Biotechnological applications of Yarrowia lipolytica: Past, present and future

Boosting succinic acid production of Yarrowia lipolytica at low pH through enhancing product tolerance and glucose metabolism

BACKGROUND

Succinic acid (SA) is an important bio-based C4 platform chemical with versatile applications, including the production of 1,4-butanediol, tetrahydrofuran, and γ-butyrolactone. The non-conventional yeast Yarrowia lipolytica has garnered substantial interest as a robust cell factory for SA production at low pH. However, the high concentrations of SA, especially under acidic conditions, can impose significant stress on microbial cells, leading to reduced glucose metabolism viability and compromised production performance. Therefore, it is important to develop Y. lipolytica strains with enhanced SA tolerance for industrial-scale SA production.

RESULTS

An SA-tolerant Y. lipolytica strain E501 with improved SA production was obtained through adaptive laboratory evolution (ALE). In a 5-L bioreactor, the evolved strain E501 produced 89.62 g/L SA, representing a 7.2% increase over the starting strain Hi-SA2. Genome resequencing and transcriptome analysis identified a mutation in the 26S proteasome regulatory subunit Rpn1, as well as genes involved in transmembrane transport, which may be associated with enhanced SA tolerance. By further fine-tuning the glycolytic pathway flux, the highest SA titer of 112.54 g/L to date at low pH was achieved, with a yield of 0.67 g/g glucose and a productivity of 2.08 g/L/h.

CONCLUSION

This study provided a robust engineered Y. lipolytica strain capable of efficiently producing SA at low pH, thereby reducing the cost of industrial SA fermentation.

Advances in Metabolic Engineering for the Accumulation of Astaxanthin Biosynthesis

Astaxanthin, a lipophilic carotenoid renowned for its strong antioxidant activity, holds significant commercial value across industries such as feed, food, and cosmetics. Although astaxanthin can be synthesized through chemical methods, it may contain toxic by-products in the synthesized astaxanthin, limiting its application in medicine or functional food. Natural astaxanthin can be extracted from algae, however, the cultivation cycle of algae is relatively longer compared to microorganisms. With the advancement of synthetic biology and metabolic engineering, the method of microbial fermentation has emerged as a promising strategy for the large-scale production of astaxanthin. This article provides a comprehensive overview of the research progress in astaxanthin biosynthesis, highlighting the use of the natural host Xanthophyllomyces dendrorhous, and the heterologous hosts Yarrowia lipolytica and Saccharomyces cerevisiae. Additionally, future research prospects are also discussed.

Assessment of the Probiotic Properties of Yarrowia lipolytica Isolated from Cold-Pressed Olive Oil

This research aimed to identify the probiotic features of Yarrowia lipolytica strains isolated from olive oils in Turkey. The in vitro survival capabilities of Y. lipolytica strains in gastric and pancreatic solutions were assessed. The hydrophobicity of Y. lipolytica strains was determined to be between 25.8% and 46.08% for xylene, 22.5% and 45.85% for chloroform, and 14.83% and 37.09% for ethyl acetate. In addition, auto-aggregation values were measured as 11.07-60.35%; 16.28-67.70% and 42.89-85.21% after 2, 4 and 24 h of incubation, respectively. The Y. lipolytica strains tested in this study demonstrated aggregation ability against the pathogens Escherichia coli ATCC 25922, Salmonella typhimurium ATCC 14028, Staphylococcus aureus ATCC 25923 and Listeria monocytogenes ATCC 7644. Antibiotic resistance and hemolytic activities were also checked to ensure the safety of the Y. lipolytica. Cholesterol removal by Y. lipolytica strains ranged from 12.30% to 47.42%, and their free radical scavenging activity varied between 2.85% and 39.10%. Out of 13 Y. lipolytica samples from 10 different olive oil sources, Y. lipolytica Y6, Y7, and Y11 exhibited the best strains with probiotic potential properties. This study discovered that Y. lipolytica with probiotic properties can be isolated in olive oil samples, a finding that has not been previously documented in the literature and may have potential industrial applications.

Modification of Yarrowia lipolytica via metabolic engineering for effective remediation of heavy metals from wastewater

With the increasing demand for heavy metals due to the advancement of industrial activities, large proportions of heavy metals have been discharged into aquatic ecosystems, causing serious harm to human health and the environment. Existing physical and chemical methods for recovering heavy metals from wastewater encounter challenges, such as low efficiency, high processing costs, and potential secondary pollution. In this study, we developed a novel approach by engineering the endogenous sulphur metabolic pathway of Yarrowia lipolytica, providing it with the ability to produce approximately 550 ppm of sulphide. Subsequently, sulphide-producing Y. lipolytica was used for the first time in heavy metal remediation. The engineered strain exhibited a high capacity to remove various heavy metals, especially achieving over 90 % for cadmium (Cd), copper (Cu) and lead (Pb). This capacity was consistent when applied to both synthetic and actual wastewater samples. Microscopic analyses revealed that sulphide-mediated biological precipitation of metal sulphides on the cell surface is responsible for their removal. Our findings demonstrate that sulphide-producing yeasts are a robust and effective bioremediation strategy for heavy metals, showing great potential for future heavy metal pollution remediation practices.

Recent advances in bio-based production of top platform chemical, succinic acid: an alternative to conventional chemistry

Succinic acid (SA) is one of the top platform chemicals with huge applications in diverse sectors. The presence of two carboxylic acid groups on the terminal carbon atoms makes SA a highly functional molecule that can be derivatized into a wide range of products. The biological route for SA production is a cleaner, greener, and promising technological option with huge potential to sequester the potent greenhouse gas, carbon dioxide. The recycling of renewable carbon of biomass (an indirect form of CO2), along with fixing CO2 in the form of SA, offers a carbon-negative SA manufacturing route to reduce atmospheric CO2 load. These attractive attributes compel a paradigm shift from fossil-based to microbial SA manufacturing, as evidenced by several commercial-scale bio-SA production in the last decade. The current review article scrutinizes the existing knowledge and covers SA production by the most efficient SA producers, including several bacteria and yeast strains. The review starts with the biochemistry of the major pathways accumulating SA as an end product. It discusses the SA production from a variety of pure and crude renewable sources by native as well as engineered strains with details of pathway/metabolic, evolutionary, and process engineering approaches for enhancing TYP (titer, yield, and productivity) metrics. The review is then extended to recent progress on separation technologies to recover SA from fermentation broth. Thereafter, SA derivatization opportunities via chemo-catalysis are discussed for various high-value products, which are only a few steps away. The last two sections are devoted to the current scenario of industrial production of bio-SA and associated challenges, along with the author's perspective.

