Genetic modification of the marine-derived yeast Yarrowia lipolytica with high-protein content using a GPI-anchor-fusion expression system

A strategy to reduce the byproduct glucose by simultaneously producing levan and single cell oil using an engineered Yarrowia lipolytica strain displaying levansucrase on the surface

Currently, levan is attracting attention due to its promising applications in the food and biomedical fields. Levansucrase synthesizes levan by polymerizing the fructosyl unit in sucrose. However, a large amount of the byproduct glucose is produced during this process. In this paper, an engineered oleaginous yeast (Yarrowia lipolytica) strain was constructed using a surface display plasmid containing the LevS gene of Gluconobacter sp. MP2116. The levansucrase activity of the engineered yeast strain reached 327.8 U/g of cell dry weight. The maximal levan concentration (58.9 g/l) was achieved within 156 h in the 5-liter fermentation. Over 81.2 % of the sucrose was enzymolyzed by the levansucrase, and the byproduct glucose was converted to 21.8 g/l biomass with an intracellular oil content of 25.5 % (w/w). The obtained oil was comprised of 91.3 % long-chain fatty acids (C16-C18). This study provides new insight for levan production and comprehensive utilization of the byproduct in levan biosynthesis.

Metabolome and Transcriptome Profiling Reveal Carbon Metabolic Flux Changes in Yarrowia lipolytica Cells to Rapamycin

Yarrowia lipolytica is an oleaginous yeast for the production of oleochemicals and biofuels. Nitrogen deficiency is beneficial to lipids biosynthesis in Y. lipolytica. Target of rapamycin (TOR) regulates the utilization of nutrients, which is inhibited in nitrogen starvation or by rapamycin treatment. However, under nitrogen-rich conditions, the lipids biosynthesis in Y. lipolytica after inhibition of TOR by rapamycin is elusive. Combining metabolomics and transcriptomics analysis, we found that rapamycin altered multiple metabolic processes of Y. lipolytica grown in nitrogen-rich medium, especially the metabolisms of amino acids and lipids. A total of 176 differentially accumulated metabolites were identified after rapamycin treatment. Rapamycin increased the levels of tryptophan, isoleucine, proline, serine, glutamine, histidine, lysine, arginine and glutamic acid, and decreased the levels of threonine, tyrosine and aspartic acid. Two fatty acids in lipid droplets, stearic acid (down-regulated) and stearidonic acid (up-regulated), were identified. The expression of 2224 genes changed significantly after rapamycin treatment. Further analysis revealed that rapamycin reduced carbon flux through lipids biosynthesis, accompanied by increased carbon flux through fatty acids degradation and amino acid (especially glutamic acid, glutamine, proline and arginine) biosynthesis. The dataset provided here is valuable for understanding the molecular mechanisms of amino acid and lipids metabolisms in oleaginous yeast.

Comparative transcriptome analysis reveals multiple functions for Mhy1p in lipid biosynthesis in the oleaginous yeast Yarrowia lipolytica

Yarrowia lipolytica is considered as a promising microbial cell factory for bio-oil production due to its ability to accumulate a large amount of lipid. However, the regulation of lipid metabolism in this oleaginous yeast is elusive. In this study, the MHY1 gene was disrupted, and 43.1% (w/w) intracellular oil based on cell dry weight was obtained from the disruptant M-MHY1, while only 30.2% (w/w) lipid based on cell dry weight was obtained from the reference strain. RNA-seq was then performed to analyze transcriptional changes during lipid biosynthesis after MHY1 gene inactivation. The expression of 1597 genes, accounting for 24.7% of annotated Y. lipolytica genes, changed significantly in the disruptant M-MHY1 during lipid biosynthesis. Differential gene expression analysis indicated that Mhy1p performs multiple functions and participates in a wide variety of biological processes, including lipid, amino acid and nitrogen metabolism. Notably, data analysis revealed increased carbon flux through lipid biosynthesis following MHY1 gene inactivation, accompanied by decreased carbon flux through amino acid biosynthesis. Moreover, Mhy1p regulates the cell cycle, and the cell cycle rate was enhanced in the disruptant M-MHY1. These results suggest that Mhy1p plays critical regulatory roles in diverse aspects of various biological processes, especially in lipid biosynthesis, amino acid and nitrogen metabolism and cell cycle. Our dataset appears to elucidate the crucial role of Mhy1p in lipid biosynthesis and serves as a resource for exploring physiological dimorphic growth in Y. lipolytica.

