合成生物技术驱动天然的真核油脂细胞工厂开发

doi:10.12211/2096-8280.2020-090

摘要/Abstract

摘要：

油脂是重要的工业原料，也是人类生存的三大营养素之一。为避免因国际环境变化导致外部资源进口遭到封锁，我国亟需建设、补充和完善油脂供给的新方式。以丰富、廉价的生物质原料替代化石原料生产食用油脂和功能性油脂，在保障国家能源安全、粮食安全方面意义重大。细菌、酵母、霉菌、微藻等多种微生物具有利用葡萄糖、木质纤维素、淀粉、甘油甚至一碳化合物等原料合成脂肪酸的能力。由于微生物，特别是产油真菌相比产油植物和动物具有生产周期短、易于大规模生产、占地少、受天气影响小、原料来源丰富等优势，近年来备受学术界和产业界重视。然而，如何获取生产效率高且鲁棒性强的微生物油脂细胞工厂，仍然面临着使能工具有限、油脂产量不高、油脂组分难以控制等诸多挑战。近年来，合成生物学技术的发展为本领域的研究提供了新的资源、工具和思路。使得产油微生物研究在遗传操作工具创制、代谢途径改造以及高附加值产品开发等方面不断获得突破。本文聚焦于真核油脂细胞工厂的开发，从天然产油底盘菌株的基因元件、遗传转化方法、基因编辑工具的开发，油脂细胞工厂代谢途径的重构/调试以及向高附加值脂质化学品方向的升级等方面，系统总结了合成生物技术驱动油脂细胞工厂开发的研究进展，可为后续研究提供借鉴。

关键词: 合成生物学, 基因编辑, 产油真菌, 代谢工程, 高附加值产品

Abstract:

Lipids are important industrial raw materials and one of the three major nutrients for human survival. In order to avoid the blockade of external resource imports due to unpredictable international market, we urgently need to build new methods for lipids supply. Biomass is the only kind of physical resource based on carbon among many renewable resources. Therefore, The production of edible and functional lipids with abundant and cheap biomass materials instead of fossil materials is of great significance in ensuring national energy security and food security. Bacteria, yeast, mold, microalgae and some other microorganisms have the potential in using glucose, lignocellulose, starch, glycerol or even one carbon compounds to synthesize fatty acids. Due to the advantages of short production cycle, easy large-scale production , less land occupation, less impact of climate change and abundant raw material sources comparing with lipips from plants and animals, microbial lipid production has attracted much attention from academia and industry in recent years. However, there are still many challenges on how to obtain efficient and robust microbial lipid cell factories, such as limited enabling tools, low lipid production and difficult control of lipid components. The development of synthetic biology then provides new resources, tools and ideas for research in this field in recent years. Thus the research of lipid producing microorganisms has made continuous breakthroughs in the creation of genetic manipulation tools, the engineering of lipip biosynthesis pathways and the development of high value-added products. This review focuses on the genetic elements of natural lipid-producing chassis strains, genetic transformation methods, genome editing tools development, the reconstruction/debugging of the metabolic pathways of lipid cell factories, and the upgrade to high value-added lipid chemicals. By systematically summarized the research progress of synthetic biotechnology in driving the development of lipid cell factories, we very much hope to provide reference for future research in this area.

Key words: synthetic biology, genome editing, oleaginous fungus, metabolic engineering, high value-added products

中图分类号:

Q812

汪庆卓, 宋萍, 黄和. 合成生物技术驱动天然的真核油脂细胞工厂开发[J]. 合成生物学, 2021, 2(6): 920-941.

Qingzhuo WANG, Ping SONG, He HUANG. Synthetic biotechnology drives the development of natural eukaryotic lipid cell factories[J]. Synthetic Biology Journal, 2021, 2(6): 920-941.

