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

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.

Tomato root specialized metabolites evolved through gene duplication and regulatory divergence within a biosynthetic gene cluster

Tremendous plant metabolic diversity arises from phylogenetically restricted specialized metabolic pathways. Specialized metabolites are synthesized in dedicated cells or tissues, with pathway genes sometimes colocalizing in biosynthetic gene clusters (BGCs). However, the mechanisms by which spatial expression patterns arise and the role of BGCs in pathway evolution remain underappreciated. In this study, we investigated the mechanisms driving acylsugar evolution in the Solanaceae. Previously thought to be restricted to glandular trichomes, acylsugars were recently found in cultivated tomato roots. We demonstrated that acylsugars in cultivated tomato roots and trichomes have different sugar cores, identified root-enriched paralogs of trichome acylsugar pathway genes, and characterized a key paralog required for root acylsugar biosynthesis, SlASAT1-LIKE (SlASAT1-L), which is nested within a previously reported trichome acylsugar BGC. Last, we provided evidence that ASAT1-L arose through duplication of its paralog, ASAT1, and was trichome-expressed before acquiring root-specific expression in the Solanum genus. Our results illuminate the genomic context and molecular mechanisms underpinning metabolic diversity in plants.

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.

The amount and chemistry of acylsugars affects sweetpotato whitefly (Bemisia tabaci) oviposition and development, and tomato yellow leaf curl virus incidence, in field grown tomato plants

The objectives of this study were to ascertain the impact of endogenous production of trichome-exuded acylsugars on insects and insect transmitted virus by evaluating tomato lines and their hybrids bred for acylsugar production under field settings on whiteflies and the whitefly-transmitted tomato yellow leaf curl virus. Specifically, we utilized a diverse array of tomato lines and hybrids bred for changes in acylsugar amount or type, grown in three field trials under natural whitefly and virus pressure, to investigate whether the amount of accumulated acylsugars and or the chemical profile of the acylsugars were associated with greater resistance to whiteflies and reduced incidence of tomato yellow leaf curl virus. There was considerable variation in the abundance of whitefly eggs and nymphs and incidence of tomato yellow leaf curl virus across experiments and between entries. Increasing amount of acylsugars accumulated by the tomato entries was associated with a reduction in the abundance of whitefly eggs and nymphs and a reduction in the incidence of tomato yellow leaf curl virus. Additionally, we identified lines with changes in several acylsugar fatty acids that were associated with decreased abundance of whitefly eggs and nymphs and reduced incidence of tomato yellow leaf curl virus. These results inform the utility of acylsugars as a host plant defense system for improving resistance to whiteflies and their transmitted viruses, with potential for reducing insecticides as a control method for whiteflies and provide breeding targets for optimization of existing acylsugar tomato lines to create lines with the most efficacious amount and chemistry of acylsugars.

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.

Acylsugar-mediated resistance as part of a multilayered defense against thrips, orthotospoviruses, and beyond

Resistant varieties are critical tools for crop production, and single-resistance genes providing strong protection against pests or pathogens are deployed in agriculture. Durability of these traits is threatened by emergence of resistance-breaking pests and pathogens. This review focuses on acylsugar-mediated resistance in tomato. Wild tomatoes have type-IV trichomes that exude chemically complex mixtures of acylsugars altering behavior and suppressing multiple pest species, and with thrips and whiteflies (WF), suppressing virus transmission, for example, Tomato spotted wilt orthotospovirus and Tomato yellow leaf curl virus, respectively. Marker-assisted selection and bioassays led to development of advanced cultivated tomato breeding lines rich in acylsugar variations, allowing acylsugar-mediated resistance to be combined with other resistance traits providing a layered defense system that reduces pest populations and virus disease prevalence. This strategy also holds promise for enhancing durability of virus resistance genes by reducing the intensity of selection for resistance-breaking variants.

Specialized metabolism by trichome-enriched Rubisco and fatty acid synthase components

Acylsugars, specialized metabolites with defense activities, are secreted by trichomes of many solanaceous plants. Several acylsugar metabolic genes (AMGs) remain unknown. We previously reported multiple candidate AMGs. Here, using multiple approaches, we characterized additional AMGs. First, we identified differentially expressed genes between high- and low-acylsugar-producing F2 plants derived from a cross between cultivated tomato (Solanum lycopersicum) and a wild relative (Solanum pennellii), which produce acylsugars that are ∼1% and ∼20% of leaf dry weight, respectively. Expression levels of many known and candidate AMGs positively correlated with acylsugar amounts in F2 individuals. Next, we identified lycopersicum-pennellii putative orthologs with higher nonsynonymous to synonymous substitutions. These analyses identified four candidate genes, three of which showed enriched expression in stem trichomes compared to underlying tissues (shaved stems). Virus-induced gene silencing confirmed two candidates, Sopen05g009610 [beta-ketoacyl-(acyl-carrier-protein) reductase; fatty acid synthase component] and Sopen07g006810 (Rubisco small subunit), as AMGs. Phylogenetic analysis indicated that Sopen05g009610 is distinct from specialized metabolic cytosolic reductases but closely related to two capsaicinoid biosynthetic reductases, suggesting evolutionary relationship between acylsugar and capsaicinoid biosynthesis. Analysis of publicly available datasets revealed enriched expression of Sopen05g009610 orthologs in trichomes of several acylsugar-producing species. Similarly, orthologs of Sopen07g006810 were identified as solanaceous trichome-enriched members, which form a phylogenetic clade distinct from those of mesophyll-expressed "regular" Rubisco small subunits. Furthermore, δ13C analyses indicated recycling of metabolic CO2 into acylsugars by Sopen07g006810 and showed how trichomes support high levels of specialized metabolite production. These findings have implications for genetic manipulation of trichome-specialized metabolism in solanaceous crops.

