Application of GC-MS for the detection of lipophilic compounds in diverse plant tissues

Finding of antibiotic compounds pyrrolo [1,2-a]pyrazine-1,4-dione, hexahydro and Cyclo(prolyl-tyrosyl) isolated from the degradation of epoxy

The investigation focused on the endophytic gram-positive microbial isolate KARE_P3, capable of degrading epoxy resin materials. This isolate produced bioactive secondary metabolic molecules with potent inhibitory effects against Staphylococcus aureus, Microbial Type Culture Collection and GenBank (MTCC 96). The study examined microbial growth and degradation mechanisms at various time points, with samples collected on the 35th and 70th days of fermentation. Three different solvents were used for extraction, and the crude metabolite was analysed using Thin Layer Chromatography (TLC), Gas Chromatography - Mass Spectrophotometry (GC-MS), Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC). These analyses revealed numerous secondary metabolites that help microbes adapt to changing environments. Further characterisation using bioautography and GC-MS identified 71 compounds, with 3-5 showing positive results. Important findings include compounds such as pyrrolo[1,2-a]pyrazine-1,4-dione, hexahydro 98% and Cyclo(prolyl-tyrosyl), which have diverse pharmaceutical applications. Antibacterial efficiency was studied using an in silico model, showing higher binding energy and inhibition rates of pyrrolo[1,2-a]pyrazine-1,4-dione and Cyclo(prolyl-tyrosyl) against Candida albicans compared to Staphylococcus epidermis. Challenges remain in the efficient sorting, recycling, and recovery of epoxy materials, crucial for future biotechnological progress.

A First Omics Data Integration Approach in Hass Avocados to Evaluate Rootstock-Scion Interactions: From Aerial and Root Plant Growth to Fruit Development

Grafting, the careful selection of rootstocks and scions, has played a crucial role maintaining Chilean avocado fruit quality standards in a scenario in which climate change and drought-related issues have considerably decreased avocado fruit production in the last fifteen years. The historical use of seedling rootstocks in Chile has experienced a recent shift towards clonal rootstocks, driven by the potential to produce more consistent and predictable crops. This research aims to compare Hass avocado plants grafted on Mexicola seedling and Dusa® clonal rootstocks in a soilless and protected system using (i) a differential expression analysis of root and leaf samples and (ii) a fruit transcriptomic and metabolomic integration analysis to improve our understanding of rootstock-scion interaction and its impact on avocado tree performance and fruit quality. The results demonstrated that no significant transcriptomic and metabolomic differences were identified at fruit level in the ready-to-eat (RTE) stage for Hass avocado fruit from both rootstocks. However, Hass avocados grafted on the clonal rootstock showed greater aerial growth and slightly increased fruit size than the seedling rootstock due to the enrichment of cell wall-remodeling genes as revealed in leaves and fruit at harvest stage.

Exploring the Significance, Extraction, and Characterization of Plant-Derived Secondary Metabolites in Complex Mixtures

Secondary metabolites are essential components for the survival of plants. Secondary metabolites in complex mixtures from plants have been adopted and documented by different traditional medicinal systems worldwide for the treatment of various human diseases. The extraction strategies are the key components for therapeutic development from natural sources. Polarity-dependent solvent-selective extraction, acidic and basic solution-based extraction, and microwave- and ultrasound-assisted extraction are some of the most important strategies for the extraction of natural products from plants. The method needs to be optimized to isolate a specific class of compounds. Therefore, to establish the mechanism of action, the characterization of the secondary metabolites, in a mixture or in their pure forms, is equally important. LC-MS, GC-MS, and extensive NMR spectroscopic strategies are established techniques for the profiling of metabolites in crude extracts. Various protocols for the extraction and characterization of a wide range of classes of compounds have been developed by various research groups and are described in this review. Additionally, the possible means of characterizing the compounds in the mixture and their uniqueness are also discussed. Hyphenated techniques are crucial for profiling because of their ability to analyze a vast range of compounds. In contrast, inherent chemical shifts make NMR an indispensable tool for structure elucidation in complex mixtures.

Proteomic and Low-Polar Metabolite Profiling Reveal Unique Dynamics in Fatty Acid Metabolism during Flower and Berry Development of Table Grapes

Grapevine development and ripening are complex processes that involve several biochemical pathways, including fatty acid and lipid metabolism. Fatty acids are essential components of lipids, which play crucial roles in fruit maturation and flavor development. However, the dynamics of fatty acid metabolism in grape flowers and berries are poorly understood. In this study, we present those dynamics and investigate the mechanisms of fatty acid homeostasis on 'Thompson Seedless' berries using metabolomic and proteomic analyses. Low-polar metabolite profiling indicated a higher abundance of fatty acids at the pre-flowering and pre-veraison stages. Proteomic analyses revealed that grape flowers and berries display unique profiles of proteins involved in fatty acid biosynthesis, triacylglycerol assembly, fatty acid β-oxidation, and lipid signaling. These findings show, for the first time, that fatty acid metabolism also plays an important role in the development of non-oil-rich tissues, opening new perspectives about lipid function and its relation to berry quality.

