- Open Access
Enhanced protopanaxadiol production from xylose by engineered Yarrowia lipolytica
- Yufen Wu†1, 2, 3,
- Shuo Xu†1, 2, 3,
- Xiao Gao1, 2, 3,
- Man Li1, 2, 3,
- Dashuai Li1, 2, 3 and
- Wenyu Lu1, 2, 3Email author
© The Author(s) 2019
- Received: 20 March 2019
- Accepted: 8 May 2019
- Published: 18 May 2019
As renewable biomass, lignocellulose remains one of the major choices for most countries in tackling global energy shortage and environment pollution. Efficient utilization of xylose, an important monosaccharide in lignocellulose, is essential for the production of high-value compounds, such as ethanol, lipids, and isoprenoids. Protopanaxadiol (PPD), a kind of isoprenoids, has important medical values and great market potential.
The engineered protopanaxadiol-producing Yarrowia lipolytica strain, which can use xylose as the sole carbon source, was constructed by introducing xylose reductase (XR) and xylitol dehydrogenase (XDH) from Scheffersomyces stipitis, overexpressing endogenous xylulose kinase (ylXKS) and heterologous PPD synthetic modules, and then 18.18 mg/L of PPD was obtained. Metabolic engineering strategies such as regulating cofactor balance, enhancing precursor flux, and improving xylose metabolism rate via XR (K270R/N272D) mutation, the overexpression of tHMG1/ERG9/ERG20 and transaldolase (TAL)/transketolase (TKL)/xylose transporter (TX), were implemented to enhance PPD production. The final Y14 strain exhibited the greatest PPD titer from xylose by fed-batch fermentation in a 5-L fermenter, reaching 300.63 mg/L [yield, 2.505 mg/g (sugar); productivity, 2.505 mg/L/h], which was significantly higher than the titer of glucose fermentation [titer, 167.17 mg/L; yield, 1.194 mg/g (sugar); productivity, 1.548 mg/L/h].
The results showed that xylose was more suitable for PPD synthesis than glucose due to the enhanced carbon flux towards acetyl-CoA, the precursor for PPD biosynthetic pathway. This is the first report to produce PPD in Y. lipolytica with xylose as the sole carbon source, which developed a promising strategy for the efficient production of high-value triterpenoid compounds.
- Yarrowia lipolytica
- Metabolic engineering
- Synthetic biology
Lignocellulose from wood in forestry and agriculture as well as industrial waste can reach 100 billion tons/year, making this biomass the most abundant renewable resource on the Earth . Efficient utilization of lignocellulose is essential for reducing demands for energy and food. Xylose is the second most abundant monosaccharide in lignocellulosic hydrolysate following glucose, accounting for nearly 35% of all monosaccharides . However, most microorganisms cannot efficiently metabolize xylose from lignocellulosic hydrolysate due to the carbon catabolite repression effect , which largely limits the applications of lignocellulose. Thus, the use of xylose has become a hot issue in the study of lignocellulose.
In recent years, great progress has been made in xylose metabolism studies. Various compounds have been successfully obtained via microbial metabolism of xylose, such as xylitol , ethanol , acetoin , fumaric acid , and polyhydroxyalkanoate . As a model organism for lipid metabolism, Yarrowia lipolytica does not naturally metabolize xylose, primarily due to low expression levels of the key enzymes involved in the xylose metabolic pathway [9–12]. However, whether the Y. lipolytica strain can grow using xylose as a substrate remains controversial [13–15]. There have been many attempts to engineer Y. lipolytica to use xylose as a substrate. Ledesma-Amaro et al.  have engineered Y. lipolytica to metabolize xylose to produce lipids and citric acid by overexpression of xylose reductase (XR) and xylitol dehydrogenase (XDH) from Scheffersomyces stipitis and endogenous xylulose kinase (ylXKS). The growth ability of engineered Y. lipolytica using xylose was identical to that of the wild type strain grown using glucose. This mutant could produce up to 80 g/L of citric acid from xylose. Li and Alper  have implemented a starvation adaptation strategy to improve the metabolic rate of xylose. They introduced a heterologous oxidoreductase pathway to optimize xylose utilization by Y. lipolytica in a stable manner; this mutant produced > 15 g/L of lipid via bioreactor fermentation, with a maximal lipid productivity of 0.19 g/L/h.
