GLYCOALKALOID METABOLISM1 is required for steroidal alkaloid glycosylation and prevention of phytotoxicity in tomato

Transcriptomic Profiling Reveals Shared Signalling Networks Between Flower Development and Herbivory-Induced Responses in Tomato

Most flowering plants must defend themselves against herbivores for survival and attract pollinators for reproduction. Although traits involved in plant defence and pollinator attraction are often localised in leaves and flowers, respectively, they will show a diffuse evolution if they share the same molecular machinery and regulatory networks. We performed RNA-sequencing to characterise and compare transcriptomic changes involved in herbivory-induced defences and flower development, in tomato leaves and flowers, respectively. We found that both the herbivory-induced responses and flower development involved alterations in jasmonic acid signalling, suppression of primary metabolism and reprogramming of secondary metabolism. We identified 411 genes that were involved in both processes, a number significantly higher than expected by chance. Genetic manipulation of key regulators of induced defences also led to the expression changes in the same genes in both leaves and flowers. Targeted metabolomic analysis showed that among closely related tomato species, jasmonic acid and α-tomatine are correlated in flower buds and herbivory-induced leaves. These findings suggest that herbivory-induced responses and flower development share a common molecular machinery and likely have coevolved in nature.

Catch-22 in specialized metabolism: balancing defense and growth

Plants are unsurpassed biochemists that synthesize a plethora of molecules in response to an ever-changing environment. The majority of these molecules, considered as specialized metabolites, effectively protect the plant against pathogens and herbivores. However, this defense most probably comes at a great expense, leading to reduction of growth (known as the 'growth-defense trade-off'). Plants employ several strategies to reduce the high metabolic costs associated with chemical defense. Production of specialized metabolites is tightly regulated by a network of transcription factors facilitating its fine-tuning in time and space. Multifunctionality of specialized metabolites-their effective recycling system by re-using carbon, nitrogen, and sulfur, thus re-introducing them back to the primary metabolite pool-allows further cost reduction. Spatial separation of biosynthetic enzymes and their substrates, and sequestration of potentially toxic substances and conversion to less toxic metabolite forms are the plant's solutions to avoid the detrimental effects of metabolites they produce as well as to reduce production costs. Constant fitness pressure from herbivores, pathogens, and abiotic stressors leads to honing of specialized metabolite biosynthesis reactions to be timely, efficient, and metabolically cost-effective. In this review, we assess the costs of production of specialized metabolites for chemical defense and the different plant mechanisms to reduce the cost of such metabolic activity in terms of self-toxicity and growth.

Plant Metabolic Gene Clusters: Evolution, Organization, and Their Applications in Synthetic Biology

Plants are a remarkable source of high-value specialized metabolites having significant physiological and ecological functions. Genes responsible for synthesizing specialized metabolites are often clustered together for a coordinated expression, which is commonly observed in bacteria and filamentous fungi. Similar to prokaryotic gene clustering, plants do have gene clusters encoding enzymes involved in the biosynthesis of specialized metabolites. More than 20 gene clusters involved in the biosynthesis of diverse metabolites have been identified across the plant kingdom. Recent studies demonstrate that gene clusters are evolved through gene duplications and neofunctionalization of primary metabolic pathway genes. Often, these clusters are tightly regulated at nucleosome level. The prevalence of gene clusters related to specialized metabolites offers an attractive possibility of an untapped source of highly useful biomolecules. Accordingly, the identification and functional characterization of novel biosynthetic pathways in plants need to be worked out. In this review, we summarize insights into the evolution of gene clusters and discuss the organization and importance of specific gene clusters in the biosynthesis of specialized metabolites. Regulatory mechanisms which operate in some of the important gene clusters have also been briefly described. Finally, we highlight the importance of gene clusters to develop future metabolic engineering or synthetic biology strategies for the heterologous production of novel metabolites.

Specific decorations of 17-hydroxygeranyllinalool diterpene glycosides solve the autotoxicity problem of chemical defense in Nicotiana attenuata

The native diploid tobacco Nicotiana attenuata produces abundant, potent anti-herbivore defense metabolites known as 17-hydroxygeranyllinalool diterpene glycosides (HGL-DTGs) whose glycosylation and malonylation biosynthetic steps are regulated by jasmonate signaling. To characterize the biosynthetic pathway of HGL-DTGs, we conducted a genome-wide analysis of uridine diphosphate glycosyltransferases (UGTs) and identified 107 family-1 UGT members. The transcript levels of three UGTs were highly correlated with the transcript levels two key HGL-DTG biosynthetic genes: geranylgeranyl diphosphate synthase (NaGGPPS) and geranyllinalool synthase (NaGLS). NaGLS's role in HGL-DTG biosynthesis was confirmed by virus-induced gene silencing. Silencing the Uridine diphosphate (UDP)-rhamnosyltransferase gene UGT91T1 demonstrated its role in the rhamnosylation of HGL-DTGs. In vitro enzyme assays revealed that UGT74P3 and UGT74P4 use UDP-glucose for the glucosylation of 17-hydroxygeranyllinalool (17-HGL) to lyciumoside I. Plants with stable silencing of UGT74P3 and UGT74P5 were severely developmentally deformed, pointing to a phytotoxic effect of the aglycone. The application of synthetic 17-HGL and silencing of the UGTs in HGL-DTG-free plants confirmed this phytotoxic effect. Feeding assays with tobacco hornworm (Manduca sexta) larvae revealed the defensive functions of the glucosylation and rhamnosylation steps in HGL-DTG biosynthesis. Glucosylation of 17-HGL is therefore a critical step that contributes to the resulting metabolites' defensive function and solves the autotoxicity problem of this potent chemical defense.

Next-Generation Mass Spectrometry Metabolomics Revives the Functional Analysis of Plant Metabolic Diversity

The remarkable diversity of specialized metabolites produced by plants has inspired several decades of research and nucleated a long list of theories to guide empirical ecological studies. However, analytical constraints and the lack of untargeted processing workflows have long precluded comprehensive metabolite profiling and, consequently, the collection of the critical currencies to test theory predictions for the ecological functions of plant metabolic diversity. Developments in mass spectrometry (MS) metabolomics have revolutionized the large-scale inventory and annotation of chemicals from biospecimens. Hence, the next generation of MS metabolomics propelled by new bioinformatics developments provides a long-awaited framework to revisit metabolism-centered ecological questions, much like the advances in next-generation sequencing of the last two decades impacted all research horizons in genomics. Here, we review advances in plant (computational) metabolomics to foster hypothesis formulation from complex metabolome data. Additionally, we reflect on how next-generation metabolomics could reinvigorate the testing of long-standing theories on plant metabolic diversity.

