Citric Acid Production in Yarrowia lipolytica SWJ-1b Yeast When Grown on Waste Cooking Oil

Bioleaching of rare earth elements from ores and waste materials: Current status, economic viability and future prospects

Rare earth elements (REEs) are critical components of numerous products widely used in many areas, and the demand for REEs is increasing dramatically in recent years. Physical-chemical leaching is commonly adopted for the recovery of REEs from ores and solid wastes, but concerns over the generation of hazards, operation safety, and environmental pollution have urged the transition to greener and more sustainable leaching methods. Bioleaching is considered an excellent alternative for the recovery of REEs. This review provided an overview on the REEs recovery from primary and secondary resources via different bioleaching strategies. The techno-economics of bioleaching for REEs recovery were highlighted, and key factors affecting the economic viability of bioleaching were identified. Finally, strategies including the utilization of low-cost substrates as feedstocks, non-sterile bioleaching, recycling and reutilization of biolixiviants, and development of robust bioleaching strains were proposed to improve the economic competitiveness of bioleaching. It is expected that this review could serve as a useful guideline on the design of more economically competitive bioleaching processes for the recovery REEs from different resources.

Considerations Regarding High Oil Density Bioreactor-Scale Fermentations of Yarrowia lipolytica Using CFD Modeling and Experimental Validation

Hydrophobic feedstocks such as waste cooking oil have recently been considered for microbial biotransformation due to their abundance, low cost, and unique advantage for lipid-derived fermentation products. Most fermentations with hydrophobic substrates are conducted at the tube or flask scale (less than 1 L total volume) or with the hydrophobic substrate comprising a small fraction of the media. Low substrate concentrations require additional feeding. Alternatively, high concentrations do not require significant dilution of the oil feedstock, which reduce volumetric requirements for larger scale fermentations. However, high-oil-density fermentations complicate efficient mixing and mass transfer challenges which are exacerbated at larger scales. To address this, computational fluid dynamics (CFD) models were explored to simulate three-phase (hydrophobic, hydrophilic, and gaseous) bench (3 L) and pilot scale (4000 L) bioreactors, highlighting challenges and potential considerations. Bioreactor fermentations of Yarrowia lipolytica strain L36DGA1 with substrate loadings of 5%, 10%, 20%, 30%, 40%, and 50% (v/v) waste cooking oil were also conducted, representing one of the highest concentrations in the reported literature. This work supports future research into and implementation of high-oil-density fermentations at the bench and pilot bioreactor scale.

Unraveling the Potential of Yarrowia lipolytica to Utilize Waste Motor Oil as a Carbon Source

This study evaluated the potential of Y. lipolytica (CBS 2075 and DSM 8218) to grow in waste motor oil (WMO) and produce valuable compounds, laying the foundation for a sustainable approach to WMO management. Firstly, yeast strains were screened for their growth on WMO (2-10 g·L-1) in microplate cultures. Despite limited growth, the CBS 2075 strain exhibited comparable growth to control conditions (without WMO), while DSM 8218 growth increased 2- and 3-fold at 5 g·L-1 and 10 g·L-1 WMO, respectively. The batch cultures in the bioreactor confirmed the best performance of DSM 8218. A two-stage fed-batch strategy-growth phase in aliphatic hydrocarbons, followed by the addition of WMO (one pulse of 5 g·L-1 or five pulses of 1 g·L-1 WMO), significantly increased biomass production and WMO assimilation by both strains. In experiments with five pulses, CBS 2075 and DSM 8218 strains reached high proteolytic activities (593-628 U·L-1) and accumulated high quantities of intracellular lipids (1.3-1.7 g·L-1). Yeast lipids, mainly composed of oleic and linoleic acids with an unsaturated/saturated fraction > 59%, meet the EU biodiesel standard EN 14214, making them suitable for biodiesel production.

