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

Metabolic regulation strategies for enhancing microbial docosahexaenoic acid production by Schizochytrium sp

Docosahexaenoic acid (DHA), one of the most important ω-3 long-chain polyunsaturated fatty acids, has attracted great attention in recent years because of its significant health benefits for human beings. Traditionally, DHA is obtained from marine fish oil, but this approach depends on marine fishing and has suffered a dramatic fall in the past few years due to overfishing and climate change, which cannot meet the increasing market demand. Microbial DHA production by oleaginous microorganisms has become the current research hotspot. Schizochytrium sp., a heterotrophic thraustochytrid, has become one of the most promising DHA producers because of its safety, fast growth and high DHA content. However, industrial DHA production by Schizochytrium sp. is severely hindered by the high production cost. Many regulation strategies have been developed to enhance DHA production through fermentation optimization and metabolic regulation. In this review, recent advances in metabolic regulation for enhancing DHA production by Schizochytrium sp. are reviewed, from the aspects of key lipogenic enzymes, precursors, transcription factors, lipid peroxidation, transport of non-esterified DHA and stress environment.

Effect of Heterologous Expression of Key Enzymes Involved in Astaxanthin and Lipid Synthesis on Lipid and Carotenoid Production in Aurantiochytrium sp

Aurantiochytrium sp., a heterotrophic microorganism, has received increasing attention for its high production of polyunsaturated fatty acids and has been widely applied in various industries. This study intended to optimize the carotenoid synthesis pathway in Aurantiochytrium sp. by metabolic engineering to increase the carotenoid content. Multi-sourced key enzyme genes involved in lipid synthesis (LPAAT and DGAT) and astaxanthin synthesis (crtZ and crtW) were selected to construct single-gene expression vectors and transformed into Aurantiochytrium sp. The results showed that the overexpression of LPAAT of Phaeodactylum tricornutum in Aurantiochytrium sp. caused an increase of 39.3% in astaxanthin, 424.7% in β-carotene, 901.8% in canthaxanthin, and 575.9% in lutein, as well as a down-regulation of 15.3% in the fatty acid content. Transcriptomics analysis revealed enhanced expression of genes involved in purine and amino acid metabolism in the transformed strains, and the down-regulation of the citric acid cycle led to an increase in the source of acetyl coenzyme A for the production of fatty acids. This study provides strong experimental evidence to support the application of increasing carotenoid levels in Aurantiochytrium sp.

Development of an enzymatic method for efficient production of DHA-enriched phospholipids through immobilized phospholipase A1 in AOT-water reverse micelles

The demand for omega-3 polyunsaturated fatty acids (PUFAs), particularly docosahexaenoic acid (DHA), has been steadily increasing due to their significant health benefits. Traditional methods for producing DHA-enriched phospholipids often suffer from low efficiency and high costs. In this study, we developed an efficient enzymatic process to prepare phospholipid-DHA, which used immobilized phospholipase A1 to catalyze transesterification in AOT-water reverse micelle systems. Initially, high concentrations of free fatty acids were produced via acid hydrolysis of algae oil followed by crystallization. Among six evaluated reverse micelle systems, one was selected for further optimization. The substrate/enzyme ratio, temperature, reaction time, and water content were optimized using single-factor experiments and response surface methodology. To enhance cost-efficiency and eco-friendly practices, substrate recycling was implemented to maximize substrate utilization. This study established a comprehensive process chain for the preparation of phospholipid-DHA, promoting its industrial production and providing a reference for the production of other phospholipid products.

Polyketide Synthase Acyltransferase Domain Swapping for Enhanced EPA Recognition and Efficient Coproduction of EPA and DHA in Schizochytrium sp

Docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) are important polyunsaturated fatty acids (PUFAs) used as nutritional supplements. The natural EPA content in Schizochytrium sp. is low, and traditional strategies to increase EPA levels often compromise DHA content or lipid accumulation, hindering industrial coproduction. This study aims to modify the PUFA synthase pathway in Schizochytrium sp. to enable high levels of EPA accumulation while maintaining high levels of DHA production. The native acyltransferase (AT) domain in the PKSB subunit was replaced with an EPA-specific AT, increasing the EPA content nearly five-fold (3.94%). Additionally, adding food-grade phenolic compounds to boost EPA accumulation and overexpressing C16 elongase to alleviate lipid synthesis inhibition increased the EPA content from 0.80 to 7.86% in a 5L bioreactor. Ultimately, EPA and DHA titers reached 3.79 and 22.06 g/L, respectively. These findings highlight the potential of Schizochytrium sp. as an efficient cell factory for sustainable EPA and DHA coproduction on an industrial scale.

Lipidomics analysis reveals the effects of Schizochytrium sp. supplementation on the lipid composition of Tan sheep meat

Schizochytrium sp. (SZ) can potentially be employed in nutritional strategies for producing high-quality sheep meat. However, the effects of SZ on the lipid composition of sheep meat are insufficiently understood. In this study, the effects of SZ supplementation on the lipid profile of Tan sheep meat were evaluated using non-targeted lipidomic techniques. Lipidomics analysis revealed 383 differential lipids (DLs) between the SZ and control groups, and there were six metabolic pathways associated with lipids, including glycerophospholipid metabolism, glycerolipid metabolism, α-linolenic acid metabolism, linoleic acid metabolism, glycine, serine and threonine metabolism, and arachidonic acid metabolism (P < 0.05). Glycerophospholipid metabolism was the core pathway of DLs; we found that phosphatidylcholine, phosphatidylserine, and lysophosphatidylcholine were the crucial lipid metabolites of this pathway. Dietary supplementation with SZ increased n-3 polyunsaturated fatty acid (PUFA), C22:6n-3, and C20:5n-3 (P < 0.05), while it decreased C18:0, saturated fatty acid (SFA), and SFA/PUFA (P < 0.05). These results indicate that SZ supplementation induces positive alterations in the lipid profile of Tan sheep meat, which is beneficial to meat quality and sheds valuable insights into the future development of functional lipids in sheep meat.

From lignocellulosic biomass to single cell oil for sustainable biomanufacturing: Current advances and prospects

As global temperatures rise and arid climates intensify, the reserves of Earth's resources and the future development of humankind are under unprecedented pressure. Traditional methods of food production are increasingly inadequate in meeting the demands of human life while remaining environmentally sustainable and resource-efficient. Consequently, the sustainable supply of lipids is expected to become a pivotal area for future food development. Lignocellulose biomass (LB), as the most abundant and cost-effective renewable resource, has garnered significant attention from researchers worldwide. Thus, bioprocessing based on LB is appearing as a sustainable model for mitigating the depletion of energy reserves and reducing carbon footprints. Currently, the transformation of LB primarily focuses on producing biofuels, such as bioethanol, biobutanol, and biodiesel, to address the energy crisis. However, there are limited reports on the production of single cell oil (SCO) from LB. This review, therefore, provides a comprehensive summary of the research progress in lignocellulosic pretreatment. Subsequently, it describes how the capability for lignocellulosic use can be conferred to cells through genetic engineering. Additionally, the current status of saccharification and fermentation of LB is outlined. The article also highlights the advances in synthetic biology aimed at driving the development of oil-producing microorganism (OPM), including genetic transformation, chassis modification, and metabolic pathway optimization. Finally, the limitations currently faced in SCO production from straw are discussed, and future directions for achieving high SCO yields from various perspectives are proposed. This review aims to provide a valuable reference for the industrial application of green SCO production.