图/表 6

参考文献 170

1	谭天伟, 苏海佳, 陈必强, 等. 绿色生物制造 [J]. 北京化工大学学报(自然科学版), 2018, 45(5): 107-118.
	TAN T W, SU H J, CHEN B Q, et al. Green bio-manufacturing[J]. Journal of Beijing University of Chemical Technology (Natural Science Edition), 2018, 45(5): 107-118.
2	WEN Z Q, ZHANG S F, ODOH C K, et al. Rhodosporidium toruloides-A potential red yeast chassis for lipids and beyond[J]. FEMS Yeast Research, 2020, 20(5): foaa038.
3	胡学超, 任路静, 胡耀池, 等. 裂殖壶菌制备二十二碳六烯酸油脂的研究历程及发展前景[J]. 食品与发酵工业, 2018, 44(11): 311-316.
	HU X C, REN L J, HU Y C, et al. Research progress and development prospect of producing docosahexaenoic acid oil by Schizochytrium sp.[J]. Food and Fermentation Industry, 2018, 44(11): 311-316.
4	SHI S, ZHAO H. Metabolic engineering of oleaginous yeasts for production of fuels and chemicals[J]. Frontiers in Microbiology, 2017, 8: 2185.
5	PATEL A, KARAGEORGOU D, ROVA E, et al. An overview of potential oleaginous microorganisms and their role in biodiesel and Omega-3 fatty acid-based industries[J]. Microorganisms, 2020, 8(3).
6	PARK Y K, NICAUD J M, LEDESMA-AMARO R. The engineering potential of Rhodosporidium toruloides as a workhorse for biotechnological applications[J]. Trends in Biotechnology, 2018, 36(3): 304-317.
7	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.
8	TAKAKU H, MATSUZAWA T, YAOI K, et al. Lipid metabolism of the oleaginous yeast Lipomyces starkeyi[J]. Applied Microbiology and Biotechnology, 2020, 104(14): 6141-6148.
9	XUE Z X, SHARPE PAMELA 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.
10	WANG Y N, ZHANG S F, POTTER M, et al. Overexpression of Delta12-fatty acid desaturase in the oleaginous yeast rhodosporidium toruloides for production of linoleic acid-rich lipids[J]. Applied Biochemistry and Biotechnology, 2016, 180(8): 1497-1507.
11	FILLET S, RONCHEL C, CALLEJO C, et al. Engineering Rhodosporidium toruloides for the production of very long-chain monounsaturated fatty acid-rich oils[J]. Applied Microbiology and Biotechnology, 2017, 101(19): 7271-7280.
12	ZHOU Y J, BUIJS N A, ZHU Z, et al. Harnessing yeast peroxisomes for biosynthesis of fatty-acid-derived biofuels and chemicals with relieved side-pathway competition[J]. Journal of the American Chemical Society, 2016, 138(47): 15368-15377.
13	ZHOU Y J J, BUIJS NICOLAAS A, ZHU Z W, et al. Production of fatty acid-derived oleochemicals and biofuels by synthetic yeast cell factories[J]. Nature Communications, 2016, 7: 11709.
14	YE Y, HUANG Y, XIA A, et al. Optimizing culture conditions for heterotrophic-assisted photoautotrophic biofilm growth of Chlorella vulgaris to simultaneously improve microalgae biomass and lipid productivity[J]. Bioresource Technology, 2018, 270: 80-87.
15	KUMAR S, GUPTA N, PAKSHIRAJAN K. Simultaneous lipid production and dairy wastewater treatment using Rhodococcus opacus in a batch bioreactor for potential biodiesel application[J]. Journal of Environmental Chemical Engineering, 2015, 3(3): 1630-1636.
16	KIM D, LEE J, HWANG Y, et al. Continuous cultivation of photosynthetic bacteria for fatty acids production[J]. Bioresource Technology, 2013, 148: 277-282.
17	ZHENG Y, LI L, LIU Q, et al. Boosting the free fatty acid synthesis of Escherichia coli by expression of a cytosolic Acinetobacter baylyi thioesterase[J]. Biotechnology for Biofuels, 2012, 5(1): 76.
18	DELLOMONACO C, CLOMBURG J M, MILLER E N, et al. Engineered reversal of the beta-oxidation cycle for the synthesis of fuels and chemicals[J]. Nature, 2011, 476(7360): 355-359.
19	XIAO Y, BOWEN C H, LIU D, et al. Exploiting nongenetic cell-to-cell variation for enhanced biosynthesis[J]. Nature Chemical Biology, 2016, 12(5): 339-344.
20	YU T, ZHOU Y J, HUANG M, et al. Reprogramming yeast metabolism from alcoholic fermentation to Lipogenesis[J]. Cell, 2018, 174(6): 1549-1558.
21	BLAZECK J, HILL A, LIU L, et al. Harnessing Yarrowia lipolytica lipogenesis to create a platform for lipid and biofuel production[J]. Nature Communications, 2014, 5: 3131.
22	QIAO K, WASYLENKO T M, ZHOU K, et al. Lipid production in Yarrowia lipolytica is maximized by engineering cytosolic redox metabolism[J]. Nature Biotechnology, 2017, 35(2): 173-177.
23	ZHAO X, HU C M, WU S G, et al. Lipid production by Rhodosporidium toruloides Y4 using different substrate feeding strategies[J]. Journal of Industrial Microbiology & Biotechnology, 2011, 38(5): 627-632.
24	LEE J J L, CHEN L W, CAO B, et al. Engineering Rhodosporidium toruloides with a membrane transporter facilitates production and separation of carotenoids and lipids in a bi-phasic culture[J]. Applied Microbiology and Biotechnology, 2016, 100(2): 869-877.
25	GUO D S, JI X J, REN L J, et al. Development of a multi-stage continuous fermentation strategy for docosahexaenoic acid production by Schizochytrium sp.[J]. Bioresource Technology, 2018, 269: 32-39.
26	SUN X M, REN L J, BI Z Q, et al. Adaptive evolution of microalgae Schizochytrium sp. under high salinity stress to alleviate oxidative damage and improve lipid biosynthesis[J]. Bioresource Technology, 2018, 267: 438-444.
27	MATSAKAS L, A-A STERIOTI, ROVA U, et al. Use of dried sweet sorghum for the efficient production of lipids by the yeast Lipomyces starkeyi CBS 1807[J]. Industrial Crops and Products, 2014, 62: 367-372.
28	HUANG C, CHEN X F, YANG X Y, et al. Bioconversion of corncob acid hydrolysate into microbial oil by the oleaginous yeast Lipomyces starkeyi[J]. Applied Biochemistry and Biotechnology, 2014, 172(4): 2197-2204.
29	HARDE S M, WANG Z, HORNE M, et al. Microbial lipid production from SPORL-pretreated Douglas fir by Mortierella isabellina[J]. Fuel, 2016, 175:64-74.
30	ANNAMALAI N, SIVAKUMAR N, OLESKOWICZ-POPIEL P. Enhanced production of microbial lipids from waste office paper by the oleaginous yeast Cryptococcus curvatus[J]. Fuel, 2018, 217: 420-426.
31	SHEN Q, CHEN Y, LIN H, et al. Agro-industrial waste recycling by Trichosporon fermentans: conversion of waste sweetpotato vines alone into lipid[J]. Environmental Science and Pollution Research, 2018, 25(9): 8793-8799.
32	CHEN J X, ZHANG X L, YAN S, et al. Lipid production from fed-batch fermentation of crude glycerol directed by the kinetic study of batch fermentations[J]. Fuel, 2017, 209:1-9.
33	KARAMEROU E E, THEODOROPOULOS C, WEBB C. Evaluating feeding strategies for microbial oil production from glycerol by Rhodotorula glutinis[J]. Engineering in Life Sciences, 2017, 17(3): 314-324.
34	MILLER K K, ALPER H S. Yarrowia lipolytica: more than an oleaginous workhorse[J]. Applied Microbiology and Biotechnology, 2019, 103(23/24): 9251-9262.
35	MADZAK C, BLANCHIN-ROLAND S, CORDERO OTERO R R, et al. Functional analysis of upstream regulating regions from the Yarrowia lipolytica XPR2 promoter[J]. Microbiology, 1999, 145(Pt 1): 75-87.
36	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.
37	BLAZECK J, LIU L, 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.
38	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.
39	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.
40	DALL M T, NICAUD J M, GAILLARDIN C. Multiple-copy integration in the yeast Yarrowia lipolytica[J]. Current Genetics, 1994, 26(1): 38-44.
41	CHEON S A, HAN E J, KANG H A, et al. Isolation and characterization of the TRP1 gene from the yeast Yarrowia lipolytica and multiple gene disruption using a TRP blaster[J]. Yeast, 2010, 20(8): 677-685.
42	OTERO R C, GAILLARDIN C. Efficient selection of hygromycin-B-resistant Yarrowia lipolytica transformants[J]. Applied Microbiology and Biotechnology, 1996, 46(2): 143-148.
43	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.
44	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.
45	JURETZEK T, LE DALL M, MAUERSBERGER S, et al. Vectors for gene expression and amplification in the yeast Yarrowia lipolytica[J]. Yeast, 2001, 18(2): 97-113.
46	LIU Y, KOH C M J, NGOH S T, et al. Engineering an efficient and tight D-amino acid-inducible gene expression system in Rhodosporidium/Rhodotorula species[J]. Microbial Cell Factories, 2015, 14: 170.
47	JOHNS A M, LOVE J, AVES S J. Four inducible promoters for controlled gene expression in the oleaginous yeast Rhodotorula toruloides[J]. Frontiers in Microbiology, 2016, 7: 1666.
48	WANG Y N, LIN X P, ZHANG S F, et al. Cloning and evaluation of different constitutive promoters in the oleaginous yeast Rhodosporidium toruloides[J]. Yeast, 2016, 33(3): 99-106.
49	LIU Y, YAP S A, KOH C M, et al. Developing a set of strong intronic promoters for robust metabolic engineering in oleaginous Rhodotorula (Rhodosporidium) yeast species[J]. Microbial Cell Factories, 2016, 15(1): 200.
50	DÍAZ T, FILLET S, CAMPOY S, et al. Combining evolutionary and metabolic engineering in Rhodosporidium toruloides for lipid production with non-detoxified wheat straw hydrolysates[J]. Applied Microbiology and Biotechnology, 2018, 102(7): 3287-3300.
51	LIN X P, WANG Y N, ZHANG S F, et al. Functional integration of multiple genes into the genome of the oleaginous yeast Rhodosporidium toruloides[J]. FEMS Yeast Research, 2014, 14(4): 547-555.
52	XUE J, BALAMURUGAN S, LI D W, et al. Glucose-6-phosphate dehydrogenase as a target for highly efficient fatty acid biosynthesis in microalgae by enhancing NADPH supply[J]. Metabolic Engineering, 2017, 41: 212-221.
53	OGURO Y, YAMAZAKI H, SHIDA Y, et al. Multicopy integration and expression of heterologous genes in the oleaginous yeast, Lipomyces starkeyi[J]. Bioscience, Biotechnology, and Biochemistry, 2015, 79(3): 512-515.
54	DAI Z Y, DENG S, CULLEY D E, et al. Agrobacterium tumefaciens-mediated transformation of oleaginous yeast Lipomyces species[J]. Applied Microbiology and Biotechnology, 2017, 101(15): 6099-6110.
55	YAN J F, CHENG R B, LIN X Z, et al. Overexpression of acetyl-CoA synthetase increased the biomass and fatty acid proportion in microalga Schizochytrium[J]. Applied Microbiology and Biotechnology, 2013, 97(5): 1933-1939.
56	LI Z, MENG T, LING X, et al. Overexpression of malonyl-CoA: ACP transacylase in Schizochytrium sp. to improve polyunsaturated fatty acid production[J]. Journal of Agricultural and Food Chemistry, 2018, 66(21): 5382-5391.