A multiomics integrative analysis of color de-synchronization with softening of 'Hass' avocado fruit: A first insight into a complex physiological disorder

Exocarp color de-synchronization with softening of 'Hass' avocado is a relevant recurrent problem for the avocado supply chain. This study aimed to unravel the mechanisms driving this de-synchronization integrating omics datasets from avocado exocarp of different storage conditions and color phenotypes. In addition, we propose potential biomarkers to predict color synchronized/de-synchronized fruit. Integration of transcriptomics, proteomics and metabolomics and network analysis revealed eight transcription factors associated with differentially regulated genes between regular air (RA) and controlled atmosphere (CA) and twelve transcription factors related to avocado fruit color de-synchronization control in ready-to-eat stage. CA was positively correlated to auxins, ethylene, cytokinins and brassinosteroids-related genes, while RA was characterized by enrichment of cell wall remodeling and abscisic acid content associated genes. At ready-to-eat higher contents of flavonoids, abscisic acid and brassinosteroids were associated with color-softening synchronized avocados. In contrast, de-synchronized fruit revealed increases of jasmonic acid, salicylic acid and auxin levels.

Phytosterols Are Involved in Sclareol-Induced Chlorophyll Reductions in Arabidopsis

Sclareol, a diterpene, has a wide range of physiological effects on plants, such as antimicrobial activity; disease resistance against pathogens; and the expression of genes encoding proteins involved in metabolism, transport, and phytohormone biosynthesis and signaling. Exogenous sclareol reduces the content of chlorophyll in Arabidopsis leaves. However, the endogenous compounds responsible for sclareol-induced chlorophyll reduction remain unknown. The phytosterols campesterol and stigmasterol were identified as compounds that reduce the content of chlorophyll in sclareol-treated Arabidopsis plants. The exogenous application of campesterol or stigmasterol dose-dependently reduced the content of chlorophyll in Arabidopsis leaves. Exogenously-applied sclareol enhanced the endogenous contents of campesterol and stigmasterol and the accumulation of transcripts for phytosterol biosynthetic genes. These results suggest that the phytosterols campesterol and stigmasterol, the production of which is enhanced in response to sclareol, contribute to reductions in chlorophyll content in Arabidopsis leaves.

Free and Esterified Tocopherols, Tocotrienols and Other Extractable and Non-Extractable Tocochromanol-Related Molecules: Compendium of Knowledge, Future Perspectives and Recommendations for Chromatographic Techniques, Tools, and Approaches Used for Tocochromanol Determination

Free and esterified (bound) tocopherols, tocotrienols and other tocochromanol-related compounds, often referred to "tocols", are lipophilic antioxidants of great importance for health. For instance, α-tocopherol is the only tocochromanol with vitamin E activity, while tocotrienols have a positive impact on health and are proposed in the prevention and therapy of so-called modern diseases. Tocopherols, tocotrienols and plastochromanol-8 are the most well-known tocochromanols; in turn, knowledge about tocodienols, tocomonoenols, and other rare tocochromanol-related compounds is limited due to several challenges in analytical chemistry and/or low concentration in plant material. The presence of free, esterified, and non-extractable tocochromanols in plant material as well as their biological function, which may be of great scientific, agricultural and medicinal importance, is also poorly studied. Due to the lack of modern protocols as well as equipment and tools, for instance, techniques suitable for the efficient and simultaneous chromatographical separation of major and minor tocochromanols, the topic requires attention and new solutions, and/or standardization, and proper terminology. This review discusses the advantages and disadvantages of different chromatographic techniques, tools and approaches used for the separation and detection of different tocochromanols in plant material and foodstuffs. Sources of tocochromanols and procedures for obtaining different tocochromanol analytical standards are also described. Finally, future challenges are discussed and perspective green techniques for tocochromanol determination are proposed along with best practice recommendations. The present manuscript aims to present key aspects and protocols related to tocochromanol determination, correct identification, and the interpretation of obtained results.

Suitability of Solvent-Assisted Extraction for Recovery of Lipophilic Phytochemicals in Sugarcane Straw and Bagasse

Sugarcane is primarily harvested to meet up to 80% of global sugar demand. Recently, lipids recovered from their biomass (straw and bagasse) have attracted much attention due to their possible utilisation in biofuel production but also by the presence of health-promoting compounds as phytosterols (i.e., improvement of cardiovascular function) or 1-octacosanol (i.e., anti-obesity). Although this fraction is commonly obtained through solid–liquid isolation, there is scarce information about how different solvents affect the composition of the extracts. This research work aimed to study whether, in sugarcane straw and bagasse samples, Soxtec extraction with widely used dichloromethane (DCM) would be suitable to recover most of the lipid classes when compared to other available solvents such as food grade ethanol (EtOH) or solvents without regulation restrictions for food and drug applications (i.e., acetone and ethyl acetate). The obtained results allow concluding that sugarcane waxes from straw and bagasse are complex lipid mixtures of polar and non-polar compounds. According to the extraction yield, the best results were obtained with ethanol (5.12 ± 0.30% and 1.97 ± 0.31%) for both straw and bagasse, respectively. The extractant greatly influenced the lipid composition of the obtained product. Thus, DCM enriched the isolates in glycerolipids (mono-, di- and triglycerides), free fatty acids, fatty alcohols, fatty aldehydes, phytosterols and hydrocarbons. On the other hand, EtOH resulted in polar isolates rich in glycolipids. Therefore, depending on the application and objectives of future research studies, the solvent to recover such lipids needs to be carefully selected.

