Selective uptake of fatty acids by the yeastYarrowia lipolytica

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.

The way forward to produce nutraceuticals from agri-food processing residues: obstacle, solution, and possibility

Food matrices contain bioactive compounds that have health benefits beyond nutritional value. The bulk of bioactive chemicals are still present in agro-industrial by-products as food matrices. Throughout the food production chain, there is a lot of agro-industrial waste that, if not managed effectively, could harm the environment, company, and how nutritiously and adequately people eat. It's important to establish processes that maximise the use of agro-industrial by-products, such as biological technologies that improve the extraction and acquisition of bioactive compounds for the food and pharmaceutical industries. As opposed to nonbiological processes, biological procedures provide high-quality, bioactive extracts with minimum toxicity and environmental impact. Fermentation and enzymatic treatment are biological processes for obtaining bioactive compounds from agro-industrial waste. In this context, this article summarises the principal bioactive components in agro-industrial byproducts and the biological methods employed to extract them. In this review efficient utilization of bioactive compounds from agro-industrial waste more effectively in food and pharmaceutical industries has been described.

Single cell protein and oil production from solid cocoa fatty acid distillates co-fed ethanol

The use of solid lipid sidestreams have been overlooked as a feedstock for the production of microbial biomass for food and feed applications and little to no recent work has examined the utilization of solid fatty acid distillates (FADs), which are a significant residue from vegetable oil processing. Yarrowia lipolytica and Rhodosporidium toruloides cultivated on cocoa fatty acid distillates (CFAD) generated final cell dry weight values > 40 g/L, with strong productivity (3.3 g/L·h) and rich protein (>45%) and lipid content (>25%). Interestingly, microbial oils were > 65% unsaturated fatty acids, compared < 20% unsaturated content in FAD. Importantly, to overcome mass-transfer limitations associated with bioconversion of solid lipid residues, ethanol was applied as a co-substrate to solubilize FAD residues. Here, FAD residues from cocoa deodorization have been demonstrated to be high energy feedstocks that represent an attractive substrate for the production of both single cell protein and oil (SCPO).

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.

Production of human milk fat substitute by engineered strains of Yarrowia lipolytica

Human milk fat has a distinctive stereoisomeric structure where palmitic acid is esterified to the middle (sn-2) position on the glycerol backbone of the triacylglycerol and unsaturated fatty acids to the outer (sn-1/3) positions. This configuration allows for more efficient nutrient absorption in the infant gut. However, the fat used in most infant formulas originates from plants, which exclude palmitic acid from the sn-2 position. Oleaginous yeasts provide an alternative source of lipids for human nutrition. However, these yeasts also exclude palmitic acid from the sn-2 position of their triacylglycerol. Here we show that Yarrowia lipolytica can be engineered to produce triacylglycerol with more than 60% of the palmitic acid in the sn-2 position, by expression of lysophosphatidic acid acyltransferases with palmitoyl-Coenzyme A specificity. The engineered Y. lipolytica strains can be cultured on glycerol, glucose, palm oil or a mixture of substrates, under nitrogen limited condition, to produce triacylglycerol with a fatty acid composition that resembles human milk fat, in terms of the major molecular species (palmitic, oleic and linoleic acids). Culture on palm oil or a mixture of glucose and palm oil produced the highest lipid titre and a triacylglycerol composition that is most similar with human milk fat. Our data show that an oleaginous yeast can be engineered to produce a human milk fat substitute (β-palmitate), that could be used as an ingredient in infant formulas.

Brine and Post-Frying Oil Management in the Fish Processing Industry—A Concept Based on Oleaginous Yeast Culture

Waste management solutions including the valorization of waste materials in biotechnological processes is an important issue needing to be explored. A significant amount of waste is being generated by the food industry. In this study, an attempt was made to utilize two fish industry wastes simultaneously—waste brine and post-frying oil from frying fish fillets in Yarrowia lipolytica culture with high single cell oil synthesis yield. Oxygenation in the culture medium had a positive effect on the biosynthesis efficiency of microbial oil, resulting in the highest content of lipids in yeast cells at the level of 0.431 g/g dm (dry mass). Y. lipolytica yeast preferentially accumulated oleic acid and linoleic acid, and the high content of linolenic acid, valuable from a nutritional point of view, was also found in microbial oil. This study proved that the use of post-frying rapeseed oil gives a chance to obtain valuable storage lipids in Y. lipolytica yeast cells via ex novo biosynthesis pathway. Furthermore, the wastewater stream could be limited using a waste brine as a solvent in medium preparation, but the brine share should not exceed 30% so as not to inhibit yeast cell growth.