Efficient synthesis of squalene by cytoplasmic-peroxisomal engineering and regulating lipid metabolism in Yarrowia lipolytica

Squalene, a high-value acyclic triterpenoid compound, is broadly used in the food and medical industries. Although the large acetyl-CoA pool and hydrophobic space of Yarrowia lipolytica are suitable for the accumulation of squalene, the current production level in Y. lipolytica is still not sufficient for industrial production. In this study, two rounds of multicopy integration of genes encoding key enzymes were performed to enhance squalene anabolic flux in the cytoplasm. Furthermore, the mevalonate pathway was imported into peroxisomes through the compartmentalization strategy, and the production of squalene was significantly increased. By augmenting the acetyl-CoA supply in peroxisomes and the cytoplasm, the squalene was boosted to 2549.1 mg/L. Finally, the squalene production reached 51.2 g/L by fed-batch fermentation in a 5-L bioreactor. This is the highest squalene production reported to date for microbial production, and this study lays the foundation for the synthesis of steroids and squalene derivatives.

Metabolic engineering of Yarrowia lipolytica for high-level production of squalene

Squalene is an important triterpene with a wide range of applications. Given the growing market demand for squalene, the development of microbial cell factories capable of squalene production is considered a sustainable method. This study aimed to investigate the squalene production potential of Yarrowia lipolytica. First, HMG-CoA reductase from Saccharomyces cerevisiae and squalene synthase from Y. lipolytica was co-overexpressed in Y. lipolytica. Second, by enhancing the supply of NADPH in the squalene synthesis pathway, the production of squalene in Y. lipolytica was effectively increased. Furthermore, by constructing an isoprenol utilization pathway and overexpressing YlDGA1, the strain YLSQ9, capable of producing 868.1 mg/L squalene, was obtained. Finally, by optimizing the fermentation conditions, the highest squalene concentration of 1628.2 mg/L (81.0 mg/g DCW) in Y. lipolytica to date was achieved. This study demonstrated the potential for achieving high squalene production using Y. lipolytica.

Key enzymes involved in the utilization of fatty acids by Saccharomyces cerevisiae: a review

Saccharomyces cerevisiae is a eukaryotic organism with a clear genetic background and mature gene operating system; in addition, it exhibits environmental tolerance. Therefore, S. cerevisiae is one of the most commonly used organisms for the synthesis of biological chemicals. The investigation of fatty acid catabolism in S. cerevisiae is crucial for the synthesis and accumulation of fatty acids and their derivatives, with β-oxidation being the predominant pathway responsible for fatty acid metabolism in this organism, occurring primarily within peroxisomes. The latest research has revealed distinct variations in β-oxidation among different fatty acids, primarily attributed to substrate preferences and disparities in the metabolic regulation of key enzymes involved in the S. cerevisiae fatty acid metabolic pathway. The synthesis of lipids, on the other hand, represents another crucial metabolic pathway for fatty acids. The present paper provides a comprehensive review of recent research on the key factors influencing the efficiency of fatty acid utilization, encompassing β-oxidation and lipid synthesis pathways. Additionally, we discuss various approaches for modifying β-oxidation to enhance the synthesis of fatty acids and their derivatives in S. cerevisiae, aiming to offer theoretical support and serve as a valuable reference for future studies.

Draft genome sequence of Yarrowia lipolytica NRRL Y-64008, an oleaginous yeast capable of growing on lignocellulosic hydrolysates

Yarrowia lipolytica is an oleaginous yeast that produces high titers of fatty acid-derived biofuels and biochemicals. It can grow on hydrophobic carbon sources and lignocellulosic hydrolysates. The genome sequence of Y. lipolytica NRRL Y-64008 is reported to aid in its development as a biotechnological chassis for producing biofuels and bioproducts.

Extending the reach of homology by using successive computational filters to find yeast pheromone genes

The mating of fungi depends on pheromones that mediate communication between two mating types. Most species use short peptides as pheromones, which are either unmodified (e.g., α-factor in Saccharomyces cerevisiae) or C-terminally farnesylated (e.g., a-factor in S. cerevisiae). Peptide pheromones have been found by genetics or biochemistry in a small number of fungi, but their short sequences and modest conservation make it impossible to detect homologous sequences in most species. To overcome this problem, we used a four-step computational pipeline to identify candidate a-factor genes in sequenced genomes of the Saccharomycotina, the fungal clade that contains most of the yeasts: we require that candidate genes have a C-terminal prenylation motif, are shorter than 100 amino acids long, and contain a proteolytic-processing motif upstream of the potential mature pheromone sequence and that closely related species contain highly conserved homologs of the potential mature pheromone sequence. Additional manual curation exploits the observation that many species carry more than one a-factor gene, encoding identical or nearly identical pheromones. From 332 Saccharomycotina genomes, we identified strong candidate pheromone genes in 241 genomes, covering 13 clades that are each separated from each other by at least 100 million years, the time required for evolution to remove detectable sequence homology among small pheromone genes. For one small clade, the Yarrowia, we demonstrated that our algorithm found the a-factor genes: deleting all four related genes in the a-mating type of Yarrowia lipolytica prevents mating.

Application of Adaptive Laboratory Evolution in Lipid and Terpenoid Production in Yeast and Microalgae

Due to the complexity of metabolic and regulatory networks in microorganisms, it is difficult to obtain robust phenotypes through artificial rational design and genetic perturbation. Adaptive laboratory evolution (ALE) engineering plays an important role in the construction of stable microbial cell factories by simulating the natural evolution process and rapidly obtaining strains with stable traits through screening. This review summarizes the application of ALE technology in microbial breeding, describes the commonly used methods for ALE, and highlights the important applications of ALE technology in the production of lipids and terpenoids in yeast and microalgae. Overall, ALE technology provides a powerful tool for the construction of microbial cell factories, and it has been widely used in improving the level of target product synthesis, expanding the range of substrate utilization, and enhancing the tolerance of chassis cells. In addition, in order to improve the production of target compounds, ALE also employs environmental or nutritional stress strategies corresponding to the characteristics of different terpenoids, lipids, and strains.

Kinetic and Regulatory Properties of Yarrowia lipolytica Aconitate Hydratase as a Model-Indicator of Cell Redox State under pH Stress

This paper presents an analysis of the regulation activity of the partially purified preparations of cellular aconitate hydratase (AH) on the yeast Yarrowia lipolytica cultivated at extreme pH. As a result of purification, enzyme preparations were obtained from cells grown on media at pH 4.0, 5.5, and 9.0, purified by 48-, 46-, and 51-fold and having a specific activity of 0.43, 0.55 and 0.36 E/mg protein, respectively. The kinetic parameters of preparations from cells cultured at extreme pH demonstrated: (1) an increase in the affinity for citrate and isocitrate; and (2) a shift in the pH optima to the acidic and alkaline side in accordance with the modulation of the medium pH. The regulatory properties of the enzyme from cells subjected to alkaline stress showed increased sensitivity to Fe²⁺ ions and high peroxide resistance. Reduced glutathione (GSH) stimulated AH, while oxidized glutathione (GSSG) inhibited AH. A more pronounced effect of both GSH and GSSG was noted for the enzyme obtained from cells grown at pH 5.5. The data obtained provide new approaches to the use of Y. lipolytica as a model of eukaryotic cells demonstrating the development of a stress-induced pathology and to conducting a detailed analysis of enzymatic activity for its correction.