Chemical Profiling of Two Italian Olea europaea (L.) Varieties Subjected to UV-B Stress

The depletion of the stratospheric ozone layer due to natural and/or anthropogenic causes decreases the amount of UV-B radiation filtered, and consequently increases the risk of potential damage to organisms. In the Mediterranean region, high UV-B indices are frequent. Even for species typical of this region, such as the olive tree, the progressive increase in UV-B radiation represents a threat. This work aimed to understand how high UV-B radiation modulates the phenolic and lipophilic profile of olive varieties, and identify metabolites that enhance olive stress tolerance. Two Italian olive varieties were subjected to chronic UV-B stress, and leaves were analyzed by gas and liquid chromatography. The results indicated that the most representative phenolic and lipophilic compounds of Giarraffa and Olivastra Seggianese were readjusted in response to UV-B stress. The Giarraffa variety seemed better suited to prolonged UV-B stress, possibly due to the higher availability of flavonoids that could help control oxidative damage, and the accumulation of hydroxycinnamic acid derivatives that could provide strong UV-B shield protection. In addition, this variety contained higher levels of fatty acids (e.g., palmitic, α-linolenic, and stearic acids), which can help to maintain membrane integrity and accumulate more sorbitol (which may serve as an osmoprotectant or act a free-radical scavenger), terpenes, and long-chain alkanes, providing higher protection against UV-B stress.

Biochemical and functional characterization of a mitochondrial citrate carrier in Arabidopsis thaliana

A homolog of the mitochondrial succinate/fumarate carrier from yeast (Sfc1p) has been found in the Arabidopsis genome, named AtSFC1. The AtSFC1 gene was expressed in Escherichia coli, and the gene product was purified and reconstituted in liposomes. Its transport properties and kinetic parameters demonstrated that AtSFC1 transports citrate, isocitrate and aconitate and, to a lesser extent, succinate and fumarate. This carrier catalyzes a fast counter-exchange transport as well as a low uniport of substrates, exhibits a higher transport affinity for tricarboxylates than dicarboxylates, and is inhibited by pyridoxal 5'-phosphate and other inhibitors of mitochondrial carriers to various degrees. Gene expression analysis indicated that the AtSFC1 transcript is mainly present in heterotrophic tissues, and fusion with a green-fluorescent protein localized AtSFC1 to the mitochondria. Furthermore, 35S-AtSFC1 antisense lines were generated and characterized at metabolic and physiological levels in different organs and at various developmental stages. Lower expression of AtSFC1 reduced seed germination and impaired radicle growth, a phenotype that was related to reduced respiration rate. These findings demonstrate that AtSFC1 might be involved in storage oil mobilization at the early stages of seedling growth and in nitrogen assimilation in root tissue by catalyzing citrate/isocitrate or citrate/succinate exchanges.

Species-independent analytical tools for next-generation agriculture

Innovative approaches are urgently required to alleviate the growing pressure on agriculture to meet the rising demand for food. A key challenge for plant biology is to bridge the notable knowledge gap between our detailed understanding of model plants grown under laboratory conditions and the agriculturally important crops cultivated in fields or production facilities. This Perspective highlights the recent development of new analytical tools that are rapid and non-destructive and provide tissue-, cell- or organelle-specific information on living plants in real time, with the potential to extend across multiple species in field applications. We evaluate the utility of engineered plant nanosensors and portable Raman spectroscopy to detect biotic and abiotic stresses, monitor plant hormonal signalling as well as characterize the soil, phytobiome and crop health in a non- or minimally invasive manner. We propose leveraging these tools to bridge the aforementioned fundamental gap with new synthesis and integration of expertise from plant biology, engineering and data science. Lastly, we assess the economic potential and discuss implementation strategies that will ensure the acceptance and successful integration of these modern tools in future farming practices in traditional as well as urban agriculture.

The Eucalyptus Cuticular Waxes Contribute in Preformed Defense Against Austropuccinia psidii

Austropuccinia psidii, the causal agent of myrtle rust, is a biotrophic pathogen whose growth and development depends on the host tissues. The uredospores of A. psidii infect Eucalyptus by engaging in close contact with the host surface and interacting with the leaf cuticle that provides important chemical and physical signals to trigger the infection process. In this study, the cuticular waxes of Eucalyptus spp. were analyzed to determine their composition or structure and correlation with susceptibility/resistance to A. psidii. Twenty-one Eucalyptus spp. in the field were classified as resistant or susceptible. The resistance/susceptibility level of six Eucalyptus spp. were validated in controlled conditions using qPCR, revealing that the pathogen can germinate on the eucalyptus surface of some species without multiplying in the host. CG-TOF-MS analysis detected 26 compounds in the Eucalyptus spp. cuticle and led to the discovery of the role of hexadecanoic acid in the susceptibility of Eucalyptus grandis and Eucalyptus phaeotricha to A. psidii. We characterized the epicuticular wax morphology of the six previously selected Eucalyptus spp. using scanning electron microscopy and observed different behavior in A. psidii germination during host infection. It was found a correlation of epicuticular morphology on the resistance to A. psidii. However, in this study, we provide the first report of considerable interspecific variation in Eucalyptus spp. on the susceptibility to A. psidii and its correlation with cuticular waxes chemical compounds that seem to play a synergistic role as a preformed defense mechanism.

