Review Open Access

Development and Perspective of Production of Terpenoids in Yeast

Synthetic Biology and Engineering. 2024, 2(1), 10003; https://doi.org/10.35534/sbe.2024.10003
Yaying Xia ,†    Congna Li ,†    Ruidi Cao    Lu Qin    Shuobo Shi *   
Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
Yaying Xia and Congna Li contributed equally.
*
Authors to whom correspondence should be addressed.

Received: 05 Jan 2024    Accepted: 02 Feb 2024    Published: 13 Feb 2024   

Abstract

Terpenoids are a large class of secondary metabolites known for their remarkable diverse biological activities, making them widely utilized in the pharmaceutical, food, cosmetic, biofuel and agricultural fields. However, the current production of terpenoids heavily relies on plant extraction and chemical synthesis, which brings about concerns regarding infield, environmental and ecological issues. With the advancements in metabolic engineering and emerging synthetic biology tools, it is now possible to sustainably produce these high value-added terpenoids using microbial chassis. Among them, yeast has emerged as a promising candidate for the heterologous biosynthesis of terpenoids due to its inherent advantages, including robustness, safety, and the availability of sufficient precursor. This review focuses on the diverse strategies employed to enable terpenoids production in yeasts. These strategies encompass metabolic engineering approaches to optimize the mevalonate pathway, protein engineering techniques to improve terpenoid biosynthesis, the applications of organelles compartmentalization, high throughput screening and global approaches for the development of efficient cell factories. Furthermore, this review discusses the future prospects and challenges associated with yeast-based terpenoid production, while also emphasizing guidelines for future studies in this field.

References

1.
Zhang Y, Nielsen J, Liu Z. Engineering yeast metabolism for production of terpenoids for use as perfume ingredients, pharmaceuticals and biofuels. FEMS Yeast Res. 2017, 17, fox080. [Google Scholar]
2.
Jiang G, Yao M, Wang Y, Xiao W, Yuan Y. A “push-pull-restrain” strategy to improve citronellol production in Saccharomyces cerevisiae. Metab. Eng. 2021, 66, 51–59. [Google Scholar]
3.
Meng X, Liu H, Xu W, Zhang W, Wang Z, Liu W. Metabolic engineering Saccharomyces cerevisiae for de novo production of the sesquiterpenoid (+)-nootkatone. Microb. Cell Factories 2020, 60, 25–36. [Google Scholar]
4.
Ju H, Zhang C, He S, Nan W, Lu W. Construction and optimization of Saccharomyces cerevisiae for synthesizing forskolin. Appl. Microbiol. Biotechnol. 2022, 106, 1933–1944. [Google Scholar]
5.
Lim SH, Baek JI, Jeon BM, Seo JW, Kim MS, Byun JY, et al. CRISPRi-guided metabolic flux engineering for enhanced protopanaxadiol production in Saccharomyces cerevisiae. Int. J. Mol. Sci. 2021, 22, 11836. [Google Scholar]
6.
Cataldo VF, Arenas N, Salgado V, Camilo C, Ibanez F, Agosin E. Heterologous production of the epoxycarotenoid violaxanthin in Saccharomyces cerevisiae. Metab. Eng. 2020, 59, 53–63. [Google Scholar]
7.
Dusséaux S, Wajn WT, Liu Y, Ignea C, Kampranis SC. Transforming yeast peroxisomes into microfactories for the efficient production of high-value isoprenoids. Proc. Natl. Acad. Sci. USA 2020, 117, 31789–31799. [Google Scholar]
8.
Ma T, Shi B, Ye Z, Li X, Liu M, Chen Y, et al. Lipid engineering combined with systematic metabolic engineering of Saccharomyces cerevisiae for high-yield production of lycopene.  Metab. Eng. 2019, 52, 134–142. [Google Scholar]
9.
Bian Q, Zhou P, Yao Z, Li M, Yu H, Ye L. Heterologous biosynthesis of lutein in S. cerevisiae enabled by temporospatial pathway control. Metab. Eng. 2021, 67, 19–28. [Google Scholar]
10.