Research progress on biosynthesis of erythritol and multi-dimensional optimization of production strategies

Erythritol, as a new type of natural sweetener, has been widely used in food, medical, cosmetics, pharmaceutical and other fields due to its unique physical and chemical properties and physiological functions. In recent years, with the continuous development of strategies such as synthetic biology, metabolic engineering, omics-based systems biology and high-throughput screening technology, people's understanding of the erythritol biosynthesis pathway has gradually deepened, and microbial cell factories with independent modification capabilities have been successfully constructed. In this review, the cheap feedstocks for erythritol synthesis are introduced in detail, the environmental factors affecting the synthesis of erythritol and its regulatory mechanism are described, and the tools and strategies of metabolic engineering involved in erythritol synthesis are summarized. In addition, the study of erythritol derivatives is helpful in expanding its application field. Finally, the challenges that hinder the effective production of erythritol are discussed, which lay a foundation for the green, efficient and sustainable production of erythritol in the future and breaking through the bottleneck of production.

Exploring the use of hexadecane by Yarrowia lipolytica: Effect of dissolved oxygen and medium supplementation

This work aimed to evaluate the effect of medium composition and volumetric oxygen transfer coefficient (kLa) on Y. lipolytica growth and production of microbial lipids and enzymes from hexadecane. In the stirred tank bioreactor, increasing kLa from 11 h-1 to 132 h-1 improved the hexadecane assimilation rate, biomass concentration, and lipids synthesis (0.90 g·L-1). A cost-effective hexadecane-based medium supplemented with corn steep liquor and a low amount of ammonium sulfate boosted lipids production up to 2.1 g·L-1, composed of palmitic, palmitoleic, oleic, and linoleic acids. The unsaturated/saturated fraction was dependent on the C/N ratio. Lipids of Y. lipolytica CBS 2075 are promising feedstock for animal feed, food additives, or the biodiesel industry. Simultaneous synthesis of extracellular lipase and protease from hexadecane was observed, which is a new feature that was not previously reported. The highest enzyme activity was obtained at the highest C/N ratio conditions. These results open new perspectives on the application of Y. lipolytica-based cultures for the biotransformation of hexadecane-polluted streams into valuable compounds, fulfilling an interesting strategy towards the circular economy concept.

Citric Acid: Properties, Microbial Production, and Applications in Industries

Citric acid finds broad applications in various industrial sectors, such as the pharmaceutical, food, chemical, and cosmetic industries. The bioproduction of citric acid uses various microorganisms, but the most commonly employed ones are filamentous fungi such as Aspergillus niger and yeast Yarrowia lipolytica. This article presents a literature review on the properties of citric acid, the microorganisms and substrates used, different fermentation techniques, its industrial utilization, and the global citric acid market. This review emphasizes that there is still much to explore, both in terms of production process techniques and emerging new applications of citric acid.

Machine Learning Models Using Data Mining for Biomass Production from Yarrowia lipolytica Fermentation

In this paper, a database of biomass production from Yarrowia lipolytica fermentation is prepared and constructed using machine learning and data mining approaches. The database is curated from 15 publications and consists of 301 rows of data with 25 predictors and 1 label. The predictors include inoculum size, temperature, pH, and time, while the label is the corresponding biomass production. The database is then divided into training, validation, and test datasets and analyzed as a supervised machine learning task for regression. Twenty-six regression models are employed and compared for their performance in predicting biomass production. The best-performing model is the Matern 5/2 Gaussian process regression model, which has the lowest root-mean-squared error of 0.75 g/L, the highest R squared of 0.90, and the lowest mean absolute error of 0.52 g/L. The t-test is used to identify the most important predictors, and 14 predictors are sufficient for creating an accurate model. These 14 predictors are fermentation time, peptone, temperature, total Kjeldahl nitrogen, shaking rate, total nitrogen, inoculum size, yeast extract, crude glycerol, glucose, oil and grease, media pH, ammonium sulfate, and olive oil. This research demonstrates the application of machine learning and data mining to estimate biomass production and gives insight into which parameters are essential for Yarrowia lipolytica fermentation.

High-yield α-humulene production in Yarrowia lipolytica from waste cooking oil based on transcriptome analysis and metabolic engineering

BACKGROUND

α-Humulene is an important biologically active sesquiterpene, whose heterologous production in microorganisms is a promising alternative biotechnological process to plant extraction and chemical synthesis. In addition, the reduction of production expenses is also an extremely critical factor in the sustainable and industrial production of α-humulene. In order to meet the requirements of industrialization, finding renewable substitute feedstocks such as low cost or waste substrates for terpenoids production remains an area of active research.

