Production of polyunsaturated fatty acids by polyketide synthases in both prokaryotes and eukaryotes

Fatty acid addition strategy redirected the metabolic flux towards an ultra-high monensin productivity of Streptomyces cinnamonensis

Monensin, a polyether ionophore antibiotic produced by Streptomyces cinnamonensis, exhibits notable anticoccidial and antitumor properties. In this study, a fatty acid addition (FAA) strategy significantly enhanced the monensin production capability of S. cinnamonensis, resulting in an unprecedented monensin titer of 17.72 g/L at 192 h, 7.36 times that of the control. Physiological assay showed the FAA markedly altered the cellular morphology, cell membrane fluidity, enzymatic activity and intracellular cofactors, thus indicating of an increased carbon flux. With transcriptional analysis at the product biosynthesis phase, 4 genes in the monensin biosynthesis cluster and 11 genes related to the oxidative stress response were observed to be upregulated. Meanwhile, genes consisting of two sugar transport systems were downregulated. For the precursors supply, genes associated with triacylglycerols (TAG) degradation (lps) and fatty acid degradation genes (fadE, fadB, fadA) were upregulated, while genes to TAG synthesis were downregulated. For the monensin synthetic pathway, 8 polyketide synthase genes, 9 modifier genes and 3 pathway-specific regulatory genes within the monensin biosynthetic gene cluster (mon) were upregulated. Consequently, the physiological and transcriptional response of S. cinnamonensis to the FAA strategy was correlated well with the monensin biosynthesis. The findings not only elucidated the de novo biosynthesis of monensin via FAA, but also offered a strategic framework for efficient production of polyketide natural products.

Improving Precursor Supply and Optimizing the Fermentation Process for High-Level Production of Docosapentaenoic Acid in Yarrowia Lipolytica

Docosapentaenoic acid (DPA) is widely applied in medicine and health products because of its important physiological functions. Using microbial cell factories for DPA production is considered a viable alternative to extracting DPA from seal oil. In this study, an engineering strategy for the efficient production of DPA was developed. First, the DPA biosynthesis pathway was successfully established in Yarrowia lipolytica. Then, the increase of acetyl-CoA by engineering citrate metabolism and malonyl-CoA by introducing a new orthogonal malonyl-CoA synthesis pathway was to further enhance DPA production. Furthermore, overexpression of glucose-6-phosphate dehydrogenase (G6PDH) and malic enzyme (ME) enhanced NADPH availability. Finally, by optimizing the fermentation conditions, the DPA content of the engineered strain reached 40.0%, and the yield reached 13.0 g/L in the 5 L bioreactor, representing the highest levels reported so far in Y. lipolytica. This study provides a promising strategy to construct microbial cell factories for fatty acid biosynthesis.

Sustainable and biotechnological production of docosahexaenoic acid from marine protists and slaughterhouse waste

Docosahexaenoic acid (DHA, 22:6n-3) is an essential omega-3 polyunsaturated fatty acid, abundant in the brain and eyes. DHA is crucial for maintaining the structural integrity and physiological functions of these vital organs. Within the brain, DHA is concentrated in the gray matter, synaptic membranes, and hippocampus. Likewise, in the eyes, substantial quantities can be found in the retina, with lower levels in the cornea and lens. Previous studies have outlined the potential for culturing marine heterotrophic protists in ways that provide cost-effective and sustainable DHA biosynthesis. Similarly, our previous work on repurposing slaughterhouse waste has highlighted this underutilized source of brain and ocular tissue, which can support the extraction of valuable nutrients such as DHA. In this review, we will examine the current state of the art related to DHA production from these two sources, explore potential applications, and outline the possible benefits that may be generated from our approaches, with an emphasis on ocular diseases.

Engineering PUFA Synthase for Enhanced Production of Polyunsaturated Fatty Acids: Insights and Applications

Polyunsaturated fatty acids (PUFAs) are essential for maintaining human health, playing a critical role in preventing cardiovascular diseases and promoting brain development. PUFAs can be synthesized through two independent biosynthetic pathways: the desaturase/elongase pathway and the PUFA synthase pathway. Among these, PUFA synthase is a crucial enzyme analogous to fatty acid synthase (FAS) and iterative polyketide synthase (PKS). Its high synthetic efficiency presents significant potential for enhancing fatty acid biosynthesis and expanding its applications. Recent in vitro and in vivo studies have progressively clarified the catalytic mechanisms of PUFA synthase, enabling the more precise engineering of this enzyme. This Review provides a comprehensive analysis of PUFA synthase, emphasizing its catalytic potential, engineering prospects, and expanding applications in fatty acid biosynthesis, offering novel insights for advancing its role in industrial and pharmaceutical innovation.

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.

Determining metabolic mechanism linking phospholipids and docosahexaenoic acid through phosphatidylcholine synthesis by phosphocholine cytidylyltransferase (CCT) overexpression in Schizochytrium sp

The polyunsaturated fatty acid (PUFA) metabolism of Schizochytrium, an excellent oil-producing microorganism, is closely related to phosphatidylcholine (PC) synthesis, which favors the migration and accumulation of docosahexaenoic acid (DHA). Phosphocholine cytidylyltransferase (CCT), a key enzyme involved in PC synthesis, profoundly impacts lipid metabolism in plants; however, few studies have focused on CCT in microorganisms. We investigated the effects of CCT overexpression on lipid metabolism in Schizochytrium sp. CCT overexpression slightly inhibited cell growth, but significantly promoted total lipid synthesis. Compared to the wild-type strain, PUFA content and DHA production in the CCT-overexpressing strain (SR21-CCT) increased by about 49% and 46%, respectively. Analysis of phospholipids and quantitative real-time PCR revealed that CCT overexpression enhanced phospholipid synthesis, especially by strengthening glycerophosphorylcholine acylation and de novo PC synthesis pathways, which promote DHA esterification to PC and DHA accumulation in triacylglycerols. This study helps decipher the mechanism correlating phospholipid metabolism and DHA production.

