Alternative Substrate Metabolism in Yarrowia lipolytica

Arabinose as an overlooked sugar for microbial bioproduction of chemical building blocks

The circular economy is anticipated to bring a disruptive transformation in manufacturing technologies. Robust and industrial scalable microbial strains that can simultaneously assimilate and valorize multiple carbon substrates are highly desirable, as waste bioresources contain substantial amounts of renewable and fermentable carbon, which is diverse. Lignocellulosic biomass (LCB) is identified as an inexhaustible and alternative resource to reduce global dependence on oil. Glucose, xylose, and arabinose are the major monomeric sugars in LCB. However, primary research has focused on the use of glucose. On the other hand, the valorization of pentose sugars, xylose, and arabinose, has been mainly overlooked, despite possible assimilation by vast microbial communities. The present review highlights the research efforts that have explicitly proven the suitability of arabinose as the starting feedstock for producing various chemical building blocks via biological routes. It begins by analyzing the availability of various arabinose-rich biorenewable sources that can serve as potential feedstocks for biorefineries. The subsequent section outlines the current understanding of arabinose metabolism, biochemical routes prevalent in prokaryotic and eukaryotic systems, and possible products that can be derived from this sugar. Further, currently, exemplar products from arabinose, including arabitol, 2,3-butanediol, 1,2,3-butanetriol, ethanol, lactic acid, and xylitol are discussed, which have been produced by native and non-native microbial strains using metabolic engineering and genome editing tools. The final section deals with the challenges and obstacles associated with arabinose-based production, followed by concluding remarks and prospects.

Elucidation of triacylglycerol catabolism in Yarrowia lipolytica: How cells balance acetyl-CoA and excess reducing equivalents

Yarrowia lipolytica is an industrial yeast that can convert waste oil to value-added products. However, it is unclear how this yeast metabolizes lipid feedstocks, specifically triacylglycerol (TAG) substrates. This study used 13C-metabolic flux analysis (13C-MFA), genome-scale modeling, and transcriptomics analyses to investigate Y. lipolytica W29 growth with oleic acid, glycerol, and glucose. Transcriptomics data were used to guide 13C-MFA model construction and to validate the 13C-MFA results. The 13C-MFA data were then used to constrain a genome-scale model (GSM), which predicted Y. lipolytica fluxes, cofactor balance, and theoretical yields of terpene products. The three data sources provided new insights into cellular regulation during catabolism of glycerol and fatty acid components of TAG substrates, and how their consumption routes differ from glucose catabolism. We found that (1) over 80% of acetyl-CoA from oleic acid is processed through the glyoxylate shunt, a pathway that generates less CO2 compared to the TCA cycle, (2) the carnitine shuttle is a key regulator of the cytosolic acetyl-CoA pool in oleic acid and glycerol cultures, (3) the oxidative pentose phosphate pathway and mannitol cycle are key routes for NADPH generation, (4) the mannitol cycle and alternative oxidase activity help balance excess NADH generated from β-oxidation of oleic acid, and (5) asymmetrical gene expressions and GSM simulations of enzyme usage suggest an increased metabolic burden for oleic acid catabolism.

Transcriptomics aids in uncovering the metabolic shifts and molecular machinery of Schizochytrium limacinum during biotransformation of hydrophobic substrates to docosahexaenoic acid

BACKGROUND

Biotransformation of waste oil into value-added nutraceuticals provides a sustainable strategy. Thraustochytrids are heterotrophic marine protists and promising producers of omega (ω) fatty acids. Although the metabolic routes for the assimilation of hydrophilic carbon substrates such as glucose are known for these microbes, the mechanisms employed for the conversion of hydrophobic substrates are not well established. Here, thraustochytrid Schizochytrium limacinum SR21 was investigated for its ability to convert oils (commercial oils with varying fatty acid composition and waste cooking oil) into ω-3 fatty acid; docosahexaenoic acid (DHA).

RESULTS

Within 72 h SR21 consumed ~ 90% of the oils resulting in enhanced biomass (7.5 g L- 1) which was 2-fold higher as compared to glucose. Statistical analysis highlights C16 fatty acids as important precursors of DHA biosynthesis. Transcriptomic data indicated the upregulation of multiple lipases, predicted to possess signal peptides for secretory, membrane-anchored and cytoplasmic localization. Additionally, transcripts encoding for mitochondrial and peroxisomal β-oxidation along with acyl-carnitine transporters were abundant for oil substrates that allowed complete degradation of fatty acids to acetyl CoA. Further, low levels of oxidative biomarkers (H2O2, malondialdehyde) and antioxidants were determined for hydrophobic substrates, suggesting that SR21 efficiently mitigates the metabolic load and diverts the acetyl CoA towards energy generation and DHA accumulation.

CONCLUSIONS

The findings of this study contribute to uncovering the route of assimilation of oil substrates by SR21. The thraustochytrid employs an intricate crosstalk among the extracellular and intracellular molecular machinery favoring energy generation. The conversion of hydrophobic substrates to DHA can be further improved using synthetic biology tools, thereby providing a unique platform for the sustainable recycling of waste oil substrates.

Toward rapid and efficient utilization of nonconventional substrates by nonconventional yeast strains

Economic and sustainable production of biofuels and chemicals necessitates utilizing abundant and inexpensive lignocellulosic biomass. Yet, Saccharomyces cerevisiae, a workhorse strain for industrial biotechnology based on starch and sugarcane-derived sugars, is not suitable for lignocellulosic bioconversion due to a lack of pentose metabolic pathways and severe inhibition by toxic inhibitors in cellulosic hydrolysates. This review underscores the potential of nonconventional yeast strains, specifically Yarrowia lipolytica and Rhodotorula toruloides, for converting underutilized carbon sources, such as xylose and acetate, into high-value products. Multi-omics studies with nonconventional yeast have elucidated the structure and regulation of metabolic pathways for efficient and rapid utilization of xylose and acetate. The review delves into the advantages of using xylose and acetate for producing biofuels and chemicals. Collectively, value-added biotransformation of nonconventional substrates by nonconventional yeast strains is a promising strategy to improve both economics and sustainability of bioproduction.

