GC–MS-based metabolomics study of the responses to arachidonic acid in Blakeslea trispora

Transcriptomic Analysis Reveals the Potential Mechanisms for Improving Carotenoid Production in Rhodosporidium toruloides Z11 under Light Stress

Carotenoids, as a type of tetraterpene compound, have been widely used in food, medical, and health areas owing to their antioxidant, immune enhancement, and disease risk reduction effects. Rhodosporidium toruloides is a promising oleaginous red yeast that can industrially synthesize carotenoids. In this study, the effects of different light exposure times and intervals on carotenoid production by R. toruloides Z11 were first investigated. Results showed that a higher carotenoid content (1.29 mg/g) can be achieved when R. toruloides Z11 was exposed to light for 12 h per day, which was increased by 1.98 times compared with that of dark cultivation. Transcriptome profiling revealed that light stress could effectively promote the gene expression levels of GGPS1 and AL1 in the carotenoid biosynthesis pathway and phr in the DNA photolysis pathway of R. toruloides. This work will provide a molecular foundation to further improve the production efficiency of carotenoids by genetic engineering.

Physarum polycephalum macroplasmodium exhibits countermeasures against TiO2 nanoparticle toxicity: A physiological, biochemical, transcriptional, and metabolic perspective

Concerns about the environmental and human health implications of TiO₂ nanoparticles (nTiO₂) are growing with their increased use in consumer and industrial products. Investigations of the underlying molecular mechanisms of nTiO₂ tolerance in organisms will assist in countering nTiO₂ toxicity. In this study, the countermeasures exhibited by the slime mold Physarum polycephalum macroplasmodium against nTiO₂ toxicity were investigated from a physiological, transcriptional, and metabolic perspective. The results suggested that the countermeasures against nTiO₂ exposure include gene-associated metabolic rearrangements in cellular pathways involved in amino acid, carbohydrate, and nucleic acid metabolism. Gene-associated nonmetabolic rearrangements involve processes such as DNA repair, DNA replication, and the cell cycle, and occur mainly when macroplasmodia are exposed to inhibitory doses of nTiO₂. Interestingly, the growth of macroplasmodia and mammal cells was significantly restored by supplementation with a combination of responsive metabolites identified by metabolome analysis. Taken together, we report a novel model organism for the study of nTiO₂ tolerance and provide insights into countermeasures taken by macroplasmodia in response to nTiO₂ toxicity. Furthermore, we also present an approach to mitigate the effects of nTiO₂ toxicity in cells by metabolic intervention.

Inhibitory mechanism of 6-Pentyl-2H-pyran-2-one secreted by Trichoderma atroviride T2 against Cylindrocarpon destructans

Root rot caused by Cylindrocarpon destructans is one of the most devastating diseases of Panax notoginseng, and Trichoderma species are potential agents for the biocontrol of fungal diseases. Thus, we screened a total of 10 Trichoderma isolates against C. destructans and selected Trichoderma atroviride T2 as an antagonistic strain for further research. 6-Pentyl-2H-pyran-2-one (6PP) was identified as an important active metabolite in the fermentation broth of the strain and exhibited antifungal activity against C. destructans. Transcriptome and metabolome analyses showed that 6PP significantly disturbed the metabolic homeostasis of C. destructans, particularly the metabolism of amino acids. By constructing a gene coexpression network, ECHS1 was identified as the hub gene correlated with 6PP stress. 6PP significantly downregulated the expression of ECHS1 at the transcriptional level and combined with the ECHS1 protein. Autophagy occurred in C. destructans cells under 6PP stress. In conclusion, 6PP may induce autophagy in C. destructans by downregulating ECHS1 at the transcriptional level and inhibiting ECHS1 protein activity. 6PP is a potential candidate for the development of new fungicides against C. destructans.

Metabolic disturbance in Korean red ginseng-induced "Shanghuo" (excessive heat)

ETHNOPHARMACOLOGICAL RELEVANCE

Northeast China is one of the Korean Red Ginseng (KRG) producing areas. As a health care product, KRG is popular amongst Chinese people. However, few studies have reported the side effects of overusing KRG.

AIM OF THE STUDY

The main purpose of this study is to explore the mechanism of Korean Red Ginseng (KRG)-induced "Shanghuo" (excessive heat).