Gerke J, Frauendorf H, Schneider D, Wintergoller M, Hofmeister T, Poehlein A, et al. Production of the fragrance geraniol in peroxisomes of a product-tolerant baker’s yeast. Front. Bioeng. Biotechnol. 2020, 8, 582052. [Google Scholar]
11.
Zhou P, Du Y, Xu N, Yue C, Ye L. Improved linalool production in Saccharomyces cerevisiae by combining directed evolution of linalool synthase and overexpression of the complete mevalonate pathway. Biochem. Eng. J. 2020, 161, 107655. [Google Scholar]
12.
Otto M, Teixeira PG, Vizcaino MI, David F, Siewers V. Integration of a multi-step heterologous pathway in Saccharomyces cerevisiae for the production of abscisic acid. Microb. Cell Factories 2019, 18, 205. [Google Scholar]
13.
Mitsui R, Nishikawa R, Yamada R, Matsumoto T, Ogino H. Construction of yeast producing patchoulol by global metabolic engineering strategy. Biotechnol. Bioeng. 2020, 117, 1348–1356. [Google Scholar]
14.
Chemler JA, Koffas MAG. Metabolic engineering for plant natural product biosynthesis in microbes. Curr. Opin. Biotechnol. 2008, 19, 597–605. [Google Scholar]
15.
Li ZJ, Wang YZ, Wang LR, Shi TQ, Sun XM, Huang H. Advanced strategies for the synthesis of terpenoids in Yarrowia lipolytica. J. Agric. Food Chem. 2021, 69, 2367–2381. [Google Scholar]
16.
Sun W, Qin L, Xue H, Yu Y, Ma Y, Wang Y, et al. Novel trends for producing plant triterpenoids in yeast. Crit. Rev. Biotechnol. 2019, 39, 618–632. [Google Scholar]
17.
Mitsui R, Yamada R. Saccharomyces cerevisiae as a microbial cell factory. In Microbial Cell Factories Engineering for Production of Biomolecules; Academic Press, Cambridge, MA, USA; 2021; pp. 319–333.
18.
Ma Y, Zu Y, Huang S, Stephanopoulos G. Engineering a universal and efficient platform for terpenoid synthesis in yeast. Proc. Natl. Acad. Sci. USA 2022, 120, e2207680120. [Google Scholar]
19.
Cao X, Wei LJ, Lin JY, Hua Q. Enhancing linalool production by engineering oleaginous yeast Yarrowia lipolytica. Bioresour. Technol. 2017, 245, 1641–1644. [Google Scholar]
20.
Ignea C, Pontini M, Maffei ME, Makris AM, Kampranis SC. Engineering monoterpene production in yeast using a synthetic dominant negative geranyl diphosphate synthase. ACS Synth. Biol. 2014, 3, 298–306. [Google Scholar]
21.
Zhao J, Bao X, Li C, Shen Y, Hou J. Improving monoterpene geraniol production through geranyl diphosphate synthesis regulation in Saccharomyces cerevisiae. Appl. Microbiol. Biotechnol. 2016, 100, 4561–4571. [Google Scholar]
22.
Yee DA, DeNicola AB, Billingsley JM, Creso JG, Subrahmanyam V, Tang Y. Engineered mitochondrial production of monoterpenes in Saccharomyces cerevisiae. Metab. Eng. 2019, 55, 76–84. [Google Scholar]
23.
Ignea C, Cvetkovic I, Loupassaki S, Kefalas P, Johnson CB, Kampranis SC, et al. Improving yeast strains using recyclable integration cassettes, for the production of plant terpenoids. Microb. Cell Fact. 2011, 10, 4. [Google Scholar]
24.
Dong C, Shi Z, Huang L, Zhao H, Xu Z, Lian J. Cloning and characterization of a panel of mitochondrial targeting sequences for compartmentalization engineering in Saccharomyces cerevisiae. Biotechnol. Bioeng. 2021, 118, 4269–4277. [Google Scholar]
25.