Antioxidant Activities of Dialium indum L. Fruit and Gas Chromatography-Mass Spectrometry (GC-MS) of the Active Fractions

The fruit of Dialium indum L. (Fabaceae) is one of the edible wild fruits native to Southeast Asia. The mesocarp is consumed as sweets while the exocarp and seed are regarded as waste. This study aimed to evaluate the antioxidant activities of the fruit by using four assays, which measure its capabilities in reducing phosphomolybdic-phosphotungstic acid reagents, neocuproine, 2,2-diphenyl-picrylhydrazyl (DPPH), and inhibiting linoleic acid peroxidation. The active fractions were then analyzed by gas chromatography-mass spectrometry (GC-MS). The results showed that the seed methanol fraction (SMF) exhibited the strongest antioxidant activity with significantly higher (p < 0.05) gallic acid equivalence (GAE), total antioxidant capacity (TAC), and DPPH radical scavenging activity (IC50 31.71; 0.88 µg/mL) than the other fractions. The exocarp dichloromethane fraction (EDF) was the discriminating fraction by having remarkable linoleic acid peroxidation inhibition (IC50 121.43; 2.97 µg/mL). A total of thirty-eight metabolites were detected in derivatized EDF and SMF with distinctive classes of phenolics and amino acids, respectively. Bioautography-guided fractionation of EDF afforded five antioxidant-enriched subfractions with four other detected phenolics. The results revealed the antioxidant properties of D. indum fruit, which has potential benefits in pharmaceutical, nutraceutical, and cosmeceutical applications.

Phytochemical profile of the rare, ancient clone Lomatia tasmanica and comparison to other endemic Tasmanian species L. tinctoria and L. polymorpha

An investigation of the previously unexamined ancient Tasmanian clone Lomatia tasmanica W. M. Curtis (Proteaceae) and two other endemic species Lomatia tinctoria R. Br. and Lomatia polymorpha (Labill.) R. Br. was undertaken. This represents the first extensive natural products study in which individual phytochemical components have been isolated and identified from these three Lomatia species. Extraction of L. tasmanica leaves provided the naphthoquinone juglone (0.34% w/w), and n-alkanes nonacosane and heptacosane (0.30% w/w combined). L. polymorpha afforded the flavonoid glycosides dihydroquercetin 3-O-β-D-xyloside (0.22% w/w) and quercetin 3-O-β-d-glucose (0.14% w/w), as well as the naphthalene glucoside 1,4,8-trihydroxynaphthalene-1-O-β-d-glucose (0.04% w/w) and 4-O-p-coumaroyl-d-glucose (0.03% w/w). In addition, both L. polymorpha and L. tinctoria contained juglone (0.32% w/w and 0.58% w/w, respectively). L. polymorpha provided tetracosan-1-ol, hexacosan-1-ol and octacosan-1-ol (0.07% w/w combined), while L. tinctoria gave nonacosane (0.13% w/w). Analysis of three individual specimens from each of the three species demonstrated consistency in the respective phytochemical profiles of these populations and tentatively suggests limited intraspecific variation.

A comparison of semi-quantitative methods suitable for establishing volatile profiles

BACKGROUND

Full scent profiles emitted by living tissues can be screened by using total ion chromatograms generated in full scan mode and gas chromatography-mass spectrometry technique using Headspace Sorptive Extraction. This allows the identification of specific compounds and their absolute quantification or relative abundance. Quantifications ideally should be based on calibration curves using standards for each compound. However, the unpredictable composition of Volatile Organic Compounds (VOCs) and lack of standards make this approach difficult. Researchers studying scent profiles therefore concentrate on identifying specific scent footprints i.e. relative abundance rather than absolute quantities. We compared several semi-quantitative methods: external calibration curves generated in the sampling system and by liquid addition of standards to stir bars, total integrated peak area per fresh weight (FW), normalized peak area per FW, semi-quantification based on internal standard abundance, semi-quantification based on the nearest n-alkane and percentage of emission. Furthermore, we explored the usage of nearest components and single calibrators for semi-quantifications.

RESULTS

Any of the semi-quantification methods based on a standard produced similar or even identical results compared to quantification by a true-standard for a compound, except for the method based on standard addition. Each method beholds advantages and disadvantages regarding level of accuracy, experimental variability, acceptance and retrieved quantities.

CONCLUSIONS

Our data shows that, except for the method of standard addition to the biological sample, the rest of the semi-quantification methods studied give highly similar statistical results. Any of the methodologies presented here can therefore be considered as valid for scent profiling. Regarding relative proportions of VOCs, the generation of calibration curves for each compound analysed is not necessary.

UV-B radiation modulates physiology and lipophilic metabolite profile in Olea europaea

Ultraviolet-B (UV-B) radiation plays an important role in plant photomorphogenesis. Whilst the morpho-functional disorders induced by excessive UV irradiation are well-known, it remains unclear how this irradiation modulates the metabolome, and which metabolic shifts improve plants' tolerance to UV-B. In this study, we use an important Mediterranean crop, Olea europaea, to decipher the impacts of enhanced UV-B radiation on the physiological performance and lipophilic metabolite profile. Young olive plants (cv. 'Galega Vulgar') were exposed for five days to UV-B biologically effective doses of 6.5 kJ m^-2 d^-1 and 12.4 kJ m^-2 d^-1. Cell cycle/ploidy, photosynthesis and oxidative stress, as well as GC-MS metabolites were assessed. Both UV-B treatments impaired net CO₂ assimilation rate, transpiration rate, photosynthetic pigments, and RuBisCO activity, but 12.4 kJ m^-2 d^-1 also decreased the photochemical quenching (qP) and the effective efficiency of PSII (Φ_PSII). UV-B treatments promoted mono/triperpene pathways, while only 12.4 kJ m^-2 d^-1 increased fatty acids and alkanes, and decreased geranylgeranyl-diphosphate. The interplay between physiology and metabolomics suggests some innate ability of these plants to tolerate moderate UV-B doses (6.5 kJ m^-2 d^-1). Also their tolerance to higher doses (12.4 kJ m^-2 d^-1) relies on plants' metabolic adjustments, where the accumulation of specific compounds such as long-chain alkanes, palmitic acid, oleic acid and particularly oleamide (which is described for the first time in olive leaves) play an important protective role. This is the first study demonstrating photosynthetic changes and lipophilic metabolite adjustments in olive leaves under moderate and high UV-B doses.