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 genetic variation in the HAIRS ABSENT (H) gene increases type-VI glandular trichomes in both wild and domesticated tomatoes

Glandular trichomes produce and exude secondary metabolites, conferring insect resistance in many crop species. Whereas some of its wild relatives are insect-resistant, tomato (Solanum lycopersicum) is not. Identifying the genetic changes that altered trichome development and biochemistry during tomato domestication would contribute to breeding for insect resistance. A mutation in the HAIRS ABSENT (H) gene, which encodes a C2H2 zinc finger protein (ZFP8), leads to reduced trichome density. Several geographic accessions of S. pimpinellifolium, the wild ancestor of domesticated tomato, have glabrous organs that resemble the phenotype caused by h. Here, we investigated allelic diversity for H in tomato and S. pimpinellifolium accessions and their associated trichome phenotypes. We also evaluated how the developmental stage can affect trichome development in glabrous and non-glabrous plants. We found that glabrous accessions of S. pimpinellifolium have different ZFP8 nucleotide sequence changes, associated with altered trichome development and density. We also found that while the glabrous appearance of h mutants is caused by a lower density of long trichomes, the density of type-VI glandular trichomes is increased, particularly in the adult stages of plant development. These insights on the genetic control of trichome development may contribute to breeding for insect resistance in tomatoes and other crops.

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.

Functions and biosynthesis of plant signaling metabolites mediating plant-microbe interactions

Covering: 2015-2022Plants and microbes have coevolved since their appearance, and their interactions, to some extent, define plant health. A reasonable fraction of small molecules plants produced are involved in mediating plant-microbe interactions, yet their functions and biosynthesis remain fragmented. The identification of these compounds and their biosynthetic genes will open up avenues for plant fitness improvement by manipulating metabolite-mediated plant-microbe interactions. Herein, we integrate the current knowledge on their chemical structures, bioactivities, and biosynthesis with the view of providing a high-level overview on their biosynthetic origins and evolutionary trajectory, and pinpointing the yet unknown and key enzymatic steps in diverse biosynthetic pathways. We further discuss the theoretical basis and prospects for directing plant signaling metabolite biosynthesis for microbe-aided plant health improvement in the future.

Tomato ARPC1 regulates trichome morphology and density and terpene biosynthesis

Based on transcriptomic analysis of wild-type and mutant tomato plants, ARPC1 was found to be important for trichome formation and development and it plays a key role in terpene synthesis. Trichomes are protruding epidermal cells in plant species. They function as the first defense layer against biotic and abiotic stresses. Despite the essential role of tomato trichomes in defense against herbivores, the understanding of their development is still incomplete. Therefore, the aim of this study was to identify genes involved in trichome formation and morphology and terpene synthesis, using transcriptomic techniques. To achieve this, we examined leaf morphology and compared the expression levels of some putative genes involved in trichome formation between wild-type (WT) and hairless-3 (hl-3) tomato mutant. The hl-3 plants displayed swollen and distorted trichomes and reduced trichome density (type I and IV) and terpene synthesis compared with that of the WT plants. Gene expression analysis showed that Actin-Related Protein Component1 (ARPC1) was expressed more highly in the WT than in the hl-3 mutant, indicating its critical role in trichome morphology and density. Additionally, the expression of MYC1 and several terpene synthase genes (TPS9, 12, 20), which are involved in type VI trichome initiation and terpene synthesis, was lower in the hl-3 mutant than in the WT plants. Moreover, transformation of the hl-3 mutant with WT ARPC1 restored normal trichome structure and density, and terpene synthesis. Structural and amino acid sequence analysis showed that there was a missplicing mutation in the hl-3 mutant, which was responsible for the abnormal trichome structure and density, and impaired terpene synthesis. Overall, the findings of this study demonstrated that ARPC1 is involved in regulating trichome structure and terpene synthesis in tomato.

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.

Characterization of trichome-specific BAHD acyltransferases involved in acylsugar biosynthesis in Nicotiana tabacum

Glandular trichomes of tobacco (Nicotiana tabacum) produce blends of acylsucroses that contribute to defence against pathogens and herbivorous insects, but the mechanism of assembly of these acylsugars has not yet been determined. In this study, we isolated and characterized two trichome-specific acylsugar acyltransferases that are localized in the endoplasmic reticulum, NtASAT1 and NtASAT2. They sequentially catalyse two additive steps of acyl donors to sucrose to produce di-acylsucrose. Knocking out of NtASAT1 or NtASAT2 resulted in deficiency of acylsucrose; however, there was no effect on acylsugar accumulation in plants overexpressing NtASAT1 or NtASAT2. Genomic analysis and profiling revealed that NtASATs originated from the T subgenome, which is derived from the acylsugar-producing diploid ancestor N. tomentosiformis. Our identification of NtASAT1 and NtASAT2 as enzymes involved in acylsugar assembly in tobacco potentially provides a new approach and target genes for improving crop resistance against pathogens and insects.

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.

