A widespread alternative squalene epoxidase participates in eukaryote steroid biosynthesis

Expanding the insight of ecological risk on the novel chiral pesticide mefentrifluconazole: Mechanism of enantioselective toxicity to earthworms (Eisenia fetida)

Continued application of new chiral fungicide mefentrifluconazole (MFZ) increases its risk to soil ecosystem. However, the toxicity of MFZ enantiomers to soil fauna and whether stereoselectivity exists remains poorly elucidated. Based on multilevel toxicity endpoints and transcriptomics, we investigated the negative effects of racemic, R-(-)-, and S-(+)-MFZ on Eisenia fetida. After exposure to S-(+) configuration at 4 mg/kg for 28 day, its reactive oxygen species levels were elevated by 15.4% compared to R-(-) configuration, inducing enantiospecific oxidative stress and transcriptional aberrations. The S-(+) isomer induced more severe cell membrane damage and apoptosis than the R-(-) isomer, and notably, the selectivity of apoptosis is probably dominated by the mitochondrial pathway. Mechanistically, differential mitochondrial stress lies in: S-(+) isomer specifically up-regulated mitochondrial cellular component compared to R-(-) isomer and identified more serious mitochondrial fission. Furthermore, S-(+) conformation down-regulated biological processes associated with ATP synthesis and metabolism, with specific inhibition of mitochondrial respiratory electron transport chain complex I and IV activity resulting in more severe electron flow disturbances. These ultimately mediated enantioselective ontogenetic process disorders, which were supported at phenotypic (weight loss), genetic, and protein (reverse modulate TCTP and Sox2 expression) levels. Our findings offer an important reference for elucidating the enantioselective toxicological mechanism of MFZ in soil fauna.

Resistance mechanisms of Saccharomyces cerevisiae against silver nanoparticles with different sizes and coatings

To investigate the underlying resistance mechanisms of Saccharomyces cerevisiae against Ag-NPs with different particle sizes and coatings, transcriptome sequencing (RNA-seq) technology was used to characterize the transcriptomes from S. cerevisiae exposed to 20-PVP-Ag, 100-PVP-Ag, 20-CIT-Ag and 100-CIT-Ag, respectively. The steroid biosynthesis was found as a general pathway for Ag-NPs stress responding, in which ERG6 and ERG3 were inhibited and ERG11, ERG25 and ERG5 were significantly up-regulated to resist the stress by supporting the later mutation and resistance and modulate drug efflux indirectly. The resistance mechanism of S. cerevisiae to 20-PVP-Ag seems different from that of 100-PVP-Ag, 20-CIT-Ag and 100-CIT-Ag. Under the 20-PVP-Ag, transmembrane transporter activity, transition metal ion homeostasis and oxidative phosphorylation pathway were main resistance pathways to enhance cell transport processes. While 100-PVP-Ag, 20-CIT-Ag and 100-CIT-Ag mainly impacted RNA binding, structural constituent of ribosome and ribosome pathway which can provide more energy to maintain the number and function of protein in cells. This study reveals the differences in resistance mechanisms of S. cerevisiae to Ag-NPs with different particle sizes and coatings, and explains several main regulatory mechanisms used to respond to silver stress. It will provide theoretical basis for the study of chemical risk assessment.

Empirical evidence for metabolic drift in plant and algal lipid biosynthesis pathways

Metabolic pathway drift has been formulated as a general principle to help in the interpretation of comparative analyses between biosynthesis pathways. Indeed, such analyses often indicate substantial differences, even in widespread pathways that are sometimes believed to be conserved. Here, our purpose is to check how much this interpretation fits to empirical data gathered in the field of plant and algal biosynthesis pathways. After examining several examples representative of the diversity of lipid biosynthesis pathways, we explain why it is important to compare closely related species to gain a better understanding of this phenomenon. Furthermore, this comparative approach brings us to the question of how much biotic interactions are responsible for shaping this metabolic plasticity. We end up introducing some model systems that may be promising for further exploration of this question.

Identification of squalene epoxidase in triterpenes biosynthesis in Poria cocos by molecular docking and CRISPR-Cas9 gene editing

BACKGROUND

Squalene epoxidase is one of the rate-limiting enzymes in the biosynthetic pathway of membrane sterols and triterpenoids. The enzyme catalyzes the formation of oxidized squalene, which is a common precursor of sterols and triterpenoids.

RESULT

In this study, the squalene epoxidase gene (PcSE) was evaluated in Poria cocos. Molecular docking between PcSE and squalene was performed and the active amino acids were identified. The sgRNA were designed based on the active site residues. The effect on triterpene synthesis in P. cocos was consistent with the results from ultra-high-performance liquid chromatography-quadruplex time-of-flight-double mass spectrometry (UHPLC-QTOF-MS/MS) analysis. The results showed that deletion of PcSE inhibited triterpene synthesis. In vivo verification of PcSE function was performed using a PEG-mediated protoplast transformation approach.

CONCLUSION

The findings from this study provide a foundation for further studies on heterologous biosynthesis of P. cocos secondary metabolites.

Identification of Incomplete Annotations of Biosynthesis Pathways in Rhodophytes Using a Multi-Omics Approach

Rhodophytes (red algae) are an important source of natural products and are, therefore, a current research focus in terms of metabolite production. The recent increase in publicly available Rhodophyte whole genome and transcriptome assemblies provides the resources needed for in silico metabolic pathway analysis. Thus, this study aimed to create a Rhodophyte multi-omics resource, utilising both genomes and transcriptome assemblies with functional annotations to explore Rhodophyte metabolism. The genomes and transcriptomes of 72 Rhodophytes were functionally annotated and integrated with metabolic reconstruction and phylogenetic inference, orthology prediction, and gene duplication analysis to analyse their metabolic pathways. This resource was utilised via two main investigations: the identification of bioactive sterol biosynthesis pathways and the evolutionary analysis of gene duplications for known enzymes. We report that sterol pathways, including campesterol, β-sitosterol, ergocalciferol and cholesterol biosynthesis pathways, all showed incomplete annotated pathways across all Rhodophytes despite prior in vivo studies showing otherwise. Gene duplication analysis revealed high rates of duplication of halide-associated haem peroxidases in Florideophyte algae, which are involved in the biosynthesis of drug-related halogenated secondary metabolites. In summary, this research revealed trends in Rhodophyte metabolic pathways that have been under-researched and require further functional analysis. Furthermore, the high duplication of haem peroxidases and other peroxidase enzymes offers insight into the potential drug development of Rhodophyte halogenated secondary metabolites.

