Functions of PKS Genes in Lipid Synthesis of Schizochytrium sp. by Gene Disruption and Metabolomics Analysis

Comparative Transcriptome Analysis Unveils Regulatory Factors Influencing Fatty Liver Development in Lion-Head Geese under High-Intake Feeding Compared to Normal Feeding

The lion-head goose is the only large goose species in China, and it is one of the largest goose species in the world. Lion-head geese have a strong tolerance for massive energy intake and show a priority of fat accumulation in liver tissue through special feeding. Therefore, the aim of this study was to investigate the impact of high feed intake compared to normal feeding conditions on the transcriptome changes associated with fatty liver development in lion-head geese. In this study, 20 healthy adult lion-head geese were randomly assigned to a control group (CONTROL, n = 10) and high-intake-fed group (CASE, n = 10). After 38 d of treatment, all geese were sacrificed, and liver samples were collected. Three geese were randomly selected from the CONTROL and CASE groups, respectively, to perform whole-transcriptome analysis to analyze the key regulatory genes. We identified 716 differentially expressed mRNAs, 145 differentially expressed circRNAs, and 39 differentially expressed lncRNAs, including upregulated and downregulated genes. GO enrichment analysis showed that these genes were significantly enriched in molecular function. The node degree analysis and centrality metrics of the mRNA-lncRNA-circRNA triple regulatory network indicate the presence of crucial functional nodes in the network. We identified differentially expressed genes, including HSPB9, Pgk1, Hsp70, ME2, malic enzyme, HSP90, FADS1, transferrin, FABP, PKM2, Serpin2, and PKS, and we additionally confirmed the accuracy of sequencing at the RNA level. In this study, we studied for the first time the important differential genes that regulate fatty liver in high-intake feeding of the lion-head goose. In summary, these differentially expressed genes may play important roles in fatty liver development in the lion-head goose, and the functions and mechanisms should be investigated in future studies.

Selectively superior production of docosahexaenoic acid in Schizochytrium sp. through engineering the fatty acid biosynthetic pathways

BACKGROUND

Schizochytrium sp. is commercially used for production of docosahexaenoic acid (DHA). Schizochytrium sp. utilizes the polyketide synthase complex (PKS) and a single type I fatty acid synthase (FAS) to synthesize polyunsaturated fatty acids and saturated fatty acids, respectively. The acyl carrier protein (ACP) domains of FAS or PKS are used to load acyl groups during fatty acids biosynthesis. Phosphopantetheinyl transferase (PPTase) transfers the pantetheine moiety from Coenzyme A to the conserved serine residue of an inactive ACP domain to produce its active form.

RESULTS

In this study, in order to improve production and content of DHA, we decreased the expression of fas, strengthened the expression of the PKS pathway, and enhanced the supply of active ACP in Schizochytrium sp. ATCC20888. Weakening the expression of fas or disruption of orfA both led to growth defect and reduction of lipid yields in the resulting strains WFAS and DPKSA, indicating that both FAS and PKS were indispensable for growth and lipid accumulation. Although WFAS had a higher DHA content in total fatty acids than the wild-type strain (WT), its growth defect and low DHA yield hinders its use for DHA production. Overexpression of the orfAB, orfC, orfC-DH (truncated orfC), or ppt promoted DHA and lipid production, respectively. The yields and contents of DHA were further increased by combined overexpression of these genes. Highest values of DHA yield (7.2 g/L) and DHA content (40.6%) were achieved in a recombinant OPKSABC-PPT, ⁓56.5% and 15.3% higher than the WT values, respectively.

CONCLUSIONS

This study demonstrates that genetic engineering of the fatty acid biosynthetic pathways provides a new strategy to enhance DHA production in Schizochytrium.

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.

