with negative autoregulation to improve strain stability and pathway yield[J]. Metabolic Engineering, 2020, 61: 79-88.
97	CHO E J, TRINH L T P, SONG Y H, et al. Bioconversion of biomass waste into high value chemicals[J]. Bioresource Technology, 2020, 298: 122386.
98	ISIKGOR F H, BECER C R J P C. Lignocellulosic biomass: a sustainable platform for the production of bio-based chemicals and polymers[J]. Polymer Chemistry, 2015, 6(25): 4497-4559.
99	SUN T, YU Y Z, WANG K F, et al. Engineering Yarrowia lipolytica to produce fuels and chemicals from xylose: a review[J]. Bioresource Technology, 2021, 337: 125484.
100	WEI W P, SHANG Y Z, ZHANG P, et al. Engineering prokaryotic transcriptional activator XylR as a xylose-inducible biosensor for transcription activation in yeast[J]. ACS Synthetic Biology, 2020, 9(5): 1022-1029.
101	WEI W P, ZHANG P, SHANG Y Z, et al. Metabolically engineering of Yarrowia lipolytica for the biosynthesis of naringenin from a mixture of glucose and xylose[J]. Bioresource Technology, 2020, 314: 123726.
102	QIU X L, XU P, ZHAO X R, et al. Combining genetically-encoded biosensors with high throughput strain screening to maximize erythritol production in Yarrowia lipolytica [J]. Metabolic Engineering, 2020, 60: 66-76.
103	张萍, 魏文平, 周英, 等. 解脂耶氏酵母中光控表达系统的构建及其应用研究[J]. 合成生物学, 2021, 2(5): 778-791.
	ZHANG P, WEI W P, ZHOU Y, et al. Construction of a light-controlled expression system and its application in Yarrowia lipolytica [J]. Synthetic Biology Journal, 2021, 2(5): 778-791.
104	WANG Z Q, YAN Y J, ZHANG H J. A single-component blue light-induced system based on EL222 in Yarrowia lipolytica [J]. International Journal of Molecular Sciences, 2022, 23(11): 6344.
105	KERKHOVEN E J. Advances in constraint-based models: methods for improved predictive power based on resource allocation constraints[J]. Current Opinion in Microbiology, 2022, 68: 102168.
106	BORDBAR A, MONK J M, KING Z A, et al. Constraint-based models predict metabolic and associated cellular functions[J]. Nature Reviews Genetics, 2014, 15(2): 107-120.
107	MAIA P, ROCHA M, ROCHA I. In silico constraint-based strain optimization methods: the quest for optimal cell factories[J]. Microbiology and Molecular Biology Reviews, 2016, 80(1): 45-67.
108	PARK B G, KIM M, KIM J, et al. Systems biology for understanding and engineering of heterotrophic oleaginous microorganisms[J]. Biotechnology Journal, 2017, 12(1): 1600104.
109	LOIRA N, DULERMO T, NICAUD J M, et al. A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica [J]. BMC Systems Biology, 2012, 6: 35.
110	PAN P C, HUA Q. Reconstruction and in silico analysis of metabolic network for an oleaginous yeast, Yarrowia lipolytica [J]. PLoS One, 2012, 7(12): e51535.
111	KAVŠČEK M, BHUTADA G, MADL T, et al. Optimization of lipid production with a genome-scale model of Yarrowia lipolytica [J]. BMC Systems Biology, 2015, 9: 72.
112	KERKHOVEN E J, POMRANING K R, BAKER S E, et al. Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica [J]. Npj Systems Biology and Applications, 2016, 2: 16005.
113	AUNG H W, HENRY S A, WALKER L P. Revising the representation of fatty acid, glycerolipid, and glycerophospholipid metabolism in the consensus model of yeast metabolism[J]. Industrial Biotechnology, 2013, 9(4): 215-228.
114	DUARTE N C, HERRGÅRD M J, PALSSON B Ø. Reconstruction and validation of Saccharomyces cerevisiae IND750, a fully compartmentalized genome-scale metabolic model[J]. Genome Research, 2004, 14(7): 1298-1309.
115	WEI S S, JIAN X X, CHEN J, et al. Reconstruction of genome-scale metabolic model of Yarrowia lipolytica and its application in overproduction of triacylglycerol[J]. Bioresources and Bioprocessing, 2017, 4: 51.
116	MISHRA P, LEE N R, LAKSHMANAN M, et al. Genome-scale model-driven strain design for dicarboxylic acid production in Yarrowia lipolytica [J]. BMC Systems Biology, 2018, 12(): 12.
117	ZHANG C, JI B Y, MARDINOGLU A, et al. Logical transformation of genome-scale metabolic models for gene level applications and analysis[J]. Bioinformatics, 2015, 31(14): 2324-2331.
