Transcriptome Analysis Reveals an Eicosapentaenoic Acid Accumulation Mechanism in a Schizochytrium sp. Mutant

Advances in multi-omics technologies for identifying metabolic engineering targets and improving lipid production in microalgae

Polyunsaturated fatty acids (PUFAs), such as γ-linolenic acid, arachidonic acid, eicosapentaenoic acid, and docosahexaenoic acid, are highly valued in the global market due to their physiological effects and health benefits. Concerns related to overfishing and marine ecosystem degradation have driven interest in microalgal lipids as a sustainable and eco-friendly alternative for PUFA production. Despite some success in commercializing microalgal lipid products, they still fail to meet global demand. Advances in high-throughput omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, have deepened the understanding of lipid biosynthesis in microalgae. This review explores the potential of multi-omics approaches to elucidate PUFA biosynthesis pathways, identify key regulatory genes, and optimize metabolic engineering strategies for enhanced lipid production. Additionally, this review discusses how multi-omics technologies address challenges in large-scale cultivation, promoting the industrialization of microalgal lipid productions. These insights provide a foundation for improving microalgal PUFA yields to meet growing global demand.

Regulatory Mechanisms of EPA and DHA Proportions in a PUFA-Producing Microalga, Schizochytrium sp. ATCC 20888: From the Biosynthesis and Storage Distribution Aspects

Schizochytrium sp. ATCC 20888 is an important species for industrial polyunsaturated fatty acids (PUFA) production. This study investigated the regulatory mechanisms affecting the proportions of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) in terms of biosynthesis and storage distribution. EPA and DHA possessed different accumulation patterns: EPA proportion increased over time, while DHA peaked at 48 h. EPA was predominantly integrated into triacylglycerol during the logarithmic phase and phosphatidylcholine during the stationary phase. Transcriptome analysis revealed that EPA synthesis involved the fatty acid synthase-elongase/desaturase system, while DHA depended mainly on PUFA synthase. Key enzymes, including elongase ELOVL7, diacylglycerol acyltransferase (g10562), and lysophosphatidylcholine acyltransferases (g8836 and g7540), show a positive correlation with EPA yield, highlighting their roles in its biosynthesis and storage. Additionally, phosphopantetheine adenylyl transferase (PPAT/COASY) and ADP-ribosylation factor 1_2 (ARF1_2) were identified as potential regulators of PUFA proportions. This study provided insights for genetic optimization of PUFA production inSchizochytrium.

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.

Application and research progress of ARTP mutagenesis in actinomycetes breeding

Atmospheric and room temperature plasma (ARTP) is an emerging artificial mutagenesis breeding technology. In comparison to traditional physical and chemical methods, ARTP technology can induce DNA damage more effectively and obtain mutation strains with stable heredity more easily after screening. It possesses advantages such as simplicity, safety, non-toxicity, and cost-effectiveness, showing high application value in microbial breeding. This article focuses on ARTP mutagenesis breeding of actinomycetes, specifically highlighting the application of ARTP mutagenesis technology in improving the performance of strains and enhancing the biosynthetic capabilities of actinomycetes. We analyzed the advantages and challenges of ARTP technology in actinomycetes breeding and summarized the common features, specific mutation sites and metabolic pathways of ARTP mutagenic strains, which could give guidance for genetic modification. It suggested that the future research work should focus on the establishment of high throughput rapid screening methods and integrate transcriptomics, proteomics, metabonomics and other omics to delve into the genetic regulations and synthetic mechanisms of the bioactive substances in ARTP mutated actinomycetes. This article aims to provide new perspectives for actinomycetes breeding through the establishment and application of ARTP mutagenesis technology, thereby promoting source innovation and the sustainable industrial development of actinomycetes.