Diversity in Chemical Structures and Biological Properties of Plant Alkaloids

Phytochemicals belonging to the group of alkaloids are signature specialized metabolites endowed with countless biological activities. Plants are armored with these naturally produced nitrogenous compounds to combat numerous challenging environmental stress conditions. Traditional and modern healthcare systems have harnessed the potential of these organic compounds for the treatment of many ailments. Various chemical entities (functional groups) attached to the central moiety are responsible for their diverse range of biological properties. The development of the characterization of these plant metabolites and the enzymes involved in their biosynthesis is of an utmost priority to deliver enhanced advantages in terms of biological properties and productivity. Further, the incorporation of whole/partial metabolic pathways in the heterologous system and/or the overexpression of biosynthetic steps in homologous systems have both become alternative and lucrative methods over chemical synthesis in recent times. Moreover, in-depth research on alkaloid biosynthetic pathways has revealed numerous chemical modifications that occur during alkaloidal conversions. These chemical reactions involve glycosylation, acylation, reduction, oxidation, and methylation steps, and they are usually responsible for conferring the biological activities possessed by alkaloids. In this review, we aim to discuss the alkaloidal group of plant specialized metabolites and their brief classification covering major categories. We also emphasize the diversity in the basic structures of plant alkaloids arising through enzymatically catalyzed structural modifications in certain plant species, as well as their emerging diverse biological activities. The role of alkaloids in plant defense and their mechanisms of action are also briefly discussed. Moreover, the commercial utilization of plant alkaloids in the marketplace displaying various applications has been enumerated.

Tomato roots secrete tomatine to modulate the bacterial assemblage of the rhizosphere

Saponins are the group of plant specialized metabolites which are widely distributed in angiosperm plants and have various biological activities. The present study focused on α-tomatine, a major saponin present in tissues of tomato (Solanum lycopersicum) plants. α-Tomatine is responsible for defense against plant pathogens and herbivores, but its biological function in the rhizosphere remains unknown. Secretion of tomatine was higher at the early growth than the green-fruit stage in hydroponically grown plants, and the concentration of tomatine in the rhizosphere of field-grown plants was higher than that of the bulk soil at all growth stages. The effects of tomatine and its aglycone tomatidine on the bacterial communities in the soil were evaluated in vitro, revealing that both compounds influenced the microbiome in a concentration-dependent manner. Numerous bacterial families were influenced in tomatine/tomatidine-treated soil as well as in the tomato rhizosphere. Sphingomonadaceae species, which are commonly observed and enriched in tomato rhizospheres in the fields, were also enriched in tomatine- and tomatidine-treated soils. Moreover, a jasmonate-responsive ETHYLENE RESPONSE FACTOR 4 mutant associated with low tomatine production caused the root-associated bacterial communities to change with a reduced abundance of Sphingomonadaceae. Taken together, our results highlight the role of tomatine in shaping the bacterial communities of the rhizosphere and suggest additional functions of tomatine in belowground biological communication.

Why and How to Dig into Plant Metabolite-Protein Interactions

Interaction between metabolites and proteins drives cellular regulatory processes within and between organisms. Recent reports highlight that numerous plant metabolites embrace multiple biological activities, beyond a sole role as substrates, products, or cofactors of enzymes, or as defense or growth-regulatory compounds. Though several technologies have been developed to identify and characterize metabolite-protein interactions, the systematic implementation of such methods in the plant field remains limited. Here, we discuss the plant metabolic space, with a specific focus on specialized metabolites and their roles, and review the technologies to study their interaction with proteins. We approach it both from a plant's perspective, to increase our understanding of plant metabolite-dependent regulatory networks, and from a human perspective, to empower agrochemical and drug discoveries.

Bitter and sweet make tomato hard to (b)eat

The glycoalkaloid saponin α-tomatine is a tomato-specific secondary metabolite that accumulates to millimolar levels in vegetative tissues and has antimicrobial and antinutritional activity that kills microbial pathogens and deters herbivorous insects. We describe recent insights into the biosynthetic pathway of α-tomatine synthesis and its regulation. We discuss the mode of action of α-tomatine by physically interacting with sterols, thereby disrupting membranes, and how tomato protects itself from its toxic action. Tomato pathogenic microbes can enzymatically hydrolyze, and thereby inactivate, α-tomatine using either of three distinct types of glycosyl hydrolases. We also describe findings that extend well beyond the simple concept of plants producing toxins and pathogens inactivating them. There are reports that toxicity of α-tomatine is modulated by external pH, that α-tomatine can trigger programmed cell death in fungi, that cellular localization matters for the impact of α-tomatine on invading microbes, and that α-tomatine breakdown products generated by microbial hydrolytic enzymes can modulate plant immune responses. Finally, we address a number of outstanding questions that deserve attention in the future.

TOMATOMET: A metabolome database consists of 7118 accurate mass values detected in mature fruits of 25 tomato cultivars

The total number of low-molecular-weight compounds in the plant kingdom, most of which are secondary metabolites, is hypothesized to be over one million, although only a limited number of plant compounds have been characterized. Untargeted analysis, especially using mass spectrometry (MS), has been useful for understanding the plant metabolome; however, due to the limited availability of authentic compounds for MS-based identification, the identities of most of the ion peaks detected by MS remain unknown. Accurate mass values of peaks obtained by high accuracy mass measurement and, if available, MS/MS fragmentation patterns provide abundant annotation for each peak. Here, we carried out an untargeted analysis of compounds in the mature fruit of 25 tomato cultivars using liquid chromatography-Orbitrap MS for accurate mass measurement, followed by manual curation to construct the metabolome database TOMATOMET (http://metabolites.in/tomato-fruits/). The database contains 7,118 peaks with accurate mass values, in which 1,577 ion peaks are annotated as members of a chemical group. Remarkably, 71% of the mass values are not found in the accurate masses detected previously in Arabidopsis thaliana, Medicago truncatula or Jatropha curcas, indicating significant chemical diversity among plant species that remains to be solved. Interestingly, substantial chemical diversity exists also among tomato cultivars, indicating that chemical profiling from distinct cultivars contributes towards understanding the metabolome, even in a single organ of a species, and can prioritize some desirable metabolic targets for further applications such as breeding.

