Fungal arachidonic acid-rich oil: research, development and industrialization

Novel Approaches to Mortierella alpina Identification and Arachidonic Acid Production Optimization

Arachidonic acid (ARA) is an integral constituent of cell structures and is instrumental for the nervous, muscular, and immune systems' functions. The sore need for this nutrient may be fulfilled via production based on the fungus Mortierella alpina. The identity of the M. alpina culture obtained from Assiut University, Egypt, was confirmed based on internal transcribed spacer DNA barcoding and elongation enzyme RNA sequencing. Liquid media glucose and peptone as carbon and nitrogen sources, respectively, and diverse micronutritional factors were adjusted for optimal biomass and ARA production. Shake flask cultivation at 25 °C for 7 days produced around 0.570 g of ARA per liter of culture. M. alpina treatment using mutagen 5-fluorouracil and octyl gallate-supplemented glucose-yeast-agar screening plates and shake-flask incubation at 25 °C, then at 20 °C, followed by aging at 10 °C, led to >3 g ARA/liter culture, a yield considered suitable for potential commercial production.

Regulation of carbon metabolic fluxes to enhance lipid and succinate production in oleaginous fungus Mortierella alpina

Mortierella alpina is popular for lipid production, but the low carbon conversion rate and lipid yield are major obstacles for its economic performance. Here, external addition of organic acids involved in tricarboxylic acid cycle was used to tune carbon flux and improve lipid production. Citrate was determined to be the best organic acid that can be used for enhancing lipid production. By the addition of citrate, the lipid titer and content were approximately 1.24 and 1.34 times higher, respectively. Meanwhile, citrate supplement also promoted the accumulation of succinate, an important value-added platform chemical. Owing to the improved lipid and succinate production through adding citrate, the carbon conversion rate of M. alpina reached up to 52.17%, much higher than that of the control group (14.11%). The addition of citrate could redistribute carbon flux by regulating the expression level of genes related to tricarboxylic acid cycle metabolism. More carbon fluxes flow to lipid and succinate synthesis, which greatly improved the carbon conversion efficiency of M. alpina. This study provides an effective and straightforward strategy with potential economic benefits to improve carbon conversion efficiency in M. alpina.

Early-life ruminal microbiome-derived indole-3-carboxaldehyde and prostaglandin D2 are effective promoters of rumen development

BACKGROUND

The function of diverse ruminal microbes is tightly linked to rumen development and host physiology. The system of ruminal microbes is an excellent model to clarify the fundamental ecological relationships among complex nutrient-microbiome-host interactions. Here, neonatal lambs are introduced to different dietary regimes to investigate the influences of early-life crosstalk between nutrients and microbiome on rumen development.

RESULTS

We find starchy corn-soybean starter-fed lambs exhibit the thickest ruminal epithelia and fiber-rich alfalfa hay-fed lambs have the thickest rumen muscle. Metabolome and metagenome data reveal that indole-3-carboxaldehyde (3-IAld) and prostaglandin D2 (PGD2) are the top characteristic ruminal metabolites associated with ruminal epithelial and muscular development, which depend on the enhanced ruminal microbial synthesis potential of 3-IAld and PGD2. Moreover, microbial culture experiment first demonstrates that Bifidobacterium pseudolongum is able to convert tryptophan into 3-IAld and Candida albicans is a key producer for PGD2. Transcriptome sequencing of the ruminal epithelia and smooth muscle shows that ruminal epithelial and muscular development is accompanied by Wnt and Ca2+ signaling pathway activation. Primary cell cultures further confirm that 3-IAld promotes ruminal epithelial cell proliferation depending on AhR-wnt/β-catenin signaling pathway and PGD2 accelerates ruminal smooth muscle cell proliferation via Ca2+ signaling pathway. Furthermore, we find that 3-IAld and PGD2 infusion promote ruminal epithelial and musculature development in lambs.

CONCLUSIONS

This study demonstrates that early-life ruminal microbiome-derived 3-IAld and PGD2 are effective promoters of rumen development, which enhances our understanding of nutrient-microbiome-host interactions in early life.

Universal and unique strategies for the production of polyunsaturated fatty acids in industrial oleaginous microorganisms

Polyunsaturated fatty acids (PUFAs), especially docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA) and arachidonic acid (ARA), are beneficial for reducing blood cholesterol and enhancing memory. Traditional PUFA production relies on extraction from plants and animals, which is unsustainable. Thus, using microorganisms as lipid-producing factories holds promise as an alternative way for PUFA production. Several oleaginous microorganisms have been successfully industrialized to date. These can be divided into universal and specialized hosts according to the products range of biosynthesis. The Yarrowia lipolytica is universal oleaginous host that has been engineered to produce a variety of fatty acids, such as γ-linolenic acid (GLA), EPA, ARA and so on. By contrast, the specialized host are used to produce only certain fatty acids, such as ARA in Mortierella alpina, EPA in Nannochloropsis, and DHA in Thraustochytrids. The metabolic engineering and fermentation strategies for improving PUFA production in universal and specialized hosts are different, which is the subject of this review. In addition, the widely applicable strategies for microbial lipid production that are not specific to individual hosts were also reviewed.

Flocculation of oleaginous green algae with Mortierella alpina fungi

Microalgae are promising sources of valuable bioproducts such as biofuels, food, and nutraceuticals. However, harvesting microalgae is challenging due to their small size and low biomass concentrations. To address this challenge, bio-flocculation of starchless mutants of Chlamydomonas reinhardtii (sta6/sta7) was investigated with Mortierella alpina, an oleaginous fungus with high concentrations of arachidonic acid (ARA). Triacylglycerides (TAG) reached 85 % of total lipids in sta6 and sta7 through a nitrogen regime. Scanning electron microscopy determined cell-wall attachment and extra polymeric substances (EPS) to be responsible for flocculation. An algal-fungal biomass ratio around 1:1 (three membranes) was optimal for bio-flocculation (80-85 % flocculation efficiency in 24 h). Nitrogen-deprived sta6/sta7 were flocculated with strains of M. alpina (NVP17b, NVP47, and NVP153) with aggregates exhibiting fatty acid profiles similar to C. reinhardtii, with ARA (3-10 % of total fatty acids). This study showcases M. alpina as a strong bio-flocculation candidate for microalgae and advances a mechanistic understanding of algal-fungal interaction.

