Functional overexpression and characterization of lipogenesis-related genes in the oleaginous yeast Yarrowia lipolytica

Molecular characterization and expression profiling of two flavohemoglobin genes play essential roles in dissolved oxygen and NO stress in Saitozyma podzolica zwy2-3

Flavohemoglobins (Fhbs) are key enzymes involved in microbial nitrosative stress resistance and nitric oxide degradation. However, the roles of Fhbs in fungi remain largely unknown. In this study, SpFhb1 and SpFhb2, two flavohemoglobin-encoding genes in Saitozyma podzolica zwy2-3 were characterized. Protein structure analysis and molecular docking showed that SpFhbs were conserved in bacteria and fungi. Phylogenetic analysis revealed that SpFhb2 may be acquired through the transfer event of independent horizontal genes from bacteria. The expression levels of SpFhb1 and SpFhb2 showed opposite trend under high/low dissolved oxygen, implying that they may exhibited different functions. Through deletion and overexpression of SpFhbs, we confirmed that SpFhbs were conducive to lipid accumulation under high stress. The sensitivities of ΔFhb mutants to NO stress were significantly increased compared with that in the WT, indicating that they were required for NO detoxification and nitrosative stress resistance in S. podzolica zwy2-3. Furthermore, SpAsg1 was identified that simultaneously regulates SpFhbs, which functions in the lipid accumulation under high/low dissolved oxygen and NO stress in S. podzolica zwy2-3. Overall, two different SpFhbs were identified in this study, providing new insights into the mechanism of lipid accumulation in fungi under high/low dissolved oxygen and NO stress.

Biomanufacturing of γ-linolenic acid-enriched galactosyldiacylglycerols: Challenges in microalgae and potential in oleaginous yeasts

γ-Linolenic acid-enriched galactosyldiacylglycerols (GDGs-GLA), as the natural form of γ-linolenic acid in microalgae, have a range of functional activities, including anti-inflammatory, antioxidant, and anti-allergic properties. The low abundance of microalgae and the structural stereoselectivity complexity impede microalgae extraction or chemical synthesis, resulting in a lack of supply of GDGs-GLA with a growing demand. At present, there is a growing interest in engineering oleaginous yeasts for mass production of GDGs-GLA based on their ability to utilize a variety of hydrophobic substrates and a high metabolic flux toward fatty acid and lipid (triacylglycerol, TAG) production. Here, we first introduce the GDGs-GLA biosynthetic pathway in microalgae and challenges in the engineering of the native host. Subsequently, we describe in detail the applications of oleaginous yeasts with Yarrowia lipolytica as the representative for GDGs-GLA biosynthesis, including the development of synthetic biology parts, gene editing tools, and metabolic engineering of lipid biosynthesis. Finally, we discuss the development trend of GDGs-GLA biosynthesis in Y. lipolytica.

A comprehensive review on microbial lipid production from wastes: research updates and tendencies

Microbial lipids have recently attracted attention as an intriguing alternative for the biodiesel and oleochemical industries to achieve sustainable energy generation. However, large-scale lipid production remains limited due to the high processing costs. As multiple variables affect lipid synthesis, an up-to-date overview that will benefit researchers studying microbial lipids is necessary. In this review, the most studied keywords from bibliometric studies are first reviewed. Based on the results, the hot topics in the field were identified to be associated with microbiology studies that aim to enhance lipid synthesis and reduce production costs, focusing on the biological and metabolic engineering involved. The research updates and tendencies of microbial lipids were then analyzed in depth. In particular, feedstock and associated microbes, as well as feedstock and corresponding products, were analyzed in detail. Strategies for lipid biomass enhancement were also discussed, including feedstock adoption, value-added product synthesis, selection of oleaginous microbes, cultivation mode optimization, and metabolic engineering strategies. Finally, the environmental implications of microbial lipid production and possible research directions were presented.

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.

Using oils and fats to replace sugars as feedstocks for biomanufacturing: Challenges and opportunities for the yeast Yarrowia lipolytica

More than 200 million tons of plant oils and animal fats are produced annually worldwide from oil, crops, and the rendered animal fat industry. Triacylglycerol, an abundant energy-dense compound, is the major form of lipid in oils and fats. While oils or fats are very important raw materials and functional ingredients for food or related products, a significant portion is currently diverted to or recovered as waste. To significantly increase the value of waste oils or fats and expand their applications with a minimal environmental footprint, microbial biomanufacturing is presented as an effective strategy for adding value. Though both bacteria and yeast can be engineered to use oils or fats as the biomanufacturing feedstocks, the yeast Yarrowia lipolytica is presented as one of the most attractive platforms. Y. lipolytica is oleaginous, generally regarded as safe, demonstrated as a promising industrial producer, and has unique capabilities for efficient catabolism and bioconversion of lipid substrates. This review summarizes the major challenges and opportunities for Y. lipolytica as a new biomanufacturing platform for the production of value-added products from oils and fats. This review also discusses relevant cellular and metabolic engineering strategies such as fatty acid transport, fatty acid catabolism and bioconversion, redox balances and energy yield, cell morphology and stress response, and bioreaction engineering. Finally, this review highlights specific product classes including long-chain diacids, wax esters, terpenes, and carotenoids with unique synthesis opportunities from oils and fats in Y. lipolytica.

Knocking out central metabolism genes to identify new targets and alternating substrates to improve lipid synthesis in Y. lipolytica

Introduction: Systematic gene knockout studies may offer us novel insights on cell metabolism and physiology. Specifically, the lipid accumulation mechanism at the molecular or cellular level is yet to be determined in the oleaginous yeast Y. lipolytica. Methods: Herein, we established ten engineered strains with the knockout of important genes involving in central carbon metabolism, NADPH generation, and fatty acid biosynthetic pathways. Results: Our result showed that NADPH sources for lipogenesis include the OxPP pathway, POM cycle, and a trans-mitochondrial isocitrate-α-oxoglutarate NADPH shuttle in Y. lipolytica. Moreover, we found that knockout of mitochondrial NAD⁺ isocitrate dehydrogenase IDH2 and overexpression of cytosolic NADP⁺ isocitrate dehydrogenase IDP2 could facilitate lipid synthesis. Besides, we also demonstrated that acetate is a more favorable carbon source for lipid synthesis when glycolysis step is impaired, indicating the evolutionary robustness of Y. lipolytica. Discussion: This systematic investigation of gene deletions and overexpression across various lipogenic pathways would help us better understand lipogenesis and engineer yeast factories to upgrade the lipid biomanufacturing platform.