Detecting early signs of heat and drought stress in Phoenix dactylifera (date palm)

Plants adapt to the environment by either long-term genome evolution or by acclimatization processes where the cellular processes and metabolism of the plant are adjusted within the existing potential in the genome. Here we studied the adaptation strategies in date palm, Phoenix dactylifera, under mild heat, drought and combined heat and drought by transcriptomic and metabolomic profiling. In transcriptomics data, combined heat and drought resembled heat response, whereas in metabolomics data it was more similar to drought. In both conditions, soluble carbohydrates, such as fucose, and glucose derivatives, were increased, suggesting a switch to carbohydrate metabolism and cell wall biogenesis. This result is consistent with the evidence from transcriptomics and cis-motif analysis. In addition, transcriptomics data showed transcriptional activation of genes related to reactive oxygen species in all three conditions (drought, heat, and combined heat and drought), suggesting increased activity of enzymatic antioxidant systems in cytosol, chloroplast and peroxisome. Finally, the genes that were differentially expressed in heat and combined heat and drought stresses were significantly enriched for circadian and diurnal rhythm motifs, suggesting new stress avoidance strategies.

Metabolite Profiling of Eastern Teaberry (Gaultheria procumbens L.) Lipophilic Leaf Extracts with Hyaluronidase and Lipoxygenase Inhibitory Activity

The phytochemical profile and anti-inflammatory activity of Gaultheria procumbens dry lipophilic leaf extracts were evaluated. Forty compounds were identified by GC-MS, representing 86.36% and 81.97% of the petroleum ether (PE) and chloroform (CHE) extracts, respectively, with ursolic acid (28.82%), oleanolic acid (10.11%), methyl benzoate (10.03%), and methyl salicylate (6.88%) dominating in CHE, and methyl benzoate (21.59%), docosane (18.86%), and octacosane (11.72%) prevailing in PE. Three components of CHE were fully identified after flash chromatography isolation and spectroscopic studies as (6S,9R)-vomifoliol (4.35%), 8-demethyl-latifolin (1.13%), and 8-demethylsideroxylin (2.25%). Hyaluronidase and lipoxygenase inhibitory activity was tested for CHE (IC50 = 282.15 ± 10.38 μg/mL and 899.97 ± 31.17 μg/mL, respectively), PE (IC50 = 401.82 ± 16.12 μg/mL and 738.49 ± 15.92 μg/mL), and nine of the main constituents versus heparin (IC50 = 366.24 ± 14.72 μg/mL) and indomethacin (IC50 = 92.60 ± 3.71 μg/mL) as positive controls. With the best activity/concentration relationships, ursolic and oleanolic acids were recommended as analytical markers for the extracts and plant material. Seasonal variation of both markers following foliar development was investigated by UHPLC-PDA. The highest levels of ursolic (5.36-5.87 mg/g DW of the leaves) and oleanolic (1.14-1.26 mg/g DW) acids were observed between August and October, indicating the optimal season for harvesting.

Tetracycline uptake and metabolism by vetiver grass (Chrysopogon zizanioides L. Nash)

Environmental contamination by antibiotics not only perturbs the ecological balance but also poses a risk to human health by promoting the development of multiantibiotic-resistant bacteria. This study focuses on identifying the biochemical pathways associated with tetracycline (TC) transformation/degradation in vetiver grass that has the potential to be used as a biological remediation system in TC-contaminated water sources. A hydroponic experimental setup was used with four initial TC concentrations (0, 5, 35, 75 ppm), and TC uptake was monitored over a 30-day period. Results show that TC transformation in the media occurred during the first 5 days, where a decrease in the parent compound and an increase in the concentration of the isomers such as epitetracycline (ETC) and anhyrotetracycline (ATC) occurred, and TC disappeared in 20 days in tanks with vetiver grass. However, the isomers ETC and ATC remained in the control tanks for the duration of the trial. Transformation products of TC in plant tissue were analyzed by using ultra HPLC high-resolution Orbitrap mass spectrometery (HRMS/MS), which indicates amide hydrolysis of TC in vetiver roots. Metabolic profiling revealed that glyoxylate metabolism, TCA cycle, biosynthesis of secondary metabolites, tryptophan metabolism, and inositol phosphate metabolism were impacted in vetiver root by TC treatment.

Metabolite profiling of Dioscorea (yam) species reveals underutilised biodiversity and renewable sources for high-value compounds

Yams (Dioscorea spp.) are a multispecies crop with production in over 50 countries generating ~50 MT of edible tubers annually. The long-term storage potential of these tubers is vital for food security in developing countries. Furthermore, many species are important sources of pharmaceutical precursors. Despite these attributes as staple food crops and sources of high-value chemicals, Dioscorea spp. remain largely neglected in comparison to other staple tuber crops of tropical agricultural systems such as cassava (Manihot esculenta) and sweet potato (Ipomoea batatas). To date, studies have focussed on the tubers or rhizomes of Dioscorea, neglecting the foliage as waste. In the present study metabolite profiling procedures, using GC-MS approaches, have been established to assess biochemical diversity across species. The robustness of the procedures was shown using material from the phylogenetic clades. The resultant data allowed separation of the genotypes into clades, species and morphological traits with a putative geographical origin. Additionally, we show the potential of foliage material as a renewable source of high-value compounds.