Yarrowia lipolytica as a biorefinery platform for effluents and solid wastes valorization - challenges and opportunities

Due to its physiological and enzymatic features, Yarrowia lipolytica produces several valuable compounds from a wide range of substrates. Appointed by some authors as an industrial workhorse, Y. lipolytica has an extraordinary ability to use unrefined and complex low-cost substrates as carbon and nitrogen sources, aiding to reduce the waste surplus and to produce added-value compounds in a cost-effective way. Dozens of review papers regarding Y. lipolytica have been published till now, proving the interest that this yeast arouses in the scientific community. However, most of them are focused on metabolic pathways involved in substrates assimilation and product formation, or the development of synthetic biology tools in order to obtain engineered strains for biotechnological applications. This paper provides an exhaustive and up-to-date revision on the application of Y. lipolytica to valorize liquid effluents and solid wastes and its role in developing cleaner biotechnological approaches, aiming to boost the circular economy. Firstly, a general overview about Y. lipolytica is introduced, describing its intrinsic features and biotechnological applications. Then, an extensive survey of the literature regarding the assimilation of oily wastes (waste cooking oils, oil cakes and olive mill wastewaters), animal fat wastes, hydrocarbons-rich effluents, crude glycerol and agro-food wastes by Y. lipolytica strains will be discussed. This is the first article that brings together the environmental issue of all such residues and their valorization as feedstock for valuable compounds production by Y. lipolytica. Finally, it will demonstrate the potential of this non-conventional yeast to be used as a biorefinery platform.

Valorization of volatile fatty acids derived from low-cost organic waste for lipogenesis in oleaginous microorganisms-A review

To meet environmental sustainability goals, microbial oils have been suggested as an alternative to petroleum-based products. At present, microbial fermentation for oil production relies on pure sugar-based feedstocks. However, these feedstocks are expensive and are in limited supply. Volatile fatty acids, which are generated as intermediates during anaerobic digestion of organic waste have emerged as a renewable feedstock that has the potential to replace conventional sugar sources for microbial oil production. They comprise short-chain (C2 to C6) organic acids and are employed as building blocks in the chemical industry. The present review discusses the use of oleaginous microorganisms for the production of biofuels and added-value products starting from volatile fatty acids as feedstocks. The review describes the metabolic pathways enabling lipogenesis from volatile fatty acids, and focuses on strategies to enhance lipid accumulation in oleaginous microorganisms by tuning the ratios of volatile fatty acids generated via anaerobic fermentation.

Animal Fat as a Substrate for Production of n-6 Fatty Acids by Fungal Solid-State Fermentation

The method of solid-state fermentation (SSF) represents a powerful technology for the fortification of animal-based by-products. Oleaginous Zygomycetes fungi are efficient microbial cell factories used in SSF to valorize a wide range of waste and rest cereal materials. The application of this fermentation technique for utilization and biotransformation of animal-based materials represents a distinguished step in their treatment. In this study, for the first time, the strain Umbelopsis isabellina CCF2412 was used for the bioconversion of animal fat by-products to the fermented bioproducts enriched with n-6 polyunsaturated fatty acids, mainly γ-linolenic acid (GLA). Bioconversion of both cereals and the animal fat by-product resulted in the production of fermented bioproducts enriched with not just GLA (maximal yield was 6.4 mg GLA/g of fermented bioproduct), but also with high yields of glucosamine. Moreover, the fermentation on the cornmeal matrix led to obtaining bioproduct enriched with β-carotene. An increased amount of β-carotene content improved the antioxidant stability of obtained fermented bioproducts. Furthermore, the application of Fourier-transform infrared spectroscopy for rapid analysis and characterization of the biochemical profile of obtained SSF bioproducts was also studied.