Potential of Mortierellaceae for polyunsaturated fatty acids production: mini review

The health benefits of polyunsaturated fatty acids (PUFAs) have encouraged the search for rich sources of these compounds. However, the supply chain of PUFAs from animals and plants presents environmental concerns, such as water pollution, deforestation, animal exploitation and interference in the trophic chain. In this way, a viable alternative has been found in microbial sources, mainly in single cell oil (SCO) production by yeast and filamentous fungi. Mortierellaceae is a filamentous fungal family world-renowned for PUFA-producing strains. For example, Mortierella alpina can be highlighted due to be industrially applied to produce arachidonic acid (20:4 n6), an important component of infant supplement formulas. Thus, the state of the art of strategies to increase PUFAs production by Mortierellaceae strains is presented in this review. Firstly, we have discussed main phylogenetic and biochemical characteristics of these strains for lipid production. Next, strategies based on physiological manipulation, using different carbon and nitrogen sources, temperature, pH and cultivation methods, which can increase PUFA production by optimizing process parameters are presented. Furthermore, it is possible to use metabolic engineering tools, controlling the supply of NADPH and co-factors, and directing the activity of desaturases and elongase to the target PUFA. Thus, this review aims to discuss the functionality and applicability of each of these strategies, in order to support future research for PUFA production by Mortierellaceae species.

Engineering Yarrowia lipolytica to produce nutritional fatty acids: Current status and future perspectives

Due to their vital physiological functions, nutritional fatty acids have great potential as nutraceutical food supplements for preventing an array of diseases such as inflammation, depression, arthritis, osteoporosis, diabetes and cancer. Microbial biosynthesis of fatty acids follows the trend of sustainable development, as it enables green, environmentally friendly and efficient production. As a natural oleaginous yeast, Yarrowia lipolytica is especially well-suited for the production of fatty acids. Moreover, it has a variety of genetic engineering tools and novel metabolic engineering strategies that make it a robust workhorse for the production of an array of value-added products. In this review, we summarize recent advances in metabolic engineering strategies for accumulating nutritional fatty acids in Y. lipolytica, including conjugated fatty acids and polyunsaturated fatty acids. In addition, the future prospects of nutritional fatty acid production using the Y. lipolytica platform are discussed in light of the current progress, challenges, and trends in this field. Finally, guidelines for future studies are also emphasized.

Physiological and proteomic responses of Chlamydomonas reinhardtii to arsenate and lead mixtures

Arsenic (As) and lead (Pb) are frequently emitted from various sources into environment, but microbial responses to their combined toxicity have not been systematically investigated. In this study, Chlamydomonas reinhardtii was exposed to two levels of arsenate (As (V), 50, 500 μg/L), Pb (II) (500, 5000 μg/L) and their mixture (50 μg/L As (V) + 500 μg/L Pb (II); 500 μg/L As (V) + 5000 μg/L Pb (II)). The growth of C. reinhardtii was inhibited more remarkably by As (V) than by Pb (II). The As stress was alleviated by Pb in the 50 μg/L As (V) + 500 μg/L Pb (II) treatment, but was enhanced upon the 500 μg/L As (V) + 5000 μg/L Pb (II) exposure, with more pronounced changes in a number of physiological parameters of the algal cells. Proteomic results showed that 71 differently expressed proteins (DEPs) in the treatment of 50 μg/L As (V) + 500 μg/L Pb (II), and 167 DEPs were identified in that of 500 μg/L As (V) + 5000 μg/L Pb (II). These proteins were involved in energy metabolism, photosynthetic carbon fixation, reactive oxygen scavenging and defense, and amino acid synthesis. Taken together, these physiological and proteomic data demonstrated that C. reinhardtii could resist the As (V) and Pb (II) combined treatments through extracellular complexation and intracellular pathways.

Engineering the Lipid and Fatty Acid Metabolism in Yarrowia lipolytica for Sustainable Production of High Oleic Oils

Oleic acid is widely applied in the chemical, material, nutritional, and pharmaceutical industries. However, the current production of oleic acid via high oleic plant oils is limited by the long growth cycle and climatic constraints. Moreover, the global demand for high oleic plant oils, especially the palm oil, has emerged as the driver of tropical deforestation causing tropical rainforest destruction, climate change, and biodiversity loss. In the present study, an alternative and sustainable strategy for high oleic oil production was established by reprogramming the metabolism of the oleaginous yeast Yarrowia lipolytica using a two-layer "push-pull-block" strategy. Specifically, the fatty acid synthesis pathway was first engineered to increase oleic acid proportion by altering the fatty acid profiles. Then, the content of storage oils containing oleic acid was boosted by engineering the synthesis and degradation pathways of triacylglycerides. The strain resulting from this two-layer engineering strategy produced the highest titer of high oleic microbial oil reaching 56 g/L with 84% oleic acid in fed-batch fermentation, representing a remarkable improvement of a 110-fold oil titer and 2.24-fold oleic acid proportion compared with the starting strain. This alternative and sustainable method for high oleic oil production shows the potential of substitute planting.