MATERIALS AND METHODS

After the baseline characteristics were evaluated, 30 healthy volunteers were administrated with 3g of KRG for 10-16 days and diagnosed with "Shanghuo". The volunteers prior to the administration of KRG were considered as the control group. The volunteers after being diagnosed with "Shanghuo" (excessive heat) were considered as "Shanghuo" group. The two groups were assessed by the tests of serum metabolic products, Succinate Dehydrogenase (SDH) activity, and mRNA expressions of adenosine monophosphate (AMP)-activated protein kinase (AMPK), PPARG Coactivator 1 Alpha (PGC-1α) and Nuclear Respiratory Factor 1 (NRF1).

RESULTS

Most of the serum metabolites in the "Shanghuo" group were increased compared with the control group, from high to low including serine, valine, heptacosane, xylose, glycerol 1-monostearate, d-glucose, 3-pyridinol, glyceryl palmitate, urea, phosphoric acid, glycerol, stearic acid, palmitic acid, cyclohexaneacetic acid. Only cholesterol was significantly reduced, The SDH activity and the mRNA expressions of AMPK, PGC-1α and NRF1 were significantly increased in the "Shanghuo" group.

CONCLUSIONS

Overconsumption of KRG could induce "Shanghuo", which has a close relationship with an accelerated TCA cycle and the increased AMPK activity.

A Negative Regulator of Carotenogenesis in Blakeslea trispora

As an ideal carotenoid producer, Blakeslea trispora has gained much attention due to its large biomass and high production of β-carotene and lycopene. However, carotenogenesis regulation in B. trispora still needs to be clarified, as few investigations have been conducted at the molecular level in B. trispora In this study, a gene homologous to carotenogenesis regulatory gene (crgA) was cloned from the mating type (-) of B. trispora, and the deduced CrgA protein was analyzed for its primary structure and domains. To clarify the crgA-mediated regulation in B. trispora, we used the strategies of gene knockout and complementation to investigate the effect of crgA expression on the phenotype of B. trispora In contrast to the wild-type strain, the crgA null mutant (ΔcrgA) was defective in sporulation but accumulated much more β-carotene (31.2% improvement at the end) accompanied by enhanced transcription of three structural genes (hmgR, carB, and carRA) for carotenoids throughout the culture time. When the wild-type copy of crgA was complemented into the crgA null mutant, sporulation, transcription of structural genes, and carotenoid production were restored to those of the wild-type strain. A gas chromatography-mass spectrometry (GC-MS)-based metabolomic approach and multivariate statistical analyses were performed to investigate the intracellular metabolite profiles. The reduced levels of tricarboxylic acid (TCA) cycle components and some amino acids and enhanced levels of glycolysis intermediates and fatty acids indicate that more metabolic flux was driven into the mevalonate (MVA) pathway; thus, the increase of precursors and fat content contributes to the accumulation of carotenoids.IMPORTANCE The zygomycete Blakeslea trispora is an important strain for the production of carotenoids on a large scale. However, the regulation mechanism of carotenoid biosynthesis is still not well understood in this filamentous fungus. In the present study, we sought to investigate how crgA influences the expression of structural genes for carotenoids, carotenoid biosynthesis, and other anabolic phenotypes. This will lead to a better understanding of the global regulation mechanism of carotenoid biosynthesis and facilitate engineering this strain in the future for enhanced production of carotenoids.

Metabolomic Profiling of Carotenoid Constituents in Physalis peruviana During Different Growth Stages by LC-MS/MS Technology

With the current ongoing changes in global food demands, natural carotenoids are preferred by consumers and are gaining attention among food scientists and producers alike. Metabolomic profiling of carotenoid constituents in Physalis peruviana during distinct on-tree growth stages was performed with liquid chromatography-tandem mass spectrometry (LC-MS/MS) technology. The results show that the β rings of β-carotene are hydroxylated with great efficiency, and there is a continual synthesis of zeaxanthin at half-ripe and full-ripe stages, which is confirmed by relating the zeaxanthin content to that of its precursor (β-carotene). Lutein was, in terms of mass intensity, the most abundant carotenoid constituent (64.61 µg/g at the half-ripe stage) observed in this study. In addition, γ-carotene, which is rare in dietary fruits and vegetables, was detected in the mature and breaker stages, albeit at a relatively low level. The results suggest that when we consider the variation in carotenoid content during different growth stages, Physalis peruviana can be considered a good source of natural carotenoids.