Enhancing fatty acid and omega-3 production in Schizochytrium sp. using developed safe-harboring expression system

BACKGROUND

Schizochytrium, a group of eukaryotic marine protists, is an oleaginous strain, making it a highly promising candidate for the production of lipid-derived products such as biofuels and omega-3 fatty acids. However, the insufficient advancement of genetic engineering tools has hindered further advancements. Therefore, the development and application of genetic engineering tools for lipid enhancement are crucial for industrial production.

RESULTS

Transgene expression in Schizochytrium often encounters challenges such as instability due to positional effects. To overcome this, we developed a safe-harbor transgene expression system. Initially, the sfGFP gene was integrated randomly, and high-expressing transformants were identified using fluorescence-activated cell sorting. Notably, HRsite 2, located approximately 3.2 kb upstream of cytochrome c, demonstrated enhanced sfGFP expression and homologous recombination efficiency. We then introduced the 3-ketoacyl-ACP reductase (KR) gene at HRsite 2, resulting in improved lipid and docosahexaenoic acid (DHA) production. Transformants with KR at HRsite 2 exhibited stable growth, increased glucose utilization, and a higher lipid content compared to those with randomly integrated transgenes. Notably, these transformants showed a 25% increase in DHA content compared to the wild-type strain.

CONCLUSION

This study successfully established a robust homologous recombination system in Schizochytrium sp. by identifying a reliable safe harbor site for gene integration. The targeted expression of the KR gene at this site not only enhanced DHA production but also maintained growth and glucose consumption rates, validating the efficacy of the safe-harbor approach. This advancement in synthetic biology and metabolic engineering paves the way for more efficient biotechnological applications in Schizochytrium sp.

Transcriptome analysis reveals the effects of Schizochytrium sp. on the meat quality attributes of Tan lambs

Schizochytrium sp., a feed additive, positively affects the quality of animal meat. In this study, the molecular mechanisms through which dietary Schizochytrium sp. affects the meat quality characteristics of Tan lambs were investigated using transcriptomic techniques. The findings demonstrate that the lambs supplemented with Schizochytrium sp. had a larger loin eye area and a higher average daily gain and intramuscular fat content (P < 0.05). They also had lower drip loss (at 24 and 48 h) and shear force (P < 0.05). Further, 745 genes were differentially expressed between lambs supplemented with Schizochytrium and the control group. Moreover, KEGG pathway analysis showed that the ECM-receptor interaction pathway, which is related to muscle generation and intramuscular fat deposition, was significantly enriched in the lambs administered a diet containing Schizochytrium sp. Herein, we identified some pivotal genes linked to muscular system development and lipid metabolism. Thus, using Schizochytrium sp. may boost the meat quality of Tan lambs by modifying the expression of genes related to hub pathways. The results supply a new basis to determine the molecular mechanisms through which Schizochytrium sp. supplementation regulates the meat quality characteristics of sheep.

Thraustochytrids as a promising source of fatty acids, carotenoids, and sterols: bioactive compound biosynthesis, and modern biotechnology

Thraustochytrids are eukaryotes and obligate marine protists. They are increasingly considered to be a promising feed additive because of their superior and sustainable application in the production of health-benefiting bioactive compounds, such as fatty acids, carotenoids, and sterols. Moreover, the increasing demand makes it critical to rationally design the targeted products by engineering industrial strains. In this review, bioactive compounds accumulated in thraustochytrids were comprehensively evaluated according to their chemical structure, properties, and physiological function. Metabolic networks and biosynthetic pathways of fatty acids, carotenoids, and sterols were methodically summarized. Further, stress-based strategies used in thraustochytrids were reviewed to explore the potential methodologies for enhancing specific product yields. There are internal relationships between the biosynthesis of fatty acids, carotenoids, and sterols in thraustochytrids since they share some branches of the synthetic routes with some intermediate substrates in common. Although there are classic synthesis pathways presented in the previous research, the metabolic flow of how these compounds are being synthesized in thraustochytrids still remains uncovered. Further, combined with omics technologies to deeply understand the mechanism and effects of different stresses is necessary, which could provide guidance for genetic engineering. While gene-editing technology has allowed targeted gene knock-in and knock-outs in thraustochytrids, efficient gene editing is still required. This critical review will provide comprehensive information to benefit boosting the commercial productivity of specific bioactive substances by thraustochytrids.

Towards Lipid from Microalgae: Products, Biosynthesis, and Genetic Engineering

Microalgae can convert carbon dioxide into organic matter through photosynthesis. Thus, they are considered as an environment-friendly and efficient cell chassis for biologically active metabolites. Microalgal lipids are a class of organic compounds that can be used as raw materials for food, feed, cosmetics, healthcare products, bioenergy, etc., with tremendous potential for commercialization. In this review, we summarized the commercial lipid products from eukaryotic microalgae, and updated the mechanisms of lipid synthesis in microalgae. Moreover, we reviewed the enhancement of lipids, triglycerides, polyunsaturated fatty acids, pigments, and terpenes in microalgae via environmental induction and/or metabolic engineering in the past five years. Collectively, we provided a comprehensive overview of the products, biosynthesis, induced strategies and genetic engineering in microalgal lipids. Meanwhile, the outlook has been presented for the development of microalgal lipids industries, emphasizing the significance of the accurate analysis of lipid bioactivity, as well as the high-throughput screening of microalgae with specific lipids.

Characterization of Three Types of Elongases from Different Fungi and Site-Directed Mutagenesis

Fatty acid elongases play crucial roles in synthesizing long-chain polyunsaturated fatty acids. Identifying more efficient elongases is essential for enhancing oleaginous microorganisms to produce high yields of target products. We characterized three elongases that were identified with distinct specificities: McELO from Mucor circinelloides, PrELO from Phytophthora ramorum, and PsELO from Phytophthora sojae. Heterologous expression in Saccharomyces cerevisiae showed that McELO preferentially elongates C16 to C18 fatty acids, PrELO targets Δ6 polyunsaturated fatty acids, and PsELO uses long chain saturated fatty acids as substrates. McELO and PrELO exhibited more homology, potentially enabling fatty acid composition remodeling and enhanced LC-PUFAs production in oleaginous microorganisms. Site-directed mutagenesis of conserved amino acids across elongase types identified residues essential for activity, supported by molecular docking. Alanine substitution of conserved polar residues led to enzyme inactivation, underscoring their importance in the condensation reaction. Our findings offer promising elongase candidates for polyunsaturated fatty acid production, contributing to the bioindustry's sustainable development.