Engineering Fatty Acid Biosynthesis in Microalgae: Recent Progress and Perspectives

Microalgal lipids hold significant potential for the production of biodiesel and dietary supplements. To enhance their cost-effectiveness and commercial competitiveness, it is imperative to improve microalgal lipid productivity. Metabolic engineering that targets the key enzymes of the fatty acid synthesis pathway, along with transcription factor engineering, are effective strategies for improving lipid productivity in microalgae. This review provides a summary of the advancements made in the past 5 years in engineering the fatty acid biosynthetic pathway in eukaryotic microalgae. Furthermore, this review offers insights into transcriptional regulatory mechanisms and transcription factor engineering aimed at enhancing lipid production in eukaryotic microalgae. Finally, the review discusses the challenges and future perspectives associated with utilizing microalgae for the efficient production of lipids.

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.

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.

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

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

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.

Effectively Improve the Astaxanthin Production by Combined Additives Regulating Different Metabolic Nodes in Phaffia rhodozyma

Astaxanthin is an important natural resource that is widely found in marine environments. Metabolic regulation is an effective method for improving astaxanthin production in Phaffia rhodozyma. Most studies have focused on single regulators, which have limited effects. In this study, 16 metabolic regulators were screened to improve astaxanthin production in high-yield and wild-type strains. Fluconazol and glutamic acid increased astaxanthin volumetric yield in MVP14 by 25.8 and 30.9%, respectively, while ethanol increased astaxanthin volumetric yield in DSM626, 29.3%. Furthermore, six additives that inhibit the competing pathways and promote the main pathway for astaxanthin synthesis were selected for combination treatment. We found that the optimal combination was penicillin, ethanol, triclosan, and fluconazol, which increased astaxanthin cell yield by 51%. Therefore, we suggest that simultaneously promoting the master pathways (mevalonate) and inhibiting competing pathways (fatty acid synthesis and ergosterol) is the best strategy to improve astaxanthin cell yield. Moreover, regulators of the biomass pathway should be avoided to improve cell yield. This study provides a technical basis for the utilisation of astaxanthin in P. rhodozyma.

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.

An Oil Hyper-Accumulator Mutant Highlights Peroxisomal ATP Import as a Regulatory Step for Fatty Acid Metabolism in Aurantiochytrium limacinum

Thraustochytrids are marine protists that naturally accumulate triacylglycerol with long chains of polyunsaturated fatty acids, such as ω3-docosahexaenoic acid (DHA). They represent a sustainable response to the increasing demand for these "essential" fatty acids (FAs). Following an attempt to transform a strain of Aurantiochytrium limacinum, we serendipitously isolated a clone that did not incorporate any recombinant DNA but contained two to three times more DHA than the original strain. Metabolic analyses indicated a deficit in FA catabolism. However, whole transcriptome analysis did not show down-regulation of genes involved in FA catabolism. Genome sequencing revealed extensive DNA deletion in one allele encoding a putative peroxisomal adenylate transporter. Phylogenetic analyses and yeast complementation experiments confirmed the gene as a peroxisomal adenylate nucleotide transporter (AlANT1), homologous to yeast ScANT1 and plant peroxisomal adenylate nucleotide carrier AtPNC genes. In yeast and plants, a deletion of the peroxisomal adenylate transporter inhibits FA breakdown and induces FA accumulation, a phenotype similar to that described here. In response to this metabolic event, several compensatory mechanisms were observed. In particular, genes involved in FA biosynthesis were upregulated, also contributing to the high FA accumulation. These results support AlANT1 as a promising target for enhancing DHA production in Thraustochytrids.

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.

Function of ORFC of the polyketide synthase gene cluster on fatty acid accumulation in Schizochytrium limacinum SR21

BACKGROUND

As a potential source of polyunsaturated fatty acids (PUFA), Schizochytrium sp. has been widely used in industry for PUFA production. Polyketide synthase (PKS) cluster is supposed to be the primary way of PUFA synthesis in Schizochytrium sp. As one of three open reading frames (ORF) in the PKS cluster, ORFC plays an essential role in fatty acid biosynthesis. However, the function of domains in ORFC in the fatty acid synthesis of Schizochytrium sp. remained unclear.