Biosynthesis of cannabinoid precursor olivetolic acid in genetically engineered Yarrowia lipolytica

Engineering microbes to produce plant-derived natural products provides an alternate solution to obtain bioactive products. Here we report a systematic approach to sequentially identify the rate-limiting steps and improve the biosynthesis of the cannabinoid precursor olivetolic acid (OLA) in Yarrowia lipolytica. We find that Pseudomonas sp LvaE encoding a short-chain acyl-CoA synthetase can efficiently convert hexanoic acid to hexanoyl-CoA. The co-expression of the acetyl-CoA carboxylase, the pyruvate dehydrogenase bypass, the NADPH-generating malic enzyme, as well as the activation of peroxisomal β-oxidation pathway and ATP export pathway are effective strategies to redirect carbon flux toward OLA synthesis. Implementation of these strategies led to an 83-fold increase in OLA titer, reaching 9.18 mg/L of OLA in shake flask culture. This work may serve as a baseline for engineering cannabinoids biosynthesis in oleaginous yeast species.

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.

Acyl-CoA:diacylglycerol acyltransferase: Properties, physiological roles, metabolic engineering and intentional control

Acyl-CoA:diacylglycerol acyltransferase (DGAT, EC 2.3.1.20) catalyzes the last reaction in the acyl-CoA-dependent biosynthesis of triacylglycerol (TAG). DGAT activity resides mainly in membrane-bound DGAT1 and DGAT2 in eukaryotes and bifunctional wax ester synthase-diacylglycerol acyltransferase (WSD) in bacteria, which are all membrane-bound proteins but exhibit no sequence homology to each other. Recent studies also identified other DGAT enzymes such as the soluble DGAT3 and diacylglycerol acetyltransferase (EaDAcT), as well as enzymes with DGAT activities including defective in cuticular ridges (DCR) and steryl and phytyl ester synthases (PESs). This review comprehensively discusses research advances on DGATs in prokaryotes and eukaryotes with a focus on their biochemical properties, physiological roles, and biotechnological and therapeutic applications. The review begins with a discussion of DGAT assay methods, followed by a systematic discussion of TAG biosynthesis and the properties and physiological role of DGATs. Thereafter, the review discusses the three-dimensional structure and insights into mechanism of action of human DGAT1, and the modeled DGAT1 from Brassica napus. The review then examines metabolic engineering strategies involving manipulation of DGAT, followed by a discussion of its therapeutic applications. DGAT in relation to improvement of livestock traits is also discussed along with DGATs in various other eukaryotic organisms.

Exploring Yeast Diversity to Produce Lipid-Based Biofuels from Agro-Forestry and Industrial Organic Residues

Exploration of yeast diversity for the sustainable production of biofuels, in particular biodiesel, is gaining momentum in recent years. However, sustainable, and economically viable bioprocesses require yeast strains exhibiting: (i) high tolerance to multiple bioprocess-related stresses, including the various chemical inhibitors present in hydrolysates from lignocellulosic biomass and residues; (ii) the ability to efficiently consume all the major carbon sources present; (iii) the capacity to produce lipids with adequate composition in high yields. More than 160 non-conventional (non-Saccharomyces) yeast species are described as oleaginous, but only a smaller group are relatively well characterised, including Lipomyces starkeyi, Yarrowia lipolytica, Rhodotorula toruloides, Rhodotorula glutinis, Cutaneotrichosporonoleaginosus and Cutaneotrichosporon cutaneum. This article provides an overview of lipid production by oleaginous yeasts focusing on yeast diversity, metabolism, and other microbiological issues related to the toxicity and tolerance to multiple challenging stresses limiting bioprocess performance. This is essential knowledge to better understand and guide the rational improvement of yeast performance either by genetic manipulation or by exploring yeast physiology and optimal process conditions. Examples gathered from the literature showing the potential of different oleaginous yeasts/process conditions to produce oils for biodiesel from agro-forestry and industrial organic residues are provided.

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

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

Bio-oil production for biodiesel industry by Yarrowia lipolytica from volatile fatty acids in two-stage batch culture

Microbial lipids-derived biodiesel is garnering much attention owing to its potential to substitute diesel fuel. In this study, lipid accumulation by Yarrowia lipolytica from volatile fatty acids (VFAs) was studied in a lab-scale stirred tank bioreactor. In batch cultures, Y. lipolytica NCYC 2904 was able to grow in 18 g·L^-1 of VFAs (acetate, propionate, and butyrate), and the addition of a co-substrate (glucose) led to a fivefold improvement in lipid concentration. Furthermore, the two-stage batch culture (growth phase in glucose (1st stage) followed by a lipogenic phase in VFAs (2nd stage)) was the best strategy to obtain the highest lipid content in the cells (37%, w/w), with aeration conditions that kept dissolved oxygen concentration between 40% and 50% of saturation during the lipogenic phase. The estimated fuel properties of biodiesel produced from Y. lipolytica NCYC 2904 lipids are comparable with those of the biodiesel produced from vegetable oils and are in accordance with the international standards (EN 14214 and ASTM D6751). The cultivation strategies herein devised enable a sustainable, eco-friendly, and economical production of microbial lipids, based on feedstocks such as VFAs that can be derived from the acidogenic fermentation of organic wastes. KEY POINTS: • Addition of glucose to VFAs enhances lipids in Y. lipolytica in batch cultures • Two-stage batch culture - growth in glucose followed by VFAs pulse - rises lipids • Dissolved oxygen of 40-50% of saturation is crucial at the lipogenic phase.