Yarrowia lipolytica contains the native mevalonate (MVA) pathway to provide precursor compounds, namely isopentenyl pyrophosphate and dimethylallyl pyrophosphate , indicating that Y. lipolytica can serve as a natural host for terpenoid synthesis. Y. lipolytica is a potential platform for producing isoprenoids using acetyl-CoA as the precursor due to its convenient genetic manipulation, robust acetyl-CoA synthesis, NADPH, and energy supply system [19–22], as S. cerevisiae lacks acetyl-CoA [23, 24]. In previous studies, biosynthesis of many terpenoids were realized in Y. lipolytica, such as farnesene, limonene, and ginsenoside compound K [25–27], and engineering strategies have been employed to enhance the production, such as codon optimization, heterologous synthetic genes introduction, synthetic pathway up-regulation, and competitive pathway down-regulation. Limonene (23.56 mg/L; 1.36 mg/g DCW) was obtained in Y. lipolytica by codon optimization and overexpression HMG1 and ERG12 genes ; The α-farnesene titer was increased by 20.8-fold by tHMG1, IDI, and ERG20 overexpression, reaching 259.98 mg/L ; The titer of ginsenoside compound K was increased to 161.8 mg/L by a combination of metabolic engineering strategies .
Protopanaxadiol (PPD) is a natural C30 isoprenoid with important medical applications owing to its anticancer, antitumor, antiviral, and antibiotic properties [28–30]. The extraction method for PPD from plants has limited applications because of shortage of ginseng plants. Therefore, strategies have been developed for PPD biosynthesis to overcome the limitations of traditional extraction processes [31, 32].
Ku70 knockout to enhance homologous recombination efficiency of Y. lipolytica
Introduction of the xylose metabolic pathway in Y. lipolytica
The natural capacity of Y. lipolytica to metabolize xylose remains unclear. To obtain xylose-fermenting strains, endogenous and heterologous pathways for xylose metabolism were introduced into Y. lipolytica. The cofactor imbalance problem can be resolved using mutated XR [43–45]. Watanabe et al.  have induced two XR gene mutations, R276H and K270R/N272D, resulting in change in preference from NADPH to NADH, which led to respectively 52- and 146-fold increases in catalytic efficiency of the mutant strains compared with that of the original strain. XYL1 and XYL2 genes from S. stipitis encoding XR (K270R/N272D) and XDH, respectively, were codon-optimized according to codon preference of Y. lipolytica and transformed into the Y1 strain, together with the ylXKS expression cassette, to produce the strain Y2 (Fig. 1). Moreover, the endogenous ylXYL1, ylXYL2, and ylXKS genes were integrated into the zeta site of Y. lipolytica using the same promoters as those of the heterologous genes to obtain the Y3 strain. Y. lipolytica ATCC 201249 could not grow in xylose medium (Fig. 2a). The Y2 series of engineered strains with the introduced heterologous xylose metabolic pathway showed a significant increase in OD600 values compared with the original strain, indicating that XR and XDH derived from S. stipitis were successfully expressed in Y. lipolytica. However, the Y3 strain overexpressing the endogenous xylose metabolism genes showed no obvious growth, indicating that endogenous XR and XDH cannot use xylose as the sole carbon source.
Strain with the highest OD600 using xylose was selected for shake flask fermentation, with Y0 and Y1 as comparisons. Results indicated that the Y2 strain alone consumed approximately 10 g/L xylose and that the growth ability using xylose remained lower than that using glucose (Fig. 2b, c). Therefore, we speculated that improving the efficiency of sugar transporters [46–48] or enhancing the adaptability of strains to xylose  can enhance xylose utilization.
Adaptation to improve xylose metabolism
PPD production in xylose-metabolizing strains of Y. lipolytica
Overexpression of the MVA pathway to enhance PPD production
The MVA pathway is the only source of precursors for the synthesis of terpenoids in Y. lipolytica [51–53]. Several key enzymes in the MVA pathway have been investigated to increase PPD production in S. cerevisiae or Y. lipolytica, such as tHMG1, ERG10, ERG12, ERG9, ERG20, and ERG13 [32, 35]. The key enzymes, tHMG1, ERG9, and ERG20, were overexpressed in Y9 (the ura3 marker in Y8 was recycled), resulting in the Y10 strain, in which PPD titer increased by 34% compared with that in the Y8 strain, reaching 80.88 mg/L, although OD600 of the cells did not change significantly (Fig. 4c). Overexpression of the MVA pathway significantly increased PPD production; however, in Y. lipolytica, PPD yield from xylose could be further increased by increasing the metabolic rate of xylose.