RESULTS

In this study, heterologous expression and overexpression were carried out to study the role of ORFC and its domains in fatty acid accumulation. Firstly, ORFC was heterologously expressed in yeast which increased the PUFA content significantly. Then, the dehydratase (DH) and enoyl reductase (ER) domains located on ORFC were overexpressed in Schizochytrium limacinum SR21, respectively. Fatty acids profile analysis showed that the contents of PUFA and saturated fatty acid were increased in the DH and ER overexpression strains, respectively. This indicated that the DH and ER domains played distinct roles in lipid accumulation. Metabolic and transcriptomic analysis revealed that the pentose phosphate pathway and triacylglycerol biosynthesis were enhanced, while the tricarboxylic acid cycle and fatty acids oxidation were weakened in DH-overexpression strain. However, the opposite effect was found in the ER-overexpression strain.

CONCLUSION

Therefore, ORFC was required for the biosynthesis of fatty acid. The DH domain played a crucial role in PUFA synthesis, whereas the ER domain might be related to saturated fatty acids (SFA) synthesis in Schizochytrium limacinum SR21. This research explored the role of ORFC in the PKS gene cluster in Schizochytrium limacinum and provided potential genetic modification strategies for improving lipid production and regulating PUFA and SFA content.

Biotechnological production of lipid and terpenoid from thraustochytrids

As fungus-like protists, thraustochytrids have been increasingly studied for their faster growth rates and high lipid content. In the 1990s, thraustochytrids were used as docosahexaenoic acid (DHA) producers for the first time. Thraustochytrids genera, such as Thraustochytrium, Schizochytrium, and Aurantiochytrium have been developed and patented as industrial strains for DHA production. The high DHA yield is attributed to its unique and efficient polyketide-like synthase (PKS) pathway. Moreover, thraustochytrids possess a completed mevalonate (MVA) pathway, so it can be used as host for terpenoid production. In order to improve strain performance, the metabolic engineering strategies have been applied to promote or disrupt intracellular metabolic pathways, such as genetic engineering and addition of chemical activators. However, it is difficult to realize industrialization only by improving strain performance. Various operation strategies were developed to enlarge the production quantities from the laboratory-scale, including two-stage cultivation strategies, scale-up technologies and bioreactor design. Moreover, an economical and effective downstream process is also an important consideration for the industrial application of thraustochytrids. Downstream costs accounts for 20-60% of the overall process costs, which represents an attractive target for increasing the cost-competitiveness of thraustochytrids, including how to improve the efficiency of lipid extraction and the further application of biomass residues. This review aims to overview the whole lipid biotechnology of thraustochytrids to provide the background information for researchers.

Structural Insights into the Trans-Acting Enoyl Reductase in the Biosynthesis of Long-Chain Polyunsaturated Fatty Acids in Shewanella piezotolerans

Two long-chain polyunsaturated fatty acids (LC-PUFAs), eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), play vital roles in human health. Similarly, two biosynthetic pathways, based on desaturase/elongase and polyketide synthase, have been implicated in the synthesis of microbial LC-PUFA. Up to now, only several microalgae, no bacteria, have been used in the commercial production of oils rich in DHA and/or EPA. Fully understanding the enzymatic mechanism in the biosynthesis of LC-PUFA would contribute significantly to produce EPA and/or DHA by the bacteria. In this study, we report a 1.998 Å-resolution crystal structure of trans-acting enoyl reductase (ER), SpPfaD, from Shewanella piezotolerans. The SpPfaD model consists of one homodimer in the asymmetric unit, and each subunit contains three domains. These include an N-terminal, a central domain forming a classic TIM barrel with a single FMN cofactor molecule bound atop the barrel, and a C-terminal domain with a lid above the TIM barrel. Furthermore, we docked oxidized nicotinamide adenine dinucleotide phosphate (NADP) and an inhibitor 2-(4-(2-((3-(5-(pyridin-2-ylthio)thiazol-2-yl)ureido)methyl)-1H-imidazole-4-yl)phenoxy)acetic acid (TUI) molecule into the active site and analyzed the inhibition and catalytic mechanisms of the enoyl reductase SpPfaD. To the best of our knowledge, this is the first crystal structure of trans-ER in the biosynthesis of bacterial polyketides.