RESULTS

In this study, we investigated the feasibility of peroxisome-engineering strain to utilize waste cooking oil (WCO) for high production of α-humulene while reducing the cost. Subsequently, transcriptome analysis revealed differences in gene expression levels with different carbon sources. The results showed that single or combination regulations of target genes identified by transcriptome were effective to enhance the α-humulene titer. Finally, the engineered strain could produce 5.9 g/L α-humulene in a 5-L bioreactor.

CONCLUSION

To the best of our knowledge, this is the first report that converted WCO to α-humulene in peroxisome-engineering strain. These findings provide valuable insights into the high-level production of α-humulene in Y. lipolytica and its utilization in WCO bioconversion.

Lipid production from lignocellulosic biomass using an engineered Yarrowia lipolytica strain

BACKGROUND

The utilization of industrial wastes as feedstock in microbial-based processes is a one of the high-potential approach for the development of sustainable, environmentally beneficial and valuable bioproduction, inter alia, lipids. Rye straw hydrolysate, a possible renewable carbon source for bioconversion, contains a large amount of xylose, inaccessible to the wild-type Yarrowia lipolytica strains. Although these oleaginous yeasts possesses all crucial genes for xylose utilization, it is necessary to induce their metabolic pathway for efficient growth on xylose and mixed sugars from agricultural wastes. Either way, biotechnological production of single cell oils (SCO) from lignocellulosic hydrolysate requires yeast genome modification or adaptation to a suboptimal environment.

RESULTS

The presented Y. lipolytica strain was developed using minimal genome modification-overexpression of endogenous xylitol dehydrogenase (XDH) and xylulose kinase (XK) genes was sufficient to allow yeast to grow on xylose as a sole carbon source. Diacylglycerol acyltransferase (DGA1) expression remained stable and provided lipid overproduction. Obtained an engineered Y. lipolytica strain produced 5.51 g/L biomass and 2.19 g/L lipids from nitrogen-supplemented rye straw hydrolysate, which represents an increase of 64% and an almost 10 times higher level, respectively, compared to the wild type (WT) strain. Glucose and xylose were depleted after 120 h of fermentation. No increase in byproducts such as xylitol was observed.

CONCLUSIONS

Xylose-rich rye straw hydrolysate was exploited efficiently for the benefit of production of lipids. This study indicates that it is possible to fine-tune a newly strain with as minimally genetic changes as possible by adjusting to an unfavorable environment, thus limiting multi-level genome modification. It is documented here the use of Y. lipolytica as a microbial cell factory for lipid synthesis from rye straw hydrolysate as a low-cost feedstock.

Engineering Yarrowia lipolytica for the sustainable production of β-farnesene from waste oil feedstock

BACKGROUND

β-Farnesene is a sesquiterpene with versatile industrial applications. The production of β-farnesene from waste lipid feedstock is an attractive method for sustainable production and recycling waste oil. Yarrowia lipolytica is an unconventional oleaginous yeast, which can use lipid feedstock and has great potential to synthesize acetyl-CoA-derived chemicals.

RESULTS

In this study, we engineered Y. lipolytica to produce β-farnesene from lipid feedstock. To direct the flux of acetyl-CoA, which is generated from lipid β-oxidation, to β-farnesene synthesis, the mevalonate synthesis pathway was compartmentalized into peroxisomes. β-Farnesene production was then engineered by the protein engineering of β-farnesene synthase and pathway engineering. The regulation of lipid metabolism by enhancing β-oxidation and eliminating intracellular lipid synthesis was further performed to improve the β-farnesene synthesis. As a result, the final β-farnesene production with bio-engineering reached 35.2 g/L and 31.9 g/L using oleic acid and waste cooking oil, respectively, which are the highest β-farnesene titers reported in Y. lipolytica.

CONCLUSIONS

This study demonstrates that engineered Y. lipolytica could realize the sustainable production of value-added acetyl-CoA-derived chemicals from waste lipid feedstock.