Application of New Yarrowia lipolytica Transformants in Production of Citrates and Erythritol from Glycerol

Citric acid and erythritol are obtained on an industrial scale using biotechnological methods. Due to the growing market demand for these products, research is underway to improve the process economics by introducing new microorganisms, in particular of the species Yarrowia lipolytica. The aim of this study was to evaluate transformants of Y. lipolytica for growth and ability to overproduce citric acids and erythritol from glycerol. The transformants were constructed by overexpressing glycerol kinase, methylcitrate synthase and mitochondrial succinate-fumarate transporter in the mutant Wratislavia 1.31. Next, strains were assessed for biosynthesis of citrate (pH 5.5; nitrogen limitation) and erythritol (pH 3.0; high osmotic pressure) from glycerol. Regardless of culture conditions strains, 1.31.GUT1/6 and 1.31.GUT1/6.CIT1/3 exhibited high rates of substrate utilization. Under conditions favoring citrate biosynthesis, both strains produced several percent more citrates, accompanied by higher erythritol production compared to the parental strain. During erythritol biosynthesis, the strain 1.31.GUT1/6.CIT1/3.E34672g obtained as a result of co-expression of all three genes stood out, producing 84.0 g/L of erythritol with yield and productivity of 0.54 g/g and 0.72 g/Lh, respectively, which places it in the group of the highest-ranked producers of erythritol among Y. lipolytica species.

Efficient Production of Triacetic Acid Lactone from Lignocellulose Hydrolysate by Metabolically Engineered Yarrowia lipolytica

Lignocellulose is a promising renewable feedstock for the bioproduction of high-value biochemicals. The poorly expressed xylose catabolic pathway was the bottleneck in the efficient utilization of the lignocellulose feedstock in yeast. Herein, multiple genetic and process engineering strategies were explored to debottleneck the conversion of xylose to the platform chemical triacetic acid lactone (TAL) in Yarrowia lipolytica. We identified that xylose assimilation generating more cofactor NADPH was favorable for the TAL synthesis. pH control improved the expression of acetyl-CoA carboxylase and generated more precursor malonyl-CoA. Combined with the suppression of the lipid synthesis pathway, 5.03 and 4.18 g/L TAL were produced from pure xylose and xylose-rich wheat straw hydrolysate, respectively. Our work removed the bottleneck of the xylose assimilation pathway and effectively upgraded wheat straw hydrolysate to TAL, which enabled us to build a sustainable oleaginous yeast cell factory to cost-efficiently produce green chemicals from low-cost lignocellulose by Y. lipolytica.

Efficient production of mycosporine-like amino acids, natural sunscreens, in Yarrowia lipolytica

BACKGROUND

Mycosporine-like amino acids (MAAs), including shinorine and porphyra-334, are gaining attention as safe natural sunscreens. The production of MAAs has been achieved in diverse microbial hosts, including Saccharomyces cerevisiae. While S. cerevisiae is the most extensively studied model yeast, the oleaginous yeast Yarrowia lipolytica has emerged as a promising candidate for the synthesis of valuable products. In this study, we explored the potential of Y. lipolytica as a host for producing MAAs, utilizing its advantages such as a robust pentose phosphate pathway flux and versatile carbon source utilization.

RESULTS

We produced MAAs in Y. lipolytica by introducing the MAA biosynthetic genes from cyanobacteria Nostoc punctiforme and Anabaena variabilis. These genes include mysA, mysB, and mysC responsible for producing mycosporine-glycine (MG) from sedoheptulose 7-phosphate (S7P). The two strains utilize different enzymes, D-Ala-D-Ala ligase homologue (MysD) in N. punctiforme and NRPS-like enzyme (MysE) in A. variabilis, for amino acid conjugation to MG. MysE specifically generated shinorine, a serine conjugate of MG, while MysD exhibited substrate promiscuity, yielding both shinorine and a small amount of porphyra-334, a threonine conjugate of MG. We enhanced MAAs production by selecting mysA, mysB, and mysC from A. variabilis and mysD from N. punctiforme based on their activities. We further improved production by strengthening promoters, increasing gene copies, and introducing the xylose utilization pathway. Co-utilization of xylose with glucose or glycerol increased MAAs production by boosting the S7P pool through the pentose phosphate pathway. Overexpressing GND1 and ZWF1, key genes in the pentose phosphate pathway, further enhanced MAAs production. The highest achieved MAAs level was 249.0 mg/L (207.4 mg/L shinorine and 41.6 mg/L of porphyra-334) in YP medium containing 10 g/L glucose and 10 g/L xylose.

CONCLUSIONS

Y. lipolytica was successfully engineered to produce MAAs, primarily shinorine. This achievement involved the introduction of MAA biosynthetic genes from cyanobacteria, establishing xylose utilizing pathway, and overexpressing the pentose phosphate pathway genes. These results highlight the potential of Y. lipolytica as a promising yeast chassis strain for MAAs production, notably attributed to its proficient expression of MysE enzyme, which remains non-functional in S. cerevisiae, and versatile utilization of carbon sources like glycerol.

Enhanced acetate utilization for value-added chemicals production in Yarrowia lipolytica by integration of metabolic engineering and microbial electrosynthesis

The limited supply of reducing power restricts the efficient utilization of acetate in Yarrowia lipolytica. Here, microbial electrosynthesis (MES) system, enabling direct conversion of inward electrons to NAD(P)H, was used to improve the production of fatty alcohols from acetate based on pathway engineering. First, the conversion efficiency of acetate to acetyl-CoA was reinforced by heterogenous expression of ackA-pta genes. Second, a small amount of glucose was used as cosubstrate to activate the pentose phosphate pathway and promote intracellular reducing cofactors synthesis. Third, through the employment of MES system, the final fatty alcohols production of the engineered strain YLFL-11 reached 83.8 mg/g dry cell weight (DCW), which was 6.17-fold higher than the initial production of YLFL-2 in shake flask. Furthermore, these strategies were also applied for the elevation of lupeol and betulinic acid synthesis from acetate in Y. lipolytica, demonstrating that our work provides a practical solution for cofactor supply and the assimilation of inferior carbon sources.

