Regulation of TG accumulation and lipid droplet morphology by the novel TLDP1 in Aurantiochytrium limacinum F26-b

Genetic Modification of Aurantiochytrium sp. 18W-13a for Enhancement of Proteolytic Activity by Heterologous Expression of Extracellular Proteases

A marine thraustochytrid, Aurantiochytrium, is a promising organism to produce docosahexaenoic acid (DHA) and squalene. Utilization of inexpensive substances such as proteins in wastes and by-products from the food industry for cultivation is a considerable option to reduce production cost; however, the proteolytic ability of Aurantiochytrium spp. is low compared to taxonomically close Shizochytrium aggregatum. We previously identified extracellular protease (extracellular protease 1, EP1) in S. aggregatum ATCC 28209 from the supernatant of the culture and found that a similar protease gene (EP2) was located downstream of the EP1 gene. In the present study, we created the transformants expressing SaEP1 and/or SaEP2 to enhance the proteolytic ability of Aurantiochytrium sp. 18W-13a strain and cultivated them in the medium containing casein as a test protein substrate. Through SDS-PAGE analysis, we confirmed that casein in the supernatant was more efficiently degraded by the transformants than the wild type, suggesting that the expressed protease(s) were properly expressed and excreted. After 4-day cultivation in the casein medium, the value of optical density at 660 nm and the cell number in the culture of the transformant that expressed both SaEP1 and SaEP2 (designated as EP12 strain) showed 1.48- and 1.38-fold higher than those of wild type, respectively. The DHA and squalene yield of the EP12 strain were respectively 158.3 and 0.23 mg L-1, and these values were 1.42- and 2.01-fold higher than those of wild type, respectively, suggesting that the EP12 created in the present study is a favorable strain for the cultivation using protein-containing medium.

Production of docosahexaenoic acid by a novel isolated Aurantiochytrium sp. 6-2 using fermented defatted soybean as a nitrogen source for sustainable fish feed development

We focused on the production of docosahexaenoic acid (DHA)-containing microbial lipids by Aurantiochytrium sp. using of defatted soybean (DS) as a nitrogen source. Defatted soybean is a plant biomass that could provide a sustainable supply at a low cost. Results showed that Aurantiochytrium sp. could not directly assimilate the DS as a nitrogen source but could grow well in a medium containing DS fermented with rice malt. When cultivated in a fermented DS (FDS) medium, Aurantiochytrium sp. showed vigorous growth with the addition of sufficient sulfate and chloride ions as inorganic nutrients without seawater salt. A novel isolated Aurantiochytrium sp. 6-2 showed 15.8 ± 3.4 g/L DHA productivity (in 54.8 ± 12.1 g/L total fatty acid production) in 1 L of the FDS medium. Therefore, DHA produced by Aurantiochytrium sp. using FDS enables a stable and sustainable DHA supply and could be an alternative source of natural DHA derived from fish oil.

A high-throughput platform enables in situ screening of fatty acid-producing strains using laser ablation electrospray ionization mass spectrometry and a Python package

Microbial fatty acid-producing strains are commonly engineered to improve their performance for industrial applications. However, it is challenging to efficiently and rapidly screen target strains for engineering. This study reported an in situ analytical platform using laser ablation electrospray ionization mass spectrometry (LAESI-MS) for fast profiling of triacylglycerols in cellular lipid droplets of Aurantiochytrium sp. colonies cultured on agar plates. LAESI-MS approach allowed for the direct acquisition of a colony cell's characteristic fingerprint mass spectrum and MS/MS facilitated the identification of triacylglycerol species containing three fatty acyl groups. The fatty acid contents of colony cells were calculated based on the intensities of triacylglycerols from their characteristic fingerprint mass spectrum. A Python package called TAFA-LEMS (Triacylglycerol to Fatty Acid by LAESI-MS) was also developed to process the high-throughput MS data and extract fatty acid contents in colony cells. The results demonstrated that the LAESI-MS platform is fast, stable, and reproducible, with a data acquisition rate of ≤2 s per sampling point and ≤13.69% RSDs of the relative contents of fatty acids. In addition, LAESI-MS was successfully performed on the analysis of P. tricornutum and Y lipolytica strains. This in situ MS platform has the potential to become a common biotechnology platform for microbial strain engineering.

