Identification of uncommon plant metabolites based on calculation of elemental compositions using gas chromatography and quadrupole mass spectrometry

The integration of metabolic and proteomic data uncovers an augmentation of the sphingolipid biosynthesis pathway during T-cell differentiation

Recent studies have highlighted the significance of cellular metabolism in the initiation of clonal expansion and effector differentiation of T cells. Upon exposure to antigens, naïve CD4+ T cells undergo metabolic reprogramming to meet their metabolic requirements. However, only few studies have simultaneously evaluated the changes in protein and metabolite levels during T cell differentiation. Our research seeks to fill the gap by conducting a comprehensive analysis of changes in levels of metabolites, including sugars, amino acids, intermediates of the TCA cycle, fatty acids, and lipids. By integrating metabolomics and proteomics data, we discovered that the quantity and composition of cellular lipids underwent significant changes in different effector Th cell subsets. Especially, we found that the sphingolipid biosynthesis pathway was commonly activated in Th1, Th2, Th17, and iTreg cells and that inhibition of this pathway led to the suppression of Th17 and iTreg cells differentiation. Additionally, we discovered that Th17 and iTreg cells enhance glycosphingolipid metabolism, and inhibition of this pathway also results in the suppression of Th17 and iTreg cell generation. These findings demonstrate that the utility of our combined metabolomics and proteomics analysis in furthering the understanding of metabolic transition during Th cell differentiation.

The role of metabolomics in informing strategies for improving photosynthesis

Photosynthesis plays a vital role in acclimating to and mitigating climate change, providing food and energy security for a population that is constantly growing, and achieving an economy with zero carbon emissions. A thorough comprehension of the dynamics of photosynthesis, including its molecular regulatory network and limitations, is essential for utilizing it as a tool to boost plant growth, enhance crop yields, and support the production of plant biomass for carbon storage. Photorespiration constrains photosynthetic efficiency and contributes significantly to carbon loss. Therefore, modulating or circumventing photorespiration presents opportunities to enhance photosynthetic efficiency. Over the past eight decades, substantial progress has been made in elucidating the molecular basis of photosynthesis, photorespiration, and the key regulatory mechanisms involved, beginning with the discovery of the canonical Calvin-Benson-Bassham cycle. Advanced chromatographic and mass spectrometric technologies have allowed a comprehensive analysis of the metabolite patterns associated with photosynthesis, contributing to a deeper understanding of its regulation. In this review, we summarize the results of metabolomics studies that shed light on the molecular intricacies of photosynthetic metabolism. We also discuss the methodological requirements essential for effective analysis of photosynthetic metabolism, highlighting the value of this technology in supporting strategies aimed at enhancing photosynthesis.

The effects of Micro/Nano-plastics exposure on plants and their toxic mechanisms: A review from multi-omics perspectives

In recent years, plastic pollution has become a global environmental problem, posing a potential threat to agricultural ecosystems and human health, and may further exacerbate global food security problems. Studies have revealed that exposure to micro/nano-plastics (MPs/NPs) might cause various aspects of physiological toxicities, including plant biomass reduction, intracellular oxidative stress burst, photosynthesis inhibition, water and nutrient absorption reduction, cellular and genotoxicity, seed germination retardation, and that the effects were closely related to MP/NP properties (type, particle size, functional groups), exposure concentration, exposure duration and plant characteristics (species, tissue, growth stage). Based on a brief review of the physiological toxicity of MPs/NPs to plant growth, this paper comprehensively reviews the potential molecular mechanism of MPs/NPs on plant growth from perspectives of multi-omics, including transcriptome, metabolome, proteome and microbiome, thus to reveal the role of MPs/NPs in plant transcriptional regulation, metabolic pathway reprogramming, protein translational and post-translational modification, as well as rhizosphere microbial remodeling at multiple levels. Meanwhile, this paper also provides prospects for future research, and clarifies the future research directions and the technologies adopted.

Plant Heterotrophic Cultures: No Food, No Growth

Plant cells are capable of uptaking exogenous organic substances. This inherited trait allows the development of heterotrophic cell cultures in various plants. The most common of them are Nicotiana tabacum and Arabidopsis thaliana. Plant cells are widely used in academic studies and as factories for valuable substance production. The repertoire of compounds supporting the heterotrophic growth of plant cells is limited. The best growth of cultures is ensured by oligosaccharides and their cleavage products. Primarily, these are sucrose, raffinose, glucose and fructose. Other molecules such as glycerol, carbonic acids, starch, and mannitol have the ability to support growth occasionally, or in combination with another substrate. Culture growth is accompanied by processes of specialization, such as elongation growth. This determines the pattern of the carbon budget. Culture ageing is closely linked to substrate depletion, changes in medium composition, and cell physiological rearrangements. A lack of substrate leads to starvation, which results in a decrease in physiological activity and the mobilization of resources, and finally in the loss of viability. The cause of the instability of cultivated cells may be the non-optimal metabolism under cultural conditions or the insufficiency of internal regulation.

A fat- and sucrose-enriched diet causes metabolic alterations in mdx mice

Duchenne muscular dystrophy (DMD), a progressive muscle disease caused by the absence of functional dystrophin protein, is associated with multiple cellular, physiological, and metabolic dysfunctions. As an added complication to the primary insult, obesity/insulin resistance (O/IR) is frequently reported in patients with DMD; however, how IR impacts disease severity is unknown. We hypothesized a high-fat, high-sucrose diet (HFHSD) would induce O/IR, exacerbate disease severity, and cause metabolic alterations in dystrophic mice. To test this hypothesis, we treated 7-wk-old mdx (disease model) and C57 mice with a control diet (CD) or an HFHSD for 15 wk. The HFHSD induced insulin resistance, glucose intolerance, and hyperglycemia in C57 and mdx mice. Of note, mdx mice on CD were also insulin resistant. In addition, visceral adipose tissue weights were increased with HFHSD in C57 and mdx mice though differed by genotype. Serum creatine kinase activity and histopathological analyses using Masson's trichrome staining in the diaphragm indicated muscle damage was driven by dystrophin deficiency but was not augmented by diet. In addition, markers of inflammatory signaling, mitochondrial abundance, and autophagy were impacted by disease but not diet. Despite this, in addition to disease signatures in CD-fed mice, metabolomic and lipidomic analyses demonstrated a HFHSD caused some common changes in C57 and mdx mice and some unique signatures of O/IR within the context of dystrophin deficiency. In total, these data revealed that in mdx mice, 15 wk of HFHSD did not overtly exacerbate muscle injury but further impaired the metabolic status of dystrophic muscle.

Enhancement of Growth and Secondary Metabolites by the Combined Treatment of Trace Elements and Hydrogen Water in Wheat Sprouts

This study aimed to evaluate the response of Triticum aestivum to hydrogen water (HW) and trace elements treated with HW. A pot experiment was conducted to assess the growth indices, secondary metabolites, and antioxidant levels. The response surface methodology (RSM) approach was used to ascertain the concentrations and significant interaction between treatments. The outcomes demonstrated that the combined treatment of Se acid and Mo oxide exhibited a notable positive effect on the growth and secondary metabolites, when treated with HW as compared to distilled water (DW). Notably, the interaction between these two treatments is significant, and the higher response was observed at the optimal concentration of 0.000005% for Se acid and 0.06% for Mo oxide. Additionally, an in vitro experiment revealed that the mixture treatment inhibits the accumulation of lipids in HepG2 hepatocytes cells. Moreover, metabolic analysis revealed that upregulated metabolites are linked to the inhibition of lipid accumulation. In addition, the analysis emphasizes that the continued benefits of higher plants as a renewable supply for chemicals compounds, especially therapeutic agents, are being expanded and amplified by these state-of-the-art technologies.