Compound K Production: Achievements and Perspectives

Compound K (CK) is one of the major metabolites found in mammalian blood and organs following oral administration of Panax plants. CK, also known as minor ginsenoside, can be absorbed in the systemic circulation. It has garnered significant attention in healthcare and medical products due to its pharmacological activities, such as antioxidation, anticancer, antiproliferation, antidiabetics, neuroprotection, and anti-atherogenic activities. However, CK is not found in natural ginseng plants but in traditional chemical synthesis, which uses toxic solvents and leads to environmental pollution during the harvest process. Moreover, enzymatic reactions are impractical for industrial CK production due to low yield and high costs. Although CK could be generated from major ginsenosides, most ginsenosides, including protopanaxatriol-oleanane and ocotillol-type, are not converted into CK by catalyzing β-glucosidase. Therefore, microbial cell systems have been used as a promising solution, providing a safe and efficient approach to CK production. This review provides a summary of various approaches for the production of CK, including chemical and enzymatic reactions, biotransformation by the human intestinal bacteria and endophytes as well as engineered microbes. Moreover, the approaches for CK production have been discussed to improve the productivity of target compounds.

Purification of Natural Pigments Violacein and Deoxyviolacein Produced by Fermentation Using Yarrowia lipolytica

Violacein and deoxyviolacein are bis-indole pigments synthesized by a number of microorganisms. The present study describes the biosynthesis of a mixture of violacein and deoxyviolacein using a genetically modified Y. lipolytica strain as a production chassis, the subsequent extraction of the intracellular pigments, and ultimately their purification using column chromatography. The results show that the optimal separation between the pigments occurs using an ethyl acetate/cyclohexane mixture with different ratios, first 65:35 until both pigments were clearly visible and distinguishable, then 40:60 to create a noticeable separation between them and recover the deoxyviolacein, and finally 80:20, which allows the recovery of the violacein. The purified pigments were then analyzed by thin-layer chromatography and nuclear magnetic resonance.

Metabolic engineering for the high-yield production of polydatin in Yarrowia lipolytica

Polydatin, a glycosylated derivative of resveratrol, has better structural stability and biological activity than resveratrol. Polydatin is the extract of Polygonum cuspidatum, which has various pharmacological effects. Owing to its Crabtree-negative characteristics and high supply of malonyl-CoA, Yarrowia lipolytica was selected to produce polydatin. Initially, the resveratrol synthetic pathway was established in Y. lipolytica. By enhancing the shikimate pathway flow, redirecting carbon metabolism, and increasing the copies of key genes, a resveratrol yield of 487.77 mg/L was obtained. In addition, by blocking the degradation of polydatin, its accumulation was successfully achieved. Finally, by optimizing the glucose concentration and supplementing with two nutritional marker genes, a high polydatin yield of 6.88 g/L was obtained in Y. lipolytica, which is the highest titer of polydatin produced in a microbial host to date. Overall, this study demonstrates that Y. lipolytica has great potential for glycoside synthesis.

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.

Leveraging substrate flexibility and product selectivity of acetogens in two-stage systems for chemical production

Carbon dioxide (CO₂ ) stands out as sustainable feedstock for developing a circular carbon economy whose energy supply could be obtained by boosting the production of clean hydrogen from renewable electricity. H₂ -dependent CO₂ gas fermentation using acetogenic microorganisms offers a viable solution of increasingly demonstrated value. While gas fermentation advances to achieve commercial process scalability, which is currently limited to a few products such as acetate and ethanol, it is worth taking the best of the current state-of-the-art technology by its integration within innovative bioconversion schemes. This review presents multiple scenarios where gas fermentation by acetogens integrate into double-stage biotechnological production processes that use CO₂ as sole carbon feedstock and H₂ as energy carrier for products' synthesis. In the integration schemes here reviewed, the first stage can be biotic or abiotic while the second stage is biotic. When the first stage is biotic, acetogens act as a biological platform to generate chemical intermediates such as acetate, formate and ethanol that become substrates for a second fermentation stage. This approach holds the potential to enhance process titre/rate/yield metrics and products' spectrum. Alternatively, when the first stage is abiotic, the integrated two-stage scheme foresees, in the first stage, the catalytic transformation of CO₂ into C₁ products that, in the second stage, can be metabolized by acetogens. This latter scheme leverages the metabolic flexibility of acetogens in efficient utilization of the products of CO₂ abiotic hydrogenation, namely formate and methanol, to synthesize multicarbon compounds but also to act as flexible catalysts for hydrogen storage or production.

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.

Efficient production of the β-ionone aroma compound from organic waste hydrolysates using an engineered Yarrowia lipolytica strain

This study demonstrates the feasibility of establishing a natural compound supply chain in a biorefinery. The process starts with the biological or chemical hydrolysis of food and agricultural waste into simple and fermentative sugars, followed by their fermentation into more complex molecules. The yeast strain, Yarrowia lipolytica, was modified by introducing high membrane affinity variants of the carotenoid cleavage dioxygenase enzyme, PhCCD1, to increase the production of the aroma compound, β-ionone. The initial hydrolysis process converted food waste or sugarcane bagasse into nutrient-rich hydrolysates containing 78.4 g/L glucose and 8.3 g/L fructose, or 34.7 g/L glucose and 20.1 g/L xylose, respectively. During the next step, engineered Y. lipolytica strains were used to produce β-ionone from these feedstocks. The yeast strain YLBI3120, carrying a modified PhCCD1 gene was able to produce 4 g/L of β-ionone with a productivity of 13.9 mg/L/h from food waste hydrolysate. This is the highest yield reported for the fermentation of this compound to date. The integrated process described in this study could be scaled up to achieve economical large-scale conversion of inedible food and agricultural waste into valuable aroma compounds for a wide range of potential applications.

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.

Effects of Inhibitors Generated by Dilute Phosphoric Acid Plus Steam-Exploded Poplar on Saccharomyces cerevisiae Growth

The pretreatment of lignocellulosic biomass is important for efficient bioethanol conversion, but causes undesirable by-products that inhibit microbial growth, conversely affecting the bioconversion efficiency. In this study, the main inhibitors derived from dilute phosphoric acid plus steam-exploded poplar wood were identified as 0.22 g/L furfural, 3.63 g/L acetic acid, 0.08 g/L syringaldehyde, etc., indicating the green nature and low toxicity of the pretreatment process. The effects of the three typical inhibitors (furfural, acetic acid, and syringaldehyde) on Saccharomyces cerevisiae 1517RM growth were analyzed and shown to prolong the lag phase of microbial growth to different degrees. In all the inhibitor groups, the ergosterol secretion was boosted, indicating low cell membrane fluidity and robustness of the strain to an adverse environment. The cell electronegativity and morphology of S. cerevisiae 1517RM also changed under different growth conditions, which was helpful for monitoring the physicochemical properties of cells. Furfural, acetic acid, and syringaldehyde had a synergistic effect on each other, providing an important reference to improving the subsequent ethanol fermentation process.

