A liquid chromatography-mass spectrometry-based metabolome database for tomato

Antibacterial and Anticancer Activity and Untargeted Secondary Metabolite Profiling of Crude Bacterial Endophyte Extracts from Crinum macowanii Baker Leaves

This study isolated and identified endophytic bacteria from the leaves of Crinum macowanii and investigated the potential of the bacterial endophyte extracts as antibacterial and anticancer agents and their subsequent secondary metabolites. Ethyl acetate extracts from the endophytes and the leaves (methanol: dichloromethane (1 : 1)) were used for antibacterial activity against selected pathogenic bacterial strains by using the broth microdilution method. The anticancer activity against the U87MG glioblastoma and A549 lung carcinoma cells was determined by the MTS (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxy-phenyl)-2-(4-sulfophenyl)-2H-tetrazolium) assay. Bacterial endophytes that were successfully isolated from C. macowanii leaves include Raoultella ornithinolytica, Acinetobacter guillouiae, Pseudomonas sp., Pseudomonas palleroniana, Pseudomonas putida, Bacillus safensis, Enterobacter asburiae, Pseudomonas cichorii, and Arthrobacter pascens. Pseudomonas cichorii exhibited broad antibacterial activity against both Gram-negative and Gram-positive pathogenic bacteria while Arthrobacter pascens displayed the least MIC of 0.0625 mg/mL. Bacillus safensis crude extracts were the only sample that showed notable cell reduction of 50% against A549 lung carcinoma cells at a concentration of 100 μg/mL. Metabolite profiling of Bacillus safensis, Pseudomonas cichorii, and Arthrobacter pascens crude extracts revealed the presence of known antibacterial and/or anticancer agents such as lycorine (1), angustine (2), crinamidine (3), vasicinol (4), and powelline. It can be concluded that the crude bacterial endophyte extracts obtained from C. macowanii leaves can biosynthesize bioactive compounds and can be bioprospected for medical application into antibacterial and anticancer agents.

Metabolic engineering of tomato fruit enriched in L-DOPA

L-DOPA, also known as Levodopa or L-3,4-dihydroxyphenylalanine, is a non-standard amino acid, and the gold standard drug for the treatment for Parkinson's Disease (PD). Recently, a gene encoding the enzyme that is responsible for its synthesis, as a precursor of the coloured pigment group betalains, was identified in beetroot, BvCYP76AD6. We have engineered tomato fruit enriched in L-DOPA through overexpression of BvCYP76AD6 in a fruit specific manner. Analysis of the transgenic fruit revealed the feasibility of accumulating L-DOPA in a non-naturally betalain-producing plant. Fruit accumulating L-DOPA also showed major effects on the fruit metabolome. Some of these changes included elevation of amino acids levels, changes in the levels of intermediates of the TCA and glycolysis pathways and reductions in the levels of phenolic compounds and nitrogen-containing specialised metabolites. Furthermore, we were able to increase the L-DOPA levels further by elevating the expression of the metabolic master regulator, MYB12, specifically in tomato fruit, together with BvCYP76AD6. Our study elucidated new roles for L-DOPA in plants, because it impacted fruit quality parameters including antioxidant capacity and firmness. The L-DOPA levels achieved in tomato fruit were comparable to the levels in other non-seed organs of L-DOPA - accumulating plants, offering an opportunity to develop new biological sources of L-DOPA by widening the repertoire of L-DOPA-accumulating plants. These tomato fruit could be used as an alternative source of this important pharmaceutical.

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Tomato fruit were engineered to synthesise and accumulate L-DOPA.

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Co-expression of the transcription factor, MYB12, doubled the levels of L-DOPA in tomato fruit.

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The accumulation of L-DOPA resulted in additional changes in the profile of primary and secondary metabolites in tomatoes.

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The L-DOPA tomato fruit exhibited improved shelf life and reduced susceptibility to Botrytis cinerea.

Integrated metabolomics and transcriptomics study of traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao reveals global metabolic profile and novel phytochemical ingredients

BACKGROUND

Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao is one of the most common herbs widely used in South and East Asia, to enhance people's health and reinforce vital energy. Despite its prevalence, however, the knowledge about phytochemical compositions and metabolite biosynthesis in Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao is very limited.

RESULTS

An integrated metabolomics and transcriptomics analysis using state-of-the-art UPLC-Q-Orbitrap mass spectrometer and advanced bioinformatics pipeline were conducted to study global metabolic profiles and phytochemical ingredients/biosynthesis in Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao. A total of 5435 metabolites were detected, from which 2190 were annotated, representing an order of magnitude increase over previously known. Metabolic profiling of Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao tissues found contents and synthetic enzymes for phytochemicals were significantly higher in leaf and stem in general, whereas the contents of the main bioactive ingredients were significantly enriched in root, underlying the value of root in herbal remedies. Using integrated metabolomics and transcriptomics data, we illustrated the complete pathways of phenylpropanoid biosynthesis, flavonoid biosynthesis, and isoflavonoid biosynthesis, in which some were first reported in the herb. More importantly, we discovered novel flavonoid derivatives using informatics method for neutral loss scan, in addition to inferring their likely synthesis pathways in Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao.

CONCLUSIONS

The current study represents the most comprehensive metabolomics and transcriptomics analysis on traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao. We demonstrated our integrated metabolomics and transcriptomics approach offers great potentials in discovering novel metabolite structure and associated synthesis pathways. This study provides novel insights into the phytochemical ingredients, metabolite biosynthesis, and complex metabolic network in herbs, highlighting the rich natural resource and nutritional value of traditional herbal plants.

Unexplored nutritive potential of tomato to combat global malnutrition

Tomato, a widely consumed vegetable crop, offers a real potential to combat human nutritional deficiencies. Tomatoes are rich in micronutrients and other bioactive compounds (including vitamins, carotenoids, and minerals) that are known to be essential or beneficial for human health. This review highlights the current state of the art in the molecular understanding of the nutritional aspects, conventional and molecular breeding efforts, and biofortification studies undertaken to improve the nutritional content and quality of tomato. Transcriptomics and metabolomics studies, which offer a deeper understanding of the molecular regulation of the tomato's nutrients, are discussed. The potential uses of the wastes from the tomato processing industry (i.e., the peels and seed extracts) that are particularly rich in oils and proteins are also discussed. Recent advancements with CRISPR/Cas mediated gene-editing technology provide enormous opportunities to enhance the nutritional content of agricultural produces, including tomatoes. In this regard, genome editing efforts with respect to biofortification in the tomato plant are also discussed. The recent technological advancements and knowledge gaps described herein aim to help explore the unexplored nutritional potential of the tomato.

Multi-Targeted Metabolic Profiling of Carotenoids, Phenolic Compounds and Primary Metabolites in Goji (Lycium spp.) Berry and Tomato (Solanum lycopersicum) Reveals Inter and Intra Genus Biomarkers

Metabolic profile is a key component of fruit quality, which is a challenge to study due to great compound diversity, especially in species with high nutritional value. This study presents optimized analytical methods for metabolic profiling in the fruits of three Solanaceae species: Lycium barbarum, Lycium chinense and Solanumlycopersicum. It includes the most important chemical classes involved in nutrition and taste, i.e., carotenoids, phenolic compounds and primary compounds. Emphasis has been placed on the systematic achievement of good extraction yields, sample stability, and high response linearity using common LC-ESI-TQ-MS and GC-EI-MS apparatuses. A set of 13 carotenoids, 46 phenolic compounds and 67 primary compounds were profiled in fruit samples. Chemometrics revealed metabolic markers discriminating Lycium and Solanum fruits but also Lycium barbarum and Lycium chinense fruits and the effect of the crop environment. Typical tomato markers were found to be lycopene, carotene, glutamate and GABA, while lycibarbarphenylpropanoids and zeaxanthin esters characterized goji (Lycium spp.) fruits. Among the compounds discriminating the Lycium species, reported here for the first time to our knowledge, chlorogenic acids, asparagine and quinic acid were more abundant in Lycium chinense, whereas Lycium barbarum accumulated more lycibarbarphenylpropanoids A-B, coumaric acid, fructose and glucose.