An efficient LC-MS method for isomer separation and detection of sugars, phosphorylated sugars, and organic acids

Assessing central carbon metabolism in plants can be challenging due to the dynamic range in pool sizes, with low levels of important phosphorylated sugars relative to more abundant sugars and organic acids. Here, we report a sensitive liquid chromatography-mass spectrometry method for analysing central metabolites on a hybrid column, where both anion-exchange and hydrophilic interaction chromatography (HILIC) ligands are embedded in the stationary phase. The liquid chromatography method was developed for enhanced selectivity of 27 central metabolites in a single run with sensitivity at femtomole levels observed for most phosphorylated sugars. The method resolved phosphorylated hexose, pentose, and triose isomers that are otherwise challenging. Compared with a standard HILIC approach, these metabolites had improved peak areas using our approach due to ion enhancement or low ion suppression in the biological sample matrix. The approach was applied to investigate metabolism in high lipid-producing tobacco leaves that exhibited increased levels of acetyl-CoA, a precursor for oil biosynthesis. The application of the method to isotopologue detection and quantification was considered through evaluating 13C-labeled seeds from Camelina sativa. The method provides a means to analyse intermediates more comprehensively in central metabolism of plant tissues.

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.

H and HL synergistically regulate jasmonate-triggered trichome formation in tomato

The development of trichomes, which protect plants against herbivores, is affected by various stresses. In tomato, previous studies showed that stress triggered JA signaling influences trichome formation, but the underlying mechanism is not fully resolved. Here, we found two C2H2 zinc finger proteins synergistically regulate JA-induced trichome formation in tomato. The naturally occurring mutations in H and its close homolog H-like gene in a spontaneous mutant, LA3172 cause severely affected trcihome development. Compared with respective single mutant, h/hl double mutant displayed more severe trichome defects in all tissues. Despite the partially redundant function, H and HL genes regulate the trichome formation in the spatially distinct manner, with HL more involved in hypocotyls and leaves, while H more involved in stems and sepals. Furthermore，the activity of H/HL is essential for JA-triggered trichome formation. JA signaling inhibitor SlJAZ2 represses the activity of H and HL via physical interaction, resulting in the activation of THM1, a negative regulator of trichome formation. Our results provide novel insight into the mechanism of the trichome formation in response to stress induced JA signaling in tomato.

The metabolic changes that effect fruit quality during tomato fruit ripening

As the most valuable organ of tomato plants, fruit has attracted considerable attention which most focus on its quality formation during the ripening process. A considerable amount of research has reported that fruit quality is affected by metabolic shifts which are under the coordinated regulation of both structural genes and transcriptional regulators. In recent years, with the development of the next generation sequencing, molecular and genetic analysis methods, lots of genes which are involved in the chlorophyll, carotenoid, cell wall, central and secondary metabolism have been identified and confirmed to regulate pigment contents, fruit softening and other aspects of fruit flavor quality. Here, both research concerning the dissection of fruit quality related metabolic changes, the transcriptional and post-translational regulation of these metabolic pathways are reviewed. Furthermore, a weighted gene correlation network analysis of representative genes of fruit quality has been carried out and the potential of the combined application of the gene correlation network analysis, fine-mapping strategies and next generation sequencing to identify novel candidate genes determinants of fruit quality is discussed.

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.

Characterization of the detrimental effects of type IV glandular trichomes on the aphid Macrosiphum euphorbiae in tomato

BACKGROUND

Glandular trichomes are essential in plants' defence against pests however, the mechanisms of action are not completely understood. While there is considerable evidence of feeding and movement impairment by trichomes, the effect on other traits is less clear. We combined laboratory and greenhouse experiments with molecular analysis to understand how glandular trichomes affect the behavior, population growth, and the expression of biomarkers involved in detoxification, primary metabolism, and developmental pathways of the aphid Macrosiphum euphorbiae. We used two isogenic tomato lines that differ in the presence of type IV glandular trichomes and production of acylsucroses; i.e.,Solanum lycopersicum cv. 'Moneymaker' and an introgressed line from Solanum pimpinellifolium (with trichomes type IV).

RESULTS

Type IV glandular trichomes affected host selection and aphid proliferation with aphids avoiding, and showing impaired multiplication on the genotype with trichomes. The exposure to type IV glandular trichomes resulted in the overexpression of detoxication markers (i.e., Hsp70, Hsp17, Hsp10); the repression of the energetic metabolism (GAPDH), and the activation of the ecdysone pathway; all these, underlying the key adaptations and metabolic trade-offs in aphids exposed to glandular trichomes.

CONCLUSION

Our results demonstrate the detrimental effect of glandular trichomes (type IV) on the aphid and put forward their mode of action. Given the prevalence of glandular trichomes in wild and cultivated Solanaceae; and of the investigated molecular biomarkers in insects in general, our results provide relevant mechanisms to understand the effect of trichomes not only on herbivorous insects but also on other trophic levels.

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.

Ancestral sequence reconstruction - An underused approach to understand the evolution of gene function in plants?

Whilst substantial research effort has been placed on understanding the interactions of plant proteins with their molecular partners, relatively few studies in plants - by contrast to work in other organisms - address how these interactions evolve. It is thought that ancestral proteins were more promiscuous than modern proteins and that specificity often evolved following gene duplication and subsequent functional refining. However, ancestral protein resurrection studies have found that some modern proteins have evolved de novo from ancestors lacking those functions. Intriguingly, the new interactions evolved as a consequence of just a few mutations and, as such, acquisition of new functions appears to be neither difficult nor rare, however, only a few of them are incorporated into biological processes before they are lost to subsequent mutations. Here, we detail the approach of ancestral sequence reconstruction (ASR), providing a primer to reconstruct the sequence of an ancestral gene. We will present case studies from a range of different eukaryotes before discussing the few instances where ancestral reconstructions have been used in plants. As ASR is used to dig into the remote evolutionary past, we will also present some alternative genetic approaches to investigate molecular evolution on shorter timescales. We argue that the study of plant secondary metabolism is particularly well suited for ancestral reconstruction studies. Indeed, its ancient evolutionary roots and highly diverse landscape provide an ideal context in which to address the focal issue around the emergence of evolutionary novelties and how this affects the chemical diversification of plant metabolism.