The history, state of the art and future prospects for oleaginous yeast research

Lipid-based biofuels, such as biodiesel and hydroprocessed esters, are a central part of the global initiative to reduce the environmental impact of the transport sector. The vast majority of production is currently from first-generation feedstocks, such as rapeseed oil, and waste cooking oils. However, the increased exploitation of soybean oil and palm oil has led to vast deforestation, smog emissions and heavily impacted on biodiversity in tropical regions. One promising alternative, potentially capable of meeting future demand sustainably, are oleaginous yeasts. Despite being known about for 143 years, there has been an increasing effort in the last decade to develop a viable industrial system, with currently around 100 research papers published annually. In the academic literature, approximately 160 native yeasts have been reported to produce over 20% of their dry weight in a glyceride-rich oil. The most intensively studied oleaginous yeast have been Cutaneotrichosporon oleaginosus (20% of publications), Rhodotorula toruloides (19%) and Yarrowia lipolytica (19%). Oleaginous yeasts have been primarily grown on single saccharides (60%), hydrolysates (26%) or glycerol (19%), and mainly on the mL scale (66%). Process development and genetic modification (7%) have been applied to alter yeast performance and the lipids, towards the production of biofuels (77%), food/supplements (24%), oleochemicals (19%) or animal feed (3%). Despite over a century of research and the recent application of advanced genetic engineering techniques, the industrial production of an economically viable commodity oil substitute remains elusive. This is mainly due to the estimated high production cost, however, over the course of the twenty-first century where climate change will drastically change global food supply networks and direct governmental action will likely be levied at more destructive crops, yeast lipids offer a flexible platform for localised, sustainable lipid production. Based on data from the large majority of oleaginous yeast academic publications, this review is a guide through the history of oleaginous yeast research, an assessment of the best growth and lipid production achieved to date, the various strategies employed towards industrial production and importantly, a critical discussion about what needs to be built on this huge body of work to make producing a yeast-derived, more sustainable, glyceride oil a commercial reality.

Metabolic Analysis of Schizochytrium Mutants With High DHA Content Achieved With ARTP Mutagenesis Combined With Iodoacetic Acid and Dehydroepiandrosterone Screening

High DHA production cost caused by low DHA titer and productivity of the current Schizochytrium strains is a bottleneck for its application in competition with traditional fish-oil based approach. In this study, atmospheric and room-temperature plasma with iodoacetic acid and dehydroepiandrosterone screening led to three mutants, 6–8, 6–16 and 6–23 all with increased growth and DHA accumulations. A LC/MS metabolomic analysis revealed the increased metabolism in PPP and EMP as well as the decreased TCA cycle might be relevant to the increased growth and DHA biosynthesis in the mutants. Finally, the mutant 6–23, which achieved the highest growth and DHA accumulation among all mutants, was evaluated in a 5 L fermentor. The results showed that the DHA concentration and productivity in mutant 6–23 were 41.4 g/L and 430.7 mg/L/h in fermentation for 96 h, respectively, which is the highest reported so far in literature. The study provides a novel strain improvement strategy for DHA-producing Schizochytrium.

Increased Lipid Production in Yarrowia lipolytica from Acetate through Metabolic Engineering and Cosubstrate Fermentation

Bioconversion of acetate, a byproduct generated in industrial processes, into microbial lipids using oleaginous yeasts offers a promising alternative for the economic utilization of acetate-containing waste streams. However, high acetate concentrations will inhibit microbial growth and metabolism. In this study, the acetate utilization capability of Yarrowia lipolytica PO1f was successively improved by overexpressing the key enzyme of acetyl-CoA synthetase (ACS), which resulted in an accumulation of 9.2% microbial lipids from acetate in shake flask fermentation. By further overexpressing the second key enzymes of acetyl-CoA carboxylase (ACC1) and fatty acid synthase (FAS) in Y. lipolytica, the lipid content was increased to 25.7% from acetate. Finally, the maximum OD₆₀₀ of 29.2 and a lipid content of 41.7% were obtained with the engineered strain by the adoption of cosubstrate (glycerol and acetate) fed-batch fermentation, which corresponded to an increase of 68 and 95%, respectively. These results presented a promising strategy for economic and efficient microbial lipid production from the waste acetate.

Bioproducts generation from carboxylate platforms by the non-conventional yeast Yarrowia lipolytica

In recent years, there has been a growing interest in the use of renewable sources for bio-based production aiming at developing sustainable and feasible approaches towards a circular economy. Among these renewable sources, organic wastes (OWs) can be anaerobically digested to generate carboxylates like volatile fatty acids (VFAs), lactic acid, and longer-chain fatty acids that are regarded as novel building blocks for the synthesis of value-added compounds by yeasts. This review discusses on the processes that can be used to create valuable molecules from OW-derived VFAs; the pathways employed by the oleaginous yeast Yarrowia lipolytica to directly metabolize such molecules; and the relationship between OW composition, anaerobic digestion, and VFA profiles. The review also summarizes the current knowledge about VFA toxicity, the pathways by which VFAs are metabolized and the metabolic engineering strategies that can be employed in Y. lipolytica to produce value-added biobased compounds from VFAs.

High-value utilization of the waste hydrolysate of Dioscorea zingiberensis for docosahexaenoic acid production in Schizochytrium sp

The starch saccharification liquid of Dioscorea zingiberensis tubers (SSLD) is a glucose-rich agro-industrial waste. Herein, SSLD was used as a novel potential carbon source for the biosynthesis of docosahexaenoic acid (DHA) in Schizochytrium sp. to achieve waste recycling and high-value utilization. Component analysis showed that SSLD contains abundant nutrients, such as glucose, amino acids, phenolics and flavonoids. When the total sugar concentration in SSLD was optimized to 90 g/L, the biomass and DHA yield reached 44.85 and 6.60 g/L, respectively, which were 32.1% and 36.92% higher than that at pure glucose culture condition. Fermentation characteristics and gene expression analysis showed that SSLD could remarkably improve cell antioxidant capacity, which is beneficial to scavenge intracellular reactive oxygen species and increase the gene expression of antioxidant enzymes in Schizochytrium sp. Hence, SSLD is an effective and economic carbon source for DHA production in Schizochytrium sp.

Exploring Proteomes of Robust Yarrowia lipolytica Isolates Cultivated in Biomass Hydrolysate Reveals Key Processes Impacting Mixed Sugar Utilization, Lipid Accumulation, and Degradation