Liu T, Li W, Chen H, Wu T, Zhu C, Zhuo M, et al. Systematic optimization of HPO-CPR to boost (+)-nootkatone synthesis in engineered Saccharomyces cerevisiae. J. Agric. Food Chem. 2022, 70, 15548–15559. [Google Scholar]
26.
Meadows AL, Hawkins KM, Tsegaye Y, Antipov E, Kim Y, Raetz L, et al. Rewriting yeast central carbon metabolism for industrial isoprenoid production. Nature 2016, 537, 694–697. [Google Scholar]
27.
Liu Y, Jiang X, Cui Z, Wang Z, Qi Q, Hou J. Engineering the oleaginous yeast Yarrowia lipolytica for production of α-farnesene. Biotechnol. Biofuels 2019, 12, 296. [Google Scholar]
28.
Guo Q, Shi TQ, Peng QQ, Sun XM, Ji XJ, Huang H. Harnessing Yarrowia lipolytica peroxisomes as a subcellular factory for alpha-humulene overproduction. J. Agric. Food Chem. 2021, 69, 13831–13837. [Google Scholar]
29.
Peng B, Plan MR, Chrysanthopoulos P, Hodson MP, Nielsen LK, Vickers CE. A squalene synthase protein degradation method for improved sesquiterpene production in Saccharomyces cerevisiae. Metab. Eng. 2017, 39, 209–219. [Google Scholar]
30.
Lu S, Deng H, Zhou C, Du Z, Guo X, Cheng Y, et al. Enhancement of β-caryophyllene biosynthesis in Saccharomyces cerevisiae via synergistic evolution of β-caryophyllene synthase and engineering the chassis. ACS Synth. Biol. 2023, 12, 1696–1707. [Google Scholar]
31.
Asadollahi MA, Maury J, Patil KR, Schalk M, Clark A, Nielsen J. Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering. Metab. Eng. 2009, 11, 328–334. [Google Scholar]
32.
Zhao Y, Zhu K, Li J, Zhao Y, Li S, Zhang C, et al. High‐efficiency production of bisabolene from waste cooking oil by metabolically engineered Yarrowia lipolytica. Microb. Biotechnol. 2021, 14, 2497–2513. [Google Scholar]
33.
Wang J, Zhu L, Li Y, Xu S, Jiang W, Liang C, et al. Enhancing geranylgeraniol production by metabolic engineering and utilization of isoprenol as a substrate in Saccharomyces cerevisiae. J. Agric. Food Chem. 2021, 69, 4480–4489. [Google Scholar]
34.
Hu T, Zhou J, Tong Y, Su P, Li X, Liu Y, et al. Engineering chimeric diterpene synthases and isoprenoid biosynthetic pathways enables high-level production of miltiradiene in yeast. Metab. Eng. 2020, 60, 87–96. [Google Scholar]
35.
Cao X, Yu W, Chen Y, Yang SC, Zhao ZK, Nielsen J, et al. Engineering yeast for high-level production of diterpenoid sclareol. Metab. Eng. 2023, 75, 19–28. [Google Scholar]
36.
Nowrouzi B, Li RA, Walls LE, d’Espaux L, Malci K, Liang L, et al. Enhanced production of taxadiene in Saccharomyces cerevisiae. Microb. Cell Fact. 2020, 19, 200. [Google Scholar]
37.
Zhu ZT, Du MM, Gao B, Tao XY, Zhao M, Ren YH, et al. Metabolic compartmentalization in yeast mitochondria: Burden and solution for squalene overproduction. Metab. Eng. 2021, 68, 232–245. [Google Scholar]
38.
Liu GS, Li T, Zhou W, Jiang M, Tao XY, Liu M, et al. The yeast peroxisome: A dynamic storage depot and subcellular factory for squalene overproduction. Metab. Eng. 2020, 57, 151–161. [Google Scholar]
39.
Kim JE, Jang IS, Son SH, Ko YJ, Cho BK, Kim SC, et al. Tailoring the Saccharomyces cerevisiae endoplasmic reticulum for functional assembly of terpene synthesis pathway. Metab. Eng. 2019, 56, 50–59. [Google Scholar]
40.