Mining and modification of Oryza sativa-derived squalene epoxidase for improved β-amyrin production in Saccharomyces cerevisiae

β-Amyrin is a pentacyclic triterpenoid and has anti-viral, anti-bacterial and anti-inflammatory activities. The synthetic pathway of β-amyrin has been analyzed and its heterogeneous synthesis has been achieved in Saccharomyces cerevisiae. Squalene epoxidase (SQE) catalyzes the oxygenation of squalene to form 2,3-oxidosqualene and is rate-limiting in the synthetic pathways of β-amyrin. The endogenous SQE in S. cerevisiae is insufficient for high production of β-amyrin. Herein, eight squalene epoxidases derived from different plants were selected and characterized in S. cerevisiae for improved biosynthesis of β-amyrin. Among them, the squalene epoxidase from Oryza sativa (OsSQE52) showed the best performance compared to other plant-derived sources. Through protein remodeling, the mutant OsSQE52L256R, obtained based on modeling analysis, increased the titer of β-amyrin by 2.43-fold compared to that in the control strain with ERG1 overexpressed under the same conditions. Moreover, the expression of OsSQE52L256R was optimized with the improvement of precursor supply to further increase the production of β-amyrin. Finally, the constructed strains produced 66.97 mg/L β-amyrin in the shake flask, which was 6.45-fold higher than the original strain. Our study provides alternative SQEs for efficient production of β-amyrin as well as other triterpenoids derived from 2,3-oxidosqualene.

Decoding the crosstalk between mevalonate metabolism and T cell function

The mevalonate pathway is an essential metabolic pathway in T cells regulating development, proliferation, survival, differentiation, and effector functions. The mevalonate pathway is a complex, branched pathway composed of many enzymes that ultimately generate cholesterol and nonsterol isoprenoids. T cells must tightly control metabolic flux through the branches of the mevalonate pathway to ensure sufficient isoprenoids and cholesterol are available to meet cellular demands. Unbalanced metabolite flux through the sterol or the nonsterol isoprenoid branch is metabolically inefficient and can have deleterious consequences for T cell fate and function. Accordingly, there is tight regulatory control over metabolic flux through the branches of this essential lipid synthetic pathway. In this review we provide an overview of how the branches of the mevalonate pathway are regulated in T cells and discuss our current understanding of the relationship between mevalonate metabolism, cholesterol homeostasis and T cell function.

Diverse uses of valuable seafood processing industry waste for sustainability: a review

Seafoods are rich in untapped bioactive compounds that have the potential to provide novel ingredients for the development of commercial functional foods and pharmaceuticals. Unfortunately, a large portion of waste or discards is generated in commercial processing setups (50-80%), which is wasted or underutilized. These by-products are a rich source of novel and valuable biomolecules, including bioactive peptides, collagen and gelatin, oligosaccharides, fatty acids, enzymes, calcium, water-soluble minerals, vitamins, carotenoids, chitin, chitosan and biopolymers. These fish components may be used in the food, cosmetic, pharmaceutical, environmental, biomedical and other industries. Furthermore, they provide a viable source for the production of biofuels. As a result, the current review emphasizes the importance of effective by-product and discard reduction techniques that can provide practical and profitable solutions. Recognizing this, many initiatives have been initiated to effectively use them and generate income for the long-term sustainability of the environment and economic framework of the processing industry. This comprehensive review summarizes the current state of the art in the sustainable valorisation of seafood by-products for human consumption. The review can generate a better understanding of the techniques for seafood waste valorisation to accelerate the sector while providing significant benefits.

Exploiting the anaerobic fermentation of alfalfa as a renewable source of squalene

BACKGROUND

The use of alfalfa is a promising response to the increasing demand for squalene. Ensiling could enhance the squalene content of fresh alfalfa and silage. To investigate and exploit the anaerobic fermentation of forage as a new squalene source, alfalfa was ensiled without (CON) or with molasses (ML) and sunflower seed oil (SSL) for 10, 40, and 70 days.

RESULTS

Naturally ensiled alfalfa was of poor quality but had up to 1.93 times higher squalene content (P < 0.001) than fresh alfalfa. The squalene-producing bacteria were found to be cocci lactic acid bacteria (LAB). Adding ML and SSL decreased squalene content (P = 0.002 and P < 0.001) by 6.89% and 11.6%, respectively. Multiple linear regression models and correlation analysis indicated that squalene synthase was the key enzyme for squalene synthesis. The addition of ML and SSL altered the structure of LAB communities, mainly decreasing the relative abundance of cocci LAB, which was responsible for squalene synthesis, and changing the fermentation products (lactic acid, propionic acid, and ammonia-N) influencing the squalene-related enzymes, thereby decreasing squalene production. Compared with squalene production from the reference bacteria (Pediococcus acidilactici Ch-2, Rhodopseudomonas palustris, Bacillus subtilis, engineered Escherichia coli), alfalfa silage had the potential to be a new squalene source.

CONCLUSION

Natural ensiled alfalfa was a promising source for squalene, and ensiling was a potential pathway to obtain novel high-yield squalene bacteria. © 2022 Society of Chemical Industry.

