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

Wo interacts with SlTCP25 to regulate type I trichome branching in tomato

Plant trichomes serve as a protective barrier against various stresses. Although the molecular mechanisms governing the initiation of trichomes have been extensively studied, the regulatory pathways underlying the trichome branching in tomato remain elusive. Here, we found that Woolly (Wo) mutant and its overexpression transgenic plants displayed branched type I trichomes. The expression level of SlTCP25, a transcription factor of type TB1 of the TCP subfamily, was obviously decreased in Wo mutant and Wo overexpressing lines. Knockout of SlTCP25 resulted in the formation of type I trichome branches on the hypocotyls. Genetic evidence showed that SlTCP25 is epistatic to Wo in the branched trichome formation. Biochemical data further indicated that Wo can directly bind to the L1-box cis-element in the SlTCP25 promoter and repress its transcription. We further determined that SlTCP25 interacts with Wo to weaken Wo-regulated the expression of SlCycB2, a trichome branching inhibitor. In addition, the number of trichome branches was significantly increased in Sltcp25Slcycb2 double mutant, suggesting that SlTCP25 and SlCycB2 coordinately repress trichome branching in wild type. In conclusion, we elucidate a molecular network governing the morphogenesis of multicellular trichomes in tomato.

Strain-Specific Features of Primary Metabolome Characteristic for Extremotolerant/Extremophilic Cyanobacteria Under Long-Term Storage

Cyanobacteria isolated from extreme habitats are promising in biotechnology due to their high adaptability to unfavorable environments and their specific natural products. Therefore, these organisms are stored under a reduced light supply in multiple collections worldwide. However, it remains unclear whether these strains maintain constitutively expressed primary metabolome features associated with their unique adaptations. To address this question, a comparative analysis of primary metabolomes of twelve cyanobacterial strains from diverse extreme habitats was performed by a combined GC-MS/LC-MS approach. The results revealed that all these cyanobacterial strains exhibited clear differences in their patterns of primary metabolites. These metabolic differences were more pronounced for the strains originating from ecologically different extreme environments. Extremotolerant terrestrial and freshwater strains contained lower strain-specifically accumulated primary metabolites than extremophilic species from habitats with high salinity and alkalinity. The latter group of strains was highly diverse in amounts of specific primary metabolites. This might indicate essentially different molecular mechanisms and metabolic pathways behind the survival of the microorganisms in saline and alkaline environments. The identified strain-specific metabolites are discussed with respect to the metabolic processes that might impact maintaining the viability of cyanobacteria during their storage and indicate unique adaptations formed in their original extreme habitats.

An In Vitro Phytohormone Survey Reveals Concerted Regulation of the Cannabis Glandular Trichome Disc Cell Proteome

Cannabis (Cannabis sativa L.) flower glandular trichomes (GTs) are the main site of cannabinoid synthesis. Phytohormones, such as jasmonic acid (JA) and salicylic acid (SA), have been shown to increase cannabinoid content in cannabis flowers, but how this is regulated remains unknown. This study aimed to understand which biological processes in GT disc cells phytohormones control by using an in vitro assay. Live GT disc cells were isolated from a high-tetrahydrocannabinol cannabis cultivar and incubated on basal media plates supplemented with either kinetin (KIN), JA, SA, abscisic acid, ethephon, gibberellic acid, brassinolide, or sodium diethyldithiocarbamate. Quantitative proteomic analysis revealed that KIN, JA, and SA caused the greatest number of changes in the GT disc cell proteome. Surprisingly, none of the treatments concertedly increased cannabinoid content or the abundance of related biosynthetic proteins in the GT, suggesting that cannabinoid increases in previous in planta phytohormone studies are likely due to other processes, such as increased GT density. As well, KIN-, JA-, and SA-treated GTs had numerous differentially abundant proteins in common. Several were key proteins for leucoplast differentiation, cuticular wax and fatty acid metabolism, and primary metabolism regulation, denoting that cytokinin, JA, and SA signalling are likely important for coordinating cannabis GT differentiation and development.