Enhanced citric acid production by a yeast Yarrowia lipolytica over-expressing a pyruvate carboxylase gene

In this study, after the expression of a pyruvate carboxylase gene (PYC) cloned from Meyerozyma guilliermondii in a marine-derived yeast Yarrowia lipolytica SWJ-1b, a transformant PG86 obtained had much higher PYC activity than Y. lipolytica SWJ-1b. At the same time, the PYC gene expression and citric acid (CA) production by the transformant PG86 were also greatly enhanced. When glucose concentration in the medium was 60.0 g L(-1), CA concentration formed by the transformant PG86 was 34.02 g L(-1), leading to a CA yield of 0.57 g g(-1) of glucose. During a 10-L fed-batch fermentation, the final concentration of CA was 101.0 ± 1.3 g L(-1), the yield was 0.89 g g(-1) of glucose, the productivity was 0.42 g L(-1) h(-1) and only 5.93 g L(-1) reducing sugar was left in the fermented medium within 240 h of the fed-batch fermentation. HPLC analysis showed that most of the fermentation products were CA.

Cloning and Characterization of a Pyruvate Carboxylase Gene from Penicillium rubens and Overexpression of the Genein the Yeast Yarrowia lipolytica for Enhanced Citric Acid Production

In this study, a pyruvate carboxylase gene (PYC1) from a marine fungus Penicillium rubens I607 was cloned and characterized. ORF of the gene (accession number: KM397349.1) had 3534 bp encoding 1177 amino acids with a molecular weight of 127.531 kDa and a PI of 6.20. The promoter of the gene was located at -1200 bp and contained a TATAA box, several CAAT boxes and a sequence 5'-SYGGRG-3'. The PYC1 deduced from the gene had no signal peptide, was a homotetramer (α4), and had the four functional domains. After expression of the PYC1 gene from the marine fungus in the marine-derived yeast Yarrowia lipolytica SWJ-1b, the transformant PR32 obtained had much higher specific pyruvate carboxylase activity (0.53 U/mg) than Y. lipolytica SWJ-1b (0.07 U/mg), and the PYC1 gene expression (133.8%) and citric acid production (70.2 g/l) by the transformant PR32 were also greatly enhanced compared to those (100 % and 27.3 g/l) by Y. lipolytica SWJ-1b. When glucose concentration in the medium was 60.0 g/l, citric acid (CA) concentration formed by the transformant PR32 was 36.1 g/l, leading to conversion of 62.1% of glucose into CA. During a 10-l fed-batch fermentation, the final concentration of CA was 111.1 ± 1.3 g/l, the yield was 0.93 g/g, the productivity was 0.46 g/l/h, and only 1.72 g/l reducing sugar was left in the fermented medium within 240 h. HPLC analysis showed that most of the fermentation products were CA. However, minor malic acid and other unknown products also existed in the culture.

Direct conversion of pretreated straw cellulose into citric acid by co-cultures of Yarrowia lipolytica SWJ-1b and immobilized Trichoderma reesei mycelium

The immobilized cellulase-producing mycelium of Trichoderma reesei was found to produce 2.9 U/ml of cellulase activity within 144 h while 2.1 U/ml of cellulase activity was produced within 120 h by the free mycelium of the same strain. When the immobilized mycelium of T. reesei was co-cultivated with the free cells of Yarrowia lipolytica SWJ-1b in flask, Y. lipolytica SWJ-1b could yield 10.7 g/l of citric acid and 3.9 g/l of isocitric acid from 40.0 g/l pretreated straw within 240 h. Under the similar conditions, Y. lipolytica SWJ-1b could yield 32.8 g/l of citric acid and 4.7 g/l of isocitric acid from 40.0 g/l pretreated straw supplemented with 20.0 g/l glucose within 288 h. When the co-cultures were grown in 10-l fermentor, Y. lipolytica SWJ-1b could yield 83.4 g/l of citric acid and 8.7 g/l of isocitric acid from 100.0 g/l of pretreated straw supplemented with 50.0 g/l glucose within 312 h.

Identifying and characterizing Yarrowia keelungensis sp. nov., an oil-degrading yeast isolated from the sea surface microlayer

Ascomycetous yeast strain SM-22 was isolated from the sea-surface microlayer near the Keelung City off the northern coast of Taiwan. This strain showed a cell surface hydrophobicity higher than 90 %, moderate UV A/B resistance, and it degraded 68 % of the total petroleum hydrocarbon content of an artificial seawater medium containing 1 % (v v(-1)) diesel oil within 15 days at 25 °C. The closest phylogenetic relative of this strain is Candida oslonensis CBS 10146(T), but it differs from strain SM-22 by a 3.7 % divergence (including 18 nucleotide substitutions and 2 gaps) in the D1/D2 domain sequence of the large subunit rRNA gene. This difference clearly suggests that the strain SM-22 represents a distinct species. Strain SM-22 does not produce ascospores on common sporulation media and it can therefore be considered an anamorph of the genus Yarrowia. Thus, the name Yarrowia keelungensis sp. nov. (type strain SM-22(T) = BCRC 23110(T) = JCM 14894(T) = CBS 11062(T)) is proposed as a novel species of genus Yarrowia.