Zhao F, Bai P, Nan W, Li D, Zhang C, Lu C, et al. A modular engineering strategy for high‐level production of protopanaxadiol from ethanol by Saccharomyces cerevisiae. AIChE J. 2018, 65, 866–874. [Google Scholar]
41.
Kim JE, Jang IS, Sung BH, Kim SC, Lee JY. Rerouting of NADPH synthetic pathways for increased protopanaxadiol production in Saccharomyces cerevisiae. Sci. Rep. 2018, 8, 15820. [Google Scholar]
42.
Choi B, Kang H, Kim S, Lee P. Organelle engineering in yeast: Enhanced production of protopanaxadiol through manipulation of peroxisome proliferation in Saccharomyces cerevisiae. Microorganisms 2022, 10, 650. [Google Scholar]
43.
Shi Y, Wang D, Li R, Huang L, Dai Z, Zhang X. Engineering yeast subcellular compartments for increased production of the lipophilic natural products ginsenosides. Metab. Eng. 2021, 67, 104–111. [Google Scholar]
44.
Wang P, Wei W, Ye W, Li X, Zhao W, Yang C, et al. Synthesizing ginsenoside Rh2 in Saccharomyces cerevisiae cell factory at high-efficiency. Cell Discov. 2019, 5, 5. [Google Scholar]
45.
Yu Y, Rasool A, Liu H, Lv B, Chang P, Song H, et al. Engineering Saccharomyces cerevisiae for high yield production of α-amyrin via synergistic remodeling of α-amyrin synthase and expanding the storage pool. Metab. Eng. 2020, 62, 72–83. [Google Scholar]
46.
Liu H, Fan J, Wang C, Li C, Zhou X. Enhanced β-amyrin synthesis in Saccharomyces cerevisiae by coupling an optimal acetyl-CoA supply pathway. J. Agr. Food Chem. 2019, 67, 3723–3732. [Google Scholar]
47.
Du MM, Zhang GG, Zhu ZT, Zhao YQ, Gao B, Tao XY, et al. Boosting the epoxidation of squalene to produce triterpenoids in Saccharomyces cerevisiae. Biotechnol. Biofuels 2023, 16, 76. [Google Scholar]
48.
Yuan W, Jiang C, Wang Q, Fang Y, Wang J, Wang M, et al. Biosynthesis of mushroom-derived type II ganoderic acids by engineered yeast. Nat. Commun. 2022, 13, 7740. [Google Scholar]
49.
Jin K, Shi X, Liu J, Yu W, Liu Y, Li J, et al. Combinatorial metabolic engineering enables the efficient production of ursolic acid and oleanolic acid in Saccharomyces cerevisiae. Bioresour. Technol. 2023, 374, 128819. [Google Scholar]
50.
Arendt P, Miettinen K, Pollier J, De Rycke R, Callewaert N, Goossens A. An endoplasmic reticulum-engineered yeast platform for overproduction of triterpenoids. Metab. Eng. 2017, 40, 165–175. [Google Scholar]
51.
Nambou K, Jian X, Zhang X, Wei L, Lou J, Madzak C, et al. Flux balance analysis inspired bioprocess upgrading for lycopene production by a metabolically engineered strain of Yarrowia lipolytica. Metabolites 2015, 5, 794–813. [Google Scholar]
52.
Zhao Y, Zhang Y, Nielsen J, Liu Z. Production of β‐carotene in Saccharomyces cerevisiae through altering yeast lipid metabolism. Biotechnol. Bioeng. 2021, 118, 2043–2052. [Google Scholar]
53.
Zhao X, Shi F, Zhan W. Overexpression of ZWF1 and POS5 improves carotenoid biosynthesis in recombinant Saccharomyces cerevisiae. Lett. Appl. Microbiol. 2015, 61, 354–360. [Google Scholar]
54.
Liu M, Zhang J, Liu X, Hou J, Qia Q. Rapid gene target tracking for enhancing β-carotene production using flow cytometry-based high-throughput screening in Yarrowia lipolytica. Appl. Environ. Microbiol. 2022, 88, e0114922. [Google Scholar]
55.