Production, Biosynthesis, and Commercial Applications of Fatty Acids From Oleaginous Fungi

Oleaginous fungi (including fungus-like protists) are attractive in lipid production due to their short growth cycle, large biomass and high yield of lipids. Some typical oleaginous fungi including Galactomyces geotrichum, Thraustochytrids, Mortierella isabellina, and Mucor circinelloides, have been well studied for the ability to accumulate fatty acids with commercial application. Here, we review recent progress toward fermentation, extraction, of fungal fatty acids. To reduce cost of the fatty acids, fatty acid productions from raw materials were also summarized. Then, the synthesis mechanism of fatty acids was introduced. We also review recent studies of the metabolic engineering strategies have been developed as efficient tools in oleaginous fungi to overcome the biochemical limit and to improve production efficiency of the special fatty acids. It also can be predictable that metabolic engineering can further enhance biosynthesis of fatty acids and change the storage mode of fatty acids.

Modelling of the Citric Acid Production from Crude Glycerol by Wild-Type Yarrowia lipolytica DSM 8218 Using Response Surface Methodology (RSM)

Crude glycerol is the main by-product of the biodiesel manufacturing industry (10% w/w). Its use as a substrate in microbial fermentations is a concrete strategy to efficiently address its market surplus. In this study, the conversion of crude glycerol to citric acid, a key biochemical in the emerging bioeconomy, by a wild-type yeast Yarrowia lipolytica DSM 8218 was modelled using the Response Surface Methodology. The model relates C/N mass ratio and crude glycerol concentration to maximize the citric acid yield in flask scale using two different N sources, yeast extract and ammonium sulphate. Under the optimal conditions (yeast extract, C/N 141, glycerol 33 g/L), the conversion yield was 0.249 g/g. The optimal conditions were used for up-scaling a fed-batch fermentation in a 2 L bioreactor highlighting a metabolic shift from mannitol to citric acid when high stirring rates were applied (800 rpm). In these conditions, a morphic transition from pseudo-mycelial form to round-shaped yeast-like cells was observed too.

Evaluation of the Potential of Lipid-Extracted Chlorella vulgaris Residue for Yarrowia lipolytica Growth at Different pH Levels

Projections show that the cultivation of microalgae will extend to the production of bio-based compounds, such as biofuels, cosmetics, and medicines. This will generate co-products or residues that will need to be valorized to reduce the environmental impact and the cost of the process. This study explored the ability of lipid-extracted Chlorella vulgaris residue as a sole carbon and nitrogen source for growing oleaginous yeasts without any pretreatment. Both wild-type Yarrowia lipolytica W29 and mutant JMY3501 (which was designed to accumulate more lipids without their remobilization or degradation) showed a similar growth rate of 0.28 h⁻¹ at different pH levels (3.5, 5.5, and 7.5). However, the W29 cell growth had the best cell number on microalgal residue at a pH of 7.5, while three times fewer cells were produced at all pH levels when JMY3501 was grown on microalgal residue. The JMY3501 growth curves were similar at pH 3.5, 5.5, and 7.5, while the fatty-acid composition differed significantly, with an accumulation of α-linolenic acid on microalgal residue at a pH of 7.5. Our results demonstrate the potential valorization of Chlorella vulgaris residue for Yarrowia lipolytica growth and the positive effect of a pH of 7.5 on the fatty acid profile.

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.

Carotenoids and Their Biosynthesis in Fungi

Carotenoids represent a class of pigmented terpenoids. They are distributed in all taxonomic groups of fungi. Most of the fungal carotenoids differ in their chemical structures to those from other organisms. The general function of carotenoids in heterotrophic organisms is protection as antioxidants against reactive oxygen species generated by photosensitized reactions. Furthermore, carotenoids are metabolized to apocarotenoids by oxidative cleavage. This review presents the current knowledge on fungal-specific carotenoids, their occurrence in different taxonomic groups, and their biosynthesis and conversion into trisporic acids. The outline of the different pathways was focused on the reactions and genes involved in not only the known pathways, but also suggested the possible mechanisms of reactions, which may occur in several non-characterized pathways in different fungi. Finally, efforts and strategies for genetic engineering to enhance or establish pathways for the production of various carotenoids in carotenogenic or non-carotenogenic yeasts were highlighted, addressing the most-advanced producers of each engineered yeast, which offered the highest biotechnological potentials as production systems.

Altering the fatty acid profile of Yarrowia lipolytica to mimic cocoa butter by genetic engineering of desaturases

Background

Demand for Cocoa butter is steadily increasing, but the supply of cocoa beans is naturally limited and under threat from global warming. One route to meeting the future demand for cocoa butter equivalent (CBE) could be to utilize microbial cell factories such as the oleaginous yeast Yarrowia lipolytica.

Results

The main goal was to achieve triacyl-glycerol (TAG) storage lipids in Y. lipolytica mimicking cocoa butter. This was accomplished by replacing the native Δ9 fatty acid desaturase (Ole1p) with homologs from other species and changing the expression of both Ole1p and the Δ12 fatty acid desaturase (Fad2p). We thereby abolished the palmitoleic acid and reduced the linoleic acid content in TAG, while the oleic acid content was reduced to approximately 40 percent of the total fatty acids. The proportion of fatty acids in TAG changed dramatically over time during growth, and the fatty acid composition of TAG, free fatty acids and phospholipids was found to be very different.

Conclusions

We show that the fatty acid profile in the TAG of Y. lipolytica can be altered to mimic cocoa butter. We also demonstrate that a wide range of fatty acid profiles can be achieved while maintaining good growth and high lipid accumulation, which, together with the ability of Y. lipolytica to utilize a wide variety of carbon sources, opens up the path toward sustainable production of CBE and other food oils.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01748-x.