Untargeted metabolomic analysis of the carotenoid-based orange coloration in Haliotis gigantea using GC-TOF-MS

Seafood coloration is typically considered an indicator of quality and nutritional value by consumers. One such seafood is the Xishi abalone (Haliotis gigantea), which displays muscle color polymorphism wherein a small subset of individuals display orange coloration of muscles due to carotenoid enrichment. However, the metabolic basis for carotenoid accumulation has not been thoroughly investigated in marine mollusks. Here, GC-TOF-MS-based untargeted metabolite profiling was used to identify key pathways and metabolites involved in differential carotenoid accumulation in abalones with variable carotenoid contents. Cholesterol was the most statistically significant metabolite that differentiated abalones with orange muscles against those with common white muscles. This observation is likely due to the competitive interactions between cholesterol and carotenoids during cellular absorption. In addition, the accumulation of carotenoids was also related to fatty acid contents. Overall, this study indicates that metabolomics can reflect physiological changes in organisms and provides a useful framework for exploring the mechanisms underlying carotenoid accumulation in abalone types.

Nano-sized TiO2 (nTiO2) induces metabolic perturbations in Physarum polycephalum macroplasmodium to counter oxidative stress under dark conditions

Nano-sized TiO₂ (nTiO₂) exerts an oxidative effect on cells upon exposure to solar or UV irradiation and ecotoxicity of the nTiO₂ is an urgent concern. Little information is available regarding the effect of TiO₂ on cells under dark conditions. Metabolomics is a unique approach to the discovery of biomarkers of nTiO₂ cytotoxicity, and leads to the identification of perturbed metabolic pathways and the mechanism underlying nTiO₂ toxicity. In the present study, gas chromatography mass spectrometry (GC/MS)-based metabolomics was performed to investigate the effect of nTiO₂ on sensitive cells (P. polycephalum macroplasmodium) under dark conditions. According to the multivariate pattern recognition analysis, at least 60 potential metabolic biomarkers related to sugar metabolism, amino acid metabolism, nucleotide metabolism, polyamine biosynthesis, and secondary metabolites pathways were significantly perturbed by nTiO₂. Notably, many metabolic biomarkers and pathways were related to anti-oxidant mechanisms in the living organism, suggesting that nTiO₂ may induce oxidative stress, even under dark conditions. This speculation was further validated by the biochemical levels of reactive oxygen species (ROS), 8-hydroxy-2-deoxyguanosine (8-OHdG), and total soluble phenols (TSP). We inferred that the oxidative stress might be related to nTiO₂-induced imbalance of cellular ROS. To the best of our knowledge, the present study is the first to investigate the nTiO₂-induced metabolic perturbations in slime mold, provide a new perspective of the mechanism underlying nTiO₂ toxicity under dark conditions, and show that metabolomics can be employed as a rapid, reliable and powerful tool to investigate the interaction among organisms, the environment, and nanomaterials.

Overexpression of Malonyl-CoA: ACP Transacylase in Schizochytrium sp. to Improve Polyunsaturated Fatty Acid Production

Polyunsaturated fatty acids (PUFAs) have been widely applied in the food and medical industry. In this study, malonyl-CoA: ACP transacylase (MAT) was overexpressed through homologous recombination to improve PUFA production in Schizochytrium. The results showed that the lipid and PUFA concentration were increased by 10.1 and 24.5% with MAT overexpression, respectively. Metabolomics analysis revealed that the intracellular tricarboxylic acid cycle was weakened and glucose absorption was accelerated in the engineered strain. In the mevalonate pathway, intracellular carotene content was decreased, and the carbon flux was then redirected toward PUFA synthesis. Furthermore, a glucose fed-batch fermentation was finally performed with the engineered Schizochytrium. The total lipid yield was further increased to 110.5 g/L, 39.6% higher than the wild strain. Docosahexaenoic acid and eicosapentaenoic acid yield were enhanced to 47.39 g/L and 1.65 g/L with an increase of 81.5 and 172.5%, respectively. This study provided an effective metabolic engineering strategy for industrial PUFA production.

Stability Study of Algerian Nigella sativa Seeds Stored under Different Conditions

In a study to determine the stability of the main volatile constituents of Nigella sativa seeds stored under several conditions, eight storage conditions were established, based on the ecological abiotic effects of air, heat, and light. Six replicates each were prepared and analyzed with Headspace-Gas Chromatography-Mass Spectrometry (HS-GC-MS) for three time points at the initial (1st day (0)), 14th (1), and 28th (2) day of storage. A targeted multivariate analysis of Principal Component Analysis revealed that the stability of the main volatile constituents of the whole seeds was better than that of the ground seeds. Exposed seeds, whole or ground, were observed to experience higher decrement of the volatile composition. These ecofactors of air, heat, and light are suggested to be directly responsible for the loss of volatiles in N. sativa seeds, particularly of the ground seeds.

