Striking natural diversity in glandular trichome acylsugar composition is shaped by variation at the Acyltransferase2 locus in the wild tomato Solanum habrochaites

Woolly mutation with the Get02 locus overcomes the polygenic nature of trichome-based pest resistance in tomato

Type-IV glandular trichomes, which only occur in the juvenile developmental phase of the cultivated tomato (Solanum lycopersicum), produce acylsugars that broadly protect against arthropod herbivory. Previously, we introgressed the capacity to retain type-IV trichomes in the adult phase from the wild tomato, Solanum galapagense, into the cultivated species cv. Micro-Tom (MT). The resulting MT-Galapagos enhanced trichome (MT-Get) introgression line contained 5 loci associated with enhancing the density of type-IV trichomes in adult plants. We genetically dissected MT-Get and obtained a subline containing only the locus on Chromosome 2 (MT-Get02). This genotype displayed about half the density of type-IV trichomes compared to the wild progenitor. However, when we stacked the gain-of-function allele of WOOLLY, which encodes a homeodomain leucine zipper IV transcription factor, Get02/Wo exhibited double the number of type-IV trichomes compared to S. galapagense. This discovery corroborates previous reports positioning WOOLLY as a master regulator of trichome development. Acylsugar levels in Get02/Wo were comparable to the wild progenitor, although the composition of acylsugar types differed, especially regarding fewer types with medium-length acyl chains. Agronomical parameters of Get02/Wo, including yield, were comparable to MT. Pest resistance assays showed enhanced protection against silverleaf whitefly (Bemisia tabaci), tobacco hornworm (Manduca sexta), and the fungus Septoria lycopersici. However, resistance levels did not reach those of the wild progenitor, suggesting the specificity of acylsugar types in the pest resistance mechanism. Our findings in trichome-mediated resistance advance the development of robust, naturally resistant tomato varieties, harnessing the potential of natural genetic variation. Moreover, by manipulating only 2 loci, we achieved exceptional results for a highly complex, polygenic trait, such as herbivory resistance in tomato.

Trading acyls and swapping sugars: metabolic innovations in Solanum trichomes

Solanaceae (nightshade family) species synthesize a remarkable array of clade- and tissue-specific specialized metabolites. Protective acylsugars, one such class of structurally diverse metabolites, are produced by AcylSugar AcylTransferases from sugars and acyl-coenzyme A esters. Published research revealed trichome acylsugars composed of glucose and sucrose cores in species across the family. In addition, acylsugars were analyzed across a small fraction of the >1200 species in the phenotypically megadiverse Solanum genus, with a handful containing inositol and glycosylated inositol cores. The current study sampled several dozen species across subclades of the Solanum to get a more detailed view of acylsugar chemodiversity. In depth characterization of acylsugars from the Clade II species Solanum melongena (brinjal eggplant) led to the identification of eight unusual structures with inositol or inositol glycoside cores, and hydroxyacyl chains. Liquid chromatography-mass spectrometry analysis of 31 additional species in the Solanum genus revealed striking acylsugar diversity with some traits restricted to specific clades and species. Acylinositols and inositol-based acyldisaccharides were detected throughout much of the genus. In contrast, acylglucoses and acylsucroses were more restricted in distribution. Analysis of tissue-specific transcriptomes and interspecific acylsugar acetylation differences led to the identification of the S. melongena AcylSugar AcylTransferase 3-Like 1 (SmASAT3-L1; SMEL4.1_12g015780) enzyme. This enzyme is distinct from previously characterized acylsugar acetyltransferases, which are in the ASAT4 clade, and appears to be a functionally divergent ASAT3. This study provides a foundation for investigating the evolution and function of diverse Solanum acylsugar structures and harnessing this diversity in breeding and synthetic biology.

Dangerous sugars: Structural diversity and functional significance of acylsugar-like defense compounds in flowering plants

Acylsugars constitute a diverse class of secondary metabolites found in many flowering plant families. Comprising sugar cores and acyl groups connected by ester and/or ether linkages, acylsugar structures vary considerably at all taxonomic levels - from populations of the same species to across species of the same family and across flowering plants, with some species producing hundreds of acylsugars in a single organ. Acylsugars have been most well-studied in the Solanaceae family, but structurally analogous compounds have also been reported in the Convolvulaceae, Martyniaceae, Geraniaceae, Rubiaceae, Rosaceae and Caryophyllaceae families. Focusing on Solanaceae and Convolvulaceae acylsugars, this review highlights their structural diversity, the potential biosynthetic mechanisms that produce this diversity, and its functional significance. Finally, we also discuss the possibility that some of this diversity is merely "noise", arising out of enzyme promiscuity and/or non-adaptive evolutionary mechanisms.

Phylogenomic analyses across land plants reveals motifs and coexpression patterns useful for functional prediction in the BAHD acyltransferase family

The BAHD acyltransferase family is one of the largest enzyme families in flowering plants, containing dozens to hundreds of genes in individual genomes. Highly prevalent in angiosperm genomes, members of this family contribute to several pathways in primary and specialized metabolism. In this study, we performed a phylogenomic analysis of the family using 52 genomes across the plant kingdom to gain deeper insights into its functional evolution and enable function prediction. We found that BAHD expansion in land plants was associated with significant changes in various gene features. Using pre-defined BAHD clades, we identified clade expansions in different plant groups. In some groups, these expansions coincided with the prominence of metabolite classes such as anthocyanins (flowering plants) and hydroxycinnamic acid amides (monocots). Clade-wise motif-enrichment analysis revealed that some clades have novel motifs fixed on either the acceptor or the donor side, potentially reflecting historical routes of functional evolution. Co-expression analysis in rice and Arabidopsis further identified BAHDs with similar expression patterns, however, most co-expressed BAHDs belonged to different clades. Comparing BAHD paralogs, we found that gene expression diverges rapidly after duplication, suggesting that sub/neo-functionalization of duplicate genes occurs quickly via expression diversification. Analyzing co-expression patterns in Arabidopsis in conjunction with orthology-based substrate class predictions and metabolic pathway models led to the recovery of metabolic processes of most of the already-characterized BAHDs as well as definition of novel functional predictions for some uncharacterized BAHDs. Overall, this study provides new insights into the evolution of BAHD acyltransferases and sets up a foundation for their functional characterization.

Natural variation meets synthetic biology: Promiscuous trichome-expressed acyltransferases from Nicotiana

Acylsugars are defensive, trichome-synthesized sugar esters produced in plants across the Solanaceae (nightshade) family. Although assembled from simple metabolites and synthesized by a relatively short core biosynthetic pathway, tremendous within- and across-species acylsugar structural variation is documented across the family. To advance our understanding of the diversity and the synthesis of acylsugars within the Nicotiana genus, trichome extracts were profiled across the genus coupled with transcriptomics-guided enzyme discovery and in vivo and in vitro analysis. Differences in the types of sugar cores, numbers of acylations, and acyl chain structures contributed to over 300 unique annotated acylsugars throughout Nicotiana. Placement of acyl chain length into a phylogenetic context revealed that an unsaturated acyl chain type was detected in a few closely related species. A comparative transcriptomics approach identified trichome-enriched Nicotiana acuminata acylsugar biosynthetic candidate enzymes. More than 25 acylsugar variants could be produced in a single enzyme assay with four N. acuminata acylsugar acyltransferases (NacASAT1-4) together with structurally diverse acyl-CoAs and sucrose. Liquid chromatography coupled with mass spectrometry screening of in vitro products revealed the ability of these enzymes to make acylsugars not present in Nicotiana plant extracts. In vitro acylsugar production also provided insights into acyltransferase acyl donor promiscuity and acyl acceptor specificity as well as regiospecificity of some ASATs. This study suggests that promiscuous Nicotiana acyltransferases can be used as synthetic biology tools to produce novel and potentially useful metabolites.