Attempt to Develop an Effective Method for the Separation of Gamma-Decalactone from Biotransformation Medium

Gamma-decalactone (GDL) is a fragrance compound obtained in the process of β-oxidation of ricinoleic acid, which is derived from the hydrolysis of castor oil. The biotechnological method of the synthesis of this lactone has been improved for over two decades, but the vast majority of research results have been based only on determining the concentration of the lactone by chromatographic methods without separating it from the biotransformation medium. In this study, we attempted to separate GDL from the medium in which the lactone was synthesized by Yarrowia lipolytica from castor oil. The effectiveness of liquid–liquid extraction, hydrodistillation, and adsorption on the porous materials (zeolite, vermiculite and resin Amberlite XAD-4) was compared. The influence of the solvent on the efficiency of GDL extraction, the influence of the acidity of the medium on the amount of GDL in the distillate, and the level of lactone adsorption on the above-mentioned adsorbents were compared by calculating the initial adsorption rate. The adsorption isotherm was determined for the most effective adsorbent. Among the five solvents tested, the most effective was diethyl ether, used at the ratio of 1:1. The extraction was characterized by higher efficiency than hydrodistillation; the difference in GDL determinations by these two methods ranged from 12.8 to 22%. The purity of the distillates was much higher than that of the extracts at 88.0 ± 3.4% compared to 53.0 ± 1.8%. The acidification of the biotransformation medium increased the concentration of the lactone in both the reaction mixture and the distillate. GDL was most efficiently adsorbed on Amberlite XAD-4 resin, for which the lactone isotherm adsorption was linear. The amount of lactone adsorbed on Amberlite XAD-4 within 1 h was approx. 80% (2.45 g), of which 1.96 g was then desorbed with ethanol. In the context of industrial applications, adsorption of GDL on Amberlite XAD-4 seems to be the most appropriate method due to material costs, the ease of the process, and low environmental burden.

A Temporal Evolution Perspective of Lipase Production by Yarrowia lipolytica in Solid-State Fermentation

Lipases are enzymes that, in aqueous or non-aqueous media, act on water-insoluble substrates, mainly catalyzing reactions on carboxyl ester bonds, such as hydrolysis, aminolysis, and (trans)esterification. Yarrowia lipolytica is a non-conventional yeast known for secreting lipases and other bioproducts; therefore, it is of great interest in various industrial fields. The production of lipases can be carried on solid-state fermentation (SSF) that utilizes solid substrates in the absence, or near absence, of free water and presents minimal problems with microbial contamination due to the low water contents in the medium. Moreover, SSF offers high volumetric productivity, targets concentrated compounds, high substrate concentration tolerance, and has less wastewater generation. In this sense, the present work provides a temporal evolution perspective regarding the main aspects of lipase production in SSF by Y. lipolytica, focusing on the most relevant aspects and presenting the potential of such an approach.

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

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

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Yarrowia lipolytica was engineered to make a human milk fat substitute.

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Palmitate was directed to the sn-2 position of triacylglycerol by expressing Chlamydomonas reinhardtii LPAAT2.

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Culture with palm oil produced a fatty acyl composition more similar with human milk fat.

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.

Physiological limitations and opportunities in microbial metabolic engineering

Metabolic engineering can have a pivotal role in increasing the environmental sustainability of the transportation and chemical manufacturing sectors. The field has already developed engineered microorganisms that are currently being used in industrial-scale processes. However, it is often challenging to achieve the titres, yields and productivities required for commercial viability. The efficiency of microbial chemical production is usually dependent on the physiological traits of the host organism, which may either impose limitations on engineered biosynthetic pathways or, conversely, boost their performance. In this Review, we discuss different aspects of microbial physiology that often create obstacles for metabolic engineering, and present solutions to overcome them. We also describe various instances in which natural or engineered physiological traits in host organisms have been harnessed to benefit engineered metabolic pathways for chemical production.

Metabolic engineering of Yarrowia lipolytica for terpenoids production: advances and perspectives

Terpenoids are a large family of natural products with diversified structures and functions that are widely used in the food, pharmaceutical, cosmetic, and agricultural fields. However, the traditional methods of terpenoids production such as plant extraction and chemical synthesis are inefficient due to the complex processes, high energy consumption, and low yields. With progress in metabolic engineering and synthetic biology, microbial cell factories provide an interesting alternative for the sustainable production of terpenoids. The non-conventional yeast, Yarrowia lipolytica, is a promising host for terpenoid biosynthesis due to its inherent mevalonate pathway, high fluxes of acetyl-CoA and NADPH, and the naturally hydrophobic microenvironment. In this review, we highlight progress in the engineering of Y. lipolytica as terpenoid biomanufacturing factories, describing the different terpenoid biosynthetic pathways and summarizing various metabolic engineering strategies, including progress in genetic manipulation, dynamic regulation, organelle engineering, and terpene synthase variants.

Yarrowia lipolytica Strains and Their Biotechnological Applications: How Natural Biodiversity and Metabolic Engineering Could Contribute to Cell Factories Improvement

Among non-conventional yeasts of industrial interest, the dimorphic oleaginous yeast Yarrowia lipolytica appears as one of the most attractive for a large range of white biotechnology applications, from heterologous proteins secretion to cell factories process development. The past, present and potential applications of wild-type, traditionally improved or genetically modified Yarrowia lipolytica strains will be resumed, together with the wide array of molecular tools now available to genetically engineer and metabolically remodel this yeast. The present review will also provide a detailed description of Yarrowia lipolytica strains and highlight the natural biodiversity of this yeast, a subject little touched upon in most previous reviews. This work intends to fill this gap by retracing the genealogy of the main Yarrowia lipolytica strains of industrial interest, by illustrating the search for new genetic backgrounds and by providing data about the main publicly available strains in yeast collections worldwide. At last, it will focus on exemplifying how advances in engineering tools can leverage a better biotechnological exploitation of the natural biodiversity of Yarrowia lipolytica and of other yeasts from the Yarrowia clade.