A single cytochrome P450 oxidase from Solanum habrochaites sequentially oxidizes 7-epi-zingiberene to derivatives toxic to whiteflies and various microorganisms

Secretions from glandular trichomes potentially protect plants against a variety of aggressors. In the tomato clade of the Solanum genus, glandular trichomes of wild species produce a rich source of chemical diversity at the leaf surface. Previously, 7-epi-zingiberene produced in several accessions of Solanum habrochaites was found to confer resistance to whiteflies (Bemisia tabaci) and other insect pests. Here, we report the identification and characterisation of 9-hydroxy-zingiberene (9HZ) and 9-hydroxy-10,11-epoxyzingiberene (9H10epoZ), two derivatives of 7-epi-zingiberene produced in glandular trichomes of S. habrochaites LA2167. Using a combination of transcriptomics and genetics, we identified a gene coding for a cytochrome P450 oxygenase, ShCYP71D184, that is highly expressed in trichomes and co-segregates with the presence of the zingiberene derivatives. Transient expression assays in Nicotiana benthamiana showed that ShCYP71D184 carries out two successive oxidations to generate 9HZ and 9H10epoZ. Bioactivity assays showed that 9-hydroxy-10,11-epoxyzingiberene in particular exhibits substantial toxicity against B. tabaci and various microorganisms including Phytophthora infestans and Botrytis cinerea. Our work shows that trichome secretions from wild tomato species can provide protection against a wide variety of organisms. In addition, the availability of the genes encoding the enzymes for the pathway of 7-epi-zingiberene derivatives makes it possible to introduce this trait in cultivated tomato by precision breeding.

Mediation of JA signalling in glandular trichomes by the woolly/SlMYC1 regulatory module improves pest resistance in tomato

Almost all plants form trichomes, which protect them against insect herbivores by forming a physical barrier and releasing chemical repellents. Glandular trichomes produce a variety of specialized defensive metabolites, including volatile terpenes. Previous studies have shown that the defence hormone jasmonic acid (JA) affects trichome development and induces terpene synthases (TPSs) but the underlying molecular mechanisms remain unclear. Here, we characterized a loss-of-function allele of the HD-ZIP IV transcription factor woolly (wo) and analysed its role in mediating JA signalling in tomato. We showed that knockout of wo led to extensive trichome defects, including structural and functional changes in type VI glandular trichomes, and a dramatic reduction in terpene levels. We further found that wo directly binds to TPS gene promoters to recruit SlMYC1, a JA signalling modulator, and that together these transcription factors promote terpene biosynthesis in tomato trichomes. The wo/SlMYC1 regulatory module is inhibited by SlJAZ2 through a competitive binding mechanism, resulting in a fine-tuned JA response in tomato trichomes. Enhanced expression of SlMYC1 substantially increased terpene levels and improved tomato resistance to spider mites. Interestingly, we also found that SlMYC1 plays an additional role in glandular cell division and expansion in type VI trichomes, independent of JA. Together, our results reveal a novel, JA-mediated regulatory mechanism that promotes insect resistance in tomato.

Integrative Metabolomic and Transcriptomic Analyses Reveal Metabolic Changes and Its Molecular Basis in Rice Mutants of the Strigolactone Pathway

Plants have evolved many metabolites to meet the demands of growth and adaptation. Although strigolactones (SLs) play vital roles in controlling plant architecture, their function in regulating plant metabolism remains elusive. Here we report the integrative metabolomic and transcriptomic analyses of two rice SL mutants, d10 (a biosynthesis mutant) and d14 (a perception mutant). Both mutants displayed a series of metabolic and transcriptional alterations, especially in the lipid, flavonoid, and terpenoid pathways. Levels of several diterpenoid phytoalexins were substantially increased in d10 and d14, together with the induction of terpenoid gene cluster and the corresponding upstream transcription factor WRKY45, an established determinant of plant immunity. The fact that WRKY45 is a target of IPA1, which acted as a downstream transcription factor of SL signaling, suggests that SLs contribute to plant defense through WRKY45 and phytoalexins. Moreover, our data indicated that SLs may modulate rice metabolism through a vast number of clustered or tandemly duplicated genes. Our work revealed a central role of SLs in rice metabolism. Meanwhile, integrative analysis of the metabolome and transcriptome also suggested that SLs may contribute to metabolite-associated growth and defense.

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.

Two BAHD Acyltransferases Catalyze the Last Step in the Shikonin/Alkannin Biosynthetic Pathway

Several Boraginaceae plants produce biologically active red naphthoquinone pigments, derivatives of the enantiomers shikonin and alkannin, which vary in acyl groups on their side chains. Compositions of shikonin/alkannin derivatives vary in plant species, but the mechanisms generating the diversity of shikonin/alkannin derivatives are largely unknown. This study describes the identification and characterization of two BAHD acyltransferases, shikonin O-acyltransferase (LeSAT1) and alkannin O-acyltransferase (LeAAT1), from Lithospermum erythrorhizon, a medicinal plant in the family Boraginaceae that primarily produces the shikonin/alkannin derivatives acetylshikonin and β-hydroxyisovalerylshikonin. Enzyme assays using Escherichia coli showed that the acylation activity of LeSAT1 was specific to shikonin, whereas the acylation activity of LeAAT1 was specific to alkannin. Both enzymes recognized acetyl-CoA, isobutyryl-CoA, and isovaleryl-CoA as acyl donors to produce their corresponding shikonin/alkannin derivatives, with both enzymes showing the highest activity for acetyl-CoA. These findings were consistent with the composition of shikonin/alkannin derivatives in intact L erythrorhizon plants and cell cultures. Genes encoding both enzymes were preferentially expressed in the roots and cell cultures in the dark in pigment production medium M9, conditions associated with shikonin/alkannin production. These results indicated that LeSAT1 and LeAAT1 are enantiomer-specific acyltransferases that generate various shikonin/alkannin derivatives.