118	JIAN X X, ZHOU S G, ZHANG C, et al. In silico identification of gene amplification targets based on analysis of production and growth coupling[J]. Biosystems, 2016, 145: 1-8.
119	MISHRA P, LEE N R, LAKSHMANAN M, et al. Genome-scale model-driven strain design for dicarboxylic acid production in Yarrowia lipolytica [J]. BMC systems biology, 2018, 12(2): 9-20.
120	KIM M, PARK B G, KIM E J, et al. In silico identification of metabolic engineering strategies for improved lipid production in Yarrowia lipolytica by genome-scale metabolic modeling[J]. Biotechnology for Biofuels, 2019, 12: 187.
121	GUO Y F, SU L Q, LIU Q, et al. Dissecting carbon metabolism of Yarrowia lipolytica type strain W29 using genome-scale metabolic modelling[J]. Computational and Structural Biotechnology Journal, 2022, 20: 2503-2511.
122	KUBICEK C P, MIKUS M, SCHUSTER A, et al. Metabolic engineering strategies for the improvement of cellulase production by Hypocrea jecorina [J]. Biotechnology for Biofuels, 2009, 2: 19.
123	WARD O P. Production of recombinant proteins by filamentous fungi[J]. Biotechnology Advances, 2012, 30(5): 1119-1139.
124	KIM H, YOO S J, KANG H A. Yeast synthetic biology for the production of recombinant therapeutic proteins[J]. FEMS Yeast Research, 2015, 15(1): 1-16.
125	WOLF K. Nonconventional yeasts in biotechnology: a handbook[M/OL]. Heidelberg: Springer Berlin, 2012[2022-11-01]. .
126	CELIŃSKA E, BORKOWSKA M, BIAŁAS W. Enhanced production of insect raw-starch-digesting alpha-amylase accompanied by high erythritol synthesis in recombinant Yarrowia lipolytica fed-batch cultures at high-cell-densities[J]. Process Biochemistry, 2017, 52: 78-85.
127	OUEPHANIT C, BOONVITTHYA N, THEERACHAT M, et al. Efficient expression and secretion of endo-1,4-β-xylanase from Penicillium citrinum in non-conventional yeast Yarrowia lipolytica directed by the native and the preproLIP2 signal peptides[J]. Protein Expression and Purification, 2019, 160: 1-6.
128	GUO Z P, DUQUESNE S, BOZONNET S, et al. Expressing accessory proteins in cellulolytic Yarrowia lipolytica to improve the conversion yield of recalcitrant cellulose[J]. Biotechnology for Biofuels, 2017, 10: 298.
129	DERAKSHAN F K, DARVISHI F, DEZFULIAN M, et al. Expression and characterization of glucose oxidase from Aspergillus niger in Yarrowia lipolytica [J]. Molecular Biotechnology, 2017, 59(8): 307-314.
130	PARK Y K, VANDERMIES M, SOUDIER P, et al. Efficient expression vectors and host strain for the production of recombinant proteins by Yarrowia lipolytica in process conditions[J]. Microbial Cell Factories, 2019, 18(1): 167.
131	CUI W, WANG Q, ZHANG F, et al. Direct conversion of inulin into single cell protein by the engineered Yarrowia lipolytica carrying inulinase gene[J]. Process Biochemistry, 2011, 46(7): 1442-1448.
132	KRISS S, ZANE G, ZANE K, et al. Waste cooking oil as substrate for single cell protein production by yeast Yarrowia lipolytica [J]. Environmental and Climate Technologies, 2020, 24(3): 457-469.
133	YANG R, CHEN Z, HU P, et al. Two-stage fermentation enhanced single-cell protein production by Yarrowia lipolytica from food waste[J]. Bioresource Technology, 2022, 361: 127677.
134	GASMI N, AYED A, AMMAR B B H, et al. Development of a cultivation process for the enhancement of human interferon alpha 2b production in the oleaginous yeast, Yarrowia lipolytica [J]. Microbial Cell Factories, 2011, 10: 90.
135	GASMI N, AYED A, NICAUD J M, et al. Design of an efficient medium for heterologous protein production in Yarrowia lipolytica: case of human interferon alpha 2b[J]. Microbial Cell Factories, 2011, 10: 38.
136	PARK J N, SONG Y, CHEON S A, et al. Essential role of YlMPO1, a novel Yarrowia lipolytica homologue of Saccharomyces cerevisiae MNN4, in mannosylphosphorylation of N- and O-linked glycans[J]. Applied and Environmental Microbiology, 2011, 77(4): 1187-1195.
137	SOONG Y H V, LIU N, YOON S, et al. Cellular and metabolic engineering of oleaginous yeast Yarrowia lipolytica for bioconversion of hydrophobic substrates into high-value products[J]. Engineering in Life Sciences, 2019, 19(6): 423-443.
