Production of tailor-made fatty acids from crude glycerol at low pH by Yarrowia lipolytica

Effects of co-fermentation with different erythritol producing abilities Yarrowia lipolytica on the flavor, functionality, and sensory characteristics of Huangjiu

Different strains play crucial roles in achieving the desired diversification of Huangjiu products. Yarrowia lipolytica strains with high (F4) and low (167) erythritol production abilities were used as adjunct cultures for Huangjiu fermentation. Physicochemical properties, volatile flavor substances, functional properties, metabolite abundance, microbial community dynamics and sensory properties of Huangjiu were evaluated. This strain promoted carbohydrate consumption. The total content of free amino acids in 167 wine significantly increased, especially with respect to sweet amino acids. Y. lipolytica promoted the production of alcohols and esters. The esters in F4 wine increased by 78.2 %, especially medium-chain and long-chain fatty acid ethyl esters, while the alcohols in 167 wine increased by 43.8 %, especially phenylethanol. Based on non-targeted metabolomic analysis, metabolites related to amino acid metabolism were highly enriched in the two groups of wines supplemented with Y. lipolytica F4 is primarily involved in tryptophan and arachidonic acid metabolism and promotes the synthesis of amino acids and their derivatives. The 167 wine contained beneficial functional metabolites involved in amino acid and carbohydrate metabolism. Y. lipolytica altered the abundance of dominant bacterial genera, with F4 increasing Lactiplantibacillus by 42.1 % and 167 enhancing Weissella by 35.9 %. Sensory analysis showed that Y. lipolytica 167 wine promoted the fruit aroma while F4 highlighted cereal aroma in the resulting wine. Therefore, applying Y. lipolytica strains with different erythritol synthesis abilities as adjunct culture are expected to produce products with distinctive flavor or functionality for rice wine or other similar beverages.

Metabolic Engineering of Yarrowia lipolytica for Enhanced De Novo Biosynthesis of Icaritin

Icaritin (ICT) is a naturally occurring flavonoid compound with notable anticancer properties, recently recognized for its efficacy in treating advanced hepatic carcinoma. Traditional methods of ICT production, including plant extraction and chemical synthesis, face challenges such as low yield and environmental concerns. This study leverages synthetic biology to construct a microbial cell factory using Yarrowia lipolytica for de novo ICT synthesis. We engineered the yeast by integrating the ICT synthesis pathway involving EsPT from Epimedium sagittatum and OsOMTm from Oryza sativa. By optimizing the metabolic pathways, including enhancing the supply of DMAPP via mevalonate pathway modifications, and fine-tuning the expression and catalytic efficiency of EsPT through truncation strategies, we significantly improved ICT yield to 247.02 mg/L─the highest microbial ICT titer reported to date. These findings lay a solid foundation for the large-scale industrial production of ICT and offer valuable insights into the biosynthesis of other flavonoid plant natural products.

Model-driven engineering of Cutaneotrichosporon oleaginosus ATCC 20509 for improved microbial oil production

Increasing demand for palm oil has drastic effects on the ecosystem as its production is unsustainable. C. oleaginosus is a yeast with great potential for microbial oil production and is a sustainable alternative to palm oil. Herein we deployed the Design-Build-Test-Learn approach to establish C. oleaginosus as an efficient fatty acid production platform. In the design step, we combined transcriptome data analysis and metabolic modeling and selected gene overexpression targets (ATP-citrate lyase, acetyl-CoA carboxylase, threonine synthase, and hydroxymethylglutaryl-CoA synthase) and media supplements (biotin, thiamine, threonine, serine, and aspartate). Characterization of transformants at various carbon-to-nitrogen (C/N) ratios, and medium supplements provided up to 56% (w/w) lipid content and a 1.4-fold increase in lipid yield on glycerol (g/g). Additionally, quadratic regressions suggested C/N ratio of 240 as the optimum value. These results and introduced pipeline for strain and medium optimization establish C. oleaginous as a sustainable alternative to palm as an oil source.

Engineered yeast Yarrowia lipolytica as a chassis for biosynthesis of fatty acids from mannitol and macroalgal biomass extracts

BACKGROUND

Yarrowia lipolytica possesses the capability to utilize many unconventional carbon sources, such as crude glycerol, alkanes and fatty acids. Despite producing polyols, such as erythritol, arabitol and mannitol, the re-utilization of mannitol is not as efficient as erythritol utilization. Genes involved in mannitol uptake and metabolism in Y. lipolytica remain undescribed. However, deletion of the EYD1 gene (YALI0F01650g), believed to encode erythritol dehydrogenase, has been found to result in a high rate of growth on media containing mannitol as the sole carbon source. Therefore this unique feature was used for further fermentation studies on media containing macroalgal mannitol extracts, obtained from the brown alga Fucus vesiculosus, to produce value-added products.