The trichome-specific acetolactate synthase NtALS1 gene, is involved in acylsugar biosynthesis in tobacco (Nicotiana tabacum L.)

MAIN CONCLUSION

NtALS1 is specifically expressed in glandular trichomes, and can improve the content of acylsugars in tobacco.

ABTRACT

The glandular trichomes of many species in the Solanaceae family play an important role in plant defense. These epidermal outgrowths exhibit specialized secondary metabolism, including the production of structurally diverse acylsugars that function in defense against insects and have substantial developmental potential for commercial uses. However, our current understanding of genes involved in acyl chain biosynthesis of acylsugars remains poor in tobacco. In this study, we identified three acetolactate synthase (ALS) genes in tobacco through homology-based gene prediction using Arabidopsis ALS. Quantitative real-time PCR (qRT-PCR) and tissue distribution analyses suggested that NtALS1 was highly expressed in the tips of glandular trichomes. Subcellular localization analysis showed that the NtALS1 localized to the chloroplast. Moreover, in the wild-type K326 variety background, we generated two ntals1 loss-of-function mutants using the CRISPR-Cas9 system. Acylsugars contents in the two ntals1 mutants were significantly lower than those in the wild type. Through phylogenetic tree analysis, we also identified NtALS1 orthologs that may be involved in acylsugar biosynthesis in other Solanaceae species. Taken together, these findings indicate a functional role for NtALS1 in acylsugar biosynthesis in tobacco.

Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity

Plants produce phylogenetically and spatially restricted, as well as structurally diverse specialized metabolites via multistep metabolic pathways. Hallmarks of specialized metabolic evolution include enzymatic promiscuity and recruitment of primary metabolic enzymes and examples of genomic clustering of pathway genes. Solanaceae glandular trichomes produce defensive acylsugars, with sidechains that vary in length across the family. We describe a tomato gene cluster on chromosome 7 involved in medium chain acylsugar accumulation due to trichome specific acyl-CoA synthetase and enoyl-CoA hydratase genes. This cluster co-localizes with a tomato steroidal alkaloid gene cluster and is syntenic to a chromosome 12 region containing another acylsugar pathway gene. We reconstructed the evolutionary events leading to this gene cluster and found that its phylogenetic distribution correlates with medium chain acylsugar accumulation across the Solanaceae. This work reveals insights into the dynamics behind gene cluster evolution and cell-type specific metabolite diversity.

Patterns of inheritance of acylsugar acyl groups in selected interspecific hybrids of genus Nicotiana

Glandular trichomes on the surface of Solanaceae species produce acyl sugars that are species-, and cultivar-specific. Acyl sugars are known to possess insecticidal, antibiotic, and hormone-like properties, and as such have great potential as a class of naturally occurring pesticides and antibiotics. The objective of this work was to analyze the acyl composition of acyl sugars in the leaf trichome exudate from selected Nicotiana species and to follow the inheritance of acyl content in their hybrids. Trichome exudates were collected, and the acyl profiles of acyl sugars were identified via GC-MS. The variations in acyl group inheritance in the hybrids (a single parent resemblance, missing, complementary, and novel groups) matched the patterns described in the literature for a variety of secondary metabolites. However, we did not find a complementation of major parental acyl groups. Instead, in some hybrids we observed a dynamic change in the proportions of acyl groups, distinguishing the acyl group profiles as novel. We observed paternal (i.e. N. tabacum cv. Turkish Samsun × N. benthamiana hybrids) and maternal (i.e. N. tabacum cv. Samsun-nn × N. otophora) inheritance patterns, novel acyl profiles (N. excelsior hybrids), and missing acyl groups (N. excelsiana). Selective inheritance of some acyl groups in the hybrids of N. benthamiana (4- and 5-methylheptanoic isomers) or N. alata (octanoate) was found. Suggestions are given to explain certain patterns of inheritance. The data presented here contribute to the body of knowledge about the effect of interspecific hybridization on the secondary metabolites by including acylsugar acyl groups that have not been studied previously.

Specialized Metabolism in a Nonmodel Nightshade: Trichome Acylinositol Biosynthesis

Plants make many biologically active, specialized metabolites, which vary in structure, biosynthesis, and the processes they influence. An increasing number of these compounds are documented to protect plants from insects, pathogens, or herbivores or to mediate interactions with beneficial organisms, including pollinators and nitrogen-fixing microbes. Acylsugars, one class of protective compounds, are made in glandular trichomes of plants across the Solanaceae family. While most described acylsugars are acylsucroses, published examples also include acylsugars with hexose cores. The South American fruit crop naranjilla (lulo; Solanum quitoense) produces acylsugars containing a myoinositol core. We identified an enzyme that acetylates triacylinositols, a function homologous to the last step in the acylsucrose biosynthetic pathway of tomato (Solanum lycopersicum). Our analysis reveals parallels between S. lycopersicum acylsucrose and S. quitoense acylinositol biosynthesis, suggesting a common evolutionary origin.