138	YUZBASHEVA E Y, AGRIMI G, YUZBASHEV T V, et al. The mitochondrial citrate carrier in Yarrowia lipolytica: its identification, characterization and functional significance for the production of citric acid[J]. Metabolic Engineering, 2019, 54: 264-274.
139	YUZBASHEVA E Y, SCARCIA P, YUZBASHEV T V, et al. Engineering Yarrowia lipolytica for the selective and high-level production of isocitric acid through manipulation of mitochondrial dicarboxylate-tricarboxylate carriers[J]. Metabolic Engineering, 2021, 65: 156-166.
140	JIANG Z N, CUI Z Y, ZHU Z W, et al. Engineering of Yarrowia lipolytica transporters for high-efficient production of biobased succinic acid from glucose[J]. Biotechnology for Biofuels, 2021, 14(1): 145.
141	ZHAO C, CUI Z Y, ZHAO X Y, et al. Enhanced itaconic acid production in Yarrowia lipolytica via heterologous expression of a mitochondrial transporter MTT[J]. Applied Microbiology and Biotechnology, 2019, 103(5): 2181-2192.
142	ZENG W Z, DU G C, CHEN J, et al. A high-throughput screening procedure for enhancing α-ketoglutaric acid production in Yarrowia lipolytica by random mutagenesis[J]. Process Biochemistry, 2015, 50(10): 1516-1522.
143	ZENG W Z, FANG F, LIU S, et al. Comparative genomics analysis of a series of Yarrowia lipolytica WSH-Z06 mutants with varied capacity for α-ketoglutarate production[J]. Journal of Biotechnology, 2016, 239: 76-82.
144	ZENG W Z, ZHANG H L, XU S, et al. Biosynthesis of keto acids by fed-batch culture of Yarrowia lipolytica WSH-Z06[J]. Bioresource Technology, 2017, 243: 1037-1043.
145	ZHANG G, WANG H, ZHANG Z, et al. Metabolic engineering of Yarrowia lipolytica for terpenoids production: advances and perspectives[J]. Critical Reviews in Biotechnology, 2022, 42(4): 618-633.
146	MAI J, LI W J, LEDESMA-AMARO R, et al. Engineering plant sesquiterpene synthesis into yeasts: a review[J]. Journal of Agricultural and Food Chemistry, 2021, 69(33): 9498-9510.
147	LI W J, CUI L W, MAI J, et al. Advances in metabolic engineering paving the way for the efficient biosynthesis of terpenes in yeasts[J]. Journal of Agricultural and Food Chemistry, 2022, 70(30): 9246-9261.
148	GOTO T, TAKAHASHI N, HIRAI S, et al. Various terpenoids derived from herbal and dietary plants function as PPAR modulators and regulate carbohydrate and lipid metabolism[J]. PPAR Research, 2010, 2010: 483958.
149	PANG Y R, ZHAO Y K, LI S L, et al. Engineering the oleaginous yeast Yarrowia lipolytica to produce limonene from waste cooking oil[J]. Biotechnology for Biofuels, 2019, 12: 241.
150	ARNESEN J A, KILDEGAARD K R, CERNUDA PASTOR M, et al. Yarrowia lipolytica strains engineered for the production of terpenoids[J]. Frontiers in Bioengineering and Biotechnology, 2020, 8: 945.
151	GUO Q, SHI T Q, PENG Q Q, et al. Harnessing Yarrowia lipolytica peroxisomes as a subcellular factory for α-humulene overproduction [J]. Journal of Agricultural and Food Chemistry, 2021, 69(46): 13831-13837.
152	MA Y R, LI W J, MAI J, et al. Engineering Yarrowia lipolytica for sustainable production of the chamomile sesquiterpene (-)-α-bisabolol[J]. Green Chemistry, 2021, 23(2): 780-787.
153	KILDEGAARD K R, ARNESEN J A, ADIEGO-PÉREZ B, et al. Tailored biosynthesis of gibberellin plant hormones in yeast[J]. Metabolic Engineering, 2021, 66: 1-11.
154	TANG W Y, WANG D P, TIAN Y, et al. Metabolic engineering of Yarrowia lipolytica for improving squalene production[J]. Bioresource Technology, 2021, 323: 124652.
155	JIN C C, ZHANG J L, SONG H, et al. Boosting the biosynthesis of betulinic acid and related triterpenoids in Yarrowia lipolytica via multimodular metabolic engineering[J]. Microbial Cell Factories, 2019, 18(1): 77.
156	MA Y S, LIU N, GREISEN P, et al. Removal of lycopene substrate inhibition enables high carotenoid productivity in Yarrowia lipolytica [J]. Nature Communications, 2022, 13: 572.
157	LARROUDE M, CELINSKA E, BACK A, et al. A synthetic biology approach to transform Yarrowia lipolytica into a competitive biotechnological producer of β-carotene[J]. Biotechnology and Bioengineering, 2018, 115(2): 464-472.