The GORKY glycoalkaloid transporter is indispensable for preventing tomato bitterness

Fruit taste is determined by sugars, acids and in some species, bitter chemicals. Attraction of seed-dispersing organisms in nature and breeding for consumer preferences requires reduced fruit bitterness. A key metabolic shift during ripening prevents tomato fruit bitterness by eliminating α-tomatine, a renowned defence-associated Solanum alkaloid. Here, we combined fine mapping with information from 150 resequenced genomes and genotyping a 650-tomato core collection to identify nine bitter-tasting accessions including the 'high tomatine' Peruvian landraces reported in the literature. These 'bitter' accessions contain a deletion in GORKY, a nitrate/peptide family transporter mediating α-tomatine subcellular localization during fruit ripening. GORKY exports α-tomatine and its derivatives from the vacuole to the cytosol and this facilitates the conversion of the entire α-tomatine pool to non-bitter forms, rendering the fruit palatable. Hence, GORKY activity was a notable innovation in the process of tomato fruit domestication and breeding.

The biosynthetic pathway of potato solanidanes diverged from that of spirosolanes due to evolution of a dioxygenase

Potato (Solanum tuberosum), a worldwide major food crop, produces the toxic, bitter tasting solanidane glycoalkaloids α-solanine and α-chaconine. Controlling levels of glycoalkaloids is an important focus on potato breeding. Tomato (Solanum lycopersicum) contains a bitter spirosolane glycoalkaloid, α-tomatine. These glycoalkaloids are biosynthesized from cholesterol via a partly common pathway, although the mechanisms giving rise to the structural differences between solanidane and spirosolane remained elusive. Here we identify a 2-oxoglutarate dependent dioxygenase, designated as DPS (Dioxygenase for Potato Solanidane synthesis), that is a key enzyme for solanidane glycoalkaloid biosynthesis in potato. DPS catalyzes the ring-rearrangement from spirosolane to solanidane via C-16 hydroxylation. Evolutionary divergence of spirosolane-metabolizing dioxygenases contributes to the emergence of toxic solanidane glycoalkaloids in potato and the chemical diversity in Solanaceae.

One goal of potato breeding is to reduce the accumulation of toxic solanidane glycoalkaloids. Here the authors show that potato DPS, a 2-oxoglutarate dependent dioxygenase, catalyzes ring rearrangement of a biosynthetic precursor to differentiate solanidanes from spirosolanes that are found in other solanaceous plants.

Controlled hydroxylations of diterpenoids allow for plant chemical defense without autotoxicity

Many plant specialized metabolites function in herbivore defense, and abrogating particular steps in their biosynthetic pathways frequently causes autotoxicity. However, the molecular mechanisms underlying their defense and autotoxicity remain unclear. Here, we show that silencing two cytochrome P450s involved in diterpene biosynthesis in the wild tobacco Nicotiana attenuata causes severe autotoxicity symptoms that result from the inhibition of sphingolipid biosynthesis by noncontrolled hydroxylated diterpene derivatives. Moreover, the diterpenes' defensive function is achieved by inhibiting herbivore sphingolipid biosynthesis through postingestive backbone hydroxylation products. Thus, by regulating metabolic modifications, tobacco plants avoid autotoxicity and gain herbivore defense. The postdigestive duet that occurs between plants and their insect herbivores can reflect the plant's solutions to the "toxic waste dump" problem of using potent chemical defenses.

Solanum steroidal glycoalkaloids: structural diversity, biological activities, and biosynthesis

Chemical structures of typical Solanum steroidal glycoalkaloids from eggplant, tomato, and potato.

High mass resolution, spatial metabolite mapping enhances the current plant gene and pathway discovery toolbox

Understanding when and where metabolites accumulate provides important cues to the gene function. Mass spectrometry imaging (MSI) enables in situ temporal and spatial measurement of a large assortment of metabolites, providing mapping information regarding their cellular distribution. To describe the current state and technical advances using MSI in plant sciences, we employed MSI to demonstrate its significant contribution to the study of plant specialised metabolism. We show that coupling MSI with: (1) RNA interference (RNAi), (2) virus induced gene silencing (VIGS), (3) agroinfiltration or (4) samples derived from plant natural variation provides great opportunities to understand the accurate gene-metabolite relationship and discover novel gene-associated metabolites. This was exemplified in three plant species (i.e. tomato, tobacco and wheat) by mapping the distribution of metabolites possessing a range of polarities. In particular, we demonstrated that MSI is able to spatially map an entire metabolic pathway, including intermediates and final products, in the intricate biosynthetic route to tomato fruit steroidal glycoalkaloids. We therefore envisage MSI as a key component of the metabolome analysis arsenal employed in plant gene discovery strategies.

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.

Analysis of wild tomato introgression lines elucidates the genetic basis of transcriptome and metabolome variation underlying fruit traits and pathogen response

Wild tomato species represent a rich gene pool for numerous desirable traits lost during domestication. Here, we exploited an introgression population representing wild desert-adapted species and a domesticated cultivar to establish the genetic basis of gene expression and chemical variation accompanying the transfer of wild-species-associated fruit traits. Transcriptome and metabolome analysis of 580 lines coupled to pathogen sensitivity assays resulted in the identification of genomic loci associated with levels of hundreds of transcripts and metabolites. These associations occurred in hotspots representing coordinated perturbation of metabolic pathways and ripening-related processes. Here, we identify components of the Solanum alkaloid pathway, as well as genes and metabolites involved in pathogen defense and linking fungal resistance with changes in the fruit ripening regulatory network. Our results outline a framework for understanding metabolism and pathogen resistance during tomato fruit ripening and provide insights into key fruit quality traits.

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.

Double infection of Wolbachia and Spiroplasma alters induced plant defense and spider mite fecundity

BACKGROUND

Herbivore-associated bacterial symbionts can change plant physiology and influence herbivore fitness. The spider mite Tetranychus truncatus is a notorious pest harboring various bacterial symbionts; however, the effect of bacterial symbionts on host plant physiology remains unclear. Here, we investigated whether infection with the endosymbionts Wolbachia and Spiroplasma altered spider mite performance on tomato plants and affected plant-induced defenses.