Autophagy Improves ARA-Rich TAG Accumulation in Mortierella alpina by Regulating Resource Allocation

The present study was designed to explore the possibility of improving lipid production in oleaginous filamentous fungus Mortierella alpina based on an autophagy regulation strategy. According to multiomics information, vacuolate-centered macroautophagy was identified as the main type of autophagy in M. alpina under nitrogen-limited conditions. Mutation of autophagy-related gene MAatg8 led to impaired fatty acid synthesis, while overexpression of both MAatg8 and phosphatidylserine decarboxylases (MApsd2) showed promoting effects on fatty acid synthesis. MAatg8 overexpression strain with external supply of ethanolamine significantly increased arachidonic acid (ARA)-rich triacylglycerol (TAG) and biomass synthesis in M. alpina, and the final fatty acid content increased by approximately 110% compared with that in the wild-type strain. Metabolomics and lipidomics analyses revealed that cell autophagy enhanced the recycling of preformed carbon, nitrogen, and lipid in mycelium, and the released carbon skeleton and energy were contributed to the accumulation of TAG in M. alpina. This study suggests that regulation of autophagy-related MAatg8-phosphatidylethanolamine (MAatg8-PE) conjugation system could be a promising strategy for attaining higher lipid production and biomass growth. The mechanism of autophagy in regulating nitrogen limitation-induced lipid accumulation elucidated in this study provides a reference for development of autophagy-based strategies for improving nutrient use efficiency and high value-added lipid production by oleaginous microorganism.

IMPORTANCE Studies have indicated that functional oil accumulation occurs in oleaginous microorganisms under nitrogen limitation. However, until now, large-scale application of nitrogen-deficiency strategies was limited by low biomass. Therefore, the identification of the critical nodes of nitrogen deficiency-induced lipid accumulation is urgently needed to further guide functional oil production. The significance of our research is in uncovering the function of cell autophagy in the ARA-rich TAG accumulation of oleaginous fungus M. alpina and demonstrating the feasibility of improving lipid production based on an autophagy regulation strategy at the molecular and omics levels. Our study proves that regulation of cell autophagy through the MAatg8-PE conjugation system-related gene overexpression or exogenous supply of ethanolamine would be an efficient strategy to increase and maintain biomass productivity when high TAG content is obtained under nitrogen deficiency, which could be useful for the development of new strategies that will achieve more biomass and maximal lipid productivity.

Process optimization and characterization of arachidonic acid oil degumming using ultrasound-assisted enzymatic method

Ultrasound assisted enzymatic method was applied to the degumming of arachidonic acid (ARA) oil produced by Mortierella alpina. The conditions of degumming process were optimized by response surface methodology with Box- Behnken design. A dephosphorization rate of 98.82% was achieved under optimum conditions of a 500 U/kg of Phospholipase A₁ (PLA₁) dosage, 2.8 mL/100 g of water volume, 120 min of ultrasonic time, and 135 W of ultrasonic power. The phosphorus content of ultrasonic assisted enzymatic degumming oil (UAEDO) was 4.79 mg/kg, which was significantly lower than that of enzymatic degumming oil (EDO, 17.98 mg/kg). Crude Oil (CO), EDO and UAEDO revealed the similar fatty acid compositions, and ARA was dominated (50.97 ~ 52.40%). The oxidation stability of UAEDO was equivalent to EDO and weaker than CO, while UAEDO presented the strongest thermal stability, followed by EDO and CO. Furthermore, aldehydes, acids and alcohols were identified the main volatile flavor components for the three oils. The proportions of major contributing components such as hexanal, nonanal, (E)-2-nonanal, (E, E)-2,4-decadienal, (E)-2-nonenal and aldehydes in UAEDO and EDO were all lower than CO. Overall, Ultrasound assisted enzymatic degumming proved to be an efficient and superior method for degumming of ARA oil.

Microbial lipid biosynthesis from lignocellulosic biomass pyrolysis products

Lipids are a biorefinery platform to prepare fuel, food and health products. They are traditionally obtained from plants, but those of microbial origin allow for a better use of land and C resources, among other benefits. Several (thermo)chemical and biochemical strategies are used for the conversion of C contained in lignocellulosic biomass into lipids. In particular, pyrolysis can process virtually any biomass and is easy to scale up. Products offer cost-effective, renewable C in the form of readily fermentable molecules and other upgradable intermediates. Although the production of microbial lipids has been studied for 30 years, their incorporation into biorefineries was only described a few years ago. As pyrolysis becomes a profitable technology to depolymerize lignocellulosic biomass into assimilable C, the number of investigations on it raises significantly. This article describes the challenges and opportunities resulting from the combination of lignocellulosic biomass pyrolysis and lipid biosynthesis with oleaginous microorganisms. First, this work presents the basics of the individual processes, and then it shows state-of-the-art processes for the preparation of microbial lipids from biomass pyrolysis products. Advanced knowledge on separation techniques, structure analysis, and fermentability is detailed for each biomass pyrolysis fraction. Finally, the microbial fatty acid platform comprising biofuel, human food and animal feed products, and others, is presented. Literature shows that the microbial lipid production from anhydrosugars, like levoglucosan, and short-chain organic acids, like acetic acid, is straightforward. Indeed, processes achieving nearly theoretical yields form the latter have been described. Some authors have shown that lipid biosynthesis from different lignin sources is biochemically feasible. However, it still imposes major challenges regarding strain performance. No report on the fermentation of pyrolytic lignin is yet available. Research on the microbial uptake of pyrolytic humins remains vacant. Microorganisms that make use of methane show promising results at the proof-of-concept level. Overall, despite some issues need to be tackled, it is now possible to conceive new versatile biorefinery models by combining lignocellulosic biomass pyrolysis products and robust oleaginous microbial cell factories.