Optimization of the xylose assimilation pathway to increase the xylose metabolism rate
Shake flask fermentation of the engineered strain Y14 using xylose to produce PPD
Fermentation of Y14 at different initial sugar concentrations
Initial sugar concentration (g/L)
Residual sugar concentration (g/L)b
PPD titer (mg/L)b
57.17 ± 1.83
81.23 ± 1.47
61.17 ± 1.31
80.45 ± 0.71
65.27 ± 1.28
120.36 ± 1.59
58.62 ± 2.22
1.0 ± 0.1
124.94 ± 2.75
87.85 ± 1.57
12.1 ± 0.9
128.94 ± 0.43
2.2 ± 0.4
82.27 ± 2.31
17.9 ± 0.8
118.55 ± 4.42
12.9 ± 0.6
80.45 ± 1.74
26.3 ± 1.2
135.21 ± 2.76
Biomass and metabolites analysis for Y14 with mixed sugars fermentation
PPD titer (mg/L)a
56.53 ± 1.23
0.178 ± 0.012
3.97 ± 0.21
68.01 ± 2.38
0.202 ± 0.061
4.28 ± 0.81
66.12 ± 1.92
0.197 ± 0.013
6.23 ± 1.02
74.04 ± 2.17
0.203 ± 0.051
7.31 ± 0.15
72.74 ± 3.28
1.973 ± 0.017
8.29 ± 1.71
83.23 ± 4.87
1.047 ± 0.082
6.38 ± 0.81
107.3 ± 1.93
2.352 ± 0.816
10.45 ± 1.38
To investigate the reason higher PPD titer were obtained using xylose than using glucose, metabolites, such as acetyl-CoA and squalene, produced by the Y14 strain at 60 h were analyzed. Acetyl-CoA is an important precursor in the MVA pathway. Cellular acetyl-CoA concentrations may be influenced by carbon sources, contributing to differences in PPD biosynthesis. The concentration of acetyl-CoA produced using xylose was higher than produced using glucose and mixed sugars (Table 2). Furthermore, we analyzed the production of squalene, which is crucial for triterpene biosynthesis via the MVA pathway (Table 2). Higher levels of squalene were produced using xylose as the sole carbon source. In the xylose medium, high acetyl-CoA production resulted in high squalene production compared with that in other media. Thus, PPD titers may be further improved by increasing squalene supply.
Fermentation by the Y14 strain for PPD production in a 5-L bioreactor
Fed-batch fermentation in 5-L bioreactor was performed to further increase PPD production (Fig. 6c, d). PPD titer was 300.63 mg/L [yield, 2.505 mg/g (sugar); productivity, 2.505 mg/L/h] using xylose. PPD synthesis quickly entered a stable period using glucose, and the highest yield was 167.17 mg/L [yield, 1.194 mg/g (sugar); productivity, 1.548 mg/L/h]. Similarly, dammarenediol-II (DMD) production was detected at the same time. DMD remained during xylose fermentation, accumulating at 24 h and peaking at 84 h, and then gradually decreased. The difference in the fed-batch fermentation results using xylose and glucose may be due to the quick consumption of glucose, which produced amount of acetyl-CoA, but for the limitations of enzymes activity of MVA pathway, carbon sources flowed to other metabolic branches, causing a reduction of acetyl-CoA used for PPD synthesis. With rapid glucose consumption, cells entered a stable phase. Insufficient supply of other precursors, such as acetyl-CoA and NADPH, resulted in slow PPD production. During xylose-feed fermentation, cells continued to grow slowly, and acetyl-CoA or NADPH were continuously supplied for PPD synthesis, reducing the loss of carbon metabolic flux. In addition, DMD accumulated a little, indicating that the supply of DMD was sufficient to be converted to PPD continuously, producing a greater titer. These results indicate that xylose has great potential for PPD production using acetyl-CoA as a precursor. Studies using S. cerevisiae for PPD production using xylose have indicated that xylose fermentation is superior to glucose fermentation in terms of the production of acetyl-CoA. Regulating the metabolic engineering strategy for xylose utilization and product synthesis can enable efficient synthesis of compounds using acetyl-CoA as a precursor and xylose as a substrate.