57	WANG F, BI Y, DIAO J, et al. Metabolic engineering to enhance biosynthesis of both docosahexaenoic acid and odd-chain fatty acids in Schizochytrium sp. S31[J]. Biotechnology for Biofuels, 2019, 12: 141.
58	JIAO X, ZHANG Y, LIU X, et al. Developing a CRISPR/Cas9 system for genome editing in the basidiomycetous yeast Rhodosporidium toruloides[J]. Biotechnology Journal, 2019, 14(7): e1900036.
59	OTOUPAL P B, ITO M, ARKIN A P, et al. Multiplexed CRISPR-Cas9 based genome editing of Rhodosporidium toruloides[J]. mSphere. 2019, 20;4(2): e00099-19.
60	DAVIDOW L S, APOSTOLAKOS D, O'DONNELL M M, et al. Integrative transformation of the yeast Yarrowia lipolytica[J]. Current Genetics, 1985, 10(1): 39-48.
61	CHEN D C, BECKERICH J M, GAILLARDIN C. One-step transformation of the dimorphic yeast Yarrowia lipolytica[J]. Applied Microbiology and Biotechnology, 1997, 48(2): 232-235.
62	WANG J H, HUNG W, TSAI S H. High efficiency transformation by electroporation of Yarrowia lipolytica[J]. Journal of Microbiology (Seoul, Korea), 2011, 49(3): 469-472.
63	TULLY M, GILBERT H J. Transformation of Rhodosporidium toruloides[J]. Gene, 1985, 36(3): 235-240.
64	LIU Y B, KOH C M J, SUN L H, et al. Characterization of glyceraldehyde-3-phosphate dehydrogenase gene RtGPD1 and development of genetic transformation method by dominant selection in oleaginous yeast Rhodosporidium toruloides[J]. Applied Microbiology and Biotechnology, 2013, 97(2): 719-729.
65	TSAI Y Y, OHASHI T, KANAZAWA T, et al. Development of a sufficient and effective procedure for transformation of an oleaginous yeast, Rhodosporidium toruloides DMKU₃-TK16[J]. Current Genetics, 2017, 63(2): 359-371.
66	ROESSLER P, MATTHEWS T, RAMSEIER T, et al. Product and process for transformation of thraustochytriales microorganisms: US2003166207-A1[P]. 2001.
67	LIPPMEIER J C, CRAWFORD K S, OWEN C B, et al. Characterization of both polyunsaturated fatty acid biosynthetic pathways in Schizochytrium sp.[J]. Lipids, 2009, 44(7): 621-630.
68	CHENG R, MA R, LI K, et al. Agrobacterium tumefaciens mediated transformation of marine microalgae Schizochytrium[J]. Microbiological Research, 2012, 167(3): 179-186.
69	REN L J, ZHUANG X Y, CHEN S L, et al. Introduction of ω-3 desaturase obviously changed the fatty acid profile and sterol content of Schizochytrium sp.[J]. Journal of Agricultural and Food Chemistry, 2015, 63(44): 9770-9776
70	CALVEY C H, WILLIS L B, JEFFRIES T W. An optimized transformation protocol for Lipomyces starkeyi[J]. Current Genetics, 2014, 60(3): 223-230.
71	OGURO Y, YAMAZAKI H, ARA S, et al. Efficient gene targeting in non-homologous end-joining-deficient Lipomyces starkeyi strains[J]. Current Genetics, 2017, 63(4): 751-763.
72	LARROUDE M, ROSSIGNOL T, NICAUD J M, et al. Synthetic biology tools for engineering Yarrowia lipolytica[J]. Biotechnology Advances, 2018, 36(8): 2150-2164.
73	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.
74	SCHWARTZ C, SHABBIR-HUSSAIN M, FROGUE K, et al. Standardized markerless gene integration for pathway engineering in Yarrowia lipolytica[J]. ACS Synthetic Biology, 2017, 6(3): 402-409.
75	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.
76	VANDERMIES M, DENIES O, NICAUD J M, et al. EYK₁ encoding erythrulose kinase as a catabolic selectable marker for genome editing in the non-conventional yeast Yarrowia lipolytica[J]. Journal of Microbiological Methods, 2017, 139: 161-164.
77	LARROUDE M, PARK Y K, SOUDIER P, et al. A modular Golden Gate toolkit for Yarrowia lipolytica synthetic biology[J]. Microbial Biotechnology, 2019, 12(6): 1249-1259.
78	WONG L, ENGEL J, JIN E, et al. YaliBricks, a versatile genetic toolkit for streamlined and rapid pathway engineering in Yarrowia lipolytica[J]. Metabolic Engineering Communications, 2017, 5: 68-77.
79	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.
80	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.
81	SCHWARTZ C M, HUSSAIN M S, BLENNER M, et al. Synthetic RNA polymerase III promoters facilitate high-efficiency CRISPR-Cas9-mediated genome editing in Yarrowia lipolytica[J]. ACS Synthetic Biology, 2016, 5(4): 356-359.
82	GAO D, 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.
83	ABDEL-MAWGOUD A M, STEPHANOPOULOS G. Improving CRISPR/Cas9-mediated genome editing efficiency in Yarrowia lipolytica using direct tRNA-sgRNA fusions[J]. Metabolic Engineering, 2020, 62: 106-115.
84	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.
85	RICHARD G F, KERREST A, LAFONTAINE I, et al. Comparative genomics of hemiascomycete yeasts: genes involved in DNA replication, repair, and recombination[J]. Molecular Biology and Evolution, 2005, 22(4): 1011-1023.
86	KRETZSCHMAR A, OTTO C, HOLZ M, et al. Increased homologous integration frequency in Yarrowia lipolytica strains defective in non-homologous end-joining[J]. Current Genetics, 2013, 59(1/2): 63-72.
87	VERBEKE J, BEOPOULOS A, NICAUD J M. Efficient homologous recombination with short length flanking fragments in Ku70 deficient Yarrowia lipolytica strains[J]. Biotechnology Letters, 2013, 35(4): 571-576.
88	SCHULTZ J C, CAO M F, ZHAO H M. Development of a CRISPR/Cas9 system for high efficiency multiplexed gene deletion in Rhodosporidium toruloides[J]. Biotechnology and Bioengineering, 2019, 116(8): 2103-2109.
89	SUN W Y, YANG X B, WANG X Y, et al. Developing a flippase-mediated maker recycling protocol for the oleaginous yeast Rhodosporidium toruloides[J]. Biotechnology Letters, 2018, 40(6): 933-940.
90	孙文怡. 基于农杆菌介导的圆红冬孢酵母遗传重组系统的研究[D].大连: 大连理工大学, 2017.
	SUN W Y. Agrobacterium-mediated genetic transformation-based genetic recombination system for Rhodosporidium toruloides[D]. Dalian: Dalian University of Technology, 2017.
91	FILLET S C, GONZÁLEZ B S, BARRENO M C R, et al. Production of microbial oils with an elevated oleic acid content: WO2016185073A1[P]. 2016.
92	KOH C M, LIU Y B, MOEHNINSI, et al. Molecular characterization of KU70 and KU80 homologues and exploitation of a KU70-deficient mutant for improving gene deletion frequency in Rhodosporidium toruloides[J]. BMC Microbiology, 2014, 14: 50.
93	GAO S L, HAN L N, ZHU L, et al. One-step integration of multiple genes into the oleaginous yeast Yarrowia lipolytica[J]. Biotechnology Letters, 2014, 36(12): 2523-2528.
94	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.
95	SCHWARTZ C, WHEELDON I. CRISPR-Cas9-mediated genome editing and transcriptional control in Yarrowia lipolytica[J]. Methods in Molecular Biology, 2018, 1772: 327-345.
96	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.
97	SCHWARTZ C, CURTIS N, LÖBS A K, et al. Multiplexed CRISPR activation of cryptic sugar metabolism enables Yarrowia lipolytica growth on cellobiose[J]. Biotechnology Journal, 2018, 13(9): e1700584.
98	YANG Z, EDWARDS H, XU P. CRISPR-Cas12a/Cpf1-assisted precise, efficient and multiplexed genome-editing in Yarrowia lipolytica[J]. Metabolic Engineering Communications, 2020, 10: e00112.
99	SUN W Y, YANG X B, WANG X Y, et al. Homologous gene targeting of a carotenoids biosynthetic gene in Rhodosporidium toruloides by Agrobacterium-mediated transformation[J]. Biotechnology Letters, 2017, 39(7): 1001-1007.
100	ZHANG S, HE Y, SEN B, et al. Alleviation of reactive oxygen species enhances PUFA accumulation in Schizochytrium sp. through regulating genes involved in lipid metabolism[J]. Metabolic Engineering Communications, 2018, 6: 39-48.
101	HAN X, ZHAO Z N, WEN Y, et al. Enhancement of docosahexaenoic acid production by overexpression of ATP-citrate lyase and acetyl-CoA carboxylase in Schizochytrium sp.[J]. Biotechnology for Biofuels2020, 13(1): 131.
102	JI X J, HUANG H. Engineering microbes to produce polyunsaturated fatty acids[J]. Trends in Biotechnology, 2019, 37(4): 344-346.
103	WANG J, LEDESMA-AMARO R, WEI Y, et al. Metabolic engineering for increased lipid accumulation in Yarrowia lipolytica-a review[J]. Bioresource Technology, 2020, 313: 123707.
104	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.
105	GU Y, XU P. Synthetic yeast brews neuroactive compounds[J]. Nature Chemical Biology, 2021, 17: 8-9.
106	MARKHAM K A, ALPER H S. Synthetic biology expands the industrial potential of Yarrowia lipolytica[J]. Trends in Biotechnology, 2018, 36(10): 1085-1095.
107	QIU X, XU P, ZHAO X, 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.
108	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.
109	GU Y, MA J, ZHU Y, 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.
110	GU Y, MA J, ZHU Y, et al. Refactoring Ehrlich pathway for high-yield 2-phenylethanol production in Yarrowia lipolytica[J]. ACS Synthetic Biology, 2020, 9(3): 623-633.
111	MATTHÄUS F, KETELHOT M, GATTER M, et al. Production of lycopene in the non-carotenoid-producing yeast Yarrowia lipolytica[J]. Applied and Environmental Microbiology, 2014, 80(5): 1660-1669.
112	KILDEGAARD K R, ADIEGO-PÉREZ B, DOMÉNECH BELDA D, et al. Engineering of Yarrowia lipolytica for production of astaxanthin[J]. Synthetic and Systems Biotechnology, 2017, 2(4): 287-294.
113	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): 1-11.
114	CAO X, WEI L J, LIN J Y, et al. Enhancing linalool production by engineering oleaginous yeast Yarrowia lipolytica[J]. Bioresource Technology, 2017, 245(pt b): 1641-1644.
115	XUE Z X, HE H X, HOLLERBACH D, et al. Identification and characterization of new Δ-17 fatty acid desaturases[J]. Applied Microbiology and Biotechnology, 2013, 97(5): 1973-1985.
116	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.
117	GAO Q, YANG J L, ZHAO X R, et al. Yarrowia lipolytica as a metabolic engineering platform for the production of very-long-chain wax esters[J]. Journal of Agricultural and Food Chemistry, 2020, 68(39): 10730-10740.
118	DOUROU M, AGGELI D, PAPANIKOLAOU S, et al. Critical steps in carbon metabolism affecting lipid accumulation and their regulation in oleaginous microorganisms[J]. Applied Microbiology and Biotechnology, 2018, 102(6): 2509-2523.
119	DULERMO T, NICAUD J M. Involvement of the G3P shuttle and β-oxidation pathway in the control of TAG synthesis and lipid accumulation in Yarrowia lipolytica[J]. Metabolic Engineering, 2011, 13(5): 482-491.