Acylsugars protect Nicotiana benthamiana against insect herbivory and desiccation

KEY MESSAGE

Nicotiana benthamiana acylsugar acyltransferase (ASAT) is required for protection against desiccation and insect herbivory. Knockout mutations provide a new resource for investigation of plant-aphid and plant-whitefly interactions. Nicotiana benthamiana is used extensively as a transient expression platform for functional analysis of genes from other species. Acylsugars, which are produced in the trichomes, are a hypothesized cause of the relatively high insect resistance that is observed in N. benthamiana. We characterized the N. benthamiana acylsugar profile, bioinformatically identified two acylsugar acyltransferase genes, ASAT1 and ASAT2, and used CRISPR/Cas9 mutagenesis to produce acylsugar-deficient plants for investigation of insect resistance and foliar water loss. Whereas asat1 mutations reduced accumulation, asat2 mutations caused almost complete depletion of foliar acylsucroses. Three hemipteran and three lepidopteran herbivores survived, gained weight, and/or reproduced significantly better on asat2 mutants than on wildtype N. benthamiana. Both asat1 and asat2 mutations reduced the water content and increased leaf temperature. Our results demonstrate the specific function of two ASAT proteins in N. benthamiana acylsugar biosynthesis, insect resistance, and desiccation tolerance. The improved growth of aphids and whiteflies on asat2 mutants will facilitate the use of N. benthamiana as a transient expression platform for the functional analysis of insect effectors and resistance genes from other plant species. Similarly, the absence of acylsugars in asat2 mutants will enable analysis of acylsugar biosynthesis genes from other Solanaceae by transient expression.

Identification of BAHD acyltransferases associated with acylinositol biosynthesis in Solanum quitoense (naranjilla)

Plants make a variety of specialized metabolites that can mediate interactions with animals, microbes, and competitor plants. Understanding how plants synthesize these compounds enables studies of their biological roles by manipulating their synthesis in vivo as well as producing them in vitro. Acylsugars are a group of protective metabolites that accumulate in the trichomes of many Solanaceae family plants. Acylinositol biosynthesis is of interest because it appears to be restricted to a subgroup of species within the Solanum genus. Previous work characterized a triacylinositol acetyltransferase involved in acylinositol biosynthesis in the Andean fruit plant Solanum quitoense (lulo or naranjilla). We characterized three additional S. quitoense trichome expressed enzymes and found that virus-induced gene silencing of each caused changes in acylinositol accumulation. pH was shown to influence the stability and rearrangement of the product of ASAT1H and could potentially play a role in acylinositol biosynthesis. Surprisingly, the in vitro triacylinositol products of these enzymes are distinct from those that accumulate in planta. This suggests that additional enzymes are required in acylinositol biosynthesis. These characterized S. quitoense enzymes, nonetheless, provide opportunities to test the biological impact and properties of these triacylinositols in vitro.

The Genetic Complexity of Type-IV Trichome Development Reveals the Steps towards an Insect-Resistant Tomato

The leaves of the wild tomato Solanum galapagense harbor type-IV glandular trichomes (GT) that produce high levels of acylsugars (AS), conferring insect resistance. Conversely, domesticated tomatoes (S. lycopersicum) lack type-IV trichomes on the leaves of mature plants, preventing high AS production, thus rendering the plants more vulnerable to insect predation. We hypothesized that cultivated tomatoes engineered to harbor type-IV trichomes on the leaves of adult plants could be insect-resistant. We introgressed the genetic determinants controlling type-IV trichome development from S. galapagense into cv. Micro-Tom (MT) and created a line named “Galapagos-enhanced trichomes” (MT-Get). Mapping-by-sequencing revealed that five chromosomal regions of S. galapagense were present in MT-Get. Further genetic mapping showed that S. galapagense alleles in chromosomes 1, 2, and 3 were sufficient for the presence of type-IV trichomes on adult organs but at lower densities. Metabolic and gene expression analyses demonstrated that type-IV trichome density was not accompanied by the AS production and exudation in MT-Get. Although the plants produce a significant amount of acylsugars, those are still not enough to make them resistant to whiteflies. We demonstrate that type-IV glandular trichome development is insufficient for high AS accumulation. The results from our study provided additional insights into the steps necessary for breeding an insect-resistant tomato.

Fruity, sticky, stinky, spicy, bitter, addictive, and deadly: evolutionary signatures of metabolic complexity in the Solanaceae

Covering: 2000-2022Plants collectively synthesize a huge repertoire of metabolites. General metabolites, also referred to as primary metabolites, are conserved across the plant kingdom and are required for processes essential to growth and development. These include amino acids, sugars, lipids, and organic acids. In contrast, specialized metabolites, historically termed secondary metabolites, are structurally diverse, exhibit lineage-specific distribution and provide selective advantage to host species to facilitate reproduction and environmental adaptation. Due to their potent bioactivities, plant specialized metabolites attract considerable attention for use as flavorings, fragrances, pharmaceuticals, and bio-pesticides. The Solanaceae (Nightshade family) consists of approximately 2700 species and includes crops of significant economic, cultural, and scientific importance: these include potato, tomato, pepper, eggplant, tobacco, and petunia. The Solanaceae has emerged as a model family for studying the biochemical evolution of plant specialized metabolism and multiple examples exist of lineage-specific metabolites that influence the senses and physiology of commensal and harmful organisms, including humans. These include, alcohols, phenylpropanoids, and carotenoids that contribute to fruit aroma and color in tomato (fruity), glandular trichome-derived terpenoids and acylsugars that contribute to plant defense (stinky & sticky, respectively), capsaicinoids in chilli-peppers that influence seed dispersal (spicy), and steroidal glycoalkaloids (bitter) from Solanum, nicotine (addictive) from tobacco, as well as tropane alkaloids (deadly) from Deadly Nightshade that deter herbivory. Advances in genomics and metabolomics, coupled with the adoption of comparative phylogenetic approaches, resulted in deeper knowledge of the biosynthesis and evolution of these metabolites. This review highlights recent progress in this area and outlines opportunities for - and challenges of-developing a more comprehensive understanding of Solanaceae metabolism.

Illuminating the lineage-specific diversification of resin glycoside acylsugars in the morning glory (Convolvulaceae) family using computational metabolomics

Acylsugars are a class of plant defense compounds produced across many distantly related families. Members of the horticulturally important morning glory (Convolvulaceae) family produce a diverse sub-class of acylsugars called resin glycosides (RGs), which comprise oligosaccharide cores, hydroxyacyl chain(s), and decorating aliphatic and aromatic acyl chains. While many RG structures are characterized, the extent of structural diversity of this class in different genera and species is not known. In this study, we asked whether there has been lineage-specific diversification of RG structures in different Convolvulaceae species that may suggest diversification of the underlying biosynthetic pathways. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was performed from root and leaf extracts of 26 species sampled in a phylogeny-guided manner. LC-MS/MS revealed thousands of peaks with signature RG fragmentation patterns with one species producing over 300 signals, mirroring the diversity in Solanaceae-type acylsugars. A novel RG from Dichondra argentea was characterized using Nuclear Magnetic Resonance spectroscopy, supporting previous observations of RGs with open hydroxyacyl chains instead of closed macrolactone ring structures. Substantial lineage-specific differentiation in utilization of sugars, hydroxyacyl chains, and decorating acyl chains was discovered, especially among Ipomoea and Convolvulus - the two largest genera in Convolvulaceae. Adopting a computational, knowledge-based strategy, we further developed a high-recall workflow that successfully explained ~72% of the MS/MS fragments, predicted the structural components of 11/13 previously characterized RGs, and partially annotated ~45% of the RGs. Overall, this study improves our understanding of phytochemical diversity and lays a foundation for characterizing the evolutionary mechanisms underlying RG diversification.

It happened again: Convergent evolution of acylglucose specialized metabolism in black nightshade and wild tomato

Plants synthesize myriad phylogenetically restricted specialized (aka “secondary”) metabolites with diverse structures. Metabolism of acylated sugar esters in epidermal glandular secreting trichomes across the Solanaceae (nightshade) family is ideal for investigating the mechanisms of evolutionary metabolic diversification. We developed methods to structurally analyze acylhexose mixtures by 2D NMR, which led to the insight that the Old World species black nightshade (Solanum nigrum) accumulates acylglucoses and acylinositols in the same tissue. Detailed in vitro biochemistry, cross-validated by in vivo virus-induced gene silencing, revealed two unique features of the four-step acylglucose biosynthetic pathway: A trichome-expressed, neofunctionalized invertase-like enzyme, SnASFF1, converts BAHD-produced acylsucroses to acylglucoses, which, in turn, are substrates for the acylglucose acyltransferase, SnAGAT1. This biosynthetic pathway evolved independently from that recently described in the wild tomato Solanum pennellii, reinforcing that acylsugar biosynthesis is evolutionarily dynamic with independent examples of primary metabolic enzyme cooption and additional variation in BAHD acyltransferases.