Combined adaptive evolution and transcriptomic profiles reveal aromatic aldehydes tolerance mechanisms in Yarrowia lipolytica

Yarrowia lipolytica is an efficient oleaginous yeast, whereas its activity is typically reduced by inhibitors present in lignocellulosic hydrolysate. Understanding the response mechanism of Y. lipolytica to hydrolysate inhibitors and developing inhibitor tolerant strains are vital to lignocellulose valorization by this promising species. In this study, through adaptive laboratory evolution on three representative aromatic aldehyde inhibitors, evolved strains were obtained. Fermentation phenotype suggested that aromatic aldehydes conversion was one main reason for high tolerance of adapted strains. Transcriptome profiling analysis and reverse metabolic engineering confirmed that overexpressing the aldehyde ketone reductase gene YALI0_B07117g and aldehyde dehydrogenase gene YALI0_B01298g effectively converted aromatic aldehyde to corresponding alcohols and acids. The potential degradation pathways for aromatic aldehyde inhibitors in Y. lipolytica XYL+ were then discussed. This study provided insights to the aromatic aldehyde degradation in Y. lipolytica and a reliable basis for the development of aromatic aldehyde tolerant strains.

Accelerostat study in conventional and microfluidic bioreactors to assess the key role of residual glucose in the dimorphic transition of Yarrowia lipolytica in response to environmental stimuli

Yarrowia lipolytica, with a diverse array of biotechnological applications, is able to grow as ovoid yeasts or filamentous hyphae depending on environmental conditions. This study has explored the relationship between residual glucose levels and dimorphism in Y. lipolytica. Under pH stress conditions, the morphological and physiological characteristics of the yeast were examined during well-controlled accelerostat cultures using both a 1 L-laboratory scale and a 1 mL-microfluidic bioreactor. The accelerostat mode, via a smooth increase of dilution rate (D), enabled the cell growth rate to increase gradually up to the cell wash-out (D ≥μmax of the strain), which was accompanied by a progressive increase in residual glucose concentration. The results showed that Y. lipolytica maintained an ovoid morphology when residual glucose concentration was below a threshold value of around 0.35-0.37 mg L^-1. Transitions towards more elongated forms were triggered at this threshold and progressively intensified with the increase in residual glucose levels. The effect of cAMP on the dimorphic transition was assessed by the exogenous addition of cAMP and the quantification of its intracellular levels during the accelerostat. cAMP has been reported to be an important mediator of environmental stimuli that inhibit filamentous growth in Y. lipolytica by activating the cAMP-PKA regulatory pathway. It was confirmed that the exogenous addition of cAMP inhibited the mycelial morphology of Y. lipolytica, even with glucose concentrations exceeding the threshold level. The results suggest that dimorphic responses in Y. lipolytica are regulated by sugar signaling pathways, most likely via the cAMP-PKA dependent pathway.

Tolerance of Yarrowia lipolytica to inhibitors commonly found in lignocellulosic hydrolysates

BACKGROUND

Lignocellulosic material is a suitable renewable carbon and energy source for microbial cell factories, such as Yarrowia lipolytica. To be accessible for microorganisms, the constituent sugars need to be released in a hydrolysis step, which as a side effect leads to the formation of various inhibitory compounds. However, the effects of these inhibitory compounds on the growth of Y. lipolytica have not been thoroughly investigated.

RESULTS

Here we show the individual and combined effect of six inhibitors from three major inhibitor groups on the growth of Y. lipolytica. We engineered a xylose consuming strain by overexpressing the three native genes XR, XDH, and XK and found that the inhibitor tolerance of Y. lipolytica is similar in glucose and in xylose. Aromatic compounds could be tolerated at high concentrations, while furfural linearly increased the lag phase of the cultivation, and hydroxymethylfurfural only inhibited growth partially. The furfural induced increase in lag phase can be overcome by an increased volume of inoculum. Formic acid only affected growth at concentrations above 25 mM. In a synthetic hydrolysate, formic acid, furfural, and coniferyl aldehyde were identified as the major growth inhibitors.

CONCLUSION

We showed the individual and combined effect of inhibitors found in hydrolysate on the growth of Y. lipolytica. Our study improves understanding of the growth limiting inhibitors found in hydrolysate and enables a more targeted engineering approach to increase the inhibitor tolerance of Y. lipolytica. This will help to improve the usage of Y. lipolytica as a sustainable microbial cell factory.

Hydrolytic secretome engineering in Yarrowia lipolytica for consolidated bioprocessing on polysaccharide resources: review on starch, cellulose, xylan, and inulin

Consolidated bioprocessing (CBP) featuring concomitant hydrolysis of renewable substrates and microbial conversion into value-added biomolecules is considered to bring substantial benefits to the overall process efficiency. The biggest challenge in developing an economically feasible CBP process is identification of bifunctional biocatalyst merging the ability to utilize the substrate and convert it to value-added product with high efficiency. Yarrowia lipolytica is known for its exceptional performance in hydrophobic substrates assimilation and storage. On the other hand, its capacity to grow on plant-derived biomass is strongly limited. Still, its high potential to simultaneously overproduce several secretory proteins makes Y. lipolytica a platform of choice for expanding its substrate range to complex polysaccharides by engineering its hydrolytic secretome. This review provides an overview of different genetic engineering strategies advancing development of Y. lipolytica strains able to grow on the following four complex polysaccharides: starch, cellulose, xylan, and inulin. Much attention has been paid to genome mining studies uncovering native potential of this species to assimilate untypical sugars, as in many cases it turns out that dormant pathways are present in Y. lipolytica's genome. In addition, the magnitude of the economic gain by CBP processing is here discussed and supported with adequate calculations based on simulated process models. KEY POINTS: • The mini-review updates the knowledge on polysaccharide-utilizing Yarrowia lipolytica. • Insight into molecular bases founding new biochemical qualities is provided. • Model industrial processes were simulated and the associated costs were calculated.

Yarrowia lipolytica as an Oleaginous Platform for the Production of Value-Added Fatty Acid-Based Bioproducts

The microbial fermentation process has been used as an alternative pathway to the production of value-added natural products. Of the microorganisms, Yarrowia lipolytica, as an oleaginous platform, is able to produce fatty acid-derived biofuels and biochemicals. Nowadays, there are growing progresses on the production of value-added fatty acid-based bioproducts in Y. lipolytica. However, there are fewer reviews performing the metabolic engineering strategies and summarizing the current production of fatty acid-based bioproducts in Y. lipolytica. To this end, we briefly provide the fatty acid metabolism, including fatty acid biosynthesis, transportation, and degradation. Then, we introduce the various metabolic engineering strategies for increasing bioproduct accumulation in Y. lipolytica. Further, the advanced progress in the production of fatty acid-based bioproducts by Y. lipolytica, including nutraceuticals, biofuels, and biochemicals, is summarized. This review will provide attractive thoughts for researchers working in the field of Y. lipolytica.