Fine-tuning mitochondrial activity in Yarrowia lipolytica for citrate overproduction

Yarrowia lipolytica is a non-conventional yeast with promising industrial potentials for lipids and citrate production. It is also widely used for studying mitochondrial respiration due to a respiratory chain like those of mammalian cells. In this study we used a genome-scale model (GEM) of Y. lipolytica metabolism and performed a dynamic Flux Balance Analysis (dFBA) algorithm to analyze and identify metabolic levers associated with citrate optimization. Analysis of fluxes at stationary growth phase showed that carbon flux derived from glucose is rewired to citric acid production and lipid accumulation, whereas the oxidative phosphorylation (OxPhos) shifted to the alternative respiration mode through alternative oxidase (AOX) protein. Simulations of optimized citrate secretion flux resulted in a pronounced lipid oxidation along with reactive oxygen species (ROS) generation and AOX flux inhibition. Then, we experimentally challenged AOX inhibition by adding n-Propyl Gallate (nPG), a specific AOX inhibitor, on Y. lipolytica batch cultures at stationary phase. Our results showed a twofold overproduction of citrate (20.5 g/L) when nPG is added compared to 10.9 g/L under control condition (no nPG addition). These results suggest that ROS management, especially through AOX activity, has a pivotal role on citrate/lipid flux balance in Y. lipolytica. All taken together, we thus provide for the first time, a key for the understanding of a predominant metabolic mechanism favoring citrate overproduction in Y. lipolytica at the expense of lipids accumulation.

Exploring the Impact of Lipid-Rich Food Industry Waste Carbon Sources on the Growth of Candida cylindracea DSM 2031

The aim of this study was to evaluate the possibility of using several lipid-rich food industry wastes in the culture medium on the growth of Candida cylindracea DSM 2031 yeast strain. Four lipid wastes from the food industry: waste fish oil, rancid ghee, waste pork lard, and waste duck processing oil were investigated. It has been shown in the laboratory scale that the above-mentioned wastes can be used to obtain biomass and produce lipolytic enzymes by the tested strain and the C. cylindracea extracellular lipase is not constitutive. High yields of biomass (12.84, 12.75, and 12.24 g/dm3) were obtained in media containing waste duck processing oil, olive oil, and waste pork lard, respectively. The highest lipolytic activity was obtained in the media containing waste fish oil and rancid ghee (0.050 and 0.047 U/cm3). During 192-h flask cultures the highest extracellular lipase activity and biomass yield were observed in the late logarithmic phase. The study showed that there is a potential for waste management to produce lipolytic enzymes or to produce yeast biomass. The use of waste substrates may contribute to lowering the costs of commercial production, and such a solution is part of the sustainable development strategy.

Production and excretion of astaxanthin by engineered Yarrowia lipolytica using plant oil as both the carbon source and the biocompatible extractant

This study aimed to develop a bioprocess using plant oil as the carbon source for lipid-assimilating yeast to produce high-value astaxanthin. Using high-oleic safflower oil as a model, efficient cell growth and astaxanthin production by the engineered Yarrowia lipolytica strain ST7403 was demonstrated, and a considerable portion of astaxanthin was found excreted into the spent oil. Astaxanthin was the predominant carotenoid in the extracellular oil phase that allowed facile in situ recovery of astaxanthin without cell lysis. Autoclaving the safflower oil medium elevated the peroxide level but it declined quickly during fermentation (reduced by 84% by day 3) and did not inhibit cell growth or astaxanthin production. In a 1.5-L fed-batch bioreactor culture with a YnB-based medium containing 20% safflower oil, and with the feeding of casamino acids, astaxanthin production reached 54 mg/L (53% excreted) in 28 days. Further improvement in astaxanthin titer and productivity was achieved by restoring leucine biosynthesis in the host, and running fed-batch fermentation using a high carbon-to-nitrogen ratio yeast extract/peptone medium containing 70% safflower oil, with feeding of additional yeast extract/peptone, to attain 167 mg/L astaxanthin (48% excreted) in 9.5 days of culture. These findings facilitate industrial microbial biorefinery development that utilizes renewable lipids as feedstocks to not only produce high-value products but also effectively extract and recover the products, including non-native ones.Key Points• Yarrowia lipolytica can use plant oil as a C-source for astaxanthin production.• Astaxanthin is excreted and accumulated in the extracellular oil phase.• Astaxanthin is the predominant carotenoid in the extracellular oil phase.• Plant oil serves as a biocompatible solvent for in situ astaxanthin extraction. Graphical abstract.