158	MA Y S, LI J B, HUANG S W, et al. Targeting pathway expression to subcellular organelles improves astaxanthin synthesis in Yarrowia lipolytica [J]. Metabolic Engineering, 2021, 68: 152-161.
159	MA T, SHI B, YE Z L, et al. Lipid engineering combined with systematic metabolic engineering of Saccharomyces cerevisiae for high-yield production of lycopene[J]. Metabolic Engineering, 2019, 52: 134-142.
160	MENG Y H, SHAO X X, WANG Y, et al. Extension of cell membrane boosting squalene production in the engineered Escherichia coli [J]. Biotechnology and Bioengineering, 2020, 117(11): 3499-3507.
161	LUO Z S, LIU N, LAZAR Z, et al. Enhancing isoprenoid synthesis in Yarrowia lipolytica by expressing the isopentenol utilization pathway and modulating intracellular hydrophobicity[J]. Metabolic Engineering, 2020, 61: 344-351.
162	GUO X Y, SUN J, LI D S, et al. Heterologous biosynthesis of (+)-nootkatone in unconventional yeast Yarrowia lipolytica [J]. Biochemical Engineering Journal, 2018, 137: 125-131.
163	ARNESEN J A, JACOBSEN I H, DANNOW DYEKJÆR J, et al. Production of abscisic acid in the oleaginous yeast Yarrowia lipolytica [J]. FEMS Yeast Research, 2022, 22(1): foac015.
164	LI D S, WU Y F, ZHANG C B, et al. Production of triterpene ginsenoside compound K in the non-conventional yeast Yarrowia lipolytica [J]. Journal of Agricultural and Food Chemistry, 2019, 67(9): 2581-2588.
165	BILAL M, XU S, IQBAL H M N, et al. Yarrowia lipolytica as an emerging biotechnological chassis for functional sugars biosynthesis[J]. Critical Reviews in Food Science and Nutrition, 2021, 61(4): 535-552.
166	JANEK T, DOBROWOLSKI A, BIEGALSKA A, et al. Characterization of erythrose reductase from Yarrowia lipolytica and its influence on erythritol synthesis[J]. Microbial Cell Factories, 2017, 16(1): 118.
167	MIROŃCZUK A M, BIEGALSKA A, DOBROWOLSKI A. Functional overexpression of genes involved in erythritol synthesis in the yeast Yarrowia lipolytica [J]. Biotechnology for Biofuels, 2017, 10: 77.
168	CHI P, WANG S Q, GE X M, et al. Efficient D-threitol production by an engineered strain of Yarrowia lipolytica overexpressing xylitol dehydrogenase gene from Scheffersomyces stipitis [J]. Biochemical Engineering Journal, 2019, 149: 107259.
169	BENAHMED A G, GASMI A, ARSHAD M, et al. Health benefits of xylitol[J]. Applied Microbiology and Biotechnology, 2020, 104(17): 7225-7237.
170	PRABHU A A, THOMAS D J, LEDESMA-AMARO R, et al. Biovalorisation of crude glycerol and xylose into xylitol by oleaginous yeast Yarrowia lipolytica [J]. Microbial Cell Factories, 2020, 19(1): 121.
171	BODE L. Human milk oligosaccharides: every baby needs a sugar mama[J]. Glycobiology, 2012, 22(9): 1147-1162.
172	HOLLANDS K, BARON C M, GIBSON K J, et al. Engineering two species of yeast as cell factories for 2′-fucosyllactose [J]. Metabolic Engineering, 2019, 52: 232-242.
173	ZHANG P, WANG Z P, SHENG J, et al. High and efficient isomaltulose production using an engineered Yarrowia lipolytica strain[J]. Bioresource Technology, 2018, 265: 577-580.
174	LI N, WANG H W, LI L J, et al. Integrated approach to producing high-purity trehalose from maltose by the yeast Yarrowia lipolytica displaying trehalose synthase (TreS) on the cell surface[J]. Journal of Agricultural and Food Chemistry, 2016, 64(31): 6179-6187.
175	王凯峰, 王金鹏, 韦萍, 等. 代谢工程改造解脂耶氏酵母生产脂肪酸及其衍生物[J]. 化工学报, 2021, 72(1): 351-365.
	WANG K F, WANG J P, WEI P, et al. Metabolic engineering of Yarrowia lipolytica to produce fatty acids and their derivatives[J]. CIESC Journal, 2021, 72(1): 351-365.
176	XU J Y, LIU N, QIAO K J, et al. Application of metabolic controls for the maximization of lipid production in semicontinuous fermentation[J]. Proceedings of the National Academy of Sciences of the United States of America, 2017, 114(27): E5308-E5316.