RESULTS

Wolbachia and Spiroplasma were mainly located in the gnathosoma and ovaries of their spider mite hosts. Wolbachia and Spiroplasma significantly improved spider mite reproductive performance in cultivated and wild-type tomato. However, in plants deficient in jasmonic acid (JA) and salicylic acid (SA), there were no significant differences in reproduction between spider mites infected with Wolbachia and Spiroplasma and uninfected mites. The results indicated that the reproduction benefits conferred by endosymbionts may relate to plant defenses. Both spider mites infected with Wolbachia and Spiroplasma and uninfected mites induced similar levels of JA and SA accumulation in tomato, whereas tomato plants damaged by spider mites infected with both Wolbachia and Spiroplasma showed lower expression levels of JA- and SA-responsive genes than those damaged by uninfected spider mites. In addition, mites infected with Wolbachia and Spiroplasma mites consumed more tomato amino acids compared to uninfected spider mites, which may have contributed to host fecundity.

CONCLUSIONS

Our results suggest that the reproduction benefits conferred by endosymbionts may be associated with changes in plant defense parameters and the concentrations of plant amino acids. The results highlight the importance of endosymbionts in interactions between spider mites and their host plants. © 2020 Society of Chemical Industry.

MicroTom Metabolic Network: Rewiring Tomato Metabolic Regulatory Network throughout the Growth Cycle

Tomato (Solanum lycopersicum) is a major horticultural crop worldwide and has emerged as a preeminent model for metabolic research. Although many research efforts have focused on the analysis of metabolite differences between varieties and species, the dynamics of metabolic changes during the tomato growth cycle and the regulatory networks that underlie these changes are poorly understood. In this study, we integrated high-resolution spatio-temporal metabolome and transcriptome data to systematically explore the metabolic landscape across 20 major tomato tissues and growth stages. In the resulting MicroTom Metabolic Network, the 540 detected metabolites and their co-expressed genes could be divided into 10 distinct clusters based on their biological functions. Using this dataset, we constructed a global map of the major metabolic changes that occur throughout the tomato growth cycle and dissected the underlying regulatory network. In addition to verifying previously well-established regulatory networks for important metabolites, we identified novel transcription factors that regulate the biosynthesis of important secondary metabolites such as steroidal glycoalkaloids and flavonoids. Our findings provide insights into spatio-temporal changes in tomato metabolism and generate a valuable resource for the study of metabolic regulatory processes in model plants.

'Hijacking' core metabolism: a new panache for the evolution of steroidal glycoalkaloids structural diversity

Steroidal glycoalkaloids (SGAs) are defense specialized metabolites produced by thousands of Solanum species. These metabolites are remarkable in structural diversity formed following modifications in their core scaffold. In recent years, it became clear that a large portion of this chemical repertoire was acquired through various molecular mechanisms involving 'hijacking' of core metabolism enzymes. This was typically accompanied by gene duplication and divergence and further neofunctionalization as well as modified subcellular localization and evolution of new substrate preferences. In this review, we highlight recent findings in the SGAs biosynthetic pathway and elaborate on similar occurrences in other chemical classes that enabled evolution of specialized metabolic pathways and its underlying structural diversity.

Elucidation of the complete biosynthetic pathway of the main triterpene glycosylation products of Panax notoginseng using a synthetic biology platform

UDP-glycosyltransferase (UGT)-mediated glycosylation is a widespread modification of plant natural products (PNPs), which exhibit a wide range of bioactivities, and are of great pharmaceutical, ecological and agricultural significance. However, functional annotation is available for less than 2% of the family 1 UGTs, which currently has 20,000 members that are known to glycosylate several classes of PNPs. This low percentage illustrates the difficulty of experimental study and accurate prediction of their function. Here, a synthetic biology platform for elucidating the UGT-mediated glycosylation process of PNPs was established, including glycosyltransferases dependent on UDP-glucose and UDP-xylose. This platform is based on reconstructing the specific PNPs biosynthetic pathways in dedicated microbial yeast chassis by the simple method of plug-and-play. Five UGT enzymes were identified as responsible for the biosynthesis of the main glycosylation products of triterpenes in Panax notoginseng, including a novel UDP-xylose dependent glycosyltransferase enzyme for notoginsenoside R1 biosynthesis. Additionally, we constructed a yeast cell factory that yields >1 g/L of ginsenoside compound K. This platform for functional gene identification and strain engineering can serve as the basis for creating alternative sources of important natural products and thereby protecting natural plant resources.

Plant terpenoid metabolism co-opts a component of the cell wall biosynthesis machinery

Glycosylation is one of the most prevalent molecular modifications in nature. Single or multiple sugars can decorate a wide range of acceptors from proteins to lipids, cell wall glycans and small molecules, dramatically affecting their activity. Here, we discovered that by 'hijacking' an enzyme of the cellulose synthesis machinery involved in cell wall assembly, plants evolved cellulose synthase-like enzymes (Csls) and acquired the capacity to glucuronidate specialized metabolites, that is, triterpenoid saponins. Apparently, endoplasmic reticulum-membrane localization of Csls and of other pathway proteins was part of evolving a new glycosyltransferase function, as plant metabolite glycosyltransferases typically act in the cytosol. Discovery of glucuronic acid transferases across several plant orders uncovered the long-pursued enzymatic reaction in the production of a low-calorie sweetener from licorice roots. Our work opens the way for engineering potent saponins through microbial fermentation and plant-based systems.

An allelic variant of GAME9 determines its binding capacity with the GAME17 promoter in the regulation of steroidal glycoalkaloid biosynthesis in tomato

Steroidal glycoalkaloids (SGAs) are cholesterol-derived molecules found in the family Solanaceae. SGA content varies among different plant species and varieties. However, the genetic mechanisms regulating SGA content remain unclear. Here, we demonstrate that genetic variation in GLYCOALKALOID METABOLISM 9 (GAME9) is responsible for the variation in SGA content in tomato (Solanum lycopersicum). During a sequential analysis we found a 1 bp substitution in the AP2/ERF binding domain of GAME9. The 1 bp substitution in GAME9 was significantly associated with high SGA content and determined the binding capacity of GAME9 with the promoter of GAME17, a core SGA biosynthesis gene. The high-SGA GAME9 allele is mainly present in S. pimpinellifolium and S. lycopersicum var. cerasiforme populations and encodes a protein that can bind the GAME17 promoter. In contrast, the low-SGA GAME9 allele is mainly present in the big-fruited varieties of S. lycopersicum and encodes a protein that shows weak binding to the GAME17 promoter. Our findings provide new insight into the regulation of SGA biosynthesis and the factors that affect the accumulation of SGA in tomato.