120	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.
121	LEDESMA-AMARO R, NICAUD J M. Yarrowia lipolytica as a biotechnological chassis to produce usual and unusual fatty acids[J]. Progress in Lipid Research, 2016, 61: 40-50.
122	LAZAR Z, LIU N, STEPHANOPOULOS G. Holistic approaches in lipid production by Yarrowia lipolytica[J]. Trends in Biotechnology, 2018, 36(11): 1157-1170.
123	ATHENSTAEDT K, JOLIVET P, BOULARD C, et al. Lipid particle composition of the yeast Yarrowia lipolytica depends on the carbon source[J]. Proteomics, 2006, 6(5): 1450-1459.
124	XU P, LI L, ZHANG F, et al. Improving fatty acids production by engineering dynamic pathway regulation and metabolic control[J]. Proceedings of the National Academy of Sciences of the United States of America, 2014, 111(31): 11299-11304.
125	YUZBASHEVA E Y, MOSTOVA E B, ANDREEVA N I, et al. A metabolic engineering strategy for producing free fatty acids by the Yarrowia lipolytica yeast based on impairment of glycerol metabolism[J]. Biotechnology and Bioengineering, 2018, 115(2): 433-443.
126	WANG G, LI D, MIAO Z, et al. Comparative transcriptome analysis reveals multiple functions for Mhy1p in lipid biosynthesis in the oleaginous yeast Yarrowia lipolytica[J]. Biochimica et Biophysica Acta Molecular and Cell Biology of Lipids, 2018, 1863(1): 81-90.
127	NIEHUS X, CRUTZ-LE COQ A M, SANDOVAL G, et al. Engineering Yarrowia lipolytica to enhance lipid production from lignocellulosic materials[J]. Biotechnology for Biofuels, 2018, 11: 11.
128	GAJDOŠ P, NICAUD J M, ČERT K M. Glycerol conversion into a single cell oil by engineered Yarrowia lipolytica[J]. Engineering in Life Sciences, 2017, 17(3): 325-332.
129	YUZBASHEVA E Y, MOSTOVA E B, ANDREEVA N I, et al. Co-expression of glucose-6-phosphate dehydrogenase and acyl-CoA binding protein enhances lipid accumulation in the yeast Yarrowia lipolytica[J]. New Biotechnology, 2017, 39(pt a): 18-21.
130	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.
131	XU P, QIAO K, STEPHANOPOULOS G. Engineering oxidative stress defense pathways to build a robust lipid production platform in Yarrowia lipolytica [J]. Biotechnology and Bioengineering, 2017, 114(7): 1521-1530.
132	WANG G, XIONG X, GHOGARE R, et al. Exploring fatty alcohol-producing capability of Yarrowia lipolytica[J]. Biotechnology for Biofuels, 2016, 9: 107.
133	XU P, QIAO K, AHN W S, et al. Engineering Yarrowia lipolytica as a platform for synthesis of drop-in transportation fuels and oleochemicals[J]. Proceedings of the National Academy of Sciences of the United States of America, 2016, 113(39): 10848-10853.
134	GAO C J, QI Q S, MADZAK C, et al. Exploring medium-chain-length polyhydroxyalkanoates production in the engineered yeast Yarrowia lipolytica[J]. Journal of Industrial Microbiology & Biotechnology, 2015, 42(9): 1255-1262.
135	QIAO K, IMAM ABIDI S H, LIU H, et al. Engineering lipid overproduction in the oleaginous yeast Yarrowia lipolytica[J]. Metabolic Engineering, 2015, 29: 56-65.
136	DULERMO T, LAZAR Z, DULERMO R, et al. Analysis of ATP-citrate lyase and malic enzyme mutants of Yarrowia lipolytica points out the importance of mannitol metabolism in fatty acid synthesis[J]. Biochimica et Biophysica Acta, 2015, 1851(9): 1107-1117.
137	LEDESMA-AMARO R, LOZANO-MARTÍNEZ P, JIMÉNEZ A, et al. Engineering Ashbya gossypii for efficient biolipid production[J]. Bioengineered, 2015, 6(2): 119-123.
138	GAO Q, CAO X, HUANG Y Y, et al. Overproduction of fatty acid ethyl esters by the oleaginous yeast Yarrowia lipolytica through metabolic engineering and process optimization[J]. ACS Synthetic Biology, 2018, 7(5): 1371-1380.
139	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.
140	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.
141	BELLOU S, TRIANTAPHYLLIDOU I E, MIZERAKIS P, et al. High lipid accumulation in Yarrowia lipolytica cultivated under double limitation of nitrogen and magnesium[J]. Journal of Biotechnology, 2016, 234: 116-126.
142	WASYLENKO T M, AHN W S, STEPHANOPOULOS G. The oxidative pentose phosphate pathway is the primary source of NADPH for lipid overproduction from glucose in Yarrowia lipolytica[J]. Metabolic Engineering, 2015, 30: 27-39.
143	ZHANG H Y, ZHANG L N, CHEN H Q, et al. Regulatory properties of malic enzyme in the oleaginous yeast, Yarrowia lipolytica, and its non-involvement in lipid accumulation[J]. Biotechnology Letters, 2013, 35(12): 2091-2098.
144	DULERMO T, TR TON B, BEOPOULOS A, et al. 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 organisation[J]. Biochimica et Biophysica Acta, 2013, 1831(9): 1486-1495.
145	MAUERSBERGER S, WANG H J, GAILLARDIN C, et al. Insertional mutagenesis in the n-alkane-assimilating yeast Yarrowia lipolytica: generation of tagged mutations in genes involved in hydrophobic substrate utilization[J]. Journal of Bacteriology, 2001, 183(17): 5102-5109.
146	JI X J, LEDESMA-AMARO R. Microbial lipid biotechnology to produce polyunsaturated fatty acids[J]. Trends in Biotechnology, 2020, 38(8): 832-834
147	HONDA D, YOKOCHI T, NAKAHARA T, et al. Molecular phylogeny of labyrinthulids and thraustochytrids based on the sequencing of 18S ribosomal RNA gene[J]. The Journal of Eukaryotic Microbiology, 1999, 46(6): 637-647.
148	YOKOYAMA R, SALLEH B, HONDA D. Taxonomic rearrangement of the genus Ulkenia sensu lato based on morphology, chemotaxonomical characteristics, and 18S rRNA gene phylogeny (Thraustochytriaceae, Labyrinthulomycetes): emendation for Ulkenia and erection of Botryochytrium, Parietichytrium, and Sicyoidochytrium gen. nov[J]. Mycoscience, 2007, 48(6): 329-341.
149	YOKOYAMA R, HONDA D. Taxonomic rearrangement of the genus Schizochytrium sensu lato based on morphology, chemotaxonomic characteristics, and 18S rRNA gene phylogeny (Thraustochytriaceae, Labyrinthulomycetes): emendation for Schizochytrium and erection of Aurantiochytrium and Oblongichytrium gen. nov[J]. Mycoscience, 2007, 48(4): 199-211.
150	SUN X M, XU Y S, HUANG H. Thraustochytrid cell factories for producing lipid compounds[J]. Trends in Biotechnology, 2021, 39(7): 648-650.
151	JI X J, REN L J, HUANG H. Omega-3 biotechnology: a green and sustainable process for omega-3 fatty acids production[J]. Frontiers in Bioengineering and Biotechnology, 2015, 3: 158.
152	BARCLAY W, WEAVER C, METZ J, et al. Development of a docosahexaenoic acid production technology using Schizochytrium: historical perspective and update[M]. Urbana, Illinois: AOCS Press, 2010: 75-96.
153	AASEN I M, ERTESVÅG H, HEGGESET T M B, et al. Thraustochytrids as production organisms for docosahexaenoic acid (DHA), squalene, and carotenoids[J]. Applied Microbiology and Biotechnology, 2016, 100(10): 4309-4321.
154	HAUVERMALE A, KUNER J, ROSENZWEIG B, et al. Fatty acid production in Schizochytrium sp.: involvement of a polyunsaturated fatty acid synthase and a type I fatty acid synthase[J]. Lipids, 2006, 41(8): 739-747.
155	RATLEDGE C. Fatty acid biosynthesis in microorganisms being used for Single Cell Oil production[J]. Biochimie, 2004, 86(11): 807-815.
156	MEESAPYODSUK D, QIU X. Biosynthetic mechanism of very long chain polyunsaturated fatty acids in Thraustochytrium sp. 26185[J]. Journal of Lipid Research, 2016, 57(10): 1854-1864.
157	GUO D S, JI X J, REN L J, et al. Development of a scale-up strategy for fermentative production of docosahexaenoic acid by Schizochytrium sp.[J]. Chemical Engineering Science, 2018, 176: 600-608.
158	CHEN C Y, YANG Y T. Combining engineering strategies and fermentation technology to enhance docosahexaenoic acid (DHA) production from an indigenous Thraustochytrium sp. BM2 strain[J]. Biochemical Engineering Journal, 2018, 179-185.
159	HUANG Z R, LIN Y K, FANG J Y. Biological and pharmacological activities of squalene and related compounds: Potential uses in cosmetic dermatology[J]. Molecules, 2009, 14(1): 540-554.
160	NAKAZAWA A, MATSUURA H, KOSE R, et al. Optimization of culture conditions of the thraustochytrid Aurantiochytrium sp. strain 18W-13a for squalene production[J]. Bioresource Technology, 2012, 109: 287-291.
161	NAKAZAWA A, KOKUBUN Y, MATSUURA H, et al. TLC screening of thraustochytrid strains for squalene production[J]. Journal of Applied Phycology, 2014, 26(1): 29-41.
162	REN L J, SUN G N, JI X J, et al. Compositional shift in lipid fractions during lipid accumulation and turnover in Schizochytrium sp.[J]. Bioresource Technology, 2014, 157: 107-113.
163	BERMAN J, ZORRILLA-LÓPEZ U, FARRÉ G, et al. Nutritionally important carotenoids as consumer products[J]. Phytochemistry Reviews, 2015, 14(5): 727-743.
164	ARMENTA R E, BURJA A, RADIANINGTYAS H, et al. Critical assessment of various techniques for the extraction of carotenoids and co-enzyme Q10 from the Thraustochytrid strain ONC-T18[J]. Journal of Agricultural and Food Chemistry, 2006, 54(26): 9752-9758.
165	CARMONA M L, NAGANUMA T, YAMAOKA Y. Identification by HPLC-MS of carotenoids of the Thraustochytrium CHN-1 strain isolated from the seto inland sea[J]. Bioscience, Biotechnology, and Biochemistry, 2003, 67(4): 884-888.
166	AKI T, HACHIDA K, YOSHINAGA M, et al. Thraustochytrid as a potential source of carotenoids[J]. Journal of the American Oil Chemists' Society, 2003, 80(8): 789-794.
167	BENITA Quilodrán, HINZPETER Ivonne, HORMAZABAL Emilio, et al. Docosahexaenoic acid (C22:6n-3, DHA) and astaxanthin production by Thraustochytriidae sp. AS4-A1 a native strain with high similitude to Ulkenia sp.: evaluation of liquid residues from food industry as nutrient sources[J]. Enzyme & Microbial Technology, 2010, 47(1/2): 24-30.
168	GAO S L, TONG Y Y, ZHU L, et al. Production of β-carotene by expressing a heterologous multifunctional carotene synthase in Yarrowia lipolytica[J]. Biotechnology Letters, 2017, 39(6): 1-7.
169	GAO S L, TONG Y Y, ZHU L, et al. Iterative integration of multiple-copy pathway genes in Yarrowia lipolytica for heterologous β-carotene production[J]. Metabolic Engineering, 2017, 41: 192-201.
170	SCHWARTZ C, FROGUE K, MISA J, et al. Host and pathway engineering for enhanced Lycopene biosynthesis in Yarrowia lipolytica[J]. Frontiers in Microbiology, 2017, 8: 2233.