Optimising a urinary extraction method for non-targeted GC-MS metabolomics

Urine is ideal for non-targeted metabolomics, providing valuable insights into normal and pathological cellular processes. Optimal extraction is critical since non-targeted metabolomics aims to analyse various compound classes. Here, we optimised a low-volume urine preparation procedure for non-targeted GC-MS. Five extraction methods (four organic acid [OA] extraction variations and a "direct analysis" [DA] approach) were assessed based on repeatability, metabolome coverage, and metabolite recovery. The DA method exhibited superior repeatability, and achieved the highest metabolome coverage, detecting 91 unique metabolites from multiple compound classes comparatively. Conversely, OA methods may not be suitable for all non-targeted metabolomics applications due to their bias toward a specific compound class. In accordance, the OA methods demonstrated limitations, with lower compound recovery and a higher percentage of undetected compounds. The DA method was further improved by incorporating an additional drying step between two-step derivatization but did not benefit from urease sample pre-treatment. Overall, this study establishes an improved low-volume urine preparation approach for future non-targeted urine metabolomics applications using GC-MS. Our findings contribute to advancing the field of metabolomics and enable efficient, comprehensive analysis of urinary metabolites, which could facilitate more accurate disease diagnosis or biomarker discovery.

Polystyrene microplastic attenuated the toxic effects of florfenicol on rice (Oryza sativa L.) seedlings in hydroponics: From the perspective of oxidative response, phototoxicity and molecular metabolism

Antibiotics and microplastics (MPs) are two emerging pollutants in agroecosystems, however the effects of co-exposure to antibiotics and MPs remain unclear. The toxicity of florfenicol (FF) and polystyrene microplastics (PS-MPs) on rice seedlings was investigated. FF and PS-MPs caused colloidal agglomeration, which changed the environmental behavior of FF. FF inhibited rice growth and altered antioxidant enzyme (superoxide dismutase, peroxidase, and catalase) activities, leading to membrane lipid peroxidation; impaired photosynthetic systems, decreased photosynthetic pigments (Chlorophyll a, Chlorophyll b, and carotene), chlorophyll precursors (Proto IX, Mg-Proto IX, and Pchlide), photosynthetic and respiratory rates. The key photosynthesis related genes (PsaA, PsaB, PsbA, PsbB, PsbC, and PsbD) were significantly down-regulated. The ultrastructure of mesophyll cells was destroyed with chloroplast swelling, membrane surface blurring, irregular thylakoid lamellar structure, and number of peroxisomes increased. PS-MPs mitigated FF toxicity, and the IBR index values showed that 10 mg∙L-1 PS-MPs were more effective. Metabolomic analysis revealed that the abundance of metabolites and metabolic pathways were altered by FF, was greater than the combined "MPs-FF" contamination. The metabolism of amino acids, sugars, and organic acids were severely interfered. Among these, 15 metabolic pathways were significantly altered, with the most significant effects on phenylalanine metabolism and the citric acid cycle (p < 0.05).

Phytophthora sojae boosts host trehalose accumulation to acquire carbon and initiate infection

Successful infection by pathogenic microbes requires effective acquisition of nutrients from their hosts. Root and stem rot caused by Phytophthora sojae is one of the most important diseases of soybean (Glycine max). However, the specific form and regulatory mechanisms of carbon acquired by P. sojae during infection remain unknown. In the present study, we show that P. sojae boosts trehalose biosynthesis in soybean through the virulence activity of an effector PsAvh413. PsAvh413 interacts with soybean trehalose-6-phosphate synthase 6 (GmTPS6) and increases its enzymatic activity to promote trehalose accumulation. P. sojae directly acquires trehalose from the host and exploits it as a carbon source to support primary infection and development in plant tissue. Importantly, GmTPS6 overexpression promoted P. sojae infection, whereas its knockdown inhibited the disease, suggesting that trehalose biosynthesis is a susceptibility factor that can be engineered to manage root and stem rot in soybean.

Phytochemical Profiling and Biological Potential of Prunus dulcis Shell Extracts

Prunus dulcis is one of the most widely cultivated species in the world. Its fruit (almond) is rich in various nutritious and bioactive compounds that exert several beneficial effects. The aim of this study was to determine the chemical profile and evaluate the biological potential in vitro of almond shell extracts. The chemical analysis of shell extracts led to the identification of 15 compounds by HPLC-DAD, of which 11 were first detected in the almond plant. Twenty-six volatile compounds were identified by the GC-MS technique; among them, seven were firstly detected in the studied plant. For the biological activities, the extracts demonstrated moderate inhibition potential against the antioxidant, antidiabetic, and cytotoxic activities. The methanol extract at 50 µg/mL showed the highest antioxidant (45%) and antidiabetic activities (45% against alpha-glucosidase and 31% against alpha-amylase extracts), while the cyclohexane and dichloromethane at 50 µg/mL showed the highest cytotoxic activity towards Hela (32.2% with cyclohexane) and RAW 264-7 (45% with dichloromethane). Overall, these findings demonstrate the potential of almond shell extracts as a source of bioactive compounds that could be applied in the pharmaceutical and medical fields.

To metabolomics and beyond: a technological portfolio to investigate cancer metabolism

Tumour cells have exquisite flexibility in reprogramming their metabolism in order to support tumour initiation, progression, metastasis and resistance to therapies. These reprogrammed activities include a complete rewiring of the bioenergetic, biosynthetic and redox status to sustain the increased energetic demand of the cells. Over the last decades, the cancer metabolism field has seen an explosion of new biochemical technologies giving more tools than ever before to navigate this complexity. Within a cell or a tissue, the metabolites constitute the direct signature of the molecular phenotype and thus their profiling has concrete clinical applications in oncology. Metabolomics and fluxomics, are key technological approaches that mainly revolutionized the field enabling researchers to have both a qualitative and mechanistic model of the biochemical activities in cancer. Furthermore, the upgrade from bulk to single-cell analysis technologies provided unprecedented opportunity to investigate cancer biology at cellular resolution allowing an in depth quantitative analysis of complex and heterogenous diseases. More recently, the advent of functional genomic screening allowed the identification of molecular pathways, cellular processes, biomarkers and novel therapeutic targets that in concert with other technologies allow patient stratification and identification of new treatment regimens. This review is intended to be a guide for researchers to cancer metabolism, highlighting current and emerging technologies, emphasizing advantages, disadvantages and applications with the potential of leading the development of innovative anti-cancer therapies.