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.

Acute and Subacute Toxicity Profiles of the Methanol Extract of Lycopersicon esculentum L. Leaves (Tomato), a Botanical with Promising In Vitro Anticancer Potential

Lycopersicon esculentum (tomato) is a plant widely used in Africa like food and to solve many health problems. The methanol crude extract of tomato recently demonstrated a good antiproliferative effect on many human cancer cell lines. The aim of this research was to evaluate the acute toxicity and subacute oral toxicity of methanolic extract from leaves of this plant. These toxicities were evaluated based on the OECD (Organization for Economic Cooperation and Development) guidelines. The assay of acute toxicity was performed using a total of 3 female rats, which received a single dose of 5000 mg/kg of methanolic extract via oral gavage. For the subacute toxicity study, 32 Wistar rats (males and females) were used. The groups were treated with three different doses of Lycopersicon esculentum methanolic extract (250, 500, and 1000 mg/kg b.w.) for 28 days and the control group received distilled water. The hematological, biochemical, and histopathological studies were performed after the sacrifice. Single dose of tomato extract caused no toxicity up to a dose of 5000 mg/kg body weight; hence, the median lethal dose (DL₅₀) of leaves of this plant was greater than this value. However, lower toxic effects could be manifested in the long-term treatment at the highest dose (1000 mg/kg) because urea level and total serum proteins significantly increased at a dose of 1000 mg/kg with respect to control. The microscopic observation showed no remarkable pathological changes on all organs in the treated groups compared with the control groups of female and male rats. These results demonstrate that single dose of tomato extract leaves is relatively nontoxic at a dose of 5000 mg/kg b.w. and prolonged use of lower doses (250 and 500 mg/kg) of L. esculentum orally should be encouraged, whereas highest dose (1000 mg/kg) should be avoided.

Rhizosphere microbiome mediates systemic root metabolite exudation by root-to-root signaling

Microbial communities associated with roots confer specific functions to their hosts, thereby modulating plant growth, health, and productivity. Yet, seminal questions remain largely unaddressed including whether and how the rhizosphere microbiome modulates root metabolism and exudation and, consequently, how plants fine tune this complex belowground web of interactions. Here we show that, through a process termed systemically induced root exudation of metabolites (SIREM), different microbial communities induce specific systemic changes in tomato root exudation. For instance, systemic exudation of acylsugars secondary metabolites is triggered by local colonization of bacteria affiliated with the genus Bacillus Moreover, both leaf and systemic root metabolomes and transcriptomes change according to the rhizosphere microbial community structure. Analysis of the systemic root metabolome points to glycosylated azelaic acid as a potential microbiome-induced signaling molecule that is subsequently exuded as free azelaic acid. Our results demonstrate that rhizosphere microbiome assembly drives the SIREM process at the molecular and chemical levels. It highlights a thus-far unexplored long-distance signaling phenomenon that may regulate soil conditioning.

Glycosylated flavonoids: fruit's concealed antifungal arsenal

Fruit defense against pathogens relies on induced and preformed mechanisms. The present contribution evaluated performed resistance of red and green mango fruit against the fungal pathogen Colletotrichum gloeosporioides and identified the main active antifungal components. High-performance liquid chromatography analysis of nonhydrolyzed mango peel extracts identified major anthocyanin peaks of glycosylated cyanidin and methylcyanidin, and flavonol peaks of glycosylated quercetin and kaempferol, which were more abundant on the 'red side' of red mango fruit. Organic extracts of red vs green mango peel were more efficient in inhibiting C. gloeosporioides. Transcriptome analysis of the mango-C. gloeosporioides interaction showed increased expression of glucosidase genes related to both fungal pathogenicity and host defense. Glucosidase treatment of organic peel extract increased its antifungal activity. Additionally, quercetin and cyanidin had significantly higher antifungal activity than their glycosylated derivatives. Peel extract volatiles treated with glucosidase had antifungal activity. GCMS analysis identified 15 volatiles after glucosidase hydrolysis, seven of them present only in red fruit. These results suggest that the fruit obtains a concealed arsenal of glycosylated flavonoids in its peel when they are hydrolyzed by β-glucosidase that is induced in both fungus and host during infection process, become more toxic to the fungal pathogen, inhibiting decay development.

Identification of α-Tomatine 23-Hydroxylase Involved in the Detoxification of a Bitter Glycoalkaloid

Tomato plants (Solanum lycopersicum) contain steroidal glycoalkaloid α-tomatine, which functions as a chemical barrier to pathogens and predators. α-Tomatine accumulates in all tissues and at particularly high levels in leaves and immature green fruits. The compound is toxic and causes a bitter taste, but its presence decreases through metabolic conversion to nontoxic esculeoside A during fruit ripening. This study identifies the gene encoding a 23-hydroxylase of α-tomatine, which is a key to this process. Some 2-oxoglutarate-dependent dioxygenases were selected as candidates for the metabolic enzyme, and Solyc02g062460, designated Sl23DOX, was found to encode α-tomatine 23-hydroxylase. Biochemical analysis of the recombinant Sl23DOX protein demonstrated that it catalyzes the 23-hydroxylation of α-tomatine and the product spontaneously isomerizes to neorickiioside B, which is an intermediate in α-tomatine metabolism that appears during ripening. Leaves of transgenic tomato plants overexpressing Sl23DOX accumulated not only neorickiioside B but also another intermediate, lycoperoside C (23-O-acetylated neorickiioside B). Furthermore, the ripe fruits of Sl23DOX-silenced transgenic tomato plants contained lower levels of esculeoside A but substantially accumulated α-tomatine. Thus, Sl23DOX functions as α-tomatine 23-hydroxylase during the metabolic processing of toxic α-tomatine in tomato fruit ripening and is a key enzyme in the domestication of cultivated tomatoes.

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.