Biosynthesis of monoterpenoid and sesquiterpenoid as natural flavors and fragrances

Terpenoids are a large class of plant-derived compounds, that constitute the main components of essential oils and are widely used as natural flavors and fragrances. The biosynthesis approach presents a promising alternative route in terpenoid production compared to plant extraction or chemical synthesis. In the past decade, the production of terpenoids using biotechnology has attracted broad attention from both academia and the industry. With the growing market of flavor and fragrance, the production of terpenoids directed by synthetic biology shows great potential in promoting future market prospects. Here, we reviewed the latest advances in terpenoid biosynthesis. The engineering strategies for biosynthetic terpenoids were systematically summarized from the enzyme, metabolic, and cellular dimensions. Additionally, we analyzed the key challenges from laboratory production to scalable production, such as key enzyme improvement, terpenoid toxicity, and volatility loss. To provide comprehensive technical guidance, we collected milestone examples of biosynthetic mono- and sesquiterpenoids, compared the current application status of chemical synthesis and biosynthesis in terpenoid production, and discussed the cost drivers based on the data of techno-economic assessment. It is expected to provide critical insights into developing translational research of terpenoid biomanufacturing.

A robust soft sensor based on artificial neural network for monitoring microbial lipid fermentation processes using Yarrowia lipolytica

Microbial oils produced by Yarrowia lipolytica offer an environmentally friendly and sustainable alternative to petroleum as well as traditional lipids from animals and plants. The accurate measurement of fermentation parameters, including the substrate concentration, dry cell weight, and lipid accumulation, is the foundation of process control, which is indispensable for industrial lipid production. However, it remains a great challenge to measure the complex parameters online during the lipid fermentation process, which is nonlinear, multivariate, and characterized by strong coupling. As a type of AI technology, the artificial neural network model is a powerful tool for handling extremely complex problems, and it can be employed to develop a soft sensor to monitor the microbial lipid fermentation process of Y. lipolytica. In this study, we first analyzed and emphasized the volume of sodium hydroxide and dissolved oxygen concentration as central parameters of the fermentation process. Then, a soft sensor based on a four-input artificial neural network model was developed, in which the input variables were fermentation time, dissolved oxygen concentration, initial glucose concentration, and additional volume of sodium hydroxide. This provides the possibility of online monitoring of dry cell weight, glucose concentration, and lipid production with high accuracy, which can be extended to similar fermentation processes characterized by the addition of bases or acids, as well as changes of the dissolved oxygen concentration.

Comparative Analysis of the Alkaline Proteolytic Enzymes of Yarrowia Clade Species and Their Putative Applications

Proteolytic enzymes are commercially valuable and have multiple applications in various industrial sectors. The most studied proteolytic enzymes produced by Yarrowia lipolytica, extracellular alkaline protease (Aep) and extracellular acid protease (Axp), were shown to be good candidates for different biotechnological applications. In this study, we performed a comprehensive analysis of the alkaline proteolytic enzymes of Yarrowia clade species, including phylogenetic studies, synteny analysis, and protease production and application. Using a combination of comparative genomics approaches based on sequence similarity, synteny conservation, and phylogeny, we reconstructed the evolutionary scenario of the XPR2 gene for species of the Yarrowia clade. Furthermore, except for the proteolytic activity of the analyzed Yarrowia clade strains, the brewers’ spent grain (BSG) was used as a substrate to obtain protein hydrolysates with antioxidant activity. For each culture, the degree of hydrolysis was calculated. The most efficient protein hydrolysis was observed in the cultures of Y. lipolytica, Y. galli, and Y. alimentaria. In contrast, the best results obtained using the 2,2-azinobis (3-ethyl-benzothiazoline-6-sulfonic acid (ABTS) method were observed for the culture medium after the growth of Y. divulgata, Y. galli, and Y. lipolytica on BSG.

Adaptive laboratory evolution boost Yarrowia lipolytica tolerance to vanillic acid

Microbial tolerance to lignocellulose-derived inhibitors, such as aromatic acids, is critical for the economical production of biofuels and biochemicals. Here, adaptive laboratory evolution was applied to improve the tolerance of Yarrowia lipolytica to a representative aromatic acid inhibitor vanillic acid. The transcriptome profiling of evolved strain suggested that the tolerance could be related to the up-regulation of RNA processing and multidrug transporting pathways. Further analysis by reverse engineering confirmed that the amplification of YALI0_F13475g coding for transcriptional coactivator and YALI0_E25201g coding for multidrug transporter conferred tolerance not only to vanillic acid but also towards ferulic acid, p-coumaric acid, p-hydroxybenzoic acid and syringic acid. These findings suggested that regulation of RNA processing and multidrug transporting pathways may be important for enhanced aromatic acid tolerance in Y. lipolytica. This study provides valuable genetic information for robust strain construction for lignocellulosic biorefinery.

Increased Cordycepin Production in Yarrowia lipolytica Using Combinatorial Metabolic Engineering Strategies

As the first nucleoside antibiotic discovered in fungi, cordycepin, with its various biological activities, has wide applications. At present, cordycepin is mainly obtained from the natural fruiting bodies of Cordyceps militaris. However, due to long production periods, low yields, and low extraction efficiency, harvesting cordycepin from natural C. militaris is not ideal, making it difficult to meet market demands. In this study, an engineered Yarrowia lipolytica YlCor-18 strain, constructed by combining metabolic engineering strategies, achieved efficient de novo cordycepin production from glucose. First, the cordycepin biosynthetic pathway derived from C. militaris was introduced into Y. lipolytica. Furthermore, metabolic engineering strategies including promoter, protein, adenosine triphosphate, and precursor engineering were combined to enhance the synthetic ability of engineered strains of cordycepin. Fermentation conditions were also optimized, after which, the production titer and yields of cordycepin in the engineered strain YlCor-18 under fed-batch fermentation were improved to 4362.54 mg/L and 213.85 mg/g, respectively, after 168 h. This study demonstrates the potential of Y. lipolytica as a cell factory for cordycepin synthesis, which will serve as the model for the green biomanufacturing of other nucleoside antibiotics using artificial cell factories.

Homologous High-Level Lipase and Single-Cell Protein Production with Engineered Yarrowia lipolytica via Scale-Up Fermentation for Industrial Applications

Yarrowia lipolytica is a promising feed additives. Here, we aimed to produce extracellular lipases and single-cell proteins (SCPs) at high levels simultaneously through fed-batch fermentation of engineered Y. lipolytica. The parameters for 500 mL shake flask cultures were optimized with a single factorial design. The resultant activity of lipase reached 880.6 U/mL after 84 h of fermentation, and 32.0 g/L fermentation broth of dry SCP was obtained at 120 h. To attain high SCP and lipase productivity, the high-density fed-batch fermentation of Y. lipolytica was scaled up in 10 L, 30 L, and 100 L fermentors. Using glycerol as the sole carbon source, the lipase activity peaked to 8083.3 U/mL, and the final dry SCP weight was 183.1 g/L at 94.6 h in 10 L fermentors. The extracellular lipase activity and SCP weight reached 11,100.0 U/mL and 173.3 g of dry SCP/L at 136 h in 30 L fermentors, respectively. Following 136 h of fed-batch fermentation, the extracellular lipase activity and dry SCP weight reached 8532.0 U/mL and 170.3 g/L in 100 L fermentors, respectively. A balance between the lipase secretion and growth of Y. lipolytica recombinant strain was achieved, indicating that an efficient fermentation strategy could promote further scale-up for industrial SCP production from engineered Y. lipolytica.