Non-invasive Raman spectroscopy for time-resolved in-line lipidomics

Oil-producing yeast cells are a valuable alternative source for palm oil production and, hence, may be one important piece of the puzzle for a more sustainable future.

CRISPR Interference and Activation to Modulate Transcription in Yarrowia lipolytica

Recent developments in RNA-guided nuclease technologies have advanced the engineering of a wide range of organisms, including the nonconventional yeast Yarrowia lipolytica. Y. lipolytica has been the focus of a range of synthetic biology and metabolic engineering studies due to its high capacity to synthesize and accumulate intracellular lipids. The CRISPR-Cas9 system from Streptococcus pyogenes has been successfully adapted and used for genome editing in Y. lipolytica. However, as engineered strains are moved closer to industrialization, the need for finer control of transcription is still present. To overcome this challenge, we have developed CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) systems to allow modulating the transcription of endogenous genes. We begin this protocol chapter by describing how to use the CRISPRi system to repress expression of any gene in Y. lipolytica. A second method describes how to use the CRISPRa system to increase expression of native Y. lipolytica genes. Finally, we describe how CRISPRi or CRISPRa vectors can be combined to enable multiplexed activation or repression of more than one gene. The implementation of CRISPRi and CRISPRa systems improves our ability to control gene expression in Y. lipolytica and promises to enable more advanced synthetic biology and metabolic engineering studies in this host.

Mapping Genetic Interactions in Human Cancer Cells Using a One-Step tRNA-CRISPR System

While well studied in yeast, mapping genetic interactions in mammalian cells has been limited due to many technical obstacles. We have recently developed a new one-step tRNA-CRISPR method called TCGI (tRNA-CRISPR for genetic interactions) which generates high-efficiency, barcode-free, and scalable pairwise CRISPR libraries to identify genetic interactions in mammalian cells. Here we describe this method in detail regarding the construction of the pairwise CRISPR libraries and performing high throughput genetic interacting screening and data analysis. This novel TCGI dramatically improves upon the current methods for mapping genetic interactions and screening drug targets for combinational therapies.

Genome editing systems across yeast species

Yeasts are used to produce a myriad of value-added compounds. Engineering yeasts into cost-efficient cell factories is greatly facilitated by the availability of genome editing tools. While traditional engineering techniques such as homologous recombination-based gene knockout and pathway integration continue to be widely used, novel genome editing systems including multiplexed approaches, bacteriophage integrases, CRISPR-Cas systems, and base editors are emerging as more powerful toolsets to accomplish rapid genome scale engineering and phenotype screening. In this review, we summarized the techniques which have been successfully implemented in model yeast Saccharomyces cerevisiae as well as non-conventional yeast species. The mechanisms and applications of various genome engineering systems are discussed and general guidelines to expand genome editing systems from S. cerevisiae to other yeast species are also highlighted.

Engineering xylose metabolism in yeasts to produce biofuels and chemicals

Xylose is the second most abundant sugar in lignocellulosic biomass. Efficient and rapid xylose utilization is essential for the economic bioconversion of lignocellulosic biomass into value-added products. Building on previous pathway engineering efforts to enable xylose fermentation in Saccharomyces cerevisiae, recent work has focused on reprogramming regulatory networks to enhance xylose utilization by engineered S. cerevisiae. Also, potential benefits of using xylose for the production of various value-added products have been demonstrated. With increasing needs of lipid-derived bioproducts, activation and enhancement of xylose metabolism in oleaginous yeasts have been attempted. This review highlights recent progress of metabolic engineering to achieve efficient and rapid xylose utilization by S. cerevisiae and oleaginous yeasts, such as Yarrowia lipolytica, Rhodosporidium toruloides, and Lipomyces starkeyi.

Lignocellulosic Biomass as a Substrate for Oleaginous Microorganisms: A Review

Microorganisms capable of accumulating lipids in high percentages, known as oleaginous microorganisms, have been widely studied as an alternative for producing oleochemicals and biofuels. Microbial lipid, so-called Single Cell Oil (SCO), production depends on several growth parameters, including the nature of the carbon substrate, which must be efficiently taken up and converted into storage lipid. On the other hand, substrates considered for large scale applications must be abundant and of low acquisition cost. Among others, lignocellulosic biomass is a promising renewable substrate containing high percentages of assimilable sugars (hexoses and pentoses). However, it is also highly recalcitrant, and therefore it requires specific pretreatments in order to release its assimilable components. The main drawback of lignocellulose pretreatment is the generation of several by-products that can inhibit the microbial metabolism. In this review, we discuss the main aspects related to the cultivation of oleaginous microorganisms using lignocellulosic biomass as substrate, hoping to contribute to the development of a sustainable process for SCO production in the near future.

Developing Methods to Circumvent the Conundrum of Chromosomal Rearrangements Occurring in Multiplex Gene Edition

CRISPR/Cas9 is a powerful tool to edit the genome of the yeast Yarrowia lipolytica. Here, we design a simple and robust method to knockout multiple gene families based on the construction of plasmids enabling the simultaneous expression of several sgRNAs. We exemplify the potency of this approach by targeting the well-characterized acyl-CoA oxidase family (POX) and the uncharacterized SPS19 family. We establish a correlation between the high lethality observed upon editing multiple loci and chromosomal translocations resulting from the simultaneous generation of several double-strand breaks (DSBs) and develop multiplex gene editing strategies. Using homologous directed recombination to reduce chromosomal translocations, we demonstrated that simultaneous editing of four genes can be achieved and constructed a strain carrying a sextuple deletion of POX genes. We explore an "excision approach" by simultaneously performing two DSBs in genes and reached 73 to 100% editing efficiency in double disruptions and 41.7% in a triple disruption. This work led to identifying SPS193 as a gene encoding a 2-4 dienoyl-CoA reductase, demonstrating the potential of this method to accelerate knowledge on gene function in expanded gene families.