菌株	底物	油脂产量/（g/L）	生产强度/[g/（L·h）]	文献
Chlorella vulgaris	CO₂/葡萄糖	41.95	0.583	[14]
Rhodococcus opacus	乳制品废水	2.2	0.023	[15]
Rhodobacter sphaeroides	乳酸/光照	—	0.028	[16]
Escherichia coli	葡萄糖	3.6	0.075	[17]
E. coli	葡萄糖	7.0	0.12	[18]
E. coli	葡萄糖	21.5	0.5	[19]
Saccharomyces cerevisiae	葡萄糖	10.4	0.087	[13]
S. cerevisiae	葡萄糖	33.4	0.17	[20]
Yarrowia lipolytica	葡萄糖	15.25	0.105	[21]
Y. lipolytica	葡萄糖	98.9	1.2	[22]
Rhodosporidium toruloides	葡萄糖	78.7	0.57	[23]
R. toruloides	葡萄糖	89.4	0.62	[24]
Schizochytrium sp.	葡萄糖	55.3	0.46	[25]
Schizochytrium sp.	葡萄糖	80.14	0.53	[26]
Lipomyces starkeyi	甜高粱茎汁	6.4	0.033	[27]
L. starkeyi	玉米棒芯水解液	8.1	0.042	[28]
Mortierella isabellina	冷杉木水解液	18.55	0.086	[29]
Cryptococcus curvatus	废纸水解液	5.75	0.08	[30]
Trichosporon fermentans	甘薯藤水解液	6.98	0.024	[31]
Trichosporon oleaginosus	生物柴油副产物	21.87		[32]
Rhodotorula glutinis	纯甘油	16.28	0.1	[33]