Lycopene, polyphenols and antioxidant activities of three characteristic tomato cultivars subjected to two drying methods

The aim of this study was to evaluate the effects of freeze drying and oven drying on appearance, chemical components and antioxidant activities of three cultivars of tomatoes. This study showed cultivar 18,131 would provide the highest phenolic contents and ABTS radical scavenging activity, and cultivar 1862 provide the highest lycopene content after oven drying. On the basis of appearance and contents of polyphenols, freeze drying showed better results. However, oven drying was found superior in decreasing degradation of lycopene. The effects of drying on the polyphenol contents varied depending on the cultivars. In addition, there is no significant difference of antioxidant activities between freeze dried and oven dried tomatoes. These results also demonstrated that freeze drying is superior in maintaining physical structure and phenolic contents of tomato slices. However, oven drying is a viable option for drying tomatoes considering both costing and contents of lycopene.

Spatial Metabolomics of the Human Kidney using MALDI Trapped Ion Mobility Imaging Mass Spectrometry

Low molecular weight metabolites are essential for defining the molecular phenotypes of cells. However, spatial metabolomics tools often lack the sensitivity, specify, and spatial resolution to provide comprehensive descriptions of these species in tissue. MALDI imaging mass spectrometry (IMS) of low molecular weight ions is particularly challenging as MALDI matrix clusters are often nominally isobaric with multiple metabolite ions, requiring high resolving power instrumentation or derivatization to circumvent this issue. An alternative to this is to perform ion mobility separation before ion detection, enabling the visualization of metabolites without the interference of matrix ions. Additional difficulties surrounding low weight metabolite visualization include high resolution imaging, while maintaining sufficient ion numbers for broad and representative analysis of the tissue chemical complement. Here, we use MALDI timsTOF IMS to image low molecular weight metabolites at higher spatial resolution than most metabolite MALDI IMS experiments (20 μm) while maintaining broad coverage within the human kidney. We demonstrate that trapped ion mobility spectrometry (TIMS) can resolve matrix peaks from metabolite signal and separate both isobaric and isomeric metabolites with different distributions within the kidney. The added ion mobility data dimension dramatically increased the peak capacity for spatial metabolomics experiments. Through this improved sensitivity, we have found >40 low molecular weight metabolites in human kidney tissue, such as argininic acid, acetylcarnitine, and choline that localize to the cortex, medulla, and renal pelvis, respectively. Future work will involve further exploring metabolomic profiles of human kidneys as a function of age, sex, and race.

A Review on the Beneficial Role of Silicon against Salinity in Non-Accumulator Crops: Tomato as a Model

Salinity is an abiotic stress that affects agriculture by severely impacting crop growth and, consequently, final yield. Considering that sea levels rise at an alarming rate of >3 mm per year, it is clear that salt stress constitutes a top-ranking threat to agriculture. Among the economically important crops that are sensitive to high salinity is tomato (Solanum lycopersicum L.), a cultivar that is more affected by salt stress than its wild counterparts. A strong body of evidence in the literature has proven the beneficial role of the quasi-essential metalloid silicon (Si), which increases the vigor and protects plants against (a)biotic stresses. This protection is realized by precipitating in the cell walls as opaline silica that constitutes a mechanical barrier to the entry of phytopathogens. With respect to Si accumulation, tomato is classified as a non-accumulator (an excluder), similarly to other members of the nightshade family, such as tobacco. Despite the low capacity of accumulating Si, when supplied to tomato plants, the metalloid improves growth under (a)biotic stress conditions, e.g., by enhancing the yield of fruits or by improving vegetative growth through the modulation of physiological parameters. In light of the benefits of Si in crop protection, the available literature data on the effects of this metalloid in mitigating salt stress in tomato are reviewed with a perspective on its use as a biostimulant, boosting the production of fruits as well as their post-harvest stability.

Quantitative trait loci analysis of seed-specialized metabolites reveals seed-specific flavonols and differential regulation of glycoalkaloid content in tomato

Given the potential health benefits (and adverse effects), of polyphenolic and steroidal glycoalkaloids in the diet there is a growing interest in fully elucidating the genetic control of their levels in foodstuffs. Here we carried out profiling of the specialized metabolites in the seeds of the Solanum pennellii introgression lines identifying 338 putative metabolite quantitative trait loci (mQTL) for flavonoids, steroidal glycoalkaloids and further specialized metabolites. Two putative mQTL for flavonols and one for steroidal glycoalkaloids were cross-validated by evaluation of the metabolite content of recombinants harboring smaller introgression in the corresponding QTL interval or by analysis of lines from an independently derived backcross inbred line population. The steroidal glycoalkaloid mQTL was localized to a chromosomal region spanning 14 genes, including a previously defined steroidal glycoalkaloid gene cluster. The flavonoid mQTL was further validated via the use of transient and stable overexpression of the Solyc12g098600 and Solyc12g096870 genes, which encode seed-specific uridine 5'-diphosphate-glycosyltransferases. The results are discussed in the context of our understanding of the accumulation of polyphenols and steroidal glycoalkaloids, and how this knowledge may be incorporated into breeding strategies aimed at improving nutritional aspects of plants as well as in fortifying them against abiotic stress.

FUNCTIONAL METABOLOMICS DECIPHER BIOCHEMICAL FUNCTIONS AND ASSOCIATED MECHANISMS UNDERLIE SMALL-MOLECULE METABOLISM

Metabolism is the collection of biochemical reactions enabled by chemically diverse metabolites, which facilitate different physiological processes to exchange substances and synthesize energy in diverse living organisms. Metabolomics has emerged as a cutting-edge method to qualify and quantify the metabolites in different biological matrixes, and it has the extraordinary capacity to interrogate the biological significance that underlies metabolic modification and modulation. Liquid chromatography combined with mass spectrometry (LC/MS), as a robust platform for metabolomics analysis, has increased in popularity over the past 10 years due to its excellent sensitivity, throughput, and versatility. However, metabolomics investigation currently provides us with only phenotype data without revealing the biochemical functions and associated mechanisms. This limitation indeed weakens the core value of metabolomics data in a broad spectrum of the life sciences. In recent years, the scientific community has actively explored the functional features of metabolomics and translated this cutting-edge approach to be used to solve key multifaceted questions, such as disease pathogenesis, the therapeutic discovery of drugs, nutritional issues, agricultural problems, environmental toxicology, and microbial evolution. Here, we are the first to briefly review the history and applicable progression of LC/MS-based metabolomics, with an emphasis on the applications of metabolic phenotyping. Furthermore, we specifically highlight the next era of LC/MS-based metabolomics to target functional metabolomes, through which we can answer phenotype-related questions to elucidate biochemical functions and associated mechanisms implicated in dysregulated metabolism. Finally, we propose many strategies to enhance the research capacity of functional metabolomics by enabling the combination of contemporary omics technologies and cutting-edge biochemical techniques. The main purpose of this review is to improve the understanding of LC/MS-based metabolomics, extending beyond the conventional metabolic phenotype toward biochemical functions and associated mechanisms, to enhance research capability and to enlarge the applicable scope of functional metabolomics in small-molecule metabolism in different living organisms.

Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) mass spectrometry imaging analysis of endogenous metabolites in cherry tomatoes

We report the spatially resolved metabolic profiling of cherry tomatoes using infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI), a mass spectrometry imaging (MSI) technique that operates at ambient conditions and requires no sample derivatization. Tomatoes were flash frozen, cryosectioned and imaged with adequate spatial resolution to distinguish between the major tissue structures of a tomato including the skin, mesocarp, endocarp, locular tissue, septum, placenta, seed and seed coating. Metabolites were imaged from 100-1200 m/z, enabling significant coverage of a diverse array of metabolites including amino acids and lipids along with the major secondary metabolite classes: terpenes, phenolics, glycosides, and alkaloids. During the metabolic profiling, we found endogenous carotenoid hydrocarbons, namely lycopene or its structural isomer β-carotene, ionized as radical cations. To our knowledge, this is the first demonstration of ionizing hydrocarbons in the MSI field.

Exploiting Natural Variation in Tomato to Define Pathway Structure and Metabolic Regulation of Fruit Polyphenolics in the Lycopersicum Complex

While the structures of plant primary metabolic pathways are generally well defined and highly conserved across species, those defining specialized metabolism are less well characterized and more highly variable across species. In this study, we investigated polyphenolic metabolism in the lycopersicum complex by characterizing the underlying biosynthetic and decorative reactions that constitute the metabolic network of polyphenols across eight different species of tomato. For this purpose, GC-MS- and LC-MS-based metabolomics of different tissues of Solanum lycopersicum and wild tomato species were carried out, in concert with the evaluation of cross-hybridized microarray data for MapMan-based transcriptomic analysis, and publicly available RNA-sequencing data for annotation of biosynthetic genes. The combined data were used to compile species-specific metabolic networks of polyphenolic metabolism, allowing the establishment of an entire pan-species biosynthetic framework as well as annotation of the functions of decoration enzymes involved in the formation of metabolic diversity of the flavonoid pathway. The combined results are discussed in the context of the current understanding of tomato flavonol biosynthesis as well as a global view of metabolic shifts during fruit ripening. Our results provide an example as to how large-scale biology approaches can be used for the definition and refinement of large specialized metabolism pathways.

Variation in secondary metabolites in a unique set of tomato accessions collected in Turkey

In this study, 50 tomato landraces grown in Turkey were investigated in terms of their secondary metabolite profiles. Each accession was planted in 2016 and 2017 in 3 replicates in an open field. In this study, color, pH and brix of the fruit samples were measured and an unbiased LCMS-based metabolomics approach was applied. Based on Principal Components Analysis (PCA) and Hierarchical Cluster Analysis (HCA) of the relative abundance levels of >250 metabolites, it could be concluded that fruit size was the most influential to the biochemical composition, rather than the geographical origin of accessions. Results indicated substantial biodiversity in various metabolites generally regarded as key to fruit quality aspects, including sugars; phenolic compounds like phenylpropanoids and flavonoids; alkaloids and glycosides of flavour-related volatile compounds. The phytochemical data provides insight into which Turkish accessions might be most promising as starting materials for the tomato processing and breeding industries.

Modulation of the Tomato Fruit Metabolome by LED Light

Metabolic profiles of tomatoes change during ripening and light can modulate the activity of relevant biochemical pathways. We investigated the effects of light directly supplied to the fruits on the metabolome of the fruit pericarp during ripening. Mature green tomatoes were exposed to well-controlled conditions with light as the only varying factor; control fruits were kept in darkness. In experiment 1 the fruits were exposed to either white light or darkness for 15 days. In experiment 2, fruits were exposed to different light spectra (blue, green, red, far-red, white) added to white background light for seven days. Changes in the global metabolome of the fruit pericarp were monitored using LCMS and GCMS (554 compounds in total). Health-beneficial compounds (carotenoids, flavonoids, tocopherols and phenolic acids) accumulated faster under white light compared to darkness, while alkaloids and chlorophylls decreased faster. Light also changed the levels of taste-related metabolites including glutamate and malate. The light spectrum treatments indicated that the addition of blue light was the most effective treatment in altering the fruit metabolome. We conclude that light during ripening of tomatoes can have various effects on the metabolome and may help with shaping the levels of key compounds involved in various fruit quality characteristics.

Cross-Species Comparison of Fruit-Metabolomics to Elucidate Metabolic Regulation of Fruit Polyphenolics Among Solanaceous Crops

Many solanaceous crops are an important part of the human daily diet. Fruit polyphenolics are plant specialized metabolites that are recognized for their human health benefits and their defensive role against plant abiotic and biotic stressors. Flavonoids and chlorogenates are the major polyphenolic compounds found in solanaceous fruits that vary in quantity, physiological function, and structural diversity among and within plant species. Despite their biological significance, the elucidation of metabolic shifts of polyphenols during fruit ripening in different fruit tissues, has not yet been well-characterized in solanaceous crops, especially at a cross-species and cross-cultivar level. Here, we performed a cross-species comparison of fruit-metabolomics to elucidate the metabolic regulation of fruit polyphenolics from three representative crops of Solanaceae (tomato, eggplant, and pepper), and a cross-cultivar comparison among different pepper cultivars (Capsicum annuum cv.) using liquid chromatography-mass spectrometry (LC-MS). We observed a metabolic trade-off between hydroxycinnamates and flavonoids in pungent pepper and anthocyanin-type pepper cultivars and identified metabolic signatures of fruit polyphenolics in each species from each different tissue-type and fruit ripening stage. Our results provide additional information for metabolomics-assisted crop improvement of solanaceous fruits towards their improved nutritive properties and enhanced stress tolerance.

Metabolite Changes during Postharvest Storage: Effects on Fruit Quality Traits

Metabolic changes occurring in ripe or senescent fruits during postharvest storage lead to a general deterioration in quality attributes, including decreased flavor and ‘off-aroma’ compound generation. As a consequence, measures to reduce economic losses have to be taken by the fruit industry and have mostly consisted of storage at cold temperatures and the use of controlled atmospheres or ripening inhibitors. However, the biochemical pathways and molecular mechanisms underlying fruit senescence in commercial storage conditions are still poorly understood. In this sense, metabolomic platforms, enabling the profiling of key metabolites responsible for organoleptic and health-promoting traits, such as volatiles, sugars, acids, polyphenols and carotenoids, can be a powerful tool for further understanding the biochemical basis of postharvest physiology and have the potential to play a critical role in the identification of the pathways affected by fruit senescence. Here, we provide an overview of the metabolic changes during postharvest storage, with special attention to key metabolites related to fruit quality. The potential use of metabolomic approaches to yield metabolic markers useful for chemical phenotyping or even storage and marketing decisions is highlighted.