This study described a strategy for enhancing PPD production through xylose fermentation with engineered Y. lipolytica. Y. lipolytica cannot naturally metabolize xylose; however, introduction of heterologous XR/XDH and overexpression of endogenous XKS successfully realized PPD biosynthesis in Y. lipolytica using xylose as the sole carbon source. Biomass and PPD production were further increased by overexpression of tHMG1/ERG9/ERG20 in MVA pathway and TAL/TKL/TX in xylose metabolic pathway. Regulation of xylose utilization pathway and product synthesis pathways through metabolic engineering can enable efficient synthesis of terpenoid compounds using xylose as a substrate, which can be a strategy for enhancing terpenoid synthesis in Y. lipolytica.
Strains, plasmids, and media
Yarrowia lipolytica ATCC 201249 was used as the parental strain for engineering, which was kindly provided by Professor Yingjin Yuan (School of Chemical Engineering and Technology, Tianjin University) . The pINA1269-LUL plasmid was used to amplify the marker ura3 with the LoxP sequence, and the pINA1269-CRE plasmid (Additional file 1: Figure S2) carrying a gene encoding CRE protein was used to recycle the marker ura3 (codon-optimized sequences were shown in Additional file 1: Table S1). All Y. lipolytica strains were cultivated in YPD or YPX medium (2% glucose or 2% xylose, respectively, 2% peptone, and 1% yeast extract) at 30 °C. SC medium (0.67% yeast nitrogen base, 2% glucose, and 2% agar) lacking leucine or uracil was used for screening Y. lipolytica transformants. LB medium (1% tryptone, 0.5% yeast extract, and 1% NaCl) supplemented with ampicillin (100 mg/L) was used for culturing Escherichia coli DH5α containing recombinant plasmids. Feed solution for fermentation contained 400 g/L xylose or glucose, 20 g/L yeast extract, and 0.5 g/L lysine. The components were sterilized separately and combined in a clean environment.
Codon-optimized xylose reductase XR (XYL1) and XDH (XYL2) derived from S. stipitis were synthesized by Wuhan Genecreate Biological Engineering Co., Ltd. The optimized nucleotide sequences of the genes are presented in Additional file 1: Table S1. The DS, PPDS, and ATR1 genes were synthesized and cloned into pUC57 plasmids by GENEWIZ (Suzhou, China), with codon optimization for Y. lipolytica. Endogenous genes encoding XKS (ylXKS), xylose transporter (TX), transketolase (TKL), transaldolase (TAL), truncated 3-hydroxy-3-methylglutaryl-coenzyme A reductase (tHMG1), farnesyl pyrophosphate synthase (ERG20), and squalene synthase (ERG9) were amplified using genomic DNA from Y. lipolytica ATCC 201249. Promoters and terminators used in the study were amplified from genomic DNA of Y. lipolytica ATCC 201249 . All primers used to amplify DNA are listed in Additional file 1: Table S2.
Strains used in this work
Yarrowia lipolytica ATCC 201249: MATA, ura3-302, leu2-270, lys8-11, pex17-ha
Y0: Ku70 deletion::LUL
Y1: zeta::exp1p-XYL1-xpr2t, gpd1p-XYL2-lip2t, tef1p-ylXKS-cyc1t
Y1: zeta::exp1p-ylXYL1-xpr2t, gpd1p-ylXYL2-lip2t, tef1p-ylXKS-cyc1t
An adaptation of xylose in Y2
An adaptation of xylose in Y3
The marker ura3 was recycled in Y4
Y6: rDNA::tef1p-DS-xpr2t, exp1p-PPDS-mig1t, gpd1p-ATR1-lip2t
Y6: rDNA::tef1p-DS-xpr2t, exp1p-PPDS-linker-ATR1-lip2t
The marker ura3 was recycled in Y8.