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

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

Comparative Transcriptome Analysis of Differentially Expressed Genes in the Testis and Ovary of Sea Urchin (Strongylocentrotus intermedius)

The quality of sea urchin gonad is important to consumers with high standards for nutrition and taste. However, few studies have been conductedon the molecular mechanisms that determine the quality of male and female sea urchins. In this study, our goal was to understand the differences and characteristics of gonad quality between sea urchin (Strongylocentrotus intermedius) males and females. The transcriptomes of males and females were obtained, with totals of 43,797,146 and 56,222,782 raw reads, respectively, comprising 128,979 transcripts and 85,745 unigenes. After comparative transcriptome analysis, a total of 6736 differentially expressed genes (DEGs) between the males and females were identified, of which 2950 genes were up-regulated and 3786 genes were down-regulated in males. We compared the expression of twelve DEGs with significant differences their expression levels and functional annotations to confirm the reliability of the RNA-Seq data. Five DEGs related to gonadal quality were found through enrichment analysis of KEGG pathways: 17β-HSD8, PGDH, FAXDC2, C4MO, and PNPLA7. Our study analyzes genes related to the taste and flavor of sea urchin gonads among the sexes and provides reference sequences and fundamental information concerning the nutrition and taste of S. intermedius gonads.

Widespread Sterol Methyltransferase Participates in the Biosynthesis of Both C4α- and C4β-Methyl Sterols

The 4-methyl steranes serve as molecular fossils and are used for studying both eukaryotic evolution and geological history. The occurrence of 4α-methyl steranes in sediments has long been considered evidence of products of partial demethylation mediated by sterol methyl oxidases (SMOs), while 4β-methyl steranes are attributed entirely to diagenetic generation from 4α-methyl steroids since possible biological sources of their precursor 4β-methyl sterols are unknown. Here, we report a previously unknown C4-methyl sterol biosynthetic pathway involving a sterol methyltransferase rather than the SMOs. We show that both C4α- and C4β-methyl sterols are end products of the sterol biosynthetic pathway in an endosymbiont of reef corals, Breviolum minutum, while this mechanism exists not only in dinoflagellates but also in eukaryotes from alveolates, haptophytes, and aschelminthes. Our discovery provides a previously untapped route for the generation of C4-methyl steranes and overturns the paradigm that all 4β-methyl steranes are diagenetically generated from the 4α isomers. This may facilitate the interpretation of molecular fossils and understanding of the evolution of eukaryotic life in general.

Microbial genetic engineering approach to replace shark livering for squalene

Squalene is generally sourced from the liver oil of deep sea sharks (Squalus spp.), in which it accounts for 40-70% of liver mass. To meet the growing demand for squalene because of its beneficial effects for human health, three to six million deep sea sharks are slaughtered each year, profoundly endangering marine ecosystems. To overcome this unsustainable practice, microbial sources of squalene might offer a viable alternative to plant- or animal-based squalene, although only a few microorganisms have been found that are capable of synthesizing up to 30% squalene of dry biomass by native biosynthetic pathways. These squalene biosynthetic pathways, on the other hand, can be genetically manipulated to transform microorganisms into 'cellular factories' for squalene overproduction.

Lipid biomarkers: molecular tools for illuminating the history of microbial life

Fossilized lipids preserved in sedimentary rocks offer singular insights into the Earth's palaeobiology. These 'biomarkers' encode information pertaining to the oxygenation of the atmosphere and oceans, transitions in ocean plankton, the greening of continents, mass extinctions and climate change. Historically, biomarker interpretations relied on inventories of lipids present in extant microorganisms and counterparts in natural environments. However, progress has been impeded because only a small fraction of the Earth's microorganisms can be cultured, many environmentally significant microorganisms from the past no longer exist and there are gaping holes in knowledge concerning lipid biosynthesis. The revolution in genomics and bioinformatics has provided new tools to expand our understanding of lipid biomarkers, their biosynthetic pathways and distributions in nature. In this Review, we explore how preserved organic molecules provide a unique perspective on the history of the Earth's microbial life. We discuss how advances in molecular biology have helped elucidate biomarker origins and afforded more robust interpretations of fossil lipids and how the rock record provides vital calibration points for molecular clocks. Such studies are open to further exploitation with the expansion of sequenced microbial genomes in accessible databases.

The Physalis floridana genome provides insights into the biochemical and morphological evolution of Physalis fruits

The fruits of Physalis (Solanaceae) have a unique structure, a lantern-like fruiting calyx known as inflated calyx syndrome (ICS) or the Chinese lantern, and are rich in steroid-related compounds. However, the genetic variations underlying the origin of these characteristic traits and diversity in Physalis remain largely unknown. Here, we present a high-quality chromosome-level reference genome assembly of Physalis floridana (~1.40 Gb in size) with a contig N50 of ~4.87 Mb. Through evolutionary genomics and experimental approaches, we found that the loss of the SEP-like MADS-box gene MBP21 subclade is likely a key mutation that, together with the previously revealed mutation affecting floral MPF2 expression, might have contributed to the origination of ICS in Physaleae, suggesting that the origination of a morphological novelty may have resulted from an evolutionary scenario in which one mutation compensated for another deleterious mutation. Moreover, the significant expansion of squalene epoxidase genes is potentially associated with the natural variation of steroid-related compounds in Physalis fruits. The results reveal the importance of gene gains (duplication) and/or subsequent losses as genetic bases of the evolution of distinct fruit traits, and the data serve as a valuable resource for the evolutionary genetics and breeding of solanaceous crops.

Off-On Squalene Epoxidase-Specific Fluorescent Probe for Fast Imaging in Living Cells

SQLE (squalene epoxidase) is a cell membrane-bound enzyme. It is a target of fungicides and may become a new target for cancer therapy. Therefore, monitoring the content and distribution of the key enzyme in living cells is very challenging. To achieve this goal, tetraphenyl ethylene-Ter (TPE-Ter) was first designed as a new fluorescent probe to SQLE based on its active cavity. Spectral experiments discovered that SQLE/TPE-Ter shows stronger emission with fast response time and low interference from other analytes. Molecular dynamics simulation clearly confirmed the complex structure of SQLE/TPE-Ter, and the key residues contribute to restriction of TPE-Ter single-molecular motion in the cavity. TPE-Ter-specific response to SQLE is successfully demonstrated in living cells such as LO2, HepG2, and fungi. Imaging of TPE-Ter-treated fungi indicates that it can be used to rapidly assess antifungal drug susceptibility (30 min at least). The present work provides a powerful tool to detect content and distribution of SQLE in living cells.