Manipulation of β-carotene levels in tomato fruits results in increased ABA content and extended shelf life

Tomato fruit ripening is controlled by the hormone ethylene and by a group of transcription factors, acting upstream of ethylene. During ripening, the linear carotene lycopene accumulates at the expense of cyclic carotenoids. Fruit-specific overexpression of LYCOPENE β-CYCLASE (LCYb) resulted in increased β-carotene (provitamin A) content. Unexpectedly, LCYb-overexpressing fruits also exhibited a diverse array of ripening phenotypes, including delayed softening and extended shelf life. These phenotypes were accompanied, at the biochemical level, by an increase in abscisic acid (ABA) content, decreased ethylene production, increased density of cell wall material containing linear pectins with a low degree of methylation, and a thicker cuticle with a higher content of cutin monomers and triterpenoids. The levels of several primary metabolites and phenylpropanoid compounds were also altered in the transgenic fruits, which could be attributed to delayed fruit ripening and/or to ABA. Network correlation analysis and pharmacological experiments with the ABA biosynthesis inhibitor, abamine, indicated that altered ABA levels were a direct effect of the increased β-carotene content and were in turn responsible for the extended shelf life phenotype. Thus, manipulation of β-carotene levels results in an improvement not only of the nutritional value of tomato fruits, but also of their shelf life.

Metabolomics profiling and biological properties of root extracts from two Asphodelus species: A. albus and A. aestivus

The pharmacological properties of Asphodelus species have been advocated previously. In this respect, the present study attempts to unravel the antioxidant and enzyme inhibitory activity of root extracts of two Asphodelus species, namely, A. albus and A. aestivus. Data gathered demonstrated that the dichloromethane (25.49, 51.30, 104.31, and 81.58 mg Trolox equivalents [TEs]/g, for 2,2-diphenyl-1-picrylhydrazyl [DPPH], 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) [ABTS], cupric ion reducing antioxidant capacity [CUPRAC], and ferric reducing antioxidant power[FRAP] assays respectively) and ethyl acetate (20.60, 41.86, 89.07, and 57.85 mg TEs/g, for DPPH, ABTS, CUPRAC, and FRAP assays respectively) extracts of A. albus roots showed highest radical scavenging and reducing potential. These findings were in accordance with total phenolic content observed which showed the highest phenolic content of A. albus dichloromethane (30.74 mg gallic acid equivalents [GAEs]/g) and ethyl acetate (23.41 mg GAEs/g) extracts. Interestingly, A. albus and A. aestivus root extracts were active inhibitors of tyrosinase and lipase, with values varying from 56.52 to 71.49 mg kojic acid equivalent/g and 34.88 to 86.32 mg orlistat equivalent/g, respectively. Flavonoids, anthraquinones, and phenolic acids were identified as main individual compounds in chemical profile analysis. This is the first report of the presence of aloin A, aloin B, and aloesin in species other than in Aloe. Scientific evidences gathered from this study claimed the biological activity of the studied Asphodelus species and provided rationale for further investigations which might lead to the development of novel pharmacophores to alleviate oxidative stress related complications, obesity, as well as, skin hyperpigmentation complications.

Distinct gene expression and secondary metabolite profiles in suppressor of prosystemin-mediated responses2 (spr2) tomato mutants having impaired mycorrhizal colonization

Arbuscular mycorrhizal fungi (AMF) colonization, sampled at 32-50 days post-inoculation (dpi), was significantly reduced in suppressor of prosystemin-mediated responses2 (spr2) mutant tomato plants impaired in the ω-3 FATTY ACID DESATURASE7 (FAD7) gene that limits the generation of linolenic acid and, consequently, the wound-responsive jasmonic acid (JA) burst. Contrary to wild-type (WT) plants, JA levels in root and leaves of spr2 mutants remained unchanged in response to AMF colonization, further supporting its regulatory role in the AM symbiosis. Decreased AMF colonization in spr2 plants was also linked to alterations associated with a disrupted FAD7 function, such as enhanced salicylic acid (SA) levels and SA-related defense gene expression and a reduction in fatty acid content in both mycorrhizal spr2 roots and leaves. Transcriptomic data revealed that lower mycorrhizal colonization efficiency in spr2 mutants coincided with the modified expression of key genes controlling gibberellin and ethylene signaling, brassinosteroid, ethylene, apocarotenoid and phenylpropanoid synthesis, and the wound response. Targeted metabolomic analysis, performed at 45 dpi, revealed augmented contents of L-threonic acid and DL-malic acid in colonized spr2 roots which suggested unfavorable conditions for AMF colonization. Additionally, time- and genotype-dependent changes in root steroid glycoalkaloid levels, including tomatine, suggested that these metabolites might positively regulate the AM symbiosis in tomato. Untargeted metabolomic analysis demonstrated that the tomato root metabolomes were distinctly affected by genotype, mycorrhizal colonization and colonization time. In conclusion, reduced AMF colonization efficiency in spr2 mutants is probably caused by multiple and interconnected JA-dependent and independent gene expression and metabolomic alterations.

Rootstock x Environment Interactions on Nitrogen-Use Efficiency in Grafted Tomato Plants at Different Phenological Stages

The use of grafting techniques for horticultural crops increases plant tolerance to various abiotic and biotic stresses. Tomato production under greenhouse conditions relies on plants grafted onto vigorous rootstocks because they sustain crops for longer periods. Growers under Mediterranean conditions usually grow crops in passive greenhouses during the summer and winter season, to provide fresh products throughout the year. No information is available with regard to the effect of the environment on nitrogen-use efficiency (NUE) in tomato plants grafted onto rootstocks with different vigor. In the present study, NUE, along with its components—uptake (NUpE) and utilization (NUtE) efficiencies—were evaluated in tomato plants grafted onto two interspecific rootstocks, conferring medium (“King Kong”) or high (“Kaiser”) vigor to the plants. The evaluations were carried out during the vegetative and reproductive stage in plants subjected to different environmental conditions resulting in different plant growth rates. The grafting treatments did not affect NUE, NUpE or NUtE in young plants, but at the reproductive stage, differences were found during the summer season (high N demand) where the vigorous rootstock increased NUpE from 55%, in non-grafted plants, to 94%, with the consequent differences in NUE. During the winter crop, no differences in NUE were found between the vigorous rootstock and non-grafted plants, but the less vigorous (cold-tolerant) rootstock enhanced NUpE. Significant positive relationships were found between plant growth rate and both NUE and NUpE, while NUtE decreased with increasing growth rate.

Antioxidant and Anti-Inflammatory Activities of the Crude Extracts of Raw and Fermented Tomato Pomace and Their Correlations with Aglycate-Polyphenols

Two tomato pomace (TP) were studied as feedstocks to obtain extracts that are rich in polyphenols. TPs prompt degradation impairs biomass safety, thus naturally present microflora were tested to perform conservation, and own lactic bacteria became predominant after 60 days of treatment. The extracts of TPs and TPs fermented (TPF) were chemically characterized and tested for antioxidant and anti-inflammatory activities. Flavonoids and phenolic acids were classed as aglycone-polyphenols (A-PP), the most bioactive polyphenol fraction. Fermentation led to a reduction of the A-PP amount, but no significant change in composition. Antioxidant power increased, despite the A-PP reduction, for the presence of fermentation metabolites having aromatic-substituent. TP and TPF both have anti-inflammatory properties that were strictly dependent upon the A-PP content. Fermentation preserved the anti-inflammatory activity and the Partial Least Square (PLS) identified as the most active molecules naringenin chalcone, kaempferol, gallic acid, and cinnamic acid, together with the definition of the active dose.

