Metabolic Engineering for Expanding the Substrate Range of Yarrowia lipolytica

Dynamic regulation combined with systematic metabolic engineering for high-level palmitoleic acid accumulation in oleaginous yeast

Palmitoleic acid (POA, C16:1Δ9) is widely recognized for its preventive and therapeutic effects in various chronic and cardiovascular diseases, but the current production practices based on plant extraction are both economically and ecologically unsustainable. Although Yarrowia lipolytica is capable of producing POA, it only accumulates to a small percentage of total fatty acids. The present study aimed to enhance the accumulation of POA by employing a two-layer engineering strategy, encompassing the modulation of the fatty acid profile and the promotion of the accumulation of POA-rich lipids. The fatty acid profile was subject to modulation through the engineering of the fatty acid metabolism by expressing heterologous specific fatty acid desaturases CeFat5 and implementing dynamic regulation based on a copper-responsive promoter. Then, the mechanism underlying this improvement of POA production capacity was elucidated. Finally, the POA-rich lipid accumulation ability was enhanced through engineering of the lipid metabolism by overexpressing the heterologous POA-specific triacylglycerol forming acyltransferase, introducing the artificial designed non-carboxylative malonyl-CoA production pathway, and preventing lipid degradation. The resulting optimized yeast strain achieved an impressive POA accumulation accounting for 50.62% of total fatty acids, marking a 37.7-fold improvement over the initial strain. Moreover, a record POA titer of 25.6 g/L was achieved in the bioreactor. Overall, this study introduces a framework for establishing efficient yeast platforms for the accumulation of valuable fatty acids.

Strategic approaches for designing yeast strains as protein secretion and display platforms

Yeast has been established as a versatile platform for expressing functional molecules, owing to its well-characterized biology and extensive genetic modification tools. Compared to prokaryotic systems, yeast possesses advanced cellular mechanisms that ensure accurate protein folding and post-translational modifications. These capabilities are particularly advantageous for the expression of human-derived functional proteins. However, designing yeast strains as an expression platform for proteins requires the integration of molecular and cellular functions. By delving into the complexities of yeast-based expression systems, this review aims to empower researchers with the knowledge to fully exploit yeast as a functional platform to produce a diverse range of proteins. This review includes an exploration of the host strains, gene cassette structures, as well as considerations for maximizing the efficiency of the expression system. Through this in-depth analysis, the review anticipates stimulating further innovation in the field of yeast biotechnology and protein engineering.

Metabolic Engineering of Yarrowia lipolytica for Conversion of Waste Cooking Oil into Omega-3 Eicosapentaenoic Acid

Omega-3 polyunsaturated fatty acids (PUFAs), especially eicosapentaenoic acid (EPA, C20:5), are crucial dietary fats known for their numerous health benefits. However, traditional sources of EPA, like fish oil, raise sustainability and environmental concerns, underscoring the need for alternative production methods. The engineered oleaginous yeast Yarrowia lipolytica has emerged as a promising candidate for sustainable production of EPA. This study explores the efficient production of EPA with an earlier engineeredY. lipolytica strain Y8412, utilizing waste cooking oil (WCO) as an alternative carbon source. While cofeeding WCO resulted in increased total lipid content, it also caused an increase in intracellular free fatty acid (FFA) levels, which can be toxic to cells and reduce EPA synthesis. To solve this issue, we first overexpressed FAA1 and GPD1 genes converting excess FFAs into triglycerides (TAGs). Additionally, we knocked out TGL3/4 genes, which encode lipases linked to lipid bodies, to minimize the degradation of TAGs back into FFAs. The modified strains significantly reduced intracellular FFA levels and improved EPA production. Notably, the TGL4 knockout strain Y8412T4- showed 57% increase in EPA production titer and nearly 50% increase in carbon conversion yield compared to the parental strain Y8412 fed with glucose only. These findings suggest that preventing TAG degradation by knocking out TGL4 is an effective approach for enhanced EPA production when WCO is used to partially replace glucose as the carbon source. This study offers an effective engineering strategy for low-cost, high-yield, and sustainable production of omega-3 fatty acids from waste feedstocks.

Insights into the methanol utilization capacity of Y. lipolytica and improvements through metabolic engineering

Methanol is a promising sustainable alternative feedstock for green biomanufacturing. The yeast Yarrowia lipolytica offers a versatile platform for producing a wide range of products but it cannot use methanol efficiently. In this study, we engineered Y. lipolytica to utilize methanol by overexpressing a methanol dehydrogenase, followed by the incorporation of methanol assimilation pathways from methylotrophic yeasts and bacteria. We also overexpressed the ribulose monophosphate (RuMP) and xylulose monophosphate (XuMP) pathways, which led to significant improvements in growth with methanol, reaching a consumption rate of 2.35 g/L in 24 h and a 2.68-fold increase in biomass formation. Metabolomics and Metabolite Flux Analysis confirmed methanol assimilation and revealed an increase in reducing power. The strains were further engineered to produce the valuable heterologous product resveratrol from methanol as a co-substrate. Unlike traditional methanol utilization processes, which are often resource-intensive and environmentally damaging, our findings represent a significant advance in green chemistry by demonstrating the potential of Y. lipolytica for efficient use of methanol as a co-substrate for energy, biomass, and product formation. This work not only contributes to our understanding of methanol metabolism in non-methylotrophic organisms but also paves the way for achieving efficient synthetic methylotrophy towards green biomanufacturing.

Novel cell factory for the production of 24-epi-ergosterol, an un-natural semi-synthetic precursor for the production of brassinolide in Yarrowia lipolytica

Brassinolide (BL) is the most bioactive plant growth regulator among Brassinosteroids (BRs), belonging to the sixth class of plant hormones. However, its low natural abundance limits large-scale agricultural applications. An unnatural sterol, 24-epi-ergosterol, was proposed as a semi-synthetic precursor for economic production of BL. Here, we constructed a synthetic pathway for 24-epi-ergosterol in Yarrowia lipolytica, which has abundant acetyl-CoA content and a hydrophobic intracellular environment. Initially, we introduced a mutant plant-derived Δ24(28) sterol reductase (Dwf1) into Y. lipolytica to enable 24-epi-ergosterol production. The production of 24-epi-ergosterol was subsequently enhanced by regulating sterol homeostasis, optimizing transcriptional regulators, and overexpressing key pathway genes. Next, the accumulation of 24-epi-ergosterol was further improved by increasing acetyl-CoA levels and adjusting lipid metabolism. Finally, the 24-epi-ergosterol production reached 1626.85 mg/L after optimizing the fermentation conditions and performing a fed-batch culture in a 2 L fermenter. This study represents the first successful de novo synthesis of 24-epi-ergosterol in Y. lipolytica, offering a novel approach for the industrial production of BL.