Dissection of complex traits of tomato in the post-genome era

We present the main advances of dissection of complex traits in tomato by omics, the genes identified to control complex traits and the application of CRISPR/Cas9 in tomato breeding. Complex traits are believed to be under the control of multiple genes, each with different effects and interaction with environmental factors. Advance development of sequencing and molecular technologies has enabled the recognition of the genomic structure of most organisms and the identification of a nearly limitless number of markers that have made it to accelerate the speed of QTL identification and gene cloning. Meanwhile, multiomics have been used to identify the genetic variations among different tomato species, determine the expression profiles of genes in different tissues and at distinct developmental stages, and detect metabolites in different pathways and processes. The combination of these data facilitates to reveal mechanism underlying complex traits. Moreover, mutants generated by mutagens and genome editing provide relatively rich genetic variation for deciphering the complex traits and exploiting them in tomato breeding. In this article, we present the main advances of complex trait dissection in tomato by omics since the release of the tomato genome sequence in 2012. We provide further insight into some tomato complex traits because of the causal genetic variations discovered so far and explore the utilization of CRISPR/Cas9 for the modification of tomato complex traits.

Candidate Gene Networks for Acylsugar Metabolism and Plant Defense in Wild Tomato Solanum pennellii

Many solanaceous plants secrete acylsugars, which are branched-chain and straight-chain fatty acids esterified to Glu or Suc. These compounds have important roles in plant defense and potential commercial applications. However, several acylsugar metabolic genes remain unidentified, and little is known about regulation of this pathway. Comparative transcriptomics between low- and high-acylsugar-producing accessions of Solanum pennellii revealed that expression levels of known and novel candidate genes (putatively encoding beta-ketoacyl-(acyl-carrier-protein) synthases, peroxisomal acyl-activating enzymes, ATP binding cassette (ABC) transporters, and central carbon metabolic proteins) were positively correlated with acylsugar accumulation, except two genes previously reported to be involved in acylglucose biosynthesis. Genes putatively encoding oxylipin metabolic proteins, subtilisin-like proteases, and other antimicrobial defense proteins were upregulated in low-acylsugar-producing accessions. Transcriptome analysis after biochemical inhibition of biosynthesis of branched-chain amino acids (precursors to branched-chain fatty acids) by imazapyr showed concentration-dependent downregulation of known and most acylsugar candidate genes, but not defense genes. Weighted gene correlation network analysis identified separate coexpressed gene networks for acylsugar metabolism (including six transcription factor genes and flavonoid metabolic genes) and plant defense (including genes putatively encoding NB-ARC and leucine-rich repeat sequences, protein kinases and defense signaling proteins, and previously mentioned defense proteins). Additionally, virus-induced gene silencing of two trichomes preferentially expressed candidate genes for straight-chain fatty acid biosynthesis confirmed their role in acylsugar metabolism.

Effects of High-Level Acylsugar-Producing Tomato Lines on the Development of Tomato Psyllids (Hemiptera: Triozidae)

Acylsugars have been shown to provide activity against numerous insect pests of tomatoes. Comparison of acylsugar levels in four tomato plant lines, FA7/AS, FA2/AS, CU071026, and 'Yellow Pear', found that the acylsugar contents in the elevated acylsugar lines were significantly higher than the commercial Yellow Pear (control) tomato plant line. Adult choice tests indicated that the tomato psyllid, Bactericera cockerelli, preferred to settle on the Yellow Pear and FA2/AS lines over the line with the highest content of acylsugars, FA7/AS, and the parental line, CU071026. The no-choice test demonstrated that adults laid fewer eggs on the high acylsugar tomato lines than on the control tomato line, Yellow Pear. For all high acylsugar lines, the relative growth index of the psyllid was significantly lower compared with the commercial line, indicating a reduced potential for population growth. Although some tomato psyllids completed their life cycle on the high acylsugar tomato plant lines, the percent survival of psyllids to the adult stage when developing on the high acylsugar lines was significantly less (range = 43.7-57.1%) than on the commercial tomato line (83.8%). All mortality occurred during the early stages of development (egg stage to third instar), which has implications for acquisition and transmission of Candidatus Liberibacter solanacearum, the causal agent of tomato vein greening disease. Therefore, with reduced attractiveness for tomato psyllids and significantly reduced survival, the high-acylsugar tomato plant lines have the potential to be part of an integrated pest management program for this pest.

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.

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.

Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds

INTRODUCTION

To date, most studies of natural variation and metabolite quantitative trait loci (mQTL) in tomato have focused on fruit metabolism, leaving aside the identification of genomic regions involved in the regulation of leaf metabolism.

OBJECTIVE

This study was conducted to identify leaf mQTL in tomato and to assess the association of leaf metabolites and physiological traits with the metabolite levels from other tissues.

METHODS

The analysis of components of leaf metabolism was performed by phenotypying 76 tomato ILs with chromosome segments of the wild species Solanum pennellii in the genetic background of a cultivated tomato (S. lycopersicum) variety M82. The plants were cultivated in two different environments in independent years and samples were harvested from mature leaves of non-flowering plants at the middle of the light period. The non-targeted metabolite profiling was obtained by gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). With the data set obtained in this study and already published metabolomics data from seed and fruit, we performed QTL mapping, heritability and correlation analyses.