Comparative metabolomic analysis provides insights into the metabolite profiles of wild and cultivated Dendrobium flexicaule

BACKGROUND

Dendrobium orchids (Dendrobium spp.) are valuable medicinal and attractive ornamental plants. Due to their limited wild resources, the size of the Dendrobium spp. population required for market demand primarily depends on artificial cultivation. However, the nutritional and therapeutic value of natural products may differ as growth conditions change. In this study, we profiled metabolites from wild and cultivated Dendrobium flexicaule (D. flexicaule) to explore the variations and interrelationships among bioactive components.

RESULTS

A total of 840 annotated metabolites were discovered, 231 of which differed significantly between wild and cultivated D. flexicaule. A comparative investigation found that the types and amounts of metabolites, particularly flavonoids, lipids, amino acids and their derivatives, varied between wild and cultivated D. flexicaule. Using metabolite correlation analysis, a series of differentially abundant metabolites were found to be significantly correlated with phytohormones such as abscisic acid (ABA), salicylic acid (SA), and zeatins, indicating that plant hormones play a role in the accumulation of specific metabolites. Furthermore, many distinct metabolites were identified as key active ingredients of traditional Chinese medicines. Additionally, 78 components were discovered to be active pharmaceutical substances against various diseases, probably contributing to the diverse medical values of wild and cultivated D. flexicaule.

CONCLUSIONS

Overall, comprehensively analyzed the metabolic profiles of wild and cultivated D. flexicaule in this study, serving as a theoretical and material foundation for quality control, health efficacy, and industrial development.

Characterisation of Cannabis glandular trichome development reveals distinct features of cannabinoid biosynthesis

KEY MESSAGE

Cannabis trichome development progresses in distinct phases that underpin the dynamic biosynthesis of cannabinoids and terpenes. This study investigates the molecular mechanisms underlying cannabinoid and terpenoid biosynthesis in glandular trichomes of Cannabis sativa (CsGTs) throughout their development. Female Cannabis sativa c. Hindu Kush were cultivated under controlled conditions, and trichome development was analysed from week 3 to week 8 of the flowering period. We employed light microscopy, quantitative metabolomics and proteomics to analyse morphological changes in trichome secretory cell development, and temporal changes in metabolite accumulation and protein abundance. Our findings identified three distinct developmental phases: pre-secretory (T3), secretory (T6), and post-secretory (T8), the first time the three phases of trichome development have been identified and investigated in CsGTs. The pre-secretory phase was characterized by smaller secretory cells, limited metabolite accumulation and elevated levels of proteins involved in protein biosynthesis and cellular development. The secretory phase exhibited the highest biosynthetic activity, marked by larger secretory cells, increased plastidal activity, central carbon metabolism, and significant accumulation of cannabinoids and terpenoids. The post-secretory phase showed a decrease in secretory cell size, reduced metabolic activity, and a decrease in the abundance of primary and secondary metabolism enzymes, although THCA continued to accumulate. Key enzymes showed dynamic changes correlating with the stages of trichome development. This study provides a comprehensive understanding of the molecular mechanisms regulating cannabinoid and terpenoid biosynthesis in CsGTs, offering insights for enhancing the production of these valuable compounds through targeted breeding and biotechnological approaches.

From dawn 'til dusk: daytime progression regulates primary and secondary metabolism in Cannabis glandular trichomes

Cannabis sativa L. glandular trichomes synthesize large amounts of secondary metabolites, predominantly cannabinoids and terpenoids. The associated demand for carbon and energy makes glandular trichomes strong sink tissues with indications that their secondary metabolism is coupled to the availability of photoassimilates. Many metabolites show diurnal patterns of flux, but it is unknown whether cannabinoids and terpenoids are regulated by time of day. We quantified cannabinoids, terpenoids, and the glandular trichome proteome over a 12 h light period in flowers of 'Hindu Kush', a high-tetrahydrocannabinol cultivar. Major cannabinoids changed significantly over the course of the day, resulting in an increase in total measured cannabinoids. Major terpenoids also changed, with sesquiterpenes generally decreasing with day progression. While monoterpenes generally did not decrease, the second most abundant, α-pinene, increased. The glandular trichome proteome changed the most within the first 6 h of the day, and analysis of differentially abundant proteins indicated up-regulation of primary metabolism. Surprisingly, key cannabinoid biosynthetic enzymes decreased with daytime progression despite increases in cannabinoid content, which indicates that daytime increases of photoassimilates are the main driver of cannabinoid regulation. This first reporting of variability of cannabinoid and terpenoid biosynthesis over the course of the day has implications for Cannabis research and production.