Characterization of thraustochytrid-specific sterol O-acyltransferase: modification of DGAT2-like enzyme to increase the sterol production in Aurantiochytrium limacinum mh0186

IMPORTANCE

Since the global market for sterols and vitamin D are grown with a high compound annual growth rate, a sustainable source of these compounds is required to keep up with the increasing demand. Thraustochytrid is a marine oleaginous microorganism that can synthesize several sterols, which are stored as SE in lipid droplets. DGAT2C is an unconventional SE synthase specific to thraustochytrids. Although the primary structure of DGAT2C shows high similarities with that of DGAT, DGAT2C utilizes sterol as an acceptor substrate instead of diacylglycerol. In this study, we examined more detailed enzymatic properties, intracellular localization, and structure-activity relationship of DGAT2C. Furthermore, we successfully developed a method to increase sterol and provitamin D3 productivity of thraustochytrid by more than threefold in the process of elucidating the function of the DGAT2C-specific N-terminal region. Our findings could lead to sustainable sterol and vitamin D production using thraustochytrid.

Uncovering global lipid accumulation routes towards docosahexaenoic acid (DHA) production in Aurantiochytrium sp. SW1 using integrative proteomic analysis

Aurantiochytrium sp., a marine thraustochytrid possesses a remarkable ability to produce lipid rich in polyunsaturated fatty acids (PUFAs), such as docosahexaenoic acid (DHA). Although gene regulation underlying lipid biosynthesis has been previously reported, proteomic analysis is still limited. In this study, high DHA accumulating strain Aurantiochytrium sp. SW1 has been used as a study model to elucidate the alteration in proteome profile under different cultivation phases i.e. growth, nitrogen-limitation and lipid accumulation. Of the total of 5146 identified proteins, 852 proteins were differentially expressed proteins (DEPs). The largest number of DEPs (488 proteins) was found to be uniquely expressed between lipid accumulating phase and growth phase. Interestingly, there were up-regulated proteins involved in glycolysis, glycerolipid, carotenoid and glutathione metabolism which were preferable metabolic routes towards lipid accumulation and DHA production as well as cellular oxidative defence. Integrated proteomic and transcriptomic data were also conducted to comprehend the gene and protein regulation underlying the lipid and DHA biosynthesis. A significant up-regulation of acetyl-CoA synthetase was observed which suggests alternative route of acetate metabolism for acetyl-CoA producer. This study presents the holistic routes underlying lipid accumulation and DHA production in Aurantiochytrium sp. SW1 and other relevant thraustochytrid.

Production of docosahexaenoic acid from spruce sugars using Aurantiochytrium limacinum

In this study lignocellulosic sugars from Norway spruce were used for production of docosahexaenoic acid (DHA) by the marine thraustochytrid Aurantiochytrium limacinum SR21. Enzymatically prepared spruce hydrolysate was combined with a complex nitrogen source and different amounts of salts. Shake flask batch cultivations revealed that addition of extra salts was not needed for optimal growth. Upscaling to fed-batch bioreactors yielded up to 55 g/L cell dry mass and a total fatty acid content of 44% (w/w) out of which 1/3 was DHA. Fourier transform infrared spectroscopy was successfully applied as a rapid method for monitoring lipid accumulation in A. limacinum SR21. Thus, this proof-of-principle study clearly demonstrates that crude spruce hydrolysates can be directly used as a novel and sustainable resource for production of DHA.

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.

PUFA synthase-independent DHA synthesis pathway in Parietichytrium sp. and its modification to produce EPA and n-3DPA

The demand for n-3 long-chain polyunsaturated fatty acids (n-3LC-PUFAs), such as docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), will exceed their supply in the near future, and a sustainable source of n-3LC-PUFAs is needed. Thraustochytrids are marine protists characterized by anaerobic biosynthesis of DHA via polyunsaturated fatty acid synthase (PUFA-S). Analysis of a homemade draft genome database suggested that Parietichytrium sp. lacks PUFA-S but possesses all fatty acid elongase (ELO) and desaturase (DES) genes required for DHA synthesis. The reverse genetic approach and a tracing experiment using stable isotope-labeled fatty acids revealed that the ELO/DES pathway is the only DHA synthesis pathway in Parietichytrium sp. Disruption of the C20 fatty acid ELO (C20ELO) and ∆4 fatty acid DES (∆4DES) genes with expression of ω3 fatty acid DES in this thraustochytrid allowed the production of EPA and n-3docosapentaenoic acid (n-3DPA), respectively, at the highest level among known microbial sources using fed-batch culture.