Engineering Xylose Isomerase and Reductase Pathways in Yarrowia lipolytica for Efficient Lipid Production

Xylose is a common monosaccharide in lignocellulosic residues that Yarrowia lipolytica cannot naturally metabolise for lipid production and therefore, heterologous xylose metabolic pathways must be engineered in this yeast to facilitate its consumption. We have compared the metabolic efficiency of two xylose metabolic pathways by developing three recombinant Y. lipolytica strains: one harbouring a xylose reductase pathway, one with a xylose isomerase pathway, and one combining both pathways, and the strains were tested for xylose consumption and lipid production at different scales. The recombinant strain with the reductase pathway that was directly isolated in selective xylose medium showed the highest lipid yield, producing up to 12.8 g/L of lipids, or 43% of the biomass dry weight, without requiring any other xylose consumption adaptive evolution process. This strain achieved a lipid yield of 0.13 g lipids/g xylose, one of the highest yields in yeast reported so far using xylose as the sole carbon and energy source. Although the strain harbouring the isomerase pathway performed better under oxygen-limiting conditions and led to higher lipid intracellular accumulation, it showed a lower xylose uptake and biomass production, rendering a lower yield under non-limiting oxygen conditions. Unexpectedly, the combination of both pathways in the same strain was less effective than the use of the reductase pathway alone.

Efficient biosynthesis of β-caryophyllene by engineered Yarrowia lipolytica

BACKGROUND

β-Caryophyllene, a sesquiterpenoid, holds considerable potential in pharmaceutical, nutraceutical, cosmetic, and chemical industries. In order to overcome the limitation of β-caryophyllene production by the extraction from plants or chemical synthesis, we aimed the microbial production of β-caryophyllene in non-conventional yeast Yarrowia lipolytica in this study.

RESULTS

Two genes, tHMG1 from S. cerevisiae to boost the mevalonate pool and QHS1 from Artemisia annua, were expressed under different promoters and copy numbers in Y. lipolytica. The co-expression of 8UAS pEYK1-QHS1 and pTEF-tHMG1 in the obese strain yielded 165.4 mg/L and 201.5 mg/L of β-caryophyllene in single and double copies, respectively. Employing the same combination of promoters and genes in wild-type-based strain with two copies resulted in a 1.36-fold increase in β-caryophyllene. The introduction of an additional three copies of 8UAS pEYK1-tHMG1 further augmented the β-caryophyllene, reaching 318.5 mg/L in flask fermentation. To maximize the production titer, we optimized the carbon source ratio between glucose and erythritol as well as fermentation condition that led to 798.1 mg/L of β-caryophyllene.

CONCLUSIONS

A biosynthetic pathway of β-caryophyllene was firstly investigated in Y. lipolytica in this study. Through the modulation of key enzyme expression, we successfully demonstrated an improvement in β-caryophyllene production. This strategy suggests its potential extension to studies involving the microbial production of various industrially relevant terpenes.

Advancing Succinic Acid Biomanufacturing Using the Nonconventional Yeast Yarrowia lipolytica

Succinic acid is an essential bulk chemical with wide-ranging applications in materials, food, and pharmaceuticals. With the advancement of biotechnology, there has been a surge in focus on low-carbon sustainable microbial synthesis methods for producing biobased succinic acid. Due to its high intrinsic acid tolerance, Yarrowia lipolytica has gained recognition as a competitive chassis for the industrial manufacture of succinic acid. This review summarizes the research progress on succinic acid biomanufacturing using Y. lipolytica. First, it introduces the major metabolic routes for succinic acid biosynthesis and the pertinent engineering approaches for building efficient cell factories. Subsequently, we offer a review of methods employed for succinic acid synthesis by Y. lipolytica utilizing alternative substrates as well as the relevant optimization strategies for the fermentation process. Finally, future research directions for improving succinic acid biomanufacturing in Y. lipolytica are delineated in light of the recent progress, obstacles, and trends in this area.

Engineering and evolution of Yarrowia lipolytica for producing lipids from lignocellulosic hydrolysates

Yarrowia lipolytica, an oleaginous yeast, shows promise for industrial fermentation due to its robust acetyl-CoA flux and well-developed genetic engineering tools. However, its lack of an active xylose metabolism restricts the conversion of cellulosic sugars to valuable products. To address this, metabolic engineering, and adaptive laboratory evolution (ALE) were applied to the Y. lipolytica PO1f strain, resulting in an efficient xylose-assimilating strain (XEV). Whole-genome sequencing (WGS) of the XEV followed by reverse engineering revealed that the amplification of the heterologous oxidoreductase pathway and a mutation in the GTPase-activating protein gene (YALI0B12100g) might be the primary reasons for improved xylose assimilation in the XEV strain. When a sorghum hydrolysate was used, the XEV strain showed superior xylose consumption and lipid production compared to its parental strain (X123). This study advances our understanding of xylose metabolism in Y. lipolytica and proposes effective metabolic engineering strategies for optimizing lignocellulosic hydrolysates.

Efficient calcium fumarate overproduction from xylose and corncob-derived xylose by engineered strains of Aureobasidium pullulans var. Aubasidani DH177

BACKGROUND

Xylose from lignocellulose is one of the most abundant and important renewable and green raw materials. It is very important how to efficiently transform xylose into useful bioproducts such as fumaric acid and so on.

RESULTS

In this study, it was found that the GC1 strain (∆gox, in which the GOX gene encoding glucose oxidase which could transform glucose into gluconic acid was removed) of A. pullulans var. aubasidani DH177 had the high ability to utilize xylose and corncob-derived xylose with CO2 fixation derived from CaCO3 to produce calcium fumarate. Overexpression of the XI gene encoding xylose isomerase, the XK gene encoding xylose kinase and the TKL gene coding for transketolase made the strain TKL-4 produce 73.1 g/L of calcium fumarate from xylose. At the same time, the transcriptional levels of the key ASS gene coding for argininosuccinate synthase and the ASL gene coding for argininosuccinate lyase in the ornithine-urea cycle (OUC) were also obviously enhanced. The results also demonstrated that the TKL-4 strain could produce more calcium fumarate from xylose and corncob-derived xylose than from glucose. During 10-liter fermentation, the TKL-4 strain could produce 88.5 g/L of calcium fumarate from xylose, the productivity was 0.52 g/h/L. Meanwhile, it could yield 85.6 g/L of calcium fumarate from corncob-derived xylose and the productivity was 0.51 g/h/L. During the same fermentation, the TKL-4 strain could transform the mixture containing 75.0 g/L glucose and 45.0 g/L xylose to produce 78.7 ± 1.1 g/L calcium fumarate.