GC-MS and LC-MS approaches for determination of tocopherols and tocotrienols in biological and food matrices

Tocopherols and tocotrienols, widely described as vitamin E derivatives, have been proven to take part in a number of important biological functions. Among them, antioxidant properties had been investigated and documented in the literature. Since tocochromanols have revealed their plausible beneficial impact on several pathological processes, such as cancerogenesis or cognitive impairment diseases, there is a growing interest in quantitative determination of these compounds in biological fluids, tissues and plant organs. However, due to vitamin E chemical features, such as lipophilic and non-polar characteristics, quantitative determination of the compounds seems to be problematic. In this paper we present current analytical approaches in tocopherols and tocotrienols determination in biological and food matrices with the use of chromatographic techniques, especially gas chromatography (GC) and high performance liquid chromatography (HPLC) coupled with mass spectrometry. Derivatization techniques applied for GC-MS analysis in the case of tocol derivatives, especially silylation and acylation, are described. Significant attention is paid to ionization process of tocopherols and tocotrienols.

Quantitative profiling of polar primary metabolites of two chickpea cultivars with contrasting responses to salinity

This study reports a GC-QqQ-MS method for the quantification of forty-eight primary metabolites from four major classes (sugars, sugar acids, sugar phosphates, and organic acids) which can be applied to a number of biological systems. The method was validated in terms of linearity, reproducibility and recovery, using both calibration standards and real samples. Additionally, twenty-eight biogenic amines and amino acids were quantified using an established LC-QqQ-MS method. Both GC-QqQ-MS and LC-QqQ-MS quantitative methods were applied to plant extracts from flower and pod tissue of two chickpea (Cicer arietinum L.) cultivars differing in their ability to tolerate salinity, which were grown under control and salt-treated conditions. Statistical analysis was applied to the data sets using the absolute concentrations of metabolites to investigate the differences in metabolite profiles between the different cultivars, plant tissues, and treatments. The method is a significant improvement of present methodology for quantitative GC-MS metabolite profiling of organic acids and sugars, and provides new insights of chickpea metabolic responses to salinity stress. It is applicable to the analysis of dynamic changes in endogenous concentrations of polar primary metabolites to study metabolic responses to environmental stresses in complex biological tissues.

Analysis of phenolic and cyclic compounds in plants using derivatization techniques in combination with GC-MS-based metabolite profiling

Metabolite profiling has been established as a modern technology platform for the description of complex chemical matrices and compound identification in biological samples. Gas chromatography coupled with mass spectrometry (GC-MS) in particular is a fast and accurate method widely applied in diagnostics, functional genomics and for screening purposes. Following solvent extraction and derivatization, hundreds of metabolites from different chemical groups can be characterized in one analytical run. Besides sugars, acids, and polyols, diverse phenolic and other cyclic metabolites can be efficiently detected by metabolite profiling. The review describes own results from plant research to exemplify the applicability of GC-MS profiling and concurrent detection and identification of phenolics and other cyclic structures.

Strategies for vitamin B6 biofortification of plants: a dual role as a micronutrient and a stress protectant

Vitamin B6 has an essential role in cells as a cofactor for several metabolic enzymes. It has also been shown to function as a potent antioxidant molecule. The recent elucidation of the vitamin B6 biosynthesis pathways in plants provides opportunities for characterizing their importance during developmental processes and exposure to stress. Humans and animals must acquire vitamin B6 with their diet, with plants being a major source, because they cannot biosynthesize it de novo. However, the abundance of the vitamin in the edible portions of the most commonly consumed plants is not sufficient to meet daily requirements. Genetic engineering has proven successful in increasing the vitamin B6 content in the model plant Arabidopsis. The added benefits associated with the enhanced vitamin B6 content, such as higher biomass and resistance to abiotic stress, suggest that increasing this essential micronutrient could be a valuable option to improve the nutritional quality and stress tolerance of crop plants. This review summarizes current achievements in vitamin B6 biofortification and considers strategies for increasing vitamin B6 levels in crop plants for human health and nutrition.

High-resolution plant metabolomics: from mass spectral features to metabolites and from whole-cell analysis to subcellular metabolite distributions

The main goal of metabolomics is the comprehensive qualitative and quantitative analysis of the time- and space-resolved distribution of all metabolites present in a given biological system. Because metabolite structures, in contrast to transcript and protein sequences, are not directly deducible from the genomic DNA sequence, the massive increase in genomic information is only indirectly of use to metabolomics, leaving compound annotation as a key problem to be solved by the available analytical techniques. Furthermore, as metabolites vary widely in both concentration and chemical behavior, there is no single analytical procedure allowing the unbiased and comprehensive structural elucidation and determination of all metabolites present in a given biological system. In this review the different approaches for targeted and non-targeted metabolomics analysis will be described with special emphasis on mass spectrometry-based techniques. Particular attention is given to approaches which can be employed for the annotation of unknown compounds. In the second part, the different experimental approaches aimed at tissue-specific or subcellular analysis of metabolites are discussed including a range of non-mass spectrometry based technologies.