Analysis of Yarrowia lipolytica growth, catabolism, and terpenoid biosynthesis during utilization of lipid-derived feedstock

This study employs biomass growth analyses and ¹³C-isotope tracing to investigate lipid feedstock utilization by Yarrowia lipolytica. Compared to glucose, oil-feedstock in the minimal medium increases the yeast's biomass yields and cell sizes, but decreases its protein content (<20% of total biomass) and enzyme abundances for product synthesis. Labeling results indicate a segregated metabolic network (the glycolysis vs. the TCA cycle) during co-catabolism of sugars (glucose or glycerol) with fatty acid substrates, which facilitates resource allocations for biosynthesis without catabolite repressions. This study has also examined the performance of a β-carotene producing strain in different growth mediums. Canola oil-containing yeast-peptone (YP) has resulted in the best β-carotene titer (121 ± 13 mg/L), two-fold higher than the glucose based YP medium. These results highlight the potential of Y. lipolytica for the valorization of waste-derived lipid feedstock.

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¹³C tracing was used to track Y. lipolytica metabolism of lipid-based feedstock.

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Y. lipolytica has a segregated flux network for lipid and sugar co-utilizations.

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Lipid feedstock and nitrogen sources affect cell morphology and optical density.

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Lipid feedstock benefits both Y. lipolytica growth and carotenoid biosynthesis.

An Overview of Potential Oleaginous Microorganisms and Their Role in Biodiesel and Omega-3 Fatty Acid-Based Industries

Microorganisms are known to be natural oil producers in their cellular compartments. Microorganisms that accumulate more than 20% w/w of lipids on a cell dry weight basis are considered as oleaginous microorganisms. These are capable of synthesizing vast majority of fatty acids from short hydrocarbonated chain (C6) to long hydrocarbonated chain (C36), which may be saturated (SFA), monounsaturated (MUFA), or polyunsaturated fatty acids (PUFA), depending on the presence and number of double bonds in hydrocarbonated chains. Depending on the fatty acid profile, the oils obtained from oleaginous microorganisms are utilized as feedstock for either biodiesel production or as nutraceuticals. Mainly microalgae, bacteria, and yeasts are involved in the production of biodiesel, whereas thraustochytrids, fungi, and some of the microalgae are well known to be producers of very long-chain PUFA (omega-3 fatty acids). In this review article, the type of oleaginous microorganisms and their expertise in the field of biodiesel or omega-3 fatty acids, advances in metabolic engineering tools for enhanced lipid accumulation, upstream and downstream processing of lipids, including purification of biodiesel and concentration of omega-3 fatty acids are reviewed.

Volatile fatty acids as novel building blocks for oil-based chemistry via oleaginous yeast fermentation

Microbial oils are proposed as a suitable alternative to petroleum-based chemistry in terms of environmental preservation. These oils have traditionally been studied using sugar-based feedstock, which implies high costs, substrate limitation, and high contamination risks. In this sense, low-cost carbon sources such as volatile fatty acids (VFAs) are envisaged as promising building blocks for lipid biosynthesis to produce oil-based bioproducts. VFAs can be generated from a wide variety of organic wastes through anaerobic digestion and further converted into lipids by oleaginous yeasts (OYs) in a fermentation process. These microorganisms can accumulate in the form of lipid bodies, lipids of up to 60% wt/wt of their biomass. In this context, OY is a promising biotechnological tool for biofuel and bioproduct generation using low-cost VFA media as substrates. This review covers recent advances in microbial oil production from VFAs. Production of VFAs via anaerobic digestion processes and the involved metabolic pathways are reviewed. The main challenges as well as recent approaches for lipid overproduction are also discussed.