177	LEDESMA AMARO R, DULERMO R, NIEHUS X, et al. Combining metabolic engineering and process optimization to improve production and secretion of fatty acids[J]. Metabolic Engineering, 2016, 38: 38-46.
178	LU R, SHI T Q, LIN L, et al. Advances in metabolic engineering of yeasts for the production of fatty acid-derived hydrocarbon fuels [J]. Green Chemical Engineering, 2022,3(4): 289-303.
179	RIGOUIN C, CROUX C, BORSENBERGER V, et al. Increasing medium chain fatty acids production in Yarrowia lipolytica by metabolic engineering[J]. Microbial Cell Factories, 2018, 17(1): 142.
180	HANKO E K R, DENBY C M, SÀNCHEZ I NOGUÉ V, et al. Engineering β-oxidation in Yarrowia lipolytica for methyl ketone production[J]. Metabolic Engineering, 2018, 48: 52-62.
181	HADDOUCHE R, POIRIER Y, DELESSERT S, et al. Engineering polyhydroxyalkanoate content and monomer composition in the oleaginous yeast Yarrowia lipolytica by modifying the β-oxidation multifunctional protein[J]. Applied Microbiology and Biotechnology, 2011, 91(5): 1327-1340.
182	GUO Y Q, SONG H L, WANG Z Y, et al. Expression of POX2 gene and disruption of POX3 genes in the industrial Yarrowia lipolytica on the γ-decalactone production[J]. Microbiological Research, 2012, 167(4): 246-252.
183	LI H B, ALPER H S. Producing biochemicals in Yarrowia lipolytica from xylose through a strain mating approach[J]. Biotechnology Journal, 2020, 15(2): e1900304.
184	XUE Z X, SHARPE P L, HONG S P, et al. Production of omega-3 eicosapentaenoic acid by metabolic engineering of Yarrowia lipolytica [J]. Nature Biotechnology, 2013, 31(8): 734-740.
185	GEMPERLEIN K, DIETRICH D, KOHLSTEDT M, et al. Polyunsaturated fatty acid production by Yarrowia lipolytica employing designed myxobacterial PUFA synthases[J]. Nature Communications, 2019, 10(1): 4055.
186	SUN M L, MADZAK C, LIU H H, et al. Engineering Yarrowia lipolytica for efficient γ-linolenic acid production[J]. Biochemical Engineering Journal, 2017, 117: 172-180.
187	LIU H H, MADZAK C, SUN M L, et al. Engineering Yarrowia lipolytica for arachidonic acid production through rapid assembly of metabolic pathway[J]. Biochemical Engineering Journal, 2017, 119: 52-58.
188	LIU H H, ZENG S Y, SHI T Q, et al. A Yarrowia lipolytica strain engineered for arachidonic acid production counteracts metabolic burden by redirecting carbon flux towards intracellular fatty acid accumulation at the expense of organic acids secretion[J]. Biochemical Engineering Journal, 2017, 128: 201-209.
189	LIU H H, WANG C, LU X Y, et al. Improved production of arachidonic acid by combined pathway engineering and synthetic enzyme fusion in Yarrowia lipolytica [J]. Journal of Agricultural and Food Chemistry, 2019, 67(35): 9851-9857.
190	XIE D M, JACKSON E N, ZHU Q. Sustainable source of omega-3 eicosapentaenoic acid from metabolically engineered Yarrowia lipolytica: from fundamental research to commercial production[J]. Applied Microbiology and Biotechnology, 2015, 99(4): 1599-1610.
191	PARK Y K, DULERMO T, LEDESMA-AMARO R, et al. Optimization of odd chain fatty acid production by Yarrowia lipolytica [J]. Biotechnology for Biofuels, 2018, 11: 158.
192	PARK Y K, LEDESMA-AMARO R, NICAUD J M. De novo biosynthesis of odd-chain fatty acids in Yarrowia lipolytica enabled by modular pathway engineering[J]. Frontiers in Bioengineering and Biotechnology, 2020, 7: 484.
193	TANG S Y, QIAN S, AKINTERINWA O, et al. Screening for enhanced triacetic acid lactone production by recombinant Escherichia coli expressing a designed triacetic acid lactone reporter[J]. Journal of the American Chemical Society, 2013, 135(27): 10099-10103.
194	SAUNDERS L P, BOWMAN M J, MERTENS J A, et al. Triacetic acid lactone production in industrial Saccharomyces yeast strains[J]. Journal of Industrial Microbiology & Biotechnology, 2015, 42(5): 711-721.
195	MARKHAM K A, PALMER C M, CHWATKO M, et al. Rewiring Yarrowia lipolytica toward triacetic acid lactone for materials generation[J]. Proceedings of the National Academy of Sciences of the United States of America, 2018, 115(9): 2096-2101
196	YU J, LANDBERG J, SHAVAREBI F, et al. Bioengineering triacetic acid lactone production in Yarrowia lipolytica for pogostone synthesis[J]. Biotechnology and Bioengineering, 2018, 115(9): 2383-2388.