Deep metabolomics revealed trajectories of jasmonate signaling-mediated primary metabolism in Arabidopsis upon Spodoptera litura herbivory

Plants defend against chewing herbivores by up-regulating jasmonic acid (JA) signaling, which activates downstream signaling cascades and produces numerous secondary metabolites that act as defense molecules against the herbivores. Although secondary metabolism always remains a focus of research, primary metabolism is also reported to be realigned upon herbivory. However, JA signaling-mediated modulation of primary metabolites and their metabolic pathways in plants are mostly unexplored. Here, we applied gas chromatography-mass spectrometry-based untargeted metabolomics aided with computational statistical frameworks on wild type Arabidopsis, mutants of active JA receptor (i.e., CORONATINE-INSENSITIVE 1, COI1-1) and downstream transcription factor (i.e., MYC2) to navigate the JA signaling-mediated primary metabolism alterations during herbivory. Pathway and metabolite's chemical class enrichment analysis revealed JA signaling is crucial for constitutive as well as herbivore-induced primary metabolism and topology of their interaction networks. JA signaling majorly modulated alterations of sugars, amino acids and related metabolites. Herbivory-mediated sugar depletion and induction of methionine for aliphatic glucosinolates are also dependent on JA signaling. Taken together, our results demonstrate trails of JA signaling-mediated primary metabolic alterations associated with herbivory.

Advancing Anticancer Drug Discovery: Leveraging Metabolomics and Machine Learning for Mode of Action Prediction by Pattern Recognition

A bottleneck in the development of new anti-cancer drugs is the recognition of their mode of action (MoA). Metabolomics combined with machine learning allowed to predict MoAs of novel anti-proliferative drug candidates, focusing on human prostate cancer cells (PC-3). As proof of concept, 38 drugs are studied with known effects on 16 key processes of cancer metabolism, profiling low molecular weight intermediates of the central carbon and cellular energy metabolism (CCEM) by LC-MS/MS. These metabolic patterns unveiled distinct MoAs, enabling accurate MoA predictions for novel agents by machine learning. The transferability of MoA predictions based on PC-3 cell treatments is validated with two other cancer cell models, i.e., breast cancer and Ewing's sarcoma, and show that correct MoA predictions for alternative cancer cells are possible, but still at some expense of prediction quality. Furthermore, metabolic profiles of treated cells yield insights into intracellular processes, exemplified for drugs inducing different types of mitochondrial dysfunction. Specifically, it is predicted that pentacyclic triterpenes inhibit oxidative phosphorylation and affect phospholipid biosynthesis, as confirmed by respiration parameters, lipidomics, and molecular docking. Using biochemical insights from individual drug treatments, this approach offers new opportunities, including the optimization of combinatorial drug applications.

Proteomics: An Essential Tool to Study Plant-Specialized Metabolism

Plants are a valuable source of specialized metabolites that provide a plethora of therapeutic applications. They are natural defenses that plants use to adapt and respond to their changing environment. Decoding their biosynthetic pathways and understanding how specialized plant metabolites (SPMs) respond to biotic or abiotic stress will provide vital knowledge for plant biology research and its application for the future sustainable production of many SPMs of interest. Here, we focus on the proteomic approaches and strategies that help with the study of plant-specialized metabolism, including the: (i) discovery of key enzymes and the clarification of their biosynthetic pathways; (ii) study of the interconnection of both primary (providers of carbon and energy for SPM production) and specialized (secondary) metabolism; (iii) study of plant responses to biotic and abiotic stress; (iv) study of the regulatory mechanisms that direct their biosynthetic pathways. Proteomics, as exemplified in this review by the many studies performed to date, is a powerful tool that forms part of omics-driven research. The proteomes analysis provides an additional unique level of information, which is absent from any other omics studies. Thus, an integrative analysis, considered versus a single omics analysis, moves us more closely toward a closer interpretation of real cellular processes. Finally, this work highlights advanced proteomic technologies with immediate applications in the field.