Knockout of a PLD gene in Schizochytrium limacinum SR21 enhances docosahexaenoic acid accumulation by modulation of the phospholipid profile

BACKGROUND

The hydrolysis and transphosphatidylation of phospholipase D (PLD) play important roles in the interconversion of phospholipids (PLs), which has been shown to profoundly impact lipid metabolism in plants. In this study, the effect of the PLD1 gene of Schizochytrium limacinum SR21 (S. limacinum SR21) on lipid metabolism was investigated.

RESULTS

PLD1 knockout had little impact on cell growth and lipid production, but it significantly improved the percentage of polyunsaturated fatty acids in lipids, of which docosahexaenoic acid (DHA) content increased by 13.3% compared to the wild-type strain. Phospholipomics and real-time quantitative PCR analysis revealed the knockout of PLD1 reduced the interexchange and increased de novo synthesis of PLs, which altered the composition of PLs, accompanied by a final decrease in phosphatidylcholine (PC) and an increase in phosphatidylinositol, lysophosphatidylcholine, and phosphatidic acid levels. PLD1 knockout also increased DHA content in triglycerides (TAGs) and decreased it in PLs.

CONCLUSIONS

These results indicate that PLD1 mainly performs the transphosphatidylation activity in S. limacinum SR21, and its knockout promotes the migration of DHA from PLs to TAGs, which is conducive to DHA accumulation and storage in TAGs via an acyl CoA-independent pathway. This study provides a novel approach for identifying the mechanism of DHA accumulation and metabolic regulation strategies for DHA production in S. limacinum SR21.

Microalgae biofuels: illuminating the path to a sustainable future amidst challenges and opportunities

The development of microalgal biofuels is of significant importance in advancing the energy transition, alleviating food pressure, preserving the natural environment, and addressing climate change. Numerous countries and regions across the globe have conducted extensive research and strategic planning on microalgal bioenergy, investing significant funds and manpower into this field. However, the microalgae biofuel industry has faced a downturn due to the constraints of high costs. In the past decade, with the development of new strains, technologies, and equipment, the feasibility of large-scale production of microalgae biofuel should be re-evaluated. Here, we have gathered research results from the past decade regarding microalgae biofuel production, providing insights into the opportunities and challenges faced by this industry from the perspectives of microalgae selection, modification, and cultivation. In this review, we suggest that highly adaptable microalgae are the preferred choice for large-scale biofuel production, especially strains that can utilize high concentrations of inorganic carbon sources and possess stress resistance. The use of omics technologies and genetic editing has greatly enhanced lipid accumulation in microalgae. However, the associated risks have constrained the feasibility of large-scale outdoor cultivation. Therefore, the relatively controllable cultivation method of photobioreactors (PBRs) has made it the mainstream approach for microalgae biofuel production. Moreover, adjusting the performance and parameters of PBRs can also enhance lipid accumulation in microalgae. In the future, given the relentless escalation in demand for sustainable energy sources, microalgae biofuels should be deemed a pivotal constituent of national energy planning, particularly in the case of China. The advancement of synthetic biology helps reduce the risks associated with genetically modified (GM) microalgae and enhances the economic viability of their biofuel production.

bZIP transcription factor FabR: Redox-dependent mechanism controlling docosahexaenoic acid biosynthesis and H2O2 stress response in Schizochytrium sp

Schizochytrium sp. is an important industrial strain for commercial production of docosahexaenoic acid (DHA), which plays essential physiological roles in infant development and human health. The regulatory network for DHA biosynthesis and lipid accumulation in Schizochytrium remains poorly understood. FabR (fatty acid biosynthesis repressor), a basic leucine zipper (bZIP) transcription factor, was transcriptionally downregulated under low-nitrogen condition. Deletion of fabR gene (mutant ΔfabR) increased production of total lipids and DHA by 30.1% and 46.5%, respectively. ΔfabR displayed H2O2 stress resistance higher than that of parental strain or complementation strain CfabR. FabR bound specifically to 7-bp pseudo-palindromic sequence 5'-ATTSAAT-3' in upstream regions and repressed transcription of fatty acid biosynthesis genes (acl, fas, pfa) and antioxidant defense genes (cat, sod1, sod2, gpx). DNA binding activity of FabR was regulated in a redox-dependent manner. Under oxidative condition, FabR forms intermolecular disulfide bonds between two Cys46 residues of dimers; its DNA binding activity is thereby lost, and the transcription of its target genes is enhanced through derepression. Our findings clarify the redox-dependent mechanism that modulates FabR activity governing lipid and DHA biosynthesis and H2O2 stress response in Schizochytrium.

Overexpression of S-R enhances the accumulation of biomass, fatty acids, and β-carotene in Schizochytrium

Strategies for enhancing biomass accumulation and increasing the production of fatty acids and β-carotene in Schizochytrium are hindered by the lack of suitable targets. In this study, S-R, a RING (really interesting new gene) finger domain-containing protein, was identified in Schizochytrium, with homologs found in the family Thraustochytriaceae. Transgenic strains overexpressing S-R showed a minor improvement in cell growth but a significant increase in total fatty acids content by 1.29- to 1.36-fold. Almost all individual saturated fatty acids exhibited significant increases, with the greatest increase observed in the C14:0 content, by 1.52- to 1.78-fold. Additionally, the β-carotene content of S-R strains was significantly upregulated. Overexpression of s-r conferred hypersaline tolerance in Schizochytrium, with a significant increase in dry cell weight, total fatty acids and β-carotene, likely due to the upregulation of glycerol and proline. This study provides a feasible strategy to engineer Thraustochytriaceae for efficient biomass and biochemical production.

Simultaneous production of high-value lipids in Schizochytrium sp. by synergism of chemical modulators

The study focuses on the simultaneous improvement of biomass, lipid, and docosahexaenoic acid (DHA) productivities in a single reactor using modulator control strategies. The efficacy of three different biochemical modulators, sesamol (Ses), 6-benzylaminopurine (6-BAP), and ethylenediaminetetraacetic acid (EDTA), as potential stimulants in augmenting the biomass, lipid, and DHA production of Schizochytrium sp. MTCC 5890 was elucidated. After 48 h of cultivation, among tested modulators, the individual supplementation of 6-BAP and Ses showed improvement in biomass, lipid, and DHA accumulation by 28.2%, 56.1%, and 87.2% and 21.7%, 47.9%, and 91%, respectively, over the non-supplemented group. In addition, the cooperative effect of selected concentrations, i.e., 10 mgL-1 6-BAP and 200 mgL-1 Ses, further increased the productivities of biomass of 13.5 gL-1d-1 ± 0.66, lipid of 7.4 gL-1d-1 ± 0.69, and DHA of 3.2 gL-1d-1 ± 1.09 representing 8%, 39%, and 69% increase over the individual addition of 6-BAP or Ses, respectively, in batch culture. Supplementation with 6-BAP + Ses at 12 h of time point eventually increased the lipid yield to 15.6 ± 0.42 gL-1 from 7.88 ± 0.31 gL-1 (control) and DHA yield to 6.4 ± 0.11 gL-1 from 2.23 ± 0.09 gL-1 (control), respectively. Furthermore, the process was optimized in continuous culture supplemented with 6-BAP + Ses for enhanced productivities. Continuous culture resulted in maximum biomass (2.04 ± 1.12 gL-1 day-1), lipid (1.0 ± 0.73 gL-1 day-1), and DHA (0.386 ± 0.22 gL-1 day-1) productivities, which were higher as compared with the batch and fed-batch processes by 26 ± 1.21%, 22 ± 1.01%, and 21 ± 0.98% and 24 ± 0.45%, 16 ± 0.38%, and 14 ± 0.12%, respectively. This work represents the potential application of the combined effect of modulators for the simultaneous enhancement of biomass production and lipid and DHA productivities. KEY POINTS: • The cumulative study of 6-BAP and sesamol proved to be more efficient in the simultaneous production of biomass, lipid, and DHA in a single reactor. • Addition of a combination of 6-BAP + Ses remarkably increased the biomass, lipid, and DHA productivities in tandem in continuous culture.