Proteome of Saccharomyces cerevisiae under paraquat stress regulated by therapeutic concentration of copper ions

Paraquat (PQ) is a non-selective herbicide with strong toxicity to humans and mammals. However, the proteome regulation of cells by PQ is still unclear, limiting the development of effective antidotes. Studies have shown that a slight excess of intracellular copper levels could be beneficial to the survival under exposure to PQ. In this study, Saccharomyces cerevisiae was used as a model to explore the regulation effect of copper ions on PQ poisoning by the approach of date independent acquisition proteomics. The results showed that toxic effect of PQ was primarily induced by oxidative damage in the mitochondria and the disorder of gene expression. The addition of Cu²⁺ involved a series of favorable reactions to cell survival under PQ stress, including activation of the mitogen-activated protein kinase signaling pathway, regulation of processes such as sulfur metabolism, carbon metabolism and gene expression in cells. The generation of glutathione, heme and steroids advantageous to cell growth under stress was also increased. These findings inferred that therapeutic concentration of copper ions could prolong the survival of cells under PQ stress.

ATP Drives Efficient Terpene Biosynthesis in Marine Thraustochytrids

Understanding carbon flux controlling mechanisms in a tangled metabolic network is an essential question of cell metabolism. Secondary metabolism, such as terpene biosynthesis, has evolved with low carbon flux due to inherent pathway constraints. Thraustochytrids are a group of heterotrophic marine unicellular protists and can accumulate terpenoids under the high-salt conditions in their natural environment. However, the mechanism behind terpene accumulation is not well understood. Here, we show that terpene biosynthesis in Thraustochytrium sp. ATCC 26185 is constrained by local thermodynamics in the mevalonate pathway. Thermodynamic analysis reveals metabolite limitation in the nondecarboxylative Claisen condensation of acetyl-coenzyme A (CoA) to the acetoacetyl-CoA step, catalyzed by the acetyl-CoA acetyltransferase (ACAT). Through a sodium-elicited mechanism, higher respiration leads to increased ATP investment into the mevalonate pathway, providing a strong thermodynamic driving force for enhanced terpene biosynthesis. Proteomic and metabolomic analyses further show that the increased ATP demands are fulfilled by shifting energy generation from carbohydrate to lipid oxidation. This study demonstrates a unique strategy in nature that uses ATP to drive a low-flux metabolic pathway, providing an alternative solution for efficient terpene metabolic engineering. IMPORTANCE Terpenoids are a large class of lipid molecules with important biological functions and diverse industrial and medicinal applications. Metabolic engineering for terpene production has been hindered by the low-flux distribution to its biosynthesis pathway. In practice, a high substrate load is generally required to reach high product titers. Here, we show that mevalonate-derived terpene biosynthesis is constrained by local pathway thermodynamics, which can only be partially relieved by increasing substrate levels. Through comparative omics and biochemical analyses, we discovered a unique mechanism for high terpene accumulation in marine protist thraustochytrids. Through a sodium-induced mechanism, thraustochytrids shift their energy metabolism from carbohydrate to lipid oxidation for enhanced ATP production, providing a strong thermodynamic driving force for efficient terpene biosynthesis. This study reveals an important mechanism in eukaryotes to overcome the thermodynamic constraint in low-flux pathways by increased ATP consumption. Engineering energy metabolism thus provides an important alternative to relieve flux constraints in low-flux and energy-consuming pathways.

Phytosterol Profiles, Genomes and Enzymes - An Overview

The remarkable diversity of sterol biosynthetic capacities described in living organisms is enriched at a fast pace by a growing number of sequenced genomes. Whereas analytical chemistry has produced a wealth of sterol profiles of species in diverse taxonomic groups including seed and non-seed plants, algae, phytoplanktonic species and other unicellular eukaryotes, functional assays and validation of candidate genes unveils new enzymes and new pathways besides canonical biosynthetic schemes. An overview of the current landscape of sterol pathways in the tree of life is tentatively assembled in a series of sterolotypes that encompass major groups and provides also peculiar features of sterol profiles in bacteria, fungi, plants, and algae.

A Water-Soluble 5/14-Carbobicyclic Steroid with a trans-9,11-Epoxy Ring from the Marine Dinoflagellate Amphidinium gibbosum: Insights into Late-Stage Diversification of Steroids

Gibbosterol A (1), a water-soluble 14-membered carbocyclic steroid with a twisted trans-9,11-epoxy ring, was discovered from the South China Sea dinoflagellate, Amphidinium gibbosum, together with its acid-induced cyclization product 2. It exhibits marked agonistic effects against human pregnane-X-receptor in a dose-dependent manner within the concentration range of 100 nM to 10 μM. Its 5/14-carbobicyclic nucleus is proposed to be originated from late-stage oxidative cleavage of the C5-C10 and C8-C9 bonds of β-sitosterol.

Dissecting cholesterol and phytosterol biosynthesis via mutants and inhibitors

Plants stand out among eukaryotes due to the large variety of sterols and sterol derivatives that they can produce. These metabolites not only serve as critical determinants of membrane structures, but also act as signaling molecules, as growth-regulating hormones, or as modulators of enzyme activities. Therefore, it is critical to understand the wiring of the biosynthetic pathways by which plants generate these distinct sterols, to allow their manipulation and to dissect their precise physiological roles. Here, we review the complexity and variation of the biosynthetic routes of the most abundant phytosterols and cholesterol in the green lineage and how different enzymes in these pathways are conserved and diverged from humans, yeast, and even bacteria. Many enzymatic steps show a deep evolutionary conservation, while others are executed by completely different enzymes. This has important implications for the use and specificity of available human and yeast sterol biosynthesis inhibitors in plants, and argues for the development of plant-tailored inhibitors of sterol biosynthesis.