197	LIU H, MARSAFARI M, WANG F, et al. Engineering acetyl-CoA metabolic shortcut for eco-friendly production of polyketides triacetic acid lactone in Yarrowia lipolytica [J]. Metabolic Engineering, 2019, 56: 60-68.
198	TRANTAS E A, KOFFAS M A G, XU P, et al. When plants produce not enough or at all: metabolic engineering of flavonoids in microbial hosts[J]. Frontiers in Plant Science, 2015, 6: 7.
199	PALMER C M, MILLER K K, NGUYEN A, et al. Engineering 4-coumaroyl-CoA derived polyketide production in Yarrowia lipolytica through a β-oxidation mediated strategy[J]. Metabolic Engineering, 2020, 57: 174-181.
200	HE Q, SZCZEPAŃSKA P, YUZBASHEV T, et al. De novo production of resveratrol from glycerol by engineering different metabolic pathways in Yarrowia lipolytica [J]. Metabolic Engineering Communications, 2020, 11: e00146.
201	LV Y K, MARSAFARI M, KOFFAS M, et al. Optimizing oleaginous yeast cell factories for flavonoids and hydroxylated flavonoids biosynthesis[J]. ACS Synthetic Biology, 2019, 8(11): 2514-2523.
202	ZHOU S H, LYU Y B, LI H Z, et al. Fine-tuning the (2S)-naringenin synthetic pathway using an iterative high-throughput balancing strategy[J]. Biotechnology and Bioengineering, 2019, 116(6): 1392-1404.
203	KALLSCHEUER N, VOGT M, STENZEL A, et al. Construction of a Corynebacterium glutamicum platform strain for the production of stilbenes and (2S)-flavanones[J]. Metabolic Engineering, 2016, 38: 47-55.
204	GAO S, LYU Y B, ZENG W Z, et al. Efficient biosynthesis of (2S)-naringenin from p-coumaric acid in Saccharomyces cerevisiae [J]. Journal of Agricultural and Food Chemistry, 2020, 68(4): 1015-1021.
205	FOWLER Z L, GIKANDI W W, KOFFAS M A G. Increased malonyl coenzyme A biosynthesis by tuning the Escherichia coli metabolic network and its application to flavanone production[J]. Applied and Environmental Microbiology, 2009, 75(18): 5831-5839.
206	AMOR I L B, HEHN A, GUEDONE E, et al. Biotransformation of naringenin to eriodictyol by Saccharomyces cerevisiea functionally expressing flavonoid 3′-hydroxylase[J]. Natural Product Communications, 2010, 5(12): 1893-1898.
207	CELIŃSKA E, KUBIAK P, BIAŁAS W, et al. Yarrowia lipolytica: the novel and promising 2-phenylethanol producer[J]. Journal of Industrial Microbiology & Biotechnology, 2013, 40(3/4): 389-392.
208	CELIŃSKA E, OLKOWICZ M, GRAJEK W. L-Phenylalanine catabolism and 2-phenylethanol synthesis in Yarrowia lipolytica—mapping molecular identities through whole-proteome quantitative mass spectrometry analysis[J]. FEMS Yeast Research, 2015, 15(5): fov041.
209	GU Y, MA J B, ZHU Y L, et al. Refactoring ehrlich pathway for high-yield 2-phenylethanol production in Yarrowia lipolytica [J]. ACS Synthetic Biology, 2020, 9(3): 623-633.
210	GU Y, MA J B, ZHU Y L, et al. Engineering Yarrowia lipolytica as a chassis for de novo synthesis of five aromatic-derived natural products and chemicals[J]. ACS Synthetic Biology, 2020, 9(8): 2096-2106.
211	TONG Y J, ZHOU J W, ZHANG L, et al. A golden-gate based cloning toolkit to build violacein pathway libraries in Yarrowia lipolytica [J]. ACS Synthetic Biology, 2021, 10(1): 115-124.
212	WRÓBEL-KWIATKOWSKA M, TURSKI W, KOCKI T, et al. An efficient method for production of kynurenic acid by Yarrowia lipolytica [J]. Yeast, 2020, 37(9/10): 541-547.
213	WRÓBEL-KWIATKOWSKA M, TURSKI W, JUSZCZYK P, et al. Improved production of kynurenic acid by Yarrowia lipolytica in media containing different honeys[J]. Sustainability, 2020, 12(22): 9424.
214	VAN DER HOEK S A, RUSNÁK M, JACOBSEN I H, et al. Engineering ergothioneine production in Yarrowia lipolytica [J]. FEBS Letters, 2022, 596(10): 1356-1364.