Two zinc-finger roteins control the initiation and elongation of long stalk trichomes in tomato

Plant glandular trichomes are epidermal secretory structures that are important for plant resistance to pests. Although several regulatory genes have been characterized in trichome development, the molecular mechanisms conferring glandular trichome morphogenesis are unclear. We observed the differences in trichomes in cultivated tomato cv. 'Moneymaker' (MM) and the wild species Solanum pimpinellifolium PI365967 (PP), and used a recombinant inbred line (RIL) population to identify the genes that control trichome development in tomato. We found that the genomic variations in two genes, H and SH, contribute to the trichome differences between MM and PP. H and SH encode two paralogous C2H2 zinc-finger proteins that function redundantly in regulating trichome formation. Loss-of-function h/sh double mutants exhibited a significantly decreased number of Type I trichomes and complete loss of long stalk trichomes. Molecular and genetic analyses further indicate that H and SH act upstream of ZFP5. Overexpression of ZFP5 partially restored the trichome defects in NIL-h^PPsh^PP. Moreover, H and SH expression is induced by high temperatures, and their mutations inhibit the elongation of trichomes that reduce the plant repellent to whiteflies. Our findings confirm that H and SH are two vital transcription factors controlling initiation and elongation of Type I and III multicellular trichomes in tomato.

Evolution-aided engineering of plant specialized metabolism

The evolution of new traits in living organisms occurs via the processes of mutation, recombination, genetic drift, and selection. These processes that have resulted in the immense biological diversity on our planet are also being employed in metabolic engineering to optimize enzymes and pathways, create new-to-nature reactions, and synthesize complex natural products in heterologous systems. In this review, we discuss two evolution-aided strategies for metabolic engineering-directed evolution, which improves upon existing genetic templates using the evolutionary process, and combinatorial pathway reconstruction, which brings together genes evolved in different organisms into a single heterologous host. We discuss the general principles of these strategies, describe the technologies involved and the molecular traits they influence, provide examples of their use, and discuss the roadblocks that need to be addressed for their wider adoption. A better understanding of these strategies can provide an impetus to research on gene function discovery and biochemical evolution, which is foundational for improved metabolic engineering. These evolution-aided approaches thus have a substantial potential for improving our understanding of plant metabolism in general, for enhancing the production of plant metabolites, and in sustainable agriculture.

Natural variation in wild tomato trichomes; selecting metabolites that contribute to insect resistance using a random forest approach

BACKGROUND

Plant-produced specialised metabolites are a powerful part of a plant's first line of defence against herbivorous insects, bacteria and fungi. Wild ancestors of present-day cultivated tomato produce a plethora of acylsugars in their type-I/IV trichomes and volatiles in their type-VI trichomes that have a potential role in plant resistance against insects. However, metabolic profiles are often complex mixtures making identification of the functionally interesting metabolites challenging. Here, we aimed to identify specialised metabolites from a wide range of wild tomato genotypes that could explain resistance to vector insects whitefly (Bemisia tabaci) and Western flower thrips (Frankliniella occidentalis). We evaluated plant resistance, determined trichome density and obtained metabolite profiles of the glandular trichomes by LC-MS (acylsugars) and GC-MS (volatiles). Using a customised Random Forest learning algorithm, we determined the contribution of specific specialised metabolites to the resistance phenotypes observed.

RESULTS

The selected wild tomato accessions showed different levels of resistance to both whiteflies and thrips. Accessions resistant to one insect can be susceptible to another. Glandular trichome density is not necessarily a good predictor for plant resistance although the density of type-I/IV trichomes, related to the production of acylsugars, appears to correlate with whitefly resistance. For type VI-trichomes, however, it seems resistance is determined by the specific content of the glands. There is a strong qualitative and quantitative variation in the metabolite profiles between different accessions, even when they are from the same species. Out of 76 acylsugars found, the random forest algorithm linked two acylsugars (S3:15 and S3:21) to whitefly resistance, but none to thrips resistance. Out of 86 volatiles detected, the sesquiterpene α-humulene was linked to whitefly susceptible accessions instead. The algorithm did not link any specific metabolite to resistance against thrips, but monoterpenes α-phellandrene, α-terpinene and β-phellandrene/D-limonene were significantly associated with susceptible tomato accessions.

CONCLUSIONS

Whiteflies and thrips are distinctly targeted by certain specialised metabolites found in wild tomatoes. The machine learning approach presented helped to identify features with efficacy toward the insect species studied. These acylsugar metabolites can be targets for breeding efforts towards the selection of insect-resistant cultivars.

Introgression of the sesquiterpene biosynthesis from Solanum habrochaites to cultivated tomato offers insights into trichome morphology and arthropod resistance

Cultivated tomatoes harboring the plastid-derived sesquiterpenes from S. habrochaites have altered type-VI trichome morphology and unveil additional genetic components necessary for piercing-sucking pest resistance. Arthropod resistance in the tomato wild relative Solanum habrochaites LA1777 is linked to specific sesquiterpene biosynthesis. The Sesquiterpene synthase 2 (SsT2) gene cluster on LA1777 chromosome 8 controls plastid-derived sesquiterpene synthesis. The main genes at SsT2 are Z-prenyltransferase (zFPS) and Santalene and Bergamotene Synthase (SBS), which produce α-santalene, β-bergamotene, and α-bergamotene in LA1777 round-shaped type-VI glandular trichomes. Cultivated tomatoes have mushroom-shaped type-VI trichomes with much smaller glands that contain low levels of monoterpenes and cytosolic-derived sesquiterpenes, not presenting the same pest resistance as in LA1777. We successfully transferred zFPS and SBS from LA1777 to cultivated tomato (cv. Micro-Tom, MT) by a backcrossing approach. The trichomes of the MT-Sst2 introgressed line produced high levels of the plastid-derived sesquiterpenes. The type-VI trichome internal storage-cavity size increased in MT-Sst2, probably as an effect of the increased amount of sesquiterpenes, although it was not enough to mimic the round-shaped LA1777 trichomes. The presence of high amounts of plastid-derived sesquiterpenes was also not sufficient to confer resistance to various tomato piercing-sucking pests, indicating that the effect of the sesquiterpenes found in the wild S. habrochaites can be insect specific. Our results provide for a better understanding of the morphology of S. habrochaites type-VI trichomes and paves the way to obtain insect-resistant tomatoes.

Genetic variation, environment and demography intersect to shape Arabidopsis defense metabolite variation across Europe

Plants produce diverse metabolites to cope with the challenges presented by complex and ever-changing environments. These challenges drive the diversification of specialized metabolites within and between plant species. However, we are just beginning to understand how frequently new alleles arise controlling specialized metabolite diversity and how the geographic distribution of these alleles may be structured by ecological and demographic pressures. Here, we measure the variation in specialized metabolites across a population of 797 natural Arabidopsis thaliana accessions. We show that a combination of geography, environmental parameters, demography and different genetic processes all combine to influence the specific chemotypes and their distribution. This showed that causal loci in specialized metabolism contain frequent independently generated alleles with patterns suggesting potential within-species convergence. This provides a new perspective about the complexity of the selective forces and mechanisms that shape the generation and distribution of allelic variation that may influence local adaptation.

Since plants cannot move, they have evolved chemical defenses to help them respond to changes in their surroundings. For example, where animals run from predators, plants may produce toxins to put predators off. This approach is why plants are such a rich source of drugs, poisons, dyes and other useful substances. The chemicals plants produce are known as specialized metabolites, and they can change a lot between, and even within, plant species. The variety of specialized metabolites is a result of genetic changes and evolution over millions of years.

Evolution is a slow process, yet plants are able to rapidly develop new specialized metabolites to protect them from new threats. Even different populations of the same species produce many distinct metabolites that help them survive in their surroundings. However, the factors that lead plants to produce new metabolites are not well understood, and it is not known how this affects genetic variation.

To gain a better understanding of this process, Katz et al. studied 797 European variants of a common weed species called Arabidopsis thaliana, which is widely studied. The investigation found that many factors affect the range of specialized metabolites in each variant. These included local geography and environment, as well as genetics and population history (demography). Katz et al. revealed a pattern of relationships between the variants that could mirror their evolutionary history as the species spread and adapted to new locations.

These results highlight the complex network of factors that affect plant evolution. Rapid diversification is key to plant survival in new and changing environments and has resulted in a wide range of specialized metabolites. As such they are of interest both for studying plant evolution and for understanding their ecology. Expanding similar work to more populations and other species will broaden the scope of our ability to understand how plants adapt to their surroundings.