Mining genes associated with furanocoumarin biosynthesis in an endangered medicinal plant, Glehnia littoralis

The endangered medicinal plant Glehnia littoralis is one of the important natural source of furanocoumarin, which has been used as mucolytic, antitussive, antitumour and antibacterial. However, the genetic information of furanocoumarin biosynthesis in G. littoralis is scarce at present. The objective of this study was to mine the putative candidate genes involved in the biosynthesis pathwayof furanocoumarin and provide references for gene identification, and functional genomics of G. littoralis. We carried out the transcriptome analysis of leaves and roots in G. littoralis, which provided a dataset for gene mining. Psoralen, imperatorin and isoimperatorin were detected in G. littoralis by high performance liquid chromatography analysis. Candidate key genes were mined based on the annotations and local BLAST with homologous sequences using BioEdit software. The relative expression of genes was analysed using quantitative real-time polymerase chain reaction. Further, the CYP450 genes were mined using phylogenetic analyses using MEGA 6.0 software. Atotal of 156,949 unigenes were generated, of which 9021 were differentially-expressed between leaves and roots. A total of 82 unigenes encoding eight enzymes in furanocoumarin biosynthetic pathway were first obtained. Seven genes that encoded key enzymes in the downstream furanocoumarin biosynthetic pathway and expressed more in roots than leaves were screened. Twenty-six candidate CYP450 unigenes expressed abundantly in roots and were chiefly concentrated in CYP71, CYP85 and CYP72 clans. Finally, we filtered 102 differentially expressed transcription factors (TFs) unigenes. The transcriptome of G. littoralis was characterized which would help to elucidate the furanocoumarin biosynthetic pathway in G. littoralis and provide an invaluable resource for further study of furanocoumarin.

Characterization of steroid 5α-reductase involved in α-tomatine biosynthesis in tomatoes

α-tomatine and dehydrotomatine are steroidal glycoalkaloids (SGAs) that accumulate in the mature green fruits, leaves, and flowers of tomatoes (Solanum lycopersicum) and function as defensive compounds against pathogens and predators. The aglycones of α-tomatine and dehydrotomatine are tomatidine and dehydrotomatidine (5,6-dehydrogenated tomatidine), and tomatidine is derived from dehydrotomatidine via four reaction steps: C3 oxidation, isomerization, C5α reduction, and C3 reduction. Our previous studies (Lee et al. 2019) revealed that Sl3βHSD is involved in the three reactions except for C5α reduction, and in the present study, we aimed to elucidate the gene responsible for the C5α reduction step in the conversion of dehydrotomatidine to tomatidine. We characterized the two genes, SlS5αR1 and SlS5αR2, which show high homology with DET2, a brassinosteroid 5α reductase of Arabidopsis thaliana. The expression pattern of SlS5αR2 is similar to those of SGA biosynthetic genes, while SlS5αR1 is ubiquitously expressed, suggesting the involvement of SlS5αR2 in SGA biosynthesis. Biochemical analysis of the recombinant proteins revealed that both of SlS5αR1 and SlS5αR2 catalyze the reduction of tomatid-4-en-3-one at C5α to yield tomatid-3-one. Then, SlS5αR1- or SlS5αR2-knockout hairy roots were constructed using CRISPR/Cas9 mediated genome editing. In the SlS5αR2-knockout hairy roots, the α-tomatine level was significantly decreased and dehydrotomatine was accumulated. On the other hand, no change in the amount of α-tomatine was observed in the SlS5αR1-knockout hairy root. These results indicate that SlS5αR2 is responsible for the C5α reduction in α-tomatine biosynthesis and that SlS5αR1 does not significantly contribute to α-tomatine biosynthesis.

Mass Spectrometry Imaging of the Spatial and Temporal Localization of Alkaloids in Nightshades

Alkaloids are common secondary metabolites found also in plants of the large family of Solanaceae, and they contribute frequently to the economic importance of these plants as food, spices, drugs, or pharmaceuticals. Matrix-assisted laser desorption/ionization mass spectrometry imaging was applied to visualize the spatial localization of the main steroidal alkaloids in diverse plant tissues of Lycopersicon esculentum, Solanum nigrum, and Solanum dulcamara. Among others, the basic aglycons, tomatidenol, tomatidine, solasodine, and soladulcine, along with their corresponding glycoalkaloids, were identified with distinct distributions within plant tissue structures and plant parts and with respect to the degree of ripeness. The alkaloids are identified by their mass and fragmentation pattern. Multivariate unsupervised principal compound analysis and the k-means clustering analysis were calculated on the basis of all peaks, automatically picked from all selected regions, with total ion count normalization resulting in characterization of the tissues and organs with respect to their chemical similarity. It can therefore be concluded that the tissue-specific localizations of alkaloids in nightshades depend upon the ripeness status and the developmental stage of the plants.

The Sweet Side of Plant-Specialized Metabolism

Glycosylation plays a major role in the structural diversification of plant natural products. It influences the properties of molecules by modifying the reactivity and solubility of the corresponding aglycones, so influencing cellular localization and bioactivity. Glycosylation of plant natural products is usually carried out by uridine diphosphate(UDP)-dependent glycosyltransferases (UGTs) belonging to the carbohydrate-active enzyme glycosyltransferase 1 (GT1) family. These enzymes transfer sugars from UDP-activated sugar moieties to small hydrophobic acceptor molecules. Plant GT1s generally show high specificity for their sugar donors and recognize a single UDP sugar as their substrate. In contrast, they are generally promiscuous with regard to acceptors, making them attractive biotechnological tools for small molecule glycodiversification. Although microbial hosts have traditionally been used for heterologous engineering of plant-derived glycosides, transient plant expression technology offers a potentially disruptive platform for rapid characterization of new plant glycosyltransferases and biosynthesis of complex glycosides.

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.

Pathways to defense metabolites and evading fruit bitterness in genus Solanum evolved through 2-oxoglutarate-dependent dioxygenases

The genus Solanum comprises three food crops (potato, tomato, and eggplant), which are consumed on daily basis worldwide and also producers of notorious anti-nutritional steroidal glycoalkaloids (SGAs). Hydroxylated SGAs (i.e. leptinines) serve as precursors for leptines that act as defenses against Colorado Potato Beetle (Leptinotarsa decemlineata Say), an important pest of potato worldwide. However, SGA hydroxylating enzymes remain unknown. Here, we discover that 2-OXOGLUTARATE-DEPENDENT-DIOXYGENASE (2-ODD) enzymes catalyze SGA-hydroxylation across various Solanum species. In contrast to cultivated potato, Solanum chacoense, a widespread wild potato species, has evolved a 2-ODD enzyme leading to the formation of leptinines. Furthermore, we find a related 2-ODD in tomato that catalyzes the hydroxylation of the bitter α-tomatine to hydroxytomatine, the first committed step in the chemical shift towards downstream ripening-associated non-bitter SGAs (e.g. esculeoside A). This 2-ODD enzyme prevents bitterness in ripe tomato fruit consumed today which otherwise would remain unpleasant in taste and more toxic.