RESULTS

The obtained strain AJD Δeyd1Dga1 was able to uptake pure and algal mannitol efficiently and produce high amounts of lipids, thanks to overexpression of the DGA1 gene (YALI0E32769g), encoding diacylglycerol (DAG) acyltransferase. The lipid content reached almost 32% of the overall dry biomass as compared to the wild type strain, where this value was more than 4 times lower. Additionally, the biomass at the end of the experiment was the highest among all of the tested strains, reaching 12.67 g/L, more than 50% higher than the control strain.

CONCLUSIONS

The results of this study shed new light on the potential for the yeast Y. lipolytica to utilize macroalgae biomass as a carbon source for production of value-added products, including biomass and lipids. Moreover, the increased mannitol utilization capabilities can provide new insight into mannitol metabolism, including its uptake, which is especially crucial, as the metabolic pathways for all polyols produced by this organism seem to be closely intertwined.

Bioengineered yeast for preventing age-related diseases

The aging process entails a multifaceted decline in the capacity to restore homeostasis in response to stress. A prevalent characteristic of many age-related diseases is the presence of low-grade chronic inflammation, a risk factor contributing significantly to morbidity and mortality in the elderly population. Specific lifestyle interventions, such as regular physical activity, targeted diet, and supplementation, can delay the accumulation of chronic age-associated conditions by mitigating inflammation processes. Bioengineered yeast-producing compounds with distinctive bioactivities, including anti-inflammatory properties, have the potential to provide rich dietary alternatives for the prevention of age-related diseases. This review highlights recent achievements in engineering effective yeast platforms, namely Saccharomyces cerevisiae and Yarrowia lipolytica, that hold promise in retarding the onset of aging and age-related ailments.

Model-based study of Yarrowia lipolytica cultivation on crude glycerol under different fermentation modes: Development of a membrane bioreactor process

Batch fermentations of the wild type Yarrowia lipolytica MUCL 28849 were performed in a bench-top bioreactor to assess crucial operating conditions. A setup of carbon to nitrogen (mol/mol) ratio equal to 34, pH = 6.0 and 52 g/L of crude glycerol showed increased lipid production and complete glycerol consumption at t = 24 h, thus, selected for further process improvement. Α semi-continuous process was implemented, where a pH drop to 4.0 at 24 h, interrupted citric acid secretion without affecting lipid production. An in-situ membrane module was employed for membrane bioreactor fermentations, where yeast cells were successfully retained with minimum fouling. The membrane bioreactor fed-batch process, resulted in a high-cell-density culture reaching 49.8 g/L of dry biomass and 4.9 g/L of lipids. An unstructured model was developed and successfully simulated operation under all fermentation modes, distinguishing diverse physiological shifts.

Engineering Yarrowia lipolytica to Produce l-Malic Acid from Glycerol

The declining availability of cheap fossil-based resources has sparked growing interest in the sustainable biosynthesis of organic acids. l-Malic acid, a crucial four-carbon dicarboxylic acid, finds extensive applications in the food, chemical, and pharmaceutical industries. Synthetic biology and metabolic engineering have enabled the efficient microbial production of l-malic acid, albeit not in Yarrowia lipolytica, an important industrial microorganism. The present study aimed to explore the potential of this fungal species for the production of l-malic acid. First, endogenous biosynthetic genes and heterologous transporter genes were overexpressed in Y. lipolytica to identify bottlenecks in the l-malic acid biosynthesis pathway grown on glycerol. Second, overexpression of isocitrate lyase, malate synthase, and malate dehydrogenase in the glyoxylate cycle pathway and introduction of a malate transporter from Schizosaccharomyces pombe significantly boosted l-malic acid production, which reached 27.0 g/L. A subsequent increase to 37.0 g/L was attained through shake flask medium optimization. Third, adaptive laboratory evolution allowed the engineered strain Po1g-CEE2+Sp to tolerate a lower pH and to accumulate a higher amount of l-malic acid (56.0 g/L). Finally, when scaling up to a 5 L bioreactor, a titer of 112.5 g/L was attained. In conclusion, this study demonstrates for the first time the successful production of l-malic acid in Y. lipolytica by combining metabolic engineering and laboratory evolution, paving the way for large-scale sustainable biosynthesis of this and other organic acids.