Yarrowia lipolytica is an oleaginous yeast exhibiting robust phenotypes beneficial for industrial biotechnology. The phenotypic diversity found within the undomesticated Y. lipolytica clade from various origins illuminates desirable phenotypic traits not found in the conventional laboratory strain CBS7504 (or W29), which include xylose utilization, lipid accumulation, and growth on undetoxified biomass hydrolysates. Currently, the related phenotypes of lipid accumulation and degradation when metabolizing nonpreferred sugars (e.g., xylose) associated with biomass hydrolysates are poorly understood, making it difficult to control and engineer in Y. lipolytica. To fill this knowledge gap, we analyzed the genetic diversity of five undomesticated Y. lipolytica strains and identified singleton genes and genes exclusively shared by strains exhibiting desirable phenotypes. Strain characterizations from controlled bioreactor cultures revealed that the undomesticated strain YB420 used xylose to support cell growth and maintained high lipid levels, while the conventional strain CBS7504 degraded cell biomass and lipids when xylose was the sole remaining carbon source. From proteomic analysis, we identified carbohydrate transporters, xylose metabolic enzymes, and pentose phosphate pathway proteins stimulated during the xylose uptake stage for both strains. Furthermore, we distinguished proteins involved in lipid metabolism (e.g., lipase, NADPH generation, lipid regulators, and β-oxidation) activated by YB420 (lipid maintenance phenotype) or CBS7504 (lipid degradation phenotype) when xylose was the sole remaining carbon source. Overall, the results relate genetic diversity of undomesticated Y. lipolytica strains to complex phenotypes of superior growth, sugar utilization, lipid accumulation, and degradation in biomass hydrolysates. IMPORTANCE Yarrowia lipolytica is an important industrial oleaginous yeast due to its robust phenotypes for effective conversion of inhibitory lignocellulosic biomass hydrolysates into neutral lipids. While lipid accumulation has been well characterized in this organism, its interconnected lipid degradation phenotype is poorly understood during fermentation of biomass hydrolysates. Our investigation into the genetic diversity of undomesticated Y. lipolytica strains, coupled with detailed strain characterization and proteomic analysis, revealed metabolic processes and regulatory elements conferring desirable phenotypes for growth, sugar utilization, and lipid accumulation in undetoxified biomass hydrolysates by these natural variants. This study provides a better understanding of the robust metabolism of Y. lipolytica and suggests potential metabolic engineering strategies to enhance its performance.

A Brief Journey into the History of and Future Sources and Uses of Fatty Acids

Fats and lipids have always had a primary role in the history of humankind, from ancient civilisations to the modern and contemporary time, going from domestic and cosmetic uses, to the first medical applications and later to the large-scale industrial uses for food, pharmaceutical, cosmetics, and biofuel production. Sources and uses of those have changed during time following the development of chemical sciences and industrial technological advances. Plants, fish, and animal fats have represented the primary source of lipids and fats for century. Nowadays, the use of fatty acid sources has taken a turn: industries are mainly interested in polyunsaturated fatty acids (PUFAs), which have beneficial properties in human health; and also, for high-value fatty acids product for innovative and green production of biofuel and feedstocks. Thus, the constant increase in demand of fatty acids, the fact that marine and vegetable sources are not adequate to meet the high level of fatty acids required worldwide and climate change, have determined the necessity of the search for renewable and sustainable sources for fatty acids. Biotechnological advances and bioengineering have started looking at the genetic modification of algae, bacteria, yeasts, seeds, and plants to develop cell factory able to produce high value fatty acid products in a renewable and sustainable manner. This innovative approach applied to FA industry is a peculiar example of how biotechnology can serve as a powerful mean to drive the production of high value fatty acid derivatives on the concept of circular bioeconomy, based on the reutilisation of organic resources for alternative and sustainable productive patterns that are environmentally friendly.

Yeasts of the Blastobotrys genus are promising platform for lipid-based fuels and oleochemicals production

Strains of the yeast genus Blastobotrys (subphylum Saccharomycotina) represent a valuable biotechnological resource for basic biochemistry research, single-cell protein, and heterologous protein production processes. Species of this genus are dimorphic, non-pathogenic, thermotolerant, and can assimilate a variety of hydrophilic and hydrophobic substrates. These can constitute a single-cell oil platform in an emerging bio-based economy as oleaginous traits have been discovered recently. However, the regulatory network of lipogenesis in these yeasts is poorly understood. To keep pace with the growing market demands for lipid-derived products, it is critical to understand the lipid biosynthesis in these unconventional yeasts to pinpoint what governs the preferential channelling of carbon flux into lipids instead of the competing pathways. This review summarizes information relevant to the regulation of lipid metabolic pathways and prospects of metabolic engineering in Blastobotrys yeasts for their application in food, feed, and beyond, particularly for fatty acid-based fuels and oleochemicals. KEY POINTS: • The production of biolipids by heterotrophic yeasts is reviewed. • Summary of information concerning lipid metabolism regulation is highlighted. • Special focus on the importance of diacylglycerol acyltransferases encoding genes in improving lipid production is made.

Sec14 family of lipid transfer proteins in yeasts

The hydrophobicity of lipids prevents their free movement across the cytoplasm. To achieve highly heterogeneous and precisely regulated lipid distribution in different cellular membranes, lipids are transported by lipid transfer proteins (LTPs) in addition to their transport by vesicles. Sec14 family is one of the most extensively studied groups of LTPs. Here we provide an overview of Sec14 family of LTPs in the most studied yeast Saccharomyces cerevisiae as well as in other selected non-Saccharomyces yeasts-Schizosaccharomyces pombe, Kluyveromyces lactis, Candida albicans, Candida glabrata, Cryptococcus neoformans, and Yarrowia lipolytica. Discussed are specificities of Sec14-domain LTPs in various yeasts, their mode of action, subcellular localization, and physiological function. In addition, quite few Sec14 family LTPs are target of antifungal drugs, serve as modifiers of drug resistance or influence virulence of pathologic yeasts. Thus, they represent an important object of study from the perspective of human health.

Lipid production by oleaginous yeasts

Microbial lipid production has been studied extensively for years; however, lipid metabolic engineering in many of the extraordinarily high lipid-accumulating yeasts was impeded by inadequate understanding of the metabolic pathways including regulatory mechanisms defining their oleaginicity and the limited genetic tools available. The aim of this review is to highlight the prominent oleaginous yeast genera, emphasizing their oleaginous characteristics, in conjunction with diverse other features such as cheap carbon source utilization, withstanding the effect of inhibitory compounds, commercially favorable fatty acid composition-all supporting their future development as economically viable lipid feedstock. The unique aspects of metabolism attributing to their oleaginicity are accentuated in the pretext of outlining the various strategies successfully implemented to improve the production of lipid and lipid-derived metabolites. A large number of in silico data generated on the lipid accumulation in certain oleaginous yeasts have been carefully curated, as suggestive evidences in line with the exceptional oleaginicity of these organisms. The different genetic elements developed in these yeasts to execute such strategies have been scrupulously inspected, underlining the major types of newly-found and synthetically constructed promoters, transcription terminators, and selection markers. Additionally, there is a plethora of advanced genetic toolboxes and techniques described, which have been successfully used in oleaginous yeasts in the recent years, promoting homologous recombination, genome editing, DNA assembly, and transformation at remarkable efficiencies. They can accelerate and effectively guide the rational designing of system-wide metabolic engineering approaches pinpointing the key targets for developing industrially suitable yeast strains.