Engineering the oleaginous yeast Yarrowia lipolytica to produce limonene from waste cooking oil

BACKGROUND

Limonene is an important biologically active natural product widely used in the food, cosmetic, nutraceutical and pharmaceutical industries. However, the low abundance of limonene in plants renders their isolation from plant sources non-economically viable. Therefore, engineering microbes into microbial factories for producing limonene is fast becoming an attractive alternative approach that can overcome the aforementioned bottleneck to meet the needs of industries and make limonene production more sustainable and environmentally friendly.

RESULTS

In this proof-of-principle study, the oleaginous yeast Yarrowia lipolytica was successfully engineered to produce both d-limonene and l-limonene by introducing the heterologous d-limonene synthase from Citrus limon and l-limonene synthase from Mentha spicata, respectively. However, only 0.124 mg/L d-limonene and 0.126 mg/L l-limonene were produced. To improve the limonene production by the engineered yeast Y. lipolytica strain, ten genes involved in the mevalonate-dependent isoprenoid pathway were overexpressed individually to investigate their effects on limonene titer. Hydroxymethylglutaryl-CoA reductase (HMGR) was found to be the key rate-limiting enzyme in the mevalonate (MVA) pathway for the improving limonene synthesis in Y. lipolytica. Through the overexpression of HMGR gene, the titers of d-limonene and l-limonene were increased to 0.256 mg/L and 0.316 mg/L, respectively. Subsequently, the fermentation conditions were optimized to maximize limonene production by the engineered Y. lipolytica strains from glucose, and the final titers of d-limonene and l-limonene were improved to 2.369 mg/L and 2.471 mg/L, respectively. Furthermore, fed-batch fermentation of the engineered strains Po1g KdHR and Po1g KlHR was used to enhance limonene production in shake flasks and the titers achieved for d-limonene and l-limonene were 11.705 mg/L (0.443 mg/g) and 11.088 mg/L (0.385 mg/g), respectively. Finally, the potential of using waste cooking oil as a carbon source for limonene biosynthesis from the engineered Y. lipolytica strains was investigated. We showed that d-limonene and l-limonene were successfully produced at the respective titers of 2.514 mg/L and 2.723 mg/L under the optimal cultivation condition, where 70% of waste cooking oil was added as the carbon source, representing a 20-fold increase in limonene titer compared to that before strain and fermentation optimization.

CONCLUSIONS

This study represents the first report on the development of a new and efficient process to convert waste cooking oil into d-limonene and l-limonene by exploiting metabolically engineered Y. lipolytica strains for fermentation. The results obtained in this study lay the foundation for more future applications of Y. lipolytica in converting waste cooking oil into various industrially valuable products.

Effect of carbon source on lipid accumulation and biodiesel production of Yarrowia lipolytica

Yarrowia lipolytica (Y. lipolytica) is an oleaginous yeast that can utilize hydrophobic substrates as carbon source to produce single-cell lipids for biodiesel production. This study attempts to increase the lipid accumulation ability of Y. lipolytica by first gradually elevating pure oil substrate concentration during the cultivation and then adding short-chain carbon compounds, such as glucose and sodium acetate, to a culture substance according to the optimal oil concentration. Results showed that Y. lipolytica cultured under 40.0 g L^-1 oil concentration showed higher lipids (2.97 g L^-1) and lipid content (37.35%, DW) compared with that cultured under 20.0 g L^-1, where the corresponding values were 1.91 g L^-1 and 24.46%. By contrast, the lipid content of Y. lipolytica increased from 37.35 to 41.50% when the substrate was changed from 40.0 g L^-1 pure oil to 5% sodium acetate combined with 95% oil under the same total carbon concentration. However, lipid accumulation did not increase even though 15% sodium acetate or 5% glucose, or 15% glucose was added to the combined substrate. Moreover, the lipid biomodification of Y. lipolytica was evident when it was cultured under the oil concentration of 20.0 g L^-1. Therefore, the lipid accumulation of Y. lipolytica can be elevated through the gradient increase of oil concentration and by adding a suitable amount of easily degradable carbon source. Furthermore, the lipid biomodification of Y. lipolytica improves biodiesel quality.