Recent advances in functional analysis of polyunsaturated fatty acid synthases

Polyunsaturated fatty acids (PUFAs) such as docosahexaenoic acid, eicosapentaenoic acid, and arachidonic acid are essential fatty acids for humans. PUFAs are biosynthesized by either desaturases/elongases from oleic acid or PUFA synthases from acetyl units. PUFA synthases are composed of three or four subunits, and each creates a specific PUFA even though the multiple catalytic domains in each subunit are very similar. We recently dissected these PUFA synthases by in vivo and in vitro experiments and elucidated how the enzymes control PUFA profiles. Moreover, for the first time, we converted a practical microalgal docosahexaenoic acid synthase into an eicosapentaenoic acid synthase based on the results.

The lipid metabolism in thraustochytrids

Thraustochytrids are unicellular heterotrophic marine protists of the Stramenopile group, often considered as non-photosynthetic microalgae. They have been isolated from a wide range of habitats including deep sea, but are mostly present in waters rich in sediments and organic materials. They are abundant in mangrove forests where they are major colonizers, feeding on decaying leaves and initiating the mangrove food web. Discovered 80 years ago, they have recently attracted considerable attention due to their biotechnological potential. This interest arises from their fast growth, their specific lipid metabolism and the improvement of the genetic tools and transformation techniques. These organisms are particularly rich in ω3-docosahexaenoic acid (DHA), an 'essential' fatty acid poorly encountered in land plants and animals but required for human health. To produce their DHA, thraustochytrids use a sophisticated system different from the classical fatty acid synthase system. They are also a potential source of squalene and carotenoids. Here we review our current knowledge about the life cycle, ecophysiology, and metabolism of these organisms, with a particular focus on lipid dynamics. We describe the different pathways involved in lipid and fatty acid syntheses, emphasizing their specificity, and we report on the recent efforts aimed to engineer their lipid metabolism.

Screening chemical modulators of benzoic acid derivatives to improve lipid accumulation in Schizochytrium limacinum SR21 with metabolomics analysis

BACKGROUND

Schizochytrium sp. is a marine fungus with great potential as an alternative commercial source of lipids rich in polyunsaturated fatty acids (PUFAs). To further increase lipid accumulation in Schizochytrium sp., the effect of exogenous additives has become one of the hotspots of current research. Although benzoic acid derivatives showed positive effects on lipid accumulation in Schizochytrium, the biochemical mechanism needs further investigation.

RESULTS

Four benzoic acid derivatives (sodium benzoate, p-aminobenzoic acid, p-methyl benzoic acid and folic acid) were screened and evaluated for their effect on lipid accumulation in Schizochytrium limacinum SR21. The lipid yield was increased by 56.84% with p-aminobenzoic acid (p-ABA) at a concentration of 200 mg/L among the four tested chemical modulators. The metabolomics analysis showed that 200 mg/L p-ABA was optimal for promoting glucose catabolism in glycolysis with an increase in the mevalonate pathway and a weakening of the tricarboxylic acid (TCA) cycle. Moreover, p-ABA increased NADPH generation by enhancing the pentose phosphate pathway (PPP), ultimately redirecting the metabolic flux to lipid synthesis. Fed-batch fermentation further proved that p-ABA could significantly increase the yield of lipid by 30.01%, reaching 99.67 g/L, and the lipid content was increased by 35.03%, reaching 71.12%. More importantly, the yields of docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) were increased by 33.28% and 42.0%, respectively.

CONCLUSION

The addition of p-ABA could promote the synthesis of tetrahydrofolate, enhancing NADPH, which ultimately promoted the flow of carbon flux to lipid synthesis. These findings provide a valuable strategy for improving the lipid accumulation in Schizochytrium by additives.