215	PARK Y K, BORDES F, LETISSE F, et al. Engineering precursor pools for increasing production of odd-chain fatty acids in Yarrowia lipolytica [J]. Metabolic Engineering Communications, 2021, 12: e00158.
216	ZHANG B X, CHEN H Q, LI M, et al. Genetic engineering of Yarrowia lipolytica for enhanced production of trans-10, cis-12 conjugated linoleic acid[J]. Microbial Cell Factories, 2013, 12: 70.
217	IMATOUKENE N, BACK A, NONUS M, et al. Fermentation process for producing CFAs using Yarrowia lipolytica [J]. Journal of Industrial Microbiology & Biotechnology, 2020, 47(4): 403-412.
218	BLITZBLAU H G, CONSIGLIO A L, TEIXEIRA P, et al. Production of 10-methyl branched fatty acids in yeast[J]. Biotechnology for Biofuels, 2021, 14(1): 12.
219	BEOPOULOS A, VERBEKE J, BORDES F, et al. Metabolic engineering for ricinoleic acid production in the oleaginous yeast Yarrowia lipolytica [J]. Applied Microbiology and Biotechnology, 2014, 98(1): 251-262.
220	RABENHORST J, GATFIELD I. Method of producing γ-decalactone using Yarrowia lipolytica strain HR 145 (DSM 12397): US06451565B1[P]. 2002-09-17. .
221	KANG W R, SEO M J, AN J U, et al. Production of δ-decalactone from linoleic acid via 13-hydroxy-9(Z)-octadecenoic acid intermediate by one-pot reaction using linoleate 13-hydratase and whole Yarrowia lipolytica cells[J].Biotechnology Letters, 2016, 38(5): 817-823.
222	MARELLA E R, DAHLIN J, DAM M I, et al. A single-host fermentation process for the production of flavor lactones from non-hydroxylated fatty acids[J]. Metabolic Engineering, 2020, 61: 427-436.
223	LI J B, MA Y S, LIU N, et al. Synthesis of high-titer alka(e)nes in Yarrowia lipolytica is enabled by a discovered mechanism[J]. Nature Communications, 2020, 11: 6198.
224	YANG K X, QIAO Y G, LI F, et al. Subcellular engineering of lipase dependent pathways directed towards lipid related organelles for highly effectively compartmentalized biosynthesis of triacylglycerol derived products in Yarrowia lipolytica [J]. Metabolic Engineering, 2019, 55: 231-238.

表征的启动子强度排序	表征方法	参考文献
pEXP1> pTEF> pGPD > pGPAT> pYAT1 >pXPR2 > pFBA1	报告蛋白：绿色荧光蛋白分析：流式细胞仪	[25]
pCTR1 > pTEF > pCTR2	报告蛋白：β-半乳糖苷酶分析：紫外-可见分光光度计	[22]
pTEFin>php4d > pTEF	报告蛋白：β-半乳糖苷酶分析：分光光度计	[26]
pTEF> pGAP > pACL2 > pICL > pIDH2 > pFAS1 > pDGA1 > pFAS2 > pZWF1 > pPOX4 > pACC1 > pIDP2	报告蛋白: 荧光素酶分析：酶标仪	[20]
pFBAin> pFBA> pTDH1 > pGPM1= pTEF	报告蛋白：β-葡萄糖醛酸酶分析：荧光微孔板读数仪	[23]

表征的启动子强度排序	表征方法	参考文献
pEXP1> pTEF> pGPD > pGPAT> pYAT1 >pXPR2 > pFBA1	报告蛋白：绿色荧光蛋白分析：流式细胞仪	[25]
pCTR1 > pTEF > pCTR2	报告蛋白：β-半乳糖苷酶分析：紫外-可见分光光度计	[22]