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.

Illumina and PacBio DNA sequencing data, de novo assembly and annotation of the genome of Aurantiochytrium limacinum strain CCAP_4062/1

The complete genome of the thraustochytrid Aurantiochytrium limacinum strain CCAP_4062/1 was sequenced using both Illumina Novaseq 6000 and third generation sequencing technology PacBio RSII in order to obtain trustworthy assembly and annotation. The reads from both platforms were combined at multiple levels in order to obtain a reliable assembly, then compared to the A. limacinum ATCCⓇ MYA1381™ reference genome. The final assembly was annotated with the help of strain CCAP_4062/1 RNAseq data. A. limacinum strain CCAP_4062/1 is an industrial strain used for the production of very long chain polyunsaturated fatty acids, like the docosahexaenoic acid that is an essential fatty acid synthesised only at very low pace in humans and vertebrates . Thraustochytrids in general and Aurantiochytrium more specifically, are used for carotenoid and squalene production as well. Beside their biotechnological interest, thraustochytrids play a crucial role in both inshore and oceanic basins ecosystems. Genome sequences will foster biotechnological as well as ecological studies.

Regulation of triglyceride metabolism in medaka (Oryzias latipes) hepatocytes by Neu3a sialidase

Fish store triglycerides (TGs) in the liver, muscle, and adipose tissue and TGs constitute an energy source upon metabolic demand. The liver generally plays important roles in lipid metabolism. Recent studies have suggested the possibility of hepatic lipid metabolic regulation by ganglioside in mammals; however, ganglioside-mediated regulation of lipid metabolism is unclear in fish. This study aimed to clarify the role of ganglioside in fish TG metabolism, with particular reference to Neu3a, a ganglioside-specific sialidase expressed in the fish liver. Under fasting conditions, there was a decrease in hepatic TG contents, and neu3a mRNA level was significantly up-regulated in the medaka liver. To determine the role of Neu3a in hepatic lipid metabolism, Neu3a stable transfectants were generated using fish liver Hepa-T1 cells. After treating Neu3a cells with oleic acid, reduction of TG was detected in comparison with the mock cells. Furthermore, lipase activity was greater in Neu3a cells than in mock cells. To examine which ganglioside regulates these events, alterations of ganglioside composition in Neu3a cells were analyzed. Neu3a cells exhibited increased level of lactosylceramide (LacCer), a Neu3 enzymatic product originating from GM3. In addition, exposure of LacCer toward Hepa-T1 cells resulted in an increase of neutral lipase activity. The present results suggest that Neu3a up-regulation in medaka under fasting condition accelerates hepatic TG degradation for energy production via GM3 desialylation.

The Nutritional and Pharmacological Potential of New Australian Thraustochytrids Isolated from Mangrove Sediments

Mangrove sediments represent unique microbial ecosystems that act as a buffer zone, biogeochemically recycling marine waste into nutrient-rich depositions for marine and terrestrial species. Marine unicellular protists, thraustochytrids, colonizing mangrove sediments have received attention due to their ability to produce large amounts of long-chain ω3-polyunsaturated fatty acids. This paper represents a comprehensive study of two new thraustochytrids for their production of valuable biomolecules in biomass, de-oiled cakes, supernatants, extracellular polysaccharide matrixes, and recovered oil bodies. Extracted lipids (up to 40% of DW) rich in polyunsaturated fatty acids (up to 80% of total fatty acids) were mainly represented by docosahexaenoic acid (75% of polyunsaturated fatty acids). Cells also showed accumulation of squalene (up to 13 mg/g DW) and carotenoids (up to 72 µg/g DW represented by astaxanthin, canthaxanthin, echinenone, and β-carotene). Both strains showed a high concentration of protein in biomass (29% DW) and supernatants (2.7 g/L) as part of extracellular polysaccharide matrixes. Alkalinization of collected biomass represents a new and easy way to recover lipid-rich oil bodies in the form of an aqueous emulsion. The ability to produce added-value molecules makes thraustochytrids an important alternative to microalgae and plants dominating in the food, pharmacological, nutraceutical, and cosmetics industries.