Steroidal glycoalkaloids (SGAs) accumulate in Solanum, but their hydroxylating enzymes are unknown. Here, the authors report 2-OXOGLUTARATE DEPENDENT DIOXYGENASE enzymes that catalyze the committed hydroxylation steps in the biosynthesis of leptinine insecticidal compounds in wild potato or non-bitter SGAs in cultivated tomato.

The Structure and Function of Major Plant Metabolite Modifications

Plants produce a myriad of structurally and functionally diverse metabolites that play many different roles in plant growth and development and in plant response to continually changing environmental conditions as well as abiotic and biotic stresses. This metabolic diversity is, to a large extent, due to chemical modification of the basic skeletons of metabolites. Here, we review the major known plant metabolite modifications and summarize the progress that has been achieved and the challenges we are facing in the field. We focus on discussing both technical and functional aspects in studying the influences that various modifications have on biosynthesis, degradation, transport, and storage of metabolites, as well as their bioactivity and toxicity. Finally, we discuss some emerging insights into the evolution of metabolic pathways and metabolite functionality.

Identification of a 3β-Hydroxysteroid Dehydrogenase/ 3-Ketosteroid Reductase Involved in α-Tomatine Biosynthesis in Tomato

α-Tomatine and dehydrotomatine are major steroidal glycoalkaloids (SGAs) that accumulate in the mature green fruits, leaves and flowers of tomato (Solanum lycopersicum), and function as defensive compounds against bacteria, fungi, insects and animals. The aglycone of dehydrotomatine is dehydrotomatidine (5,6-dehydrogenated tomatidine, having the Δ5,6 double bond; the dehydro-type). The aglycone of α-tomatine is tomatidine (having a single bond between C5 and C6; the dihydro-type), which is believed to be derived from dehydrotomatidine via four reaction steps: C3 oxidation, isomerization, C5 reduction and C3 reduction; however, these conversion processes remain uncharacterized. In the present study, we demonstrate that a short-chain alcohol dehydrogenase/reductase designated Sl3βHSD is involved in the conversion of dehydrotomatidine to tomatidine in tomato. Sl3βHSD1 expression was observed to be high in the flowers, leaves and mature green fruits of tomato, in which high amounts of α-tomatine are accumulated. Biochemical analysis of the recombinant Sl3βHSD1 protein revealed that Sl3βHSD1 catalyzes the C3 oxidation of dehydrotomatidine to form tomatid-4-en-3-one and also catalyzes the NADH-dependent C3 reduction of a 3-ketosteroid (tomatid-3-one) to form tomatidine. Furthermore, during co-incubation of Sl3βHSD1 with SlS5αR1 (steroid 5α-reductase) the four reaction steps converting dehydrotomatidine to tomatidine were completed. Sl3βHSD1-silenced transgenic tomato plants accumulated dehydrotomatine, with corresponding decreases in α-tomatine content. Furthermore, the constitutive expression of Sl3βHSD1 in potato hairy roots resulted in the conversion of potato SGAs to the dihydro-type SGAs. These results demonstrate that Sl3βHSD1 is a key enzyme involved in the conversion processes from dehydrotomatidine to tomatidine in α-tomatine biosynthesis.

Next-Gen Approaches to Flavor-Related Metabolism

Although flavor is an essential element for consumer acceptance of food, breeding programs have focused primarily on yield, leading to significant declines in flavor for many vegetables. The deterioration of flavor quality has concerned breeders; however, the complexity of this trait has hindered efforts to improve or even maintain it. Recently, the integration of flavor-associated metabolic profiling with other omics methodologies derived from big data has become a prominent trend in this research field. Here, we provide an overview of known metabolites contributing to flavor in the major vegetables as well as genetic analyses of the relevant metabolic pathways based on different approaches, especially multi-omics. We present examples demonstrating how omics analyses can help us to understand the accomplishments of historical flavor breeding practices and implement further improvements. The integration of genetics, cultivation, and postharvest practices with genome-scale data analyses will create enormous potential for further flavor quality improvements.

Identification of genes involved in fruit development/ripening in Capsicum and development of functional markers

The molecular mechanism of the underlying genes involved in the process of fruit ripening in Capsicum (family Solanaceae) is not clearly known. In the present study, we identified orthologs of 32 fruit development/ripening genes of tomato in Capsicum, and validated their expression in fruit development stages in C. annuum, C. frutescens, and C. chinense. In silico expression analysis using transcriptome data identified a total of 12 out of 32 genes showing differential expression during different stages of fruit development in Capsicum. Real time expression identified gene LOC107847473 (ortholog of MADS-RIN) had substantially higher expression (>500 folds) in breaker and mature fruits, which suggested the non-climacteric ripening behaviour of Capsicum. However, differential expression of Ehtylene receptor 2-like (LOC107873245) gene during fruit maturity supported the climacteric behaviour of only C. frutescens (hot pepper). Furthermore, development of 49 gene based simple sequence repeat (SSR) markers would help in selection of identified genes in Capsicum breeding.

Exploring the sound-modulated delay in tomato ripening through expression analysis of coding and non-coding RNAs

Background and Aims

Sound is omnipresent in nature. Recent evidence supports the notion that naturally occurring and artificially generated sound waves induce inter- and intracellular changes in plants. These changes, in turn, lead to diverse physiological changes, such as enhanced biotic and abiotic stress responses, in both crops and model plants.

Methods

We previously observed delayed ripening in tomato fruits exposed to 1 kHz sound vibrations for 6 h. Here, we evaluated the molecular mechanism underlying this delaying fruit ripening by performing RNA-sequencing analysis of tomato fruits at 6 h, 2 d, 5 d and 7 d after 1 kHz sound vibration treatment.