Towards the Physiological Understanding of Yarrowia lipolytica Growth and Lipase Production Using Waste Cooking Oils

The yeast Yarrowia lipolytica is an industrially relevant microorganism, which is able to convert low-value wastes into different high-value, bio-based products, such as enzymes, lipids, and other important metabolites. Waste cooking oil (WCO) represents one of the main streams generated in the food supply chain, especially from the domestic sector. The need to avoid its incorrect disposal makes this waste a resource for developing bioprocesses in the perspective of a circular bioeconomy. To this end, the strain Y. lipolytica W29 was used as a platform for the simultaneous production of intracellular lipids and extracellular lipases. Three different minimal media conditions with different pH controls were utilized in a small-scale (50 mL final volume) screening strategy, and the best condition was tested for an up-scaling procedure in higher volumes (800 mL) by selecting the best-performing possibility. The tested media were constituted by YNB media with high nitrogen restriction (1 g L−1 (NH4)2SO4) and different carbon sources (3% w v−1 glucose and 10% v v−1 WCO) with different levels of pH controls. Lipase production and SCO content were analyzed. A direct correlation was found between decreasing FFA availability in the media and increasing SCO levels and lipase activity. The simultaneous production of extracellular lipase (1.164 ± 0.025 U mL−1) and intracellular single-cell oil accumulation by Y. lipolytica W29 growing on WCO demonstrates the potential and the industrial relevance of this biorefinery model.

Phosphorus and Nitrogen Limitation as a Part of the Strategy to Stimulate Microbial Lipid Biosynthesis

Microbial lipids called a sustainable alternative to traditional vegetable oils invariably capture the attention of researchers. In this study, the effect of limiting inorganic phosphorus (KH2PO4) and nitrogen ((NH4)2SO4) sources in lipid-rich culture medium on the efficiency of cellular lipid biosynthesis by Y. lipolytica yeast has been investigated. In batch cultures, the carbon source was rapeseed waste post-frying oil (50 g/dm3). A significant relationship between the concentration of KH2PO4 and the amount of lipids accumulated has been revealed. In the shake-flask cultures, storage lipid yield was correlated with lower doses of phosphorus source in the medium. In bioreactor culture in mineral medium with (g/dm3) 3.0 KH2PO4 and 3.0 (NH4)2SO4, the cellular lipid yield was 47.5% (w/w). Simultaneous limitation of both phosphorus and nitrogen sources promoted lipid accumulation in cells, but at the same time created unfavorable conditions for biomass growth (0.78 gd.m./dm3). Increased phosphorus availability with limited cellular access to nitrogen resulted in higher biomass yields (7.45 gd.m./dm3) than phosphorus limitation in a nitrogen-rich medium (4.56 gd.m./dm3), with comparable lipid yields (30% and 32%). Regardless of the medium composition, the yeast preferentially accumulated oleic and linoleic acids as well as linolenic acid up to 8.89%. Further, it is crucial to determine the correlation between N/P molar ratios, biomass growth and efficient lipid accumulation. In particular, considering the contribution of phosphorus as a component of coenzymes in many metabolic pathways, including lipid biosynthesis and respiration processes, its importance as a factor in the cultivation of the oleaginous microorganisms was highlighted.

α-Farnesene production from lipid by engineered Yarrowia lipolytica

Producing high value-added products from waste lipid feedstock by microbial cell factory has great advantages to minimize the pollution as well as improve the economic value of wasted oils and fats. Yarrowia lipolytica is a non-conventional oleaginous yeast and can grow on a variety of hydrophobic substrates. In this study, we explored its ability to synthesize α-farnesene, an important sesquiterpene, using lipid feedstock. Based on the α-farnesene production strain, we constructed previously, we identified that Erg12 was the key limiting factor to further increase the α-farnesene production. The α-farnesene production was improved by 35.8% through increasing the copy number of ERG12 and FSERG20 on oleic acid substrate. Expression of heterologous VHb further improved α-farnesene production by 12.7%. Combining metabolic engineering with the optimization of fermentation conditions, the α-farnesene titer and yield reached 10.2 g/L and 0.1 g/g oleic acid, respectively, in fed-batch cultivation. The α-farnesene synthesis ability on waste cooking oil and other edible oils were also explored. Compared with using glucose as carbon source, using lipid substrates obtained higher α-farnesene yield and titer, but lower by-products accumulation, demonstrating the advantage of Y. lipolytica to synthesize high value-added products using lipid feedstock.