CONCLUSIONS

This indicated that the TKL-4 strain constructed in this study indeed could actively transform xylose and corncob-derived xylose into calcium fumarate through the green ways.

Synthesis of β-ionone from xylose and lignocellulosic hydrolysate in genetically engineered oleaginous yeast Yarrowia lipolytica

β-ionone, an apocarotenoid derived from a C40 terpenoid has an intense, woody smell and a low odor threshold that has been widely used in as an ingredient in food and cosmetics. Yarrowia lipolytica is a promising host for β-ionone production because of its oleaginous nature, its ability to produce high levels of acetyl-CoA (an important precursor for terpenoids), and the availability of synthetic biology tools to engineer the organism. In this study, β-carotene-producing Y. lipolytica strain XK17 was employed for β-ionone biosynthesis. First, we explored the effect of different sources of carotenoid cleavage dioxygenase (CCD) genes on β-ionone production. A high-yielding strain rUinO-D14 with 122 mg/L of β-ionone was obtained by screening promoters combined with rDNA mediated multi-round iterative transformations to optimize the expression of the CCD gene of Osmanthus fragrans. Second, to further develop a high-level production strain for β-ionone, we optimized key genes in the mevalonate pathway by multi-round iterative transformations mediated by non-homologous end joining, combined with a protein tagging strategy. Finally, the introduction of a heterologous oxidoreductase pathway enabled the engineered Y. lipolytica strain to use xylose as a sole carbon source and produce β-ionone. In addition, the potential for use of lignocellulosic hydrolysate as the carbon source for β-ionone production showed that the NHA-A31 strain had a high β-ionone productivity level. This study demonstrates that engineered Y. lipolytica can be used for the efficient, green and sustainable production of β-ionone.

Advances and perspectives in genetic expression and operation for the oleaginous yeast Yarrowia lipolytica

The utilization of industrial biomanufacturing has emerged as a viable and sustainable alternative to fossil-based resources for producing functional chemicals. Moreover, advancements in synthetic biology have created new opportunities for the development of innovative cell factories. Notably, Yarrowia lipolytica, an oleaginous yeast that is generally regarded as safe, possesses several advantageous characteristics, including the ability to utilize inexpensive renewable carbon sources, well-established genetic backgrounds, and mature genetic manipulation methods. Consequently, there is increasing interest in manipulating the metabolism of this yeast to enhance its potential as a biomanufacturing platform. Here, we reviewed the latest developments in genetic expression strategies and manipulation tools related to Y. lipolytica, particularly focusing on gene expression, chromosomal operation, CRISPR-based tool, and dynamic biosensors. The purpose of this review is to serve as a valuable reference for those interested in the development of a Y. lipolytica microbial factory.

Efficient Production of the Colorless Carotenoid Phytoene in Yarrowia lipolytica through Metabolic Engineering

Phytoene, a colorless carotenoid with unique ultraviolet (UV)-B absorption properties, offers potential for applications in functional food, cosmetics, and therapeutics. However, their low natural yield poses a challenge for large-scale production. This study aims to enhance phytoene production in the oleaginous yeast Yarrowia lipolytica by introducing a heterologous phytoene synthase gene combined with metabolic engineering approaches. We enhanced phytoene synthesis by overexpressing key genes in the mevalonate pathway and compartmentalizing the biosynthetic pathway within peroxisomes. Moreover, we inhibited the glyoxylate cycle to increase the accumulation of peroxisomal acetyl-CoA available for phytoene production. Our engineered strains demonstrated a significant increase in phytoene production, reaching up to 1.34 g/L titer and 58.74 mg/gDCW yield in the flask-scale fed-batch culture, which are the highest levels reported to date. These results underscore the potential of Y. lipolytica as a robust platform for producing phytoenes and other terpenoids on an industrial scale, offering valuable insights for future efforts in metabolic engineering.

Understanding xylose transport in yeasts

Xylose constitutes the second major sugar fraction of the plant-derived lignocellulosic biomass, which is the most abundantly available and renewable feedstock for microbial fermentations. Hence, comprehensive utilization of xylose is crucial from the perspective of sustainable development of bio-based products, such as fuels, fine chemicals, and high-value compounds. Due to several inherent advantages, various species and strains of yeast are employed to produce these biomolecules. With the advancement of genetic engineering in yeast, lignocellulosic biomass has begun to be commercialized for producing various bioproducts required in the food, fuel, pharmaceutical, chemical, and cosmetics industries. The increasing demands of these bioproducts worldwide lead to a necessity of utilizing xylose efficiently for yeast fermentation strategies together with/replacing glucose for more economic sustainability. However, yeast fermentation processes mostly employ glucose; hence, our understanding of xylose utilization by yeast has not been as scrupulous as it should have been. There has been a remarkable increase in the number of studies conducted on xylose utilization and metabolism in yeasts in the past decade. Our objective in this chapter is to highlight the key advancements and novel approaches in this area and to integrate our understanding of xylose metabolism in yeasts, which can help culminate into commercializing strategies in the future for the development of important bioproducts.

Enhanced Antioxidant, Antifungal, and Herbicidal Activities through Bioconversion of Diosgenin by Yarrowia lipolytica P01a

This study explores the bioconversion of diosgenin by Yarrowia lipolytica P01a, focusing on enhancing the antioxidant, antifungal, and herbicidal activities of the resulting extracts. The bioconversion process, involving glycosylation and hydroxylation, produced significant amounts of protodioscin and soyasaponin I. The extracts showed superior antioxidant activity, with up to 97.02% inhibition of ABTS· radicals and 33.30% inhibition of DPPH· radicals at 1000 mg L-1 of diosgenin. Antifungal assays revealed strong inhibitory effects against Botrytis cinerea, Alternaria sp., and Aspergillus niger, with maximum inhibition rates of 67.34%, 35.63%, and 65.53%, respectively. Additionally, the herbicidal activity of the bioconverted extracts was comparable to commercial herbicides, achieving 100% inhibition of seed germination in both monocotyledonous and dicotyledonous plants. These findings suggest that the Y. lipolytica P01a-mediated bioconversion of diosgenin could provide a sustainable and eco-friendly alternative for developing natural biofungicides and bioherbicides.