RESULTS

Changes in metabolite contents were evident in the ILs that are potentially important with respect to stress responses and plant physiology. By analyzing the obtained data, we identified 42 positive and 76 negative mQTL involved in carbon and nitrogen metabolism.

CONCLUSIONS

Overall, these findings allowed the identification of S. lycopersicum genome regions involved in the regulation of leaf primary carbon and nitrogen metabolism, as well as the association of leaf metabolites with metabolites from seeds and fruits.

QTL mapping of insect resistance components of Solanum galapagense

QTLs for insect resistance parameters, trichome type IV development, and more than 200 non-volatile metabolites, including 76 acyl sugars, all co-locate at the end of Chromosome 2 of Solanum galapagense. Host plant resistance is gaining importance as more and more insecticides are being banned due to environmental concerns. In tomato, resistance towards insects is found in wild relatives and has been attributed to the presence of glandular trichomes and their specific phytochemical composition. In this paper, we describe the results from a large-scale QTL mapping of data from whitefly resistance tests, trichome phenotyping and a comprehensive metabolomics analysis in a recombinant inbred line population derived from a cross between the cultivated Solanum lycopersicum and the wild relative S. galapagense, which is resistant to a range of pest insects. One major QTL (Wf-1) was found to govern the resistance against two different whitefly species. This QTL co-localizes with QTLs for the presence of trichomes type IV and V, as well as all 76 acyl sugars detected and about 150 other non-volatile phytochemicals, including methyl esters of the flavonols myricetin and quercetin. Based on these results, we hypothesize that Wf-1 is regulating the formation of glandular trichome type IV on the leaf epidermis, enabling the production and accumulation of bioactive metabolites in this type of trichomes.

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.

Evolutionary Diversification of Primary Metabolism and Its Contribution to Plant Chemical Diversity

Plants produce a diverse array of lineage-specific specialized (secondary) metabolites, which are synthesized from primary metabolites. Plant specialized metabolites play crucial roles in plant adaptation as well as in human nutrition and medicine. Unlike well-documented diversification of plant specialized metabolic enzymes, primary metabolism that provides essential compounds for cellular homeostasis is under strong selection pressure and generally assumed to be conserved across the plant kingdom. Yet, some alterations in primary metabolic pathways have been reported in plants. The biosynthetic pathways of certain amino acids and lipids have been altered in specific plant lineages. Also, two alternative pathways exist in plants for synthesizing primary precursors of the two major classes of plant specialized metabolites, terpenoids and phenylpropanoids. Such primary metabolic diversities likely underlie major evolutionary changes in plant metabolism and chemical diversity by acting as enabling or associated traits for the evolution of specialized metabolic pathways.

Trait discovery and editing in tomato

Tomato (Solanum lycopersicum), which is used for both processing and fresh markets, is a major crop species that is the top ranked vegetable produced over the world. Tomato is also a model species for research in genetics, fruit development and disease resistance. Genetic resources available in public repositories comprise the 12 wild related species and thousands of landraces, modern cultivars and mutants. In addition, high quality genome sequences are available for cultivated tomato and for several wild relatives, hundreds of accessions have been sequenced, and databases gathering sequence data together with genetic and phenotypic data are accessible to the tomato community. Major breeding goals are productivity, resistance to biotic and abiotic stresses, and fruit sensorial and nutritional quality. New traits, including resistance to various biotic and abiotic stresses and root architecture, are increasingly being studied. Several major mutations and quantitative trait loci (QTLs) underlying traits of interest in tomato have been uncovered to date and, thanks to new populations and advances in sequencing technologies, the pace of trait discovery has considerably accelerated. In recent years, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing (GE) already proved its remarkable efficiency in tomato for engineering favorable alleles and for creating new genetic diversity by gene disruption, gene replacement, and precise base editing. Here, we provide insight into the major tomato traits and underlying causal genetic variations discovered so far and review the existing genetic resources and most recent strategies for trait discovery in tomato. Furthermore, we explore the opportunities offered by CRISPR/Cas9 and their exploitation for trait editing in tomato.

Upregulation of Skin-Aging Biomarkers in Aged NHDF Cells by a Sucrose Ester Extract from the Agroindustrial Waste of Physalis peruviana Calyces

As part of a search for new sustainable plant sources of valuable compounds, the EtOAc extract of the discarded calyces of Physalis peruviana fruit was selected for its significant antiaging activity. Eight new sucrose esters (SEs), named peruvioses F-M (1-8), along with three known SEs, peruvioses A (9), peruviose B (10), and nicandrose D (11), were isolated. Their structures were elucidated by comprehensive analyses of their NMR and MS data. A global fragmentation pattern of these SEs was established from their MS data. The SE extract (SEE) at a concentration of 0.5 mg L^-1 upregulated multiple skin-aging biomarkers, namely, collagen I, elastin, and fibrillin-1, in aged normal human dermal fibroblast cells. A 36% increase in collagen I was observed. The elastin and fibrillin-1 contents were fully recovered, and an increase of at least 10% in the production of elastin was observed.