Development of Schizochytrium sp. strain HS01 with high-DHA and low-saturated fatty acids production by multi-pronged adaptive evolution

PURPOSE

Docosahexaenoic acid (DHA) is an important omega-3 unsaturated fatty acid and has been widely applied in medicine, food additives, and feed ingredients. The fermentative production of DHA using microorganisms, including Schizochytrium sp., attracted much attention due to its high production efficiency and environment friendly properties. An efficient laboratory evolution approach was used to improve the strain's performance in this study.

METHODS

A multi-pronged laboratory evolution approach was applied to evolve high-yield DHA-producing Schizochytrium strain. We further employed comparative transcriptional analysis to identify transcriptional changes between the screened strain HS01 and its parent strain GS00.

RESULTS

After multiple generations of ALE, a strain HS01 with higher DHA content and lower saturated fatty acids content was obtained. Low nitrogen conditions were important for enhancing DHA biosynthesis in HS01. The comparative transcriptional analysis results indicated that during the fermentation process of HS01, the expression of key enzymes in the glycolysis, the pentose phosphate pathway and the tricarboxylic acid cycle were up-regulated, while the expression of polyketide synthase genes and fatty acid synthesis genes were similar to those in GS00.

CONCLUSION

The results suggest that the improved DHA production capacity of HS01 is not due to enhancement of the DHA biosynthesis pathway, but rather related to modulation of central metabolism pathways.

Enhancing the biomass and docosahexaenoic acid-rich lipid accumulation of Schizochytrium sp. in propionate wastewater

In order to find a more effective way to obtain docosahexaenoic acid (DHA) rich lipid from Schizochytrium sp., a widespread propionate wastewater (PW) is used. PW is a common industrial and domestic wastewater, and transforming it into valuable products is a potential treatment method. Schizochytrium sp. is a rapidly growing oleaginous organism, which has been used commercially for DHA production. Herein, PW is completely used for DHA production by Schizochytrium sp. by genetic engineering and fermentation optimization, which can alleviate the increasingly tense demand for water resources and environmental pollution caused by industrial wastewater. Firstly, the methylmalonyl-CoA mutase (MCM) was overexpressed in Schizochytrium sp. to enhance the metabolism of propionate, then the engineered strain of overexpressed MCM (OMCM) can effectively use propionate. Then, the effects of PW with different concentration of propionate were investigated, and results showed that OMCM can completely replace clean water with PW containing 5 g L-1 propionate. Furthermore, in the fed-batch fermentation, the OMCM obtained the highest biomass of 113.4 g L-1 and lipid yield of 64.4 g L-1 in PW condition, which is 26.8% and 51.7% higher than that of wild type (WT) in PW condition. Moreover, to verify why overexpression of MCM can promote DHA and lipid accumulation, the comparative metabolomics, ATP production level, the antioxidant system, and the transcription of key genes were investigated. Results showed that ATP induced by PW condition could drive the synthesis of DHA, and remarkably improve the antioxidant capacity of cells by enhancing the carotenoids production. Therefore, PW can be used as an effective and economical substrate and water source for Schizochytrium sp. to accumulate biomass and DHA.

Efficient Biosynthesis of Odd-Chain Fatty Acids via Regulating the Supply and Consumption of Propionyl-CoA in Schizochytrium sp

Odd chain fatty acids (OCFAs) are high-value-added compounds with great application in the field of food and medicine. As an oleaginous microorganism, Schizochytrium sp. has the potential to produce OCFAs efficiently. Propionyl-CoA is used as a precursor to synthesize OCFAs through the fatty acid synthetase (FAS) pathway, so its flow direction determines the yield of OCFAs. Here, different substrates were assessed to promote propionyl-CoA supply for OCFA accumulation. Moreover, the methylmalonyl-CoA mutase (MCM) was identified as the key gene responsible for propionyl-CoA consumption, which promotes the propionyl-CoA to enter into the tricarboxylic acid cycle rather than the FAS pathway. As one of the classic B₁₂-dependent enzymes, the activity of MCM can be inhibited in the absence of B₁₂. As expected, the OCFA accumulation was greatly increased. However, the removal of B₁₂ caused growth limitation. Furthermore, the MCM was knocked out to block the consumption of propionyl-CoA and to maintain cell growth; results showed that the engineered strain achieved the OCFAs titer of 2.82 g/L, which is 5.76-fold that of wild type. Last, a fed-batch co-feeding strategy was developed, resulting in the highest reported OCFAs titer of 6.82 g/L. This study provides guidance for the microbial production of OCFAs.

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.

Microbial production of odd-chain fatty acids

Odd-chain fatty acids (OcFAs) and their derivatives have attracted much attention due to their beneficial physiological effects and their potential to be alternatives to advanced fuels. However, cells naturally produce even-chain fatty acids (EcFAs) with negligible OcFAs. In the process of biosynthesis of fatty acids (FAs), the acetyl-CoA serves as the starter unit for EcFAs, and propionyl-CoA works as the starter unit for OcFAs. The lack of sufficient propionyl-CoA, the precursor, is usually regarded as the main restriction for large-scale bioproduction of OcFAs. In recent years, synthetic biology strategies have been used to modify several microorganisms to produce more propionyl-CoA that would enable an efficient biosynthesis of OcFAs. This review discusses several reported and potential metabolic pathways for propionyl-CoA biosynthesis, followed by advances in engineering several cell factories for OcFAs production. Finally, trends and challenges of synthetic biology driven OcFAs production are discussed.

De novo bio-production of odd-chain fatty acids in Saccharomyces cerevisiae through a synthetic pathway via 3-hydroxypropionic acid

Odd-chain fatty acids (OCFAs) and their derivatives have attracted increasing attention due to their wide applications in the chemical, fuel, and pharmaceutical industry. However, most natural fatty acids are even-chained, and OCFAs are rare. In this work, a novel pathway was designed and established for de novo synthesis of OCFAs via 3-hydroxypropionic acid (3-HP) as the intermediate in Saccharomyces cerevisiae. First, the OCFAs biosynthesis pathway from 3-HP was confirmed, followed by an optimization of the precursor 3-HP. After combining these strategies, a de novo production of OCFAs at 74.8 mg/L was achieved, and the percentage of OCFAs in total lipids reached 20.3%, reaching the highest ratio of de novo-produced OCFAs. Of the OCFAs produced by the engineered strain, heptadecenoic acid (C17:1) and heptadecanoic acid (C17:0) accounted for 12.1% and 7.6% in total lipid content, respectively. This work provides a new and promising pathway for the de novo bio-production of OCFAs.