Transcriptomic profiling of an evolved Yarrowia lipolytica strain: tackling hexanoic acid fermentation to increase lipid production from short-chain fatty acids

BACKGROUND

Short-chain fatty acids (SCFAs) are cost-effective carbon sources for an affordable production of lipids. Hexanoic acid, the acid with the longest carbon chain in the SCFAs pool, is produced in anaerobic fermentation of organic residues and its use is very challenging, even inhibiting oleaginous yeasts growth.

RESULTS

In this investigation, an adaptive laboratory evolution (ALE) was performed to improve Yarrowia lipolytica ACA DC 50109 tolerance to high hexanoic acid concentrations. Following ALE, the transcriptomic analysis revealed several genetic adaptations that improved the assimilation of this carbon source in the evolved strain compared to the wild type (WT). Indeed, the evolved strain presented a high expression of the up-regulated gene YALI0 E16016g, which codes for FAT1 and is related to lipid droplets formation and responsible for mobilizing long-chain acids within the cell. Strikingly, acetic acid and other carbohydrate transporters were over-expressed in the WT strain.

CONCLUSIONS

A more tolerant yeast strain able to attain higher lipid content under the presence of high concentrations of hexanoic acid has been obtained. Results provided novel information regarding the assimilation of hexanoic acid in yeasts.

Efficient production of 2'-fucosyllactose in unconventional yeast Yarrowia lipolytica

2'-Fucosyllactose (2'-FL) has great application value as a nutritional component and the whole cell biosynthesis of 2'-FL has become the focus of current research. Yarrowia lipolytica has great potential in oligosaccharide synthesis and large-scale fermentation. In this study, systematic engineering of Y. lipolytica for efficient 2'-FL production was performed. By fusing different protein tags, the synthesis of 2'-FL was optimized and the ubiquitin tag was demonstrated to be the best choice to increase the 2'-FL production. By iterative integration of the related genes, increasing the precursor supply, and promoting NADPH regeneration, the 2'-FL synthesis was further improved. The final 2'-FL titer, 41.10 g/L, was obtained in the strain F5-1. Our work reports the highest 2'-FL production in Y. lipolytica, and demonstrates that Y. lipolytica is an efficient microbial chassis for the synthesis of oligosaccharides.

Energy recovery from agro-forest wastes through hydrothermal carbonization coupled with hydrothermal Co-gasification: Effects of succinic acid on hydrochars and H2 production

Aiming to upgrade agro-forest wastes into value-added solid and gaseous fuels in the present investigation, hydrothermal carbonization (HTC) of spruce (SP), canola hull (CH), and canola meal (CM) was optimized in terms of operating conditions, maximizing the higher heating value of hydrochars. The optimal operating conditions were achieved at HTC temperature, reaction time, and solid-to-liquid ratio of 260 ^°C, 60 min, and 0.2 g mL^-1, respectively. At the optimum condition, succinic acid (0.05-0.1 M) was used as HTC reaction medium to investigate the effects of acidic medium on the fuel characteristics of hydrochars. The succinic acid assisted HTC was found to eliminate ash-forming minerals e.g., K, Mg, and Ca from hydrochar backbones. The calorific values, H/C and O/C atomic ratios of hydrochars were in the range of 27.6-29.8 MJ kg^-1, 0.8-1.1, and 0.1-0.2, respectively, indicating the biomass upgrading into coal-like solid fuels. Finally, hydrothermal gasification of hydrochars with their corresponding HTC aqueous phase (HTC-AP) was assessed. Gasification of CM resulted in a relatively high H₂ yield of 4.9-5.5 mol kg^-1 followed by that for SP with 4.0-4.6 mol H₂ per kg of hydrochars. Results suggest that hydrochars and HTC-AP have a great potential for H₂ production via hydrothermal co-gasification, while suggesting HTC-AP reuse.

In-depth analysis of erythrose reductase homologs in Yarrowia lipolytica

The unconventional yeast Yarrowia lipolytica produces erythritol as an osmoprotectant to adapt to osmotic stress. In this study, the array of putative erythrose reductases, responsible for the conversion of d-erythrose to erythritol, was analyzed. Single knockout and multiple knockout strains were tested for their ability to produce polyols in osmotic stress conditions. Lack of six of the reductase genes does not affect erythritol significantly, as the production of this polyol is comparable to the control strain. Deletion of eight of the homologous erythrose reductase genes resulted in a 91% decrease in erythritol synthesis, a 53% increase in mannitol synthesis, and an almost 8-fold increase in arabitol synthesis as compared to the control strain. Additionally, the utilization of glycerol was impaired in the media with induced higher osmotic pressure. The results of this research may shed new light on the production of arabitol and mannitol from glycerol by Y. lipolytica and help to develop strategies for further modification in polyol pathways in these microorganisms.