菌株	底物	油脂产量/（g/L）	生产强度/[g/（L·h）]	文献
Chlorella vulgaris	CO₂/葡萄糖	41.95	0.583	[14]
Rhodococcus opacus	乳制品废水	2.2	0.023	[15]
Rhodobacter sphaeroides	乳酸/光照	—	0.028	[16]
Escherichia coli	葡萄糖	3.6	0.075	[17]
E. coli	葡萄糖	7.0	0.12	[18]
E. coli	葡萄糖	21.5	0.5	[19]
Saccharomyces cerevisiae	葡萄糖	10.4	0.087	[13]
S. cerevisiae	葡萄糖	33.4	0.17	[20]
Yarrowia lipolytica	葡萄糖	15.25	0.105	[21]
Y. lipolytica	葡萄糖	98.9	1.2	[22]
Rhodosporidium toruloides	葡萄糖	78.7	0.57	[23]
R. toruloides	葡萄糖	89.4	0.62	[24]
Schizochytrium sp.	葡萄糖	55.3	0.46	[25]
Schizochytrium sp.	葡萄糖	80.14	0.53	[26]
Lipomyces starkeyi	甜高粱茎汁	6.4	0.033	[27]
L. starkeyi	玉米棒芯水解液	8.1	0.042	[28]
Mortierella isabellina	冷杉木水解液	18.55	0.086	[29]
Cryptococcus curvatus	废纸水解液	5.75	0.08	[30]
Trichosporon fermentans	甘薯藤水解液	6.98	0.024	[31]
Trichosporon oleaginosus	生物柴油副产物	21.87		[32]
Rhodotorula glutinis	纯甘油	16.28	0.1	[33]