Function of the Polyketide Synthase Domains of Schizochytrium sp. on Fatty Acid Synthesis in Yarrowia lipolytica

It is well known that polyunsaturated fatty acids (PUFAs) in Schizochytrium sp. are mainly synthesized via the polyketide synthase (PKS) pathway. However, the specific mechanism of PKS in fatty acid synthesis is still unclear. In this work, the functions of ORFA, ORFB, ORFC, and their individual functional domain genes on fatty acid synthesis were investigated through heterologous expression in Yarrowia lipolytica. The results showed that the expression of ORFA, ORFB, ORFC, and their individual functional domains all led to the increase of the very long-chain PUFA content (mainly eicosapentaenoic acid). Furthermore, the transcriptomic analysis showed that except for the 3-ketoacyl-ACP synthase (KS) domain of ORFB, the expression of an individual functional domain, including malonyl-CoA: ACP acyltransferase, 3-hydroxyacyl-ACP dehydratase (DH), 3-ketoacyl-ACP reductase, and KS domains of ORFA, acyltransferase domains of ORFB, and two DH domains of ORFC resulted in upregulation of the tricarboxylic acid cycle and pentose phosphate pathway, downregulation of the triacylglycerol biosynthesis, fatty acid synthesis pathway, and β-oxidation in Yarrowia lipolytica. These results provide a theoretical basis for revealing the function of PKS in fatty acid synthesis in Y. lipolytica and elucidate the possible mechanism for PUFA biosynthesis.

Elucidation of sterol biosynthesis pathway and its co-regulation with fatty acid biosynthesis in the oleaginous marine protist Schizochytrium sp

Sterols constitute vital structural and regulatory components of eukaryotic cells. In the oleaginous microorganism Schizochytrium sp. S31, the sterol biosynthetic pathway primarily produces cholesterol, stigmasterol, lanosterol, and cycloartenol. However, the sterol biosynthesis pathway and its functional roles in Schizochytrium remain unidentified. Through Schizochytrium genomic data mining and a chemical biology approach, we first in silico elucidated the mevalonate and sterol biosynthesis pathways of Schizochytrium. The results showed that owing to the lack of plastids in Schizochytrium, it is likely to use the mevalonate pathway as the terpenoid backbone pathway to supply isopentenyl diphosphate for the synthesis of sterols, similar to that in fungi and animals. In addition, our analysis revealed a chimeric organization of the Schizochytrium sterol biosynthesis pathway, which possesses features of both algae and animal pathways. Temporal tracking of sterol profiles reveals that sterols play important roles in Schizochytrium growth, carotenoid synthesis, and fatty acid synthesis. Furthermore, the dynamics of fatty acid and transcription levels of genes involved in fatty acid upon chemical inhibitor-induced sterol inhibition reveal possible co-regulation of sterol synthesis and fatty acid synthesis, as the inhibition of sterol synthesis could promote the accumulation of fatty acid in Schizochytrium. Sterol and carotenoid metabolisms are also found possibly co-regulated, as the inhibition of sterols led to decreased carotenoid synthesis through down-regulating the gene HMGR and crtIBY in Schizochytrium. Together, elucidation of the Schizochytrium sterol biosynthesis pathway and its co-regulation with fatty acid synthesis lay the essential foundation for engineering Schizochytrium for the sustainable production of lipids and high-value chemicals.

Modulating DHA-Producing Schizochytrium sp. toward Astaxanthin Biosynthesis via a Seamless Genome Editing System

Schizochytrium sp. is commercially used for the production of docosahexaenoic acid (DHA). Some strains of Schizochytrium sp. are also known to produce low amounts of carotenoids, including astaxanthin and β-carotene. In order to enhance the production of astaxanthin in Schizochytrium sp., we established a seamless genome editing system with a dual selection marker for rapid screening of positive transformants. By using this system, we strengthened the endogenous mevalonate pathway, enhanced the supply of geranylgeranyl diphosphate and β-carotene, upregulated endogenous β-carotene hydroxylase, and introduced the algal astaxanthin pathway. The highest astaxanthin production in the engineered Schizochytrium sp. was achieved at 8.1 mg/L (307.1 μg/g dry cell weight) under shake-flask conditions, which was 2.6-fold higher than that in the start strain. Meanwhile, the percentage of DHA to total fatty acids was not obviously affected. We then eliminated the dual selection marker by using the Cre-loxP recombination system, and the engineered strain was ready for iterative editing. The developed system could be applied to seamlessly engineer DHA-producing Schizochytrium sp. toward astaxanthin and other value-added terpenoids, which broadens the application of this strain.

Functional analysis of the dehydratase domains of the PUFA synthase from Emiliania huxleyi in Escherichia coli and Arabidopsis thaliana

BACKGROUND

Polyunsaturated fatty acid (PUFA) synthase is a multi-domain mega-enzyme that effectively synthesizes a series of PUFAs in marine microorganisms. The dehydratase (DH) domain of a PUFA synthase plays a crucial role in double bond positioning in fatty acids. Sequencing results of the coccolithophore Emiliania huxleyi (E. huxleyi, Eh) indicated that this species contains a PUFA synthase with multiple DH domains. Therefore, the current study, sought to define the functions of these DH domains (EhDHs), by cloning and overexpressing the genes encoding FabA-like EhDHs in Escherichia coli (E. coli) and Arabidopsis thaliana (A. thaliana).

RESULTS

A complementation test showed that the two FabA-like DH domains could restore DH function in a temperature-sensitive (Ts) mutant. Meanwhile, overexpression of FabA-like EhDH₁ and EhDH₂ domains increased the production of unsaturated fatty acids (UFAs) in recombinant E. coli by 43.5-32.9%, respectively. Site-directed mutagenesis analysis confirmed the authenticity of active-site residues in these domains. Moreover, the expression of tandem EhDH₁-DH₂ in A. thaliana altered the fatty acids content, seed weight, and germination rate.

CONCLUSIONS

The two FabA-like DH domains in the E. huxleyi PUFA synthase function as 3-hydroxyacyl-acyl carrier protein dehydratase in E. coli. The expression of these domains in E. coli and A. thaliana can alter the fatty acid profile in E. coli and increase the seed lipid content and germination rate in A. thaliana. Hence, introduction of DH domains controlling the dehydration process of fatty acid biosynthesis in plants might offer a new strategy to increase oil production in oilseed plants.