Overexpression of Key Sterol Pathway Enzymes in Two Model Marine Diatoms Alters Sterol Profiles in Phaeodactylum tricornutum

Sterols are a class of triterpenoid molecules with diverse functional roles in eukaryotic cells, including intracellular signaling and regulation of cell membrane fluidity. Diatoms are a dominant eukaryotic phytoplankton group that produce a wide diversity of sterol compounds. The enzymes 3-hydroxy-3-methyl glutaryl CoA reductase (HMGR) and squalene epoxidase (SQE) have been reported to be rate-limiting steps in sterol biosynthesis in other model eukaryotes; however, the extent to which these enzymes regulate triterpenoid production in diatoms is not known. To probe the role of these two metabolic nodes in the regulation of sterol metabolic flux in diatoms, we independently over-expressed two versions of the native HMGR and a conventional, heterologous SQE gene in the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum. Overexpression of these key enzymes resulted in significant differential accumulation of downstream sterol pathway intermediates in P. tricornutum. HMGR-mVenus overexpression resulted in the accumulation of squalene, cycloartenol, and obtusifoliol, while cycloartenol and obtusifoliol accumulated in response to heterologous NoSQE-mVenus overexpression. In addition, accumulation of the end-point sterol 24-methylenecholesta-5,24(24’)-dien-3β-ol was observed in all P. tricornutum overexpression lines, and campesterol increased three-fold in P. tricornutum lines expressing NoSQE-mVenus. Minor differences in end-point sterol composition were also found in T. pseudonana, but no accumulation of sterol pathway intermediates was observed. Despite the successful manipulation of pathway intermediates and individual sterols in P. tricornutum, total sterol levels did not change significantly in transformed lines, suggesting the existence of tight pathway regulation to maintain total sterol content.

Four new polyhydroxylated steroids from the South Sea sponge Plakortis sp

Four new polyhydroxylated steroids plaksterols A-D (1-4), together with two known related steroids ergost-7,9(11),22-trien-3β,5α,6α-triol (5) and ergosta-6β-methoxy-7,22-diene-3β,5α-diol (6), were isolated from methanol extract of the South China Sea marine sponge Plakortis sp. Their structures were identified by spectroscopic analysis, including NMR, MS, and IR. The cytotoxicity of the polyhydroxylated steroids were evaluated, and compound 6 showed moderate inhibitory activities against K562, HL-60 and BEL-7402 cells.

Phenotypic trait variability as an indication of adaptive capacity in a cosmopolitan marine diatom

Determining the adaptive capacity of marine phytoplankton is important in predicting changes in phytoplankton responses to ocean warming. Phytoplankton may consist of high levels of standing phenotypic and genetic variability, the basis of rapid evolution; however, few studies have quantified trait variability within and amongst closely related diatom species. Using 35 clonal cultures of the ubiquitous marine diatom Leptocylindrus isolated from six locations, spanning 2000 km of the south-eastern Australian coastline, we found evidence of significant intraspecific morphological and metabolic trait variability, which for 8 of 9 traits (growth rate, biovolume, C:N, silica deposition, silica incorporation rate, chl-a, and photosynthetic efficiency under dark adapted, growth irradiance, and high-light adaptation) were greater within a species than between species. Moreover, only two traits revealed a latitudinal trend with strains isolated from lower latitudes showing significantly higher silicification rates and protein:lipid content compared to their higher latitude counterparts. These data mirror recent studies on diatom intraspecific genetic diversity, which has found comparable levels of genetic diversity at a single site to those thousands of kilometres apart, and provide evidence of a functional role of diatom diversity that will allow for rapid adaptation via ecological selection on standing variation in response to changing conditions.

Mining of squalene as a value-added byproduct from DHA producing marine thraustochytrid cultivated on food waste hydrolysate

The commercial production of docosahexaenoic acid (DHA) from oleaginous microorganisms is getting more attention due to several advantages over fish oils. The processing cost became a major bottleneck for commercialization of DHA from microorganisms. The most of cost shares in the feedstock to cultivate the microorganisms and downstream processing. The cost of feedstock can be compensated with the utilization of substrate from waste stream whereas production of value-added chemicals boosts the economic viability of nutraceutical production. In the present study, the docosahexaenoic acid (DHA)-producing marine protist Aurantiochytrium sp. T66 was cultivated on post-consumption food waste hydrolysate for the mining of squalene. After 120 h of cultivation, cell dry weight was 14.7 g/L, of which 6.34 g/L (43.13%; w/w) were lipids. DHA accounted for 2.15 g/L (34.05%) of total extracted lipids or 0.15 g/g_CDW. Maximum squalene concentration and yield were 1.05 g/L and 69.31 mg/g_CDW, respectively. Hence, utilization of food waste represents an excellent low-cost strategy for cultivating marine oleaginous thraustochytrids and produce squalene as a byproduct of DHA.

Sterol Evolution: Cholesterol Synthesis in Animals Is Less a Required Trait Than an Acquired Taste

Although cholesterol is considered a vital lipid for animals, not all animals can make cholesterol. A new study employing that celebrated elegant worm, Caenorhabditis elegans, investigates mechanisms that evolved in a sterol auxotroph to enable survival without sterol synthesis.

Comparative analysis and natural evolution of squalene epoxidase in three Fritillaria species

Fritillariae Bulbus are the most commonly used antitussive and edible herbs in China. Based on UPLC-QTOF-MS and UPLC-QQQ-MS, the validated MRM-based non-targeted quantitative method was applied to determinate the contents of 48 Fritillaria alkaloids (FAs) in three Fritillaria species (F. thunbergii Miq., F. unibracteata and F. ussuriensis). The RNA-Seq results showed that gene transcript levels have different expression patterns in three Fritillaria species. Based on transcriptome data, the full-length cDNA sequences of squalene epoxidase gene were cloned and characterized. Natural evolution of squalene epoxidase genes resulted in four mutations (C236R, M489L, G510A and K517R) in three Fritillaria species. Molecular docking analysis showed that the 236 residue is located inside the pocket and the binding center while other three residues are located on the surface of the protein. Functional verification indicated the mutations of SQE (C236R) could effectively increase the activity of SQE and obtain higher yield of 2,3-oxidosqualene in recombinant yeast. And the mutations of SQE (M489L and G510A), which increased the hydrophobicity of the protein surface, could also enhance the activity of SQE. This study provides major insights into the metabolites differentiation of FAs biosynthesis, and a firm foundation for the quality control and metabolic engineering of Fritillariae bulbus.