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.

Citric Acid Production of Yeasts: An Overview

Background

Citric acid, an intermediate product of the Krebs cycle, has a wide usage area in the food industry since it has some functions such as acidulant, flavouring agent, preservative and antioxidant. Although molds are the most commonly used microorganisms in the citric acid production, it is known that there are significant advantages of using yeasts.

Purpose and scope

The microbial citric acid production mechanism needs to be well understood to make production more efficient. In this study, the yeasts used in the production, fermentation types and the factors affecting production were reviewed with studies.

Methodology

Although production of citric acid can be produced by chemical synthesis, the fermentation is preferred because of its low cost and ease of use. More than 90% of citric acid produced in the world is obtained by fermentation.

Results

Yarrowia lipolytica, Candida zeylanoides and Candida oleophila are evaluated for citric acid production with substrates such as molasses, glucose, sucrose and glycerol. On the other hand, there is great interest in developing processes with new substrates and/ or microorganisms.

Conclusion

Although the microbial strain is an important factor, the factors such as carbon, phosphorus and nitrogen sources, aeration, the presence of trace elements and pH are also parameters affecting the production.

Overexpression of Citrate Synthase Increases Isocitric Acid Biosynthesis in the Yeast Yarrowia lipolytica

Yarrowia lipolytica is a non-conventional yeast producing valuable compounds, such as citric acids, from renewable raw materials. This study investigated the impact of citrate synthase overexpression on the biosynthesis of citric and isocitric acid in Y. lipolytica. Two transformants of Y. lipolytica A101.1.31 strain (efficient citric acid producer), overexpressing CIT1 or CIT2 gene (encoding proteins with citrate synthase activity), were constructed. The results revealed that overexpression of either of these genes enhances citrate synthase activity. Additionally, the cit1 knockout strain was unable to use propionate as the sole carbon source, which proves that CIT1 gene encodes a dual activity protein–citrate and 2-methylcitrate synthase. In the overexpressing mutants, a significant increase in isocitric acid biosynthesis was observed. Both CIT1 and CIT2 overexpressing strains produced citric and isocitric acid from vegetable oil in a ratio close to 1 (CA/ICA ratio for wild-type strain was 4.12).

Oil crop wastes as substrate candidates for enhancing erythritol production by modified Yarrowia lipolytica via one-step solid state fermentation

Oil crop wastes are attractive feedstocks in microbial processes due to their low cost. However, the product yields can be limited by their undesirable nitrogen surplus. Present study proposed a one-step solid state fermentation (SSF) method for producing erythritol from unrefined oil crop wastes using a modified strain Y. lipolytica M53-S. Enhanced erythritol production (185.4 mg/gds) was obtained from peanut press cake mixed with 40% sesame meal and 10% waste cooking oil. The process was performed at pH 4.0 in 5 L flasks, with initial moisture content, NaCl addition, and inoculum size of 70%, 0.02 g/gds, and 7.5 × 10⁴ cells/gds, respectively. This procedure showed advantages in terms of lower material cost than that of submerged fermentation and shorter culture cycle (96 h) than other SSF processes. In repeated-batch fermentation, erythritol was continuously produced for seven cycles. This study presents a feasible approach in developing an efficient erythritol cultivation from nitrogen-rich wastes.

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.

Organic Wastes as Feedstocks for Non-Conventional Yeast-Based Bioprocesses

Non-conventional yeasts are efficient cell factories for the synthesis of value-added compounds such as recombinant proteins, intracellular metabolites, and/or metabolic by-products. Most bioprocess, however, are still designed to use pure, ideal sugars, especially glucose. In the quest for the development of more sustainable processes amid concerns over the future availability of resources for the ever-growing global population, the utilization of organic wastes or industrial by-products as feedstocks to support cell growth is a crucial approach. Indeed, vast amounts of industrial and commercial waste simultaneously represent an environmental burden and an important reservoir for recyclable or reusable material. These alternative feedstocks can provide microbial cell factories with the required metabolic building blocks and energy to synthesize value-added compounds, further representing a potential means of reduction of process costs as well. This review highlights recent strategies in this regard, encompassing knowledge on catabolic pathways and metabolic engineering solutions developed to endow cells with the required metabolic capabilities, and the connection of these to the synthesis of value-added compounds. This review focuses primarily, but not exclusively, on Yarrowia lipolytica as a yeast cell factory, owing to its broad range of naturally metabolizable carbon sources, together with its popularity as a non-conventional yeast.