Substrate specificities of two ketosynthases in eukaryotic microalgal and prokaryotic marine bacterial DHA synthases

Highly reducing iterative polyketide synthases (HR-iPKSs) are huge enzyme complexes with multiple catalytic domains that biosynthesize polyketides by intrinsically programmed iterative carbon chain extensions and reductions. Unlike most HR-iPKSs, which possess a single ketosynthase (KS) domain for all carbon chain elongations, polyunsaturated fatty acid (PUFA) synthases contain two KS domains. We previously examined the substrate specificities of two KS domains of prokaryotic marine PUFA synthases with several acyl-ACP intermediates and showed that the two KS domains are utilized differentially depending on the carbon chain length. In this study, we investigated two KS domains in a eukaryotic microalgal DHA synthase, KSA and KSB, which show low similarities to those of prokaryotic marine enzymes, together with almost all the acyl-ACP intermediates. C6-, C12-, and C18-ACPs were exclusively accepted by KSA while KSB utilized C-8. C14- and C20-ACPs. In contrast, both KSA and KSB showed activities against C2-, C4-, and C10-ACPs. A general tendency was observed in which both the prokaryotic KS and the eukaryotic KS recognized the acyl structures in the vicinity of the thioester in ACP substrates except for short-chain substrates.

Recent Advancements and Strategies for Omega-3 Fatty Acid Production in Yeast

Recently, the biosynthesis of omega-3 fatty acids (ω3 FAs) in yeast has witnessed significant advancements. Notably, eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) play crucial roles in overall human growth, encompassing neurological development, cardiovascular health, and immune function. However, traditional sources of ω3 FAs face limitations such as environmental concerns. Yeast, as a genetically tractable organism, offers a promising alternative for its sustainable production. Recent advancements and strategies in yeast through metabolic engineering led to significant improvements in ω3 FA production, including the optimization of metabolic pathways, enhancement of precursor supplies, and manipulation of gene expression. Moreover, innovative bioprocess approaches, such as fermentation conditions and bioreactor design, have been devised to further maximize its yields. This review aims to comprehensively summarize recent strategies in ω3 FA production within yeast systems, highlighting their contribution to meeting global ω3 FA demand while mitigating environmental impact and ensuring food security.

The chemical ecology and physiological functions of type I polyketide natural products: the emerging picture

Covering: up to 2024.For many years, the value of complex polyketides lay in their medical properties, including their antibiotic and antifungal activities, with little consideration paid to their native functions. However, more recent evidence gathered from the study of inter-organismal interactions has revealed the influence of these metabolites upon the ecological adaptation and distribution of their hosts, as well as their modes of communication. The increasing number of sequenced genomes and associated transcriptomes has also unveiled the widespread occurrence of the underlying biosynthetic enzymes across all kingdoms of life, and the important contributions they make to physiological events specific to each organism. This review depicts the diversity of roles fulfilled by type I polyketides, particularly in light of studies carried out during the last decade, providing an initial overall picture of their diverse functions.

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.

Shewanella is a putative producer of polyunsaturated fatty acids in the gut soil of the composting earthworm Eisenia fetida

Polyunsaturated fatty acids (PUFAs) play a crucial role in aiding bacteria to adapt to extreme and stressful environments. While there is a well-established understanding of their production, accrual, and transfer within marine ecosystems, knowledge about terrestrial environments remains limited. Investigation of the intestinal microbiome of earthworms has illuminated the presence of PUFAs presumably of microbial origin, which contrasts with the surrounding soil. To comprehensively study this phenomenon, a multi-faceted approach was employed, combining fatty acid analysis with amplicon sequencing of the PfaA-KS domain of the anaerobic fatty acid synthase gene (pfa), as well as the 16S rRNA and 18S rRNA genes. This methodology was applied to scrutinize the gut microbiome of Eisenia fetida, its compost-based dietary source, and the resultant castings. This study unveiled a distinct gut soil ecosystem from input compost and output castings in fatty acid profile as well as type and abundance of organisms. 16S sequencing provided insights into the microbial composition, showing increased relative abundance of certain Pseudomonadota, including Shewanellaceae, and Planctomycetota, including Gemmataceae within the gut microbiome compared to input bulk soil compost, while Actinomycetota and Bacillota were relatively enriched compared to the casted feces. Sequencing of the PfaA-KS domain revealed amplicon sequence variants (ASVs) belonging primarily to Shewanella. Intriguingly, the 20C PUFAs were identified only in gut soil samples, though PfaA-KS sequence abundance was highest in output castings, indicating a unique metabolism occurring only in the gut. Overall, the results indicate that Shewanella can explain PUFA enrichment in the gut environment because of the pfa gene presence detected via PfaA-KS sequence data.IMPORTANCEPrior research has demonstrated that earthworm microbiomes can potentially harbor polyunsaturated fatty acids (PUFAs) that are not found within their residing soil environment. Moreover, distinct indicator species have been pinpointed for various microbial genera in earthworm microbiomes. Nevertheless, none of these studies have integrated metataxonomic and fatty acid analyses to explore the origin of PUFA synthesis in any earthworm species, with the objective of identifying the specific organisms and locations responsible for this production. This study suggests that earthworms accumulate PUFAs produced from bacteria, especially Shewanella, activated through the gut ecosystem.

Structural analysis of a membrane-associated delta-6 fatty acid desaturase from Prorocentrum micans

Delta-6 fatty acid desaturases, which play key roles in the biosynthesis of polyunsaturated fatty acids (PUFAs), are membrane-associated enzymes that present significant challenges for isolation and purification, complicating their structural characterization. Here we report the identification and structure-function analysis of a novel Δ6 fatty acid desaturase (PmD6) from the marine alga Prorocentrum micans with substrate preference to α-linolenic acid (18:3n-3). Structural modeling revealed a mushroom-like structure of PmD6 formed by four transmembrane α-helices as a stem and three cytoplasmic domains as a cap. Structural alignment identified several key residues positioned around the substrate tunnel and catalytic center in PmD6. Functional analysis of these residues by site-directed mutagenesis showed that Tyr226, Trp235, Phe345, and Ser349, facing the middle region of the substrate tunnel of PmD6, played critical roles in defining the structure for acceptance of substrates. Thr200, Leu391, and Met389, surrounding the end of the substrate tunnel, had roles in interaction with the methyl end of substrates. Asp255, close to a metal iron in the catalytic center, was essential for catalytic reaction by supporting the regional structure. These results have provided mechanistic insights into the structure-function relationship of membrane-bound front-end fatty acid desaturases.