Comparative metabolic profiling of olive leaf extracts from twelve different cultivars collected in both fruiting and flowering seasons

Olea europaea is an economically significant crop native to Mediterranean countries. Its leaves exhibit several biological properties associated to their chemical composition. The aqueous ethanolic extracts of olive leaves from twelve different cultivars were analyzed by high performance liquid chromatography coupled to photodiode array and electrospray ionization mass spectrometry (HPLC/PDA/ESI-MS/MS). A total of 49 phytochemicals were identified in both positive and negative ionization modes. The identified compounds belonged to four classes of secondary metabolites including secoiridoids, flavonoids, pentacyclic triterpenoids and various phenolic compounds. Seasonal variation in chemical composition among the studied cultivars was apparent in autumn and spring. Secologanoside, oleuropein, hydroxy-oleuropein, demethyl oleuropein, gallocatechin, luteolin-O-hexoside, diosmetin, oleanolic acid and maslinic acid were detected in all cultivars in both seasons. Oleuropein-O-deoxyhexoside was tentatively identified for the first time in olive leaf extracts; detected only in the Spanish cultivar Picual (PIC) collected in spring. Also, dihydroxy-oxooleanenoic acid and hydroxy-oxooleanenoic acid, two bioactive pentacyclic triterpenes, were identified. Principle component analysis (PCA) showed good discrimination among the studied cultivars in terms of their botanical origin. This study is considered the first study for non-targeted metabolic profiling of different olive leaf cultivars cultivated in Egypt.

Derivatization Strategies in Flavor Analysis: An Overview over the Wine and Beer Scenario

Wine and beer are the most appreciated and consumed beverages in the world. This success is mainly due to their characteristic taste, smell, and aroma, which can delight consumer’s palates. These olfactory characteristics are produced from specific classes of volatile compounds called “volatile odor-active compounds” linked to different factors such as age and production. Given the vast market of drinking beverages, the characterization of these odor compounds is increasingly important. However, the chemical complexity of these beverages has led the scientific community to develop several analytical techniques for extracting and quantifying these molecules. Even though the recent “green-oriented” trend is directed towards direct preparation-free procedures, for some class of analytes a conventional step like derivatization is unavoidable. This review is a snapshot of the most used derivatization strategies developed in the last 15 years for VOAs’ determination in wine and beer, the most consumed fermented beverages worldwide and among the most complex ones. A comprehensive overview is provided for every method, whereas pros and cons are critically analyzed and discussed. Emphasis was given to miniaturized methods which are more consistent with the principles of “green analytical chemistry”.

Application of Metabolomics in Childhood Leukemia Diagnostics

Metabolomics is a new field of science dealing with the study and analysis of metabolites formed in living cells. The biological fluids used in this test method are: blood, blood plasma, serum, cerebrospinal fluid, saliva and urine. The most popular methods of assessing the composition of metabolites include nuclear magnetic resonance spectroscopy and mass spectrometry (MS) in combination with gas chromatography–MS or liquid chromatography–MS. Metabolomics is used in many areas of medicine. The variability of biochemical processes in neoplastic cells in relation to healthy cells is the starting point for this type of research. The aim of the research currently being carried out is primarily to find biomarkers for quick diagnosis of the disease, assessment of its advancement and treatment effectiveness. The development of metabolomics may also contribute to the individualization of treatment of patients, adjusting drugs depending on the metabolic profile, and thus may improve the effectiveness of therapy, reduce side effects and help to improve the quality of life of patients. Here, we review the current and potential applications of metabolomics, focusing on its use as a biomarker method for childhood leukemia.

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Comparing the Chemical Profiles of Plant-Based and Traditional Meats Using GC–MS-Based Metabolomics

As the consumer interest and market for plant-based meat alternatives grows, understanding the nutritional differences between alternative and traditional meats is essential. This article describes an untargeted gas chromatography–mass spectrometry (GC–MS)-based metabolomics approach that compares the chemical profiles of a popular plant-based meat alternative and grass-fed ground beef using a GC system coupled to a GC–MS device. The samples were derivatized to simplify the chromatographic process and render the polar metabolites more volatile for GC–MS analysis. Statistical and multivariate analysis of the acquired and processed GC–MS data revealed that 90% of the annotated compounds differed between the plant-based alternative meat and the grass-fed ground beef samples. The ground beef and plant-based products each contained several compounds that were found in much smaller quantities, or not at all, in the other product. These results indicate differences in organic composition even though the nutritional labels on the back of the products were nearly identical. Heat maps, principal component analysis (PCA) score plots, variable importance plots (VIPs), and the clustering of compounds into metabolite classes provided further insights into the differences between the two types of meat products. The biological significance of the comparative data was studied using online databases and pathway analysis tools.

Application of Metabolomics in Fungal Research

Metabolomics is an essential method to study the dynamic changes of metabolic networks and products using modern analytical techniques, as well as reveal the life phenomena and their inherent laws. Currently, more and more attention has been paid to the development of metabolic histochemistry in the fungus field. This paper reviews the application of metabolomics in fungal research from five aspects: identification, response to stress, metabolite discovery, metabolism engineering, and fungal interactions with plants.

Uncovering nasopharyngeal carcinoma from chronic rhinosinusitis and healthy subjects using routine medical tests via machine learning

Nasopharyngeal carcinoma (NPC) is one of the most common types of cancers in South China and Southeast Asia. Clinical data has shown that early detection is essential for improving treatment effectiveness and survival rate. Unfortunately, because the early symptoms of NPC are rather minor and similar to that of diseases such as Chronic Rhinosinusitis (CRS), early detection is a challenge. This paper proposes using machine learning methods to detect NPC using routine medical test data, namely Random Forest (RF), Support Vector Machine (SVM), and Artificial Neural Network (ANN), k-Nearest-Neighbor (KNN) and Logistic Regression (LR). We collected a dataset containing 523 newly diagnosed NPC patients before treatment, 501 newly diagnosed CRS patients before treatment as well as 600 healthy controls. The routine medical test data including age, gender, blood test features, liver function test features, and urine sediment test features. For comparison, we also used data from Epstein-Barr Virus (EBV) antibody tests, which is a specialized test not included among routine medical tests. In our first test, all four methods were tested on classifying NPC vs CRS vs controls; RF gives the best overall performance. Using only routine medical test data, it gives an accuracy of 83.1%, outperforming LR by 12%. In our second test, using only routine medical test data, when classifying NPC vs non-NPC (i.e. CRS or controls), RF achieves an accuracy of 88.2%. In our third test, when classifying NPC vs. controls, RF using only routine test data achieves an accuracy significantly better than RF using only EBV antibody data. Finally, in our last test, RF trained with NPC vs controls, using routine test data only, continued to perform well on an entirely separate dataset. This is a promising result because preliminary NPC detection using routine medical data is easy and inexpensive to implement. We believe this approach will play an important role in the detection and treatment of NPC in the future.