Aseptic production of citric and isocitric acid from crude glycerol by genetically modified Yarrowia lipolytica

The unconventional yeast Yarrowia lipolytica is known for its capacity to produce citric or isocitric acid from glycerol. In this study a reduction of production cost was achieved by using cheap crude glycerol and conducting the production at pH 3 to prevent bacterial contamination. In this study a Y. lipolytica strain overexpressing Gut1 and Gut2 was used. For the modified strain, crude glycerol proved to be an excellent substrate for production of citric/isocitric acids in aseptic conditions, as the final concentration of these compounds reached 75.9 ± 1.8 g L^-1 after 7 days of batch production. Interestingly, the concentration of isocitric acid was 42.5 ± 2.4 g L^-1, which is one of the highest concentrations of isocitric acid obtained from a waste substrate. In summary, these data show that organic acids can be efficiently produced by the yeast Y. lipolytica from crude glycerol without any prior purification in aseptic conditions.

Enhanced squalene biosynthesis in Yarrowia lipolytica based on metabolically engineered acetyl-CoA metabolism

As a bioactive triterpenoid, squalene is widely used in the food industry, cosmetics, and pharmacology. Squalene's major commercial sources are the liver oil of deep-sea sharks and plant oils. In this study, we focused on the enhancement of squalene biosynthesis in Yarrowia lipolytica, with particular attention to the engineering of acetyl-CoA metabolism based on genome-scale metabolic reaction network analysis. Although the overexpression of the rate-limiting endogenous ylHMG1 (3-hydroxy-3-methylglutaryl-CoA reductase gene) could improve squalene synthesis by 3.2-fold over that by the control strain, the availability of the key intracellular precursor, acetyl-CoA, was found to play a more significant role in elevating squalene production. Analysis of metabolic networks with the newly constructed genome-scale metabolic model of Y. lipolytica iYL_2.0 showed that the acetyl-CoA pool size could be increased by redirecting carbon flux of pyruvate dehydrogenation towards the ligation of acetate and CoA or the cleavage of citrate to form oxaloacetate and acetyl-CoA. The overexpression of either acetyl-CoA synthetase gene from Salmonella enterica (acs*) or the endogenous ATP citrate lyase gene (ylACL1) resulted in a more than 50% increase in the cytosolic acetyl-CoA level. Moreover, iterative chromosomal integration of the ylHMG1, asc*, and ylACL1 genes resulted in a significant improvement in squalene production (16.4-fold increase in squalene content over that in the control strain). We also found that supplementation with 10 mM citrate in a flask culture further enhanced squalene production to 10 mg/g DCW. The information obtained in this study demonstrates that rationally engineering acetyl-CoA metabolism to ensure the supply of this key metabolic precursor is an efficient strategy for the enhancement of squalene biosynthesis.

Effects of osmotic pressure and pH on citric acid and erythritol production from waste cooking oil by Yarrowia lipolytica

Erythritol and citric acid could be produced from waste cooking oil (WCO) by Yarrowia lipolytica under different medium conditions, and osmotic pressure together with pH were considered to be the critical factors in this process. High osmotic pressure (2.76 osmol/L) combined with low pH (pH 3.0) promoted the highest yield of erythritol (21.8 g/L) accompanied by low-producing citric acid (2.5 g/L). By contrast, the highest citric acid biosynthesis (12.6 g/L) was detected under a pH of 6.0 and an osmotic pressure of 0.75 osmol/L, when only 4.0 g/L of erythritol was yielded. Moreover, lipase activities in these two media were also detected, and pH 3.0-OP 2.76 was supposed to be more beneficial to lipase activity. Biochemical pathways involved in the biosynthesis of erythritol and citric acid were subsequently investigated, and the products yielded from WCO were assumed to be correlated with the activities of transketolase, erythrose reductase, citrate synthase, and glycerol kinase. However, RT-PCR analysis revealed that mRNA levels of these enzymes did not significantly differ, confirming that metabolic flux regulations of erythritol and citric acid mostly took place at the post-transcriptional level.