Oleaginous Yeasts as Cell Factories for the Sustainable Production of Microbial Lipids by the Valorization of Agri-Food Wastes

The agri-food industry annually produces huge amounts of crops residues and wastes, the suitable management of these products is important to increase the sustainability of agro-industrial production by optimizing the entire value chain. This is also in line with the driving principles of the circular economy, according to which residues can become feedstocks for novel processes. Oleaginous yeasts represent a versatile tool to produce biobased chemicals and intermediates. They are flexible microbial factories able to grow on different side-stream carbon sources such as those deriving from agri-food wastes, and this characteristic makes them excellent candidates for integrated biorefinery processes through the production of microbial lipids, known as single cell oils (SCOs), for different applications. This review aims to present an extensive overview of research progress on the production and use of oleaginous yeasts and present discussions on the current bottlenecks and perspectives of their exploitation in different sectors, such as foods, biofuels and fine chemicals.

Recent advances in lipid metabolic engineering of oleaginous yeasts

With the increasing demand to develop a renewable and sustainable biolipid feedstock, several species of non-conventional oleaginous yeasts are being explored. Apart from the platform oleaginous yeast Yarrowia lipolytica, the understanding of metabolic pathway and, therefore, exploiting the engineering prospects of most of the oleaginous species are still in infancy. However, in the past few years, enormous efforts have been invested in Rhodotorula, Rhodosporidium, Lipomyces, Trichosporon, and Candida genera of yeasts among others, with the rapid advancement of engineering strategies, significant improvement in genetic tools and techniques, generation of extensive bioinformatics and omics data. In this review, we have collated these recent progresses to make a detailed and insightful summary of the major developments in metabolic engineering of the prominent oleaginous yeast species. Such a comprehensive overview would be a useful resource for future strain improvement and metabolic engineering studies for enhanced production of lipid and lipid-derived chemicals in oleaginous yeasts.

Isolation and characterization of Lipomyces starkeyi mutants with greatly increased lipid productivity following UV irradiation

The oleaginous yeast Lipomyces starkeyi is an intriguing lipid producer that can produce triacylglycerol (TAG), a feedstock for biodiesel production. We previously reported that the L. starkeyi mutant E15 with high levels of TAG production compared with the wild-type was efficiently obtained using Percoll density gradient centrifugation. However, considering its use for biodiesel production, it is necessary to further improve the lipid productivity of the mutant. In this study, we aimed to obtain mutants with better lipid productivity than E15, evaluate its lipid productivity, and analyze lipid synthesis-related gene expression in the wild-type and mutant strains. The mutants E15-11, E15-15, and E15-25 exhibiting higher lipid productivity than E15 were efficiently isolated from cells exposed to ultraviolet light using Percoll density gradient centrifugation. They exhibited approximately 4.5-fold higher lipid productivity than the wild-type on day 3. The obtained mutants did not exhibit significantly different fatty acid profiles than the wild-type and E15 mutant strains. E15-11, E15-15, and E15-25 exhibited higher expression of acyl-CoA synthesis- and Kennedy pathway-related genes than the wild-type and E15 mutant strains. Activation of the pentose phosphate pathway, which supplies NADPH, was also observed. These results suggested that the increased expression of acyl-CoA synthesis- and Kennedy pathway-related genes plays a vital role in lipid productivity in the oleaginous yeast L. starkeyi.

The native acyltransferase-coding genes DGA1 and DGA2 affect lipid accumulation in Blastobotrys raffinosifermentans differently when overexpressed

Blastobotrys raffinosifermentans is an ascomycetous yeast with biotechnological applications, recently shown to be an oleaginous yeast accumulating lipids under nitrogen limitation. Diacylglycerol acyltransferases (DGATs) act in the lipid storage pathway, in the last step of triacylglycerol biosynthesis. Two DGAT families are widespread in eukaryotes. We first checked that B. raffinosifermentans strain LS3 possessed both types of DGAT, and we then overexpressed the native DGAT-encoding genes, DGA1 and DGA2, separately or together. DGA2 (from the DGAT1 family) overexpression was sufficient to increase lipid content significantly in LS3, to up to 26.5% of dry cell weight (DCW), 1.6 times the lipid content of the parental strain (16.90% of DCW) in glucose medium under nitrogen limitation. By contrast, DGA1 (of the DGAT2 type) overexpression led to a large increase (up to 140-fold) in the amount of the corresponding transcript, but had no effect on overall lipid content relative to the parental strain. Analysis of the expression of the native genes over time in the parental strain revealed that DGA2 transcript levels quadrupled between 8 and 24 h in the N-limited lipogenic medium, whereas DGA1 transcript levels remained stable. This survey highlights the predominant role of the DGAT1 family in lipid accumulation and demonstrates the suitability of B. raffinosifermentans for engineering for lipid production.

Metabolic Engineering for Unusual Lipid Production in Yarrowia lipolytica

Using microorganisms as lipid-production factories holds promise as an alternative method for generating petroleum-based chemicals. The non-conventional yeast Yarrowia lipolytica is an excellent microbial chassis; for example, it can accumulate high levels of lipids and use a broad range of substrates. Furthermore, it is a species for which an array of efficient genetic engineering tools is available. To date, extensive work has been done to metabolically engineer Y. lipolytica to produce usual and unusual lipids. Unusual lipids are scarce in nature but have several useful applications. As a result, they are increasingly becoming the targets of metabolic engineering. Unusual lipids have distinct structures; they can be generated by engineering endogenous lipid synthesis or by introducing heterologous enzymes to alter the functional groups of fatty acids. In this review, we describe current metabolic engineering strategies for improving lipid production and highlight recent researches on unusual lipid production in Y. lipolytica.