The Puzzling Conservation and Diversification of Lipid Droplets from Bacteria to Eukaryotes

Membrane compartments are amongst the most fascinating markers of cell evolution from prokaryotes to eukaryotes, some being conserved and the others having emerged via a series of primary and secondary endosymbiosis events. Membrane compartments comprise the system limiting cells (one or two membranes in bacteria, a unique plasma membrane in eukaryotes) and a variety of internal vesicular, subspherical, tubular, or reticulated organelles. In eukaryotes, the internal membranes comprise on the one hand the general endomembrane system, a dynamic network including organelles like the endoplasmic reticulum, the Golgi apparatus, the nuclear envelope, etc. and also the plasma membrane, which are linked via direct lateral connectivity (e.g. between the endoplasmic reticulum and the nuclear outer envelope membrane) or indirectly via vesicular trafficking. On the other hand, semi-autonomous organelles, i.e. mitochondria and chloroplasts, are disconnected from the endomembrane system and request vertical transmission following cell division. Membranes are organized as lipid bilayers in which proteins are embedded. The budding of some of these membranes, leading to the formation of the so-called lipid droplets (LDs) loaded with hydrophobic molecules, most notably triacylglycerol, is conserved in all clades. The evolution of eukaryotes is marked by the acquisition of mitochondria and simple plastids from Gram-positive bacteria by primary endosymbiosis events and the emergence of extremely complex plastids, collectively called secondary plastids, bounded by three to four membranes, following multiple and independent secondary endosymbiosis events. There is currently no consensus view of the evolution of LDs in the Tree of Life. Some features are conserved; others show a striking level of diversification. Here, we summarize the current knowledge on the architecture, dynamics, and multitude of functions of the lipid droplets in prokaryotes and in eukaryotes deriving from primary and secondary endosymbiosis events.

Lipid and DHA-production in Aurantiochytrium sp. - Responses to nitrogen starvation and oxygen limitation revealed by analyses of production kinetics and global transcriptomes

Thraustochytrids of the genera Schizochytrium and Aurantiochytrium accumulate oils rich in the essential, marine n3 fatty acid docosahexaenoic acid (DHA). DHA production in Aurantiochytrium sp T66 was studied with the aim to provide more knowledge about factors that affect the DHA-productivities and the contributions of the two enzyme systems used for fatty acid synthesis in thraustochytrids, fatty acid synthetase (FAS) and PUFA-synthase. Fermentations with nitrogen starvation, which is well-known to initiate lipid accumulation in oleaginous organisms, were compared to fermentations with nitrogen in excess, obtained by oxygen limitation. The specific productivities of fatty acids originating from FAS were considerably higher under nitrogen starvation than with nitrogen in excess, while the specific productivities of DHA were the same at both conditions. Global transcriptome analysis showed significant up-regulation of FAS under N-deficient conditions, while the PUFA-synthase genes were only marginally upregulated. Neither of them was upregulated under O₂-limitation where nitrogen was in excess, suggesting that N-starvation mainly affects the FAS and may be less important for the PUFA-synthase. The transcriptome analysis also revealed responses likely to be related to the generation of reducing power (NADPH) for fatty acid synthesis.

A thraustochytrid-specific lipase/phospholipase with unique positional specificity contributes to microbial competition and fatty acid acquisition from the environment