Ma Y, Li J, Huang S, Stephanopoulos G. Targeting pathway expression to subcellular organelles improves astaxanthin synthesis in Yarrowia lipolytica. Metab. Eng. 2021, 68, 152–161. [Google Scholar]
56.
Kildegaard KR, Adiego-Pérez B, Doménech Belda D, Khangura JK, Holkenbrink C, Borodina I. Engineering of Yarrowia lipolytica for production of astaxanthin. Synth. Syst. Biotechnol. 2017, 2, 287–294. [Google Scholar]
57.
Liu S, Yi H, Zhan H, Wang L, Wang J, Li Y, et al. Gibberellic acid‐induced fatty acid metabolism and ABC transporters promote astaxanthin production in Phaffia rhodozyma. J. Appl. Microbiol. 2021, 132, 390–400. [Google Scholar]
58.
Liscum L, Finer-Moore J, Stroud RM, Luskey KL, Brown MS, Goldstein JL. Domain structure of 3-hydroxy-3-methylglutaryl coenzyme A reductase, a glycoprotein of the endoplasmic reticulum. J. Biol. Chem. 1985, 260, 522–530. [Google Scholar]
59.
Zhang G, Wang H, Zhang Z, Verstrepen KJ, Wang Q, Dai Z. Metabolic engineering of Yarrowia lipolytica for terpenoids production: advances and perspectives. Crit. Rev. Biotechnol. 2022, 42, 618–633. [Google Scholar]
60.
Mantzouridou F, Tsimidou MZ. Observations on squalene accumulation in Saccharomyces cerevisiae due to the manipulation of HMG2 and ERG6. FEMS Yeast Res. 2010, 10, 699–707. [Google Scholar]
61.
Li W, Cui L, Mai J, Shi TQ, Lin L, Zhang ZG, et al. Advances in metabolic engineering paving the way for the efficient biosynthesis of terpenes in yeasts. J. Agric. Food Chem. 2022, 70, 9246–9261. [Google Scholar]
62.
Chatzivasileiou AO, Ward V, Edgar SM, Stephanopoulos G. Two-step pathway for isoprenoid synthesis. Proc. Natl. Acad. Sci. USA 2019, 116, 506–511. [Google Scholar]
63.
Zhang C, Hong K. Production of terpenoids by synthetic biology approaches. Biotechnol. Bioeng. 2020, 8, 347. [Google Scholar]
64.
Kwak S, Yun EJ, Lane S, Oh EJ, Kim KH, Jin YS. Redirection of the glycolytic flux enhances isoprenoid production in Saccharomyces cerevisiae. Biotechnol. J. 2019, 15, e1900173. [Google Scholar]
65.
Dinday S, Ghosh S. Recent advances in triterpenoid pathway elucidation and engineering. Biotechnol. Adv. 2023, 68, 108214. [Google Scholar]
66.
Kirby J, Romanini DW, Paradise EM, Keasling JD. Engineering triterpene production in Saccharomyces cerevisiae–β‐amyrin synthase from Artemisia annua. FEBS J. 2008, 275, 1852–1859. [Google Scholar]
67.
Bröker JN, Müller B, van Deenen N, Prüfer D, Schulze Gronover C. Upregulating the mevalonate pathway and repressing sterol synthesis in Saccharomyces cerevisiae enhances the production of triterpenes. Appl. Microbiol. Biotechnol. 2018, 102, 6923–6934. [Google Scholar]
68.
Guo H, Wang H, Chen T, Guo L, Blank LM, Ebert BE, et al. Engineering critical amino acid residues of lanosterol synthase to improve the production of triterpenoids in Saccharomyces cerevisiae. ACS Synth. Biol. 2022, 11, 2685–2696. [Google Scholar]
69.
Sun W, Xue H, Liu H, Lv B, Yu Y, Wang Y, et al. Controlling chemo- and regioselectivity of a plant P450 in yeast cell toward rare licorice triterpenoid biosynthesis. ACS Catal. 2020, 10, 4253–4260. [Google Scholar]
70.