Integration of Metabolomics and Transcriptomics Reveal the Mechanism Underlying Accumulation of Flavonols in Albino Tea Leaves

Albino tea plants (Camellia sinensis) have been reported to possess highly inhibited metabolism of flavonoids compared to regular green tea leaves, which improves the quality of the tea made from these leaves. However, the mechanisms underlying the metabolism of catechins and flavonols in albino tea leaves have not been well elucidated. In this study, we analyzed a time series of leaf samples in the greening process from albino to green in a thermosensitive leaf-color tea mutant using metabolomics and transcriptomics. The total content of polyphenols dramatically decreased, while flavonols (such as rutin) were highly accumulated in albino leaves compared to in green leaves. After treatment with increasing environment temperature, total polyphenols and catechins were increased in albino mutant tea leaves; however, flavonols (especially ortho-dihydroxylated B-rings such as rutin) were decreased. Meanwhile, weighted gene co-expression network analysis of RNA-seq data suggested that the accumulation of flavonols was highly correlated with genes related to reactive oxygen species scavenging. Histochemical localization further demonstrated that this specific accumulation of flavonols might be related to their biological functions in stress tolerance. These findings suggest that the temperature-stimulated accumulation of total polyphenols and catechins in albino mutant tea leaves was highly induced by enhanced photosynthesis and accumulation of its products, while the initial accumulation and temperature inhibition of flavonols in albino mutant tea leaves were associated with metabolism related to oxidative stress. In conclusion, our results indicate that the biosynthesis of flavonoids could be driven by many different factors, including antioxidation and carbon skeleton storage, under favorable and unfavorable circumstances, respectively. This work provides new insights into the drivers of flavonoid biosynthesis in albino tea leaves, which will further help to increase tea quality by improving cultivation measures.

Classification of sugarcane genotypes susceptible and resistant to the initial attack of sugarcane borer Diatraea saccharalis using epicuticular wax composition

Identifying compounds present in the sugarcane epicuticular wax and using these compounds to classify the genotypes susceptible and resistant to the initial attack of sugarcane borer (Diatraea saccharalis) was the aim of this study. A greenhouse experiment was performed in a factorial scheme with and without borer infestation using genotypes previously characterized as resistant or susceptible in field-based experiments. Sugarcane whorls of six-month-old plants were collected before (BI) and after (AI) 72 h of sugarcane borer infestation. The sugarcane epicuticular wax was extracted in both times, i.e., BI and AI and its chemical composition was assessed by gas chromatography coupled to mass spectrometry (GC-MS). Twenty-five compounds were identified for both BI and AI. Classification models were built using partial least squares for discriminant analysis (PLS-DA) and linear discriminant analysis (LDA). Variable selection methods were used to improve the classification models. Ordered predictors selection for discriminant analysis (OPSDA) selected compounds that correctly classified all the test samples before borer infestation (Error = 0.000), and exhibited the most suitable classification parameters for the test set after borer infestation (Error = 0.111). The C30 pentacyclic triterpene friedelin and a high alcohol/aldehyde ratio were associated with the classification of resistant genotypes. Our findings have applicability in developing a screening methodology for breeding programs interested in identifying genotypes resistant to the initial feeding of sugarcane borer.

Data dimensionality reduction technique for clustering problem of metabolomics data

In metabolomics studies, independent analyses or replicating the metabolite concentration measurements are often performed to anticipate errors. On the other hand, the size of the dataset is increasing. For clustering purposes, obtaining representative information chemically from independent analyses is needed. The objective of this study is to develop a data reduction method such that a dataset that represents chemical information is obtained. Overall a proper data reduction method would simplify the clustering of metabolite data. We propose the modified Weiszfeld algorithm (MWA) to reduce independent analyses. To obtain comprehensive results, we compare MWA with some other well-known reduction methods, including PCA, CMDS, LE, and LLE. Then reduced datasets are clustered using the fuzzy c-means (FCM) algorithm with the Tang Sun Sun (TSS) index and silhouette index as the cluster validity indices. The results show that MWA, together with PCA, present the optimal number of clusters, namely four clusters. This result aligns with the optimal number of clusters before dimensionality reduction. The present results show that MWA is robust to perform dimensionality reduction of independent analyses while maintaining chemical information on the reduced dataset. Therefore, we recommend the reliability of MWA as one of the chemometric techniques, and the present finding has enriched chemometric techniques in metabolomics studies.

A long noncoding RNA functions in high-light-induced anthocyanin accumulation in apple by activating ethylene synthesis

Anthocyanin production in apple (Malus domestica) fruit and their consequent coloration can be induced by high-light treatment. The hormone ethylene is also essential for this coloration, but the regulatory relationships that link ethylene and light with anthocyanin-associated coloration are not well defined. In this study, we observed that high-light treatment of apple fruit increased anthocyanin accumulation more than moderate-light treatment did and was the main contributor of induced ethylene production and activation of anthocyanin biosynthesis. A transcriptome study of light-treated apple fruit suggested that a long noncoding RNA (lncRNA), MdLNC610, the corresponding gene of which is physically located downstream from the 1-aminocyclopropane-1-carboxylate oxygenase (ACO) ethylene biosynthesis gene MdACO1, likely affects anthocyanin biosynthesis under high-light treatment. Expression and promoter β-glucuronidase reporter analyses further showed that MdLNC610 upregulates expression of MdACO1 and so likely participates in high-light-induced ethylene biosynthesis. Overexpression of MdACO1 and MdLNC610 in apple fruit and calli indicated that a major increase in MdLNC610 expression activates MdACO1 expression, thereby causing an increase in ethylene production and anthocyanin levels. These results suggest that MdLNC610 participates in the regulation of high-light-induced anthocyanin production by functioning as a positive regulator to promote MdACO1 expression and ethylene biosynthesis. Our study provides insights into the relationship between mRNA and lncRNA networks in the ethylene biosynthetic pathway and anthocyanin accumulation in apple fruit.

Research Progress and Trends in Metabolomics of Fruit Trees

Metabolomics is an indispensable part of modern systems biotechnology, applied in the diseases' diagnosis, pharmacological mechanism, and quality monitoring of crops, vegetables, fruits, etc. Metabolomics of fruit trees has developed rapidly in recent years, and many important research results have been achieved in combination with transcriptomics, genomics, proteomics, quantitative trait locus (QTL), and genome-wide association study (GWAS). These research results mainly focus on the mechanism of fruit quality formation, metabolite markers of special quality or physiological period, the mechanism of fruit tree's response to biotic/abiotic stress and environment, and the genetics mechanism of fruit trait. According to different experimental purposes, different metabolomic strategies could be selected, such as targeted metabolomics, non-targeted metabolomics, pseudo-targeted metabolomics, and widely targeted metabolomics. This article presents metabolomics strategies, key techniques in metabolomics, main applications in fruit trees, and prospects for the future. With the improvement of instruments, analysis platforms, and metabolite databases and decrease in the cost of the experiment, metabolomics will prompt the fruit tree research to achieve more breakthrough results.

A feedback loop engaging propionate catabolism intermediates controls mitochondrial morphology

D-2-Hydroxyglutarate (D-2HG) is an α-ketoglutarate-derived mitochondrial metabolite that causes D-2-hydroxyglutaric aciduria, a devastating developmental disorder. How D-2HG adversely affects mitochondria is largely unknown. Here, we report that in Caenorhabditis elegans, loss of the D-2HG dehydrogenase DHGD-1 causes D-2HG accumulation and mitochondrial damage. The excess D-2HG leads to a build-up of 3-hydroxypropionate (3-HP), a toxic metabolite in mitochondrial propionate oxidation, by inhibiting the 3-HP dehydrogenase HPHD-1. We demonstrate that 3-HP binds the MICOS subunit MIC60 (encoded by immt-1) and inhibits its membrane-binding and membrane-shaping activities. We further reveal that dietary and gut bacteria affect mitochondrial health by modulating the host production of 3-HP. These findings identify a feedback loop that links the toxic effects of D-2HG and 3-HP on mitochondria, thus providing important mechanistic insights into human diseases related to D-2HG and 3-HP.