Comparative transcriptomics analysis-guided metabolic engineering of Yarrowia lipolytica for improved erythritol and fructooligosaccharides production

Currently, fructooligosaccharides (FOS) are converted from sucrose by purified enzymes or fungal cells, but these methods are costly and time-consuming. Here, the optimal fermentation conditions for strain E326 were determined through fermentation optimization: initial glucose 200 g/L, NaCl 25 g/L, inoculum volume 20 %, dissolved oxygen 20-30 %, pH 3, and glucose feeding concentration 100 g/L, which increased erythritol titer by 1.5 times. The co-expression of HGT1 and APC11 genes alleviated the erythritol synthesis stagnation, shorten the fermentation time by 16.7 %, and increased the erythritol productivity by 17.2 %. The episomal plasmids based on yeast mitochondrial replication origins (mtORIs) were constructed to surface display fructosyltransferase, effectively utilizing waste yeast cells generated during erythritol fermentation. Under the conditions of 60℃ and pH 6, the FOS yield reached 65 %, which to our best of knowledge is so-far the highest yield of FOS obtained. These findings will contribute to the industrial production of erythritol and FOS.

Probiotic Yeasts: A Developing Reality?

Yeasts are gaining increasing attention for their potential health benefits as probiotics in recent years. Researchers are actively searching for new yeast strains with probiotic properties (i.e, Debaryomyces hansenii; Kluyveromyces marxianus; Yarrowia lipolytica; Pichia hudriavzevii; and Torulaspora delbrueckii) from various sources, including traditional fermented foods, the human gut, and the environment. This exploration is expanding the pool of potential probiotic yeasts beyond the well-studied Saccharomyces boulardii. Research suggests that specific yeast strains possess properties that could be beneficial for managing conditions like inflammatory bowel disease, irritable bowel syndrome, skin disorders, and allergies. Additionally, probiotic yeasts may compete with pathogenic bacteria for adhesion sites and nutrients, thereby inhibiting their growth and colonization. They might also produce antimicrobial compounds that directly eliminate harmful bacteria. To achieve these goals, the approach that uses probiotics for human health is changing. Next-generation yeast probiotics are emerging as a powerful new approach in the field of live biotherapeutics. By using genetic engineering, scientists are able to equip these tools with specialized capabilities. However, most research on these probiotic yeasts is still in its early stages, and more clinical trials are needed to confirm their efficacy and safety for various health conditions. This review could provide a brief overview of the situation in this field.

Yeast-insect interactions in southern Africa: Tapping the diversity of yeasts for modern bioprocessing

Yeast-insect interactions are one of the most interesting long-standing relationships whose research has contributed to our understanding of yeast biodiversity and their industrial applications. Although insect-derived yeast strains are exploited for industrial fermentations, only a limited number of such applications has been documented. The search for novel yeasts from insects is attractive to augment the currently domesticated and commercialized production strains. More specifically, there is potential in tapping the insects native to southern Africa. Southern Africa is home to a disproportionately high fraction of global biodiversity with a cluster of biomes and a broad climate range. This review presents arguments on the roles of the mutualistic relationship between yeasts and insects, the presence of diverse pristine environments and a long history of spontaneous food and beverage fermentations as the potential source of novelty. The review further discusses the recent advances in novelty of industrial strains of insect origin, as well as various ancient and modern-day industries that could be improved by use yeasts from insect origin. The major focus of the review is on the relationship between insects and yeasts in southern African ecosystems as a potential source of novel industrial yeast strains for modern bioprocesses.

Genome-scale transcriptional activation by non-homologous end joining-mediated integration in Yarrowia lipolytica

BACKGROUND

Genome-scale screening can be applied to efficiently mine for unknown genes with phenotypes of interest or special functions. It is also useful to identify new targets for engineering desirable properties of cell factories.

RESULTS

Here, we designed a new approach for genome-scale transcription activation using non-homologous end joining (NHEJ)-mediated integration in Yarrowia lipolytica. We utilized this approach to screen for genes that, upon activation, confer phenotypes including improved acetic acid tolerance and xylose metabolism. The candidates were validated using gene overexpression, and functional changes including improved growth performance under multiple stressors and activated pentose metabolism were identified.

CONCLUSIONS

This study provides a simple and effective approach to randomly activate endogenous genes and mine for key targets associated with phenotypes of interest. The specific gene targets identified here will be useful for cell factory construction and biorefining lignocellulose.

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.

Engineered yeasts and lignocellulosic biomaterials: shaping a new dimension for biorefinery and global bioeconomy

The next milestone of synthetic biology research relies on the development of customized microbes for specific industrial purposes. Metabolic pathways of an organism, for example, depict its chemical repertoire and its genetic makeup. If genes controlling such pathways can be identified, scientists can decide to enhance or rewrite them for different purposes depending on the organism and the desired metabolites. The lignocellulosic biorefinery has achieved good progress over the past few years with potential impact on global bioeconomy. This principle aims to produce different bio-based products like biochemical(s) or biofuel(s) from plant biomass under microbial actions. Meanwhile, yeasts have proven very useful for different biotechnological applications. Hence, their potentials in genetic/metabolic engineering can be fully explored for lignocellulosic biorefineries. For instance, the secretion of enzymes above the natural limit (aided by genetic engineering) would speed-up the down-line processes in lignocellulosic biorefineries and the cost. Thus, the next milestone would greatly require the development of synthetic yeasts with much more efficient metabolic capacities to achieve basic requirements for particular biorefinery. This review gave comprehensive overview of lignocellulosic biomaterials and their importance in bioeconomy. Many researchers have demonstrated the engineering of several ligninolytic enzymes in heterologous yeast hosts. However, there are still many factors needing to be well understood like the secretion time, titter value, thermal stability, pH tolerance, and reactivity of the recombinant enzymes. Here, we give a detailed account of the potentials of engineered yeasts being discussed, as well as the constraints associated with their development and applications.