菌株	工具	原理	载体	转化方法	文献
Yarrowia lipolytica	Golden Gate或Biobrick体外多片段组装；	体外分子砌块组装，体内同源重组（双交换）	线性化质粒	醋酸锂转化	[77-78]
Y. lipolytica	体内多片段组装	同源重组（双交换）	线性化DNA片段	醋酸锂转化	[93]
Y. lipolytica	Cre-lox重组酶系统	位点特异性重组	复制型质粒	醋酸锂转化	[75-76]
Y. lipolytica	基于rDNA或zeta位点的多拷贝整合	同源重组（单交换或双交换）	自杀质粒或者线性化片段	醋酸锂转化	[45, 79]
Y. lipolytica	染色体随机整合	非同源末端连接	线性化片段	醋酸锂转化	[94]
Y. lipolytica	CRISPR/Cas9介导的基因编辑，单基因或多基因敲除、整合	Cas9切割基因组后，宿主启动同源重组及非同源末端连接修复	复制型质粒	醋酸锂转化或电转化	[74,80-83]
Y. lipolytica	CRISPR/dCas9介导的转录抑制	失去切割活性的Cas9结合在靶标序列可阻碍转录正常进行	复制型质粒	醋酸锂转化	[95-96]
Y. lipolytica	CRISPR/dCas9介导的转录激活	失去切割活性的Cas9结合在启动子区域，招募激活因子后可上调转录	复制型质粒	醋酸锂转化	[97]
Y. lipolytica	CRISPR/Cpf1介导的基因编辑	Cas9切割基因组后，宿主进行非同源末端连接修复	复制型质粒	醋酸锂转化	[98]
Y. lipolytica	CRISPR/Cas9辅助的碱基编辑系统	胞嘧啶脱氨酶作用后，宿主碱基对由C-G转变为T-A	复制型质粒	醋酸锂转化	[84]
Rhodosporidium toruloides	CRISPR/Cas9基因编辑，单基因或多基因敲除	非同源末端连接	Ti质粒	农杆菌介导转化	[88]
R. toruloides	CRISPR/Cas9基因编辑，单基因或多基因敲除	非同源末端连接	自杀质粒	醋酸锂化学转化	[59]
R. toruloides	CRISPR/Cas9基因编辑，单基因或整合，多基因敲除	非同源末端连接或同源重组	Ti质粒	农杆菌介导转化	[58]
R. toruloides	等位基因替换	同源重组（双交换）	Ti质粒	农杆菌介导转化	[92, 99]
R. toruloides	重组酶系统(Cre-loxP, Flipase-FRT, I-SceI）	位点特异性重组	自杀质粒或Ti质粒	农杆菌介导转化或PEG介导原生质体转化	[89-91]
R. toruloides	染色体随机整合	非同源末端连接	Ti质粒	农杆菌介导转化	[51, 64]
R. toruloides	染色体随机整合	非同源末端连接	自杀质粒	PEG介导原生质体转化	[63]
R. toruloides	染色体随机整合	非同源末端连接	线性化DNA片段	电转化	[52]
Schizochytrium sp.	染色体定点整合	同源重组（双交换）	（线性化的）自杀质粒	电穿孔转化	[56-57,69, 100]
Schizochytrium sp. TIO1101	染色体定点整合	同源重组（单交换）	线性化自杀质粒	电穿孔转化	[55]
Schizochytrium sp.	染色体随机整合	非同源末端连接	线性化自杀质粒	电穿孔转化	[101]
Schizochytrium sp.	染色体随机整合	非同源末端连接	Ti质粒	农杆菌介导转化	[68]
Lipomyces starkeyi	染色体随机整合	非同源末端连接	Ti质粒	农杆菌介导转化	[54]
L. starkeyi	染色体定点整合	同源重组（双交换）	线性化的自杀质粒	PEG介导原生质体转化	[53, 71]

菌株	工具	原理	载体	转化方法	文献
Yarrowia lipolytica	Golden Gate或Biobrick体外多片段组装；	体外分子砌块组装，体内同源重组（双交换）	线性化质粒	醋酸锂转化	[77-78]
Y. lipolytica	体内多片段组装	同源重组（双交换）	线性化DNA片段	醋酸锂转化	[93]
Y. lipolytica	Cre-lox重组酶系统	位点特异性重组	复制型质粒	醋酸锂转化	[75-76]
Y. lipolytica	基于rDNA或zeta位点的多拷贝整合	同源重组（单交换或双交换）	自杀质粒或者线性化片段	醋酸锂转化	[45, 79]
Y. lipolytica	染色体随机整合	非同源末端连接	线性化片段	醋酸锂转化	[94]
Y. lipolytica	CRISPR/Cas9介导的基因编辑，单基因或多基因敲除、整合	Cas9切割基因组后，宿主启动同源重组及非同源末端连接修复	复制型质粒	醋酸锂转化或电转化	[74,80-83]
Y. lipolytica	CRISPR/dCas9介导的转录抑制	失去切割活性的Cas9结合在靶标序列可阻碍转录正常进行	复制型质粒	醋酸锂转化	[95-96]
Y. lipolytica	CRISPR/dCas9介导的转录激活	失去切割活性的Cas9结合在启动子区域，招募激活因子后可上调转录	复制型质粒	醋酸锂转化	[97]
Y. lipolytica	CRISPR/Cpf1介导的基因编辑	Cas9切割基因组后，宿主进行非同源末端连接修复	复制型质粒	醋酸锂转化	[98]
Y. lipolytica	CRISPR/Cas9辅助的碱基编辑系统	胞嘧啶脱氨酶作用后，宿主碱基对由C-G转变为T-A	复制型质粒	醋酸锂转化	[84]
Rhodosporidium toruloides	CRISPR/Cas9基因编辑，单基因或多基因敲除	非同源末端连接	Ti质粒	农杆菌介导转化	[88]
R. toruloides	CRISPR/Cas9基因编辑，单基因或多基因敲除	非同源末端连接	自杀质粒	醋酸锂化学转化	[59]
R. toruloides	CRISPR/Cas9基因编辑，单基因或整合，多基因敲除	非同源末端连接或同源重组	Ti质粒	农杆菌介导转化	[58]
R. toruloides	等位基因替换	同源重组（双交换）	Ti质粒	农杆菌介导转化	[92, 99]
R. toruloides	重组酶系统(Cre-loxP, Flipase-FRT, I-SceI）	位点特异性重组	自杀质粒或Ti质粒	农杆菌介导转化或PEG介导原生质体转化	[89-91]
R. toruloides	染色体随机整合	非同源末端连接	Ti质粒	农杆菌介导转化	[51, 64]
R. toruloides	染色体随机整合	非同源末端连接	自杀质粒	PEG介导原生质体转化	[63]
R. toruloides	染色体随机整合	非同源末端连接	线性化DNA片段	电转化	[52]
Schizochytrium sp.	染色体定点整合	同源重组（双交换）	（线性化的）自杀质粒	电穿孔转化	[56-57,69, 100]
Schizochytrium sp. TIO1101	染色体定点整合	同源重组（单交换）	线性化自杀质粒	电穿孔转化	[55]
Schizochytrium sp.	染色体随机整合	非同源末端连接	线性化自杀质粒	电穿孔转化	[101]
Schizochytrium sp.	染色体随机整合	非同源末端连接	Ti质粒	农杆菌介导转化	[68]
Lipomyces starkeyi	染色体随机整合	非同源末端连接	Ti质粒	农杆菌介导转化	[54]
L. starkeyi	染色体定点整合	同源重组（双交换）	线性化的自杀质粒	PEG介导原生质体转化	[53, 71]