Migration through a Major Andean Ecogeographic Disruption as a Driver of Genetic and Phenotypic Diversity in a Wild Tomato Species

Evolutionary dynamics at the population level play a central role in creating the diversity of life on our planet. In this study, we sought to understand the origins of such population-level variation in mating systems and defensive acylsugar chemistry in Solanum habrochaites—a wild tomato species found in diverse Andean habitats in Ecuador and Peru. Using Restriction-site-Associated-DNA-Sequencing (RAD-seq) of 50 S. habrochaites accessions, we identified eight population clusters generated via isolation and hybridization dynamics of 4–6 ancestral populations. Detailed characterization of mating systems of these clusters revealed emergence of multiple self-compatible (SC) groups from progenitor self-incompatible populations in the northern part of the species range. Emergence of these SC groups was also associated with fixation of deleterious alleles inactivating acylsugar acetylation. The Amotape-Huancabamba Zone—a geographical landmark in the Andes with high endemism and isolated microhabitats—was identified as a major driver of differentiation in the northern species range, whereas large geographical distances contributed to population structure and evolution of a novel SC group in the central and southern parts of the range, where the species was also inferred to have originated. Findings presented here highlight the role of the diverse ecogeography of Peru and Ecuador in generating population differentiation, and enhance our understanding of the microevolutionary processes that create biological diversity.

Glandular trichome-derived sesquiterpenes of wild tomato accessions (Solanum habrochaites) affect aphid performance and feeding behavior

Glandular trichomes of tomato produce a number of secondary metabolites including terpenes that contribute to host plant resistance against pests. While glandular trichomes of cultivated tomato Solanum lycopersicum primarily accumulate a monoterpene blend, those of wild tomato species like Solanum habrochaites produce various sesquiterpenes. Previous studies have shown that glandular trichome derived terpenes in cultivated and wild tomato species have repellent and toxic activity against multiple biting-chewing herbivores. In contrast, considerably less is known about the effect of these glandular trichome derived terpenes on piercing-sucking herbivores such as aphids. Here, we have screened a collection of S. habrochaites accessions representing five chemotypes that produce distinct sets of sesquiterpenes to identify those affecting the potato aphid (Macrosiphum euphorbiae). Non-choice assays demonstrated that the longevity and fecundity of M. euphorbiae was significantly reduced when kept on the leaf surface of S. habrochaites accessions producing β-caryophyllene and α-humulene, or α-santalene, α-bergamotene, and β-bergamotene, respectively. When M. euphorbiae apterae were feeding on artificial diets with added terpene containing leaf dip extracts, the same β-caryophyllene/α-humulene and α-santalene/α-bergamotene/β-bergamotene producing S. habrochaites accessions were found to affect aphid survivorship and feeding behavior as indicated by gel saliva investment and honeydew production. Olfactometer assays revealed that the sesquiterpenes emitted from these S. habrochaites accessions also have repellent activity against M. euphorbiae alatae affecting their choice behavior prior to landing on host plants. Assays performed with pure sesquiterpene compounds and an introgression line carrying respective S. habrochaites terpene biosynthetic genes in the S. lycopersicum background confirmed that β-caryophyllene/α-humulene and α-santalene/α-bergamotene/β-bergamotene were responsible for the observed effects on performance, feeding and choice behavior of M. euphorbiae.

An Integrated Analytical Approach Reveals Trichome Acylsugar Metabolite Diversity in the Wild Tomato Solanum pennellii

Acylsugars constitute an abundant class of pest- and pathogen-protective Solanaceae family plant-specialized metabolites produced in secretory glandular trichomes. Solanum pennellii produces copious triacylated sucrose and glucose esters, and the core biosynthetic pathway producing these compounds was previously characterized. We performed untargeted metabolomic analysis of S. pennellii surface metabolites from accessions spanning the species range, which indicated geographic trends in the acylsugar profile and revealed two compound classes previously undescribed from this species, tetraacylglucoses and flavonoid aglycones. A combination of ultrahigh-performance liquid chromatography–high resolution mass spectrometry (UHPLC–HR-MS) and NMR spectroscopy identified variations in the number, length, and branching pattern of acyl chains, and the proportion of sugar cores in acylsugars among accessions. The new dimensions of acylsugar variation revealed by this analysis further indicate variation in the biosynthetic and degradative pathways responsible for acylsugar accumulation. These findings provide a starting point for deeper investigation of acylsugar biosynthesis, an understanding of which can be exploited through crop breeding or metabolic engineering strategies to improve the endogenous defenses of crop plants.

Trichomes form genotype-specific microbial hotspots in the phyllosphere of tomato

BACKGROUND

The plant phyllosphere is a well-studied habitat characterized by low nutrient availability and high community dynamics. In contrast, plant trichomes, known for their production of a large number of metabolites, are a yet unexplored habitat for microbes. We analyzed the phyllosphere as well as trichomes of two tomato genotypes (Solanum lycopersicum LA4024, S. habrochaites LA1777) by targeting bacterial 16S rRNA gene fragments.

RESULTS

Leaves, leaves without trichomes, and trichomes alone harbored similar abundances of bacteria (10⁸-10⁹ 16S rRNA gene copy numbers per gram of sample). In contrast, bacterial diversity was found significantly increased in trichome samples (Shannon index: 4.4 vs. 2.5). Moreover, the community composition was significantly different when assessed with beta diversity analysis and corresponding statistical tests. At the bacterial class level, Alphaproteobacteria (23.6%) were significantly increased, whereas Bacilli (8.6%) were decreased in trichomes. The bacterial family Sphingomonadacea (8.4%) was identified as the most prominent, trichome-specific feature; Burkholderiaceae and Actinobacteriaceae showed similar patterns. Moreover, Sphingomonas was identified as a central element in the core microbiome of trichome samples, while distinct low-abundant bacterial families including Hymenobacteraceae and Alicyclobacillaceae were exclusively found in trichome samples. Niche preferences were statistically significant for both genotypes and genotype-specific enrichments were further observed.

CONCLUSION

Our results provide first evidence of a highly specific trichome microbiome in tomato and show the importance of micro-niches for the structure of bacterial communities on leaves. These findings provide further clues for breeding, plant pathology and protection as well as so far unexplored natural pathogen defense strategies.

Effects of Water Deficit and Heat Stress on Nicotiana langsdorffii Metabolomic Pattern Modified by Insertion of rolD Gene from Agrobacterium rhizogenes

Abiotic stresses are major factors that negatively affect plant growth and productivity. Plants have developed complex strategies to ensure their survival and reproduction under adverse conditions, activating mechanisms that involve changes at different metabolic levels. In order to select stress-resistant species, research has focused on molecular studies and genetic engineering, showing promising results. In this work, the insertion of the rolD gene from Agrobacterium rhizogenes into Nicotiana langsdorffii plants is investigated, in order to assess the potential of this genetic modification towards mitigating water and heat stresses. Different approaches were combined: a high-throughput metabolomics and ionomics study was performed, together with the determination of important plant phytohormones. The aim was to identify the influence of abiotic stresses on plants and to highlight the effects of the rolD genetic modification on plant stress response. The most relevant compounds for each kind of stress were identified, belonging mainly to the classes of lipids, acyl sugars, glycosides, and amino acid derivatives. Water stress (WS) determined a decrease of elements and secondary metabolites, while amino acids and their derivatives increased, proving to be key molecules in this type of stress. RolD plants exposed to high temperature stress (HS) presented higher dry weight levels than controls, as well as increased amounts of K and adenosine and lower levels of damage-associated metabolites, suggesting the increased resistance of rolD-modified plants toward HS.

Integrative Transcriptomic and Metabolic Analyses Provide Insights into the Role of Trichomes in Tea Plant (Camellia Sinensis)

Trichomes, which develop from epidermal cells, are regarded as one of the key features that are involved in the evaluation of tea quality and tea germplasm resources. The metabolites from trichomes have been well characterized in tea products. However, little is known regarding the metabolites in fresh tea trichomes and the molecular differences in trichomes and tea leaves per se. In this study, we developed a method to collect trichomes from tea plant tender shoots, and their main secondary metabolites, including catechins, caffeine, amino acids, and aroma compounds, were determined. We found that the majority of these compounds were significantly less abundant in trichomes than in tea leaves. RNA-Seq was used to investigate the differences in the molecular regulatory mechanism between trichomes and leaves to gain further insight into the differences in trichomes and tea leaves. In total, 52.96 Gb of clean data were generated, and 6560 differentially expressed genes (DEGs), including 4471 upregulated and 2089 downregulated genes, were identified in the trichomes vs. leaves comparison. Notably, the structural genes of the major metabolite biosynthesis pathways, transcription factors, and other key DEGs were identified and comparatively analyzed between trichomes and leaves, while trichome-specific genes were also identified. Our results provide new insights into the differences between tea trichomes and leaves at the metabolic and transcriptomic levels, and open up new doors to further recognize and re-evaluate the role of trichomes in tea quality formation and tea plant growth and development.