Optimization of culture conditions for enhanced Dunaliella salina productions in mixotrophic culture

Dunaliella salina (D. salina) is a green microalga known for its tendency to produce lipid and β-carotene. Fatty acid profile, lipid and β-carotene productions of the microalga D. salina cultivated under different mixotrophic conditions were assayed. Notably, in spite of a broad spectrum of substrates served, mixotrophic cultivations slightly affected the fatty acid composition, and as a result C16:0 and C18:0, C18:1, C18:2 and C18:3 were identified as main fatty acids. Lipid in dry weight biomass (DWB) hit a high of 24.3% at 5% of NaCL and linolenic acid in lipid reached a peak of 9.15% at 15% of NaCL in medium containing glucose and equal amounts of yeast extract and soy bean powder. One-factor-at-a-time was applied to elucidate the substrates which had noticeable impacts on β-carotene production. Glucose, meat peptone, titanium dioxide nanoparticles (TiO₂ NPs), pH 7.5 and 5% NaCL were identified as key process parameters impacting β-carotene production. Following, the concentration of glucose, meat peptone and TiO₂ NPs were optimized by using response surface method. The highest content of β-carotene, 25.23 mg/g DWB, was obtained in medium composed of (g/L); 22.92 glucose, 5 meat peptone and 0.002 TiO₂ NPs.

Heterologous Production of Polyunsaturated Fatty Acids in E. coli Using Δ5-Desaturase Gene from Microalga Isochrysis Sp

Eicosapentaenoic acid (EPA) and arachidonic acid (ARA) are long-chain polyunsaturated fatty acids (PUFAs) that play a significant role in human growth and development, which deficiency can trigger several metabolic-related diseases. Since the availability of PUFA sources is limited, there arises a need to explore alternative sources. Therefore, the present study aimed to investigate whether an Escherichia coli which are engineered with Δ5Des-Iso gene isolated from Isochrysis sp. could be utilized to synthesize PUFAs. Full-length gene Δ5Des-Iso (1149 bp) was isolated from Isochrysis sp. that encodes 382 amino acids and identified as Δ5-desatruase gene using different bioinformatic analysis. Heterologous gene expression was carried out in E. coli having Δ5Des-Iso with precursor fatty acids. The Δ5Des-Iso produced novel fatty acids of EPA (ω-3) and ARA (ω-6) as respective products were identified by GC-MS. Gene expression and PUFA synthesis in E. coli were optimized by temperature, time, and concentrations of precursor fatty acid substrates. Δ5Des-Iso RNA transcript level was inversely proportional to the time and fatty acid synthesis. And, the significant production of EPA (4.1 mg/g) and ARA (8.3 mg/g) in total fatty acids was observed in E. coli grown at 37 °C for 24 h with 25 μM of external fatty acid substrate as an optimum growth conditions. E. coli could be used as alternative organism to synthesis PUFAs and widely applicable in many nutraceuticals and pharmaceuticals industry for human use.

Optimization of carbon source efficiency for lipid production with the oleaginous yeast Saitozyma podzolica DSM 27192 applying automated continuous feeding

BACKGROUND

Biotechnologically produced microbial lipids are of interest as potential alternatives for crude and plant oils. Their lipid profile is similar to plant oils and can therefore be a substitute for the production of biofuels, additives for food and cosmetics industry as well as building blocks for oleochemicals. Commercial microbial lipids production, however, is still not profitable and research on process optimization and cost reduction is required. This study reports on the process optimization using glucose or xylose with the unconventional oleaginous yeast Saitozyma podzolica DSM 27192 aiming to reduce the applied carbon source amount without sacrificing lipid productivity.

RESULTS

By optimizing the process parameters temperature and pH, lipid productivity was enhanced by 40%. Thereupon, by establishing a two-phase strategy with an initial batch phase and a subsequent fed-batch phase for lipid production in which a constant sugar concentration of about 10 g/L was maintained, resulted in saving of ~ 41% of total glucose and ~ 26% of total xylose. By performing the automated continuous sugar feed the total sugar uptake was improved to ~ 91% for glucose and ~ 92% for xylose and thus, prevented waste of unused carbon source in the cultivation medium. In addition, reduced glucose cultivation resulted in to 28% higher cell growth and 19% increase of lipid titer. By using xylose, the by-product xylonic acid was identified for the first time as by-product of S. podzolica.

CONCLUSIONS

These findings provide a broad view of different cultivation process strategies with subsequent comparison and evaluation for lipid production with S. podzolica. Additionally, new biotechnological characteristics of this yeast were highlighted regarding the ability to produce valuable organic acids from sustainable and renewable sugars.

Metabolomics analysis reveals the role of oxygen control in the nitrogen limitation induced lipid accumulation in Mortierella alpina

Lipid hyperaccumulation in oleaginous microorganisms is generally induced by nitrogen limitation, while oxygen supply can influence biomass growth and cell metabolism. Although strategies based on nitrogen limitation or oxygen control have been extensively explored and applied in various oleaginous microorganisms, the role of oxygen supply in nitrogen limitation induced lipid hyperaccumulation still remains unclear. Here, we systematically surveyed the effects of oxygen supply on the oleaginous fungus M. alpina cultured in nitrogen limited conditions through integration of physiochemical parameters and metabolomics analysis. Our results indicated that a high oxygen supply promoted carbon/nitrogen consumption and was used for rapid biomass synthesis, while either high or low oxygen supply conditions were adverse to lipid and ARA accumulation. Different oxygen supply level significantly affected the balance between fermentation for lipid synthesis and respiration for energy generation. Under nitrogen limitation, a suitable oxygen supply promoted the recycling of preformed nitrogen and increased the redirection of carbon towards fatty acid synthesis through the hub centred around glutamic acid coupled to the intermediate metabolism of carbon in the TCA cycle, while a high oxygen supply favored the respiration process and enhanced the degradation of LC-PUFAs, rather than fermentation for fatty acid synthesis. This system-level insight reveals the underlying metabolic mechanism of oxygen control in nitrogen limitation induced lipid accumulation, and provides theoretical support for the integration of oxygen control with nutrient supply for efficient microbial oil production.