Genome-scale metabolic modelling common cofactors metabolism in microorganisms

The common cofactors ATP/ADP, NAD(P)(H), and acetyl-CoA/CoA are indispensable participants in biochemical reactions in industrial microbes. To systematically explore the effects of these cofactors on cell growth and metabolic phenotypes, the first genome-scale cofactor metabolic model, icmNX6434, including 6434 genes, 1782 metabolites, and 6877 reactions, was constructed from 14 genome-scale metabolic models of 14 industrial strains. The origin, consumption, and interactions of these common cofactors in microbial cells were elucidated by the icmNX6434 model, and they played important roles in cell growth. The essential cofactor modules contained 2480 genes and 2948 reactions; therefore, improving cofactor biosynthesis, directing these cofactors into essential metabolic pathways, as well as avoiding cofactor utilization during byproduct biosynthesis and futile cycles, are three ways to increase cell growth. The effects of these common cofactors on the distribution and rate of the carbon flux in four universal modes, as well as an optimized metabolic flux, could be obtained by manipulating cofactor availability and balance. Significant changes in the ATP, NAD(H), NADP(H), or acetyl-CoA concentrations triggered relevant metabolic responses to acidic, oxidative, heat, and osmotic stress. Globally, the model icmNX6434 provides a comprehensive platform to elucidate the physiological effects of these cofactors on cell growth, metabolic flux, and industrial robustness. Moreover, the results of this study are a further example of using a consensus genome-scale metabolic model to increase our understanding of key biological processes.

Metabolic engineering of Ustilago trichophora TZ1 for improved malic acid production

Ustilago trichophora RK089 has been found recently as a good natural malic acid producer from glycerol. This strain has previously undergone adaptive laboratory evolution for enhanced substrate uptake rate resulting in the strain U. trichophora TZ1. Medium optimization and investigation of process parameters enabled titers and rates that are able to compete with those of organisms overexpressing major parts of the underlying metabolic pathways. Metabolic engineering can likely further increase the efficiency of malate production by this organism, provided that basic genetic tools and methods can be established for this rarely used and relatively obscure species.

Here we investigate and adapt existing molecular tools from U. maydis for use in U. trichophora. Selection markers from U. maydis that confer carboxin, hygromycin, nourseothricin, and phleomycin resistance are applicable in U. trichophora. A plasmid was constructed containing the ip-locus of U. trichophora RK089, resulting in site-specific integration into the genome. Using this plasmid, overexpression of pyruvate carboxylase, two malate dehydrogenases (mdh1, mdh2), and two malate transporters (ssu1, ssu2) was possible in U. trichophora TZ1 under control of the strong P_etef promoter. Overexpression of mdh1, mdh2, ssu1, and ssu2 increased the product (malate) to substrate (glycerol) yield by up to 54% in shake flasks reaching a titer of up to 120 g L⁻¹. In bioreactor cultivations of U. trichophora TZ1 P_etefssu2 and U. trichophora TZ1 P_etefmdh2 a drastically lowered biomass formation and glycerol uptake rate resulted in 29% (Ssu1) and 38% (Mdh2) higher specific production rates and 38% (Ssu1) and 46% (Mdh2) increased yields compared to the reference strain U. trichophora TZ1. Investigation of the product spectrum resulted in an 87% closed carbon balance with 134 g L⁻¹ malate and biomass (73 g L⁻¹), succinate (20 g L⁻¹), CO₂ (¹7 g L⁻¹), and α-ketoglutarate (8 g L⁻¹) as main by-products.

These results open up a wide range of possibilities for further optimization, especially combinatorial metabolic engineering to increase the flux from pyruvate to malic acid and to reduce by-product formation.

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Metabolic engineering tools established for U. trichophora

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Potentially carbon neutral process through CO₂ co-metabolism

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Optimized malic acid production from glycerol by overexpression of rTCA cycle

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Specific production rate and yield increased up to 38% and 46%, respectively

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.