Perspectives for Using CO2 as a Feedstock for Biomanufacturing of Fuels and Chemicals

Microbial cell factories offer an eco-friendly alternative for transforming raw materials into commercially valuable products because of their reduced carbon impact compared to conventional industrial procedures. These systems often depend on lignocellulosic feedstocks, mainly pentose and hexose sugars. One major hurdle when utilizing these sugars, especially glucose, is balancing carbon allocation to satisfy energy, cofactor, and other essential component needs for cellular proliferation while maintaining a robust yield. Nearly half or more of this carbon is inevitably lost as CO2 during the biosynthesis of regular metabolic necessities. This loss lowers the production yield and compromises the benefit of reducing greenhouse gas emissions-a fundamental advantage of biomanufacturing. This review paper posits the perspectives of using CO2 from the atmosphere, industrial wastes, or the exhausted gases generated in microbial fermentation as a feedstock for biomanufacturing. Achieving the carbon-neutral or -negative goals is addressed under two main strategies. The one-step strategy uses novel metabolic pathway design and engineering approaches to directly fix the CO2 toward the synthesis of the desired products. Due to the limitation of the yield and efficiency in one-step fixation, the two-step strategy aims to integrate firstly the electrochemical conversion of the exhausted CO2 into C1/C2 products such as formate, methanol, acetate, and ethanol, and a second fermentation process to utilize the CO2-derived C1/C2 chemicals or co-utilize C5/C6 sugars and C1/C2 chemicals for product formation. The potential and challenges of using CO2 as a feedstock for future biomanufacturing of fuels and chemicals are also discussed.

Biotechnological production of omega-3 fatty acids: current status and future perspectives

Omega-3 fatty acids, including alpha-linolenic acids (ALA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA), have shown major health benefits, but the human body's inability to synthesize them has led to the necessity of dietary intake of the products. The omega-3 fatty acid market has grown significantly, with a global market from an estimated USD 2.10 billion in 2020 to a predicted nearly USD 3.61 billion in 2028. However, obtaining a sufficient supply of high-quality and stable omega-3 fatty acids can be challenging. Currently, fish oil serves as the primary source of omega-3 fatty acids in the market, but it has several drawbacks, including high cost, inconsistent product quality, and major uncertainties in its sustainability and ecological impact. Other significant sources of omega-3 fatty acids include plants and microalgae fermentation, but they face similar challenges in reducing manufacturing costs and improving product quality and sustainability. With the advances in synthetic biology, biotechnological production of omega-3 fatty acids via engineered microbial cell factories still offers the best solution to provide a more stable, sustainable, and affordable source of omega-3 fatty acids by overcoming the major issues associated with conventional sources. This review summarizes the current status, key challenges, and future perspectives for the biotechnological production of major omega-3 fatty acids.

Application of adaptive laboratory evolution for Yarrowia lipolytica: A comprehensive review

Adaptive laboratory evolution is an innovative approach utilized by researchers to enhance the characteristics of microorganisms in the field of biology. With the advancement of this technology, it is now being extended to non-model strains. Yarrowia lipolytica, an oleaginous yeast with significant industrial potential, stands out among the non-conventional fungi. However, the activity of Yarrowia lipolytica is frequently affected by specific substances and environmental factors, necessitating the development of techniques to address these challenges. This manuscript provides an overview of adaptive laboratory evolution experiments conducted on Yarrowia lipolytica, and categorizes the contents into two aspects including improving lignocellulose utilization and enhancing the production in Yarrowia lipolytica. Additionally, we selected several representative examples to illustrate how adaptive laboratory evolution can be combined with other techniques to elucidate the potential mechanisms underlying strain evolution. Lastly, we anticipate a promising future for adaptive laboratory evolution technology and Yarrowia lipolytica in tandem.

Microbial engineering for shikimate biosynthesis

Shikimate, a precursor to the antiviral drug oseltamivir (Tamiflu®), can influence aromatic metabolites and finds extensive use in antimicrobial, antitumor, and cardiovascular applications. Consequently, various strategies have been developed for chemical synthesis and plant extraction to enhance shikimate biosynthesis, potentially impacting environmental conditions, economic sustainability, and separation and purification processes. Microbial engineering has been developed as an environmentally friendly approach for shikimate biosynthesis. In this review, we provide a comprehensive summary of microbial strategies for shikimate biosynthesis. These strategies primarily include chassis construction, biochemical optimization, pathway remodelling, and global regulation. Furthermore, we discuss future perspectives on shikimate biosynthesis and emphasize the importance of utilizing advanced metabolic engineering tools to regulate microbial networks for constructing robust microbial cell factories.

Cinnamic acid and p-coumaric acid are metabolized to 4-hydroxybenzoic acid by Yarrowia lipolytica

Yarrowia lipolytica has been explored as a potential production host for flavonoid synthesis due to its high tolerance to aromatic acids and ability to supply malonyl-CoA. However, little is known about its ability to consume the precursors cinnamic and p-coumaric acid. In this study, we demonstrate that Y. lipolytica can consume these precursors through multiple pathways that are partially dependent on the cultivation medium. By monitoring the aromatic acid concentrations over time, we found that cinnamic acid is converted to p-coumaric acid. We identified potential proteins with a trans-cinnamate 4-monooxygenase activity in Y. lipolytica and constructed a collection of 15 knock-out strains to identify the genes responsible for the reaction. We identified YALI1_B28430g as the gene encoding for a protein that converts cinnamic acid to p-coumaric acid (designated as TCM1). By comparing different media compositions we found that complex media components (casamino acids and yeast extract) induce this pathway. Additionally, we discover the conversion of p-coumaric acid to 4-hydroxybenzoic acid. Our findings provide new insight into the metabolic capabilities of Y. lipolytica and hold great potential for the future development of improved strains for flavonoid production.