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.

Production, Transport, Fate and Effects of Lipids in the Marine Environment

Lipids form energy storage depots, cellular barriers and signaling molecules. They are generated and metabolized by enzymes under the influence of biotic and abiotic factors, and some-the long-chain polyunsaturated ω3 and ω6 fatty acids and cholesterol-are essential for optimal health in marine organisms. In addition, lipids have direct and indirect roles in the control of buoyancy in marine fauna ranging from copepods to whales. Phytoplankton account for about half of the planet's carbon fixation, and about half of that carbon goes into lipids. Lipids are an important component of the ocean's ability to sequester carbon away from the atmosphere through sinking and especially after transfer to zooplankton. Phytoplankton are the main suppliers of ω3 polyunsaturated fatty acids (PUFAs) in the marine environment. They also supply cholesterol and many phytosterols to ocean ecosystems; however, genomics is indicating that members of the Cnidaria, Rotifera, Annelida, and Mollusca phyla also have the endogenous capacity for the de novo synthesis of ω3 PUFAs as well as phytosterols. It has been predicted that ω3 long-chain PUFAs will decrease in marine organisms with climate change, with implications for human consumption and for carbon sequestration; however, the responses of ω3 PUFA supply to future conditions are likely to be quite diverse.

Biosynthetic mechanisms of omega-3 polyunsaturated fatty acids in microalgae

Marine microalgae are the primary producers of ω3 polyunsaturated fatty acids (PUFAs), such as octadecapentaenoic acid (OPA, 18:5n-3) and docosahexaenoic acid (DHA, 22:6n-3) for food chains. However, the biosynthetic mechanisms of these PUFAs in the algae remain elusive. To study how these fatty acids are synthesized in microalgae, a series of radiolabeled precursors were used to trace the biosynthetic process of PUFAs in Emiliania huxleyi. Feeding the alga with 14C-labeled acetic acid in a time course showed that OPA was solely found in glycoglycerolipids such as monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG) synthesized plastidically by sequential desaturations while DHA was exclusively found in phospholipids synthesized extraplastidically. Feeding the alga with 14C-labeled α-linolenic acid (ALA), linoleic acid (LA), and oleic acid (OA) showed that DHA was synthesized extraplastidically from fed ALA and LA, but not from OA, implying that the aerobic pathway of DHA biosynthesis is incomplete with missing a Δ12 desaturation step. The in vitro enzymatic assays with 14C-labeled malonyl-CoA showed that DHA was synthesized from acetic acid by a PUFA synthase. These results provide the first and conclusive biochemistry evidence that OPA is synthesized by a plastidic aerobic pathway through sequential desaturations with the last step of Δ3 desaturation, while DHA is synthesized by an extraplastidic anaerobic pathway catalyzed by a PUFA synthase in the microalga.

Transcriptional, post-transcriptional, and post-translational regulation of polyunsaturated fatty acid synthase genes in Aurantiochytrium limacinum strain BL10: Responses to nitrogen starvation

Under nitrogen deficient conditions, the Aurantiochytrium limacinum strain BL10 greatly increases the production of docosahexaenoic acid (DHA) and n-6 docosapentaenoic acid. Researchers have yet to elucidate the mechanism by which BL10 promotes the activity of polyunsaturated fatty acid synthase (Pfa), which plays a key role in the synthesis of polyunsaturated fatty acid (PUFA). Analysis in the current study revealed that in nitrogen-depleted environments, BL10 boosts the transcription and synthesis of proteins by facilitating the expression of pfa genes via transcriptional regulation. It was also determined that BL10 adjusts the lengths of the 5'- and 3'-untranslated regions (suggesting post-transcriptional regulation) and modifies the ratio of two Pfa1 isoforms to favor PUFA production via post-translational regulation (ubiquitination). These findings clarify the exceptional DHA production of BL10 and provide additional insights into the regulatory mechanisms of PUFA biosynthesis in Aurantiochytrium.

Ameliorating microalgal OMEGA production using omics platforms

Over the past decade, the focus on omega (ω)-3 fatty acids from microalgae has intensified due to their diverse health benefits. Bioprocess optimization has notably increased ω-3 fatty acid yields, yet understanding of the genetic architecture and metabolic pathways of high-yielding strains remains limited. Leveraging genomics, transcriptomics, proteomics, and metabolomics tools can provide vital system-level insights into native ω-3 fatty acid-producing microalgae, further boosting production. In this review, we explore 'omics' studies uncovering alternative pathways for ω-3 fatty acid synthesis and genome-wide regulation in response to cultivation parameters. We also emphasize potential targets to fine-tune in order to enhance yield. Despite progress, an integrated omics platform is essential to overcome current bottlenecks in optimizing the process for ω-3 fatty acid production from microalgae, advancing this crucial field.

Application of synthetic biology strategies to promote biosynthesis of fatty acids and their derivatives

Fatty acids and their derivatives are indispensable biomolecules in all organisms, and can be used as intermediates in the synthesis of pharmaceuticals, biofuels and pesticides, and thus their demand has increased dramatically in recent years. In addition to serving as structural components of cell membranes and metabolic energy, fatty acids and their derivatives can also be used as signal transduction and regulatory bioactive molecules to regulate cell functions. Biosynthesis of fatty acids and their derivatives through microbial catalysis provides green and alternative options to meet the goal. However, the low biosynthetic titer of fatty acids and their derivatives limits their industrial production and application. In this review, we first summarize the metabolic pathways and related enzymes of fatty acids and their derivatives biosynthesis. Then, the strategies and research progress of biosynthesis of fatty acids and derivatives through metabolic and enzyme engineering were reviewed. The biosynthesis of saturated fatty acids (medium chain fatty acids and long chain fatty acids), bioactive fatty acids (PUFAs, oxylipins, ether lipids), and their derivatives with microbial and enzymatic catalysis were respectively summarized. Finally, synthetic biology strategies to improve fatty acids and their derivatives production through enzyme rational design, carbon metabolism flux, cofactors balance, and metabolic pathways design were discussed. The review provides references and prospects for fatty acids and their derivatives biosynthesis and industrial production.