Engineering Strategies for Efficient Bioconversion of Glycerol to Value-Added Products by Yarrowia lipolytica

Yarrowia lipolytica has been a valuable biotechnological workhorse for the production of commercially important biochemicals for over 70 years. The knowledge gained so far on the native biosynthetic pathways, as well as the availability of numerous systems and synthetic biology tools, enabled not only the regulation and the redesign of the existing metabolic pathways, but also the introduction of novel synthetic ones; further consolidating the position of the yeast in industrial biotechnology. However, for the development of competitive and sustainable biotechnological production processes, bioengineering should be reinforced by bioprocess optimization strategies. Although there are many published reviews on the bioconversion of various carbon sources to value-added products by Yarrowia lipolytica, fewer works have focused on reviewing up-to-date strain, medium, and process engineering strategies with an aim to emphasize the significance of integrated engineering approaches. The ultimate goal of this work is to summarize the necessary knowledge and inspire novel routes to manipulate at a systems level the yeast biosynthetic machineries by combining strain and bioprocess engineering. Due to the increasing surplus of biodiesel-derived waste glycerol and the favored glycerol-utilization metabolic pathways of Y. lipolytica over other carbon sources, the present review focuses on pure and crude glycerol-based biomanufacturing.

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.

Remodelling metabolism for high-level resveratrol production in Yarrowia lipolytica

Resveratrol is a polyphenol with numerous applications in food, pharma, and cosmetics. Lack of precursors and low titer are the main problems hindering industrial scale resveratrol production. Based on previous prescreening, expressing the combination of FjTAL, Pc4CL1 and VvSTS achieved the best resveratrol titer. This was further improved to 235.1 mg/L through engineering the shikimic acid pathway, applying a modular enzyme assembly of Pc4CL1 and VvSTS, enhancing p-coumaric acid supply and diverting glycolytic flux toward erythrose-4-phosphate. The titer was increased to 819.1 mg/L following two rounds of multicopy integration of resveratrol biosynthesis and malonyl-CoA supply, respectively. The titer reached 22.5 g/L with a yield on glucose of 65.5 mg/g using an optimum fed-batch strategy in a 5 L bioreactor with morphology control. This research is the highest report on the de novo production of resveratrol in Yarrowia lipolytica and the findings lay a solid foundation for other producing polyphenols.

An overview on the conversion of glycerol to value-added industrial products via chemical and biochemical routes

Glycerol is a common by-product of industrial biodiesel syntheses. Due to its properties, availability, and versatility, residual glycerol can be used as a raw material in the production of high value-added industrial inputs and outputs. In particular, products like hydrogen, propylene glycol, acrolein, epichlorohydrin, dioxalane and dioxane, glycerol carbonate, n-butanol, citric acid, ethanol, butanol, propionic acid, (mono-, di-, and triacylglycerols), cynamoil esters, glycerol acetate, benzoic acid, and other applications. In this context, the present study presents a critical evaluation of the innovative technologies based on the use of residual glycerol in different industries, including the pharmaceutical, textile, food, cosmetic, and energy sectors. Chemical and biochemical catalysts in the transformation of residual glycerol are explored, along with the factors to be considered regarding the choice of catalyst route used in the conversion process, aiming at improving the production of these industrial products.

Tailoring and optimizing fatty acid production by oleaginous yeasts through the systematic exploration of their physiological fitness

Background

The use of palm oil for our current needs is unsustainable. Replacing palm oil with oils produced by microbes through the conversion of sustainable feedstocks is a promising alternative. However, there are major technical challenges that must be overcome to enable this transition. Foremost among these challenges is the stark increase in lipid accumulation and production of higher content of specific fatty acids. Therefore, there is a need for more in-depth knowledge and systematic exploration of the oil productivity of the oleaginous yeasts. In this study, we cultivated Cutaneotrichosporon oleaginosus and Yarrowia lipolytica at various C/N ratios and temperatures in a defined medium with glycerol as carbon source and urea as nitrogen source. We ascertained the synergistic effect between various C/N ratios of a defined medium at different temperatures with Response Surface Methodology (RSM) and explored the variation in fatty acid composition through Principal Component Analysis.