Engineering Yarrowia lipolytica as a Chassis for De Novo Synthesis of Five Aromatic-Derived Natural Products and Chemicals

Yarrowia lipolytica is a novel microbial chassis to upgrade renewable low-cost carbon feedstocks to high-value commodity chemicals and natural products. In this work, we systematically characterized and removed the rate-limiting steps of the shikimate pathway and achieved de novo synthesis of five aromatic chemicals in Y. lipolytica. We determined that eliminating amino acids formation and engineering feedback-insensitive DAHP synthases are critical steps to mitigate precursor competition and relieve the feedback regulation of the shikimate pathway. Further overexpression of heterologous phosphoketolase and deletion of pyruvate kinase provided a sustained metabolic driving force that channels E4P (erythrose 4-phosphate) and PEP (phosphoenolpyruvate) precursors through the shikimate pathway. Precursor competing pathways and byproduct formation pathways were also blocked by inactivating chromosomal genes. To demonstrate the utility of our engineered chassis strain, three natural products, 2-phenylethanol (2-PE), p-coumaric acid, and violacein, which were derived from phenylalanine, tyrosine, and tryptophan, respectively, were chosen to test the chassis performance. We obtained 2426.22 ± 48.33 mg/L of 2-PE, 593.53 ± 28.75 mg/L of p-coumaric acid, 12.67 ± 2.23 mg/L of resveratrol, 366.30 ± 28.99 mg/L of violacein, and 55.12 ± 2.81 mg/L of deoxyviolacein from glucose in a shake flask. The 2-PE production represents a 286-fold increase over the initial strain (8.48 ± 0.50 mg/L). Specifically, we obtained the highest 2-PE, violacein, and deoxyviolacein titer ever reported from the de novo shikimate pathway in yeast. These results set up a new stage of engineering Y. lipolytica as a sustainable biorefinery chassis strain for de novo synthesis of aromatic compounds with economic values.

Rhodosporidium toruloides - A potential red yeast chassis for lipids and beyond

The red yeast Rhodosporidium toruloides naturally produces microbial lipids and carotenoids. In the past decade or so, many studies demonstrated R. toruloides as a promising platform for lipid production owing to its diverse substrate appetites, robust stress resistance and other favorable features. Also, significant progresses have been made in genome sequencing, multi-omic analysis and genome-scale modeling, thus illuminating the molecular basis behind its physiology, metabolism and response to environmental stresses. At the same time, genetic parts and tools are continuously being developed to manipulate this distinctive organism. Engineered R. toruloides strains are emerging for enhanced production of conventional lipids, functional lipids as well as other interesting metabolites. This review updates those progresses and highlights future directions for advanced biotechnological applications.

Patterns of Lignocellulosic Sugar Assimilation and Lipid Production by Newly Isolated Yeast Strains From Chilean Valdivian Forest

Three yeast strains were isolated from decaying wood of Chilean Valdivian forest and identified as Meyerozyma guilliermondii, Scheffersomyces coipomensis, and Sugiyamaella paludigena. These strains were able to efficiently grow on the major monomers contained in Pinus spp. and Eucalyptus spp. wood that includes glucose (Glc), xylose (Xyl), and mannose (Man), showing at 28 °C higher uptake rates for Man, and in some cases for Glc, than for Xyl, used as single carbon sources. Nevertheless, in cultures performed on sugar mixtures, the strains displayed a notable preference for Glc. Additionally, in sugar mixtures, the absence of regulatory mechanisms in sugar assimilation (e.g., catabolic repression) was observed and documented when the activities of several enzymes involved in sugar assimilation (i.e., phosphoglucose isomerase, phosphomannose isomerase, and xylulokinase) were determined. The activity of the key enzymes involved in the onset of lipid accumulation (i.e., NAD⁺-ICDH) and in fatty acid (FA) biosynthesis (i.e., ATP:CL) indicated a significant accumulation of storage lipids (i.e., up to 24%, w/w) containing oleic and palmitic acids as the major components. The present paper is the first report on the potential of M. guilliermondii, S. coipomensis, and S. paludigena as oleaginous yeasts. We conclude that the new isolates, being able to simultaneously assimilate the major lignocellulosic sugars and efficiently convert them into oily biomass, present a biotechnological potential which deserve further investigation.

Bioproduction of succinic acid from xylose by engineered Yarrowia lipolytica without pH control

BACKGROUND

Xylose is the most prevalent sugar available in hemicellulose fraction of lignocellulosic biomass (LCB) and of great interest for the green economy. Unfortunately, most of the cell factories cannot inherently metabolize xylose as sole carbon source. Yarrowia lipolytica is a non-conventional yeast that produces industrially important metabolites. The yeast is able to metabolize a large variety of substrates including both hydrophilic and hydrophobic carbon sources. However, Y. lipolytica lacks effective metabolic pathway for xylose uptake and only scarce information is available on utilization of xylose. For the economica feasibility of LCB-based biorefineries, effective utilization of both pentose and hexose sugars is obligatory.

RESULTS

In the present study, succinic acid (SA) production from xylose by Y. lipolytica was examined. To this end, Y. lipolytica PSA02004 strain was engineered by overexpressing pentose pathway cassette comprising xylose reductase (XR), xylitol dehydrogenase (XDH) and xylulose kinase (XK) gene. The recombinant strain exhibited a robust growth on xylose as sole carbon source and produced substantial amount of SA. The inhibition of cell growth and SA formation was observed above 60 g/L xylose concentration. The batch cultivation of the recombinant strain in a bioreactor resulted in a maximum biomass concentration of 7.3 g/L and SA titer of 11.2 g/L with the yield of 0.19 g/g. Similar results in terms of cell growth and SA production were obtained with xylose-rich hydrolysate derived from sugarcane bagasse. The fed-batch fermentation yielded biomass concentration of 11.8 g/L (OD600: 56.1) and SA titer of 22.3 g/L with a gradual decrease in pH below 4.0. Acetic acid was obtained as a main by-product in all the fermentations.

CONCLUSION

The recombinant strain displayed potential for bioconversion of xylose to SA. Further, this study provided a new insight on conversion of lignocellulosic biomass into value-added products. To the best of our knowledge, this is the first study on SA production by Y. lipolytica using xylose as a sole carbon source.