A High-Throughput Extraction and Analysis Method for Steroidal Glycoalkaloids in Tomato

Tomato steroidal glycoalkaloids (tSGAs) are a class of cholesterol-derived metabolites uniquely produced by the tomato clade. These compounds provide protection against biotic stress due to their fungicidal and insecticidal properties. Although commonly reported as being anti-nutritional, both in vitro as well as pre-clinical animal studies have indicated that some tSGAs may have a beneficial impact on human health. However, the paucity of quantitative extraction and analysis methods presents a major obstacle for determining the biological and nutritional functions of tSGAs. To address this problem, we developed and validated the first comprehensive extraction and ultra-high-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) quantification method for tSGAs. Our extraction method allows for up to 16 samples to be extracted simultaneously in 20 min with 93.0 ± 6.8 and 100.8 ± 13.1% recovery rates for tomatidine and alpha-tomatine, respectively. Our UHPLC-MS/MS method was able to chromatographically separate analytes derived from 18 tSGA peaks representing 9 different tSGA masses, as well as two internal standards, in 13 min. Tomato steroidal glycoalkaloids that did not have available standards were annotated using high resolution mass spectrometry as well as product ion scans that provided fragmentation data. Lastly, we utilized our method to survey a variety of commonly consumed tomato-based products. Total tSGA concentrations ranged from 0.2 to 3.4 mg/serving and represent some of the first reported tSGA concentrations in tomato-based products. Our validation studies indicate that our method is sensitive, robust, and able to be used for a variety of applications where concentrations of biologically relevant tSGAs need to be quantified.

Characterization of metabolite profiles of white and green spears of asparagus officinalis L. from Caoxian, East China

China is the largest planting country of asparagus (Asparagus officinalis L.) in the world. Caoxian, as the famous asparagus township in China, enjoys a reputation for producing asparagus with high yield and good quality, due to its unique geological characteristic. In this study, a method of reverse-phase ultraperformance liquid chromatography coupled with electrospray tandem mass spectrometry (RP-UPLC-ESI-MS/MS) was established for profiling metabolites from three segments (tip, mid, and base) of 'Caoxian white and green Asparagus'. A total of 114 metabolites were identified, among them, 43 were found for the first time in this vegetable. Principal component analysis (PCA) and hierarchical cluster analysis (HCA) was applied to provide an overview of the metabolite profiles of Caoxian asparagus and to separate different segments of spears. The variables most decisive to discriminate among segments included 9 of the metabolites tentatively identified. This study will help to improve the protection of Caoxian asparagus geographical indication.

A comparative metabolomics analysis of the components of heartwood and sapwood in Taxus chinensis (Pilger) Rehd

Taxus chinensis is a well-known gymnosperm with great ornamental and medicinal value. Its purple red brown heartwood (HW) has many attributes such as straight texture, high density, mechanical strength, rich elasticity and corrosion resistance that is highly prized commercially. T. chinensis sapwood (SW), in comparison, lacks these important traits. At present, little is known about the differences of metabolites between the SW and HW in T. chinensis. Widely targeted metabolic profiling was performed to analyze the metabolic profiles of HW and SW in T. chinensis using Liquid Chromatography-Electrospray Ionization-Mass Spectrometry (LC-EI-MS). A total of 607 metabolites were detected in HW and SW. Among them, 146 metabolites were significantly higher, and 167 metabolites significantly lower, in HW as compared to SW. These differential metabolites were mainly involved in metabolic pathways and biosynthesis of secondary metabolites, such as flavonoids, flavone and flavonol, phenylpropanoids and antibiotics. Moreover, 71 flavonoids and isoflavones were found to be significantly different between HW and SW. Our results show the difference of components between the HW and SW, which has potential significance to further elucidate the mechanism of HW color formation. The results will provide insight into the metabolites associated with wood color formation and useful information for understanding the metabolites associated with wood quality.

Advances in Omics Approaches for Abiotic Stress Tolerance in Tomato

Tomato, one of the most important crops worldwide, has a high demand in the fresh fruit market and processed food industries. Despite having considerably high productivity, continuous supply as per the market demand is hard to achieve, mostly because of periodic losses occurring due to biotic as well as abiotic stresses. Although tomato is a temperate crop, it is grown in almost all the climatic zones because of widespread demand, which makes it challenge to adapt in diverse conditions. Development of tomato cultivars with enhanced abiotic stress tolerance is one of the most sustainable approaches for its successful production. In this regard, efforts are being made to understand the stress tolerance mechanism, gene discovery, and interaction of genetic and environmental factors. Several omics approaches, tools, and resources have already been developed for tomato growing. Modern sequencing technologies have greatly accelerated genomics and transcriptomics studies in tomato. These advancements facilitate Quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS). However, limited efforts have been made in other omics branches like proteomics, metabolomics, and ionomics. Extensive cataloging of omics resources made here has highlighted the need for integration of omics approaches for efficient utilization of resources and a better understanding of the molecular mechanism. The information provided here will be helpful to understand the plant responses and the genetic regulatory networks involved in abiotic stress tolerance and efficient utilization of omics resources for tomato crop improvement.

Extractable impurities from fluoropolymer-based membrane filters - interference in high-throughput, untargeted analysis

The removal of particles using fluoropolymer-based membrane filters is usually done so to prolong the life span of an analytical column, prevent hardware damage, and reduce signal suppression. Ironically, these membrane filters tend to leach impurities into the samples as the samples are filtered through them. These impurities have the potential to affect the researcher's interpretation in high-throughput, non-targeted analysis. In this study, extractable impurities from different brands of fluoropolymer-based membrane filters present in the filtrate filtered using the said filters were investigated. The results demonstrated that different brand membrane filters and materials tend to elute vastly different numbers of impurities. There were instances whereby the extractable impurities persisted in both the membrane filter and the filtrate despite the filter being pre-conditioned (up to 3 times). Principle component analysis revealed that filtrates at different purge intervals are distant from the unfiltered samples. Pre-conditioning of the PTFE membrane filters could potentially reduce the number of extractable impurities across the tested brands. PVDF filtrates, however, tend to co-cluster with their respective brands, thus suggesting that dissimilarity persists in brands following conditioning. As such, pre-conditioning of the PTFE membrane filters should be encouraged so as to reduce false positive results, while the use of PVDF membrane filters for mass-spectrometry-based untargeted analysis is not advisable as extractable impurities would still persist after 3 rounds of conditioning. Neither the use of different filter brands, nor the use of different filter materials in a sample batch are encouraged as different membrane materials or brands could potentially elute varying impurities.

A classification of liquid chromatography mass spectrometry techniques for evaluation of chemical composition and quality control of traditional medicines

Natural products (NPs) and traditional medicines (TMs) are used for treatment of various diseases and also to develop new drugs. However, identification of drug leads within the immense biodiversity of living organisms is a challenging task that requires considerable time, labor, and computational resources as well as the application of modern analytical instruments. LC-MS platforms are widely used for both drug discovery and quality control of TMs and food supplements. Moreover, a large dataset generated during LC-MS analysis contains valuable information that could be extracted and handled by means of various data mining and statistical tools. Novel sophisticated LC-MS based approaches are being introduced every year. Therefore, this review is prepared for the scientists specialized in pharmacognosy and analytical chemistry of NPs as well as working in related areas, in order to navigate them in the world of diverse LC-MS based techniques and strategies currently employed for NP discovery and dereplication, quality control, pattern recognition and sample comparison, and also in targeted and untargeted metabolomic studies. The suggested classification system includes the following LC-MS based procedures: elemental composition determination, isotopic fine structure analysis, mass defect filtering, de novo identification, clustering of the compounds in Molecular Networking (MN), diagnostic fragment ion (or neutral loss) filtering, manual dereplication using MS/MS data, database-assisted peak annotation, annotation of spectral trees, MS fingerprinting, feature extraction, bucketing of LC-MS data, peak profiling, predicted metabolite screening, targeted quantification of biomarkers, quantitative analysis of multi-component system, construction of chemical fingerprints, multi-targeted and untargeted metabolite profiling.