Quantitative Trait Loci Analysis Identifies a Prominent Gene Involved in the Production of Fatty Acid-Derived Flavor Volatiles in Tomato

To gain insight into the genetic regulation of lipid metabolism in tomato, we conducted metabolic trait loci (mQTL) analysis following the lipidomic profiling of fruit pericarp and leaf tissue of the Solanum pennellii introgression lines (IL). To enhance mapping resolution for selected fruit-specific mQTL, we profiled the lipids in a subset of independently derived S. pennellii backcross inbred lines, as well as in a near-isogenic sub-IL population. We identified a putative lecithin:cholesterol acyltransferase that controls the levels of several lipids, and two members of the class III lipase family, LIP1 and LIP2, that were associated with decreased levels of diacylglycerols (DAGs) and triacylglycerols (TAGs). Lipases of this class cleave fatty acids from the glycerol backbone of acylglycerols. The released fatty acids serve as precursors of flavor volatiles. We show that LIP1 expression correlates with fatty acid-derived volatile levels. We further confirm the function of LIP1 in TAG and DAG breakdown and volatile synthesis using transgenic plants. Taken together, our study extensively characterized the genetic architecture of lipophilic compounds in tomato and demonstrated at molecular level that release of free fatty acids from the glycerol backbone can have a major impact on downstream volatile synthesis.

Phylogenomic Mining of the Mints Reveals Multiple Mechanisms Contributing to the Evolution of Chemical Diversity in Lamiaceae

The evolution of chemical complexity has been a major driver of plant diversification, with novel compounds serving as key innovations. The species-rich mint family (Lamiaceae) produces an enormous variety of compounds that act as attractants and defense molecules in nature and are used widely by humans as flavor additives, fragrances, and anti-herbivory agents. To elucidate the mechanisms by which such diversity evolved, we combined leaf transcriptome data from 48 Lamiaceae species and four outgroups with a robust phylogeny and chemical analyses of three terpenoid classes (monoterpenes, sesquiterpenes, and iridoids) that share and compete for precursors. Our integrated chemical-genomic-phylogenetic approach revealed that: (1) gene family expansion rather than increased enzyme promiscuity of terpene synthases is correlated with mono- and sesquiterpene diversity; (2) differential expression of core genes within the iridoid biosynthetic pathway is associated with iridoid presence/absence; (3) generally, production of iridoids and canonical monoterpenes appears to be inversely correlated; and (4) iridoid biosynthesis is significantly associated with expression of geraniol synthase, which diverts metabolic flux away from canonical monoterpenes, suggesting that competition for common precursors can be a central control point in specialized metabolism. These results suggest that multiple mechanisms contributed to the evolution of chemodiversity in this economically important family.

Acylsugar amount and fatty acid profile differentially suppress oviposition by western flower thrips, Frankliniella occidentalis, on tomato and interspecific hybrid flowers

Tomatoes (Solanum lycopersicum L.) have been bred to exude higher amounts or different types of the specialized plant metabolites, acylsugars, from type IV trichomes. Acylsugars are known to deter several herbivorous insect pests, including the western flower thrips (WFT), Frankliniella occidentalis (Pergande); however, all previous studies investigated the effect of acylsugars on leaves, or acylsugar extracts obtained from leaves. In spite of the WFT predilection for flowers, there is a gap in knowledge about flower defenses against thrips damage. This is especially important in light of their capacity to acquire and inoculate viruses in the genus Orthotospovirus, such as Tomato spotted wilt orthotospovirus (TSWV), in flowers. Therefore, we turned our attention to assessing thrips oviposition differences on flowers of 14 entries, including 8 interspecific hybrids, 5 tomato lines bred for specific acylsugar-related characteristics (type IV trichome densities, acylsugar amount, sugar moiety and fatty acid profile), and a fresh market tomato hybrid, Mt. Spring, which only produces trace amounts of acylsugars. Our results show that the density of the acylsugar droplet bearing type IV trichomes is greatest on sepals, relative to other flower structures, and accordingly, WFT avoids oviposition on sepals in favor of trichome-sparse petals. In concordance with past studies, acylsugar amount was the most important acylsugar-related characteristic suppressing WFT oviposition. Certain acylsugar fatty acids, specifically i-C5, i-C9 and i-C11, were also significantly associated with changes in WFT oviposition. These results support continued breeding efforts to increase acylsugar amounts and explore modifications of fatty acid profile and their roles in deterring thrips oviposition. The finding that acylsugar production occurs and reduces thrips oviposition in tomato flowers will be important in efforts to use acylsugar-mediated resistance to reduce incidence of orthotospoviruses such as TSWV in tomato by deterring virus transmission and development of thrips vector populations in the crop.

Genetic mapping identifies loci that influence tomato resistance against Colorado potato beetles

The Colorado potato beetle (CPB; Leptinotarsa decemlineata Say), the most economically important insect pest on potato (Solanum tuberosum L.), also feeds on other Solanaceae, including cultivated tomato (Solanum lycopersicum L.). We used tomato genetic mapping populations to investigate natural variation in CPB resistance. CPB bioassays with 74 tomato lines carrying introgressions of Solanum pennellii in S. lycopersicum cv. M82 identified introgressions from S. pennellii on chromosomes 1 and 6 conferring CPB susceptibility, whereas introgressions on chromosomes 1, 8 and 10 conferred higher resistance. Mapping of CPB resistance using 113 recombinant inbred lines derived from a cross between S. lycopersicum cv UC-204B and Solanum galapagense identified significant quantitative trait loci on chromosomes 6 and 8. In each case, the S. galapagense alleles were associated with lower leaf damage and reduced larval growth. Results of both genetic mapping approaches converged on the same region of chromosome 6, which may have important functions in tomato defense against CPB herbivory. Although genetic mapping identified quantitative trait loci encompassing known genes for tomato acyl sugar and glycoalkaloid biosynthesis, experiments with acyl sugar near-isogenic lines and transgenic GAME9 glycoalkaloid-deficient and overproducing lines showed no significant effect of these otherwise insect-defensive metabolites on CPB performance.