A thrips vector of tomato spotted wilt virus responds to tomato acylsugar chemical diversity with reduced oviposition and virus inoculation

There is increasing evidence that acylsugars deter insect pests and plant virus vectors, including the western flower thrips (WFT), Frankliniella occidentalis (Pergande), vector of tomato spotted wilt virus (TSWV). Acylsugars are sugar-polyesters composed of saturated, un-saturated, and variously branched short and long chain fatty acids (FAs) esterified to a glucose (acylglucose) or sucrose (acylsucrose) moiety. We sought to understand how acylsucrose amount and composition of associated FA profiles interacted to mediate resistance to WFT oviposition and TSWV inoculation on tomato leaves. Towards this goal, we examined WFT oviposition and TSWV inoculation behavior on tomato lines bred to exude varying amounts of acylsucrose in association with diverse FA profiles. Our data show that as acylsucrose amounts increased, WFT egg-laying (oviposition) decreased and TSWV inoculation was suppressed. Western flower thrips also responded to FA profiles that included iC4, iC11, nC12 and nC10 FA. These findings support improving acylsugar-mediated resistance against WFT by breeding tomatoes exuding greater amounts of acylsucrose associated with specific FA profiles. We show that increasing acylsucrose amount output by type IV trichomes and selecting for particular FA profiles through advanced breeding profoundly affects WFT behavior in ways that benefit management of WFT as direct pests and as TSWV vectors.

Variations of Secondary Metabolites among Natural Populations of Sub-Antarctic Ranunculus Species Suggest Functional Redundancy and Versatility

Plants produce a high diversity of metabolites which help them sustain environmental stresses and are involved in local adaptation. However, shaped by both the genome and the environment, the patterns of variation of the metabolome in nature are difficult to decipher. Few studies have explored the relative parts of geographical region versus environment or phenotype in metabolomic variability within species and none have discussed a possible effect of the region on the correlations between metabolites and environments or phenotypes. In three sub-Antarctic Ranunculus species, we examined the role of region in metabolite differences and in the relationship between individual compounds and environmental conditions or phenotypic traits. Populations of three Ranunculus species were sampled across similar environmental gradients in two distinct geographical regions in îles Kerguelen. Two metabolite classes were studied, amines (quantified by high-performance liquid chromatography and fluorescence spectrophotometry) and flavonols (quantified by ultra-high-performance liquid chromatography with triple quadrupole mass spectrometry). Depending on regions, the same environment or the same trait may be related to different metabolites, suggesting metabolite redundancy within species. In several cases, a given metabolite showed different or even opposite relations with the same environmental condition or the same trait across the two regions, suggesting metabolite versatility within species. Our results suggest that metabolites may be functionally redundant and versatile within species, both in their response to environments and in their relation with the phenotype. These findings open new perspectives for understanding evolutionary responses of plants to environmental changes.

Tip of the trichome: evolution of acylsugar metabolic diversity in Solanaceae

Acylsugars are insecticidal plant specialized metabolites produced in the Solanaceae (nightshade family). Despite having simple constituents, these compounds are unusually structurally diverse. Their structural variations in phylogenetically closely related species enable comparative biochemical approaches to understand acylsugar biosynthesis and pathway diversification. Thus far, varied enzyme classes contributing to their synthesis were characterized in cultivated and wild tomatoes, including from core metabolism - isopropylmalate synthase (Leu) and invertase (carbon) - and a group of evolutionarily related BAHD acyltransferases known as acylsucrose acyltransferases. Gene duplication and neofunctionalization of these enzymes drove acylsugar diversification both within and beyond tomato. The broad set of evolutionary mechanisms underlying acylsugar diversity in Solanaceae make this metabolic network an exemplar for detailed understanding of the evolution of metabolic form and function.

Trichome Independent Resistance against Western Flower Thrips in Tomato

Western flower thrips (WFT) are a major pest on many crops, including tomato. Thrips cause yield losses, not only through feeding damage, but also by the transmission of viruses of which the Tomato Spotted Wilt Virus is the most important one. In cultivated tomato, genetic diversity is extremely low, and all commercial lines are susceptible to WFT. Several wild relatives are WFT resistant and these resistances are based on glandular trichome-derived traits. Introgression of these traits in cultivated lines did not lead to WFT resistant commercial varieties so far. In this study, we investigated WFT resistance in cultivated tomato using a F2 population derived from a cross between a WFT susceptible and a WFT resistant cultivated tomato line. We discovered that this WFT resistance is independent of glandular trichome density or trichome-derived volatile profiles and is associated with three QTLs on chromosomes 4, 5 and 10. Foliar metabolic profiles of F3 families with low and high WFT feeding damage were clearly different. We identified α-tomatine and a phenolic compound as potential defensive compounds. Their causality and interaction need further investigation. Because this study is based on cultivated tomato lines, our findings can directly be used in nowadays breeding programs.

Evolution of metabolic novelty: A trichome-expressed invertase creates specialized metabolic diversity in wild tomato

Plants produce a myriad of taxonomically restricted specialized metabolites. This diversity-and our ability to correlate genotype with phenotype-makes the evolution of these ecologically and medicinally important compounds interesting and experimentally tractable. Trichomes of tomato and other nightshade family plants produce structurally diverse protective compounds termed acylsugars. While cultivated tomato (Solanum lycopersicum) strictly accumulates acylsucroses, the South American wild relative Solanum pennellii produces copious amounts of acylglucoses. Genetic, transgenic, and biochemical dissection of the S. pennellii acylglucose biosynthetic pathway identified a trichome gland cell-expressed invertase-like enzyme that hydrolyzes acylsucroses (Sopen03g040490). This enzyme acts on the pyranose ring-acylated acylsucroses found in the wild tomato but not on the furanose ring-decorated acylsucroses of cultivated tomato. These results show that modification of the core acylsucrose biosynthetic pathway leading to loss of furanose ring acylation set the stage for co-option of a general metabolic enzyme to produce a new class of protective compounds.

Ethylene signaling regulates natural variation in the abundance of antifungal acetylated diferuloylsucroses and Fusarium graminearum resistance in maize seedling roots

The production and regulation of defensive specialized metabolites play a central role in pathogen resistance in maize (Zea mays) and other plants. Therefore, identification of genes involved in plant specialized metabolism can contribute to improved disease resistance. We used comparative metabolomics to identify previously unknown antifungal metabolites in maize seedling roots, and investigated the genetic and physiological mechanisms underlying their natural variation using quantitative trait locus mapping and comparative transcriptomics approaches. Two maize metabolites, smilaside A (3,6-diferuloyl-3',6'-diacetylsucrose) and smiglaside C (3,6-diferuloyl-2',3',6'-triacetylsucrose), were identified that could contribute to maize resistance against Fusarium graminearum and other fungal pathogens. Elevated expression of an ethylene signaling gene, ETHYLENE INSENSITIVE 2 (ZmEIN2), co-segregated with a decreased smilaside A : smiglaside C ratio. Pharmacological and genetic manipulation of ethylene availability and sensitivity in vivo indicated that, whereas ethylene was required for the production of both metabolites, the smilaside A : smiglaside C ratio was negatively regulated by ethylene sensitivity. This ratio, rather than the absolute abundance of these two metabolites, was important for maize seedling root defense against F. graminearum. Ethylene signaling regulates the relative abundance of the two F. graminearum-resistance-related metabolites and affects resistance against F. graminearum in maize seedling roots.

Non-volatile natural products in plant glandular trichomes: chemistry, biological activities and biosynthesis

The investigation methods, chemistry, bioactivities, and biosynthesis of non-volatile natural products involving 489 compounds in plant glandular trichomes are reviewed.

Evolution of a flipped pathway creates metabolic innovation in tomato trichomes through BAHD enzyme promiscuity

Plants produce hundreds of thousands of structurally diverse specialized metabolites via multistep biosynthetic networks, including compounds of ecological and therapeutic importance. These pathways are restricted to specific plant groups, and are excellent systems for understanding metabolic evolution. Tomato and other plants in the nightshade family synthesize protective acylated sugars in the tip cells of glandular trichomes on stems and leaves. We describe a metabolic innovation in wild tomato species that contributes to acylsucrose structural diversity. A small number of amino acid changes in two acylsucrose acyltransferases alter their acyl acceptor preferences, resulting in reversal of their order of reaction and increased product diversity. This study demonstrates how small numbers of amino acid changes in multiple pathway enzymes can lead to diversification of specialized metabolites in plants. It also highlights the power of a combined genetic, genomic and in vitro biochemical approach to identify the evolutionary mechanisms leading to metabolic novelty.

Plants produce large numbers of structurally diverse metabolites through multistep pathways that often use the same precursors. Here the authors utilize the pathway leading to the production of acylated sucroses in the tomato plant to illustrate how metabolite diversity can arise through biochemical pathway evolution.