Metabolic and Process Engineering for Producing the Peach-Like Aroma Compound γ-Decalactone in Yarrowia lipolytica

Due to its strong and unique peach-like aroma, γ-decalactone is widely used in dairy products and other foods or beverages. The oleaginous yeast Yarrowia lipolytica, which is generally regarded as safe, has shown great potential in the production of this flavor compound. Recently, the development of metabolic and process engineering has enabled the application of Y. lipolytica for the production of γ-decalactone. This Review summarizes the relevant biosynthesis and degradation pathways of Y. lipolytica, after which the related metabolic engineering strategies to increase the accumulation of γ-decalactone are summarized. In addition, the factors affecting γ-decalactone accumulation in Y. lipolytica are introduced, and corresponding process optimization strategies are discussed. Finally, the current research needs are analyzed to search for remaining challenges and future directions in this field.

Enhancing erythritol production from crude glycerol in a wild-type Yarrowia lipolytica by metabolic engineering

Background: Erythritol is a zero-calorie sweetener that is widely used in the food, pharmaceutical, and medical industries. Crude glycerol is the main by-product of biodiesel, and the effective utilization of crude glycerol will help to improve biodiesel viability. Previous studies on the production of erythritol from Y. lipolytica using crude glycerol as a carbon source have focused on optimizing the fermentation process of the mutant Y. lipolytica Wratislavia K1, while metabolic engineering has not been successfully applied. Results: To this end, we engineered the yeast Y. lipolytica to increase the productivity of this strain. Wild strains tolerant to high concentrations of crude glycerol were screened and identified. A series of rational metabolic approaches were employed to improve erythritol production. Among them, the engineered strain Y-04, obtained by tandem overexpression of GUT1 and GUT2, significantly increased glycerol assimilation by 33.3%, which was consistent with the results of RT-qPCR analysis. The effects of tandem overexpression of GUT1, GUT2, TKL1, and TAL1 on erythritol synthesis were also evaluated. The best results were obtained using a mutant that overexpressed GUT1, GUT2, and TKL1 and knocked out EYD1. The final Y-11 strain produced 150 g/l erythritol in a 5-L bioreactor with a yield and productivity of 0.62 g/g and 1.25 g/l/h, respectively. To the best of our knowledge, this is the highest erythritol yield and productivity from crude glycerol ever reported in Y. lipolytica. Conclusion: This work demonstrated that overexpression of GUT1, GUT2, and TKL1 and knockdown of EYD1 could be used to improve crude glycerol utilization and erythritol synthesis in Y. lipolytica. The process parameters such as erythritol yield and productivity were significantly elevated, which is valuable for industrial applications. Crude glycerol, as a carbon source, could efficiently restrict the synthesis of by-products while enhancing the generation of erythritol, compared to glucose. This indicates considerable potential for synthesizing value-added products from crude glycerol by Y. lipolytica.

Nonconventional Yeasts Engineered Using the CRISPR-Cas System as Emerging Microbial Cell Factories

Because the petroleum-based chemical synthesis of industrial products causes serious environmental and societal issues, biotechnological production using microorganisms is an alternative approach to achieve a more sustainable economy. In particular, the yeast Saccharomyces cerevisiae is widely used as a microbial cell factory to produce biofuels and valuable biomaterials. However, product profiles are often restricted due to the Crabtree-positive nature of S. cerevisiae, and ethanol production from lignocellulose is possibly enhanced by developing alternative stress-resistant microbial platforms. With desirable metabolic pathways and regulation in addition to strong resistance to diverse stress factors, nonconventional yeasts (NCY) may be considered an alternative microbial platform for industrial uses. Irrespective of their high industrial value, the lack of genetic information and useful gene editing tools makes it challenging to develop metabolic engineering-guided scaled-up applications using yeasts. The recently developed clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (Cas) system is a powerful gene editing tool for NCYs. This review describes the current status of and recent advances in promising NCYs in terms of industrial and biotechnological applications, highlighting CRISPR-Cas9 system-based metabolic engineering strategies. This will serve as a basis for the development of novel yeast applications.

Simultaneous Production and Immobilization of Lipase Using Pomegranate-Seed Residue: A New Biocatalyst for Hydrolysis Reactions and Structured Lipids Synthesis

Pomegranate-seed residue (PSR) was used in a new strategy for the simultaneous production of Yarrowia lipolytica lipase by submerged fermentation and its immobilization by adsorption. This biocatalyst—the fermented solid residue containing the adsorbed lipase (fermPSR)—was evaluated in hydrolysis reactions and in structured lipid synthesis. In shake flasks, yeast extract and urea were the best nitrogen sources for lipase production with PSR and their simultaneous use increased the lipase production even further. This result was confirmed in a 3.5-liter bioreactor, with lipase activity in an extracellular medium of 40 U/mL. A maximum reaction rate (Vmax) of 49.5 µmol/min/g, a Michaelis–Menten constant (Km) of 207 µmol/L, and a turnover number (Kcat) of 130 s−1 were determined for the new biocatalyst, fermPSR, for the hydrolysis of p-nitrophenyl laurate (p-NPL) into p-nitrophenol. The conversion of p-NPL into p-nitrophenol in subsequent reactions confirmed fermPSR’s potential for industrial hydrolytic reactions. The production of structured lipids from vegetable oil and free fatty acids by fermPSR evidences the versatility of this new biocatalyst.

High-level de novo biosynthesis of cordycepin by systems metabolic engineering in Yarrowia lipolytica

Cordycepin is a nucleoside antibiotic with various biological activities, which has wide applications in the area of cosmetic and medicine industries. However, the current production of cordycepin is costly and time-consuming. To construct the promising cell factory for high-level cordycepin production, firstly, the design and construction of cordycepin biosynthetic pathway were performed in Yarrowia lipolytica. Secondly, the adaptivity between cordycepin biosynthetic pathway and Y. lipolytica was enhanced by enzyme fusion and integration site engineering. Then, the production of cordycepin was improved by the enhancement of adenosine supply. Furthermore, through modular engineering, the production of cordycepin was achieved at 3588.59 mg/L from glucose. Finally, 3249.58 mg/L cordycepin with a yield of 76.46 mg/g total sugar was produced by the engineered strain from the mixtures of glucose and molasses. This research is the first report on the de novo high-level production of cordycepin in the engineered Y. lipolytica.