Y9: POX1::Fbainp-tHMG1-xpr2t, gpd1p-erg9-cyc1t, exp1p-erg20-lip2t
The marker ura3 was recycled in Y10.
Y11: POX2::exp1p-TKL-mig1t, tef1p-TAL-lip2t
The marker ura3 was recycled in Y12.
Y13: POX3:: Pfba1-TX-cyc1t
Cells were cultured in 5 mL SC medium for 7 days. Then, cells were washed using sterile water and transferred to 5 mL SC medium containing 20 g/L xylose (without glucose) for 10 days at 30 °C. Cells were washed again with sterile water and transferred to solid SC medium plates (20 g/L xylose) to culture single colonies, followed by culture in 5 mL selection medium containing xylose (without glucose) to select single colonies. The process was repeated 2–3 times.
Transcriptional gene expression studies by RT-qPCR
Samples were taken at exponential phase. RNAs was extracted using RNA extraction kit (TIANGEN, China). PrimeScriptTM RT reagent Kit with gDNA Eraser from TaKaRa was used to convent mRNA into cDNA. SYBR® Premix Ex TaqTM II Kit from TaKaRa was used for reverse transcription-quantitative real-time PCR (RT-qPCR). The primers are listed in Additional file 1: Table S3. Triplicate qPCRs were performed. CT (threshold cycle number) values of target genes were normalized using the erg5 gene as reference. The data obtained were analyzed by applying the 2−ΔΔCT method .
Fermentation in shake flasks
Yarrowia lipolytica strains stored at − 80 °C in 25% glycerol were inoculated into 5 mL YPD medium as the seed culture for 24 h at 30 °C while shaking at 220 rpm, and the culture was transferred to 250-mL shake flasks loaded with 50 mL YPD or YPX medium at an initial optical density at 600 nm (OD600) of 0.5 under the same cultivation conditions for 4 days. All shake flask fermentation experiments were performed in three parallel experimental groups.
As seed culture for batch fermentation in 5-L bioreactors (Bailun, Shanghai, China), 5 mL preculture was transferred to 150 mL YPD medium in 500-mL shake flasks and cultivated for 24 h at 30 °C while shaking at 220 rpm. The seed medium was inoculated in a 5-L bioreactor at an initial OD600 of 0.5 in 2 L YPD or YPX medium. Temperature was maintained at 30 °C, and pH was maintained at 6.0 by adding 20% ammonia water or 3 M H2SO4. Rotating speed was set at 450 rpm, with an air flow rate of 2 vvm. For fed-batch fermentation in the 5-L bioreactor, 100 mL feed solution was added every 12 h when the sugar was depleted.
PPD extraction and analysis
PPD was extracted using n-butanol, as previously described . The mixture of fermentation broth and n-butanol was centrifuged at 11,564×g for 10 min, and the n-butanol phase was collected for analysis. Samples were analyzed by LC/APCI/MS and quantified by HPLC, as previously reported . Standards were purchased from Meilun Biotechnology Co., Ltd (Dalian, China).
Cell growth was determined by measuring the OD600 using a UV–VIS spectrophotometer. Concentrations of glucose and xylose were measured using a refractive index detector (Shodex RI-201H) equipped with an Elite P230II pump (Elite Analytical Instruments Co., Ltd., China) and an Aminex HPX-87H column (Bio-Rad, USA). Temperatures of the column and detector were 65 °C and 40 °C, respectively. The mobile phase was 5 mM H2SO4 at a flow rate of 0.6 mL/min. Acetyl-CoA was analyzed using the Acetyl-CoA ELISA Kit (Shanghai Shuangying Co., Ltd., China). Squalene was analyzed using the Elite HPLC system equipped with an Elite P230II high-pressure pump, UV detection at 203 nm, and the Hypersil C18 column (4.6 mm × 250 mm, 5 µm). Methanol was used as the mobile phase at a flow rate of 1 mL/min.
This work was financially supported by the National Natural Science Foundation of China (No. 21878220) and the Major Research Plan of Tianjin [No. 16YFXTSF00460].
YW, XG and DL designed the experiments. YW, SX and ML performed the experiments. YW, XG and WL wrote the manuscript. All authors read and approved the final manuscript.
Ethics approval and consent to participate
Consent for publication
The authors declare that they have no competing interests.
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