A new optimization strategy for MALDI FTICR MS tissue analysis for untargeted metabolomics using experimental design and data modeling

Ultra-high-resolution imaging mass spectrometry using matrix-assisted laser desorption ionization (MALDI) MS coupled to a Fourier transform ion cyclotron resonance (FTICR) mass analyzer is a powerful technique for the visualization of small molecule distribution within biological tissues. The FTICR MS provides ultra-high resolving power and mass accuracy that allows large molecular coverage and molecular formula assignments, both essential for untargeted metabolomics analysis. These performances require fine optimizations of the MALDI FTICR parameters. In this context, this study proposes a new strategy, using experimental design, for the optimization of ion transmission voltages and MALDI parameters, for tissue untargeted metabolomics analysis, in both positive and negative ionization modes. These experiments were conducted by assessing the effects of nine factors for ion transmission voltages and four factors for MALDI on the number of peaks, the weighted resolution, and the mean error within m/z 150-1000 mass range. For this purpose, fractional factorial designs were used with multiple linear regression (MLR) to evaluate factor effects and to optimize parameter values. The optimized values of ion transmission voltages (RF amplitude TOF, RF amplitude octopole, frequency transfer optic, RF frequency octopole, deflector plate, funnel 1, skimmer, funnel RF amplitude, time-of-flight, capillary exit), MALDI parameters (laser fluence, number of laser shots), and detection parameters (data size, number of scans) led to an increase of 32% and 18% of the number of peaks, an increase of 8% and 39% of the resolution, and a decrease of 56% and 34% of the mean error in positive and negative ionization modes, respectively. Graphical abstract.

A comparative study of UHPLC/Orbitrap MS metabolomics profiles and biological properties of Asphodeline taurica from Bulgaria and Turkey

The present investigation attempts to compare the pharmacological properties and phytochemical profile of four extracts (ethyl acetate, dichloromethane, methanol, and water) of Asphodeline taurica (Pall.) Endl. roots from Bulgaria and Turkey. The Bulgarian ethyl acetate extract displayed the highest antioxidant activity in the DPPH, CUPRAC, and phosphomolybdenum assay, and strongest inhibition against α-amylase and α-glucosidase. The Turkish aqueous extract exhibited the strongest ABTS scavenging and ferric reducing power while its methanol extract was the most effective acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) inhibitor. On the other hand, the Turkish dichloromethane extract showed the highest lipase inhibition. UHPLC/Orbitrap MS analysis showed a wide array of individual phenolics; six free anthraquinones, two bianthraquinones, three bianthracenes, three anthraquinone glycosides and one bianthracen glycoside were identified. The present data suggest that A. taurica roots can be considered as a valuable source of biologically active phytocompounds with functional properties for the cosmetic and pharmaceutical industries.

Co-Culture Systems for the Production of Secondary Metabolites: Current and Future Prospects

Microorganisms are the great sources of Natural Products (NPs); these are imperative to their survival apart from conferring competitiveness amongst each other within their environmental niches. Primary and secondary metabolites are the two major classes of NPs that help in cell development, where antimicrobial activity is closely linked with secondary metabolites. To capitalize on the effects of secondary metabolites, co-culture methods have been often used to develop an artificial microbial community that promotes the action of these metabolites. Different analytical techniques will subsequently be employed based on the metabolite specificity and sensitivity to further enhance the metabolite induction. Liquid Chromatography-Mass Spectrometry (LC-MS) and Gas Chromatography (GC)-MS are commonly used for metabolite separation while Nuclear Magnetic Resonance (NMR) and Mass Spectrometry (MS) have been used as tools to elucidate the structure of compounds. This review intends to discuss current systems in use for co-culture in addition to its advantages, with discourse into the investigation of specific techniques in use for the detailed study of secondary metabolites. Further advancements and focus on co-culture technologies are required to fully realize the massive potential in synthetic biological systems.

Antimicrobial Activity of Various Parts of Tomato Plants Varied with Different Solvent Extracts

The antimicrobial activity of acetone, hexane, dichloromethane, and methanol extracts from leaves, stems, immature green fruits, and red fruits of tomato plants was examined against six phytopathogens. The minimum inhibitory concentration (MIC) of the acetonic extracts from these four plant parts was lower than that of the other solvents. Among the acetonic extracts, tomato leaves had a lower MIC than the other tomato parts. The acetonic extract from tomato leaves was therefore selected as a source of antimicrobial substances. The acetonic extract from tomato leaves inhibited mycelial growth of Fusarium oxysporum f. sp. lycopersici, Glomerella cingulata, and Rhizoctonia solani. Mycelial growth of R. solani treated with acetone extract from leaves showed more susceptibility than the other phytopathogens. Using 0.31 mg/ml of the acetonic extract from leaves, mycelial growth of R. solani on days 1, 2, and 3 decreased by 50.0, 52.1, and 64.0%, respectively, compared with acetone solvent treatment. The antimicrobial compounds effective against R. solani were identified as linolenic acid and caffeic acid by bioautography and GC-MS. These two compounds were used to treat six phytopathogens to confirm their antimicrobial activities. Linolenic acid inhibited mycelial growth of R. solani, while caffeic acid showed only slight antimicrobial activity. Results indicated that we propose extracts from tomato leaves which included antimicrobial compounds may provide a new lead in the pursuit of new biological sources of agrochemical candidates.

Analysis of metabolic changes in Trichoderma asperellum TJ01 at different fermentation time-points by LC-QQQ-MS

Trichoderma spp. are among the most widely recognized biocontrol fungi used to inhibit pathogens and promote plant growth. These functions are related to primary and secondary metabolites. This study investigated the different metabolites in Trichoderma asperellum TJ01 cultured for 24 and 72 h using liquid chromatography with triple-quadrupole mass spectrometry. Compared to the 24 h culture of T. asperellum TJ01, the 72 h culture with amino acid metabolism tended to decrease while sugar and lipid metabolisms tended to increase. Furthermore, the 72 h culture had a higher proportion of upregulated flavonoids, in combination with a higher proportion of downregulated alkaloids, and equal proportions of upregulated and downregulated polyphenols and hormones. This study also identified a few valuable medicinal substances such as trigonelline and 5-hydroxytryptophan in T. asperellum TJ01 fermentation cultures.

Metabolomics Provides Valuable Insight for the Study of Durum Wheat: A Review

Metabolomics is increasingly being applied in various fields offering a highly informative tool for high-throughput diagnostics. However, in plant sciences, metabolomics is underused, even though plant studies are relatively easy and cheap when compared to those on humans and animals. Despite their importance for human nutrition, cereals, and especially wheat, remain understudied from a metabolomics point of view. The metabolomics of durum wheat has been essentially neglected, although its genetic structure allows the inference of common mechanisms that can be extended to other wheat and cereal species. This review covers the present achievements in durum wheat metabolomics highlighting the connections with the metabolomics of other cereal species (especially bread wheat). We discuss the metabolomics data from various studies and their relationships to other "-omics" sciences, in terms of wheat genetics, abiotic and biotic stresses, beneficial microbes, and the characterization and use of durum wheat as feed, food, and food ingredient.

Identification of potential human urinary biomarkers for tomato juice intake by mass spectrometry-based metabolomics

PURPOSE

Dietary biomarkers allow the accurate and objective determination of the dietary intake of humans and can thus be valuable for investigating the relation between consumption of foods and biochemical as well as physiological responses. The objective of this study was the identification of potential urinary biomarkers for consumption of tomato juice.