Comparative Transcriptomic Analysis on the Effect of Sesamol on the Two-Stages Fermentation of Aurantiochytrium sp. for Enhancing DHA Accumulation

Aurantiochytrium is a well-known long-chain polyunsaturated fatty acids (PUFAs) producer, especially docosahexaenoic acid (DHA). In order to reduce the cost or improve the productivity of DHA, many researchers are focusing on exploring the high-yield strain, reducing production costs, changing culture conditions, and other measures. In this study, DHA production was improved by a two-stage fermentation. In the first stage, efficient and cheap soybean powder was used instead of conventional peptone, and the optimization of fermentation conditions (optimal fermentation conditions: temperature 28.7 °C, salinity 10.7‱, nitrogen source concentration 1.01 g/L, and two-nitrogen ratio of yeast extract to soybean powder 2:1) based on response surface methodology resulted in a 1.68-fold increase in biomass concentration. In the second stage, the addition of 2.5 mM sesamol increased the production of fatty acid and DHA by 93.49% and 98.22%, respectively, as compared to the optimal culture condition with unadded sesamol. Transcriptome analyses revealed that the addition of sesamol resulted in the upregulation of some genes related to fatty acid synthesis and antioxidant enzymes in Aurantiochytrium. This research provides a low-cost and effective culture method for the commercial production of DHA by Aurantiochytrium sp.

Dual stress factors adaptive evolution for high EPA production in Schizochytrium sp. and metabolomics mechanism analysis

Eicosapentaenoic acid (EPA) is a vital ɷ-3 polyunsaturated fatty acid (PUFA) for human body with various physiological functions. In this study, we proposed an adaptive evolutionary strategy based on high-temperature and high-oxygen two-factor stress to increase the EPA production capacity of Schizochytrium. High-temperature stress was used to increase EPA yield, and high oxygen was implemented to continuously stimulate cell growth and lipid accumulation. The biomass and EPA production of ALE-D50 reached 35.33 g/L and 1.54 g/L, which were 43.85% and 71.11% higher than that of the original strain, respectively. Lower in vivo reactive oxygen species levels indicated that the evolved strain possessed stronger antioxidant activity. Liquid chromatography-mass spectrometry metabolomics showed that enhanced glucose consumption and glycolysis metabolism, as well as a weakened tricarboxylic acid cycle and reduced amino acid metabolic tributaries in the evolved strain, might be associated with increased growth and EPA synthesis. Finally, the lipid production and EPA production in a fed-batch fermentation were further increased to 48.93 g/L and 3.55 g/L, improving by 54.30% and 90.86%, respectively. This study provides a novel pathway for promoting EPA biosynthesis in Schizochytrium.

Squalene production under oxygen limitation by Schizochytrium sp. S31 in different cultivation systems

The triterpene squalene is widely used in the food, cosmetics and pharmaceutical industries due to its antioxidant, antistatic and anti-carcinogenic properties. It is usually obtained from the liver of deep sea sharks, which are facing extinction. Alternative production organisms are marine protists from the family Thraustochytriaceae, which produce and store large quantities of various lipids. Squalene accumulation in thraustochytrids is complex, as it is an intermediate in sterol biosynthesis. Its conversion to squalene 2,3-epoxide is the first step in sterol synthesis and is heavily oxygen dependent. Hence, the oxygen supply during cultivation was investigated in our study. In shake flask cultivations, a reduced oxygen supply led to increased squalene and decreased sterol contents and yields. Oxygen-limited conditions were applied to bioreactor scale, where squalene accumulation and growth of Schizochytrium sp. S31 was determined in batch, fed-batch and continuous cultivation. The highest dry matter (32.03 g/L) was obtained during fed-batch cultivation, whereas batch cultivation yielded the highest biomass productivity (0.2 g/L*h-1). Squalene accumulation benefited from keeping the microorganisms in the growth phase. Therefore, the highest squalene content of 39.67 ± 1.34 mg/g was achieved by continuous cultivation (D = 0.025 h-1) and the highest squalene yield of 1131 mg/L during fed-batch cultivation. Volumetric and specific squalene productivity both reached maxima in the continuous cultivation at D = 0.025 h-1 (6.94 ± 0.27 mg/L*h-1 and 1.00 ± 0.03 mg/g*h-1, respectively). Thus, the choice of a suitable cultivation method under oxygen-limiting conditions depends heavily on the process requirements. KEY POINTS: • Measurements of respiratory activity and backscatter light of thraustochytrids • Oxygen limitation increased squalene accumulation in Schizochytrium sp. S31 • Comparison of different cultivation methods under oxygen-limiting conditions.