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.

Comparative analysis of gut microbiome of mangrove brachyuran crabs revealed patterns of phylosymbiosis and codiversification

The acquisition of microbial symbionts enables animals to rapidly adapt to and exploit novel ecological niches, thus significantly enhancing the evolutionary fitness and success of their hosts. However, the dynamics of host-microbe interactions and their evolutionary implications remain largely underexplored in marine invertebrates. Crabs of the family Sesarmidae (Crustacea: Brachyura) are dominant inhabitants of mangrove forests and are considered keystone species there. Their rapid diversification, particularly after adopting a plant-feeding lifestyle, is believed to have been facilitated by symbiotic gut microbes, enabling successful colonization of intertidal and terrestrial environments. To investigate the patterns and mechanisms shaping the microbial communities and the role of microbes in the evolution of Sesarmidae, we characterized and compared the gut microbiome compositions across 43 crab species from Sesarmidae and other mangrove-associated families using 16S metabarcoding. We found that the gut microbiome assemblages in crabs are primarily determined by host identity, with a secondary influence from environmental factors such as microhabitat and sampling location, and to a lesser extent influenced by biological factors such as sex and gut region. While patterns of phylosymbiosis (i.e. when microbial community relationships recapitulate the phylogeny of their hosts) were consistently observed in all beta-diversity metrics analysed, the strength of phylosymbiosis varied across crab families. This suggests that the bacterial assemblages in each family were differentially shaped by different degrees of host filtering and/or other evolutionary processes. Notably, Sesarmidae displayed signals of cophylogeny with its core gut bacterial genera, which likely play crucial functional roles in their hosts by providing lignocellulolytic enzymes, essential amino acids, and fatty acids supplementation. Our results support the hypothesis of microbial contribution to herbivory and terrestrialization in mangrove crabs, highlighting the tight association and codiversification of the crab holobiont.

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.

Transcriptomics aids in uncovering the metabolic shifts and molecular machinery of Schizochytrium limacinum during biotransformation of hydrophobic substrates to docosahexaenoic acid

BACKGROUND

Biotransformation of waste oil into value-added nutraceuticals provides a sustainable strategy. Thraustochytrids are heterotrophic marine protists and promising producers of omega (ω) fatty acids. Although the metabolic routes for the assimilation of hydrophilic carbon substrates such as glucose are known for these microbes, the mechanisms employed for the conversion of hydrophobic substrates are not well established. Here, thraustochytrid Schizochytrium limacinum SR21 was investigated for its ability to convert oils (commercial oils with varying fatty acid composition and waste cooking oil) into ω-3 fatty acid; docosahexaenoic acid (DHA).

RESULTS

Within 72 h SR21 consumed ~ 90% of the oils resulting in enhanced biomass (7.5 g L- 1) which was 2-fold higher as compared to glucose. Statistical analysis highlights C16 fatty acids as important precursors of DHA biosynthesis. Transcriptomic data indicated the upregulation of multiple lipases, predicted to possess signal peptides for secretory, membrane-anchored and cytoplasmic localization. Additionally, transcripts encoding for mitochondrial and peroxisomal β-oxidation along with acyl-carnitine transporters were abundant for oil substrates that allowed complete degradation of fatty acids to acetyl CoA. Further, low levels of oxidative biomarkers (H2O2, malondialdehyde) and antioxidants were determined for hydrophobic substrates, suggesting that SR21 efficiently mitigates the metabolic load and diverts the acetyl CoA towards energy generation and DHA accumulation.

CONCLUSIONS

The findings of this study contribute to uncovering the route of assimilation of oil substrates by SR21. The thraustochytrid employs an intricate crosstalk among the extracellular and intracellular molecular machinery favoring energy generation. The conversion of hydrophobic substrates to DHA can be further improved using synthetic biology tools, thereby providing a unique platform for the sustainable recycling of waste oil substrates.

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.

Metagenomic and metabolomic analysis of the effect of bleaching on unsaturated fatty acid synthesis pathways in coral symbionts

Unsaturated fatty acids (UFAs) are known to play a vital role in regulating stress resistance and metabolism in corals. Nevertheless, a comprehensive understanding of the microbial and functional composition of the UFA synthesis pathway (UFASP) remains lacking. This study employed metagenome and metabolome to investigate the microbial community, function, and metabolic response of UFASP in reef-building corals inhabiting the Nansha Islands. Our findings revealed significantly higher diversity for the UFASP microbe in bleached corals compared to unbleached corals. Furthermore, principal coordinates analysis (PCoA) and taxonomy assessments exhibited notable distinctions in the microbe between the two coral states. Notably, the dominant microorganisms involved in UFASP were Dinophyceae, Sordariomycetes, Ulvophyceae, and Chlorophyceae. Bleaching resulted in a considerable increase in fungal abundance within coral symbionts. A total of 12 KEGG Orthology (KO) were identified in UFASP, with PCoA analysis indicating significant differences in their abundance between bleached and unbleached corals. UFASP's beta-Oxidation module exhibited reduced abundance in bleached corals. Contribution analysis highlighted the participation of Symbiodiniaceae, Ascomycota, Chlorophyta, Proteobacteria, and Actinobacteria in UFASP. Notably, Symbiodiniaceae and Ascomycota were the major contributors to two UFASP modules, with the latter displaying greater involvement in bleached corals. Furthermore, significant differences in n3 and n6-family metabolites were observed between bleached and unbleached corals. Notably, bleaching induced a reduction in metabolites of Symbiodiniaceae, while an increase in the multiple UFAs abundance was detected in bleached corals. These findings suggest that bleaching-induced alterations coral symbionts composition directly impact the functionality of UFASP, ultimately affecting the corals' capacity to adapt to stress.