Opportunities in phytochemistry, ecophysiology and wood research via laser ablation direct analysis in real time imaging-mass spectrometry

Analysis of wood transects in a manner that preserves the spatial distribution of the metabolites present is highly desirable to among other things: (1) facilitate ecophysiology studies that reveal the association between chemical make-up and environmental factors or climatic events over time; and (2) investigate the mechanisms of the synthesis and trafficking of small molecules within specialised tissues. While a variety of techniques could be applied to achieve these goals, most remain challenging and impractical. Laser ablation direct analysis in real time imaging-mass spectrometry (LADI-MS) was successfully used to survey the chemical profile of wood, while also preserving the small-molecule spatial distributions. The tree species Entandrophragma candollei Harms, Millettia laurentii DeWild., Pericopsis elata (Harms) Meeuwen, Dalbergia nigra (Vell.) Benth. and Dalbergia normandii Bosser & R.Rabev were analysed. Several compounds were associated with anatomical features. A greater diversity was detected in the vessels and parenchyma compared with the fibres. Analysis of single vessels revealed that the chemical fingerprint used for timber identification is mainly determined by vessel content. Laser ablation direct analysis in real time imaging-mass spectrometry offers unprecedented opportunities to investigate the distribution of metabolites within wood samples, while circumventing the issues associated with previous methods. This technique opens up new vistas for the discovery of small-molecule biomarkers that are linked to environmental events.

Gas Chromatography-Mass Spectrometry (GC-MS) Analysis of Candida auris Metabolites

Unique metabolic features allow fungi to colonize and persist within the human host. Investigations of unique metabolic fingerprints of a pathogenic fungus can provide a more complete understanding of the infection process and an interpretation of associations between genotype and phenotype. Gas chromatography-mass spectrometry (GC-MS) has proved to be one of the most powerful analytical techniques used for qualitative and quantitative detection of cellular metabolites. This technique has been used for comparative metabolomic analyses of both intracellular and secreted metabolites under variable conditions. This book chapter describes the use of GC-MS in the detection of both intracellular and secreted metabolites from Candida auris, a newly emerging fungal pathogen representing a serious global health threat due to its multidrug resistance profile. The identified fungal metabolites are compared using available software in order to assign a correlation between the pattern of accumulation of metabolites and behavior of the organism.

Environmental exposures associated with honey bee health

Bee health is declining on a global scale, yet the exact causes and their interactions responsible for the decline remain unknown. To more objectively study bee health, recently biomarkers have been proposed as an essential tool, because they can be rapidly quantified and standardized, serving as a comparable measure across bee species and varying environments. Here, we used a systems biology approach to draw associations between endogenous and exogenous chemical profiles, with pesticide exposure, or the abundance of the 21 most common honey bee diseases. From the analysis we identified chemical biomarkers for both pesticide exposure and bee diseases along with the mechanistic biological pathways that may influence disease onset and progression. We found a total of 2352 chemical features, from 30 different hives, sampled from seven different locations. Of these, a total of 1088 significant associations were found that could serve as chemical biomarker profiles for predicting both pesticide exposure and the presence of diseases in a bee colony. In almost all cases we found novel external environmental exposures within the top seven associations with bee diseases and pesticide exposures, with the majority having previously unknown connections to bee health. We highlight the exposure-outcome paradigm and its ability to identify previously uncategorized interactions from different environmental exposures associated with bee diseases, pesticides, mechanisms, and potential synergistic interactions of these that are responsible for honey bee health decline.

Time-series eco-metabolomics reveals extensive reshuffling in metabolome during transition from cold acclimation to de-acclimation in an alpine shrub

Recording environmentally induced variations in the metabolome in plants can be a promising approach for understanding the complex patterns of metabolic regulation and their eco-physiological consequences. Here, we studied metabolome-wide changes and eco-physiological adjustments occurring across the year at high elevation environments in the leaf tissue of Rhododendron anthopogon, an alpine evergreen shrub of the Himalaya. New leaves of R. anthopogon appear after the snow-melt and remain intact even when the plants get covered under snow (November-June). During this whole period, they may undergo several physiological and biochemical adjustments in response to fluctuating temperatures and light conditions. To understand these changes, we analyzed eco-physiological traits, that is, freezing resistance, dry matter content and % of nitrogen and the overall metabolome across 10 different time-points, from August until the snowfall in November 2017, and then from June to August 2018. As anticipated, the freezing resistance increased toward the onset of winters. The leaf tissues exhibited a complete reshuffling of the metabolome during the growth cycle and time-points segregated into four clusters directly correlating with distinct phases of acclimation: non-acclimation (August 22, 2017; August 14, 2018), early cold acclimation (September 12, September 29, October 11, 2017), late cold acclimation (October 23, November 4, 2017), and de-acclimation (June 15, June 28, July 14, 2018). Cold acclimation involved metabolic progression (101 metabolites) with an increase of up to 19.4-fold (gentiobiose), whereas de-acclimation showed regression (120 metabolites) with a decrease of up to 30-fold (sucrose). The changes in the metabolome during de-acclimation were maximum and were not just a reversal of cold acclimation. Our results provided insights into the direction and magnitude of physiological changes in Rhododendron anthopogon that occurred across the year.

Characterization of key lipids for binding and generating aroma compounds in roasted mutton by UPLC-ESI-MS/MS and Orbitrap Exploris GC

Lipids are the key aroma formation substrates and retainers relevant to the flavor quality. The lipids in the roasted mutton were investigated by UPLC-ESI-MS/MS and Orbitrap Exploris GC. The results showed that a total of 2488 lipids from 24 subclasses were identified in the roasted mutton, including 28.21% triglyceride (TG), 14.87% phosphatidylcholine (PC), and 11.03% phosphatidylethanolamine (PE). TG (16:0_18:1_18:1) and TG (18:0_18:0_18:1) might be the predominant lipids for binding aroma compounds. 488 Differential lipids from 20 subclasses were observed based on VIP > 1 and p < 0.05. The 61 out of 488 differential lipids, especially PC and PE, might predominantly contribute to the formation of aroma compounds. A total of 13 aroma compounds were determined as the characteristic odorants in the roasted mutton, including hexanal, heptanal, and 1-octen-3-ol. PC (30: 6) and PC (28: 3) were the potential markers for the discrimination of roasted mutton.