Metabolomics analysis reveals 6-benzylaminopurine as a stimulator for improving lipid and DHA accumulation of Aurantiochytriumsp

BACKGROUND

Phytohormones are chemical messengers that have a positive effect on biodiesel production of microalgae at low concentrations. However, the effect of phytohormone 6-benzylaminopurine on lipid and docosahexaenoic acid (DHA) production in marine DHA-producer Aurantiochytrium has never been reported. In this study, a GC-MS-based metabolomics method combined with a multivariate analysis is applied to reveal the metabolic mechanism of 6-benzylaminopurine enhancing production of lipid and DHA in Aurantiochytrium sp.YLH70.

RESULTS

In total, 71 metabolites were identified by GC-MS. The PCA model revealed that 76.9% of metabolite variation was related to 6-benzylaminopurine treatment, and overall metabolomics profiles between the 6-benzylaminopurine and control groups were clearly discriminated. Forty-six metabolites identified by the PLS-DA model were responsible for responding to 6-benzylaminopurine. Metabolic analysis showed that 6-benzylaminopurine could accelerate the rate of utilization of glucose in Aurantiochytrium sp. YLH70, and the metabolic flux from glycolysis, TCA cycle and mevalonate pathway to fatty acids biosynthesis was promoted. Moreover, the anti-stress mechanism in Aurantiochytrium sp.YLH70 might be induced by 6-benzylaminopurine.

CONCLUSION

Metabolomics is a suitable tool to discover the metabolic mechanism for improving lipid and DHA accumulation in a microorganism. 6-benzylaminopurine has the potential to stimulate lipid and DHA production of Aurantiochytrium sp.YLH70 for industrial purposes. © 2015 The Authors. Journal of Chemical Technology & Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Analytical methodology for metabolomics study of adherent mammalian cells using NMR, GC-MS and LC-HRMS

We developed a methodology for the analysis of intracellular metabolites using nuclear magnetic resonance spectrometry (NMR), gas-chromatography coupled with mass spectrometry (GC-MS), and liquid chromatography coupled with high resolution mass spectrometry (LC-HRMS). The main steps for analysis of adherent cells in order to recover the widest possible range of intracellular compounds are blocking metabolic activity by quenching and extraction of intracellular metabolites. We explored three protocols to quench NSC-34 cell metabolism and four different extraction methods, analyzed by NMR. On the basis of the number of metabolites extracted and their relative standard deviation (RSD) analyzed by NMR, the most reproducible protocol [quenching by MeOH at -40 °C and extraction with CH2Cl2/MeOH/H2O (3:3:2)] was used to obtain intracellular media to be analyzed by GC-MS and LC-HRMS. GC-MS analysis was optimized by three oximation procedures followed by silylation derivatization and these were compared to silylation alone. Using reversed-phase liquid chromatography (C18), four different gradients for LC-MS were compared. The analytical protocols were determined to establish the reliability and suitability of sample treatments required to achieve the correct biological analysis of untargeted mammalian cell metabolomics.

Metabolic responses in Candida tropicalis to complex inhibitors during xylitol bioconversion

During xylitol fermentation, Candida tropicalis is often inhibited by inhibitors in hemicellulose hydrolysate. The mechanisms involved in the metabolic responses to inhibitor stress and the resistances to inhibitors are still not clear. To understand the inhibition mechanisms and the metabolic responses to inhibitors, a GC/MS-based metabolomics approach was performed on C. tropicalis treated with and without complex inhibitors (CI, including furfural, phenol and acetic acid). Partial least squares discriminant analysis was used to determine the metabolic variability between CI-treated groups and control groups, and 25 metabolites were identified as possible entities responsible for the discrimination caused by inhibitors. We found that xylose uptake rate and xylitol oxidation rate were promoted by CI treatment. Metabolomics analysis showed that the flux from xylulose to pentose phosphate pathway increased, and tricarboxylic acid cycle was disturbed by CI. Moreover, the changes in levels of 1,3-propanediol, trehalose, saturated fatty acids and amino acids showed different mechanisms involved in metabolic responses to inhibitor stress. The increase of 1,3-propanediol was considered to be correlated with regulating redox balance and osmoregulation. The increase of trehalose might play a role in protein stabilization and cellular membranes protection. Saturated fatty acids could cause the decrease of membrane fluidity and make the plasma membrane rigid to maintain the integrity of plasma membrane. The deeper understanding of the inhibition mechanisms and the metabolic responses to inhibitors will provide us with more information on the metabolism regulation during xylitol bioconversion and the construction of industrial strains with inhibitor tolerance for better utilization of bioresource.