Results

By applying RSM, we determined a temperature of 30 °C and a C/N ratio of 175 g/g to enable maximal oil production by C. oleaginosus and a temperature of 21 °C and a C/N ratio of 140 g/g for Y. lipolytica. We increased production by 71% and 66% respectively for each yeast compared to the average lipid accumulation in all tested conditions. Modulating temperature enabled us to steer the fatty acid compositions. Accordingly, switching from higher temperature to lower cultivation temperature shifted the production of oils from more saturated to unsaturated by 14% in C. oleaginosus and 31% in Y. lipolytica. Higher cultivation temperatures resulted in production of even longer saturated fatty acids, 3% in C. oleaginosus and 1.5% in Y. lipolytica.

Conclusions

In this study, we provided the optimum C/N ratio and temperature for C. oleaginosus and Y. lipolytica by RSM. Additionally, we demonstrated that lipid accumulation of both oleaginous yeasts was significantly affected by the C/N ratio and temperature. Furthermore, we systematically analyzed the variation in fatty acids composition and proved that changing the C/N ratio and temperature steer the composition. We have further established these oleaginous yeasts as platforms for production of tailored fatty acids.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01956-5.

Lipid production from lignocellulosic biomass using an engineered Yarrowia lipolytica strain

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Two-stage fermentation enhanced single-cell protein production by Yarrowia lipolytica from food waste

The resource utilization of food waste is crucial, and single-cell protein (SCP) is attracting much attention due to its high value. This study aimed to convert food waste to SCP by Yarrowia lipolytica. It was found the chemical oxygen demand (COD) removal rate 77 ± 1.70% was achieved at 30 g COD/L with the protein content of biomass only 24.1 ± 0.4% w/w biomass dry weight (BDW) in one-stage fermentation system. However, the protein content was significantly increased to 38.8 ± 0.2% w/w BDW with the COD removal rate 85.5 ± 0.7% by a two-stage fermentation process, where the food waste was firstly anaerobically fermented to volatile fatty acids and then converted to SCP with Yarrowia lipolytica. Transcriptomic analysis showed that the expression of SCP-producing genes including ATP citrate (pro-S)-lyase and fumarate hydratase class II were up-regulated in the two-stage transformation, resulting in more organic degradation for SCP synthesis.

Isopropanol biosynthesis from crude glycerol using fatty acid precursors via engineered oleaginous yeast Yarrowia lipolytica

Background

Isopropanol is widely used as a biofuel and a disinfectant. Chemical preparation of isopropanol destroys the environment, which makes biological preparation of isopropanol necessary. Previous studies focused on the use of expensive glucose as raw material. Therefore, the microbial cell factory that ferments isopropanol with cheap raw materials will provide a greener way to produce isopropanol.

Results

This study converted crude glycerol into isopropanol using Y. lipolytica. As a microbial factory, the active natural lipid and fatty acid synthesis pathway endows Y. lipolytica with high malonyl-CoA production capacity. Acetoacetyl-CoA synthase (nphT7) and isopropanol synthesis genes are integrated into the Y. lipolytica genome. The nphT7 gene uses the accumulated malonyl-CoA to synthesize acetoacetyl-CoA, which increases isopropanol production. After medium optimization, the best glycerol medium was found and resulted in a 4.47-fold increase in isopropanol production. Fermenter cultivation with pure glycerol medium resulted in a maximum isopropanol production of 1.94 g/L. In a crude glycerol fermenter, 1.60 g/L isopropanol was obtained, 82.53% of that achieved with pure glycerol. The engineered Y. lipolytica in this study has the highest isopropanol titer reported.

Conclusions

The engineered Y. lipolytica successfully produced isopropanol by using crude glycerol as a cheap carbon source. This is the first study demonstrating the use of Y. lipolytica as a cell factory to produce isopropanol. In addition, this is also a new attempt to accumulate lipid synthesis precursors to synthesize other useful chemicals by integrating exogenous genes in Y. lipolytica.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01890-6.