Tomato fruit photosynthesis is seemingly unimportant in primary metabolism and ripening but plays a considerable role in seed development

Fruit of tomato (Solanum lycopersicum), like those from many species, have been characterized to undergo a shift from partially photosynthetic to truly heterotrophic metabolism. While there is plentiful evidence for functional photosynthesis in young tomato fruit, the rates of carbon assimilation rarely exceed those of carbon dioxide release, raising the question of its role in this tissue. Here, we describe the generation and characterization of lines exhibiting a fruit-specific reduction in the expression of glutamate 1-semialdehyde aminotransferase (GSA). Despite the fact that these plants contained less GSA protein and lowered chlorophyll levels and photosynthetic activity, they were characterized by few other differences. Indeed, they displayed almost no differences in fruit size, weight, or ripening capacity and furthermore displayed few alterations in other primary or intermediary metabolites. Although GSA antisense lines were characterized by significant alterations in the expression of genes associated with photosynthesis, as well as with cell wall and amino acid metabolism, these changes were not manifested at the phenotypic level. One striking feature of the antisense plants was their seed phenotype: the transformants displayed a reduced seed set and altered morphology and metabolism at early stages of fruit development, although these differences did not affect the final seed number or fecundity. Taken together, these results suggest that fruit photosynthesis is, at least under ambient conditions, not necessary for fruit energy metabolism or development but is essential for properly timed seed development and therefore may confer an advantage under conditions of stress.

Enhanced levels of vitamin B(6) increase aerial organ size and positively affect stress tolerance in Arabidopsis

Vitamin B₆ is an essential nutrient in the human diet derived primarily from plant sources. While it is well established as a cofactor for numerous metabolic enzymes, more recently, vitamin B₆ has been implicated as a potent antioxidant. The de novo vitamin B₆ biosynthesis pathway in plants has recently been unraveled and involves only two proteins, PDX1 and PDX2. To provide more insight into the effect of the compound on plant development and its role as an antioxidant, we have overexpressed the PDX proteins in Arabidopsis, generating lines with considerably higher levels of the vitamin in comparison with other recent attempts to achieve this goal. Interestingly, it was possible to increase the level of only one of the two catalytically active PDX1 proteins at the protein level, providing insight into the mechanism of vitamin B₆ homeostasis in planta. Vitamin B₆ enhanced lines have considerably larger vegetative and floral organs and although delayed in pre-reproductive development, do not have an altered overall morphology. The vitamin was observed to accumulate in seeds and the enhancement of its levels was correlated with an increase in their size and weight. This phenotype is predominantly a consequence of embryo enlargement as reflected by larger cells. Furthermore, plants that overaccumulate the vitamin have an increased tolerance to oxidative stress providing in vivo evidence for the antioxidant functionality of vitamin B₆. In particular, the plants show an increased resistance to paraquat and photoinhibition, and they attenuate the cell death response observed in the conditional flu mutant.

Quantification of α- and β-amyrin in rat plasma by gas chromatography-mass spectrometry: application to preclinical pharmacokinetic study

α- and β-Amyrins are naturally occurring triterpenes with a wide range of biological activities. In this study, a reliable GC-MS method was developed and validated for the quantification of α- and β-amyrins in rat plasma. The calibration curves were linear (R(2) > 0.996) with a limit of quantification of 1.0 ng ml(-1) for both α- and β-amyrins. The precision and repeatability of this method was good as the relative standard deviation were 12% or less. The absolute recovery ranged from 71% to 89%, while the analytical recovery ranged from 95% to 99%. The pharmacokinetic profiles of α- and β-amyrins in rats were subsequently investigated in Sprague-Dawley rats. β-Amyrin was administered intravenously and also orally in two forms, namely, as a suspension of the pure compound and the crude plant extract. α-Amyrin was administered orally as a suspension of the crude plant extract. β-Amyrin had a very long terminal elimination half-life (t(1/2λz) = 610 ± 179 min) and extremely slow clearance (Cl = 2.04 ± 0.24 ml min(-1) kg(-1)). The absolute oral bioavailability of β-amyrin in the crude plant extract was about fourfold higher than that in the suspension of pure form (3.83% vs 0.86%). When given in crude plant extract, both α- and β-amyrins had a similar dose normalized C(max). This reliable GC-MS method will enable further pharmacokinetic investigations of α- and β-amyrins.

Complex assembly and metabolic profiling of Arabidopsis thaliana plants overexpressing vitamin B₆ biosynthesis proteins

In plants, vitamin B₆ biosynthesis requires the activity of PDX1 and PDX2 proteins. Arabidopsis thaliana encodes for three PDX1 proteins, named PDX1.1, 1.2, and 1.3, but only one PDX2. Here, we show in planta complex assembly of PDX proteins, based on split-YFP and FPLC assays, and can demonstrate their presence in higher complexes of around 750 kDa. Metabolic profiling of plants ectopically expressing the different PDX proteins indicates a negative influence of PDX1.2 on vitamin B₆ biosynthesis and a correlation between aberrant vitamin B6 content, PDX1 gene expression, and light sensitivity specifically for PDX1.3. These findings provide first insights into in planta vitamin B₆ synthase complex assembly and new information on how the different PDX proteins affect plant metabolism.