Evaluation and Transcriptome Analysis of the Novel Oleaginous Microalga Lobosphaera bisecta (Trebouxiophyceae, Chlorophyta) for Arachidonic Acid Production

Arachidonic acid (AA) is an omega-6 long-chain polyunsaturated fatty acid and is important for human health. The coccoid green microalga Lobosphaera bisecta has been reported to be able to accumulate high AA content under certain conditions. Nutrient management and light intensity had significant effects on the biomass and accumulation of lipids and AA in L. bisecta SAG2043. Both a high nitrogen concentration (18 mM) and high light intensity (bilateral light-300 μmol m⁻² s⁻¹) were beneficial to the growth of L. bisecta, and the replacement of culture medium further enhanced the biomass, which reached 8.9 g L⁻¹. Low nitrogen concentration (3.6 mM) and high light significantly promoted the accumulation of lipids and AA. The highest lipid and AA content reached 54.0% and 10.8% of dry weight, respectively. Lipid compositions analysis showed that 88.2% of AA was distributed within the neutral lipids. We then reconstructed the lipid metabolic pathways of L. bisecta for the first time, and demonstrated that the upregulation of a key desaturase and elongase in the Δ6 pathway was conducive to the accumulation of fatty acids toward AA synthesis. L. bisecta SAG2043 exhibits high biomass, lipid and AA production. It may be a potential candidate for AA production.

Evaluation of Downstream Processing, Extraction, and Quantification Strategies for Single Cell Oil Produced by the Oleaginous Yeasts Saitozyma podzolica DSM 27192 and Apiotrichum porosum DSM 27194

Single cell oil (SCO) produced by oleaginous yeasts is considered as a sustainable source for biodiesel and oleochemicals since its production does not compete with food or feed and high yields can be obtained from a wide variety of carbon sources, e.g., acetate or lignocellulose. Downstream processing is still costly preventing the broader application of SCO. Direct transesterification of freeze-dried biomass is widely used for analytical purposes and for biodiesel production but it is energy intensive and, therefore, expensive. Additionally, only fatty acid esters are produced limiting the subsequent applications. The harsh conditions applied during direct esterification might also damage high-value polyunsaturated fatty acids. Unfortunately, universal downstream strategies effective for all yeast species do not exist and methods have to be developed for each yeast species due to differences in cell wall composition. Therefore, the aim of this study was to evaluate three industrially relevant cell disruption methods combined with three extraction systems for the SCO extraction of two novel, unconventional oleaginous yeasts, Saitozyma podzolica DSM 27192 and Apiotrichum porosum DSM 27194, based on cell disruption efficiency, lipid yield, and oil quality. Bead milling (BM) and high pressure homogenization (HPH) were effective cell disruption methods in contrast to sonification. By combining HPH (95% cell disruption efficiency) with ethanol-hexane-extraction 46.9 ± 4.4% lipid/CDW of S. podzolica were obtained which was 2.7 times higher than with the least suitable combination (ultrasound + Folch). A. porosum was less affected by cell disruption attempts. Here, the highest disruption efficiency was 74% after BM and the most efficient lipid recovery method was direct acidic transesterification (27.2 ± 0.5% fatty acid methyl esters/CDW) after freeze drying. The study clearly indicates cell disruption is the decisive step for SCO extraction. At disruption efficiencies of >90%, lipids can be extracted at high yields, whereas at lower cell disruption efficiencies, considerable amounts of lipids will not be accessible for extraction regardless of the solvents used. Furthermore, it was shown that hexane-ethanol which is commonly used for extraction of algal lipids is also highly efficient for yeasts.

Tetrahydrobiopterin Plays a Functionally Significant Role in Lipogenesis in the Oleaginous Fungus Mortierella alpina

Tetrahydrobiopterin (BH₄) is well-known as a cofactor of phenylalanine hydroxylase (PAH) and nitric oxide synthase (NOS), but its exact role in lipogenesis is unclear. In this study, the GTP cyclohydrolase I (GTPCH) gene was overexpressed to investigate the role of BH₄ in lipogenesis in oleaginous fungus Mortierella alpina. Transcriptome data analysis reveal that GTPCH expression was upregulated when nitrogen was exhausted, resulting in lipid accumulation. Significant changes were also found in the fatty acid profile of M. alpina grown on medium that contained a GTPCH inhibitor relative to that of M. alpina grown on medium that lacked the inhibitor. GTPCH overexpression in M. alpina (the MA-GTPCH strain) led to a sevenfold increase in BH₄ levels and enhanced cell fatty acid synthesis and poly-unsaturation. Increased levels of nicotinamide adenine dinucleotide phosphate (NADPH) and upregulated expression of NADPH-producing genes in response to enhanced BH₄ levels were also observed, which indicate a novel aspect of the NADPH regulatory mechanism. Increased BH₄ levels also enhanced phenylalanine hydroxylation and nitric oxide synthesis, and the addition of an NOS or a PAH inhibitor in the MA-GTPCH and control strain cultures decreased fatty acid accumulation, NADPH production, and the transcript levels of NADPH-producing genes. Our research suggests an important role of BH₄ in lipogenesis and that the phenylalanine catabolism and arginine-nitric oxide pathways play an integrating role in translating the effects of BH₄ on lipogenesis by regulating the cellular NADPH pool. Thus, our findings provide novel insights into the mechanisms of efficient lipid biosynthesis regulation in oleaginous microorganisms and lay a foundation for the genetic engineering of these organisms to optimize their dietary fat yield.

Recent Advances of CRISPR/Cas9-Based Genetic Engineering and Transcriptional Regulation in Industrial Biology

Industrial biology plays a crucial role in the fields of medicine, health, food, energy, and so on. However, the lack of efficient genetic engineering tools has restricted the rapid development of industrial biology. Recently, the emergence of clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system brought a breakthrough in genome editing technologies due to its high orthogonality, versatility, and efficiency. In this review, we summarized the barriers of CRISPR/Cas9 and corresponding solutions for efficient genetic engineering in industrial microorganisms. In addition, the advances of industrial biology employing the CRISPR/Cas9 system were compared in terms of its application in bacteria, yeast, and filamentous fungi. Furthermore, the cooperation between CRISPR/Cas9 and synthetic biology was discussed to help build complex and programmable gene circuits, which can be used in industrial biotechnology.