Waste fat biodegradation and biomodification by Yarrowia lipolytica and a bacterial consortium composed of Bacillus spp. and Pseudomonas putida

Fats, oils, and greases (FOGs) are a particular environmental threat. Biodegradation of FOGs is a challenge and in this study the biodegradation of waste cooking fats, namely butter and olive oil, was studied using a non-conventional yeast, Yarrowia lipolytica strain LFMB 20, and a bioaugmentation product consisting of Bacillus spp. and Pseudomonas putida CP1 strain. The microorganisms were grown aerobically in shake-flask experiments in an enriched medium supplemented with ca 0.85% w/v of waste fat. Analysis of the remaining substrate showed a removal of ca 90% of the fat by the yeast at the end of the incubation, while the bacteria removed ca 95% of both fats. Growth rate, biomass production and biomass yield per unit of fat consumed were all higher for the yeast compared to the bacterial consortium. The bacterial consortium exhibited autolysis and a significant decrease in its DCW value at the late growth phases of both fat substrate cultures. The main fatty acids (FAs) present in both fats were linoleic (Δ9,12C18:2), oleic (Δ9C18:1), palmitic (C16:0), palmitoleic (Δ9C16:1) and stearic (C18:0) acid. Both the bacterial consortium and Y. lipolytica preferentially removed Δ9C18:1 from the medium, while a negative selectivity against C18:0 was reported. Both inocula produced microbial mass that contained intra-cellular lipid quantities, but the bacterial consortium gave significantly higher lipid in DCW values compared with the yeast (maximum values up to ca 63% w/w for the butter and ca 42% w/w for the olive oil while the respective values for both lipids were 22% ± 2% w/w for Y. lipolytica). In all cases, intra-cellular lipids in DCW values decreased during the late growth phases, while their FA composition differed with those of the substrate fat.

Systematic analysis of the lysine acetylome reveals diverse functions of lysine acetylation in the oleaginous yeast Yarrowia lipolytica

Lysine acetylation of proteins, a major post-translational modification, plays a critical regulatory role in almost every aspects in both eukaryotes and prokaryotes. Yarrowia lipolytica, an oleaginous yeast, is considered as a model for bio-oil production due to its ability to accumulate a large amount of lipids. However, the function of lysine acetylation in this organism is elusive. Here, we performed a global acetylproteome analysis of Y. lipolytica ACA-DC 50109. In total, 3163 lysine acetylation sites were identified in 1428 proteins, which account for 22.1% of the total proteins in the cell. Fifteen conserved acetylation motifs were detected. The acetylated proteins participate in a wide variety of biological processes. Notably, a total of 65 enzymes involved in lipid biosynthesis were found to be acetylated. The acetylation sites are distributed in almost every type of conserved domains in the multi-enzymatic complexes of fatty acid synthetases. The provided dataset probably illuminates the crucial role of reversible acetylation in oleaginous microorganisms, and serves as an important resource for exploring the physiological role of lysine acetylation in eukaryotes.

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.

Engineering Yarrowia lipolytica for Enhanced Production of Lipid and Citric Acid

Increasing demand for plant oil for food, feed, and fuel production has led to food-fuel competition, higher plant lipid cost, and more need for agricultural land. On the other hand, the growing global production of biodiesel has increased the production of glycerol as a by-product. Efficient utilization of this by-product can reduce biodiesel production costs. We engineered Yarrowia lipolytica (Y. lipolytica) at various metabolic levels of lipid biosynthesis, degradation, and regulation for enhanced lipid and citric acid production. We used a one-step double gene knock-in and site-specific gene knock-out strategy. The resulting final strain combines the overexpression of homologous DGA1 and DGA2 in a POX-deleted background, and deletion of the SNF1 lipid regulator. This increased lipid and citric acid production in the strain under nitrogen-limiting conditions (C/N molar ratio of 60). The engineered strain constitutively accumulated lipid at a titer of more than 4.8 g/L with a lipid content of 53% of dry cell weight (DCW). The secreted citric acid reached a yield of 0.75 g/g (up to ~45 g/L) from pure glycerol in 3 days of batch fermentation using a 1-L bioreactor. This yeast cell factory was capable of simultaneous lipid accumulation and citric acid secretion. It can be used in fed-batch or continuous bioprocessing for citric acid recovery from the supernatant, along with lipid extraction from the harvested biomass.