Bioengineering to Accelerate Biodiesel Production for a Sustainable Biorefinery

Biodiesel is an alternative, carbon-neutral fuel compared to fossil-based diesel, which can reduce greenhouse gas (GHGs) emissions. Biodiesel is a product of microorganisms, crop plants, and animal-based oil and has the potential to prosper as a sustainable and renewable energy source and tackle growing energy problems. Biodiesel has a similar composition and combustion properties to fossil diesel and thus can be directly used in internal combustion engines as an energy source at the commercial level. Since biodiesel produced using edible/non-edible crops raises concerns about food vs. fuel, high production cost, monocropping crisis, and unintended environmental effects, such as land utilization patterns, it is essential to explore new approaches, feedstock and technologies to advance the production of biodiesel and maintain its sustainability. Adopting bioengineering methods to produce biodiesel from various sources such as crop plants, yeast, algae, and plant-based waste is one of the recent technologies, which could act as a promising alternative for creating genuinely sustainable, technically feasible, and cost-competitive biodiesel. Advancements in genetic engineering have enhanced lipid production in cellulosic crops and it can be used for biodiesel generation. Bioengineering intervention to produce lipids/fat/oil (TGA) and further their chemical or enzymatic transesterification to accelerate biodiesel production has a great future. Additionally, the valorization of waste and adoption of the biorefinery concept for biodiesel production would make it eco-friendly, cost-effective, energy positive, sustainable and fit for commercialization. A life cycle assessment will not only provide a better understanding of the various approaches for biodiesel production and waste valorization in the biorefinery model to identify the best technique for the production of sustainable biodiesel, but also show a path to draw a new policy for the adoption and commercialization of biodiesel.

The Consumption of Amino Acids and Production of Volatile Aroma Compounds by Yarrowia lipolytica in Brewers’ Wort

The yeast Yarrowia lipolytica is well known for its versatile production of metabolites from various substrates, but, although isolated from, e.g., wild-fermented Belgian Sour beers, it is rarely considered a starter culture in fermented beverages. In this study, we aimed to elucidate the ability of Y. lipolytica to ferment brewers’ wort containing iso-α-acid for 7 days at low and high aeration and at 20 °C and 30 °C, with a special focus on amino acid consumption and production of volatile aroma compounds. Y. lipolytica was able to grow in the wort under all four conditions, although the growth was inhibited. Furthermore, it only consumed glucose and fructose, and no ethanol was formed. Moreover, under high aeration conditions, Y. lipolytica consumed 75–80% of the amino acids in the wort. Interestingly, no esters were produced during the fermentations, and only five higher alcohols (1-propanol, 2-methyl-1-propanol, 3-methyl-1-butanol, 3-methyl-3-buten-1-ol, and 2-phenylethanol), two aldehydes (3-methylbutanal and (E)-2-nonenal), two ketones (cyclopentanone and 9-oxabicyclo [6.1.0]nonan-4-one), one fatty acid (3-methyl-butanoic acid), and one benzene derivate (1,2,4-trimethyl-benzene) were produced. These results may contribute to the potential use of Y. lipolytica in a traditional brewery for the production of novel beers; e.g., alcohol-free beer.

Papiliotrema laurentii: general features and biotechnological applications

Papiliotrema laurentii, previously classified as Cryptococcus laurentii, is an oleaginous yeast that has been isolated from soil, plants, and agricultural and industrial residues. This variety of habitats reflects the diversity of carbon sources that it can metabolize, including monosaccharides, oligosaccharides, glycerol, organic acids, and oils. Compared to other oleaginous yeasts, such as Yarrowia lipolytica and Rhodotorula toruloides, there is little information regarding its genetic and physiological characteristics. From a biotechnological point of view, P. laurentii can produce surfactants, enzymes, and high concentrations of lipids, which can be used as feedstock for fatty acid-derived products. Moreover, it can be applied for the biocontrol of phytopathogenic fungi, contributing to quality maintenance in post- and pre-harvest fruits. It can also improve mycorrhizal colonization, nitrogen nutrition, and plant growth. P. laurentii is also capable of degrading polyester and diesel derivatives and acting in the bioremediation of heavy metals. In this review, we present the current knowledge about the basic and applied aspects of P. laurentii, underscoring its biotechnological potential and future perspectives. KEY POINTS: • The physiological characteristics of P. laurentii confer a wide range of biotechnological applications. • The regulation of the acetyl-CoA carboxylase in P. laurentii is different from most other oleaginous yeasts. • The GEM is a valuable tool to guide the construction of engineered P. laurentii strains with improved features for bio-based products.

An overview about the approaches used in the production of alpha-ketoglutaric acid with their applications

Alpha ketoglutaric acid is a biological compound found naturally in the human body. It plays an important role in the cell metabolism and has a role in various metabolic pathways including Kreb’s cycle, protein metabolism and so on. Keto glutaric acid is chemically prepared from succinic acid and oxalic acid. It is a direct precursor of glutamic acid and triazines. It can be produced by oxidative decarboxylation of isocitrate by isocitrate dehydrogenase. The yeast Yarrowia lipolytica is used as a prospective producer of alpha ketoglutaric acid from ethanol. The capability to synthesize Keto glutaric acid has so far been investigated for many microorganisms such as Pseudomonas fluoroscens , Bacillus subtilis etc. P. fluoroscens have the ability to synthesize a huge amount of alpha ketoglutaric acid in a glycerol medium supplemented with manganese (Mn). The Mangnese has a significant impact on glycerol metabolism resulting in the buildup of alpha ketoglutaric acid. The metabolism of succinate may result in the production of alpha ketoglutarate. Despite its importance in TCA cycle, alpha ketoglutaric acid buildup as an intermediate product of bacterial glucose oxidation. Along with chemical synthesis and microbial fermentation, enzymatic transformation can also be used to produce alpha ketoglutaric acid. Biodiesel waste is considered as cheap and renewable carbon source for the development of alpha ketoglutaric acid. Alpha ketoglutarate is used for kidney disease, intestinal and stomach disorders and many other conditions. It also plays an important role in the food industry as food and nutrient enhancers. The review is covering all the aspects related with the Alpha ketoglutaric acid production, utilization and product recovery.

Development and expansion of the CRISPR/Cas9 toolboxes for powerful genome engineering in yeast

Yeasts represent a group of the microorganisms most frequently seen in biotechnology. Recently, the class 2 type II CRISPR system (CRISPR/Cas9) has become the principal toolbox for genome editing. By efficiently implementing genetic manipulations such as gene integration/knockout, base editor, and transcription regulation, the development of biotechnological applications in yeasts has been extensively promoted. The genome-level tools based on CRISPR/Cas9, used for screening and identifying functional genes/gene clusters, are also advancing. In general, CRISPR/Cas9-assisted editing tools have gradually become standardized and function as host-orthogonal genetic systems, which results in time-saving for strain engineering and biotechnological application processes. In this review, we summarize the key points of the basic elements in the CRISPR/Cas9 system, including Cas9 variants, guide RNA, donors, and effectors. With a focus on yeast, we have also introduced the development of various CRISPR/Cas9 systems and discussed their future possibilities.