Oleaginous yeasts for biochemicals, biofuels and food from lignocellulose-hydrolysate and crude glycerol

Microbial lipids produced from lignocellulose and crude glycerol (CG) can serve as sustainable alternatives to vegetable oils, whose production is, in many cases, accompanied by monocultures, land use changes or rain forest clearings. Our projects aim to understand the physiology of microbial lipid production by oleaginous yeasts, optimise the production and establish novel applications of microbial lipid compounds. We have established methods for fermentation and intracellular lipid quantification. Following the kinetics of lipid accumulation in different strains, we found high variability in lipid formation even between very closely related oleaginous yeast strains on both, wheat straw hydrolysate and CG. For example, on complete wheat straw hydrolysate, we saw that one Rhodotorula glutinis strain, when starting assimilating D-xylosealso assimilated the accumulated lipids, while a Rhodotorula babjevae strain could accumulate lipids on D-xylose. Two strains (Rhodotorula toruloides CBS 14 and R. glutinis CBS 3044) were found to be the best out of 27 tested to accumulate lipids on CG. Interestingly, the presence of hemicellulose hydrolysate stimulated glycerol assimilation in both strains. Apart from microbial oil, R. toruloides also produces carotenoids. The first attempts of extraction using the classical acetone-based method showed that β-carotene is the major carotenoid. However, there are indications that there are also substantial amounts of torulene and torularhodin, which have a very high potential as antioxidants.

Combining Metabolic Engineering and Lipid Droplet Storage Engineering for Improved α-Bisabolene Production in Yarrowia Lipolytica

Bisabolene is a bioactive sesquiterpene with a wide range of applications in food, cosmetics, medicine, and aviation fuels. Microbial production offers a green, efficient, and sustainable alternative. In this study, we focused on improving the titers of α-bisabolene in Yarrowia lipolytica by applying two strategies, (i) optimizing the metabolic flux of α-bisabolene biosynthetic pathway and (ii) sequestering α-bisabolene in lipid droplet, thus alleviating its inherent toxicity to host cells. We showed that overexpression of DGA1 and OLE1 to increase lipid content and unsaturated fatty acid levels was essential for boosting the α-bisabolene synthesis when supplemented with auxiliary carbon sources. The final engineered strain Po1gαB10 produced 1954.3 mg/L α-bisabolene from the waste cooking oil under shake flask fermentation, which was 96-fold higher than the control strain Po1gαB0. At the time of writing, our study represents the highest reported α-bisabolene titer in the engineered Y. lipolytica cell factory. This work describes novel strategies to improve the bioproduction of α-bisabolene that potentially may be applicable for other high-value terpene products.

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.

The microbial food revolution

Our current food system relies on unsustainable practices, which often fail to provide healthy diets to a growing population. Therefore, there is an urgent demand for new sustainable nutrition sources and processes. Microorganisms have gained attention as a new food source solution, due to their low carbon footprint, low reliance on land, water and seasonal variations coupled with a favourable nutritional profile. Furthermore, with the emergence and use of new tools, specifically in synthetic biology, the uses of microorganisms have expanded showing great potential to fulfil many of our dietary needs. In this review, we look at the different applications of microorganisms in food, and examine the history, state-of-the-art and potential to disrupt current foods systems. We cover both the use of microbes to produce whole foods out of their biomass and as cell factories to make highly functional and nutritional ingredients. The technical, economical, and societal limitations are also discussed together with the current and future perspectives.

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.

Combination of a Push-Pull-Block Strategy with a Heterologous Xylose Assimilation Pathway toward Lipid Overproduction from Lignocellulose in Yarrowia lipolytica

The production of biodiesel using microbial lipids derived from renewable lignocellulosic biomass is considered a promising strategy to reduce environmental pressure and promote the green energy transition. The hydrolysates of lignocellulosic biomass are rich in glucose and xylose, which makes it crucial to efficiently utilize both sugars. Here, we combined metabolic engineering and adaptive laboratory evolution (ALE) to construct an engineered Yarrowia lipolytica strain that can efficiently produce lipids from glucose and xylose. First, the "Push-Pull-Block" strategy was adopted to increase lipid content to 73.42% of the dry cell weight (DCW). Then, a heterologous xylose-utilization pathway was integrated into the engineered strain, which was subjected to ALE. The final evolved strain could accumulate 53.64% DCW of lipids from xylose, and the lipid titer reached 16.25 g/L. This work sheds light on the potential of microbial lipid overproduction from lignocellulose using engineered Y. lipolytica.

What makes Yarrowia lipolytica well suited for industry?

Yarrowia lipolytica possesses natural and engineered traits that make it a good host for the industrial bioproduction of chemicals, fuels, foods, and pharmaceuticals. In recent years, academic and industrial researchers have assessed its potential, developed synthetic biology techniques, improved its features, scaled its processes, and identified its limitations. Both publications and patents related to Y. lipolytica have shown a drastic increase during the past decade. Here, we discuss the characteristics of this yeast that make it suitable for industry and the remaining challenges for its wider use at large scale. We present evidence herein that shows the importance and potential of Y. lipolytica in bioproduction such that it may soon be one of the preferred choices of industry.

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

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

Oleaginous yeasts: Time to rethink the definition?

Oleaginous yeasts are typically defined as those able to accumulate more than 20% of their cell dry weight as lipids or triacylglycerides. Research on these yeasts has increased lately fuelled by an interest to use biotechnology to produce lipids and oleochemicals that can substitute those coming from fossil fuels or offer sustainable alternatives to traditional extractions (e.g., palm oil). Some oleaginous yeasts are attracting attention both in research and industry, with Yarrowia lipolytica one of the best-known and studied ones. Oleaginous yeasts can be found across several clades and different metabolic adaptations have been found, affecting not only fatty acid and neutral lipid synthesis, but also lipid particle stability and degradation. Recently, many novel oleaginous yeasts are being discovered, including oleaginous strains of the traditionally considered non-oleaginous Saccharomyces cerevisiae. In the face of this boom, a closer analysis of the definition of "oleaginous yeast" reveals that this term has instrumental value for biotechnology, while it does not give information about distinct types of yeasts. Having this perspective in mind, we propose to expand the term "oleaginous yeast" to those able to produce either intracellular or extracellular lipids, not limited to triacylglycerides, in at least one growth condition (including ex novo lipid synthesis). Finally, a critical look at Y. lipolytica as a model for oleaginous yeasts shows that the term "oleaginous" should be reserved only for strains and not species and that in the case of Y. lipolytica, it is necessary to distinguish clearly between the lipophilic and oleaginous phenotype.