Thraustochytrids are heterotrophic marine protists that are considered as important decomposers in the marine ecosystem; however, how they digest and uptake lipid nutrients from the environment is largely unknown. Genomic clustering analysis using thraustochytrid draft genome databases revealed that novel proteins with a Lipase_3 domain are commonly present in thraustochytrids, including Aurantiochytrium limacinum. After heterologous expression and His tag-based purification, protein ID: 145138 was identified as lipase/phospholipase capable of hydrolyzing triacylglycerol (TG) and phosphatidylcholine (PC). 145138 was secreted into the medium, and deletion of the 145138 gene in A. limacinum reduced the degradation of extracellular lipids. Fatty acids generated by 145138 were reused for the biosynthesis of PC and TG, and 145138 allowed A. limacinum to survive in the medium containing TG as a sole carbon source. 145138 hydrolyzed all the acyl-ester linkages of TG; however, the enzyme showed strict positional specificity toward phospholipids, generating 2-acyl lysophospholipids. The 2-acyl lysophospholipids showed stronger antimicrobial activity compared with 1-acyl lysophospholipids. These results suggested that 145138 is a bifunctional enzyme that contributes to the acquisition of lipid nutrients from the environment, as well as to generate antimicrobial lysophospholipids that are beneficial for competition with bacteria over lipid nutrients in the marine environment.

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.

The glycerol-3-phosphate acyltransferase PLAT2 functions in the generation of DHA-rich glycerolipids in Aurantiochytrium limacinum F26-b

Thraustochytrids possess docosahexaenoic acid (DHA, 22:6n-3) as acyl chain(s) of triacylglycerol (TG) and phosphatidylcholine (PC), some of which contain multiple DHAs. However, little is known about how these DHA-rich glycerolipids are produced in thraustochytrids. In this study, we identified PLAT2 in Aurantiochytrium limacinum F26-b as a glycerol-3-phosphate (G3P) acyltransferase (GPAT) by heterologous expression of the gene in budding yeast. Subsequently, we found that GPAT activity was reduced by disruption of the PLAT2 gene in A. limacinum, resulting in a decrease in DHA-containing lysophosphatidic acid (LPA 22:6). Conversely, overexpression of PLAT2 increased both GPAT activity and LPA 22:6. These results indicate that PLAT2 is a GPAT that transfers DHA to G3P in vivo as well as in vitro. Overexpression of the PLAT2 gene increased the production of a two DHA-containing diacylglycerol (DG 44:12), followed by an increase in the three DHA-containing TG (TG 66:18), two-DHA-containing TG (TG 60:12), and two DHA-containing PC (PC 44:12). However, overexpression of PLAT2 did not increase DHA-free DG (DG32:0), which was preferentially converted to three 16:0-containing TG (TG 48:0) but not two 16:0-containing PC (PC 32:0). Collectively, we revealed that DHA-rich glycerolipids are produced from a precursor, LPA 22:6, which is generated by incorporating DHA to G3P by PLAT2 in the A. limacinum.

Enhanced saturated fatty acids accumulation in cultures of newly-isolated strains of Schizochytrium sp. and Thraustochytriidae sp. for large-scale biodiesel production

Heterotrophic marine protists (Thraustochytrids) have received increasingly global attention as a renewable, sustainable and alternative source of biodiesel because of their high ability of saturated fatty acids (SFAs) accumulation. Yet, the influence of extrinsic factors (nutrients and environmental conditions) on thraustochytrid culture and optimal conditions for high SFAs production are poorly described. In the present study, two different thraustochytrid strains, Schizochytrium sp. PKU#Mn4 and Thraustochytriidae sp. PKU#Mn16 were studied for their growth and SFAs production profiles under various conditions (carbon, nitrogen, temperature, pH, KH₂PO₄, salinity, and agitation speed). Of the culture conditions, substrates (C and N) source and conc., temperature, and agitation speed significantly influenced the cell growth and SFAs production of both strains. Although both the strains were capable of growth and SFAs production in the broad range of culture conditions, their physiological responses to KH₂PO₄, pH, and salinity were dissimilar. Under their optimal batch culture conditions, peak SFAs productions of 3.3g/L and 2.2g/L with 62% and 49% SFAs contents (relative to total fatty acids) were achieved, respectively. The results of 5-L fed-batch fermentation under optimal conditions showed a nearly 4.5-fold increase in SFAs production (i.e., 7.5g/L) by both strains compared to unoptimized conditions. Of the two strains, the quality of biodiesel produced from the fatty acids of PKU#Mn4 met the biodiesel standard defined by ASTM6751. This study, to the knowledge of the authors, is the first comprehensive report of optimal fermentation conditions demonstrating enhanced SFAs production by strains belonging to two different thraustochytrid genera and provides the basis for large-scale biodiesel production.