Time-resolved multi-omics analysis reveals the role of nutrient stress-induced resource reallocation for TAG accumulation in oleaginous fungus Mortierella alpina

BACKGROUND

Global resource reallocation is an established critical strategy through which organisms deal with environmental stress. The regulation of intracellular lipid storage or utilization is one of the most important strategies for maintaining energy homeostasis and optimizing growth. Oleaginous microorganisms respond to nitrogen deprivation by inducing lipid hyper accumulation; however, the associations between resource allocation and lipid accumulation are poorly understood.

RESULTS

Here, the time-resolved metabolomics, lipidomics, and proteomics data were generated in response to nutrient availability to examine how metabolic alternations induced by nitrogen deprivation drive the triacylglycerols (TAG) accumulation in M. alpina. The subsequent accumulation of TAG under nitrogen deprivation was a consequence of the reallocation of carbon, nitrogen sources, and lipids, rather than an up-regulation of TAG biosynthesis genes. On one hand, nitrogen deprivation induced the down-regulation of isocitrate dehydrogenase level in TCA cycle and redirected glycolytic flux of carbon from amino acid biosynthesis into fatty acids' synthesis; on the other hand, nitrogen deprivation induced the up-regulation of cell autophagy and ubiquitin-mediated protein proteolysis which resulted in a recycling of preformed protein nitrogen and carbon. Combining with the up-regulation of glutamate decarboxylase and succinic semialdehyde dehydrogenase in GABA shunt, and the phosphoenolpyruvate carboxykinase in the central hub involving pyruvate/phosphoenolpyruvate/oxaloacetate, the products from nitrogen-containing compounds degradation were recycled to be intermediates of TCA cycle and be shunted toward de novo biosynthesis of fatty acids. We found that nitrogen deprivation increased the protein level of phospholipase C/D that contributes to degradation of phosphatidylcholine and phosphatidylethanolamine, and supplied acyl chains for TAG biosynthesis pathway. In addition, ATP from substrate phosphorylation was presumed to be a critical factor regulation of the global resource allocation and fatty acids' synthesis rate.

CONCLUSIONS

The present findings offer a panoramic view of resource allocation by M. alpina in response to nutrient stress and revealed a set of intriguing associations between resource reallocation and TAG accumulation. This system-level insight provides a rich resource with which to explore in-depth functional characterization and gain information about the strategic combination of strain development and process integration to achieve optimal lipid productivity under nutrient stress.

Ultra Performance Liquid Chromatography-Q Exactive Orbitrap/Mass Spectrometry-Based Lipidomics Reveals the Influence of Nitrogen Sources on Lipid Biosynthesis of Mortierella alpina

The objective of the present study was to reveal the effects of four types of nitrogen sources (soymeal, yeast extract, KNO₃, and ammonium tartrate) on the lipid metabolism of the oleaginous fungus Mortierella alpina using untargeted lipidomics, targeted fatty acid, and reverse transcription quantitative polymerase chain reaction (RT-qPCR) analysis. Our results showed clear differences in the contents and compositions of lipids between four types of nitrogen sources. Soymeal and ammonium tartrate supplementation favored the accumulation of triglycerides with arachidonic acid (ARA) and C_16-18 fatty acids, respectively. These results were further validated by our targeted fatty acid analysis. RT-qPCR analysis of related genes in M. alpina between the four nitrogen source conditions found that soymeal supplementation dramatically increased the expression of GPAT, ELOVL, and Δ12/Δ6 desaturase. Our findings provided new insights into the regulation of lipid biosynthesis in M. alpina and potential avenues for genetic manipulation and highlighted the importance of an optimal nitrogen source for ARA-rich oil production.

Improved Production of Arachidonic Acid by Combined Pathway Engineering and Synthetic Enzyme Fusion in Yarrowia lipolytica

Arachidonic acid (ARA, C20:4) is a typical ω-6 polyunsaturated fatty acid with special functions. Using Yarrowia lipolytica as an unconventional chassis, we previously showed the performance of the Δ-6 pathway in ARA production. However, a significant increase in the Δ-9 pathway has rarely been reported. Herein, the Δ-9 pathway from Isochrysis galbana was constructed via pathway engineering, allowing us to synthesize ARA at 91.5 mg L^-1. To further improve the ARA titer, novel enzyme fusions of Δ-9 elongase and Δ-8 desaturase were redesigned in special combinations containing different linkers. Finally, with the integrated pathway engineering and synthetic enzyme fusion, a 29% increase in the ARA titer, up to 118.1 mg/L, was achieved using the reconstructed strain RH-4 that harbors the rigid linker (GGGGS). The results show that the combined pathway and protein engineering can significantly facilitate applications of Y. lipolytica.

Role of Adenosine Monophosphate Deaminase during Fatty Acid Accumulation in Oleaginous Fungus Mortierella alpina

In oleaginous micro-organisms, nitrogen limitation activates adenosine monophosphate deaminase (AMPD) and promotes lipogenesis via the inhibition of isocitrate dehydrogenase. We found that the overexpression of homologous AMPD in Mortierella alpina favored lipid synthesis over cell growth. Total fatty acid content in the recombinant strain was 15.0-34.3% higher than that in the control, even though their biomass was similar. During the early fermentation stage, the intracellular AMP level reduced by 40-60%, together with a 1.9-2.7-fold increase in citrate content compared with the control, therefore provided more precursors for fatty acid synthesis. Moreover, the decreased AMP level resulted in metabolic reprogramming, reflected by the blocked TCA cycle and reduction of amino acids, distributing more carbon to lipid synthesis pathways. By coupling the energy balance with lipogenesis, this study provides new insights into cell metabolism under nitrogen-limited conditions and targets the regulation of fatty acid accumulation in oleaginous micro-organisms.