Exogenous glycine and serine promote growth and antifungal activity of Penicillium citrinum W1 from the south-west Indian Ocean

PcPAF is a novel antifungal protein identified by our recent study, which is produced by a fungal strain Penicillium citrinum W1 isolated from a south-west Indian Ocean sediment sample. The present study identified glycine as a potential metabolite which increased the fungal growth and promoted antifungal activity. Then, GC/MS based metabolomics was used to disclose the metabolic mechanism manipulated by glycine. With the aid of unsupervised hierarchical clustering analysis and supervised orthogonal partial least-squares-discriminant analysis, the intracellular metabolite profiles were distinguished among two glycine-treated groups and control. 43 and 47 significantly varied metabolites were detected in 2.5 mM or 5 mM glycine-treated groups and involved in seven and eight pathways, respectively. Furthermore, exogenous serine, which is converted from glycine, showed the same potential as glycine did. Our findings not only identify glycine and serine as nutrients which promoted P. citrinum W1 growth and increased antifungal activity, but also highlight the way to utilize metabolomics for an understanding of metabolic mechanism manipulated by an exogenous compound.

Gas chromatography-mass spectrometry of biofluids and extracts

Gas chromatography-mass spectrometry (GC-MS) has been widely used in metabonomics analyses of biofluid samples. Biofluids provide a wealth of information about the metabolism of the whole body and from multiple regions of the body that can be used to study general health status and organ function. Blood serum and blood plasma, for example, can provide a comprehensive picture of the whole body, while urine can be used to monitor the function of the kidneys, and cerebrospinal fluid (CSF) will provide information about the status of the brain and central nervous system (CNS). Different methods have been developed for the extraction of metabolites from biofluids, these ranging from solvent extracts, acids, heat denaturation, and filtration. These methods vary widely in terms of efficiency of protein removal and in the number of metabolites extracted. Consequently, for all biofluid-based metabonomics studies, it is vital to optimize and standardize all steps of sample preparation, including initial extraction of metabolites. In this chapter, recommendations are made of the optimum experimental conditions for biofluid samples for GC-MS, with a particular focus on blood serum and plasma samples.

Metabolic regulation of α-linolenic acid on β-carotene synthesis in Blakeslea trispora revealed by a GC-MS-based metabolomic approach

ALA promoted β-carotene production in two ways: increasing the dissolved oxygen and decreasing the consumption of acetyl-CoA.

Sample collection and preparation of biofluids and extracts for gas chromatography-mass spectrometry

To maximize the utility of gas chromatography-mass spectrometry (GC-MS) in metabonomics research, all stages of the experimental design should be standardized, including sample collection, storage, preparation, and sample separation. Moreover, the prerequisite for any GC-MS analysis is that a compound must be volatile and thermally stable if it is to be analyzed using this technique. Since many metabolites are nonvolatile and polar in nature, they are not readily amenable to analysis by GC-MS and require initial chemical derivatization of the polar functional groups in order to reduce the polarity and to increase the thermal stability and volatility of the analytes. In this chapter, an overview is presented of the optimum approach to sample collection, storage, and preparation for gas chromatography-mass spectrometry-based metabonomics with particular focus on urine samples as example of biofluids.

Metabolomic profiling of Rhodosporidium toruloides grown on glycerol for carotenoid production during different growth phases

Carotenoid production from three strains of Rhodosporidium toruloides grown on glycerol was studied. A time-dependent metabolomics approach was used to understand its metabolism on glycerol and mechanism for carotenoid production in three strains during different growth phases (1, 4, 7, and 12 days). Strain CBS 5490 was the highest carotenoid producer (28.5 mg/L) and had a unique metabolic profile. In this strain, metabolites belonging to the TCA cycle and amino acids were produced in lower amounts, as compared to the other strains. On the other hand, it produced the highest amounts of carotenoid and fatty acid metabolites. This indicated that the lower production of the TCA cycle and amino acid metabolites promoted energy and metabolic flux toward the carotenoid and fatty acid synthesis metabolic pathways. This study shows that metabolomic profiling is a useful tool to gain insight into the metabolic pathways in the cell and to shed light on the different molecular mechanisms between strains.