Development of Hypertolerant Strain of Yarrowia lipolytica Accumulating Succinic Acid Using High Levels of Acetate

Acetate is emerging as a promising feedstock for biorefineries as it can serve as an alternate carbon source for microbial cell factories. In this study, we expressed acetyl-CoA synthase in Yarrowia lipolytica PSA02004PP, and the recombinant strain grew on acetate as the sole carbon source and accumulated succinic acid or succinate (SA). Unlike traditional feedstocks, acetate is a toxic substrate for microorganisms; therefore, the recombinant strain was further subjected to adaptive laboratory evolution to alleviate toxicity and improve tolerance against acetate. At high acetate concentrations, the adapted strain Y. lipolytica ACS 5.0 grew rapidly and accumulated lipids and SA. Bioreactor cultivation of ACS 5.0 with 22.5 g/L acetate in a batch mode resulted in a maximum cell OD₆₀₀ of 9.2, with lipid and SA accumulation being 0.84 and 5.1 g/L, respectively. However, its fed-batch cultivation yielded a cell OD₆₀₀ of 23.5, SA titer of 6.5 g/L, and lipid production of 1.5 g/L with an acetate uptake rate of 0.2 g/L h, about 2.86 times higher than the parent strain. Cofermentation of acetate and glucose significantly enhanced the SA titer and lipid accumulation to 12.2 and 1.8 g/L, respectively, with marginal increment in cell growth (OD₆₀₀: 26.7). Furthermore, metabolic flux analysis has drawn insights into utilizing acetate for the production of metabolites that are downstream to acetyl-CoA. To the best of our knowledge, this is the first report on SA production from acetate by Y. lipolytica and demonstrates a path for direct valorization of sugar-rich biomass hydrolysates with elevated acetate levels to SA.

A comprehensive assessment of Yarrowia lipolytica and its interactions with metals: Current updates and future prospective

The non-conventional yeast Yarrowia lipolytica has been popular as a model system for understanding biological processes such as dimorphism and lipid accumulation. The organism can efficiently utilize hydrophobic substrates (hydrocarbons and triglycerides) thereby rendering it relevant in bioremediation of oil polluted environments. The current review focuses on the interactions of this fungus with metal pollutants and its potential application in bioremediation of metal contaminated locales. This fungus is intrinsically equipped with a variety of physiological and biochemical features that enable it to tide over stress conditions induced by the presence of metals. Production of enzymes such as phosphatases, reductases and superoxide dismutases are worth a special mention. In the presence of metals, levels of inherently produced metal binding proteins (metallothioneins) and the pigment melanin are seen to be elevated. Morphological alterations with respect to biofilm formation and dimorphic transition from yeast to mycelial form are also induced by certain metals. The biomass of Y. lipolytica is inherently important as a biosorbent and cell surface modification, process optimization or whole cell immobilization techniques have aided in improving this capability. In the presence of metals such as mercury, cadmium, copper and uranium, the culture forms nanoparticulate deposits. In addition, on account of its intrinsic reductive ability, Y. lipolytica is being exploited for synthesizing nanoparticles of gold, silver, cadmium and selenium with applications as antimicrobial compounds, location agents for bioimaging and as feed supplements. This versatile organism thus has great potential in interacting with various metals and addressing problems related to their pollutant status.

Engineering Yarrowia lipolytica to Produce Itaconic Acid From Waste Cooking Oil

Itaconic acid (IA) is a high-value organic acid with a plethora of industrial applications. In this study, we seek to develop a microbial cell factory that could utilize waste cooking oil (WCO) as raw material for circular and cost-effective production of the abovementioned biochemical. Specifically, we expressed cis-aconitic acid decarboxylase (CAD) gene from Aspergillus terreus in either the cytosol or peroxisome of Yarrowia lipolytica and assayed for production of IA on WCO. To further improve production yield, the 10 genes involved in the production pathway of acetyl-CoA, an intermediate metabolite necessary for the synthesis of cis-aconitic acid, were individually overexpressed and investigated for their impact on IA production. To minimize off-target flux channeling, we had also knocked out genes related to competing pathways in the peroxisome. Impressively, IA titer up to 54.55 g/L was achieved in our engineered Y. lipolytica in a 5 L bioreactor using WCO as the sole carbon source.

Yarrowia lipolytica as an Alternative and Valuable Source of Nutritional and Bioactive Compounds for Humans

Yarrowia lipolytica, an oleagineous species of yeast, is a carrier of various important nutrients. The biomass of this yeast is an extensive source of protein, exogenous amino acids, bioavailable essenctial trace minerals, and lipid compounds as mainly unsaturated fatty acids. The biomass also contains B vitamins, including vitamin B12, and many other bioactive components. Therefore, Y. lipolytica biomass can be used in food supplements for humans as safe and nutritional additives for maintaining the homeostasis of the organism, including for vegans and vegetarians, athletes, people after recovery, and people at risk of B vitamin deficiencies.

Nutrient biomass production from agro-industrial residues using Yarrowia lipolytica: screening and optimization of growing conditions

Abstract The possibility of using agro-industrial residues in bioconversion processes advances with the development of biotechnology and the search for processes in which is possible to add commercial value to previously discarded products. These processes should be low cost, easy to control and chemical-free. The yeast Yarrowia lipolytica (YL) is widely used to produce lipids, enzymes, citric acid, and proteins, among others. This study aimed to evaluate the capacity of this yeast to use agro-industrial residues as a source of carbon without adding extra carbohydrate sources for the development of cells. The study evaluated the production of proteins and lipids from different carbon sources as well as the optimization of the process (agitation, temperature, and nitrogen source). Indeed, YL produced 22.3% of protein and 9.4% of lipids in dry biomass, a 179% of protein and 660% of lipid increase from raw material, respectively, when using cassava residues as a carbon source. However, lipase production was low, indicating that the strain had priority for cell growth.

Harnessing Yarrowia lipolytica Peroxisomes as a Subcellular Factory for α-Humulene Overproduction

The sesquiterpene α-humulene has been shown to have anti-inflammatory and anticancer activities, which has led to its vast application potential in medicine. However, α-humulene production methods including phytoextraction and chemical synthesis currently were limited to low yield, high costs, and expensive catalysts, which cannot meet the increasing market demand. In this study, Yarrowia lipolytica was developed as a robust cell factory for α-humulene production. The peroxisome in Y. lipolytica was first engineered to boost the synthesis of the sesquiterpene α-humulene. By compartmentalization of the α-humulene biosynthesis pathway, improving ATP and acetyl-CoA supply, and optimizing the gene copy numbers of rate-limiting enzymes, the engineered strain GQ2012 could produce 3.2 g/L α-humulene in a 5 L bioreactor, the highest α-humulene titer reported so far. Our study provides a valuable reference for highly sustainable production of terpenoids by peroxisome engineering in Y. lipolytica.