Characterization of Trichome-Expressed BAHD Acyltransferases in Petunia axillaris Reveals Distinct Acylsugar Assembly Mechanisms within the Solanaceae

Acylsugars are synthesized in the glandular trichomes of the Solanaceae family and are implicated in protection against abiotic and biotic stress. Acylsugars are composed of either sucrose or glucose esterified with varying numbers of acyl chains of differing length. In tomato (Solanum lycopersicum), acylsugar assembly requires four acylsugar acyltransferases (ASATs) of the BAHD superfamily. Tomato ASATs catalyze the sequential esterification of acyl-coenzyme A thioesters to the R4, R3, R3', and R2 positions of sucrose, yielding a tetra-acylsucrose. Petunia spp. synthesize acylsugars that are structurally distinct from those of tomato. To explore the mechanisms underlying this chemical diversity, a Petuniaaxillaris transcriptome was mined for trichome preferentially expressed BAHDs. A combination of phylogenetic analyses, gene silencing, and biochemical analyses coupled with structural elucidation of metabolites revealed that acylsugar assembly is not conserved between tomato and petunia. In P. axillaris, tetra-acylsucrose assembly occurs through the action of four ASATs, which catalyze sequential addition of acyl groups to the R2, R4, R3, and R6 positions. Notably, in P. axillaris, PaxASAT1 and PaxASAT4 catalyze the acylation of the R2 and R6 positions of sucrose, respectively, and no clear orthologs exist in tomato. Similarly, petunia acylsugars lack an acyl group at the R3' position, and congruently, an ortholog of SlASAT3, which catalyzes acylation at the R3' position in tomato, is absent in P. axillaris Furthermore, where putative orthologous relationships of ASATs are predicted between tomato and petunia, these are not supported by biochemical assays. Overall, these data demonstrate the considerable evolutionary plasticity of acylsugar biosynthesis.

Evolutionary routes to biochemical innovation revealed by integrative analysis of a plant-defense related specialized metabolic pathway

The diversity of life on Earth is a result of continual innovations in molecular networks influencing morphology and physiology. Plant specialized metabolism produces hundreds of thousands of compounds, offering striking examples of these innovations. To understand how this novelty is generated, we investigated the evolution of the Solanaceae family-specific, trichome-localized acylsugar biosynthetic pathway using a combination of mass spectrometry, RNA-seq, enzyme assays, RNAi and phylogenomics in different non-model species. Our results reveal hundreds of acylsugars produced across the Solanaceae family and even within a single plant, built on simple sugar cores. The relatively short biosynthetic pathway experienced repeated cycles of innovation over the last 100 million years that include gene duplication and divergence, gene loss, evolution of substrate preference and promiscuity. This study provides mechanistic insights into the emergence of plant chemical novelty, and offers a template for investigating the ~300,000 non-model plant species that remain underexplored.

There are about 300,000 species of plant on Earth, which together produce over a million different small molecules called metabolites. Plants use many of these molecules to grow, to communicate with each other or to defend themselves against pests and disease. Humans have co-opted many of the same molecules as well; for example, some are important nutrients while others are active ingredients in medicines.

Many plant metabolites are found in almost all plants, but hundreds of thousands of them are more specialized and only found in small groups of related plant species. These specialized metabolites have a wide variety of structures, and are made by different enzymes working together to carry out a series of biochemical reactions.

Acylsugars are an example of a group of specialized metabolites with particularly diverse structures. These small molecules are restricted to plants in the Solanaceae family, which includes tomato and tobacco plants. Moghe et al. have now focused on acylsugars to better understand how plants produce the large diversity of chemical structures found in specialized metabolites, and how these processes have evolved over time.

An analysis of over 35 plant species from across the Solanaceae family revealed hundreds of acylsugars, with some plants accumulating 300 or more different types of these specialized metabolites. Moghe et al. then looked at the enzymes that make acylsugars from a poorly studied flowering plant called Salpiglossis sinuata, partly because it produces a large diversity of these small molecules and partly because it sits in a unique position in the Solanaceae family tree. The activities of the enzymes were confirmed both in test tubes and in plants. This suggested that many of the enzymes were “promiscuous”, meaning that they could likely use a variety of molecules as starting points for their chemical reactions. This finding could help to explain how this plant species can make such a wide variety of acylsugars. Moghe et al. also discovered that many of the enzymes that make acylsugars are encoded by genes that were originally copies of other genes and that have subsequently evolved new activities.

Plant scientists and plant breeders value tomato plants that produce acylsugars because these natural chemicals protect against pests like whiteflies and spider mites. A clearer understanding of the diversity of acylsugars in the Solanaceae family, as well as the enzymes that make these specialized metabolites, could help efforts to breed crops that are more resistant to pests. Some of the enzymes related to those involved in acylsugar production could also help to make chemicals with pharmaceutical value. These new findings might also eventually lead to innovative ways to produce these chemicals on a large scale.

Loss of type-IV glandular trichomes is a heterochronic trait in tomato and can be reverted by promoting juvenility

Glandular trichomes are structures with widespread distribution and deep ecological significance. In the Solanum genus, type-IV glandular trichomes provide resistance to insect pests. The occurrence of these structures is, however, poorly described and controversial in cultivated tomato (Solanum lycopersicum). Optical and scanning electron microscopy were used to screen a series of well-known commercial tomato cultivars, revealing the presence of type-IV trichomes on embryonic (cotyledons) and juvenile leaves. A tomato line overexpressing the microRNA miR156, known to promote heterochronic development, and mutants affecting KNOX and CLAVATA3 genes possessed type-IV trichomes in adult leaves. A re-analysis of the Woolly (Wo) mutant, previously described as enhancing glandular trichome density, showed that this effect only occurs at the juvenile phase of vegetative development. Our results suggest the existence of at least two levels of regulation of multicellular trichome formation in tomato: one enhancing different types of trichomes, such as that controlled by the WOOLLY gene, and another dependent on developmental stage, which is fundamental for type-IV trichome formation. Their combined manipulation could represent an avenue for biotechnological engineering of trichome development in plants.

O-Acyl Sugars Protect a Wild Tobacco from Both Native Fungal Pathogens and a Specialist Herbivore

O-Acyl sugars (O-AS) are abundant trichome-specific metabolites that function as indirect defenses against herbivores of the wild tobacco Nicotiana attenuata; whether they also function as generalized direct defenses against herbivores and pathogens remains unknown. We characterized natural variation in O-AS among 26 accessions and examined their influence on two native fungal pathogens, Fusarium brachygibbosum U4 and Alternaria sp. U10, and the specialist herbivore Manduca sexta At least 15 different O-AS structures belonging to three classes were found in N. attenuata leaves. A 3-fold quantitative variation in total leaf O-AS was found among the natural accessions. Experiments with natural accessions and crosses between high- and low-O-AS accessions revealed that total O-AS levels were associated with resistance against herbivores and pathogens. Removing O-AS from the leaf surface increased M. sexta growth rate and plant fungal susceptibility. O-AS supplementation in artificial diets and germination medium reduced M. sexta growth and fungal spore germination, respectively. Finally, silencing the expression of a putative branched-chain α-ketoacid dehydrogenase E1 β-subunit-encoding gene (NaBCKDE1B) in the trichomes reduced total leaf O-AS by 20% to 30% and increased susceptibility to Fusarium pathogens. We conclude that O-AS function as direct defenses to protect plants from attack by both native pathogenic fungi and a specialist herbivore and infer that their diversification is likely shaped by the functional interactions among these biotic stresses.

Multi-Omics of Tomato Glandular Trichomes Reveals Distinct Features of Central Carbon Metabolism Supporting High Productivity of Specialized Metabolites

Glandular trichomes are metabolic cell factories with the capacity to produce large quantities of secondary metabolites. Little is known about the connection between central carbon metabolism and metabolic productivity for secondary metabolites in glandular trichomes. To address this gap in our knowledge, we performed comparative metabolomics, transcriptomics, proteomics, and ¹³C-labeling of type VI glandular trichomes and leaves from a cultivated (Solanum lycopersicum LA4024) and a wild (Solanum habrochaites LA1777) tomato accession. Specific features of glandular trichomes that drive the formation of secondary metabolites could be identified. Tomato type VI trichomes are photosynthetic but acquire their carbon essentially from leaf sucrose. The energy and reducing power from photosynthesis are used to support the biosynthesis of secondary metabolites, while the comparatively reduced Calvin-Benson-Bassham cycle activity may be involved in recycling metabolic CO₂ Glandular trichomes cope with oxidative stress by producing high levels of polyunsaturated fatty acids, oxylipins, and glutathione. Finally, distinct mechanisms are present in glandular trichomes to increase the supply of precursors for the isoprenoid pathways. Particularly, the citrate-malate shuttle supplies cytosolic acetyl-CoA and plastidic glycolysis and malic enzyme support the formation of plastidic pyruvate. A model is proposed on how glandular trichomes achieve high metabolic productivity.