An evolutionarily conserved metabolite inhibits biofilm formation in Escherichia coli K-12

Methylerythritol cyclodiphosphate (MEcPP) is an intermediate in the biosynthesis of isoprenoids in plant plastids and in bacteria, and acts as a stress signal in plants. Here, we show that MEcPP regulates biofilm formation in Escherichia coli K-12 MG1655. Increased MEcPP levels, triggered by genetic manipulation or oxidative stress, inhibit biofilm development and production of fimbriae. Deletion of fimE, encoding a protein known to downregulate production of adhesive fimbriae, restores biofilm formation in cells with elevated MEcPP levels. Limited proteolysis-coupled mass spectrometry (LiP-MS) reveals that MEcPP interacts with the global regulatory protein H-NS, which is known to repress transcription of fimE. MEcPP prevents the binding of H-NS to the fimE promoter. Therefore, our results indicate that MEcPP can regulate biofilm formation by modulating H-NS activity and thus reducing fimbriae production. Further research is needed to test whether MEcPP plays similar regulatory roles in other bacteria.

Sleeping but not defenceless: seed dormancy and protection

To ensure their vital role in disseminating the species, dormant seeds have developed adaptive strategies to protect themselves against pathogens and predators. This is orchestrated through the synthesis of an array of constitutive defences that are put in place in a developmentally regulated manner, which are the focus of this review. We summarize the defence activity and the nature of the molecules coming from the exudate of imbibing seeds that leak into their vicinity, also referred to as the spermosphere. As a second layer of protection, the dual role of the seed coat will be discussed; as a physical barrier and a multi-layered reservoir of defence compounds that are synthesized during seed development. Since imbibed dormant seeds can persist in the soil for extensive periods, we address the question of whether during this time a constitutively regulated defence programme is switched on to provide further protection, via the well-defined pathogenesis-related (PR) protein family. In addition, we review the hormonal and signalling pathways that might be involved in the interplay between dormancy and defence and point out questions that need further attention.

Coordinated metabolic adaptation of Arabidopsis thaliana to high light

In plants, exposure to high light irradiation induces various stress responses, which entail complex metabolic rearrangements. To explore these dynamics, we conducted time‐course experiments spanning 2 min to 72 h with Arabidopsis thaliana under high and control light. Comparative metabolomics, transcriptomics, redox proteomics, and stable isotope labeling on leaf rosettes identified a series of synchronous and successive responses that provide a deeper insight into well‐orchestrated mechanisms contributing to high‐light acclimation. We observed transient transcriptome downregulation related to light harvesting and electron flow before the profound remodeling of the photosynthetic apparatus. Throughout the entire time course, redox homeostasis is tightly balanced between downregulation of production and enhanced transformation of NADPH accompanied by redistribution of reducing equivalents across several subcellular compartments. In both light conditions, C4 acids such as malate and fumarate are produced via anaplerosis. In carbon units, their accumulation in vacuoles surpasses plastidic levels of starch and intensifies notably under high light. In parallel, citrate synthesis from pyruvate is significantly hindered diurnally. Isotopic labeling in 2‐oxoglutarate and glutamate suggests a moderate de novo synthesis of C5 acids from a vacuolar citrate reservoir during the light phase while they are largely renewed during the night. In the absence of a diurnal clockwise flow through the tricarboxylic acid (TCA) cycle, increased oxidation of photorespiratory glycine takes over as a source of reductants to fuel mitochondrial ATP production. These findings, along with previous research, contribute to a model integrating redox balance and linking increased carbon assimilation and nitrogen metabolism, especially in the context of an incomplete TCA cycle.

Multi-Omics Analyses of Lettuce (Lactuca sativa) Reveals Primary Metabolism Reorganization Supporting Distinct Features of Secondary Metabolism Induced by Supplementing UV-A Radiation