METHODS

In the course of a dietary intervention study, the human urine metabolome of a study cohort was compared between a tomato-free diet and after intake of tomato juice by application of an LC-HRMS-based metabolomics approach. The data acquisition was achieved using an orbitrap mass spectrometer, followed by multistage data processing and univariate as well as multivariate statistical analysis to identify discriminating features.

RESULTS

Statistical analysis revealed several unique features detectable after tomato juice intake. The most discriminating markers were putatively identified as hydroxylated and sulfonated metabolites of esculeogenin B, aglycone of the steroidal glycoalkaloid esculeoside B recently found in tomato juice. Furthermore, the β-carboline alkaloids tangutorid E and F and glucuronidated derivatives thereof were identified in urine.

CONCLUSIONS

Steroidal glycoalkaloids in tomato juice are cleaved after ingestion, and hydroxylated and sulfonated metabolites of their aglycones might serve as urinary biomarkers for tomato juice intake. Similarly, β-carboline alkaloids and glucuronidated derivatives were identified as potential urinary biomarkers. Both the aglycones of the steroidal alkaloids and the β-carboline alkaloids might exhibit biological activities worth investigating.

Swift metabolite changes and leaf shedding are milestones in the acclimation process of grapevine under prolonged water stress

BACKGROUND

Grape leaves provide the biochemical substrates for berry development. Thus, understanding the regulation of grapevine leaf metabolism can aid in discerning processes fundamental to fruit development and berry quality. Here, the temporal alterations in leaf metabolism in Merlot grapevine grown under sufficient irrigation and water deficit were monitored from veraison until harvest.

RESULTS

The vines mediated water stress gradually and involving multiple strategies: osmotic adjustment, transcript-metabolite alteration and leaf shedding. Initially stomatal conductance and leaf water potential showed a steep decrease together with the induction of stress related metabolism, e.g. up-regulation of proline and GABA metabolism and stress related sugars, and the down-regulation of developmental processes. Later, progressive soil drying was associated with an incremental contribution of Ca²⁺ and sucrose to the osmotic adjustment concomitant with the initiation of leaf shedding. Last, towards harvest under progressive stress conditions following leaf shedding, incremental changes in leaf water potential were measured, while the magnitude of perturbation in leaf metabolism lessened.

CONCLUSIONS

The data present evidence that over time grapevine acclimation to water stress diversifies in temporal responses encompassing the alteration of central metabolism and gene expression, osmotic adjustments and reduction in leaf area. Together these processes mitigate leaf water stress and aid in maintaining the berry-ripening program.

The effect of isolation methods of tomato pollen on the results of metabolic profiling

INTRODUCTION

Untargeted metabolomics is a powerful tool to detect hundreds of metabolites within a given tissue and to compare the metabolite composition of samples in a comprehensive manner. However, with regard to pollen research such comprehensive metabolomics approaches are yet not well developed. To enable isolation of pollen that is tightly enclosed within the anthers of the flower, such as immature pollen, the current pollen isolation protocols require the use of a watery solution. These protocols raise a number of concerns for their suitability in metabolomics analyses, in view of possible metabolic activities in the pollen and contamination with anther metabolites.

OBJECTIVES

We assessed the effect of different sample preparation procedures currently used for pollen isolation for their suitability to perform metabolomics of tomato pollen.

METHODS

Pollen were isolated using different methods and the metabolic profiles were analysed by liquid chromatography-mass spectrometry (LC-MS).

RESULTS

Our results demonstrated that pollen isolation in a watery solution led to (i) rehydration of the pollen grains, inducing marked metabolic changes in flavonoids, phenylpropanoids and amino acids and thus resulting in a metabolite profile that did not reflect the one of mature dry pollen, (ii) hydrolysis of sucrose into glucose and fructose during subsequent metabolite extraction, unless the isolated and rehydrated pollen were lyophilized prior to extraction, and (iii) contamination with anther-specific metabolites, such as alkaloids, thus compromising the metabolic purity of the pollen fraction.

CONCLUSION

We conclude that the current practices used to isolate pollen are suboptimal for metabolomics analyses and provide recommendations on how to improve the pollen isolation protocol, in order to obtain the most reliable metabolic profile from pollen tissue.

Salinity in Autumn-Winter Season and Fruit Quality of Tomato Landraces

Tomato landraces, originated by adaptive responses to local habitats, are considered a valuable resource for many traits of agronomic interest, including fruit nutritional quality. Primary and secondary metabolites are essential determinants of fruit organoleptic quality, and some of them, such as carotenoids and phenolics, have been associated with beneficial proprieties for human health. Landraces' fruit taste and flavour are often preferred by consumers compared to the commercial varieties' ones. In an autumn-winter greenhouse hydroponic experiment, the response of three Southern-Italy tomato landraces (Ciettaicale, Linosa and Corleone) and one commercial cultivar (UC-82B) to different concentrations of sodium chloride (0 mM, 60 mM or 120 mM NaCl) were evaluated. At harvest, no losses in marketable yield were noticed in any of the tested genotypes. However, under salt stress, fresh fruit yield as well as fruit calcium concentration were higher affected in the commercial cultivar than in the landraces. Furthermore, UC-82B showed a trend of decreasing lycopene and total antioxidant capacity with increasing salt concentration, whereas no changes in these parameters were observed in the landraces under 60 mM NaCl. Landraces under 120 mM NaCl accumulated more fructose and glucose in the fruits, while salt did not affect hexoses levels in UC-82B. Ultra-performance liquid chromatography-tandem mass spectrometry analysis revealed differential accumulation of glycoalkaloids, phenolic acids, flavonoids and their derivatives in the fruits of all genotypes under stress. Overall, the investigated Italian landraces showed a different behaviour compared to the commercial variety UC-82B under moderate salinity stress, showing a tolerable compromise between yield and quality attributes. Our results point to the feasible use of tomato landraces as a target to select interesting genetic traits to improve fruit quality under stress conditions.

The effects of dietary tomato powder (Solanum lycopersicum L.) supplementation on the haematological, immunological, serum biochemical and antioxidant parameters of growing rabbits

Using nutritional antioxidants in livestock systems is considered the key in improving animal production. The current study assumes that dietary tomato powder (TP) supplementation positively affects haemato-immunological, biochemical, and antioxidant parameters for New Zealand rabbits. A total of 30 rabbits (45 days old) were assigned to three groups, including a diet with no additives (control), and two dietary treatments with the providing of 1% or 2% TP. Mass spectrometric study for TP methanolic extract showed some phenolic compounds. Consumption of TP supplemented diets significantly (p < 0.001) affected body weight gain and feed efficiency. Red blood cells and white blood cells count exhibited a significant increase (p < 0.001) in both TP groups compared with the control. In addition to, feeding rabbits on TP enhanced cell-mediated and humoral immune responses through a significant increase in phagocytosis, chemotaxis, and levels of immunoglobulins (TIg, IgG, IgM and IgA). Supplementation of TP significantly (p < 0.01) reduced lipid profile induces except high-density lipoprotein cholesterol values. A remarkable significant (p < 0.001) effect on serum and hepatic oxidative stress responses were observed with TP addition. Ultimately, TP supplementation could play a potential role as a growth and health enhancer for fattening rabbits.