工程菌	宿主	遗传操作	产物	产量	底物	培养方式
S14G19O-ACC1 Y-4311^a[125]	ATCC 20460	敲除甘油-3-磷酸脱氢酶（Gpd1和Gut2）和氧化物酶体基质蛋白Pex10；过表达乙酰辅酶A羧化酶 ACC1	游离脂肪酸	2.03 g/L	甘油和正十二烷	摇瓶
M-MHY1^[126]	ACA-DC 50109	敲除C2H2锌指蛋白Mhy1	三乙酰甘油酯	43.1% (DCW)	葡萄糖	摇瓶
ylXYL+Obese-XA^[127]	PO1d	敲除酰基辅酶A氧化酶（POX1-6）和脂肪酶Tgl4；过表达DAG酰基转移酶DGA1、磷酸转酮酶XPKA、乙酸激酶ACK、乙酰辅酶A合成酶ACS2、磷酸转乙酰酶XA、木糖还原酶XR、木糖醇脱氢酶XDH和木酮糖激酶XK	三乙酰甘油酯	16.5 g/L	蔗糖	发酵罐
JMY3580^[128]	ATCC 20460	敲除DAG酰基转移酶（Dga1、Dga2和Lro1）和酰基辅酶A甾醇酰基转移酶；过表达DAG酰基转移酶DGA2	脂肪酸	9.9 g/L	甘油	摇瓶
ADgm-hi^a[22]	Po1g	过表达乙酰辅酶A羧化酶 ACC1、DAG酰基转移酶DGA1、NAD⁺激酶YEF和3-磷酸甘油醛脱氢酶GapC	脂肪酸甲酯	98.9 g/L	葡萄糖	发酵罐
W29 (Dpex10 ZWF1 ACBP)^[129]	ATCC 20460	敲除氧化物酶体基质蛋白Pex10；过表达葡萄糖-6-磷酸脱氢酶ZWF	三乙酰甘油酯	30% (DCW)	葡萄糖	摇瓶
Po1f-6-D^[130]	PO1f	过表达来源Mortierella alpina的Δ6去饱和酶	γ-亚油酸	71.6 mg/L	葡萄糖	摇瓶
ALDH^[131]	PO1g	过表达乙酰辅酶A羧化酶ACC1、DAG酰基转移酶DGA1、醛脱氢酶EcAldH（来源于E. coli）、葡萄糖-6-磷酸脱氢酶ZWF（来源于S. cerevisiae）、谷胱甘肽二硫还原酶GSR和硫氧还蛋白还原酶TRX	三乙酰甘油酯	72.7 g/L	葡萄糖	发酵罐
Tafar1-5copy-Δdga1 fao1^[132]	PO1f	敲除DAG酰基转移酶Dga1和脂肪醇氧化酶Fao1；过表达脂肪酰辅酶A还原酶Tafar1	脂肪醇	690.21 mg/L	甘油	发酵罐
AD pYLXP-ylFAS1-EcTesA^[133]	PO1g	表达脂肪酸合酶FAS1和硫脂酶EcTesA（来源于E. coli）	游离脂肪酸	9.67 g/L	葡萄糖	发酵罐
AD pYLXP-AbAtfA-scCat2^[133]	PO1g	表达蜡酯合酶AbAtfA（来源于A. baylyi ADP1）和肉碱乙酰转移酶scCat2	脂肪酸乙酯	142.5 mg/L	葡萄糖	摇瓶
AD pYLXP- Maqu2220-EcfadD^[133]	PO1g	表达脂酰辅酶A合成酶Maqu2220和EcfadD（来源于Marinobacter aquaeolei和E. coli）	脂肪酸醇	2.15 g/L	葡萄糖	摇瓶
AD pYLXP-MmCAR-BsuSfp-PmADO^[133]	PO1g	表达羧酸还原酶MmCAR（来源于M. marinum）、磷酸泛酰巯基乙胺基转移酶BsuSfp（来源于Bacillus subtilis）和醛脱甲氧化酶PmADO（Prochlorococcus marinus）	脂肪烷烃	23.3 mg/L	葡萄糖	摇瓶
AD pYLXP-ylACC1-ylDGA1-scCat2^[133]	PO1g	表达乙酰辅酶A羧化酶ACC1、DAG酰基转移酶DGA1和肉碱乙酰转移酶Cat2	三乙酰甘油酯	66.4 g/L	葡萄糖	发酵罐
PMOC^[134]	PO1h	表达聚羟基脂肪酸合成酶PhaC1	聚羟基链烷酸酯	1.11 g/L	正十二烷	摇瓶
YL-ad9^[135]	PO1f	过表达乙酰辅酶A羧化酶 ACC1、DAG酰基转移酶DGA1和硬脂酰辅酶A去饱和酶SCD	三乙酰甘油酯	55 g/L	葡萄糖	发酵罐
Y4305^[9]	ATCC 20362	敲除氧化物酶体基质蛋白Pex10、脂肪酶1、固醇载体蛋白scp2和未知功能基因yali0c1871；过表达C_16/18延伸酶和Δ12、Δ9、Δ8、Δ5和Δ17去饱和酶	ω-3 二十碳五烯酸	15%(DCW)	葡萄糖	摇瓶