Microbial cell factories for the production of three-carbon backbone organic acids from agro-industrial wastes

At present, mass production of basic and valuable commodities is dependent on linear petroleum-based industries, which ultimately makes the depletion of finite natural reserves and accumulation of non-biodegradable and hazardous wastes. Therefore, an ecofriendly and sustainable solution should be established for a circular economy where infinite resources, such as agro-industrial wastes, are fully utilized as substrates in the production of target value-added chemicals. Hereby, recent advances in metabolic engineering strategies and techniques used in the development of microbial cell factories for enhanced production of three-carbon platform chemicals such as lactic acid, propionic acid, and 3-hydroxypropionic acid are discussed. Further developments and future perspectives in the production of these organic acids from agro-industrial wastes from the dairy, sugar, and biodiesel industries are also highlighted to demonstrate the importance of waste-based biorefineries for organic acid production.

Advancing Yarrowia lipolytica as a superior biomanufacturing platform by tuning gene expression using promoter engineering

Yarrowia lipolytica is recognized as an excellent non-conventional yeast in the field of biomanufacturing, where it is used as a host to produce oleochemicals, terpenes, organic acids, polyols and recombinant proteins. Consequently, metabolic engineering of this yeast is becoming increasingly popular to advance it as a superior biomanufacturing platform, of which promoters are the most basic elements for tuning gene expression. Endogenous promoters of Yarrowia lipolytica were reviewed, which are the basis for promoter engineering. The engineering strategies, such as hybrid promoter engineering, intron enhancement promoter engineering, and transcription factor-based inducible promoter engineering are described. Additionally, the applications of Yarrowia lipolytica promoter engineering to rationally reconstruct biosynthetic gene clusters and improve the genome-editing efficiency of the CRISPR-Cas systems were reviewed. Finally, research needs and future directions for promoter engineering are also discussed in this review.

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.

Engineering Yarrowia lipolytica to produce advanced biofuels: Current status and perspectives

Energy security and global climate change have necessitated the development of renewable energy with net-zero emissions. As alternatives to traditional fuels used in heavy-duty vehicles, advanced biofuels derived from fatty acids and terpenes have similar properties to current petroleum-based fuels, which makes them compatible with existing storage and transportation infrastructures. The fast development of metabolic engineering and synthetic biology has shown that microorganisms can be engineered to convert renewable feedstocks into these advanced biofuels. The oleaginous yeast Yarrowia lipolytica is rapidly emerging as a valuable chassis for the sustainable production of advanced biofuels derived from fatty acids and terpenes. Here, we provide a summary of the strategies developed in recent years for engineering Y. lipolytica to synthesize advanced biofuels. Finally, efficient biotechnological strategies for the production of these advanced biofuels and perspectives for future research are also discussed.

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.

Microbial lipids from organic wastes: Outlook and challenges

Microbial lipids have recently drawn a lot of attention as renewable sources for biochemicals production. Strong research efforts have been addressed to efficiently use organic wastes as carbon source for microbial lipids, which would definitively increase the profitability of the production process and boost a bio-based economy. This review compiles interesting traits of oleaginous microorganisms and highlights current trends on microbial- and process-oriented approaches to maximize microbial oil production from inexpensive substrates like lignocellulosic sugars, volatile fatty acids and glycerol. Furthermore, downstream processes such as cell harvesting or lipid extraction, that are decisive for the cost-effectiveness of the process, are discussed. To underpin microbial oils within the so demanded circular economy, associated challenges, recent advances and possible industrial applications that are also identified in this review.

Rye and Oat Agricultural Wastes as Substrate Candidates for Biomass Production of the Non-Conventional Yeast Yarrowia lipolytica

The aim of this study was to test rye straw, rye bran and oat bran hydrolysates as substrates for growth of the yeast Yarrowia lipolytica, a microorganism known to have large biotechnological potential. First, after the combined process of acid-enzymatic hydrolysis, the concentration and composition of fermentable monosaccharides in the obtained hydrolysates were analyzed. Glucose was the main sugar, followed by xylose and arabinose. Rye bran hydrolysate had the highest sugar content—80.8 g/L. The results showed that this yeast was able to grow on low-cost medium and produce biomass that could be used as a feed in the form of single cell protein. The biomass of yeast grown in oat bran hydrolysate was over 9 g/L after 120 h, with the biomass total yield and total productivity values of 0.141 g/g and 0.078 g/h, respectively. The protein contents in yeast biomass were in the range of 30.5–44.5% of dry weight. Results obtained from Y. lipolytica cultivated in rye bran showed high content of exogenous amino acid (leucine 3.38 g, lysine 2.93 g, threonine 2.31 g/100 g of dry mass) and spectrum of unsaturated fatty acid with predominantly oleic acid—59.28%. In conclusion, these results demonstrate that lignocellulosic agricultural waste, after hydrolysis, could be efficiently converted to feed-related yeast biomass.