UV can serve as an effective light spectrum for regulating plant secondary metabolites, while relevant studies on UV-A are much less extensive than those on UV-B. A comprehensive understanding of the selective effects of UV-A on different secondary metabolites and the specific features of primary metabolism that drive these effects is still lacking. To address this knowledge gap, we conducted a study to analyze the dynamic changes in the metabolome and transcriptome of lettuce leaves irradiated with red plus UV-A light (monochromatic red light as control). Generally, UV-A promoted the synthesis of most phenylpropanoids and terpenoids originating from the shikimate and methylerythritol phosphate (MEP) pathway in plastids but sacrificed the synthesis of terpenoids derived from the mevalonate (MVA) pathway, particularly sesquiterpenes. Increased precursors supply for the shikimate and MEP pathway under UV-A was directly supported by the activation of the Calvin-Benson cycle and phosphoenolpyruvate transport. Whereas, along with phosphoenolpyruvate transport, the TCA cycle was restrained, causing deprivation of the MVA pathway precursor. In addition, UV-A also activated the plastidic oxidative branch of the pentose phosphate pathway, photorespiration, and malate shuttle, to ensure a sufficient supply of nitrogen, circulation homeostasis of the Calvin-Benson cycle, and energy balance, thus indirectly supporting UV-A-induced specific secondary metabolic output. This study provides a comprehensive framework for understanding the flexible primary-secondary metabolism interactions that are able to produce specific metabolites favorable for adaptation to environmental stimuli.

Plant terpenoid biosynthetic network and its multiple layers of regulation

Terpenoids constitute one of the largest and most chemically diverse classes of primary and secondary metabolites in nature with an exceptional breadth of functional roles in plants. Biosynthesis of all terpenoids begins with the universal five‑carbon building blocks, isopentenyl diphosphate (IPP) and its allylic isomer dimethylallyl diphosphate (DMAPP), which in plants are derived from two compartmentally separated but metabolically crosstalking routes, the mevalonic acid (MVA) and methylerythritol phosphate (MEP) pathways. Here, we review the current knowledge on the terpenoid precursor pathways and highlight the critical hidden constraints as well as multiple regulatory mechanisms that coordinate and homeostatically govern carbon flux through the terpenoid biosynthetic network in plants.

B Vitamins: An Update on Their Importance for Plant Homeostasis

B vitamins are a source of coenzymes for a vast array of enzyme reactions, particularly those of metabolism. As metabolism is the basis of decisions that drive maintenance, growth, and development, B vitamin-derived coenzymes are key components that facilitate these processes. For over a century, we have known about these essential compounds and have elucidated their pathways of biosynthesis, repair, salvage, and degradation in numerous organisms. Only now are we beginning to understand their importance for regulatory processes, which are becoming an important topic in plants. Here, I highlight and discuss emerging evidence on how B vitamins are integrated into vital processes, from energy generation and nutrition to gene expression, and thereby contribute to the coordination of growth and developmental programs, particularly those that concern maintenance of a stable state, which is the foundational tenet of plant homeostasis.

Spatiotemporal formation of glands in plants is modulated by MYB-like transcription factors

About one third of vascular plants develop glandular trichomes, which produce defensive compounds that repel herbivores and act as a natural biofactory for important pharmaceuticals such as artemisinin and cannabinoids. However, only a few regulators of glandular structures have been characterized so far. Here we have identified two closely-related MYB-like genes that redundantly inhibit the formation of glandular cells in tomatoes, and they are named as GLAND CELL REPRESSOR (GCR) 1 and 2. The GCR genes highly express in the apical cells of tomato trichomes, with expression gradually diminishing as the cells transition into glands. The spatiotemporal expression of GCR genes is coordinated by a two-step inhibition process mediated by SlTOE1B and GCRs. Furthermore, we demonstrate that the GCR genes act by suppressing Leafless (LFS), a gene that promotes gland formation. Intriguingly, homologous GCR genes from tobacco and petunia also inhibit gland formation, suggesting that the GCR-mediated repression mechanism likely represents a conserved regulatory pathway for glands across different plant species.

A method to determine antifungal activity in seed exudates by nephelometry

BACKGROUND

One of the levers towards alternative solutions to pesticides is to improve seed defenses against pathogens, but a better understanding is needed on the type and regulation of existing pathways during germination. Dormant seeds are able to defend themselves against microorganisms during cycles of rehydration and dehydration in the soil. During imbibition, seeds leak copious amounts of exudates. Here, we developed a nephelometry method to assay antimicrobial activity (AA) in tomato seed exudates as a proxy to assess level of defenses.