Maize Zmcyp710a8 Mutant as a Tool to Decipher the Function of Stigmasterol in Plant Metabolism

Sterols are integral components of membrane lipid bilayers in eukaryotic organisms and serve as precursors to steroid hormones in vertebrates and brassinosteroids (BR) in plants. In vertebrates, cholesterol is the terminal sterol serving both indirect and direct roles in cell signaling. Plants synthesize a mixture of sterols including cholesterol, sitosterol, campesterol, and stigmasterol but the signaling role for the free forms of individual plant sterols is unclear. Since stigmasterol is the terminal sterol in the sitosterol branch and produced from a single enzymatic step, modifying stigmasterol concentration may shed light on its role in plant metabolism. Although Arabidopsis has been the model of choice to study sterol function, the functional redundancy of AtCYP710A genes and the presence of brassicasterol may hinder our ability to test the biological function of stigmasterol. We report here the identification and characterization of ZmCYP710A8, the sole maize C-22 sterol desaturase involved in stigmasterol biosynthesis and the identification of a stigmasterol-free Zmcyp710a8 mutant. ZmCYP710A8 mRNA expression pattern correlated with transcripts for several sterol biosynthesis genes and loss of stigmasterol impacted sterol composition. Exogenous stigmasterol also had a stimulatory effect on mRNA for ZmHMGR and ZmSMT2. This demonstrates the potential of Zmcyp710a8 in understanding the role of stigmasterol in modulating sterol biosynthesis and global cellular metabolism. Several amino acids accumulate in the Zmcyp710a8 mutant, offering opportunity for genetic enhancement of nutritional quality of maize. Other cellular metabolites in roots and shoots of maize and Arabidopsis were also impacted by genetic modification of stigmasterol content. Yet lack of obvious developmental defects in Zmcyp710a8 suggest that stigmasterol might not be essential for plant growth under normal conditions. Nonetheless, the Zmcyp710a8 mutant reported here is of great utility to advance our understanding of the additional roles of stigmasterol in plant metabolism. A number of biological and agronomic questions can be interrogated using this tool such as gene expression studies, spatio-temporal localization of sterols, cellular metabolism, pathway regulation, physiological studies, and crop improvement.

Metabolomics analysis of grains of wheat infected and noninfected with Tilletia controversa Kühn

Dwarf bunt caused by the pathogen Tilletia controversa Kühn is one of the most serious quarantine diseases of winter wheat. Metabolomics studies provide detailed information about the biochemical changes at the cell and tissue levels of plants. In the present study, a liquid chromatography/mass spectrometry (LC/MS) metabolomics approach was used to investigate the changes in the grain metabolomics of infected and noninfected with T. controversa samples. PCA suggested that T. controversa-infected and noninfected samples were separated during the interaction. LC/MS analysis showed that 62 different metabolites were recorded in the grains, among which a total of 34 metabolites were upregulated and 28 metabolites were downregulated. Prostaglandins (PGs) and 9-hydroxyoctadecadienoic acids (9-HODEs) are fungal toxin-related substances, and their expression significantly increased in T. controversa-infected grains. Additionally, the concentrations of cucurbic acid and octadecatrienoic acid changed significantly after pathogen infection, which play a large role in plant defense. The eight different metabolic pathways activated during T. controversa and wheat plant interactions included phenylalanine metabolism, isoquinoline alkaloid biosynthesis, starch and sucrose metabolism, tyrosine metabolism, sphingolipid metabolism, arginine and proline metabolism, alanine, aspartate, and glutamate metabolism, and tryptophan metabolism. In conclusion, we found differences in the metabolic profiles of wheat grains after T. controversa infection. To our knowledge, this is the first study to evaluate the metabolites in wheat grains after T. controversa infection.

Lipoteichoic acid from Bifidobacterium animalis subsp. lactis BPL1: a novel postbiotic that reduces fat deposition via IGF-1 pathway

Obesity and its related metabolic disorders, such as diabetes and cardiovascular disease, are major risk factors for morbidity and mortality in the world population. In this context, supplementation with the probiotic strain Bifidobacterium animalis subsp. lactis BPL1 (CECT8145) has been shown to ameliorate obesity biomarkers. Analyzing the basis of this observation and using the pre-clinical model Caenorhabditis elegans, we have found that lipoteichoic acid (LTA) of BPL1 is responsible for its fat-reducing properties and that this attribute is preserved under hyperglycaemic conditions. This fat-reducing capacity of both BPL1 and LTA-BPL1 is abolished under glucose restriction, as a result of changes in LTA chemical composition. Moreover, we have demonstrated that LTA exerts this function through the IGF-1 pathway, as does BPL1 strain. These results open the possibility of using LTA as a novel postbiotic, whose beneficial properties can be applied therapeutically and/or preventively in metabolic syndrome and diabetes-related disorders.

Simultaneous Determination of Polyamines and Steroids in Human Serum from Breast Cancer Patients Using Liquid Chromatography-Tandem Mass Spectrometry

A simultaneous quantitative profiling method for polyamines and steroids using liquid chromatography-tandem mass spectrometry was developed and validated. We applied this method to human serum samples to simultaneously evaluate polyamine and steroid levels. Chemical derivatization was performed using isobutyl chloroformate to increase the sensitivity of polyamines. The method was validated, and the matrix effects were in the range of 78.7-126.3% and recoveries were in the range of 87.8-123.6%. Moreover, the intra-day accuracy and precision were in the ranges of 86.5-116.2% and 0.6-21.8%, respectively, whereas the inter-day accuracy and precision were in the ranges of 82.0-119.3% and 0.3-20.2%, respectively. The linearity was greater than 0.99. The validated method was used to investigate the differences in polyamine and steroid levels between treated breast cancer patients and normal controls. In our results, N-acetyl putrescine, N-acetyl spermidine, cadaverine, 1,3-diaminopropane, and epitestosterone were significantly higher in the breast cancer patient group. Through receiver operating characteristic curve analysis, all metabolites that were significantly increased in patient groups with areas under the curve >0.8 were shown. This mass spectrometry-based quantitative profiling method, used for the investigation of breast cancer, is also applicable to androgen-dependent diseases and polyamine-related diseases.

A Significant Change in Free Amino Acids of Soybean (Glycine max L. Merr) through Ethylene Application

In this study, the changes in free amino acids of soybean leaves after ethylene application were characterized based on quantitative and metabolomic analyses. All essential and nonessential amino acids in soybean leaves were enhanced by fivefold (250 to 1284 mg/100 g) and sixfold (544 to 3478 mg/100 g), respectively, via ethylene application. In particular, it was found that asparagine is the main component, comprising approximately 41% of the total amino acids with a twenty-five fold increase (78 to 1971 mg/100 g). Moreover, arginine and branched chain amino acids (Val, Leu, and Ile) increased by about 14 and 2-5 times, respectively. The increase in free amino acid in stem was also similar to the leaves. The metabolites in treated and untreated soybean leaves were systematically identified by gas chromatography-mass spectrometry (GC-MS), and partial variance discriminant analysis (PLS-DA) scores and heat map analysis were given to understand the changes of each metabolite. The application of ethylene may provide good nutrient potential for soybean leaves.

Metabolomics reveals the within-plant spatial effects of shading on tea plants

It is well known that green tea made from fully developed leaves located at the base of young shoots is of lower quality than that made from the still developing leaves located on the top of the shoot. It has additionally been shown that plant shading can significantly improve green tea quality. Here, we aimed to get more insight into the effects of shading on the overall metabolome in different parts of the tea shoots. To do this, field-grown tea plants were shaded by coverage with either a straw layer or a black net, both blocking the daylight intensity for more than 90%. Both the first (i.e. still developing) leaf and the fourth (i.e. fully developed) leaf, as well as the stem of young shoots were harvested and subjected to complementary untargeted metabolomics approaches, using accurate mass LC-Orbitrap-Fourier transform mass spectrometry (FTMS) for profiling both semi-polar and lipid-soluble compounds and GC-TOF-MS for profiling polar compounds. In total, 1419 metabolites were detected. Shading resulted in a decreased ratio of polyphenols to amino acids (which improves the quality of green tea) and lower levels of galloylated catechins in the shoots. The positive effect of shading on the amino acid/catechin ratio was more pronounced in the fully developed (fourth) than in the developing (first) leaves. Furthermore, many metabolites, especially organic acids, carbohydrates and amino acids, showed differential or opposite responses to the shading treatments between the three shoot tissues investigated, suggesting a within-plant spatial regulation or transport/redistribution of carbon and nitrogen resources between the tissues of the growing young shoots. This work provides new insight into the spatial effects of shading on tea plants, which could further help to increase tea quality by improving cultivation measures for plant shading.