Enhancing docosahexaenoic acid production in Aurantiochytrium species using atmospheric and room temperature plasma mutagenesis and comprehensive multi-omics analysis

Aurantiochytrium sp. belongs to marine heterotrophic single-cell protist, which is an important decomposer in marine ecosystem. Aurantiochytrium sp. has gained notoriety because of its ability to accumulate high-value docosahexaenoic acid (DHA), but the key factors of DHA synthesis were unclear at present. In this study, Atmospheric and Room Temperature Plasma technology was applied to the mutagenic breeding of Aurantiochytrium sp., and transcriptomics and proteomics were adopted to analyze the DHA-biosynthesis mechanism. According to the growth and DHA accumulation profiles, the mutant strain Aurantiochytrium sp. R2A35 was selected. The DHA content in total lipids was greatly improved from 49.39 % of the wild strain R2 to 63.69 % of the mutant strain. Moreover, the DHA content in the biomass of Aurantiochytrium sp. R2A35 as 39.72 % was the highest DHA productivity reported so far. The differentially expressed genes distinguished from transcriptome and the TMT-identified differential proteins distinguished from proteome confirmed that the expression of acetyl-CoA carboxylase and ketoacyl reductase was up-regulated by 4.78-fold and 6.95-fold, respectively and the fatty acid synthase was concurrently down-regulated by 2.79-fold, so that more precursor was transported to the polyketide synthase pathway, thereby increasing the DHA yield in Aurantiochytrium sp. R2A35. This research would provide reference for the DHA metabolism process and contribute to the understanding of the decomposer - Aurantiochytrium sp. in marine ecosystems.

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.

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.

Distinct gut microbial communities and functional predictions in divergent ophiuroid species: host differentiation, ecological niches, and adaptation to cold-water habitats

IMPORTANCE

Gastrointestinal microorganisms are critical to the survival and adaptation of hosts, and there are few studies on the differences and functions of gastrointestinal microbes in widely distributed species. This study investigated the gut microbes of two ophiuroid species (Ophiura sarsii and its subspecies O. sarsii vadicola) in cold-water habitats of the Northern Pacific Ocean. The results showed that a combination of host and environmental factors shapes the intestinal microbiota of ophiuroids. There was a high similarity in microbial communities between the two groups living in different regions, which may be related to their similar ecological niches. These microorganisms played a vital role in the ecological success of ophiuroids as the foundation for their adaptation to cold-water environments. This study revealed the complex relationship between hosts and their gut microbes, providing insights into the role they play in the adaptation and survival of marine species.

Effects of microbial-converted ancient permafrost organic carbon on the growth and reproduction of Daphnia magna

Immense amounts of ancient (radiocarbon age over 200 years) organic carbon (OC) from permafrost are released into aquatic systems. Ancient terrestrial OC exists in numerous aquatic ecosystems. It has been reported that ancient OC can be incorporated by consumers in aquatic ecosystems, but the effect of ancient OC on the growth of consumers has rarely been studied. In this study, we extracted ancient dissolved organic carbon (DOC) from frozen soils in an alpine lake catchment. After a 6-day microbial conversion period, the contents of ω3 and ω6 polyunsaturated fatty acids (PUFAs) in ancient DOC increased. Proteobacteria and Actinobacteria were the primary taxa consuming the permafrost DOC and generating fatty acids. In addition to the exclusive diet of soil DOC (containing bacteria) or Chlorella pyrenoidosa, mixed diets of Chlorella pyrenoidosa, and ancient DOC (containing bacteria) in ratios of 2:1, 1:1, and 1:2 (by carbon concentration) were used to feed Daphnia magna. We discovered that Daphnia reared on the mixture with the DOC:Chlorella ratio of 1:2 had the highest contents of ω3 PUFAs and FAs. Daphnia reared exclusively on Chlorella and the mixture with the DOC:Chlorella ratio of 1:2 had the largest body size (3.1-3.4 mm) and the highest offspring production (95.5-96.2 ind-1). Daphnia fed on mixed diets exhibited higher intrinsic rates of population growth (0.48-0.53 d-1) compared to those fed exclusively on Chlorella pyrenoidosa, or ancient DOC plus bacteria. Overall, ancient soil OC converted by bacteria can act as a valuable supplement to algae food to promote Daphnia growth.

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.

Review of Eukaryote Cellular Membrane Lipid Composition, with Special Attention to the Fatty Acids

Biological membranes, primarily composed of lipids, envelop each living cell. The intricate composition and organization of membrane lipids, including the variety of fatty acids they encompass, serve a dynamic role in sustaining cellular structural integrity and functionality. Typically, modifications in lipid composition coincide with consequential alterations in universally significant signaling pathways. Exploring the various fatty acids, which serve as the foundational building blocks of membrane lipids, provides crucial insights into the underlying mechanisms governing a myriad of cellular processes, such as membrane fluidity, protein trafficking, signal transduction, intercellular communication, and the etiology of certain metabolic disorders. Furthermore, comprehending how alterations in the lipid composition, especially concerning the fatty acid profile, either contribute to or prevent the onset of pathological conditions stands as a compelling area of research. Hence, this review aims to meticulously introduce the intricacies of membrane lipids and their constituent fatty acids in a healthy organism, thereby illuminating their remarkable diversity and profound influence on cellular function. Furthermore, this review aspires to highlight some potential therapeutic targets for various pathological conditions that may be ameliorated through dietary fatty acid supplements. The initial section of this review expounds on the eukaryotic biomembranes and their complex lipids. Subsequent sections provide insights into the synthesis, membrane incorporation, and distribution of fatty acids across various fractions of membrane lipids. The last section highlights the functional significance of membrane-associated fatty acids and their innate capacity to shape the various cellular physiological responses.

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.