Inference of Regulatory System for TAG Biosynthesis in Lipomyces starkeyi

Improving the bioproduction ability of efficient host microorganisms is a central aim in bioengineering. To control biosynthesis in living cells, the regulatory system of the whole biosynthetic pathway should be clearly understood. In this study, we applied our network modeling method to infer the regulatory system for triacylglyceride (TAG) biosynthesis in Lipomyces starkeyi, using factor analyses and structural equation modeling to construct a regulatory network model. By factor analysis, we classified 89 TAG biosynthesis-related genes into nine groups, which were considered different regulatory sub-systems. We constructed two different types of regulatory models. One is the regulatory model for oil productivity, and the other is the whole regulatory model for TAG biosynthesis. From the inferred oil productivity regulatory model, the well characterized genes DGA1 and ACL1 were detected as regulatory factors. Furthermore, we also found unknown feedback controls in oil productivity regulation. These regulation models suggest that the regulatory factor induction targets should be selected carefully. Within the whole regulatory model of TAG biosynthesis, some genes were detected as not related to TAG biosynthesis regulation. Using network modeling, we reveal that the regulatory system is helpful for the new era of bioengineering.

Metabolic engineering for increased lipid accumulation in Yarrowia lipolytica - A Review

Current energy security and climate change policies encourage the development and utilization of bioenergy. Oleaginous yeasts provide a particularly attractive platform for the sustainable production of biofuels and industrial chemicals due to their ability to accumulate high amounts of lipids. In particular, microbial lipids in the form of triacylglycerides (TAGs) produced from renewable feedstocks have attracted considerable attention because they can be directly used in the production of biodiesel and oleochemicals analogous to petrochemicals. As an oleaginous yeast that is generally regarded as safe, Yarrowia lipolytica has been extensively studied, with large amounts of data on its lipid metabolism, genetic tools, and genome sequencing and annotation. In this review, we highlight the newest strategies for increasing lipid accumulation using metabolic engineering and summarize the research advances on the overaccumulation of lipids in Y. lipolytica. Finally, perspectives for future engineering approaches are proposed.

Disrupting a phospholipase A2 gene increasing lipid accumulation in the oleaginous yeast Yarrowia lipolytica

AIMS

Phospholipase A₂ (PLA₂ ) is a diverse superfamily that hydrolyzes fatty acyl ester bonds at the sn-2 position of phospholipids. The correlation between phospholipid metabolism and the anabolism of neutral lipids remains unclear in yeasts. This study aims to explore the effects of PLA₂ on lipid accumulation in the oleaginous yeast Yarrowia lipolytica.

METHODS AND RESULTS

This study identified an actively expressed phospholipase A₂ gene (PLA2-3, YAIL0_E16060g) in Y. lipolytica by quantitative PCR analysis. The gene PLA2-3 was disrupted in the strain po1gΔKu70 by homologous recombination and in the strain po1g-G3 by a CRISPR-Cas9 system, which caused an increase in stress sensitivity while the cell growth was not altered under fermentative conditions. Lipid production was performed in both flasks and bioreactors. The results showed that the lipid titre and lipid content were improved over 25% and 8-30%, respectively, in PLA2-3 disrupted strains compared to the controls.

CONCLUSIONS

Disruption of the phospholipase PLA2-3 gene could effectively improve lipid production in Y. lipolytica.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study presented a strategy on improving the lipid production of oleaginous yeasts and a similar strategy might be used in other oleaginous microbes.

The influence of transketolase on lipid biosynthesis in the yeast Yarrowia lipolytica

Background

During the pentose phosphate pathway (PPP), two important components, NADPH and pentoses, are provided to the cell. Previously it was shown that this metabolic pathway is a source of reducing agent for lipid synthesis from glucose in the yeast Yarrowia lipolytica. Y. lipolytica is an attractive microbial host since it is able to convert untypical feedstocks, such as glycerol, into oils, which subsequently can be transesterified to biodiesel. However, the lipogenesis process is a complex phenomenon, and it still remains unknown which genes from the PPP are involved in lipid synthesis.

Results

To address this problem we overexpressed five genes from this metabolic pathway: transaldolase (TAL1, YALI0F15587g), transketolase (TKL1, YALI0E06479g), ribulose-phosphate 3-epimerase (RPE1, YALI0C11880g) and two dehydrogenases, NADP⁺-dependent glucose-6-phosphate dehydrogenase (ZWF1, YALI0E22649g) and NADP⁺-dependent 6-phosphogluconate dehydrogenase (GND1, YALI0B15598g), simultaneously with diacylglycerol acyltransferase (DGA1, YALI0E32769g) and verified each resulting strain’s ability to synthesize fatty acid growing on both glycerol and glucose as a carbon source. Our results showed that co-expression of DGA1 and TKL1 results in higher SCO synthesis, increasing lipid content by 40% over the control strain (DGA1 overexpression).

Conclusions

Simultaneous overexpression of DGA1 and TKL1 genes results in a higher lipid titer independently from the fermentation conditions, such as carbon source, pH and YE supplementation.

Effects of a high-cultivation temperature on the physiology of three different Yarrowia lipolytica strains

Despite the increasing relevance, ranging from academic research to industrial applications, only a limited number of non-conventional, oleaginous Yarrowia lipolytica strains are characterized in detail. Therefore, we analyzed three strains in regard to their metabolic and physiological properties, especially with respect to important characteristics of a production strain. By investigating different cultivation conditions and media compositions, similarities and differences between the distinct strain backgrounds could be derived. Especially sugar alcohol production, as well as an agglomeration of cells were found to be connected with growth at high temperatures. In addition, sugar alcohol production was independent of high substrate concentrations under these conditions. To investigate the genotypic basis of particular traits, including growth characteristics and metabolite concentrations, genomic analysis were performed. We found sequence variations for one third of the annotated proteins but no obvious link to all phenotypic features.

Efficient xylose utilization leads to highest lipid productivity in Candida tropicalis SY005 among six yeast strains grown in mixed sugar medium

Six local isolates of yeasts were screened for cell mass and lipid production in mixed glucose and xylose medium. Candida tropicalis SY005 and Trichosporon (Apiotrichum) loubieri SY006 showed significant lipid accumulation of 24.6% and 32% (dry cell weight), respectively when grown in medium containing equal mass of both the sugars. SY005 produced relatively higher cell mass of 9.66 gL^-1 due to higher rate of sugar consumption, which raised the lipid productivity of the organism to 0.792 gL^-1day^-1 as compared to 0.446 gL^-1day^-1 in SY006. When grown with each sugar separately, the xylose consumption rate of SY005 was found to be 0.55 gL^-1 h^-1 after 4 days as compared to 0.52 gL^-1 h^-1 for SY006. Transcript expression of the high affinity xylose transporter (Cthaxt), xylose reductase (Ctxyl1), and xylitol dehydrogenase (Ctxyl2) of SY005 was monitored to unravel such high rate of sugar consumption. Expression of all the three genes was observed to vary in mixed sugars with Cthaxt exhibiting the highest expression in presence of only xylose. Expression levels of both Ctxyl1 and Ctxyl2, involved in xylose catabolism, were maximum during 24-48 h of growth, indicating that xylose utilization started in the presence of glucose, which was depleted in the medium after 96 h. Together, the present study documents that C. tropicalis SY005 consumes xylose concomitant to glucose during early period of growth, and it is a promising yeast strain for viable production of storage lipid or other high-value oleochemicals utilizing lignocellulose hydrolysate.