Cuticular hydrocarbons and sucrose esters as chemotaxonomic markers of wild and cultivated tomato species (Solanum section Lycopersicon)

The tomato (Solanum lycopersicum L.) is one of the most important vegetables worldwide. Due to the limited genetic variability, wild related species are considered as potential gene pool for breeding cultivated plants with enriched genetic basis. Taxonomic relations between tomato species at the level of single groups and taxa still remain, however, not fully resolved. Hence, in addition to already reported classification based on the morphology of the plants and molecular markers, we proposed chemotaxonomic approach to unveil some aspects of tomato taxonomy. Cuticular hydrocarbons and surface sucrose esters (SEs) were used as chemotaxonomic markers. Classification based on the cuticular hydrocarbon profile was in good agreement with other taxonomic studies as long as between-species differences were taken into account. Clear separation of the common tomato and closely related species from the majority of S. pennellii accessions was obtained. In the same time, however, S. pennellii revealed broad variation: based on the results, three highly distinct types of these plants were proposed, among them one type was very similar to cultivated tomato and its relatives. Addition of SEs profiles to the dataset did not impair the classification, but clarified the position of S. pennellii. The results suggest possible hybrid origin of some of S. pennellii and wild S. lycopersicum accessions, and the approach proposed has a potential to identify such hybrid plant lines.

Natural variability in acyl moieties of sugar esters produced by certain tobacco and other Solanaceae species

A unique feature of glandular trichomes of plants in the botanical family Solanaceae is that they produce sugar esters (SE), chemicals that have been shown to possess insecticidal, antifungal, and antibacterial properties. Sugar esters of tobacco (Nicotiana tabacum) provide pest resistance, and are important flavor precursors in oriental tobacco cultivars. Acyl moieties of SEs in Nicotiana spp., petunia, and tomato are shown to vary with respect to carbon length and isomer structure (2-12 carbon chain length; anteiso-, iso-, and straight-chain). Sugar esters and their acyl groups could serve as a model to explore the basis of phenotypic diversity and adaptation to natural and agricultural environments. However, information on the diversity of acyl composition among species, cultivars, and accessions is lacking. Herein, described is the analysis of SE acyl groups found in 21 accessions of Nicotiana obtusifolia (desert tobacco), six of Nicotiana occidentalis subsp. hesperis, three of Nicotiana alata, two of N. occidentalis, four modern tobacco cultivars, five petunia hybrids, and one accession each of a primitive potato (Solanum berthaultii) and tomato (Solanum pennellii). A total of 20 different acyl groups was observed that were represented differently among cultivars, species, and accessions. In Nicotiana species, acetate and iso- and anteiso-branched acids prevailed. Straight-chain groups (2-8 carbons) were prominent in petunias, while octanoic acid was prominent in N. alata and N. × sanderae. Two unexpected acyl groups, 8-methyl nonanoate and decanoate were found in N. occidentalis subsp. hesperis. Longer chain groups were found in the petunia, tomato, and potato species studied.

Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies

The identification of metabolites by mass spectrometry constitutes a major bottleneck which considerably limits the throughput of metabolomics studies in biomedical or plant research. Here, we present a novel approach to analyze metabolomics data from untargeted, data-independent LC-MS/MS measurements. By integrated analysis of MS(1) abundances and MS/MS spectra, the identification of regulated metabolite families is achieved. This approach offers a global view on metabolic regulation in comparative metabolomics. We implemented our approach in the web application "MetFamily", which is freely available at http://msbi.ipb-halle.de/MetFamily/ . MetFamily provides a dynamic link between the patterns based on MS(1)-signal intensity and the corresponding structural similarity at the MS/MS level. Structurally related metabolites are annotated as metabolite families based on a hierarchical cluster analysis of measured MS/MS spectra. Joint examination with principal component analysis of MS(1) patterns, where this annotation is preserved in the loadings, facilitates the interpretation of comparative metabolomics data at the level of metabolite families. As a proof of concept, we identified two trichome-specific metabolite families from wild-type tomato Solanum habrochaites LA1777 in a fully unsupervised manner and validated our findings based on earlier publications and with NMR.

Comparative Biochemistry and In Vitro Pathway Reconstruction as Powerful Partners in Studies of Metabolic Diversity

There are estimated to be >300,000 plant species, producing >200,000 metabolites. Many of these metabolites are restricted to specific plant lineages and are referred to as "specialized" metabolites. These serve varied functions in plants including defense against biotic and abiotic stresses, plant-plant and plant-microbe communication, and pollinator attraction. These compounds also have important applications in agriculture, medicine, skin care, and in diverse aspects of human culture. The specialized metabolic repertoire of plants can vary even within and between closely related species, in terms of the number and classes of specialized metabolites as well as their structural variants. This phenotypic variation can be exploited to discover the underlying variation in the metabolic enzymes. We describe approaches for using the diversity of specialized metabolites and variation in enzyme structure and function to identify novel enzymatic activities and understand the structural basis for these differences. The knowledge obtained from these studies will provide new modules for the synthetic biology toolbox.

Acylsugar Acylhydrolases: Carboxylesterase-Catalyzed Hydrolysis of Acylsugars in Tomato Trichomes

Glandular trichomes of cultivated tomato (Solanum lycopersicum) and many other species throughout the Solanaceae produce and secrete mixtures of sugar esters (acylsugars) on the plant aerial surfaces. In wild and cultivated tomato, these metabolites consist of a sugar backbone, typically glucose or sucrose, and two to five acyl chains esterified to various positions on the sugar core. The aliphatic acyl chains vary in length and branching and are transferred to the sugar by a series of reactions catalyzed by acylsugar acyltransferases. A phenotypic screen of a set of S. lycopersicum M82 × Solanum pennellii LA0716 introgression lines identified a dominant genetic locus on chromosome 5 from the wild relative that affected total acylsugar levels. Genetic mapping revealed that the reduction in acylsugar levels was consistent with the presence and increased expression of two S. pennellii genes (Sopen05g030120 and Sopen05g030130) encoding putative carboxylesterase enzymes of the α/β-hydrolase superfamily. These two enzymes, named ACYLSUGAR ACYLHYDROLASE1 (ASH1) and ASH2, were shown to remove acyl chains from specific positions of certain types of acylsugars in vitro. A survey of related genes in M82 and LA0716 identified another trichome-expressed ASH gene on chromosome 9 (M82, Solyc09g075710; LA0716, Sopen09g030520) encoding a protein with similar activity. Characterization of the in vitro activities of the SpASH enzymes showed reduced activities with acylsugars produced by LA0716, presumably contributing to the high-level production of acylsugars in the presence of highly expressed SpASH genes.

Single-Cell Metabolite Profiling of Stalk and Glandular Cells of Intact Trichomes with Internal Electrode Capillary Pressure Probe Electrospray Ionization Mass Spectrometry

In this report, we developed the pressure probe electrospray ionization-mass spectrometry with internal electrode capillary (IEC-PPESI-MS) which enables high spatial-resolution cell sampling, precise postsampling manipulation, and high detection sensitivity. Using this technique, a comparative in situ single-cell metabolite profiling of stalk and glandular cells, the two adjacent cell types comprising a trichome unit in tomato plants (Solanum lycopersicum L.), were performed to clarify the extent of metabolic differentiation between two cell types as well as among different types of trichomes. Owing to high sensitivity of the system, less than a picoliter cell sap from a single stalk cell sufficiently yielded a number of peaks of amino acids, organic acids, carbohydrates, and flavonoids. The minimal cell sap removal from a stalk cell without severe disturbance of trichome structure enabled sequential analysis of adjacent glandular cell on the same trichome, which showed the presence of striking differences in metabolite compositions between two adjacent cell types. Comparison among different types of trichome also revealed significant variations in metabolite profiles, particularly in flavonoids and acyl sugars compositions. Some metabolites were found only in specific cell types or particular trichome types. Although extensive metabolomics analysis of glandular cells of tomato trichomes has been previously documented, this is the first report describing cell-to-cell variations in metabolite compositions of stalk and glandular cells as well as in different trichome types. Further application of this technique may provide new insights into distinct metabolism in plant cells displaying variations in shape, size, function and physicochemical properties.