Metabolic Reconfiguration in C. elegans Suggests a Pathway for Widespread Sterol Auxotrophy in the Animal Kingdom

Cholesterol is one of the hallmarks of animals. In vertebrates, the cholesterol synthesis pathway (CSP) is the primary source of cholesterol that has numerous structural and regulative roles [1]. Nevertheless, the few invertebrates tested for cholesterol synthesis show complete sterol auxotrophy [2-6], raising questions about how animals thrive without cholesterol synthesis and about the prevalence of sterol auxotrophy in animals. In the nematode Caenorhabditis elegans (C. elegans), sterols are the precursors of the steroid hormone dafachronic acid that coordinates development to adulthood [7, 8]; thus, sterol-deprived C. elegans arrest at the diapause "dauer" larval stage [9]. Using this system, we have identified a pathway that converts plant and fungal sterols into cholesterol through the activity of enzymes with sequence similarity to specific human CSP enzymes. Based on this finding, we propose that two critical steps shaped the evolution of animal sterol auxotrophy: (1) the loss of the orthologs of the first three enzymes of the CSP and (2) the co-opting of other downstream enzymes of the CSP for the utilization of dietary sterols. Using this mechanistic signature, we studied the evolution of cholesterol auxotrophy across the animal kingdom. Complete sets of CSP enzymes in basal animals suggest that the loss of cholesterol synthesis occurred during animal evolution. A sterol auxothropy signature in the genomes of many invertebrates, including nematodes and most arthropods, suggests widespread cholesterol auxotrophy in animals. Thus, we propose that this co-opted pathway supports widespread cholesterol auxotrophy by interkingdom interactions between cholesterol-auxotrophic animals and sterol-producing fungi and plants.

Extrachromosomal Genetic Engineering of the Marine Diatom Phaeodactylum tricornutum Enables the Heterologous Production of Monoterpenoids

Geraniol is a commercially relevant plant-derived monoterpenoid that is a main component of rose essential oil and used as insect repellent. Geraniol is also a key intermediate compound in the biosynthesis of the monoterpenoid indole alkaloids (MIAs), a group of over 2000 compounds that include high-value pharmaceuticals. As plants naturally produce extremely small amounts of these molecules and their chemical synthesis is complex, industrially sourcing these compounds is costly and inefficient. Hence, microbial hosts suitable to produce MIA precursors through synthetic biology and metabolic engineering are currently being sought. Here, we evaluated the suitability of a eukaryotic microalga, the marine diatom Phaeodactylum tricornutum, for the heterologous production of monoterpenoids. Profiling of endogenous metabolism revealed that P. tricornutum, unlike other microbes employed for industrial production of terpenoids, accumulates free pools of the precursor geranyl diphosphate. To evaluate the potential for larger synthetic biology applications, we engineered P. tricornutum through extrachromosomal, episome-based expression, for the heterologous biosynthesis of the MIA intermediate geraniol. By profiling the production of geraniol resulting from various genetic and cultivation arrangements, P. tricornutum reached the maximum geraniol titer of 0.309 mg/L in phototrophic conditions. This work provides (i) a detailed analysis of P. tricornutum endogenous terpenoid metabolism, (ii) a successful demonstration of extrachromosomal expression for metabolic pathway engineering with potential gene-stacking applications, and (iii) a convincing proof-of-concept of the suitability of P. tricornutum as a novel production platform for heterologous monoterpenoids, with potential for complex pathway engineering aimed at the heterologous production of MIAs.

Emerging Technologies in Algal Biotechnology: Toward the Establishment of a Sustainable, Algae-Based Bioeconomy

Mankind has recognized the value of land plants as renewable sources of food, medicine, and materials for millennia. Throughout human history, agricultural methods were continuously modified and improved to meet the changing needs of civilization. Today, our rapidly growing population requires further innovation to address the practical limitations and serious environmental concerns associated with current industrial and agricultural practices. Microalgae are a diverse group of unicellular photosynthetic organisms that are emerging as next-generation resources with the potential to address urgent industrial and agricultural demands. The extensive biological diversity of algae can be leveraged to produce a wealth of valuable bioproducts, either naturally or via genetic manipulation. Microalgae additionally possess a set of intrinsic advantages, such as low production costs, no requirement for arable land, and the capacity to grow rapidly in both large-scale outdoor systems and scalable, fully contained photobioreactors. Here, we review technical advancements, novel fields of application, and products in the field of algal biotechnology to illustrate how algae could present high-tech, low-cost, and environmentally friendly solutions to many current and future needs of our society. We discuss how emerging technologies such as synthetic biology, high-throughput phenomics, and the application of internet of things (IoT) automation to algal manufacturing technology can advance the understanding of algal biology and, ultimately, drive the establishment of an algal-based bioeconomy.

Diatoms synthesize sterols by inclusion of animal and fungal genes in the plant pathway

Diatoms are ubiquitous microalgae that have developed remarkable metabolic plasticity and gene diversification. Here we report the first elucidation of the complete biosynthesis of sterols in the lineage. The study has been carried out on the bloom-forming species Skeletonema marinoi and Cyclotella cryptica that synthesise an ensemble of sterols with chemotypes of animals (cholesterol and desmosterol), plants (dihydrobrassicasterol and 24-methylene cholesterol), algae (fucosterol) and marine invertebrates (clionasterol). In both species, sterols derive from mevalonate through cyclization of squalene to cycloartenol by cycloartenol synthase. The pathway anticipates synthesis of cholesterol by enzymes of the phytosterol route in plants, as recently reported in Solanaceae. Major divergences stem from reduction of Δ24(28) and Δ24(25) double bonds which, in diatoms, are apparently dependent on sterol reductases of fungi, algae and animals. Phylogenetic comparison revealed a good level of similarity between the sterol biosynthetic genes of S. marinoi and C. cryptica with those in the genomes of the other diatoms sequenced so far.