RESULTS

A protocol is described to determine the level of AA against the nonhost filamentous fungus Alternaria brassicicola in the exudates of tomato seeds and seedlings. The fungal and exudate concentrations can be adjusted to modulate the assay sensitivity, thereby providing a large window of AA detection. We established that AA in dormant seeds depends on the genotype. It ranged from very strong AA to complete absence of AA, even after prolonged imbibition. AA depends also on the stages of germination and seedling emergence. Exudates from germinated seeds and seedlings showed very strong AA, while those from dormant seeds exhibited less activity for the same imbibition time. The exudate AA did not impact the growth of a pathogenic fungus host of tomato, Alternaria alternata, illustrating the adaptation of this fungus to its host.

CONCLUSIONS

We demonstrate that our nephelometry method is a simple yet powerful bioassay to quantify AA in seed exudates. Different developmental stages from dormant seed to seedlings show different levels of AA in the exudate that vary between genotypes, highlighting a genetic diversity x developmental stage interaction in defense. These findings will be important to identify molecules in the exudates conferring antifungal properties and obtain a better understanding of the regulatory and biosynthetic pathways through the lifecycle of seeds, from dormant seeds until seedling emergence.

Jasmonates Coordinate Secondary with Primary Metabolism

Jasmonates (JAs), including jasmonic acid (JA), its precursor 12-oxo-phytodienoic acid (OPDA) and its derivatives jasmonoyl-isoleucine (JA-Ile), methyl jasmonate (MeJA), cis-jasmone (CJ) and other oxylipins, are important in the regulation of a range of ecological interactions of plants with their abiotic and particularly their biotic environments. Plant secondary/specialized metabolites play critical roles in implementing these ecological functions of JAs. Pathway and transcriptional regulation analyses have established a central role of JA-Ile-mediated core signaling in promoting the biosynthesis of a great diversity of secondary metabolites. Here, we summarized the advances in JAs-induced secondary metabolites, particularly in secondary metabolites induced by OPDA and volatile organic compounds (VOCs) induced by CJ through signaling independent of JA-Ile. The roles of JAs in integrating and coordinating the primary and secondary metabolism, thereby orchestrating plant growth-defense tradeoffs, were highlighted and discussed. Finally, we provided perspectives on the improvement of the adaptability and resilience of plants to changing environments and the production of valuable phytochemicals by exploiting JAs-regulated secondary metabolites.

Shifts in carbon partitioning by photosynthetic activity increase terpenoid synthesis in glandular trichomes

Several commercially important secondary metabolites are produced and accumulated in high amounts by glandular trichomes, giving the prospect of using them as metabolic cell factories. Due to extremely high metabolic fluxes through glandular trichomes, previous research focused on how such flows are achieved. The question regarding their bioenergetics became even more interesting with the discovery of photosynthetic activity in some glandular trichomes. Despite recent advances, how primary metabolism contributes to the high metabolic fluxes in glandular trichomes is still not fully elucidated. Using computational methods and available multi-omics data, we first developed a quantitative framework to investigate the possible role of photosynthetic energy supply in terpenoid production and next tested experimentally the simulation-driven hypothesis. With this work, we provide the first reconstruction of specialised metabolism in Type-VI photosynthetic glandular trichomes of Solanum lycopersicum. Our model predicted that increasing light intensities results in a shift of carbon partitioning from catabolic to anabolic reactions driven by the energy availability of the cell. Moreover, we show the benefit of shifting between isoprenoid pathways under different light regimes, leading to a production of different classes of terpenes. Our computational predictions were confirmed in vivo, demonstrating a significant increase in production of monoterpenoids while the sesquiterpenes remained unchanged under higher light intensities. The outcomes of this research provide quantitative measures to assess the beneficial role of chloroplast in glandular trichomes for enhanced production of secondary metabolites and can guide the design of new experiments that aim at modulating terpenoid production.

Cell-type-specific metabolism in plants

Every plant organ contains tens of different cell types, each with a specialized function. These functions are intrinsically associated with specific metabolic flux distributions that permit the synthesis of the ATP, reducing equivalents and biosynthetic precursors demanded by the cell. Investigating such cell-type-specific metabolism is complicated by the mosaic of different cells within each tissue combined with the relative scarcity of certain types. However, techniques for the isolation of specific cells, their analysis in situ by microscopy, or modeling of their function in silico have permitted insight into cell-type-specific metabolism. In this review we present some of the methods used in the analysis of cell-type-specific metabolism before describing what we know about metabolism in several cell types that have been studied in depth; (i) leaf source and sink cells; (ii) glandular trichomes that are capable of rapid synthesis of specialized metabolites; (iii) guard cells that must accumulate large quantities of the osmolytes needed for stomatal opening; (iv) cells of seeds involved in storage of reserves; and (v) the mesophyll and bundle sheath cells of C4 plants that participate in a CO₂ concentrating cycle. Metabolism is discussed in terms of its principal features, connection to cell function and what factors affect the flux distribution. Demand for precursors and energy, availability of substrates and suppression of deleterious processes are identified as key factors in shaping cell-type-specific metabolism.