In vitro reconstruction and analysis of evolutionary variation of the tomato acylsucrose metabolic network

Plant glandular secreting trichomes are epidermal protuberances that produce structurally diverse specialized metabolites, including medically important compounds. Trichomes of many plants in the nightshade family (Solanaceae) produce O-acylsugars, and in cultivated and wild tomatoes these are mixtures of aliphatic esters of sucrose and glucose of varying structures and quantities documented to contribute to insect defense. We characterized the first two enzymes of acylsucrose biosynthesis in the cultivated tomato Solanum lycopersicum. These are type I/IV trichome-expressed BAHD acyltransferases encoded by Solyc12g006330--or S. lycopersicum acylsucrose acyltransferase 1 (Sl-ASAT1)--and Solyc04g012020 (Sl-ASAT2). These enzymes were used--in concert with two previously identified BAHD acyltransferases--to reconstruct the entire cultivated tomato acylsucrose biosynthetic pathway in vitro using sucrose and acyl-CoA substrates. Comparative genomics and biochemical analysis of ASAT enzymes were combined with in vitro mutagenesis to identify amino acids that influence CoA ester substrate specificity and contribute to differences in types of acylsucroses that accumulate in cultivated and wild tomato species. This work demonstrates the feasibility of the metabolic engineering of these insecticidal metabolites in plants and microbes.

A Feedback-Insensitive Isopropylmalate Synthase Affects Acylsugar Composition in Cultivated and Wild Tomato

Acylsugars are insecticidal specialized metabolites produced in the glandular trichomes of plants in the Solanaceae family. In the tomato clade of the Solanum genus, acylsugars consist of aliphatic acids of different chain lengths esterified to sucrose, or less frequently to glucose. Through liquid chromatography-mass spectrometry screening of introgression lines, we previously identified a region of chromosome 8 in the Solanum pennellii LA0716 genome (IL8-1/8-1-1) that causes the cultivated tomato Solanum lycopersicum to shift from producing acylsucroses with abundant 3-methylbutanoic acid acyl chains derived from leucine metabolism to 2-methylpropanoic acid acyl chains derived from valine metabolism. We describe multiple lines of evidence implicating a trichome-expressed gene from this region as playing a role in this shift. S. lycopersicum M82 SlIPMS3 (Solyc08g014230) encodes a functional end product inhibition-insensitive version of the committing enzyme of leucine biosynthesis, isopropylmalate synthase, missing the carboxyl-terminal 160 amino acids. In contrast, the S. pennellii LA0716 IPMS3 allele found in IL8-1/8-1-1 encodes a nonfunctional truncated IPMS protein. M82 transformed with an SlIPMS3 RNA interference construct exhibited an acylsugar profile similar to that of IL8-1-1, whereas the expression of SlIPMS3 in IL8-1-1 partially restored the M82 acylsugar phenotype. These IPMS3 alleles are polymorphic in 14 S. pennellii accessions spread throughout the geographical range of occurrence for this species and are associated with acylsugars containing varying amounts of 2-methylpropanoic acid and 3-methylbutanoic acid acyl chains.

Integrative Approaches to Enhance Understanding of Plant Metabolic Pathway Structure and Regulation

Huge insight into molecular mechanisms and biological network coordination have been achieved following the application of various profiling technologies. Our knowledge of how the different molecular entities of the cell interact with one another suggests that, nevertheless, integration of data from different techniques could drive a more comprehensive understanding of the data emanating from different techniques. Here, we provide an overview of how such data integration is being used to aid the understanding of metabolic pathway structure and regulation. We choose to focus on the pairwise integration of large-scale metabolite data with that of the transcriptomic, proteomics, whole-genome sequence, growth- and yield-associated phenotypes, and archival functional genomic data sets. In doing so, we attempt to provide an update on approaches that integrate data obtained at different levels to reach a better understanding of either single gene function or metabolic pathway structure and regulation within the context of a broader biological process.

Metabolomics-Inspired Insight into Developmental, Environmental and Genetic Aspects of Tomato Fruit Chemical Composition and Quality

Tomato was one of the first plant species to be evaluated using metabolomics and remains one of the best characterized, with tomato fruit being both an important source of nutrition in the human diet and a valuable model system for the development of fleshy fruits. Additionally, given the broad habitat range of members of the tomato clade and the extensive use of exotic germplasm in tomato genetic research, it represents an excellent genetic model system for understanding both metabolism per se and the importance of various metabolites in conferring stress tolerance. This review summarizes technical approaches used to characterize the tomato metabolome to date and details insights into metabolic pathway structure and regulation that have been obtained via analysis of tissue samples taken under different developmental or environmental circumstance as well as following genetic perturbation. Particular attention is paid to compounds of importance for nutrition or the shelf-life of tomatoes. We propose furthermore how metabolomics information can be coupled to the burgeoning wealth of genome sequence data from the tomato clade to enhance further our understanding of (i) the shifts in metabolic regulation occurring during development and (ii) specialization of metabolism within the tomato clade as a consequence of either adaptive evolution or domestication.

Metabolomic analysis of wild and transgenic Nicotiana langsdorffii plants exposed to abiotic stresses: unraveling metabolic responses

Nicotiana langsdorffii plants, wild and transgenic for the Agrobacterium rhizogenes rol C gene and the rat glucocorticoid receptor (GR) gene, were exposed to different abiotic stresses (high temperature, water deficit, and high chromium concentrations). An untargeted metabolomic analysis was carried out in order to investigate the metabolic effects of the inserted genes in response to the applied stresses and to obtain a comprehensive profiling of metabolites induced during abiotic stresses. High-performance liquid chromatography separation (HPLC) coupled to high-resolution mass spectrometry (HRMS) enabled the identification of more than 200 metabolites, and statistical analysis highlighted the most relevant compounds for each plant treatment. The plants exposed to heat stress showed a unique set of induced secondary metabolites, some of which were known while others were not previously reported for this kind of stress; significant changes were observed especially in lipid composition. The role of trichome, as a protection against heat stress, is here suggested by the induction of both acylsugars and glykoalkaloids. Water deficit and Cr(VI) stresses resulted mainly in enhanced antioxidant (HCAs, polyamine) levels and in the damage of lipids, probably as a consequence of reactive oxygen species (ROS) production. Moreover, the ability of rol C expression to prevent oxidative burst was confirmed. The results highlighted a clear influence of GR modification on plant stress response, especially to water deficiency-a phenomenon whose applications should be further investigated. This study provides new insights into the field of system biology and demonstrates the importance of metabolomics in the study of plant functioning. Graphical Abstract Untargeted metabolomic analysis was applied to wild type, GR and RolC modified Nicotiana Langsdorffii plants exposed to heat, water and Cr(VI) stresses. The key metabolites, highly affected by stress application, were identified, allowing to outline the main metabolic responses to stress in each plant genotype.

Functionally divergent alleles and duplicated Loci encoding an acyltransferase contribute to acylsugar metabolite diversity in Solanum trichomes

Glandular trichomes from tomato (Solanum lycopersicum) and other species in the Solanaceae produce and secrete a mixture of O-acylsugars (aliphatic esters of sucrose and glucose) that contribute to insect defense. Despite their phylogenetic distribution and diversity, relatively little is known about how these specialized metabolites are synthesized. Mass spectrometric profiling of acylsugars in the S. lycopersicum x Solanum pennellii introgression lines identified a chromosome 11 locus containing a cluster of BAHD acyltransferases with one gene (named Sl-ASAT3) expressed in tip cells of type I trichomes where acylsugars are made. Sl-ASAT3 was shown to encode an acyl-CoA-dependent acyltransferase that catalyzes the transfer of short (four to five carbons) branched acyl chains to the furanose ring of di-acylsucrose acceptors to produce tri-acylsucroses, which can be further acetylated by Sl-ASAT4 (previously Sl-AT2). Among the wild tomatoes, diversity in furanose ring acyl chains on acylsucroses was most striking in Solanum habrochaites. S. habrochaites accessions from Ecuador and northern Peru produced acylsucroses with short (≤C5) or no acyl chains on the furanose ring. Accessions from central and southern Peru had the ability to add short or long (up to C12) acyl chains to the furanose ring. Multiple ASAT3-like sequences were found in most accessions, and their in vitro activities correlated with observed geographical diversity in acylsugar profiles.

Dependence of negative-mode electrospray ionization response factors on mobile phase composition and molecular structure for newly-authenticated neutral acylsucrose metabolites

Amounts of newly-purified acylsugars were authenticated by saponification and stable isotope dilution UHPLC/MS/MS; acylsugar electrospray ionization response factors were determined.