Rapid metabolic profiling of Nicotiana tabacum defence responses against Phytophthora nicotianae using direct infrared laser desorption ionization mass spectrometry and principal component analysis

BACKGROUND

Successful defence of tobacco plants against attack from the oomycete Phytophthora nicotianae includes a type of local programmed cell death called the hypersensitive response. Complex and not completely understood signaling processes are required to mediate the development of this defence in the infected tissue. Here, we demonstrate that different families of metabolites can be monitored in small pieces of infected, mechanically-stressed, and healthy tobacco leaves using direct infrared laser desorption ionization orthogonal time-of-flight mass spectrometry. The defence response was monitored for 1 - 9 hours post infection.

RESULTS

Infrared laser desorption ionization orthogonal time-of-flight mass spectrometry allows rapid and simultaneous detection in both negative and positive ion mode of a wide range of naturally occurring primary and secondary metabolites. An unsupervised principal component analysis was employed to identify correlations between changes in metabolite expression (obtained at different times and sample treatment conditions) and the overall defence response.A one-dimensional projection of the principal components 1 and 2 obtained from positive ion mode spectra was used to generate a Biological Response Index (BRI). The BRI obtained for each sample treatment was compared with the number of dead cells found in the respective tissue. The high correlation between these two values suggested that the BRI provides a rapid assessment of the plant response against the pathogen infection. Evaluation of the loading plots of the principal components (1 and 2) reveals a correlation among three metabolic cascades and the defence response generated in infected leaves. Analysis of selected phytohormones by liquid chromatography electrospray ionization mass spectrometry verified our findings.

CONCLUSION

The described methodology allows for rapid assessment of infection-specific changes in the plant metabolism, in particular of phenolics, alkaloids, oxylipins, and carbohydrates. Moreover, potential novel biomarkers can be detected and used to predict the quality of plant infections.

Vitamin B6: Killing two birds with one stone?

Vitamin B6 comprises a group of compounds that are involved in a surprisingly high diversity of biochemical reactions. Actually, most of these reactions are co-catalyzed by a single B6 vitamer, pyridoxal 5'-phosphate, making it a crucial and versatile co-factor in many metabolic processes in the cell. In addition, it has been demonstrated in recent years that vitamin B6 has a second important function by being an effective antioxidant. Because of these two characteristics the vitamin is an interesting compound to study in plants. This review provides a brief overview and update on such important aspects like vitamin B6-dependent enzymes and known biosynthetic pathways in plants, phenotypes of plant mutants affected in vitamin B6 biosynthesis, and the potential benefits of modifying vitamin B6 content in plants.

Vitamin B6 deficient plants display increased sensitivity to high light and photo-oxidative stress

BACKGROUND

Vitamin B6 is a collective term for a group of six interconvertible compounds: pyridoxine, pyridoxal, pyridoxamine and their phosphorylated derivatives. Vitamin B6 plays essential roles as a cofactor in a range of biochemical reactions. In addition, vitamin B6 is able to quench reactive oxygen species in vitro, and exogenously applied vitamin B6 protects plant cells against cell death induced by singlet oxygen (1O2). These results raise the important question as to whether plants employ vitamin B6 as an antioxidant to protect themselves against reactive oxygen species.

RESULTS

The pdx1.3 mutation affects the vitamin B6 biosynthesis enzyme, pyridoxal synthase (PDX1), and leads to a reduction of the vitamin B6 concentration in Arabidopsis thaliana leaves. Although leaves of the pdx1.3 Arabidopsis mutant contained less chlorophyll than wild-type leaves, we found that vitamin B6 deficiency did not significantly impact photosynthetic performance or shoot and root growth. Chlorophyll loss was associated with an increase in the chlorophyll a/b ratio and a selective decrease in the abundance of several PSII antenna proteins (Lhcb1/2, Lhcb6). These changes were strongly dependent on light intensity, with high light amplifying the difference between pdx1.3 and the wild type. When leaf discs were exposed to exogenous 1O2, lipid peroxidation in pdx1.3 was increased relative to the wild type; this effect was not observed with superoxide or hydrogen peroxide. When leaf discs or whole plants were exposed to excess light energy, 1O2-mediated lipid peroxidation was enhanced in leaves of the pdx1.3 mutant relative to the wild type. High light also caused an increased level of 1O2 in vitamin B6-deficient leaves. Combining the pdx1.3 mutation with mutations affecting the level of 'classical' quenchers of 1O2 (zeaxanthin, tocopherols) resulted in a highly photosensitive phenotype.

CONCLUSION

This study demonstrates that vitamin B6 has a function in the in vivo antioxidant defense of plants. Thus, the antioxidant activity of vitamin B6 inferred from in vitro studies is confirmed in planta. Together with the finding that chloroplasts contain vitamin B6 compounds, the data show that vitamin B6 functions as a photoprotector that limits 1O2 accumulation in high light and prevents 1O2-mediated oxidative damage.

What can metabolomics learn from genomics and proteomics?

After nearly a decade, metabolomics has begun to acquire some credence in the scientific community although its acceptance cannot be compared with that of its forerunners, genomics and proteomics. The legitimization of metabolomics as a valid scientific entity depends on the size of the research community it influences. By far the most effective medium for inoculation is the web infrastructure: public servers that accommodate experimental data, simple formats and guidelines for their interpretation, and connectivity between data and tools for analysis. When these elements satisfy the condition to initiate a social epidemic, metabolomics will be accepted as a fundamental data-driven science that can unite hitherto independently conducted research disciplines.