Trichome-Specific Analysis and Weighted Gene Co-Expression Correlation Network Analysis (WGCNA) Reveal Potential Regulation Mechanism of Artemisinin Biosynthesis in Artemisia annua

Trichomes are attractive cells for terpenoid biosynthesis and accumulation in Artemisia annua. However, the molecular process underlying the trichome of A. annua is not yet fully elucidated. In this study, an analysis of multi-tissue transcriptome data was performed to examine trichome-specific expression patterns. A total of 6646 genes were screened and highly expressed in trichomes, including artemisinin biosynthetic genes such as amorpha-4,11-diene synthase (ADS) and cytochrome P450 monooxygenase (CYP71AV1). Mapman and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that trichome-specific genes were mainly enriched in lipid metabolism and terpenoid metabolism. These trichome-specific genes were analyzed by a weighted gene co-expression network analysis (WGCNA), and the blue module linked to terpenoid backbone biosynthesis was determined. Hub genes correlated with the artemisinin biosynthetic genes were selected based on TOM value. ORA, Benzoate carboxyl methyltransferase (BAMT), Lysine histidine transporter-like 8 (AATL1), Ubiquitin-like protease 1 (Ulp1) and TUBBY were revealed as key hub genes induced by methyl jasmonate (MeJA) for regulating artemisinin biosynthesis. In summary, the identified trichome-specific genes, modules, pathways and hub genes provide clues and shed light on the potential regulatory mechanisms of artemisinin biosynthesis in trichomes in A. annua.

Morphological characterization of intraspecific variation for trichome traits in tomato (Solanum lycopersicum)

Trichomes, the hairlike protuberances in plants, have been well known to act as the first line of defense against herbivores, and abiotic stresses, along with other structural defenses such as spines, thorns, and waxes. We previously reported the tremendous variation in trichome traits among different wild and cultivated Solanum species and demonstrated that trichomes types and density are traditionally miscalculated and often misnamed. However, intraspecific variation in trichome traits is poorly understood, although this has implications for stress tolerance and resistance breeding programs in economically important crop species and can also mediate ecological interactions at multiple trophic levels in their wild congeners. In this study, using tomato as a model, we characterized the trichomes from 10 commonly grown varieties using a minimal sample prep desktop scanning electron microscopy, and followed up with estimating their dimensions across the varieties and trichome types. We hypothesized that although trichome number may vary, the varieties will have similar trichome types, based on current literature. Our results show that there is significant variation for trichome number as well as dimensions of trichome types among these varieties. Furthermore, when we separately analyzed the number and dimensions of commonly found glandular and non-glandular trichomes, the results were consistent with broad assessment of trichomes, showing consistent variation among varieties, suggesting that trichome studies should not be limited to basic classification into glandular and non-glandular, and should accommodate the sub-types and their dimensions.

A HD-ZIP transcription factor specifies fates of multicellular trichomes via dosage-dependent mechanisms in tomato

Hair-like structures are shared by most living organisms. The hairs on plant surfaces, commonly referred to as trichomes, form diverse types to sense and protect against various stresses. However, it is unclear how trichomes differentiate into highly variable forms. Here, we show that a homeodomain leucine zipper (HD-ZIP) transcription factor named Woolly controls the fates of distinct trichomes in tomato via a dosage-dependent mechanism. The autocatalytic reinforcement of Woolly is counteracted by an autoregulatory negative feedback loop, creating a circuit with a high or low Woolly level. This biases the transcriptional activation of separate antagonistic cascades that lead to different trichome types. Our results identify the developmental switch of trichome formation and provide mechanistic insights into the progressive fate specification in plants, as well as a path to enhancing plant stress resistance and the production of beneficial chemicals.

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.