Citramalate synthase yields a biosynthetic pathway for isoleucine and straight- and branched-chain ester formation in ripening apple fruit

A plant pathway that initiates with the formation of citramalate from pyruvate and acetyl-CoA by citramalate synthase (CMS) is shown to contribute to the synthesis of α-ketoacids and important odor-active esters in apple (Malus × domestica) fruit. Microarray screening led to the discovery of a gene with high amino acid similarity to 2-isopropylmalate synthase (IPMS). However, functional analysis of recombinant protein revealed its substrate preference differed substantially from IPMS and was more typical of CMS. MdCMS also lacked the regulatory region present in MdIPMS and was not sensitive to feedback inhibition. 13C-acetate feeding of apple tissue labeled citramalate and α-ketoacids in a manner consistent with the presence of the citramalate pathway, labeling both straight- and branched-chain esters. Analysis of genomic DNA (gDNA) revealed the presence of two nearly identical alleles in "Jonagold" fruit (MdCMS_1 and MdCMS_2), differing by two nonsynonymous single-nucleotide polymorphisms (SNPs). The mature proteins differed only at amino acid 387, possessing either glutamine387 (MdCMS_1) or glutamate387 (MdCMS_2). Glutamate387 was associated with near complete loss of activity. MdCMS expression was fruit-specific, increasing severalfold during ripening. The translated protein product was detected in ripe fruit. Transient expression of MdCMS_1 in Nicotiana benthamiana induced the accumulation of high levels of citramalate, whereas MdCMS_2 did not. Domesticated apple lines with MdCMS isozymes containing only glutamate387 produced a very low proportion of 2-methylbutanol- and 2-methylbutanoate (2MB) and 1-propanol and propanoate (PROP) esters. The citramalate pathway, previously only described in microorganisms, is shown to function in ripening apple and contribute to isoleucine and 2MB and PROP ester biosynthesis without feedback regulation.

Metabolomic Elucidation of the Effect of Sucrose on the Secondary Metabolite Profiles in Melissa officinalis by Ultraperformance Liquid Chromatography-Mass Spectrometry

Sucrose induces flavonoid accumulation in plants as a defense mechanism against various stresses. However, the relationship between the biosynthesis of flavonoids as secondary metabolites and sucrose levels remains unknown. To understand the change in flavonoid biosynthesis by sucrose, we conducted secondary metabolite profiling in Melissa officinalis treated with different levels of sucrose using ultraperformance liquid chromatography/quadrupole time-of-flight mass spectrometry. The partial least squares-discriminant and hierarchical clustering analyses showed significant differences in secondary metabolite profiles in M. officinalis at 50, 150, and 300 mM sucrose levels. The levels of 3 flavonoids such as quercetin 3-O-β-d-glucosyl-(1→2)-β-d-glucoside, 6-methoxyaromadendrin 3-O-acetate, and 3-hydroxycoumarin and 19 flavonoids including 6-methoxyaromadendrin 3-O-acetate, aureusidin, iridin, flavonol 3-O-(6-O-malonyl-β-d-glucoside) quercetin 3-O-glucoside, and rutin increased at 150 and 300 mM sucrose, respectively, compared to 50 mM sucrose, indicating that the flavonoids were accumulated in M. officinalis by a higher concentration of sucrose. This is the first investigation of the change in individual flavonoids as secondary metabolites in M. officinalis by varying sucrose levels, and the results demonstrate that the sucrose causes the accumulation of certain flavonoids as a defense mechanism against osmotic stress.

Identification of biomarkers to diagnose diseases and find adverse drug reactions by metabolomics

Metabolomics has been widely used for investigating the biological functions of disease expression and has the potential to discover biomarkers in circulating biofluids or tissue extracts that reflect in phenotypic changes. Metabolic profiling has advantages because of the use of unbiased techniques, including multivariate analysis, and has been applied in pharmacological studies to predict therapeutic and adverse reactions of drugs, which is called pharmacometabolomics (PMx). Nuclear magnetic resonance (NMR)- and mass spectrometry (MS)-based metabolomics has contributed to the discovery of recent disease biomarkers; however, the optimal strategy for the study purpose must be selected from many established protocols, methodologies and analytical platforms. Additionally, information on molecular localization in tissue is essential for further functional analyses related to therapeutic and adverse effects of drugs in the process of drug development. MS imaging (MSI) is a promising technology that can visualize molecules on tissue surfaces without labeling and thus provide localized information. This review summarizes recent uses of MS-based global and wide-targeted metabolomics technologies and the advantages of the MSI approach for PMx and highlights the PMx technique for the biomarker discovery of adverse drug effects.

Dehydroquinate dehydratase/shikimate dehydrogenases involved in gallate biosynthesis of the aluminum-tolerant tree species Eucalyptus camaldulensis

Eucalyptus camaldulensis EcDQD/SDH2 and 3 combine gallate formation, dehydroquinate dehydratase, and shikimate dehydrogenase activities. They are candidates for providing the essential gallate for the biosynthesis of the aluminum-detoxifying metabolite oenothein B. The tree species Eucalyptus camaldulensis shows exceptionally high tolerance against aluminum, a widespread toxic metal in acidic soils. In the roots of E. camaldulensis, aluminum is detoxified via the complexation with oenothein B, a hydrolyzable tannin. In our approach to elucidate the biosynthesis of oenothein B, we here report on the identification of E. camaldulensis enzymes that catalyze the formation of gallate, which is the phenolic constituent of hydrolyzable tannins. By systematical screening of E. camaldulensis dehydroquinate dehydratase/shikimate dehydrogenases (EcDQD/SDHs), we found two enzymes, EcDQD/SDH2 and 3, catalyzing the NADP⁺-dependent oxidation of 3-dehydroshikimate to produce gallate. Based on extensive in vitro assays using recombinant EcDQD/SDH2 and 3 enzymes, we present for the first time a detailed characterization of the enzymatic gallate formation activity, including the cofactor preferences, pH optima, and kinetic constants. Sequence analyses and structure modeling suggest the gallate formation activity of EcDQD/SDHs is based on the reorientation of 3-dehydroshikimate in the catalytic center, which facilitates the proton abstraction from the C5 position. Additionally, EcDQD/SDH2 and 3 maintain DQD and SDH activities, resulting in a 3-dehydroshikimate supply for gallate formation. In E. camaldulensis, EcDQD/SDH2 and 3 are co-expressed with UGT84A25a/b and UGT84A26a/b involved in hydrolyzable tannin biosynthesis. We further identified EcDQD/SDH1 as a "classical" bifunctional plant shikimate pathway enzyme and EcDQD/SDH4a/b as functional quinate dehydrogenases of the NAD⁺/NADH-dependent clade. Our data indicate that in E. camaldulensis the enzymes EcDQD/SDH2 and 3 provide the essential gallate for the biosynthesis of the aluminum-detoxifying metabolite oenothein B.