Key Results

Bioinformatic analysis of differentially expressed genes and non-coding small RNAs revealed that some of these genes are involved in plant hormone and cell wall modification processes. Ethylene and cytokinin biosynthesis and signalling-related genes were downregulated by sound vibration treatment, whereas genes involved in flavonoid, phenylpropanoid and glucan biosynthesis were upregulated. Furthermore, we identified two sound-specific microRNAs and validated the expression of the pre-microRNAs and the mRNAs of their target genes.

Conclusions

Our results indicate that sound vibration helps to delay fruit ripening through the sophisticated regulation of coding and non-coding RNAs and transcription factor genes.

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.

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.

Distinct Signatures of Host Defense Suppression by Plant-Feeding Mites

Tomato plants are attacked by diverse herbivorous arthropods, including by cell-content-feeding mites, such as the extreme generalist Tetranychus urticae and specialists like Tetranychus evansi and Aculops lycopersici. Mite feeding induces plant defense responses that reduce mite performance. However, T. evansi and A. lycopersici suppress plant defenses via poorly understood mechanisms and, consequently, maintain a high performance on tomato. On a shared host, T. urticae can be facilitated by either of the specialist mites, likely due to the suppression of plant defenses. To better understand defense suppression and indirect plant-mediated interactions between herbivorous mites, we used gene-expression microarrays to analyze the transcriptomic changes in tomato after attack by either a single mite species (T. urticae, T. evansi, A. lycopersici) or two species simultaneously (T. urticae plus T. evansi or T. urticae plus A. lycopersici). Additionally, we assessed mite-induced changes in defense-associated phytohormones using LC-MS/MS. Compared to non-infested controls, jasmonates (JAs) and salicylate (SA) accumulated to higher amounts upon all mite-infestation treatments, but the response was attenuated after single infestations with defense-suppressors. Strikingly, whereas 8 to 10% of tomato genes were differentially expressed upon single infestations with T. urticae or A. lycopersici, respectively, only 0.1% was altered in T. evansi-infested plants. Transcriptome analysis of dual-infested leaves revealed that A. lycopersici primarily suppressed T. urticae-induced JA defenses, while T. evansi dampened T. urticae-triggered host responses on a transcriptome-wide scale. The latter suggests that T. evansi not solely down-regulates plant gene expression, but rather directs it back towards housekeeping levels. Our results provide valuable new insights into the mechanisms underlying host defense suppression and the plant-mediated facilitation of competing herbivores.

Analysis of the mechanisms regulating the expression of isoprenoid biosynthesis genes in hydroponically-grown Nicotiana benthamiana plants using virus-induced gene silencing

Secondary metabolites in plants play important roles in defence against biotic and abiotic stresses. Although the biosynthesis pathways of secondary metabolites have been extensively studied, the regulatory mechanism of gene expression involved in these pathways remains poorly understood. In this study, we develop a virus-induced gene silencing (VIGS) system that enables a rapid analysis of the regulatory mechanism of genes involved in the biosynthesis of isoprenoids, one of the largest groups in secondary metabolites, using hydroponically-grown Nicotiana benthamiana. Using VIGS, we successfully reduced the transcript levels of 3-hydroxy-3-methylglutaryl-CoA reductase 1 (HMGR1), cycloartenol synthase 1 (CAS1), sterol side chain reductase 2 (SSR2) and S-adenosyl-L-Met-dependent C-24 sterol methyltransferase 1 (SMT1) in leaf, stem and root tissues in approximately 2 weeks. We identified novel feedback and feed-forward regulation of isoprenoid biosynthesis genes when CAS1, which encodes a key enzyme involved in the biosynthesis of sterols and steroidal glycoalkaloids, was down-regulated. Furthermore, the regulation of these genes differed among different tissues. These results demonstrate that our system can rapidly analyse the regulatory mechanisms involved in the biosynthesis of secondary metabolites.

Generation of α-solanine-free hairy roots of potato by CRISPR/Cas9 mediated genome editing of the St16DOX gene

Potato (Solanum tuberosum) is a major food crop, while the most tissues of potato accumulates steroidal glycoalkaloids (SGAs) α-solanine and α-chaconine. Since SGAs confer a bitter taste on human and show the toxicity against various organisms, reducing the SGA content in the tubers is requisite for potato breeding. However, generation of SGA-free potato has not been achieved yet, although silencing of several SGA biosynthetic genes led a decrease in SGAs. Here, we show that the knockout of St16DOX encoding a steroid 16α-hydroxylase in SGA biosynthesis causes the complete abolition of the SGA accumulation in potato hairy roots. Nine candidate guide RNA (gRNA) target sequences were selected from St16DOX by in silico analysis, and the two or three gRNAs were introduced into a CRISPR/Cas9 vector designated as pMgP237-2A-GFP that can express multiplex gRNAs based on the pre-tRNA processing system. To establish rapid screening of the candidate gRNAs that can efficiently mutate the St16DOX gene, we used a potato hairy root culture system for the introduction of the pMgP237 vectors. Among the transgenic hairy roots, two independent lines showed no detectable SGAs but accumulated the glycosides of 22,26-dihydroxycholesterol, which is the substrate of St16DOX. Analysis of the two lines with sequencing exhibited the mutated sequences of St16DOX with no wild-type sequences. Thus, generation of SGA-free hairy roots of tetraploid potato was achieved by the combination of the hairy root culture and the pMgP237-2A-GFP vector. This experimental system is useful to evaluate the efficacy of candidate gRNA target sequences in the short-term.

Metabolic Gene Clusters in Eukaryotes

In bacteria, more than half of the genes in the genome are organized in operons. In contrast, in eukaryotes, functionally related genes are usually dispersed across the genome. There are, however, numerous examples of functional clusters of nonhomologous genes for metabolic pathways in fungi and plants. Despite superficial similarities with operons (physical clustering, coordinate regulation), these clusters have not usually originated by horizontal gene transfer from bacteria, and (unlike operons) the genes are typically transcribed separately rather than as a single polycistronic message. This clustering phenomenon raises intriguing questions about the origins of clustered metabolic pathways in eukaryotes and the significance of clustering for pathway function. Here we review metabolic gene clusters from fungi and plants, highlight commonalities and differences, and consider how these clusters form and are regulated. We also identify opportunities for future research in the areas of large-scale genomics, synthetic biology, and experimental evolution.

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.