Glycerol conversion into a single cell oil by engineered Yarrowia lipolytica

Oleaginous yeasts are considered as natural single cell oil producers. Engineering the lipid biosynthetic pathway has the potential to increase lipid accumulation by these yeasts. In Yarrowia lipolytica, three diacylglycerol acyltransferases encoded by LRO1, DGA1, and DGA2 genes are involved in lipid formation. Strain JMY3580 was constructed by overexpressing DGA2 gene in Q4 strain (dga1Δ dga2Δ lro1Δ are1Δ). Reconstruction of triacylglycerol synthesis pathway led to significant improvement in lipid accumulation. Strain JMY3580 accumulated over 40% of lipids in biomass, while lipid accumulation in wild-type strain was not able to exceed 20% when grown on a glycerol-based medium with carbon to nitrogen ratio of 90. Higher lipid accumulation (over 50%) was achieved in fed-batch grown cells when glycerol was added during cultivation. The best biomass yield was 18.5 g/L after 144 h with total fatty acid yield 9.9 g/L. Fatty acid composition was altered when Dga2p was the only diacylglycerol acyltransferase present in yeast cells, especially lower percentage of linoleic acid was present in lipids of JMY3580. Microbial oil prepared by conversion of glycerol by genetically engineered Y. lipolytica could be applied for various value-added products based on single cell oils.

Combining metabolic engineering and process optimization to improve production and secretion of fatty acids

Microbial oils are sustainable alternatives to petroleum for the production of chemicals and fuels. Oleaginous yeasts are promising source of oils and Yarrowia lipolytica is the most studied and engineered one. Nonetheless the commercial production of biolipids is so far limited to high value products due to the elevated production and extraction costs. In order to contribute to overcoming these limitations we exploited the possibility of secreting lipids to the culture broth, uncoupling production and biomass formation and facilitating the extraction. We therefore considered two synthetic approaches, Strategy I where fatty acids are produced by enhancing the flux through neutral lipid formation, as typically occurs in eukaryotic systems and Strategy II where the bacterial system to produce free fatty acids is mimicked. The engineered strains, in a coupled fermentation and extraction process using alkanes, secreted the highest titer of lipids described so far, with a content of 120% of DCW.

Production of Palmitoleic and Linoleic Acid in Oleaginous and Nonoleaginous Yeast Biomass

We investigated the possibility of utilizing both oleaginous yeast species accumulating large amounts of lipids (Yarrowia lipolytica, Rhodotorula glutinis, Trichosporon cutaneum, and Candida sp.) and traditional biotechnological nonoleaginous ones (Kluyveromyces polysporus, Torulaspora delbrueckii, and Saccharomyces cerevisiae) as potential producers of dietetically important major fatty acids. The main objective was to examine the cultivation conditions that would induce a high ratio of dietary fatty acids and biomass. Though genus-dependent, the type of nitrogen source had a higher influence on biomass yield than the C/N ratio. The nitrogen source leading to the highest lipid accumulation was potassium nitrate, followed by ammonium sulfate, which is an ideal nitrogen source supporting, in both oleaginous and nonoleaginous species, sufficient biomass growth with concomitantly increased lipid accumulation. All yeast strains displayed high (70–90%) content of unsaturated fatty acids in total cell lipids. The content of dietary fatty acids of interest, namely, palmitoleic acid and linoleic acid, reached in Kluyveromyces and Trichosporon strains over 50% of total fatty acids and the highest yield, over 280 mg per g of dry cell weight of these fatty acids, was observed in Trichosporon with ammonium sulfate as nitrogen source at C/N ratio 70.