Metabolomics revealing the response of rice (Oryza sativa L.) exposed to polystyrene microplastics

Large amounts of microplastics accumulate in the agricultural soil. Microplastics would stress the crops but the underlying mechanism remains unclear. Herein, a laboratory exposure and field trials were carried out to investigate the response of rice (Oryza sativa L. II You. 900) to stress induced by polystyrene microplastics (PS-MPs) using a metabolomic approach. After laboratory exposure for 21 days, the decreases in shoot biomass of rice exposed to low, medium and high doses of PS-MPs were 13.1% (CV = 4.1%), 18.8% (CV = 3.7%), and 40.3% (CV = 9.2%), respectively, while the antioxidant enzymes showed an inverted upper-U shape when exposed to PS-MPs. A total of 24 samples from three exposure dose levels were included in the metabolic analysis. The metabolites of 12 amino acids, 16 saccharides, 26 organic acids and 17 others (lipids and polyols) in leaves decreased after the exposure to both 50 mg L^-1 and 250 mg L^-1 PS-MPs doses with hydroponically-cultured. The inhibition of perturbed biological pathway causes the biosynthesis of amino acids, nucleic acids, fatty acids and some secondary metabolites decreased which indicate that the energy expenditure exceeded the substance accumulation. In order to further validate the effects of PS-MPs on rice leaves obtained from the laboratory-scale experiments, a field-trial experiment was conducted. After 142 days of cultivation in farmland, the results with a maximum of 25.9% lower biomass in the crops exposed with PS-MPs. As such, the presence of PS-MPs may affect rice production by altering the metabolic systems of rice. Long-term exposure of PS-MPs to rice might be a potential risk to rice safety and quality.

Evaluation of Sample Preparation Methods for Inter-Laboratory Metabolomics Investigation of Streptomyces lividans TK24

In the past two decades, metabolomics has proved to be a valuable tool with many potential applications in different areas of science. However, there are still some challenges that need to be addressed, particularly for multicenter studies. These challenges are mainly attributed to various sources of fluctuation and unwanted variations that can be introduced at pre-analytical, analytical, and/or post-analytical steps of any metabolomics experiment. Thus, this study aimed at using Streptomyces lividans TK24 as the model organism in a cross-laboratory experiment in Manchester and Leuven to evaluate the reproducibility of a standard sample preparation method, and determine the optimal sample format (cell extract or quenched biomass) required to preserve the metabolic profile of the cells during cross-lab sample transportation and storage. Principal component analysis (PCA) scores plot of the gas chromatography-mass spectrometry (GC-MS) data from both laboratories displayed clear growth-dependent clustering patterns which was in agreement with the Procrustes analysis findings. In addition, the data generated in Manchester displayed tight clustering of cell pellets (quenched biomass) and metabolite extracts, confirming the stability of both sample formats during the transportation and storage period.

Biochemical and Genetic Analysis of 4-Hydroxypyridine Catabolism in Arthrobacter sp. Strain IN13

N-Heterocyclic compounds are widely spread in the biosphere, being constituents of alkaloids, cofactors, allelochemicals, and artificial substances. However, the fate of such compounds including a catabolism of hydroxylated pyridines is not yet fully understood. Arthrobacter sp. IN13 is capable of using 4-hydroxypyridine as a sole source of carbon and energy. Three substrate-inducible proteins were detected by comparing protein expression profiles, and peptide mass fingerprinting was performed using MS/MS. After partial sequencing of the genome, we were able to locate genes encoding 4-hydroxypyridine-inducible proteins and identify the kpi gene cluster consisting of 16 open reading frames. The recombinant expression of genes from this locus in Escherichia coli and Rhodococcus erytropolis SQ1 allowed an elucidation of the biochemical functions of the proteins. We report that in Arthrobacter sp. IN13, the initial hydroxylation of 4-hydroxypyridine is catalyzed by a flavin-dependent monooxygenase (KpiA). A product of the monooxygenase reaction is identified as 3,4-dihydroxypyridine, and a subsequent oxidative opening of the ring is performed by a hypothetical amidohydrolase (KpiC). The 3-(N-formyl)-formiminopyruvate formed in this reaction is further converted by KpiB hydrolase to 3-formylpyruvate. Thus, the degradation of 4-hydroxypyridine in Arthrobacter sp. IN13 was analyzed at genetic and biochemical levels, elucidating this catabolic pathway.

Metabolomics should be deployed in the identification and characterization of gene-edited crops

Gene-editing techniques are currently revolutionizing biology, allowing far greater precision than previous mutagenic and transgenic approaches. They are becoming applicable to a wide range of plant species and biological processes. Gene editing can rapidly improve a range of crop traits, including disease resistance, abiotic stress tolerance, yield, nutritional quality and additional consumer traits. Unlike transgenic approaches, however, it is not facile to forensically detect gene-editing events at the molecular level, as no foreign DNA exists in the elite line. These limitations in molecular detection approaches are likely to focus more attention on the products generated from the technology than on the process in itself. Rapid advances in sequencing and genome assembly increasingly facilitate genome sequencing as a means of characterizing new varieties generated by gene-editing techniques. Nevertheless, subtle edits such as single base changes or small deletions may be difficult to distinguish from normal variation within a genotype. Given these emerging scenarios, downstream 'omics' technologies reflective of edited affects, such as metabolomics, need to be used in a more prominent manner to fully assess compositional changes in novel foodstuffs. To achieve this goal, metabolomics or 'non-targeted metabolite analysis' needs to make significant advances to deliver greater representation across the metabolome. With the emergence of new edited crop varieties, we advocate: (i) concerted efforts in the advancement of 'omics' technologies, such as metabolomics, and (ii) an effort to redress the use of the technology in the regulatory assessment for metabolically engineered biotech crops.

Comparative analysis of metabolite profiles from Panax herbs in specific tissues and cultivation conditions reveals the strategy of accumulation

Panax ginseng is one of the most valuable medicinal plants in the world, and wild-forest (WG) and artificial-forest (AG) ginseng are very popular in the ginseng market, with ginsenosides constituting a majority of the bioactives. Research on the biochemical and physiological patterns of metabolic accumulation in different tissues of ginseng cultivated under various conditions is relatively scarce. We profiled metabolites using GC/MS and LC/MS to explore the bioactive component changes and interrelationships that occur in 7 tissues of WG and AG. In total, 149 primary metabolites and 46 secondary compounds were found in aboveground and belowground tissues. Metabolite changes associated with primary and secondary biochemistry were observed, and the levels of ginsenoside F2 and other compounds showed a significant correlation by statistical analysis in ginseng under both cultivation methods, as observed for secondary compounds and C and N metabolites. In addition, the number of secondary components was higher in the aboveground parts than in the belowground parts, showing a different pattern, and the same accumulation pattern of compounds involved in C and N metabolism was observed in individual plant tissues, but the high rate of photosynthesis and energy metabolism in WG provided energy for the biosynthesis of secondary compounds. Furthermore, artificial neural network models explained the variation in the secondary compounds very well via the combination of several different metabolites from WG and AG. Finally, C and N metabolism plays a key role in secondary compound biosynthesis in specific tissues and cultivation conditions and highlights large-scale metabolite patterns in WG and AG.