Perspectives for Glyco-Engineering of Recombinant Biopharmaceuticals from Microalgae

Microalgae exhibit great potential for recombinant therapeutic protein production, due to lower production costs, immunity to human pathogens, and advanced genetic toolkits. However, a fundamental aspect to consider for recombinant biopharmaceutical production is the presence of correct post-translational modifications. Multiple recent studies focusing on glycosylation in microalgae have revealed unique species-specific patterns absent in humans. Glycosylation is particularly important for protein function and is directly responsible for recombinant biopharmaceutical immunogenicity. Therefore, it is necessary to fully characterise this key feature in microalgae before these organisms can be established as industrially relevant microbial biofactories. Here, we review the work done to date on production of recombinant biopharmaceuticals in microalgae, experimental and computational evidence for N- and O-glycosylation in diverse microalgal groups, established approaches for glyco-engineering, and perspectives for their application in microalgal systems. The insights from this review may be applied to future glyco-engineering attempts to humanize recombinant therapeutic proteins and to potentially obtain cheaper, fully functional biopharmaceuticals from microalgae.

Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift

Inferring genome-scale metabolic networks in emerging model organisms is challenged by incomplete biochemical knowledge and partial conservation of biochemical pathways during evolution. Therefore, specific bioinformatic tools are necessary to infer biochemical reactions and metabolic structures that can be checked experimentally. Using an integrative approach combining genomic and metabolomic data in the red algal model Chondrus crispus, we show that, even metabolic pathways considered as conserved, like sterols or mycosporine-like amino acid synthesis pathways, undergo substantial turnover. This phenomenon, here formally defined as "metabolic pathway drift," is consistent with findings from other areas of evolutionary biology, indicating that a given phenotype can be conserved even if the underlying molecular mechanisms are changing. We present a proof of concept with a methodological approach to formalize the logical reasoning necessary to infer reactions and molecular structures, abstracting molecular transformations based on previous biochemical knowledge.

Co-production of DHA and squalene by thraustochytrid from forest biomass

Omega-3 fatty acids, and specifically docosahexaenoic acid (DHA), are important and essential nutrients for human health. Thraustochytrids are recognised as commercial strains for nutraceuticals production, they are group of marine oleaginous microorganisms capable of co-synthesis of DHA and other valuable carotenoids in their cellular compartment. The present study sought to optimize DHA and squalene production by the thraustochytrid Schizochytrium limacinum SR21. The highest biomass yield (0.46 g/g_substrate) and lipid productivity (0.239 g/g_substrate) were observed with 60 g/L of glucose, following cultivation in a bioreactor, with the DHA content to be 67.76% w/w_{total lipids}. To reduce costs, cheaper feedstocks and simultaneous production of various value-added products for pharmaceutical or energy use should be attempted. To this end, we replaced pure glucose with organosolv-pretreated spruce hydrolysate and assessed the simultaneous production of DHA and squalene from S. limacinum SR21. After the 72 h of cultivation period in bioreactor, the maximum DHA content was observed to 66.72% w/w_{total lipids} that was corresponded to 10.15 g/L of DHA concentration. While the highest DHA productivity was 3.38 ± 0.27 g/L/d and squalene reached a total of 933.72 ± 6.53 mg/L (16.34 ± 1.81 mg/g_CDW). In summary, we show that the co-production of DHA and squalene makes S. limacinum SR21 appropriate strain for commercial-scale production of nutraceuticals.

Levels of Diatom Minor Sterols Respond to Changes in Temperature and Salinity

Diatoms are a broadly distributed and evolutionarily diversified group of microalgae that produce a diverse range of sterol compounds. Sterols are triterpenoids that play essential roles in membrane-related processes in eukaryotic cells. Some sterol compounds possess bioactivities that promote human health and are currently used as nutraceuticals. The relationship between sterol diversity in diatoms and their acclimation to different environments is not well understood. In this study, we investigated the occurrence of different sterol types across twelve diatom species, as well as the effect of temperature reduction and changes in salinity on the sterol contents of three model diatom species. In the diatoms Thalassiosira pseudonana, Phaeodactylum tricornutum and Chaetoceros muelleri, we found that changes in the relative contents of minor sterols accompanied shifts in temperature and salinity. This may be indicative of acquired adaptive traits in diatom metabolism.

Methyl jasmonate promote protostane triterpenes accumulation by up-regulating the expression of squalene epoxidases in Alisma orientale

Protostane triterpenes, which are found in Alisma orientale, are tetracyclic triterpenes with distinctive pharmacological activities. The natural distribution of protostane triterpenes is limited mainly to members of the botanical family Alismataceae. Squalene epoxidase (SE) is the key rate-limiting enzyme in triterpene biosynthesis. In this study, we report the characterization of two SEs from A. orientale. AoSE1 and AoSE2 were expressed as fusion proteins in E. coli, and the purified proteins were used in functional research. In vitro enzyme assays showed that AoSE1 and AoSE2 catalyze the formation of oxidosqualene from squalene. Immunoassays revealed that the tubers contain the highest levels of AoSE1 and AoSE2. After MeJA induction, which is the main elicitor of triterpene biosynthesis, the contents of 2,3-oxidosqualene and alisol B 23-acetate increased by 1.96- and 2.53-fold, respectively. In addition, the expression of both AoSE proteins was significantly increased at four days after MeJA treatment. The contents of 2,3-oxidosqualene and alisol B 23-acetate were also positively correlated with AoSEs expression at different times after MeJA treatment. These results suggest that AoSE1 and AoSE2 are the key regulatory points in protostane triterpenes biosynthesis, and that MeJA regulates the biosynthesis of these compounds by increasing the expression of AoSE1 and AoSE2.