Deciphering and engineering the polyunsaturated fatty acid synthase pathway from eukaryotic microorganisms

Polyunsaturated fatty acids (PUFAs) are important nutrients that play important roles in human health. In eukaryotes, PUFAs can be de novo synthesized through two independent biosynthetic pathways: the desaturase/elongase pathway and the PUFA synthase pathway. Among them, PUFAs synthesized through the PUFA synthase pathway typically have few byproducts and require fewer reduction equivalents. In the past 2 decades, numerous studies have been carried out to identify, analyze and engineer PUFA synthases from eukaryotes. These studies showed both similarities and differences between the eukaryotic PUFA synthase pathways and those well studied in prokaryotes. For example, eukaryotic PUFA synthases contain the same domain types as those in prokaryotic PUFA synthases, but the number and arrangement of several domains are different; the basic functions of same-type domains are similar, but the properties and catalytic activities of these domains are somewhat different. To further utilize the PUFA synthase pathway in microbial cell factories and improve the productivity of PUFAs, many challenges still need to be addressed, such as incompletely elucidated PUFA synthesis mechanisms and the difficult genetic manipulation of eukaryotic hosts. In this review, we provide an updated introduction to the eukaryotic PUFA synthase pathway, summarize the functions of domains and propose the possible mechanisms of the PUFA synthesis process, and then provide future research directions to further elucidate and engineer the eukaryotic PUFA synthase pathway for the maximal benefits of humans.

Significance of mitochondrial fatty acid β-oxidation for the survivability of Aurantiochytrium limacinum ATCC MYA-1381 during sugar starvation

Thraustochytrids are marine protists that accumulate large amounts of palmitic acid and docosahexaenoic acid in lipid droplets. Random insertional mutagenesis was adopted for Aurantiochytrium limacinum ATCC MYA-1381 to search for genes that regulate lipid metabolism in thraustochytrids. A mutant strain, M17, was selected because of its significant decrease in myristic acid, palmitic acid, and triacylglycerol contents and cell growth defect. Genome analysis revealed that the gene encoding for mitochondrial electron-transfer flavoprotein ubiquinone oxidoreductase (ETFQO) was lacking in the M17 strain. This mutant strain exhibited a growth defect at the stationary phase, possibly due to stagnation of mitochondrial fatty acid β-oxidation and branched-chain amino acid degradation, both of which were caused by lack of ETFQO. This study shows the usability of random insertional mutagenesis to obtain mutants of lipid metabolism in A. limacinum and clarifies that ETFQO is integral for survival under sugar starvation in A. limacinum.

Investigating the Bioconversion Potential of Volatile Fatty Acids: Use of Oleaginous Yeasts Rhodosporidium toruloides and Cryptococcus curvatus towards the Sustainable Production of Biodiesel and Odd-Chain Fatty Acids

Oleaginous yeasts have attracted increasing scientific interest as single cell oil (SCO) producers. SCO can be used as a fossil-free fuel substitute, but also as a source of rarely found odd-chain fatty acids (OCFAs), such as C15, C17, and C25 fatty acids which have a wide range of nutritional and biological applications. Volatile fatty acids (VFAs) have gained interest as sustainable carbon source for yeasts. This study aims to improve current knowledge on yeast species that yield high amounts of SCO using VFAs as a carbon source. Specifically, the growth of the promising yeasts Cryptococcus curvatus and Rhodotorula toruloides was evaluated on individual VFAs, such as acetic, propionic, and butyric acid. C. curvatus proved to be more tolerant in higher concentrations of VFAs (up to 60 g/L), while butyric acid favored biomass and lipid conversion (0.65 and 0.23 g/gsubstrate, respectively). For R. toruloides, butyric acid favored biomass conversion (0.48 g/gsubstrate), but lipid conversion was favored using acetic acid, instead (0.14 g/gsubstrate). Propionic acid induced the formation of OCFAs, which yielded higher amounts for C. curvatus (up to 2.17 g/L). VFAs derived from the anaerobic digestion of brewer’s spent grain were tested as a cost-competitive carbon source and illustrated the significance of the combination of different VFAs in the quality of the produced SCO, by improving the biodiesel properties and OCFAs production.

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.

Strategic Development of Aurantiochytrium sp. Mutants With Superior Oxidative Stress Tolerance and Glucose-6-Phosphate Dehydrogenase Activity for Enhanced DHA Production Through Plasma Mutagenesis Coupled With Chemical Screening

Thraustochytrids, such as Aurantiochytrium and Schizochytrium, have been shown as a promising sustainable alternative to fish oil due to its ability to accumulate a high level of docosahexaenoic acid (DHA) from its total fatty acids. However, the low DHA volumetric yield by most of the wild type (WT) strain of thraustochytrids which probably be caused by the low oxidative stress tolerance as well as a limited supply of key precursors for DHA biosynthesis has restricted its application for industrial application. Thus, to enhance the DHA production, we aimed to generate Aurantiochytrium SW1 mutant with high tolerance toward oxidative stress and high glucose-6 phosphate dehydrogenase (G6PDH) activities through strategic plasma mutagenesis coupled with chemical screening. The WT strain (Aurantiochytrium sp. SW1) was initially exposed to plasma radiation and was further challenged with zeocin and polydatin, generating a mutant (YHPM1) with a 30, 65, and 80% higher overall biomass, lipid, and DHA production in comparison with the parental strains, respectively. Further analysis showed that the superior growth, lipid, and DHA biosynthesis of the YHMP1 were attributed not only to the higher G6PDH and enzymes involved in the oxidative defense such as superoxide dismutase (SOD) and catalase (CAT) but also to other key metabolic enzymes involved in lipid biosynthesis. This study provides an effective approach in developing the Aurantiochytrium sp. mutant with superior DHA production capacity that has the potential for industrial applications.

Production of Docosahexaenoic Acid and Odd-Chain Fatty Acids by Microalgae Schizochytrium limacinum Grown on Waste-Derived Volatile Fatty Acids

Heterotrophic microalgae are recognized as a source of bioactive compounds. However, there are still some drawbacks for their use at an industrial scale associated with the high cost of glucose, the main carbon source in heterotrophic cultures. In recent years, significant efforts have been made to investigate more sustainable carbon sources to produce biomass. In this study, the capacity of Schizochytrium limacinum to grow on waste-derived volatile fatty acids and the effect that their use produces on biomass and fatty acids profiles were investigated. Acetic, propionic, butyric, valeric and caproic acid were evaluated independently, as well as in a synthetic mixture (VFA). The use of acetic and butyric resulted in a good biomass productivity, while the use of valeric and propionic acid resulted in higher content of odd-chain fatty acids (OCFA), increasingly investigated due to their potential benefits for human health. The use of industrial waste-derived VFA as a potential carbon source was validated through the utilization of biowaste derived effluents from a volatile fatty acid platform. The biomass produced was of 18.5 g/L, 54.0% lipids, 46.3% docosahexaenoic acid (DHA) and 25.0% OCFA, concluding that waste derived VFA can produce DHA and OCFA in a suitable ratio of DHA/OCFA with potential industrial applications.