Examination of gammarid transcriptomes reveals a widespread occurrence of key metabolic genes from epibiont bdelloid rotifers in freshwater species

Previous data revealed the unexpected presence of genes encoding for long-chain polyunsaturated fatty acid (LC-PUFA) biosynthetic enzymes in transcriptomes from freshwater gammarids but not in marine species, even though closely related species were compared. This study aimed to clarify the origin and occurrence of selected LC-PUFA biosynthesis gene markers across all published gammarid transcriptomes. Through systematic searches, we confirmed the widespread occurrence of sequences from seven elongases and desaturases involved in LC-PUFA biosynthesis, in transcriptomes from freshwater gammarids but not marine species, and clarified that such occurrence is independent from the gammarid species and geographical origin. The phylogenetic analysis established that the retrieved elongase and desaturase sequences were closely related to bdelloid rotifers, confirming that multiple transcriptomes from freshwater gammarids contain contaminating rotifers' genetic material. Using the Adineta steineri genome, we investigated the genomic location and exon-intron organization of the elongase and desaturase genes, establishing they are all genome-anchored and, importantly, identifying instances of horizontal gene transfer. Finally, we provide compelling evidence demonstrating Bdelloidea desaturases and elongases enable these organisms to perform all the reactions for de novo biosynthesis of PUFA and, from them, LC-PUFA, an advantageous trait when considering the low abundance of these essential nutrients in freshwater environments.

Examination of Secondary Metabolite Biosynthesis in Apicomplexa

Natural product discovery has traditionally relied on the isolation of small molecules from producing species, but genome-sequencing technology and advances in molecular biology techniques have expanded efforts to a wider array of organisms. Protists represent an underexplored kingdom for specialized metabolite searches despite bioinformatic analysis that suggests they harbor distinct biologically active small molecules. Specifically, pathogenic apicomplexan parasites, responsible for billions of global infections, have been found to possess multiple biosynthetic gene clusters, which hints at their capacity to produce polyketide metabolites. Biochemical studies have revealed unique features of apicomplexan polyketide synthases, but to date, the identity and function of the polyketides synthesized by these megaenzymes remains unknown. Herein, we discuss the potential for specialized metabolite production in protists and the possible evolution of polyketide biosynthetic gene clusters in apicomplexan parasites. We then focus on a polyketide synthase from the apicomplexan Toxoplasma gondii to discuss the unique domain architecture and properties of these proteins when compared to previously characterized systems, and further speculate on the possible functions for polyketides in these pathogenic parasites.

Integrative miRNA-mRNA network analysis to identify crucial pathways of salinity adaptation in brain transcriptome of Labeo rohita

Introduction: Brain being the master regulator of the physiology of animal, the current study focuses on the gene expression pattern of the brain tissue with special emphasis on regulation of growth, developmental process of an organism and cellular adaptation of Labeo rohita against unfavourable environmental conditions. Methods: RNA-seq study was performed on collected brain samples at 8ppt salt concentration and analyzed for differential gene expression, functional annotation and miRNA-mRNA regulatory network. Results: We found that 2450 genes were having significant differential up and down regulation. The study identified 20 hub genes based on maximal clique centrality algorithm. These hub genes were mainly involved in various signaling pathways, energy metabolism and ion transportation. Further, 326 up and 1214 down regulated genes were found to be targeted by 7 differentially expressed miRNAs i.e., oni-miR-10712, oni-miR-10736, ssa-miR-221-3p, ssa-miR-130d-1-5p, ssa-miR-144-5p and oni-miR-10628. Gene ontology analysis of these differentially expressed genes led to the finding that these genes were involved in signal transduction i.e., calcium, FOXO, PI3K-AKT, TGF-β, Wnt and p53 signalling pathways. Differentially expressed genes were also involved in regulation of immune response, environmental adaptation i.e., neuroactive ligand-receptor interaction, ECM-receptor interaction, cell adhesion molecules and circadian entrainment, osmoregulation and energy metabolism, which are critical for salinity adaptation. Discussion: The findings of whole transcriptomic study on brain deciphered the miRNA-mRNA interaction patterns and pathways associated with salinity adaptation of L. rohita.

Improved polyketide production in C. glutamicum by preventing propionate-induced growth inhibition

Corynebacterium glutamicum is a promising host for production of valuable polyketides. Propionate addition, a strategy known to increase polyketide production by increasing intracellular methylmalonyl-CoA availability, causes growth inhibition in C. glutamicum. The mechanism of this inhibition was unclear before our work. Here we provide evidence that accumulation of propionyl-CoA and methylmalonyl-CoA induces growth inhibition in C. glutamicum. We then show that growth inhibition can be relieved by introducing methylmalonyl-CoA-dependent polyketide synthases. With germicidin as an example, we used adaptive laboratory evolution to leverage the fitness advantage of polyketide production in the presence of propionate to evolve improved germicidin production. Whole-genome sequencing revealed mutations in germicidin synthase, which improved germicidin titer, as well as mutations in citrate synthase, which effectively evolved the native glyoxylate pathway to a new methylcitrate pathway. Together, our results show that C. glutamicum is a capable host for polyketide production and we can take advantage of propionate growth inhibition to drive titers higher using laboratory evolution or to screen for production of polyketides.

Polyunsaturated Fatty Acids: Conversion to Lipid Mediators, Roles in Inflammatory Diseases and Dietary Sources

Polyunsaturated fatty acids (PUFAs) are important components of the diet of mammals. Their role was first established when the essential fatty acids (EFAs) linoleic acid and α-linolenic acid were discovered nearly a century ago. However, most of the biochemical and physiological actions of PUFAs rely on their conversion to 20C or 22C acids and subsequent metabolism to lipid mediators. As a generalisation, lipid mediators formed from n-6 PUFAs are pro-inflammatory while those from n-3 PUFAs are anti-inflammatory or neutral. Apart from the actions of the classic eicosanoids or docosanoids, many newly discovered compounds are described as Specialised Pro-resolving Mediators (SPMs) which have been proposed to have a role in resolving inflammatory conditions such as infections and preventing them from becoming chronic. In addition, a large group of molecules, termed isoprostanes, can be generated by free radical reactions and these too have powerful properties towards inflammation. The ultimate source of n-3 and n-6 PUFAs are photosynthetic organisms which contain Δ-12 and Δ-15 desaturases, which are almost exclusively absent from animals. Moreover, the EFAs consumed from plant food are in competition with each other for conversion to lipid mediators. Thus, the relative amounts of n-3 and n-6 PUFAs in the diet are important. Furthermore, the conversion of the EFAs to 20C and 22C PUFAs in mammals is rather poor. Thus, there has been much interest recently in the use of algae, many of which make substantial quantities of long-chain PUFAs or in manipulating oil crops to make such acids. This is especially important because fish oils, which are their main source in human diets, are becoming limited. In this review, the metabolic conversion of PUFAs into different lipid mediators is described. Then, the biological roles and molecular mechanisms of such mediators in inflammatory diseases are outlined. Finally, natural sources of PUFAs (including 20 or 22 carbon compounds) are detailed, as well as recent efforts to increase their production.