Wang F, Lv X, Xie W, Zhou P, Zhu Y, Yao Z, et al. Combining Gal4p-mediated expression enhancement and directed evolution of isoprene synthase to improve isoprene production in Saccharomyces cerevisiae. Metab. Eng. 2017, 39, 257–266. [Google Scholar]
71.
Hammer SK, Avalos JL. Harnessing yeast organelles for metabolic engineering. Nat. Chem. Biol. 2017, 13, 823–832. [Google Scholar]
72.
Weinert BT, Iesmantavicius V, Moustafa T, Schölz C, Wagner SA, Magnes C, et al. Acetylation dynamics and stoichiometry in Saccharomyces cerevisiae. Mol. Syst. Biol. 2014, 10, 833. [Google Scholar]
73.
Van der Klei IJ, Veenhuis M. Yeast peroxisomes: Function and biogenesis of a versatile cell organelle. Trends Microbiol. 1997, 5, 502–509. [Google Scholar]
74.
Leavell MD, Singh AH, Kaufmann-Malaga BB. High-throughput screening for improved microbial cell factories, perspective and promise. Curr. Opin. Biotechnol. 2020, 62, 22–28. [Google Scholar]
75.
Takekana M, Yoshida T, Yoshida E, Ono S, Horie S, Vavricka CJ, et al. Online SFE-SFC-MS/MS colony screening: A high-throughput approach for optimizing (-)-limonene production. J. Chromatogr. B 2023, 1215, 123588. [Google Scholar]
76.
Ko YS, Kim JW, Lee JA, Han T, Kim GB, Park JE, et al. Tools and strategies of systems metabolic engineering for the development of microbial cell factories for chemical production. Chem. Soc. Rev. 2020, 49, 4615–4636. [Google Scholar]
77.
Zhu J, An T, Zha W, Gao K, Li T, Zi J. Manipulation of IME4 expression, a global regulation strategy for metabolic engineering in Saccharomyces cerevisiae. Acta Pharm. Sin. B 2023, 13, 2795–2806. [Google Scholar]
78.
Yang H, Yang L, Du X, He N, Jiang Z, Zhu Y, et al. Metabolomics of astaxanthin biosynthesis and corresponding regulation strategies in Phaffia rhodozyma. Yeast 2023, 40, 254–264. [Google Scholar]
79.
Dahal S, Yurkovich JT, Xu H, Palsson BO, Yang L. Synthesizing systems biology knowledge from omics using genome-scale models. Proteomics 2020, 20, 1900282. [Google Scholar]
80.
Paramasivan K, Abdulla A, Gupta N, Mutturi S. In silico target-based strain engineering of Saccharomyces cerevisiae for terpene precursor improvement. Integr. Biol. 2022, 14, 25–36. [Google Scholar]
81.
Kim GB, Kim WJ, Kim HU, Lee SY. Machine learning applications in systems metabolic engineering. Curr. Opin. Biotechnol. 2020, 64, 1–9. [Google Scholar]
82.
Costello Z, Martin HG. A machine learning approach to predict metabolic pathway dynamics from time-series multiomics data. NPJ Syst. Biol. Appl. 2018, 4, 19. [Google Scholar]
83.
Chen L, Cai C, Chen V, Lu X. Learning a hierarchical representation of the yeast transcriptomic machinery using an autoencoder model. BMC Bioinformat. 2016, 17, 9. [Google Scholar]
84.
Ma J, Yu MK, Fong S, Ono K, Sage E, Demchak B, et al. Using deep learning to model the hierarchical structure and function of a cell. Nat. Methods 2018, 15, 290–298. [Google Scholar]
85.
Mukherjee M, Blair RH, Wang ZQ. Machine-learning guided elucidation of contribution of individual steps in the mevalonate pathway and construction of a yeast platform strain for terpenoid production. Metab. Eng. 2022, 74, 139–149. [Google Scholar]
86.
Chen M, Li M, Ye L, Yu H. Construction of canthaxanthin-producing yeast by combining spatiotemporal regulation and pleiotropic drug resistance engineering. ACS Synth. Biol. 2022, 11, 325–333. [Google Scholar]
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