OSBPL2 deficiency upregulate SQLE expression increasing intracellular cholesterol and cholesteryl ester by AMPK/SP1 and SREBF2 signalling pathway

Previous studies have shown that oxysterol binding protein like 2 (OSBPL2) knockdown is closely related to cholesterol metabolism. However, whether there is a direct relation between OSBPL2 and cholesterol synthesis is unknown. This study explored the mechanism of OSBPL2 deficiency in the upregulation of squalene epoxidase (SQLE) and the subsequent accumulation of intracellular cholesterol and cholesteryl ester. Here, we constructed an OSBPL2-deleted HeLa cell line using CRISPR/Cas9 technology, screened differentially expressed genes and examined the transcriptional regulation of SQLE using a dual-luciferase reporter gene. RNA-seq analysis showed that SQLE was upregulated significantly and the dual luciferase reporter gene assay revealed that two new functional transcription factor binding sites of Sp1 transcription factor (SP1) and sterol regulatory element-binding transcription factor 2 (SREBF2) in the SQLE promoter participated in the SQLE transcription and expression. In addition, we also observed that OSBPL2 deletion inhibited the AMPK signalling pathway and that the inhibition of AMPK signalling promoted SP1 and SREBF2 entry into the nuclear to upregulate SQLE expression. Therefore, these data support that OSBPL2 deficiency upregulates SQLE expression and increases the accumulation of cholesterol and cholesteryl ester by suppressing AMPK signalling, which provides new evidence of the connection between OSBPL2 and cholesterol synthesis.

Diatom isoprenoids: Advances and biotechnological potential

Diatoms are among the most productive and ecologically important groups of microalgae in contemporary oceans. Due to their distinctive metabolic and physiological features, they offer exciting opportunities for a broad range of commercial and industrial applications. One such feature is their ability to synthesize a wide diversity of isoprenoid compounds. However, limited understanding of how these molecules are synthesized have until recently hindered their exploitation. Following comprehensive genomic and transcriptomic analysis of various diatom species, the biosynthetic mechanisms and regulation of the different branches of the pathway are now beginning to be elucidated. In this review, we provide a summary of the recent advances in understanding diatom isoprenoid synthesis and discuss the exploitation potential of diatoms as chassis for high-value isoprenoid synthesis.

Relationship between acyl-lipid and sterol metabolisms in diatoms

Diatoms are a phylum of unicellular photosynthetic eukaryotes living in oceans and fresh waters, characterized by the complexity of their plastid, resulting from a secondary endosymbiosis event. In the model diatom Phaeodactylum tricornutum, fatty acids (FAs) are synthesized from acetyl-CoA in the stroma of the plastid, producing palmitic acid. FAs are elongated and desaturated to form very-long chain polyunsaturated fatty acids (VLC-PUFAs) in domains of the endomembrane system that need to be identified. Synthesis of VLC-PUFAs is coupled with their import to the core of the plastid via the so-called "omega" pathway. The biosynthesis of sterols in diatoms is likely to be localized in the endoplasmic reticulum as well as using precursors deriving from the mevalonate pathway, using acetyl-CoA as initial substrate. These metabolic modules can be characterized functionally by genetic analyzes or chemical treatments with appropriate inhibitors. Some 'metabolic modules' are characterized by a very low level of metabolic intermediates. Since some chemical treatments or genetic perturbation of lipid metabolism induce the accumulation of these intermediates, channeling processes are possibly involved, suggesting that protein-protein interactions might occur between enzymes within large size complexes or metabolons. At the junction of these modules, metabolic intermediates might therefore play dramatic roles in directing carbon fluxes from one direction to another. Here, acetyl-CoA seems determinant in the balance between TAGs and sterols. Future lines of research and potential utilization for biotechnological applications are discussed.

Phytosterol biosynthesis and production by diatoms (Bacillariophyceae)

Diatoms are abundant unicellular marine photosynthetic algae that have genetically diversified their physiology and metabolism while adapting to numerous environments. The metabolic repertoire of diatoms presents opportunities to characterise the biosynthesis and production of new and potentially valuable microalgal compounds, including sterols. Sterols of plant origin, known as phytosterols, have been studied for health benefits including demonstrated cholesterol-lowering properties. In this review we summarise sterol diversity, the unique metabolic features of sterol biosynthesis in diatoms, and prospects for the extraction of diatom phytosterols in comparison to existing sources. We also review biotechnological efforts to manipulate diatom biosynthesis, including culture conditions and avenues for the rational engineering of metabolism and cellular regulation.

Simultaneous production of DHA and squalene from Aurantiochytrium sp. grown on forest biomass hydrolysates

BACKGROUND

Recent evidence points to the nutritional importance of docosahexaenoic acid (DHA) in the human diet. Thraustochytrids are heterotrophic marine oleaginous microorganisms capable of synthesizing high amounts of DHA, as well as other nutraceutical compounds such as squalene, in their cellular compartment. Squalene is a natural triterpene and an important biosynthetic precursor to all human steroids. It has a wide range of applications in the cosmetic and pharmaceutical industries, with benefits that include boosting immunity and antioxidant activity. Apart from its nutritional quality, it can also be utilized for high-grade bio-jet fuel by catalytic conversion.

RESULTS

In the present study, the potential of thraustochytrid strain Aurantiochytrium sp. T66 to produce DHA and squalene was evaluated. When the strain was cultivated on organosolv-pretreated birch hydrolysate (30 g/L glucose) in flask, it resulted in 10.39 g/L of cell dry weight and 4.98 g/L of total lipids, of which 25.98% was DHA. In contrast, when the strain was grown in a bioreactor, cell dry weight, total lipid, and DHA increased to 11.24 g/L, 5.90 g/L, and 35.76%, respectively. The maximum squalene yield was 69.31 mg/g_CDW (0.72 g/L) when the strain was cultivated in flask, but it increased to 88.47 mg/g_CDW (1.0 g/L), when cultivation shifted to a bioreactor.

CONCLUSIONS

This is the first report demonstrating the utilization of low cost non-edible lignocellulosic feedstock to cultivate the marine oleaginous microorganism Aurantiochytrium sp. for the production of nutraceutical vital compounds. Owing to the simultaneous generation of DHA and squalene, the strain is suitable for industrial-scale production of nutraceuticals.