High-efficiency production of bisabolene from waste cooking oil by metabolically engineered Yarrowia lipolytica

The natural plant product bisabolene serves as a precursor for the production of a wide range of industrially relevant chemicals. However, the low abundance of bisabolene in plants renders its isolation from plant sources non-economically viable. Therefore, creation of microbial cell factories for bisabolene production supported by synthetic biology and metabolic engineering strategies presents a more competitive and environmentally sustainable method for industrial production of bisabolene. In this proof-of-principle study, for the first time, we engineered the oleaginous yeast Yarrowia lipolytica to produce α-bisabolene, β-bisabolene and γ-bisabolene through heterologous expression of the α-bisabolene synthase from Abies grandis, the β-bisabolene synthase gene from Zingiber officinale and the γ-bisabolene synthase gene from Helianthus annuus respectively. Subsequently, two metabolic engineering approaches, including overexpression of the endogenous mevalonate pathway genes and introduction of heterologous multidrug efflux transporters, were employed in order to improve bisabolene production. Furthermore, the fermentation conditions were optimized to maximize bisabolene production by the engineered Y. lipolytica strains from glucose. Finally, we explored the potential of the engineered Y. lipolytica strains for bisabolene production from the waste cooking oil. To our knowledge, this is the first report of bisabolene production in Y. lipolytica using metabolic engineering strategies. These findings provide valuable insights into the engineering of Y. lipolytica for a higher-level production of bisabolene and its utilization in converting waste cooking oil into various industrially valuable products.

Disrupting putative N-glycosylation site N17 in lipase Lip11 of Yarrowia lipolytica yielded a catalytically efficient and thermostable variant accompanying conformational changes

Lip11 gene from oleaginous yeast Yarrowia lipolytica MSR80 was recombinantly expressed in Pichia pastoris X33. Native secretion signal present in its sequence resulted in 92 % expression in comparison to α-secretion factor which resulted to 900 U/L in the extracellular broth. Catalytic triad in Lip11, like most lipases, was formed by serine, histidine, and aspartate residues. While point mutation disrupting putative glycosylation site (N389) present towards the C-terminus ruinously effected its stability and catalytic activity, disruption of the first putative glycosylation site (N17) located towards the N-terminus presented interesting insights. Mutation resulted in a variant N1 exhibiting higher thermal and acid stability; a t_1/2 of 198 min was obtained at 50 °C and it retained almost 80 % activity following incubation at pH 3. Catalytic efficiency was improved by 2.7 fold and a 10 °C rise in temperature optima was accompanied by higher relative activity in acidic range. Thermal stability corresponded to convoying structural modifications in the tertiary structure, findings of fluorescence spectroscopy suggested. Thermal fluorescence studies revealed a Tm of 65 °C for both Lip11 and N1 and λmax of Lip11 exhibited a blue shift upon refolding while no shift in the λmax of N1 was observed. A resilient tertiary structure which could fold back to its native confirmation upon thermal denaturation and increase in surface-exposed hydrophobic residues as revealed by ANS binding assay summed up to thermal stability of N1. Furthermore, circular dichroism data disclosed an alternate ratio of alpha-helices and beta-sheets; respective values changed from 36 % and 8%-27% and 19 %. Following mutation, substrate specificity remained unaffected and similar to native protein, N1 showed activation in presence of organic solvents and most divalent cations.

Orotic acid production by Yarrowia lipolytica under conditions of limited pyrimidine

Orotic acid (OA) is an intermediate of the pyrimidine biosynthesis with high industrial relevance due to its use as precursor for production of biochemical pyrimidines or its use as carrier molecule in drug formulations. It can be produced by fermentation of microorganisms with engineered pyrimidine metabolism. In this study, we surprisingly discovered the yeast Yarrowia lipolytica as a powerful producer of OA. The overproduction of OA in the Y. lipolytica strain PO1f was found to be caused by the deletion of the URA3 gene which prevents the irreversible decarboxylation of OA to uridine monophosphate. It was shown that the lack of orotidine-5'-phosphate decarboxylase was the reason for the accumulation of OA inside the cell since a rescue mutant of the URA3 deletion in Y. lipolytica PO1f completely prevented the OA secretion into the medium. In addition, pyrimidine limitation in the cell massively enhanced the OA accumulation followed by secretion due to intense overflow metabolism during bioreactor cultivations. Accordingly, supplementation of the medium with 200 mg/L uracil drastically decreased the OA overproduction by 91%. OA productivity was further enhanced in fed-batch cultivation with glucose and ammonium sulfate feed to a maximal yield of 9.62 ± 0.21 g/L. Y. lipolytica is one of three OA overproducing yeasts described in the literature so far, and in this study, the highest productivity was shown. This work demonstrates the potential of Y. lipolytica as a possible production organism for OA and provides a basis for further metabolic pathway engineering to optimize OA productivity.

Engineering Yarrowia lipolytica to produce fuels and chemicals from xylose: A review

The production of chemicals and fuels from lignocellulosic biomass has great potential industrial applications due to its economic feasibility and environmental attractiveness. However, the utilized microorganisms must be able to use all the sugars present in lignocellulosic hydrolysates, especially xylose, the second most plentiful monosaccharide on earth. Yarrowia lipolytica is a good candidate for producing various valuable products from biomass, but this yeast is unable to catabolize xylose efficiently. The development of metabolic engineering facilitated the application of Y. lipolytica as a platform for the bioconversion of xylose into various value-added products. Here, we reviewed the research progress on natural xylose-utilization pathways and their reconstruction in Y. lipolytica. The progress and emerging trends in metabolic engineering of Y. lipolytica for producing chemicals and fuels are further introduced. Finally, challenges and future perspectives of using lignocellulosic hydrolysate as substrate for Y. lipolytica are discussed.

Metabolic engineering of the oleaginous yeast Yarrowia lipolytica PO1f for production of erythritol from glycerol

BACKGROUND

Sugar alcohols are widely used as low-calorie sweeteners in the food and pharmaceutical industries. They can also be transformed into platform chemicals. Yarrowia lipolytica, an oleaginous yeast, is a promising host for producing many sugar alcohols. In this work, we tested whether heterologous expression of a recently identified sugar alcohol phosphatase (PYP) from Saccharomyces cerevisiae would increase sugar alcohol production in Y. lipolytica.

RESULTS

Y. lipolytica was found natively to produce erythritol, mannitol, and arabitol during growth on glucose, fructose, mannose, and glycerol. Osmotic stress is known to increase sugar alcohol production, and was found to significantly increase erythritol production during growth on glycerol. To better understand erythritol production from glycerol, since it was the most promising sugar alcohol, we measured the expression of key genes and intracellular metabolites. Osmotic stress increased the expression of several key genes in the glycerol catabolic pathway and the pentose phosphate pathway. Analysis of intracellular metabolites revealed that amino acids, sugar alcohols, and polyamines are produced at higher levels in response to osmotic stress. Heterologous overexpression of the sugar alcohol phosphatase increased erythritol production and glycerol utilization in Y. lipolytica. We further increased erythritol production by increasing the expression of native glycerol kinase (GK), and transketolase (TKL). This strain was able to produce 27.5 ± 0.7 g/L erythritol from glycerol during batch growth and 58.8 ± 1.68 g/L erythritol during fed-batch growth in shake-flasks experiments. In addition, the glycerol utilization was increased by 2.5-fold. We were also able to demonstrate that this strain efficiently produces erythritol from crude glycerol, a major byproduct of the biodiesel production.