Zinc finger protein LipR represses docosahexaenoic acid and lipid biosynthesis in Schizochytrium sp

The heterotrophic marine microalgae Schizochytrium sp. is an important industrial producer of docosahexaenoic acid (DHA). Increased production of DHA and lipids in Schizochytrium sp. have been achieved by standard fermentation optimization and metabolic engineering methods; however, regulatory mechanisms for DHA and lipid biosynthesis remain unknown. In this study, the C2H2 zinc finger protein LipR was identified in Schizochytrium sp. ATCC20888 by transcriptional analysis. Deletion of the lipR gene significantly (p< 0.001) increased production of total lipids and DHA by (respectively) 33% and 48%. LipR repressed DHA and lipid production by directly inhibiting transcription of polyunsaturated fatty acid (PUFA) and fatty acid synthase (FAS) genes (pfa1, pfa2, pfa3, fas). Specific binding of LipR to 9-bp recognition sequence 5'-(C/A)(A/G)CCATCTT-3' in upstream regions of target genes was demonstrated by electrophoretic mobility shift assays (EMSAs) and DNase I footprinting assays. Expression of several key genes (acc, acl, ampD, fabD, mae, zwf, dga1) related to levels of precursors and NADPH, and to triacylglycerol storage rate, were also directly repressed by LipR. Our findings, taken together, indicate that the evolutionarily unique regulator LipR is an essential repressor of DHA and saturated fatty acid biosynthesis in Schizochytrium sp. Importance Regulatory mechanisms for DHA and saturated fatty acid biosynthesis in the heterotrophic marine microalgae Schizochytrium sp. are unclear. We demonstrate here that deletion of the gene (lipR) encoding the C2H2 zinc finger protein LipR promotes DHA and saturated fatty acid production in this genus. LipR acts as a key repressor of such production by binding to 9-bp consensus sequence 5'-(C/A)(A/G)CCATCTT-3' in the upstream regions of polyunsaturated fatty acid and fatty acid synthase genes (pfa1, pfa2, pfa3, fas), and genes related to levels of precursors and NADPH (acc, acl, ampD, fabD, mae, zwf), and to triacylglycerol storage rate (dga1). This is the first demonstration that a regulator inhibits synthesis of DHA and lipids in Schizochytrium sp. by directly controlling transcription of PUFA synthase and fas genes. Manipulation of the lipR gene provides a potential strategy for enhancing accumulation of polyunsaturated fatty acids and lipids in thraustochytrids.

Microalgal metabolic engineering strategies for the production of fuels and chemicals

Microalgae are promising sustainable resources because of their ability to convert CO₂ into biofuels and chemicals directly. However, the industrial production and economic feasibility of microalgal bioproducts are still limited. As such, metabolic engineering approaches have been undertaken to enhance the productivities of microalgal bioproducts. In the last decade, impressive advances in microalgae metabolic engineering have been made by developing genetic engineering tools and multi-omics analysis. This review presents comprehensive microalgal metabolic pathways and metabolic engineering strategies for producing lipids, long chain-polyunsaturated fatty acids, terpenoids, and carotenoids. Additionally, promising metabolic engineering approaches specific to target products are summarized. Finally, this review discusses current challenges and provides future perspectives for the effective production of chemicals and fuels via microalgal metabolic engineering.

Development of an Efficient Gene Editing Tool in Schizochytrium sp. and Improving Its Lipid and Terpenoid Biosynthesis

Schizochytrium sp. HX-308 is a marine microalga with fast growth and high lipid content, which has potential as microbial cell factories for lipid compound biosynthesis. It is significant to develop efficient genetic editing tool and discover molecular target in Schizochytrium sp. HX-308 for lipid compound biosynthesis. In this study, we developed an efficient gene editing tool in HX-308 which was mediated by Agrobacterium tumefaciens AGL-1. Results showed that the random integration efficiency reached 100%, and the homologous recombination efficiency reached about 30%. Furthermore, the metabolic pathway of lipid and terpenoid biosynthesis were engineered. Firstly, the acetyl-CoA c-acetyltransferase was overexpressed in HX-308 with a strong constitutive promoter. With the overexpression of acetyl-CoA c-acetyltransferase, more acetyl-CoA was used to synthesize terpenoids, and the production of squalene, β-carotene and astaxanthin was increased 5.4, 1.8, and 2.4 times, respectively. Interestingly, the production of saturated fatty acids and polyunsaturated fatty acids also changed. Moreover, three Acyl-CoA oxidase genes which catalyze the first step of β-oxidation were knocked out using homologous recombination. Results showed that the production of lipids increased in the three knock-out strains. Our results demonstrated that the A. tumefaciens-mediated transformation method will be of great use for the study of function genes, as well as developing Schizochytrium sp. as a strong cell factory for producing high value products.

Metabolomics-based engineering for biofuel and bio-based chemical production in microalgae and cyanobacteria: A review

Metabolomics, an essential tool in modern synthetic biology based on the design-build-test-learn platform, is useful for obtaining a detailed understanding of cellular metabolic mechanisms through comprehensive analyses of the metabolite pool size and its dynamic changes. Metabolomics is critical to the design of a rational metabolic engineering strategy by determining the rate-limiting reaction and assimilated carbon distribution in a biosynthetic pathway of interest. Microalgae and cyanobacteria are promising photosynthetic producers of biofuels and bio-based chemicals, with high potential for developing a bioeconomic society through bio-based carbon neutral manufacturing. Metabolomics technologies optimized for photosynthetic organisms have been developed and utilized in various microalgal and cyanobacterial species. This review provides a concise overview of recent achievements in photosynthetic metabolomics, emphasizing the importance of microalgal and cyanobacterial cell factories that satisfy industrial requirements.

A Two-Stage Adaptive Laboratory Evolution Strategy to Enhance Docosahexaenoic Acid Synthesis in Oleaginous Thraustochytrid

Thraustochytrid is a promising algal oil resource with the potential to meet the demand for docosahexaenoic acid (DHA). However, oils with high DHA content produced by genetic modified thraustochytrids are not accepted by the food and pharmaceutical industries in many countries. Therefore, in order to obtain non-transgenic strains with high DHA content, a two-stage adaptive laboratory evolution (ALE) strategy was applied to the thraustochytrid Aurantiochytrium sp. Heavy-ion irradiation technique was first used before the ALE to increase the genetic diversity of strains, and then two-step ALE: low temperature based ALE and ACCase inhibitor quizalofop-p-ethyl based ALE were employed in enhancing the DHA production. Using this strategy, the end-point strain E-81 with a DHA content 51% higher than that of the parental strain was obtained. The performance of E-81 strain was further analyzed by component analysis and quantitative real-time PCR. The results showed that the enhanced in lipid content was due to the up-regulated expression of key enzymes in lipid accumulation, while the increase in DHA content was due to the increased transcriptional levels of polyunsaturated fatty acid synthase. This study demonstrated a non-genetic approach to enhance lipid and DHA content in non-model industrial oleaginous strains.