Dynamic process and mechanism of crude oil release from silty intertidal sediment under different influencing factors

Under tidal scouring, residual petroleum in the intertidal sediment after oil spills could release again, causing secondary pollution in the marine ecosystem. The current study aimed to investigate the dynamic process and principles of crude oil release from silty intertidal sediment under different influencing factors and screened for the key factors. In this paper, the fitting equations and correlation between the release amount and various factors were explored through the single-factor and orthogonal experiments. Then, the key influencing factors were selected for multi-factor fitting of the release amount. The results showed that the oil release amount rose with the increase in oil concentration, oscillation frequency, and release time, but decreased with an increase in salinity. As the pH decreased, the oil release amount increased. The relationship between release amount and concentration/oscillation frequency can be equipped by the polynomial equation, and the average R² was 0.95 and 0.84, respectively. The release amount can be fitted by the Lagergren pseudo-second-order kinetic equation with time, with the average R² 0.89. The pH was negatively correlated with the release amount in the fresh contaminated sediment but positively correlated with the weathered one. The correlation between each factor and oil release amount was ranked (from large to small) as oil concentration, oscillation frequency, salinity, time, and pH. At last, a polynomial equation can be fitted between the key influencing factors (oil concentration and oscillation frequency) and the release amount. The results can provide a theoretical basis for predicting the secondary pollution owing to the oil re-release from intertidal sediment.

Understanding and application of Bacillus nitrogen regulation: A synthetic biology perspective

BACKGROUND

Nitrogen sources play an essential role in maintaining the physiological and biochemical activity of bacteria. Nitrogen metabolism, which is the core of microorganism metabolism, makes bacteria able to autonomously respond to different external nitrogen environments by exercising complex internal regulatory networks to help them stay in an ideal state. Although various studies have been put forth to better understand this regulation in Bacillus, and many valuable viewpoints have been obtained, these views need to be presented systematically and their possible applications need to be specified.

AIM OF REVIEW

The intention is to provide a deep and comprehensive understanding of nitrogen metabolism in Bacillus, an important industrial microorganism, and thereby apply this regulatory logic to synthetic biology to improve biosynthesis competitiveness. In addition, the potential researches in the future are also discussed.

KEY SCIENTIFIC CONCEPT OF REVIEW

Understanding the meticulous regulation process of nitrogen metabolism in Bacillus not only could facilitate research on metabolic engineering but also could provide constructive insights and inspiration for studies of other microorganisms.

Brown seaweed hydrolysate as a promising growth substrate for biomass and lipid synthesis of the yeast yarrowia lipolytica

Biomass of the brown algae Fucus vesiculosus and Saccharina latissima is a promising, renewable feedstock because of the high growth rate, accessibility and content of glucose and mannitol. Saccharification of seaweeds is a simple process due to the lack of lignocellulose in the cell wall. The high content of glucose and mannitol makes these seaweeds an attractive feedstock for lipid production in the yeast Yarrowia lipolytica. This study demonstrated that hydrolysates of brown algae biomass can be applied as a substrate for synthesis of yeast biomass and lipids without any supplementation. To increase the lipid titer in yeast biomass, we employed an engineered strain of Y. lipolytica overexpressing DGA1/DGA2. In consequence, the C/N ratio has a lower impact on lipid synthesis. Moreover, the applied substrates allowed for high synthesis of unsaturated fatty acids (UFA); the level exceeded 90% in the fatty acid pool. Oleic (C18:1) and linoleic acids (C18:2) achieved the highest content. The study showed that Y. lipolytica is able to grow on the seaweed hydrolysate and produces a high content of UFA in the biomass.

Identification of genome integration sites for developing a CRISPR-based gene expression toolkit in Yarrowia lipolytica

With the rapid development of synthetic biology, the oleaginous yeast Yarrowia lipolytica has become an attractive microorganism for chemical production. To better optimize and reroute metabolic pathways, we have expanded the CRISPR-based gene expression toolkit of Y. lipolytica. By sorting the integration sites associated with high expression, new neutral integration sites associated with high expression and high integration efficiency were identified. Diverse genetic components, including promoters and terminators, were also characterized to expand the expression range. We found that in addition to promoters, the newly characterized terminators exhibited large variations in gene expression. These genetic components and integration sites were then used to regulate genes involved in the lycopene biosynthesis pathway, and different levels of lycopene production were achieved. The CRISPR-based gene expression toolkit developed in this study will facilitate the genetic engineering of Y. lipolytica.

Valorization of Low-Cost Substrates for the Production of Odd Chain Fatty Acids by the Oleaginous Yeast Yarrowia lipolytica

Odd-chain fatty acids (OCFAs) have recently gained interest as target compounds in microbial production due to their diverse applications in the medical, pharmaceutical and chemical industries for the production of biofuels. Yarrowia lipolytica is a promising oleaginous yeast that has the ability to accumulate high quantities of fatty acids. However, the use of Y. lipolytica oils is still under research, in order to decrease the production costs related to the fermentation process and improve economic feasibility. In this work, sugar beet molasses (10–50 g/L) and crude glycerol (30 g/L) were used as the main carbon sources to reduce the processing costs of oil production from a genetically engineered Y. lipolytica strain. The effects of medium composition were studied on biomass production, lipid content, and OCFAs profile. Lipid production by yeast growing on molasses (20 g/L sucrose) and crude glycerol reached 4.63 ± 0.95 g/L of culture medium. OCFAs content represented 58% of the total fatty acids in lipids, which corresponds to ≈2.69 ± 0.03 g/L of culture medium. The fermentation was upscaled to 5 L bioreactors and fed-batch co-feeding increased OCFA accumulation in Y. lipolytica by 56% compared to batch cultures.

Dissecting carbon metabolism of Yarrowia lipolytica type strain W29 using genome-scale metabolic modelling

Yarrowia lipolytica is a widely-used chassis cell in biotechnological applications. It has recently gained extensive research interest owing to its extraordinary ability of producing industrially valuable biochemicals from a variety of carbon sources. Genome-scale metabolic models (GSMMs) enable analyses of cellular metabolism for engineering various industrial hosts. In the present study, we developed a high-quality GSMM iYli21 for Y. lipolytica type strain W29 by extensive manual curation with Biolog experimental data. The model showed a high accuracy of 85.7% in predicting nutrient utilization. Transcriptomics data were integrated to delineate cellular metabolism of utilizing six individual metabolites as sole carbon sources. Comparisons showed that 302 reactions were commonly used, including those from TCA cycle, oxidative phosphorylation, and purine metabolism for energy and material supply. Whereas glycolytic reactions were employed only when glucose and glycerol used as sole carbon sources, gluconeogenesis and fatty acid oxidation reactions were specifically employed when fatty acid, alkane and glycerolipid were the sole carbon sources. Further test of 46 substrates for generating 5 products showed that hexanoate outcompeted other compounds in terms of maximum theoretical yield owing to the lowest carbon loss for energy supply. This newly generated model iYli21 will be a valuable tool in dissecting metabolic mechanism and guiding metabolic engineering of this important industrial cell factory.