Both decrease in ACL1 gene expression and increase in ICL1 gene expression in marine-derived yeast Yarrowia lipolytica expressing INU1 gene enhance citric acid production from inulin

In this study, some of the ATP-citrate lyase genes (ACL1) were deleted and the copy number of the iso-citrate lyase gene (ICL1) was increased in the marine-derived yeast Yarrowia lipolytica SWJ-1b displaying the recombinant inulinase. It was found that lipid content and iso-citric acid in the transformant 30 obtained were greatly reduced and citric acid production was greatly enhanced. It was also found that the ACL1 gene expression and ATP-citrate lyase activity in the transformant 30 were declined and the ICL1 gene expression and iso-citrate lyase activity were promoted. During the 2-l fermentation, 84.0 g/l of citric acid and 1.8 g/l of iso-citric acid in the fermented medium were attained from 10.0 % of inulin by the transformant 30 within 214 h. The results showed that only 0.36 % of the residual reducing sugar and 1.0 % of the residual total sugar were left in the fermented medium, suggesting that 89.6 % of the total sugar was used for citric acid production and cell growth by the transformant 30.

Disruption of the MIG1 gene enhances lipid biosynthesis in the oleaginous yeast Yarrowia lipolytica ACA-DC 50109

In this study, the MIG1 gene in the oleaginous yeast Yarrowia lipolytica ACA-DC 50109 (the parent yeast) was disrupted and the disruptant M25 obtained could grow in yeast nitrogen base-N5000 medium without uracil or the medium with 2-deoxy-D-glucose. It was found that the cells of the disruptant M25 had more lipid bodies than those of its parent yeast. The disruptant M25 contained 48.7% (w/w) of oil based on its cell weight while the parent yeast only contained 36.0% (w/w) of oil. Transcript levels of many genes relevant to lipid biosynthesis in the disruptant M25 were enhanced compared to those of the same genes in the parent yeast. However, transcript level of the MFE1 gene, one of the genes relevant to fatty acid degradation was reduced in the disruptant M25 compared to that of the same gene in the parent yeast. Such changes in gene expression profile may cause the increased lipid biosynthesis in the disruptant M25. Biosynthesis of C18:1 fatty acid in the disruptant M25 was greatly enhanced compared to that in the parent yeast.

Molecular characterization and expression of microbial inulinase genes

Many genes encoding exo- and endo-inulinases from bacteria, yeasts and filamentous fungi have been cloned and characterized. All the inulinases have several conserved motifs, such as WMND(E)PNGL, RDP, EC(V)P, SVEVF, Q and FS(T), which play an important role in inulinase catalysis and substrate binding. However, the exo-inulinases produced by yeasts has no conserved motif SVEVF and the yeasts do not produce any endo-inulinase. Exo- and endo-inulinases found in different microorganisms cluster separately at distant positions from each other. Most of the cloned inulinase genes have been expressed in Yarrowia lipolytica, Saccharomyces cerevisiae, Pichia pastoris, Klyuveromyces lactis and Escherichia coli, respectively. The recombinant inulinases produced and the engineered hosts using the cloned inulinase genes have many potential applications. Expression of most of the inulinase genes is repressed by glucose and fructose and induced by inulin and sucrose. However, the detailed mechanisms of the repression and induction are still unknown.

Biotechnological potential of inulin for bioprocesses

Inulin consists of linear chains of β-2,1-linked D-fructofuranose molecules terminated by a glucose residue through a sucrose-type linkage at the reducing end. In this review article, inulin and its applications in bioprocesses are overviewed. The tubers of many plants, such as Jerusalem artichoke, chicory, dahlia, and yacon contain a large amount of inulin. Inulin can be actively hydrolyzed by microbial inulinases to produce fructose, glucose and inulooligosaccharides (IOS). The fructose and glucose formed can be further transformed into ethanol, single-cell protein, single cell oil and other useful products by different microorganisms. IOS formed have many functions. Therefore, inulin can be widely used in food, feed, pharmaceutical, chemical and biofuels industries.

Expression of the inulinase gene from the marine-derived Pichia guilliermondii in Saccharomyces sp. W0 and ethanol production from inulin

It has been confirmed that Saccharomyces sp. W0 can produce high concentration of ethanol. In this study, the INU1 gene cloned from the marine-derived Pichia guilliermondii was transformed into uracil mutant of Saccharomyces sp. W0. The positive transformant Inu-66 obtained could produce 34.2 U ml⁻¹ of extracellular inulinase within 72 h of cultivation. It was found that 15.2 U of inulinase activity per one gram of inulin was suitable for inulin hydrolysis and ethanol production by the transformant Inu-66. During the small-scale fermentation, 13.7 ml of ethanol in 100 ml of medium was produced and 99.1% of the added inulin was utilized by the transformant. During the 2 l fermentation, 14.9% (v/v) of ethanol was produced from inulin and 99.5% of the added inulin was converted into ethanol, CO₂ and cell mass.