Pathway Grafting for Polyunsaturated Fatty Acids Production in Ashbya gossypii through Golden Gate Rapid Assembly

Here we present a Golden Gate assembly system adapted for the rapid genomic engineering of the industrial fungus Ashbya gossypii. This biocatalyst is an excellent biotechnological chassis for synthetic biology applications and is currently used for the industrial production of riboflavin. Other bioprocesses such as the production of folic acid, nucleosides, amino acids and biolipids have been recently reported in A. gossypii. In this work, an efficient assembly system for the expression of heterologous complex pathways has been designed. The expression platform comprises interchangeable DNA modules, which provides flexibility for the use of different loci for integration, selection markers and regulatory sequences. The functionality of the system has been applied to engineer strains able to synthesize polyunsaturated fatty acids (up to 35% of total fatty acids). The production of the industrially relevant arachidonic, eicosapentanoic and docosahexanoic acids remarks the potential of A. gossypii to produce these functional lipids.

Characterization of an Omega-3 Desaturase From Phytophthora parasitica and Application for Eicosapentaenoic Acid Production in Mortierella alpina

Omega-3 long-chain polyunsaturated fatty acids (LC-PUFAs) have important therapeutic and nutritional benefits in humans. In the biosynthesis pathways of these LC-PUFAs, omega-3 desaturase plays a critical role. In this study, we report a new omega-3 desaturase (PPD17) from Phytophthora parasitica. This desaturase shares high similarities with the known omega-3 desaturases and was expressed in Saccharomyces cerevisiae for the activity and substrate specificity research. The desaturase has a wide omega-6 fatty acid substrate, containing both 18C and 20C fatty acids, and exhibits a strong activity of delta-17 desaturase but a weak activity of delta-15 desaturase. The new desaturase converted the omega-6 arachidonic acid (AA, C20:4) to EPA (an omega-3 LC-PUFA, C20:5) with a substrate conversion rate of 70%. To obtain a high EPA-producing strain, we transformed PPD17 into Mortierella alpina, an AA-producing filamentous fungus. The EPA content of the total fatty acids in reconstruction strains reached 31.5% and was followed by the fermentation optimization of the EPA yield of up to 1.9 g/L. This research characterized a new omega-3 desaturase and provides a possibility of industrially producing EPA using M. alpina.

Enhancing oil production and harvest by combining the marine alga Nannochloropsis oceanica and the oleaginous fungus Mortierella elongata

BACKGROUND

Although microalgal biofuels have potential advantages over conventional fossil fuels, high production costs limit their application in the market. We developed bio-flocculation and incubation methods for the marine alga, Nannochloropsis oceanica CCMP1779, and the oleaginous fungus, Mortierella elongata AG77, resulting in increased oil productivity.

RESULTS

By growing separately and then combining the cells, the M. elongata mycelium could efficiently capture N. oceanica due to an intricate cellular interaction between the two species leading to bio-flocculation. Use of a high-salt culture medium induced accumulation of triacylglycerol (TAG) and enhanced the contents of polyunsaturated fatty acids (PUFAs) including arachidonic acid and docosahexaenoic acid in M. elongata. To increase TAG productivity in the alga, we developed an effective, reduced nitrogen-supply regime based on ammonium in environmental photobioreactors. Under optimized conditions, N. oceanica produced high levels of TAG that could be indirectly monitored by following chlorophyll content. Combining N. oceanica and M. elongata to initiate bio-flocculation yielded high levels of TAG and total fatty acids, with ~ 15 and 22% of total dry weight (DW), respectively, as well as high levels of PUFAs. Genetic engineering of N. oceanica for higher TAG content in nutrient-replete medium was accomplished by overexpressing DGTT5, a gene encoding the type II acyl-CoA:diacylglycerol acyltransferase 5. Combined with bio-flocculation, this approach led to increased production of TAG under nutrient-replete conditions (~ 10% of DW) compared to the wild type (~ 6% of DW).

CONCLUSIONS

The combined use of M. elongata and N. oceanica with available genomes and genetic engineering tools for both species opens up new avenues to improve biofuel productivity and allows for the engineering of polyunsaturated fatty acids.

Heavy ion mutagenesis combined with triclosan screening provides a new strategy for improving the arachidonic acid yield in Mortierella alpina

BACKGROUND

Arachidonic acid (ARA), which is a ω-6 polyunsaturated fatty acid, has a wide range of biological activities and is an essential component of cellular membranes in some human tissues. Mortierella alpina is the best strain for industrial production of ARA. To increase its yield of arachidonic acid, heavy ion beam irradiation mutagenesis of Mortierella alpina was carried out in combination with triclosan and octyl gallate treatment.

RESULTS

The obtained mutant strain F-23 ultimately achieved an ARA yield of 5.26 g L^- 1, which is 3.24 times higher than that of the wild-type strain. In addition, quantitative real-time PCR confirmed that the expression levels of fatty acid synthase (FAS), Δ5-desaturase, Δ6-desaturase, and Δ9-desaturase were all significantly up-regulated in the mutant F-23 strain, especially Δ6- and Δ9-desaturase, which were up-regulated 3- and 2-fold, respectively.

CONCLUSIONS

This study confirmed a feasible mutagenesis breeding strategy for improving ARA production and provided a mutant of Mortierella alpina with high ARA yield.