pTEFin>php4d > pTEF	报告蛋白：β-半乳糖苷酶分析：分光光度计	[26]
pTEF> pGAP > pACL2 > pICL > pIDH2 > pFAS1 > pDGA1 > pFAS2 > pZWF1 > pPOX4 > pACC1 > pIDP2	报告蛋白: 荧光素酶分析：酶标仪	[20]
pFBAin> pFBA> pTDH1 > pGPM1= pTEF	报告蛋白：β-葡萄糖醛酸酶分析：荧光微孔板读数仪	[23]

模型名称	基因数	代谢物数	反应数	代谢区室数	准确性	年份	参考文献
iNL895	895	1847	1989	16	0.65	2012	[109]
iYL619_PCP	619	849	1142	2	0.83	2012	[110]
iMK735	735	1111	1336	8	0.80	2015	[111]
iYali4	901	1683	1985	16	Not determined	2016	[112]
iYL_2.0	645	1083	1471	4	0.97	2017	[115]
iYLI647	647	1119	1347	8	0.80	2018	[116]
iYli21	1058	1868	2285	16	0.86	2022	[121]

模型名称	基因数	代谢物数	反应数	代谢区室数	准确性	年份	参考文献
iNL895	895	1847	1989	16	0.65	2012	[109]
iYL619_PCP	619	849	1142	2	0.83	2012	[110]
iMK735	735	1111	1336	8	0.80	2015	[111]
iYali4	901	1683	1985	16	Not determined	2016	[112]
iYL_2.0	645	1083	1471	4	0.97	2017	[115]
iYLI647	647	1119	1347	8	0.80	2018	[116]
iYli21	1058	1868	2285	16	0.86	2022	[121]

种类	产品	生产规模	生产水平	参考文献
有机酸	柠檬酸	1L 生物反应器	97.1 g/L	[138]
	异柠檬酸	1L 生物反应器	136.7 g/L	[139]
	琥珀酸	1L 生物反应器	101.4 g/L	[140]
	衣康酸	5L 生物反应器	22.03 g/L	[141]
	α-酮戊二酸	3L 生物反应器	67.4 g/L	[144]
	丙酮酸	3L 生物反应器	39.1 g/L	[144]
萜烯类	柠檬烯	摇瓶	35.9 mg/L	[150]
	α-法尼烯	1L 生物反应器	25.55 g/L	[56]
	β-法尼烯	摇瓶	955 mg/L	[150]
	α-葎草烯	5L 生物反应器	3.2 g/L	[151]
	(-)-α-红没药醇	5L 生物反应器	4.4 g/L	[57]
	脱落酸	摇瓶	263.5 mg/L	[163]
	赤霉素3	摇瓶	17.29 mg/L	[153]
	赤霉素4	摇瓶	12.81 mg/L	[153]
	角鲨烯	摇瓶	731.18 mg/L	[154]
	桦木酸	摇瓶	51.87 mg/L	[155]
	人参皂苷CK	5L 生物反应器	161.8 mg/L	[164]
	番茄红素	3L 生物反应器	17.6 g/L	[156]
	β-胡萝卜素	5L 生物反应器	6.5 g/L	[157]
	虾青素	摇瓶	858 mg/L	[158]
功能糖及糖醇类	赤藓糖醇	3L生物反应器	148 g/L	[102]
	D-苏糖醇	摇瓶	112 g/L	[168]
	木糖醇	摇瓶	53.2 g/L	[170]
	2′-岩藻糖基乳糖	2L 生物反应器	24 g/L	[172]
	异麦芽酮糖	10L 生物反应器	572.1 g/L	[173]
	海藻糖	3L 生物反应器	219 g/L	[174]
脂肪酸及衍生物类	奇数链脂肪酸(C₁₅～C₁₉)	摇瓶	1.87 g/L	[215]
	(10E,12Z)十八碳二烯酸	5L 生物反应器	4 g/L	[216]
	油酸	5L 生物反应器	46.23 g/L	[78]
	α-亚麻酸	2L 生物反应器	1.42 g/L	[183]
	γ-亚麻酸	摇瓶	71.6 mg/L	[186]
	花生四烯酸	摇瓶	118.1 mg/L	[189]
	二十碳五烯酸	摇瓶	占总脂肪酸的56.6%	[184]
	二十二碳六烯酸	1L 生物反应器	350 mg/L	[185]
	环丙烷脂肪酸(C₁₇、C₁₉)	5L 生物反应器	7.49 g/L	[217]
	10-甲基支链脂肪酸	1L 生物反应器	1.2 g/L	[218]
	蓖麻油酸	摇瓶	12 g/L	[219]
	甲基酮	0.5L 生物反应器	314.8 mg/L	[180]
	聚羟基脂肪酸酯	摇瓶	占细胞干重7.3%	[181]
	γ-癸内酯	300L 生物反应器	12.3 g/L	[220]
	δ-癸内酯	摇瓶	1.9 g/L	[221]
	γ-十二内酯	1L 生物反应器	282 mg/L	[222]
	烷（烯）烃	摇瓶	1.47 g/L	[223]
	烯烃	摇瓶	554.4 mg/L	[224]
聚酮类和黄酮类	三乙酸内酯	3L 生物反应器	(35.9±3.9) g/L	[195]
	白藜芦醇	5L 生物反应器	430 mg/L	[200]
	柚皮素	3L 生物反应器	898 mg/L	[199]
	圣草酚	摇瓶	134.2 mg/L	[96]
氨基酸衍生物类	2-苯乙醇	摇瓶	2669.54 mg/L	[209]
	对香豆酸	摇瓶	(593.53 ± 28.75) mg/L	[210]
	紫杆菌素	摇瓶	(366.30 ± 28.99) mg/L	[210]
	犬尿酸	5L 生物反应器	培养液：68 mg/L 生物量：542 mg/kg	[213]
	麦角硫因	1L 生物反应器	1.63 g/L	[214]