A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data

Rhodosporidium toruloides is a red, basidiomycetes yeast that can accumulate a large amount of lipids and produce carotenoids. To better assess this non-model yeast's metabolic capabilities, we reconstructed a genome-scale model of R. toruloides IFO0880's metabolic network (iRhto1108) accounting for 2204 reactions, 1985 metabolites and 1108 genes. In this work, we integrated and supplemented the current knowledge with in-house generated biomass composition and experimental measurements pertaining to the organism's metabolic capabilities. Predictions of genotype-phenotype relations were improved through manual curation of gene-protein-reaction rules for 543 reactions leading to correct recapitulations of 84.5% of gene essentiality data (sensitivity of 94.3% and specificity of 53.8%). Organism-specific macromolecular composition and ATP maintenance requirements were experimentally measured for two separate growth conditions: (i) carbon and (ii) nitrogen limitations. Overall, iRhto1108 reproduced R. toruloides's utilization capabilities for 18 alternate substrates, matched measured wild-type growth yield, and recapitulated the viability of 772 out of 819 deletion mutants. As a demonstration to the model's fidelity in guiding engineering interventions, the OptForce procedure was applied on iRhto1108 for triacylglycerol overproduction. Suggested interventions recapitulated many of the previous successful implementations of genetic modifications and put forth a few new ones.

Overexpression of delta-12 desaturase in the yeast Schwanniomyces occidentalis enhances the production of linoleic acid

The oleaginous yeast Schwanniomyces occidentalis was previously isolated because of its excellent suitability to convert lignocellulosic hydrolysates into triacyl glycerides: it is able to use a broad range of sugars and is able to tolerate high concentrations of lignocellulosic hydrolysate inhibitors. Compared to other oleaginous yeasts S. occidentalis however produces a low content of unsaturated fatty acids. We show here that the linoleic acid content can be significantly improved by (over)expression Δ12-desaturases derived from S. occidentalis and Fusarium moniliforme. Expression was stable for the homologous expression but decreased during heterologous expression. Both homologous and heterologous expression of mCherry-Δ12-desaturase led to a 4-fold increase in linoleic acid from 0.02 g/g biomass to 0.08 g/g biomass resulting in the production of 2.23 g/L and 2.05 g/L of linoleic acid.

Common aspects in the engineering of yeasts for fatty acid- and isoprene-based products

The biosynthetic pathways for most lipophilic metabolites share several common principles. These substances are built almost exclusively from acetyl-CoA as the donor for the carbon scaffold and NADPH is required for the reductive steps during biosynthesis. Due to their hydrophobicity, the end products are sequestered into the same cellular compartment, the lipid droplet. In this review, we will summarize the efforts in the metabolic engineering of yeasts for the production of two major hydrophobic substance classes, fatty acid-based lipids and isoprenoids, with regard to these common aspects. We will compare and discuss the results of genetic engineering strategies to construct strains with enhanced synthesis of the precursor acetyl-CoA and with modified redox metabolism for improved NADPH supply. We will also discuss the role of the lipid droplet in the storage of the hydrophobic product and review the strategies to either optimize this organelle for higher capacity or to achieve excretion of the product into the medium.

Cellular and metabolic engineering of oleaginous yeast Yarrowia lipolytica for bioconversion of hydrophobic substrates into high-value products

The non-conventional oleaginous yeast Yarrowia lipolytica is able to utilize both hydrophilic and hydrophobic carbon sources as substrates and convert them into value-added bioproducts such as organic acids, extracellular proteins, wax esters, long-chain diacids, fatty acid ethyl esters, carotenoids and omega-3 fatty acids. Metabolic pathway analysis and previous research results show that hydrophobic substrates are potentially more preferred by Y. lipolytica than hydrophilic substrates to make high-value products at higher productivity, titer, rate, and yield. Hence, Y. lipolytica is becoming an efficient and promising biomanufacturing platform due to its capabilities in biosynthesis of extracellular lipases and directly converting the extracellular triacylglycerol oils and fats into high-value products. It is believed that the cell size and morphology of the Y. lipolytica is related to the cell growth, nutrient uptake, and product formation. Dimorphic Y. lipolytica demonstrates the yeast-to-hypha transition in response to the extracellular environments and genetic background. Yeast-to-hyphal transition regulating genes, such as YlBEM1, YlMHY1 and YlZNC1 and so forth, have been identified to involve as major transcriptional factors that control morphology transition in Y. lipolytica. The connection of the cell polarization including cell cycle and the dimorphic transition with the cell size and morphology in Y. lipolytica adapting to new growth are reviewed and discussed. This review also summarizes the general and advanced genetic tools that are used to build a Y. lipolytica biomanufacturing platform.

Understanding lipogenesis by dynamically profiling transcriptional activity of lipogenic promoters in Yarrowia lipolytica

Lipogenesis is a complicated process involving global transcriptional reprogramming of lipogenic pathways. It is commonly believed that nitrogen starvation triggers a metabolic shift that reroutes carbon flux from Krebs cycles to lipogenesis. In this study, we systematically surveyed and dynamically profiled the transcriptional activity of 22 lipogenic promoters aiming to delineate a picture how nitrogen starvation regulates lipogenesis in Y. lipolytica. These lipogenic promoters drive the expression of critical pathways that are responsible for the generation of reducing equivalents (NADPH), carbon backbones (acetyl-CoA, malonyl-CoA, DHAP, etc.), synthesis and degradation of fatty acids. Specifically, our investigated promoters span across an array of metabolic pathways, including glycolysis, Krebs cycle, pentose phosphate pathway, mannitol cycle, glutamine-GABA cycle, fatty acid and lipid synthesis, glyoxylate, β-oxidation, and POM (pyruvate-oxaloacetate-malate) cycle. Our work provides evidences that mannitol cycle, glutamine-GABA cycle and amino acid degradation, pyruvate oxidation, and acetate assimilation pathways are lipogenesis-related steps involved in generating cytosolic NADPH and acetyl-CoA precursors. This systematic investigation and dynamic profiling of lipogenic promoters may help us better understand lipogenesis, facilitate the formulation of structure-based kinetic models, as well as develop efficient cell factories for fuels and chemical production in oleaginous species.