An Online Respiratory Quotient-Feedback Strategy of Feeding Yeast Extract for Efficient Arachidonic Acid Production by Mortierella alpina

Mortierella alpina (M. alpina) is well known for arachidonic acid (ARA) production. However, low efficiency and unstableness are long existed problems for industrial production of ARA by M. alpina due to the lack of online regulations. The aim of the present work is to develop an online-regulation strategy for efficient and stable ARA production in industry. The strategy was developed in 50 L fermenters and then applied in a 200 m3 fermenter. Results indicated that yeast extract (YE) highly increased cell growth in shake flask, it was then used in bioreactor fermentation by various feeding strategies. Feeding YE to control respiratory quotient (RQ) at 1.1 during 0-48 h and at 1.5 during 48-160 h, dry cell weight, and ARA titer reached 53.1 and 11.49 g/L in 50 L fermenter, which were increased by 79.4 and 36.9% as compared to that without YE feeding, respectively. Then, the online RQ-feedback strategy was applied in 200 m3 bioreactor fermentation and an average ARA titer of 16.82 g/L was obtained from 12 batches, which was 41.0% higher than the control batches. This is the first report on successful application of online RQ-feedback control of YE in ARA production, especially in an industrial scale of 200 m3 fermentation. It could be applied to other industrial production of microbial oil by oleaginous microorganisms.

Arachidonic acid: Physiological roles and potential health benefits - A review

It is time to shift the arachidonic acid (ARA) paradigm from a harm-generating molecule to its status of polyunsaturated fatty acid essential for normal health. ARA is an integral constituent of biological cell membrane, conferring it with fluidity and flexibility, so necessary for the function of all cells, especially in nervous system, skeletal muscle, and immune system. Arachidonic acid is obtained from food or by desaturation and chain elongation of the plant-rich essential fatty acid, linoleic acid. Free ARA modulates the function of ion channels, several receptors and enzymes, via activation as well as inhibition. That explains its fundamental role in the proper function of the brain and muscles and its protective potential against Schistosoma mansoni and S. haematobium infection and tumor initiation, development, and metastasis. Arachidonic acid in cell membranes undergoes reacylation/deacylation cycles, which keep the concentration of free ARA in cells at a very low level and limit ARA availability to oxidation. Metabolites derived from ARA oxidation do not initiate but contribute to inflammation and most importantly lead to the generation of mediators responsible for resolving inflammation and wound healing. Endocannabinoids are oxidation-independent ARA derivatives, critically important for brain reward signaling, motivational processes, emotion, stress responses, pain, and energy balance. Free ARA and metabolites promote and modulate type 2 immune responses, which are critically important in resistance to parasites and allergens insult, directly via action on eosinophils, basophils, and mast cells and indirectly by binding to specific receptors on innate lymphoid cells. In conclusion, the present review advocates the innumerable ARA roles and considerable importance for normal health.

CRISPR/Cas9-based genome editing of the filamentous fungi: the state of the art

In recent years, a variety of genetic tools have been developed and applied to various filamentous fungi, which are widely applied in agriculture and the food industry. However, the low efficiency of gene targeting has for many years hampered studies on functional genomics in this important group of microorganisms. The emergence of CRISPR/Cas9 genome-editing technology has sparked a revolution in genetic research due to its high efficiency, versatility, and easy operation and opened the door for the discovery and exploitation of many new natural products. Although the application of the CRISPR/Cas9 system in filamentous fungi is still in its infancy compared to its common use in E. coli, yeasts, and mammals, the deep development of this system will certainly drive the exploitation of fungal diversity. In this review, we summarize the research progress on CRISPR/Cas9 systems in filamentous fungi and finally highlight further prospects in this area.

Effects of aeration on metabolic profiles of Mortierella alpina during the production of arachidonic acid

To investigate the metabolic regulation against oxygen supply, comparative metabolomics was performed to explore the metabolic responses of Mortierella alpina in the process of arachidonic acid (ARA) production. More than 110 metabolites involved in Embden–Meyerhof–Parnas pathway, pentose phosphate pathway, tricarboxylic acid cycle, inositol phosphate metabolism, fatty acid biosynthesis, and amino acid metabolism were identified by gas chromatography–mass spectrometry. Samples at different aeration rates were clearly distinguished by principal components analysis and partial least squares analysis, indicating that oxygen supply had a profound effect on the metabolism of M. alpina. Eleven major metabolites were identified as potential biomarkers to be primarily responsible for the difference of metabolism. Further study of metabolic changes with the relevant pathways demonstrated that the levels of several intermediate metabolites in relation to central carbon metabolism changed remarkably via both processes and citrate and malate was supposed to play vital roles in polyunsaturated acid (PUFA) synthesis. Increase of myo-inositol and sorbitol were probably for osmo-regulation and redox balance, while enhanced phosphoric acid and pyroglutamic acid were supposed to have function in the activation of signal transduction pathway for stress resistance. The present study provides a novel insight into the metabolic responses of M. alpina to aeration rates and the metabolic characteristics during the ARA fermentation.

Reactive Oxygen Species-Mediated Cellular Stress Response and Lipid Accumulation in Oleaginous Microorganisms: The State of the Art and Future Perspectives

Microbial oils, which are mainly extracted from yeasts, molds, and algae, have been of considerable interest as food additives and biofuel resources due to their high lipid content. While these oleaginous microorganisms generally produce only small amounts of lipids under optimal growth conditions, their lipid accumulation machinery can be induced by environmental stresses, such as nutrient limitation and an inhospitable physical environmental. As common second messengers of many stress factors, reactive oxygen species (ROS) may act as a regulator of cellular responses to extracellular environmental signaling. Furthermore, increasing evidence indicates that ROS may act as a mediator of lipid accumulation, which is associated with dramatic changes in the transcriptome, proteome, and metabolome. However, the specific mechanisms of ROS involvement in the crosstalk between extracellular stress signaling and intracellular lipid synthesis require further investigation. Here, we summarize current knowledge on stress-induced lipid biosynthesis and the putative role of ROS in the control of lipid accumulation in oleaginous microorganisms. Understanding such links may provide guidance for the development of stress-based strategies to enhance microbial lipid production.