Lipid production on free fatty acids by oleaginous yeasts under non-growth conditions

Microbial lipids produced by oleaginous yeasts serve as promising alternatives to traditional oils and fats for the production of biodiesel and oleochemicals. To improve its techno-economics, it is pivotal to use wastes and produce high quality lipids of special fatty acid composition. In the present study, four oleaginous yeasts were tested to use free fatty acids for lipid production under non-growth conditions. Microbial lipids of exceptionally high fatty acid relative contents, e.g. those contained over 70% myristic acid or 80% oleic acid, were produced that may be otherwise inaccessible by growing cells on various carbon sources. It was found that Cryptococcus curvatus is a robust strain that can efficiently use oleic acid as well as even-numbered saturated fatty acids with carbon atoms ranging from 10 to 20. Our results provided new opportunity for the production of functional lipids and for the exploitation of organic wastes rich in free fatty acids.

Yarrowia lipolytica and pollutants: Interactions and applications

Yarrowia lipolytica is a dimorphic, non-pathogenic, ascomycetous yeast species with distinctive physiological features and biochemical characteristics that are significant in environment-related matters. Strains naturally present in soils, sea water, sediments and waste waters have inherent abilities to degrade hydrocarbons such as alkanes (short and medium chain) and aromatic compounds (biphenyl and dibenzofuran). With the application of slow release fertilizers, design of immobilization techniques and development of microbial consortia, scale-up studies and in situ applications have been possible. In general, hydrocarbon uptake in this yeast is mediated by attachment to large droplets (via hydrophobic cell surfaces) or is aided by surfactants and emulsifiers. Subsequently, the internalized hydrocarbons are degraded by relevant enzymes innately present in the yeast. Some wild-type or recombinant strains also detoxify nitroaromatic (2,4,6-trinitrotoluene), halogenated (chlorinated and brominated hydrocarbons) and organophosphate (methyl parathion) compounds. The yeast can tolerate some metals and detoxify them via different biomolecules. The biomass (unmodified, in combination with sludge, magnetically-modified and in the biofilm form) has been employed in the biosorption of hexavalent chromium ions from aqueous solutions. Yeast cells have also been applied in protocols related to nanoparticle synthesis. The treatment of oily and solid wastes with this yeast reduces chemical oxygen demand or value-added products (single cell oil, single cell protein, surfactants, organic acids and polyalcohols) are obtained. On account of all these features, the microorganism has established a place for itself and is of considerable value in environment-related applications.

Compositional shift in lipid fractions during lipid accumulation and turnover in Schizochytrium sp

Single cell oils (SCOs), a complex lipid system, contains neutral lipids (NLs), polar lipids (PLs) and unsaponifiable matters (UMs). To investigate the dynamic changes and the metabolic competition mechanism of different components of SCOs, changes in lipid composition of Schizochytrium sp. were monitored in lipid accumulation and turnover stages. Lipid content could reach 69.98% in biomass during the lipid accumulation stage, while, after the exhaustion of glucose, the content decreased to 45.51% and 20.6g/L non-oil biomass was synthesis. Polyunsaturated fatty acids (PUFAs) were easier to bind with PLs. NLs were preferentially converted to PLs during lipid turnover stage, accompanied by the degradation of saturated fatty acids and the increase of UMs. Meanwhile, a positive correlation between the synthesis of PUFAs and unsaponifiable matters exited in Schizochytrium sp., and increasing the content of UMs from 45 to 100mg/L could increase the PUFA percentage from 64% to 74% effectively.

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.

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.

Utilization of biodiesel by-products for biogas production

This contribution reviews the possibility of using the by-products from biodiesel production as substrates for anaerobic digestion and production of biogas. The process of biodiesel production is predominantly carried out by catalyzed transesterification. Besides desired methylesters, this reaction provides also few other products, including crude glycerol, oil-pressed cakes, and washing water. Crude glycerol or g-phase is heavier separate liquid phase, composed mainly by glycerol. A couple of studies have demonstrated the possibility of biogas production, using g-phase as a single substrate, and it has also shown a great potential as a cosubstrate by anaerobic treatment of different types of organic waste or energy crops. Oil cakes or oil meals are solid residues obtained after oil extraction from the seeds. Another possible by-product is the washing water from raw biodiesel purification, which is an oily and soapy liquid. All of these materials have been suggested as feasible substrates for anaerobic degradation, although some issues and inhibitory factors have to be considered.