The metabolism and genetic regulation of lipids in the oleaginous yeast Yarrowia lipolytica

The biotechnological potential of Yarrowia lipolytica, as a single cell oil-producing microorganism, is presented in this review. Although initially this yeast species was considered as a lipid-degrading, recently, it was reclassified as a lipid-producing microorganism, since it has been reported to be capable of accumulating diverse desirable fatty acids after metabolic pathway engineering. In the first part of the present document, a general revision of the oil metabolic pathways and the capacity of oil production in Y. lipolytica is presented. The single cell oil produced by these metabolic engineering strategies has been designed by optimization, introduction, or suppression of new pathways to increase yield on lipid production. Later on, the genetic regulation systems and the lipid composition generated by this yeast for industrial purposes are discussed. These lipids could be safely used in the chemical food and biofuel industries, due to their high proportion of oleic acid. This document emphasizes in the overviewing at Y. lipolytica as an ideal oil cell factory, and as an excellent model to produce single cell oil.

Metabolic engineering to enhance biosynthesis of both docosahexaenoic acid and odd-chain fatty acids in Schizochytrium sp. S31

BACKGROUND

Docosahexaenoic acid (DHA, C22:6) and odd-chain fatty acids (OCFAs, C15:0 and C17:0) have attracted great interest, since they have been widely used in food and therapeutic industries, as well as chemical industry, such as biodiesel production and improvement. The oil-producing heterotrophic microalgae Schizochytrium sp. 31 is one of main DHA-producing strains. Recently, it was found that Schizochytrium can also synthesize OCFAs; however, contents and titers of DHA and OCFAs in Schizochytrium are still low, which limit its practical application.

RESULTS

In this study, we found that acetyl-CoA carboxylase suffered from a feedback inhibition by C16-CoA in Schizochytrium, and relief of the inhibition resulted in improved both lipid content and the ratio of OCFAs in total fatty acids. Based on this finding, a novel strategy for elevating both DHA and OCFAs contents was established. First, the total lipid accumulation was increased by overexpressing a malic enzyme from Crypthecodinium cohnii to elevate NADPH supply. Second, the inhibition effect on acetyl-CoA carboxylase was relieved by overexpressing a codon-optimized ELO3 gene from Mortierella alpina, which encodes an elongase enzyme responsible for converting C16 into C18 fatty acids. After the above two-step engineering, contents of DHA and OCFAs were increased by 1.39- and 3.30-fold, reaching a level of 26.70 and 25.08% of dry cell weight, respectively, which are the highest contents reported so far for Schizochytrium. The titers of DHA and OCFAs were elevated by 1.08- and 2.57-fold, reaching a level of 3.54 and 3.32 g/L, respectively. Notably, the OCFAs titer achieved was 2.66-fold higher than the highest reported in Escherichia coli (1.25 g/L), implying potential value for industry application. To reveal the potential metabolic mechanism for the enhanced biosynthesis of both DHA and OCFAs, LC-MS metabolomic analysis was employed and the results showed that the pentose phosphate pathway and the glycolysis pathway were strengthened and intracellular propionyl-CoA concentration were also significantly increased in the engineered Schizochytrium, suggesting an increased supply of NADPH, acetyl-CoA, and propionyl-CoA for DHA and OCFAs accumulation.

CONCLUSIONS

The discovery provides a new source of OCFAs production, and proposes a new strategy to improve contents and titers of both DHA and OCFAs in Schizochytrium. These will be valuable for improving commercial potential of Schizochytrium and guiding the engineering strategy in other fatty acids producing heterotrophic microalga.

Metabolic engineering in the host Yarrowia lipolytica

The nonconventional, oleaginous yeast, Yarrowia lipolytica is rapidly emerging as a valuable host for the production of a variety of both lipid and nonlipid chemical products. While the unique genetics of this organism pose some challenges, many new metabolic engineering tools have emerged to facilitate improved genetic manipulation in this host. This review establishes a case for Y. lipolytica as a premier metabolic engineering host based on innate metabolic capacity, emerging synthetic tools, and engineering examples. The metabolism underlying the lipid accumulation phenotype of this yeast as well as high flux through acyl-CoA precursors and the TCA cycle provide a favorable metabolic environment for expression of relevant heterologous pathways. These properties allow Y. lipolytica to be successfully engineered for the production of both native and nonnative lipid, organic acid, sugar and acetyl-CoA derived products. Finally, this host has unique metabolic pathways enabling growth on a wide range of carbon sources, including waste products. The expansion of carbon sources, together with the improvement of tools as highlighted here, have allowed this nonconventional organism to act as a cellular factory for valuable chemicals and fuels.

Overproduction of Fatty Acid Ethyl Esters by the Oleaginous Yeast Yarrowia lipolytica through Metabolic Engineering and Process Optimization

Recent advances in the production of biofuels by microbes have attracted attention due to increasingly limited fossil fuels. Biodiesels, especially fatty acid ethyl esters (FAEEs), are considered a potentially fully sustainable fuel in the near future due to similarities with petrodiesels and compatibility with existing infrastructure. However, biosynthesis of FAEEs is limited by the supply of precursor lipids and acetyl-CoA. In the present study, we explored the production potential of an engineered biosynthetic pathway coupled to the addition of ethanol in the oleaginous yeast Yarrowia lipolytica. This type of yeast is able to supply a greater amount of precursor lipids than species typically used. To construct the FAEEs synthesis pathway, WS genes that encode wax ester synthases (WSs) from different species were codon-optimized and heterologously expressed in Y. lipolytica. The most productive engineered strain was found to express a WS gene from Marinobacter hydrocarbonoclasticus strain DSM 8798. To stepwisely increase FAEEs production, we optimized the promoter of WS overexpression, eliminated β-oxidation by deleting the PEX10 gene in our engineered strains, and redirected metabolic flux toward acetyl-CoA. The new engineered strain, coupled with an optimized ethanol concentration, led to an approximate 5.5-fold increase in extracellular FAEEs levels compared to the wild-type strain and a maximum FAEEs titer of 1.18 g/L in shake flask cultures. In summary, the present study demonstrated that an engineered Y. lipolytica strain possessed a high capacity for FAEEs production and may serve as a platform for more efficient biodiesel production in the future.