Metabolomics of Solanum lycopersicum Infected with Phytophthora infestans Leads to Early Detection of Late Blight in Asymptomatic Plants

Tomato crops suffer attacks of various pathogens that cause large production losses. Late blight caused by Phytophthora infestans is a devastating disease in tomatoes because of its difficultly to control. Here, we applied metabolomics based on liquid chromatography⁻mass spectrometry (LC-MS) and metabolic profiling by matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) in combination with multivariate data analysis in the early detection of late blight on asymptomatic tomato plants and to discriminate infection times of 4, 12, 24, 36, 48, 60, 72 and 96 h after inoculation (hpi). MALDI-MS and LC-MS profiles of metabolites combined with multivariate data analysis are able to detect early-late blight-infected tomato plants, and metabolomics based on LC-MS discriminates infection times in asymptomatic plants. We found the metabolite tomatidine as an important biomarker of infection, saponins as early infection metabolite markers and isocoumarin as early and late asymptomatic infection marker along the post infection time. MALDI-MS and LC-MS analysis can therefore be used as a rapid and effective method for the early detection of late blight-infected tomato plants, offering a suitable tool to guide the correct management and application of sanitary defense approaches. LC-MS analysis also appears to be a suitable tool for identifying major metabolites of asymptomatic late blight-infected tomato plants.

Identification of a freshness marker metabolite in stored soybean sprouts by comprehensive mass-spectrometric analysis of carbonyl compounds

The objective of this study was to identify metabolites that quantitatively indicate degrees of freshness of soybean sprouts. Self-cultivated soybean sprouts were stored at 5 °C, 10 °C or 20 °C, and respiratory CO2 production rates were monitored using gas chromatography during storage. Carbonyl compounds (CCs) were analyzed comprehensively using mass-spectroscopic metabolomics analyses. CCs were derivatized using dansyl hydrazine (DH) and were then analyzed using high performance liquid chromatography-electrospray ionization tandem mass spectrometry (HPLC-MS/MS) with multiplexed multiple reaction monitoring (MRM). In the MRM chromatogram, 171 to 358 peaks were observed from stored soybean sprouts. Principle component analysis and discriminant analysis (PCA-DA) selected the CC-DH derivative ion with a m/z 512 at a retention time of 9.34 min as the most significant metabolite. Searching online metabolomics databases and matching fragment patterns of product ion mass spectra of an authentic standard revealed abscisic acid is a freshness marker of soybean sprouts.

Modulation of steroidal glycoalkaloid biosynthesis in tomato (Solanum lycopersicum) by jasmonic acid

Jasmonic acid (JA) is a phytohormone involved in plant development and defense. A major role of JA is the enhancement of secondary metabolite production, such as response to herbivory. Systemin is a bioactive plant peptide of 18 amino acids that contributes to the induction of local and systemic defense responses in tomato (Solanum lycopersicum) through JA biosynthesis. The overexpression of systemin (PS-OE) results in constitutive JA accumulation and enhances pest resistance in plants. Conversely, mutant plants affected in linolenic acid synthesis (spr2) are negatively compromised in the production of JA which favors damage and oviposition by insect herbivores. With undirected mass fingerprinting analyses, we found global metabolic differences between genotypes with modified jasmonic acid production. The spr2 mutants were enriched in di-unsaturated fatty acids and generally showed more changes. The PS-OE genotype produced an unidentified compound with a mass-to-charge ratio of 695 (MZ695). Most strikingly, the steroidal glycoalkaloid biosynthesis was negatively affected in the spr2 genotype. Complementation with jasmonic acid could restore the tomatine pathway, which strongly suggests the control of steroidal glycoalkaloid biosynthesis by jasmonic acid. spr2 plants were more susceptible to fungal infection with Fusarium oxysporum f.sp. ciceris, but not to bacterial infection with Clavibacter michiganensis subsp. michiganensis which supports the involvement of steroidal glycoalkaloids in the plant response against fungi.

Drought-induced susceptibility for Cenangium ferruginosum leads to progression of Cenangium-dieback disease in Pinus koraiensis

Recently, the occurrence of "Cenangium-dieback" has been frequent and devastating. Cenangium-dieback is caused by an endophytic fungus Cenangium ferruginosum in stressed pine trees. Progression of the disease in terms of molecular interaction between host and pathogen is not well studied and there is a need to develop preventive strategies. Thus, we simulated disease conditions and studied the associated transcriptomics, metabolomics, and hormonal changes. Pinus koraiensis seedlings inoculated with C. ferruginosum were analyzed both under drought and well-watered conditions. Transcriptomic analysis suggested decreased expression of defense-related genes in C. ferruginosum-infected seedlings experiencing water-deficit. Further, metabolomic analysis indicated a decrease in the key antimicrobial terpenoids, flavonoids, and phenolic acids. Hormonal analysis revealed a drought-induced accumulation of abscisic acid and a corresponding decline in the defense-associated jasmonic acid levels. Pathogen-associated changes were also studied by treating C. ferruginosum with metabolic extracts from pine seedlings (with and without drought) and polyethylene glycol to simulate the effects of direct drought. From RNA sequencing and metabolomic analysis it was determined that drought did not directly induce pathogenicity of C. ferruginosum. Collectively, we propose that drought weakens pine immunity, which facilitates increased C. ferruginosum growth and results in conversion of the endophyte into the phytopathogen causing dieback.

The Chemistry behind Tomato Quality

Tomato is one of the most widely consumed fresh vegetables in the industrialized world and an important source of healthy constituents of the human diet. Despite the unique flavor characteristics of tomatoes, which make them extremely valuable in cooking, and their recognized beneficial role in the diet, the quality of tomato was traditionally only considered in connection to external appearances. As it happened with other highly requested crops, breeding programs of tomato focused their efforts on developing new varieties with higher yields and stress resistance, with better uniformity in fruit size, brighter color and prolonged shelf life. The downside of these strategies was that organoleptic features and nutritional value were often neglected, with a detrimental effect on commercial tomatoes. Over the last years, there has been an increase in consumers’ demand for tasty and healthy products. This aspect, paired with novel and multidisciplinary approaches to tomato research, allowed both sensory and nutritional qualities to be reconsidered as valuable parameters in breeding. In this review we describe the main chemical constituents of tomato, focusing on the flavor compounds (both volatile and non-volatile compounds) and secondary metabolites. Particular attention is paid to their beneficial effects on human health and their relevance to the overall quality of tomato.

Identification of spoilage by Alicyclobacillus bacteria in tomato-based products by UHPLC-MS/MS

In recent years, there have been some cases of alteration of tomato derivatives by Alicyclobacilli spp. The spoilage was reported by consumers who felt odors and abnormal tastes ("bad") of products. In this work, an untarget approach with Q-Exactive™ Quadrupole-Orbitrap Mass Spectrometer has been used to identify metabolites associated with the alteration of tomato puree by Alicyclobacillus bacteria. The study was carried out on tomato puree found positive for the presence of Alicyclobacillus spores. The germination and growth of native spores were induced through incubation at 65°C under static conditions for 5 days. For microbial concentration below 100 ufc/mL, negative growth was considered. The samples arising from incubation were submitted to UHPL-HRMS/MS analysis. To find compounds related to microbial growth, data obtained by UHPLC-MS/MS analysis were processed with Thermo Fisher Compound Discoverer™ 2.0 software. We compared samples grouped according to microbial growth: positive growth vs negative growth. Five compounds were identified and confirmed by analysis performed on authentic standards. To other compounds, we have assigned a putative identity. The HRMS approach using Q-Exactive™ Quadrupole-Orbitrap Mass Spectrometer has proven to be an important and powerful tool for identification of compounds which could be used as marker molecules in cases of suspected spoilage by Alicyclobacillus bacteria in tomato derivatives.