Engineering Nutritionally Improved Edible Plant Oils

In contrast to traditional breeding, which relies on the identification of mutants, metabolic engineering provides a new platform to modify the oil composition in oil crops for improved nutrition. By altering endogenous genes involved in the biosynthesis pathways, it is possible to modify edible plant oils to increase the content of desired components or reduce the content of undesirable components. However, introduction of novel nutritional components such as omega-3 long-chain polyunsaturated fatty acids needs transgenic expression of novel genes in crops. Despite formidable challenges, significant progress in engineering nutritionally improved edible plant oils has recently been achieved, with some commercial products now on the market.

Low dissolved oxygen supply functions as a global regulator of the growth and metabolism of Aurantiochytrium sp. PKU#Mn16 in the early stages of docosahexaenoic acid fermentation

BACKGROUND

Thraustochytrids accumulate lipids with a high content of docosahexaenoic acid (DHA). Although their growth and DHA content are significantly affected by the dissolved oxygen (DO) supply, the role of DO on the transcriptional regulation of metabolism and accumulation of intracellular metabolites remains poorly understood. Here we investigate the effects of three different DO supply conditions (10%, 30%, and 50%) on the fed-batch culture of the Aurantiochytrium PKU#Mn16 strain to mainly reveal the differential gene expressions and metabolite profiles.

RESULTS

While the supply of 10% DO significantly reduced the rates of biomass and DHA production in the early stages of fermentation, it achieved the highest amounts of biomass (56.7 g/L) and DHA (6.0 g/L) on prolonged fermentation. The transcriptome analyses of the early stage (24 h) of fermentation revealed several genes involved in the central carbon, amino acid, and fatty acid metabolism, which were significantly downregulated at a 10% DO level. The comparative metabolomics results revealed the accumulation of several long-chain fatty acids, amino acids, and other metabolites, supporting the transcriptional regulation under the influence of a low oxygen supply condition. In addition, certain genes involved in antioxidative systems were downregulated under 10% DO level, suggesting a lesser generation of reactive oxygen species that lead to oxidative damage and fatty acid oxidation.

CONCLUSIONS

The findings of this study suggest that despite the slow growth and metabolism in the early stage of fermentation of Aurantiochytrium sp. PKU#Mn16, a constant supply of low dissolved oxygen can yield biomass and DHA content better than that with high oxygen supply conditions. The critical information gained in this study will help to further improve DHA production through bioprocess engineering strategies.

Rapid remodeling of the soil lipidome in response to a drying-rewetting event

BACKGROUND

Microbiomes contribute to multiple ecosystem services by transforming organic matter in the soil. Extreme shifts in the environment, such as drying-rewetting cycles during drought, can impact the microbial metabolism of organic matter by altering microbial physiology and function. These physiological responses are mediated in part by lipids that are responsible for regulating interactions between cells and the environment. Despite this critical role in regulating the microbial response to stress, little is known about microbial lipids and metabolites in the soil or how they influence phenotypes that are expressed under drying-rewetting cycles. To address this knowledge gap, we conducted a soil incubation experiment to simulate soil drying during a summer drought of an arid grassland, then measured the response of the soil lipidome and metabolome during the first 3 h after wet-up.

RESULTS

Reduced nutrient access during soil drying incurred a replacement of membrane phospholipids, resulting in a diminished abundance of multiple phosphorus-rich membrane lipids. The hot and dry conditions increased the prevalence of sphingolipids and lipids containing long-chain polyunsaturated fatty acids, both of which are associated with heat and osmotic stress-mitigating properties in fungi. This novel finding suggests that lipids commonly present in eukaryotes such as fungi may play a significant role in supporting community resilience displayed by arid land soil microbiomes during drought. As early as 10 min after rewetting dry soil, distinct changes were observed in several lipids that had bacterial signatures including a rapid increase in the abundance of glycerophospholipids with saturated and short fatty acid chains, prototypical of bacterial membrane lipids. Polar metabolites including disaccharides, nucleic acids, organic acids, inositols, and amino acids also increased in abundance upon rewetting. This rapid metabolic reactivation and growth after rewetting coincided with an increase in the relative abundance of firmicutes, suggesting that members of this phylum were positively impacted by rewetting.

CONCLUSIONS

Our study revealed specific changes in lipids and metabolites that are indicative of stress adaptation, substrate use, and cellular recovery during soil drying and subsequent rewetting. The drought-induced nutrient limitation was reflected in the lipidome and polar metabolome, both of which rapidly shifted (within hours) upon rewet. Reduced nutrient access in dry soil caused the replacement of glycerophospholipids with phosphorus-free lipids and impeded resource-expensive osmolyte accumulation. Elevated levels of ceramides and lipids with long-chain polyunsaturated fatty acids in dry soil suggest that lipids likely play an important role in the drought tolerance of microbial taxa capable of synthesizing these lipids. An increasing abundance of bacterial glycerophospholipids and triacylglycerols with fatty acids typical of bacteria and polar metabolites suggest a metabolic recovery in representative bacteria once the environmental conditions are conducive for growth. These results underscore the importance of the soil lipidome as a robust indicator of microbial community responses, especially at the short time scales of cell-environment reactions. Video Abstract.