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.

Golden Gate Multigene Assembly Method for Yarrowia lipolytica

The oleaginous yeast Yarrowia lipolytica has emerged as a powerful alternative for biolipid production due to its high capacity for lipid accumulation. Genetic engineering and synthetic biology are promoted forward to improve production and reroute metabolism for high-value compound synthesis. In this context, efficient, modular, and high-throughput compatible cloning and expression system are required to speed up and rationalize research in this field. Here, we present the fast and modular Golden Gate cloning strategy for the construction of multigene expression vectors and their transformation into Y. lipolytica. As an example, we used the heterologous expression of the carotenoid pathway by cloning three genes involved in this pathway in only one vector allowing reaching production of β-carotene after a single transformation.

Engineering Yeast Yarrowia lipolytica for Methanol Assimilation

Conferring methylotrophy on industrial microorganisms would enable the production of diverse products from one-carbon feedstocks and contribute to establishing a low-carbon society. Rebuilding methylotrophs, however, requires a thorough metabolic refactoring and is highly challenging. Only recently was synthetic methylotrophy achieved in model microorganisms─Escherichia coli and baker's yeast Saccharomyces cerevisiae. Here, we have engineered industrially important yeast Yarrowia lipolytica to assimilate methanol. Through rationally constructing a chimeric assimilation pathway, rewiring the native metabolism for improved precursor supply, and laboratory evolution, we improved the methanol assimilation from undetectable to a level of 1.1 g/L per 72 h and enabled methanol-supported cellular maintenance. By transcriptomic analysis, we further found that fine-tuning of methanol assimilation and ribulose monophosphate/xylulose monophosphate (RuMP/XuMP) regeneration and strengthening formate dehydrogenation and the serine pathway were beneficial for methanol assimilation. This work paves the way for creating synthetic methylotrophic yeast cell factories for low-carbon economy.

D-Xylose Sensing in Saccharomyces cerevisiae: Insights from D-Glucose Signaling and Native D-Xylose Utilizers

Extension of the substrate range is among one of the metabolic engineering goals for microorganisms used in biotechnological processes because it enables the use of a wide range of raw materials as substrates. One of the most prominent examples is the engineering of baker's yeast Saccharomyces cerevisiae for the utilization of d-xylose, a five-carbon sugar found in high abundance in lignocellulosic biomass and a key substrate to achieve good process economy in chemical production from renewable and non-edible plant feedstocks. Despite many excellent engineering strategies that have allowed recombinant S. cerevisiae to ferment d-xylose to ethanol at high yields, the consumption rate of d-xylose is still significantly lower than that of its preferred sugar d-glucose. In mixed d-glucose/d-xylose cultivations, d-xylose is only utilized after d-glucose depletion, which leads to prolonged process times and added costs. Due to this limitation, the response on d-xylose in the native sugar signaling pathways has emerged as a promising next-level engineering target. Here we review the current status of the knowledge of the response of S. cerevisiae signaling pathways to d-xylose. To do this, we first summarize the response of the native sensing and signaling pathways in S. cerevisiae to d-glucose (the preferred sugar of the yeast). Using the d-glucose case as a point of reference, we then proceed to discuss the known signaling response to d-xylose in S. cerevisiae and current attempts of improving the response by signaling engineering using native targets and synthetic (non-native) regulatory circuits.

Yarrowia lipolytica chassis strains engineered to produce aromatic amino acids via the shikimate pathway

Yarrowia lipolytica is widely used as a microbial producer of lipids and lipid derivatives. Here, we exploited this yeast's potential to generate aromatic amino acids by developing chassis strains optimized for the production of phenylalanine, tyrosine and tryptophan. We engineered the shikimate pathway to overexpress a combination of Y. lipolytica and heterologous feedback-insensitive enzyme variants. Our best chassis strain displayed high levels of de novo Ehrlich metabolite production (up to 0.14 g l-1 in minimal growth medium), which represented a 93-fold increase compared to the wild-type strain (0.0015 g l-1 ). Production was further boosted to 0.48 g l-1 when glycerol, a low-cost carbon source, was used, concomitantly to high secretion of phenylalanine precursor (1 g l-1 ). Among these metabolites, 2-phenylethanol is of particular interest due to its rose-like flavour. We also established a production pathway for generating protodeoxyviolaceinic acid, a dye derived from tryptophan, in a chassis strain optimized for chorismate, the precursor of tryptophan. We have thus demonstrated that Y. lipolytica can serve as a platform for the sustainable de novo bio-production of high-value aromatic compounds, and we have greatly improved our understanding of the potential feedback-based regulation of the shikimate pathway in this yeast.

Recent Advances in Biotechnological Itaconic Acid Production, and Application for a Sustainable Approach

Intense research has been conducted to produce environmentally friendly biopolymers obtained from renewable feedstock to substitute fossil-based materials. This is an essential aspect for implementing the circular bioeconomy strategy, expressly declared by the European Commission in 2018 in terms of "repair, reuse, and recycling". Competent carbon-neutral alternatives are renewable biomass waste for chemical element production, with proficient recyclability properties. Itaconic acid (IA) is a valuable platform chemical integrated into the first 12 building block compounds the achievement of which is feasible from renewable biomass or bio-wastes (agricultural, food by-products, or municipal organic waste) in conformity with the US Department of Energy. IA is primarily obtained through fermentation with Aspergillus terreus, but nowadays several microorganisms are genetically engineered to produce this organic acid in high quantities and on different substrates. Given its trifunctional structure, IA allows the synthesis of various novel biopolymers, such as drug carriers, intelligent food packaging, antimicrobial biopolymers, hydrogels in water treatment and analysis, and superabsorbent polymers binding agents. In addition, IA shows antimicrobial, anti-inflammatory, and antitumor activity. Moreover, this biopolymer retains qualities like environmental effectiveness, biocompatibility, and sustainability. This manuscript aims to address the production of IA from renewable sources to create a sustainable circular economy in the future. Moreover, being an essential monomer in polymer synthesis it possesses a continuous provocation in the biopolymer chemistry domain and technologies, as defined in the present review.

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.