CONCLUSIONS

We demonstrated the application of a promising enzyme for increasing erythritol production in Y. lipolytica. We were further able to boost production by combining the expression of this enzyme with other approaches known to increase erythritol production in Y. lipolytica. This suggest that this new enzyme provides an orthogonal route for boosting production and can be stacked with existing designs known to increase sugar alcohol production in yeast such as Y. lipolytica. Collectively, this work establishes a new route for increasing sugar alcohol production and further develops Y. lipolytica as a promising host for erythritol production from cheap substrates such as glycerol.

Yarrowia lipolytica, health benefits for animals

The yeast Yarrowia lipolytica has been industrially adopted for docosahexaenoic acid and eicosapentaenoic acid production under good manufacturing practices over 2 decades. In recent years, it has claimed attention for novel biotechnological applications, such as a functional feed additive for animals. Studies have demonstrated that this yeast is safe and has probiotic and nutritional properties for mammals, birds, fish, crustaceans, and molluscs. Animals fed Y. lipolytica enhanced productive and immune parameters, as well as modulated microbiome, fatty acid composition, and biochemical profiles. Additionally, some Y. lipolytica-derived compounds have improved productive performance, immune status, and disease resistance in animals. Therefore, the aim of this review is to identify and discuss research advances on the potential use of this yeast for animals of economic interest. Challenges, opportunities, and trends were identified and envisioned in the near future for this industrially produced yeast. KEY POINTS: • Yarrowia lipolytica has probiotic and nutritional effects in animals. • Lipase2, EPA, and β-glucan from Y. lipolytica have health benefits for animals. • Y. lipolytica is envisioned in terrestrial and aquatic animal production systems.

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.

Co-Cultivation of Two Bacillus Strains for Improved Cell Growth and Enzyme Production to Enhance the Degradation of Aflatoxin B1

Bacillus sp. H16v8 and Bacillus sp. HGD9229 were identified as Aflatoxin B₁ (AFB₁) degrader in nutrient broth after a 12 h incubation at 37 °C. The degradation efficiency of the two-strain supernatant on 100 μg/L AFB₁ was higher than the bacterial cells and cell lysate. Moreover, degradations of AFB₁ were strongly affected by the metal ions in which Cu²⁺ stimulated the degradation and Zn²⁺ inhibited the degradation. The extracellular detoxifying enzymes produced by co-cultivation of two strains were isolated and purified by ultrafiltration. The molecular weight range of the detoxifying enzymes was 20-25 kDa by SDS-PAGE. The co-culture of two strains improved the total cell growth with the enhancement of the total protein content and detoxifying enzyme production. The degradation efficiency of the supernatant from mixed cultures increased by 87.7% and 55.3% compared to Bacillus sp. H16v8 and HGD9229, individually. Moreover, after the degradation of AFB₁, the four products of the lower toxicity were identified by LC-Triple TOF-MS with the two proposed hypothetical degradation pathways.

Dual Regulation of Cytoplasm and Peroxisomes for Improved Α-Farnesene Production in Recombinant Pichia pastoris

Microbial production of α-farnesene from renewable raw materials is a feasible alternative to traditional petroleum craft. Recently, the research on improving α-farnesene production in Pichia pastoris mainly focused on cytoplasmic engineering, while comprehensive engineering of multiple subcellular compartments is rarely reported. Here, we first sought to confirm that the isopentenol utilization pathway (IUP) could act as a two-step shortcut for IPP synthesis in P. pastoris peroxisomes. In addition, we proposed dual regulation of cytoplasm and peroxisomes to boost α-farnesene synthesis in P. pastoris X33, thus the resultant strain produced 2.18 ± 0.04 g/L, which was 1.3 times and 2.1 times than that of the strain only with peroxisomal or cytoplasmic engineering, respectively. The α-farnesene production achieved 2.56 ± 0.04 g/L in shake flasks after carbon source cofeeding, which was the highest reported production in worldwide literatures to the best of my knowledge. Therefore, we propose these strategies as efficient approaches to enhancing α-farnesene production in P. pastoris, which might bring new ideas for the biosynthesis of high-value compounds.

Conferring thermotolerant phenotype to wild-type Yarrowia lipolytica improves cell growth and erythritol production

In microbial engineering, heat stress is an important environmental factor modulating cell growth, metabolic flux distribution and the synthesis of target products. Yarrowia lipolytica, as a GARS (generally recognized as safe) nonconventional yeast, has been widely used in the food industry, especially as the host of erythritol production. Biomanufacturing economics is limited by the high operational cost of cooling energy in large-scale fermentation. It is of great significance to select thermotolerant Y. lipolytica to reduce the cooling cost and elucidate the heat-resistant mechanism at molecular level. For this purpose, we performed adaptive evolution and obtained a thermotolerant strain named Y. lipolytica BBE-18. Transcriptome analysis allows us to identify four genes in thiamine metabolism pathway that are responsible for the complicated thermotolerant phenotype. The heat-resistant phenotype was validated with the model strain Y. lipolytica Po1f by overexpression of single and combined genes. Then, conferring the thermotolerant phenotype to the wild-type Y. lipolytica BBE-17 enable the strain to produce three-times more erythritol of the control strain with 3°C higher than optimal cultivation temperature. To our knowledge, this is the first report on engineering heat-resistant phenotype to improve the erythritol production in Y. lipolytica. However, due to the increase of culture temperature, a large amount of adenosine triphosphate is consumed to ensure the life activities of Y. lipolytica which limits the potential of cell synthetic products to a certain extent. Even so, this study provides a reference for Y. lipolytica to produce other products under high temperature.

Engineering the oleaginous yeast Yarrowia lipolytica for β-farnesene overproduction

β-farnesene is a sesquiterpenoid with various industrial applications which is now commercially produced by a Saccharomyces cerevisiae strain obtained by random mutagenesis and genetic engineering. We rationally designed a genetically defined Yarrowia lipolytica through recovery of L-leucine biosynthetic route, gene dosage optimization of β-farnesene synthase and disruption of the competition pathway. The resulting β-farnesene titer was improved from 8 to 345 mg L^-1 . Finally, the strategy for decreasing the lipid accumulation by individually and iteratively knocking out four acyltransferases encoding genes was adopted. The result displayed that β-farnesene titer in the engineered strain CIBT6304 in which acyltransferases (DGA1 and DGA2) were deleted increased by 45% and reached 539 mg L^-1 (88 mg g^-1 DCW). Using fed-batch fermentation, CIBT6304 could produce the highest β-farnesene titer (22.8 g L^-1 ) among the genetically defined strains. This study will provide the foundation of engineering Y. lipolytica to produce other terpenoids more cost-efficiently.