Protist–Lactic Acid Bacteria Co-Culture as a Strategy to Bioaccumulate Polyunsaturated Fatty Acids in the Protist Aurantiochytrium sp. T66

Thraustochytrids are aquatic unicellular protists organisms that represent an important reservoir of a wide range of bioactive compounds, such as essential polyunsaturated fatty acids (PUFAs) such as arachidonic acid (ARA), docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), which are involved in the regulation of the immune system. In this study, we explore the use of co-cultures of Aurantiochytrium sp. and bacteria as a biotechnological tool capable of stimulating PUFA bioaccumulation. In particular, the co-culture of lactic acid bacteria and the protist Aurantiochytrium sp. T66 induce PUFA bioaccumulation, and the lipid profile was evaluated in cultures at different inoculation times, with two different strains of lactic acid bacteria capable of producing the tryptophan dependent auxins, and one strain of Azospirillum sp., as a reference for auxin production. Our results showed that the Lentilactobacillus kefiri K6.10 strain inoculated at 72 h gives the best PUFA content (30.89 mg g−1 biomass) measured at 144 h of culture, three times higher than the control (8.87 mg g−1 biomass). Co-culture can lead to the generation of complex biomasses with higher added value for developing aquafeed supplements.

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.

Labelling of eicosapentaenoic acid with stable isotope 13C in the marine bacterium Shewanella marinintestina

Eicosapentaenoic acid (EPA) is an essential omega-3 polyunsaturated fatty acid that plays a critical role in marine life. It is present in several marine animals, including fish, but the primary producers of EPA are phytoplankton and specific marine bacteria. Although most of the EPA present in marine animals come from phytoplankton, the bacterial input into the marine EPA food web is still unknown. The labelling of EPA within a bacterial strain could be a viable strategy to help revealing this contribution. In this work, Shewanella marinintestina IRL 567, a marine bacterium isolated from fish guts and known to produce EPA, was labelled with the stable isotope ¹³C at small (250-mL shake flask), bench (2.5-L shake flask), and pilot scale (50-L stirred tank bioreactor). Growing the bacterium with ¹³C-acetate in the culture medium demonstrated that EPA was de-novo synthesized utilizing acetate as precursor. ¹³C incorporation into the EPA molecule resulted in values as high as 95.5% of the synthesized EPA being labelled in small scale, 95.9% in bench scale and 91.5% in pilot scale. This simple method to label EPA proved to be effective and therefore it could be a valuable tool to follow the fate of bacterial EPA into higher trophic levels.

Efficient Co-production of Docosahexaenoic Acid Oil and Carotenoids in Aurantiochytrium sp. Using a Light Intensity Gradient Strategy

Aurantiochytrium is a promising source of docosahexaenoic acid (DHA) and carotenoids, but their synthesis is influenced by environmental stress factors. In this study, the effect of different light intensities on the fermentation of DHA oil and carotenoids using Aurantiochytrium sp. TZ209 was investigated. The results showed that dark culture and low light intensity conditions did not affect the normal growth of cells, but were not conducive to the accumulation of carotenoids. High light intensity promoted the synthesis of DHA and carotenoids, but caused cell damage, resulting in a decrease of oil yield. To solve this issue, a light intensity gradient strategy was developed, which markedly improved the DHA and carotenoid content without reducing the oil yield. This strategy produced 30.16 g/L of microalgal oil with 15.11 g/L DHA, 221 µg/g astaxanthin, and 386 µg/g β-carotene. This work demonstrates that strain TZ209 is a promising DHA producer and provides an efficient strategy for the co-production of DHA oil together with carotenoids.

New alternative sources of omega-3 fish oil

Long-chain omega-3 polyunsaturated fatty acids such as eicosapentaenoic and docosahexaenoic acids play an important role in brain growth and development, as well as in the health of the body. These fatty acids are traditionally found in seafood, such as fish, fish oils, and algae. They can also be added to food or consumed through dietary supplements. Due to a lack of supply to meet current demand and the potential for adverse effects from excessive consumption of fish and seafood, new alternatives are being sought to achieve the recommended levels in a safe and sustainable manner. New sources have been studied and new production mechanisms have been developed. These new proposals, as well as the importance of these fatty acids, are discussed in this paper.

Construction of Glucose-6-Phosphate Dehydrogenase Overexpression Strain of Schizochytrium sp. H016 to Improve Docosahexaenoic Acid Production

Docosahexaenoic acid (DHA) is an important omega-3 polyunsaturated fatty acid (PUFA) that plays a critical physiological role in human health. Schizochytrium sp. is considered an excellent strain for DHA production, but the synthesis of DHA is limited by the availability of nicotinamide adenine dinucleotide phosphate (NADPH). In this study, the endogenous glucose-6-phosphate dehydrogenase (G6PD) gene was overexpressed in Schizochytrium sp. H016. Results demonstrated that G6PD overexpression increased the availability of NADPH, which ultimately altered the fatty acid profile, resulting in a 1.91-fold increase in DHA yield (8.81 g/L) and increased carbon flux by shifting it from carbohydrate and protein synthesis to lipid production. Thus, G6PD played a vital role in primary metabolism. In addition, G6PD significantly increased DHA content and lipid accumulation by 31.47% and 40.29%, respectively. The fed-batch fermentation experiment results showed that DHA production reached 17.01 g/L in the overexpressing G6PD strain. These results elucidated the beneficial effects of NADPH on the synthesis of PUFA in Schizochytrium sp. H016, which may be a potential target for metabolic engineering. Furthermore, this study provides a promising regulatory strategy for the large-scale production of DHA in Schizochytrium sp.

Efficient co-production of EPA and DHA by Schizochytrium sp. via regulation of the polyketide synthase pathway

Presently, the supply of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) traditionally produced by marine fisheries will be insufficient to meet their market demand in food industry. Thus a sustainable alternative source is urgently required. Schizochytrium sp. is an ideal producer of DHA; however, its ability to co-produce DHA and EPA has not yet been proved. Herein, we first described a cobalamin-independent methionine synthase-like (MetE-like) complex, which contains independent acyltransferase and 3-ketoacyl synthase domains, independent of the traditional polyketide synthase (PKS) system. When the MetE-like complex was activated, the EPA content was increased from 1.26% to 7.63%, which is 6.06-folds higher than that in the inactivated condition. Through lipidomics, we find that EPA is more inclined to be stored as triglyceride. Finally, the EPA production was enhanced from 4.19 to 29.83 (mg/g cell dry weight) using mixed carbon sources, and the final yield reached 2.25 g/L EPA and 9.59 g/L DHA, which means that Schizochytrium sp. has great market potential for co-production of EPA and DHA.

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

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

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.