Production of polyunsaturated fatty acids by Schizochytrium (Aurantiochytrium) spp

Diverse health benefits are associated with dietary consumption of omega-3 long-chain polyunsaturated fatty acids (ω-3 LC-PUFA), particularly docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA). Traditionally, these fatty acids have been obtained from fish oil, but limited supply, variably quality, and an inability to sustainably increase production for a rapidly growing market, are driving the quest for alternative sources. DHA derived from certain marine protists (heterotrophic thraustochytrids) already has an established history of commercial production for high-value dietary use, but is too expensive for use in aquaculture feeds, a much larger potential market for ω-3 LC-PUFA. Sustainable expansion of aquaculture is prevented by its current dependence on wild-caught fish oil as the source of ω-3 LC-PUFA nutrients required in the diet of aquacultured animals. Although several thraustochytrids have been shown to produce DHA and EPA, there is a particular interest in Schizochytrium spp. (now Aurantiochytrium spp.), as some of the better producers. The need for larger scale production has resulted in development of many strategies for improving productivity and production economics of ω-3 PUFA in Schizochytrium spp. Developments in fermentation technology and metabolic engineering for enhancing LC-PUFA production in Schizochytrium spp. are reviewed.

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.

Progress of metabolic engineering for the production of eicosapentaenoic acid

Eicosapentaenoic Acid (EPA) is an essential ω-3 polyunsaturated fatty acid for human health. Currently, high-quality EPA production is largely dependent on the extraction of fish oil, but this unsustainable approach cannot meet its rising market demand. Biotechnological approaches for EPA production from microorganisms have received increasing attention due to their suitability for large-scale production and independence of the seasonal or climate restrictions. This review summarizes recent research on different microorganisms capable of producing EPA, such as microalgae, bacteria, and fungi, and introduces the different EPA biosynthesis pathways. Notably, some novel engineering strategies have been applied to endow and improve the abilities of microorganisms to synthesize EPA, including the construction and optimization of the EPA biosynthesis pathway, an increase in the acetyl-CoA pool supply, the increase of NADPH and the inhibition of competing pathways. This review aims to provide an updated summary of EPA production.

Multiproduct biorefinery from marine thraustochytrids towards a circular bioeconomy

Microalgal biotechnology research continues to expand due to largely unexplored marine environments and growing consumer interest in healthy products. Thraustochytrids, which are marine oleaginous protists, are known for their production of bioactives with significant applications in nutraceuticals, pharmaceuticals, and aquaculture. A wide range of high-value biochemicals, such as nutritional supplements (omega-3 fatty acids), squalene, exopolysaccharides (EPSs), enzymes, aquaculture feed, and biodiesel and pigment compounds, have been investigated. We discuss thraustochytrids as potential feedstocks to produce various bioactive compounds and advocate developing a biorefinery to offset production costs. We anticipate that future advances in cell manufacturing, lipidomic analysis, and nanotechnology-guided lipid extraction would facilitate large-scale cost-competitive production through these microbes.

Customizing lipids from oleaginous microbes: leveraging exogenous and endogenous approaches

To meet the growing demands of the oleochemical industry, tailored lipid sources are expanding to oleaginous microbes. To control the fatty acid composition of microbial lipids, ground-breaking exogenous and endogenous approaches are being developed. Exogenous approaches employ extracellular tools such as product-specific feedstocks, process optimization, elicitors, and magnetic and mechanical energy, whereas endogenous approaches leverage biology through the use of product-specific microbes, adaptive laboratory evolution (ALE), and the creation of custom strains via random and targeted cellular engineering. We consolidate recent advances from both fields into a review that will serve as a resource for those striving to fulfill the vision of microbial cell factories for tailored lipid production.

Method Development Progress in Genetic Engineering of Thraustochytrids

Thraustochytrids are unicellular, heterotrophic marine eukaryotes. Some species are known to store surplus carbon as intracellular lipids, and these also contain the long-chain polyunsaturated fatty acid docosahexaenoic acid (DHA). Most vertebrates are unable to synthesize sufficient amounts of DHA, and this fatty acid is essential for, e.g., marine fish, domesticated animals, and humans. Thraustochytrids may also produce other commercially valuable fatty acids and isoprenoids. Due to the great potential of thraustochytrids as producers of DHA and other lipid-related molecules, a need for more knowledge on this group of organisms is needed. This necessitates the ability to do genetic manipulation of the different strains. Thus far, this has been obtained for a few strains, while it has failed for other strains. Here, we systematically review the genetic transformation methods used for different thraustochytrid strains, with the aim of aiding studies on strains not yet successfully transformed. The designs of transformation cassettes are also described and compared. Moreover, the potential problems when trying to establish transformation protocols in new thraustochytrid species/strains are discussed, along with suggestions utilized in other organisms to overcome similar challenges. The approaches discussed in this review could be a starting point when designing protocols for other non-model organisms.

Obtaining High-Purity Docosahexaenoic Acid Oil in Thraustochytrid Aurantiochytrium through a Combined Metabolic Engineering Strategy

High-purity docosahexaenoic acid (DHA) resources are insufficient in the pharmaceutical and food industries. Although many efforts have attempted to obtain the high-purity DHA production, few reports have been successful. Here, a combined metabolic engineering strategy was employed to increase the DHA purity in the oleaginous thraustochytrid Aurantiochytrium. The strategy includes both partial deactivation of the competing pathway of DHA biosynthesis, by disrupting one copy of the fatty acid synthase gene, and strengthening of substrate supply and triacylglycerol synthesis, by the overexpression of acetyl-CoA carboxylase and diacylglycerol acyltransferase. With this strategy, a final mutant was obtained with a DHA purity of 61% in total fatty acids and a content of 331 mg/g dry cell weight. This study provides an advanced strategy for sustainable high-purity DHA production and highlights the strategy for producing designer oils in industrial oleaginous microorganisms.

Lipid metabolism research in oleaginous fungus Mortierella alpina: Current progress and future prospects

The oleaginous fungus Mortierella alpina has distinct advantages in long-chain PUFAs production, and it is the only source for dietary arachidonic acid (ARA) certificated by FDA and European Commission. This review provides an overall introduction to M. alpina, including its major research methods, key factors governing lipid biosynthesis, metabolic engineering and omics studies. Currently, the research interests in M. alpina focus on improving lipid yield and fatty acid desaturation degree by enhancing fatty acid precursors and the reducing power NADPH, and genetic manipulation on PUFAs synthetic pathways is carried to optimise fatty acid composition. Besides, multi-omics studies have been applied to elucidate the global regulatory mechanism of lipogenesis in M. alpina. However, research challenges towards achieving a lipid cell factory lie in strain breeding and cost control due to the coenocytic mycelium, long fermentation period and insufficient conversion rate from carbon to lipid. We also proposed future research goals based on a multilevel regulating strategy: obtaining ideal chassis by directional evolution and high-throughput screening; rewiring central carbon metabolism and inhibiting competitive pathways by multi-gene manipulation system to enhance carbon to lipid conversion rate; optimisation of protein function based on post-translational modification; application of dynamic fermentation strategies suitable for different fermentation phases. By reviewing the comprehensive research progress of this oleaginous fungus, we aim to further comprehend the fungal lipid metabolism and provide reference information and guidelines for the exploration of microbial oils from the perspectives of fundamental research to industrial application.