Genomic and metabolic profiling of two tomato contrasting cultivars for tolerance to Tuta absoluta

Dissimilar patterns of variants affecting genes involved in response to herbivory, including those leading to difference in VOC production, were identified in tomato lines with contrasting response to Tuta absoluta. Tuta absoluta is one of the most destructive insect pest affecting tomato production, causing important yield losses both in open field and greenhouse. The selection of tolerant varieties to T. absoluta is one of the sustainable approaches to control this invasive leafminer. In this study, the genomic diversity of two tomato varieties, one tolerant and the other susceptible to T. absoluta infestation was explored, allowing us to identify chromosome regions with highly dissimilar pattern. Genes affected by potential functional variants were involved in several processes, including response to herbivory and secondary metabolism. A metabolic analysis for volatile organic compounds (VOCs) was also performed, highlighting a difference in several classes of chemicals in the two genotypes. Taken together, these findings can aid tomato breeding programs aiming to develop tolerant plants to T. absoluta.

Proteomics of Reproductive Development, Fruit Ripening, and Stress Responses in Tomato

The fruits of the tomato crop (Solanum lycopersicum L.) are increasingly consumed by humans worldwide. Due to their rich nutritional quality, pharmaceutical properties, and flavor, tomato crops have gained a salient role as standout crops among other plants. Traditional breeding and applied functional research have made progress in varying tomato germplasms to subdue biotic and abiotic stresses. Proteomic investigations within a span of few decades have assisted in consolidating the functional genomics and transcriptomic research. However, due to the volatility and dynamicity of proteins in the regulation of various biosynthetic pathways, there is a need for continuing research in the field of proteomics to establish a network that could enable a more comprehensive understanding of tomato growth and development. With this view, we provide a comprehensive review of proteomic studies conducted on the tomato plant in past years, which will be useful for future breeders and researchers working to improve the tomato crop.

Plant secondary metabolic responses to global climate change: A meta-analysis in medicinal and aromatic plants

Plant secondary metabolites (SMs) play crucial roles in plant-environment interactions and contribute greatly to human health. Global climate changes are expected to dramatically affect plant secondary metabolism, yet a systematic understanding of such influences is still lacking. Here, we employed medicinal and aromatic plants (MAAPs) as model plant taxa and performed a meta-analysis from 360 publications using 1828 paired observations to assess the responses of different SMs levels and the accompanying plant traits to elevated carbon dioxide (eCO₂ ), elevated temperature (eT), elevated nitrogen deposition (eN) and decreased precipitation (dP). The overall results showed that phenolic and terpenoid levels generally respond positively to eCO₂ but negatively to eN, while the total alkaloid concentration was increased remarkably by eN. By contrast, dP promotes the levels of all SMs, while eT exclusively exerts a positive influence on the levels of phenolic compounds. Further analysis highlighted the dependence of SM responses on different moderators such as plant functional types, climate change levels or exposure durations, mean annual temperature and mean annual precipitation. Moreover, plant phenolic and terpenoid responses to climate changes could be attributed to the variations of C/N ratio and total soluble sugar levels, while the trade-off supposition contributed to SM responses to climate changes other than eCO₂ . Taken together, our results predicted the distinctive SM responses to diverse climate changes in MAAPs and allowed us to define potential moderators responsible for these variations. Further, linking SM responses to C-N metabolism and growth-defence balance provided biological understandings in terms of plant secondary metabolic regulation.

Excretion of triacylglycerol as a matrix lipid facilitating apoplastic accumulation of a lipophilic metabolite shikonin

Plants produce a large variety of lipophilic metabolites, many of which are secreted by cells and accumulated in apoplasts. These compounds often play a role to protect plants from environmental stresses. However, little is known about how these lipophilic compounds are secreted into apoplastic spaces. In this study, we used shikonin-producing cultured cells of Lithospermum erythrorhizon as an experimental model system to analyze the secretion of lipophilic metabolites, taking advantage of its high production rate and the clear inducibility in culture. Shikonin derivatives are lipophilic red naphthoquinone compounds that accumulate exclusively in apoplastic spaces of these cells and also in the root epidermis of intact plants. Microscopic analysis showed that shikonin is accumulated in the form of numerous particles on the cell wall. Lipidomic analysis showed that L. erythrorhizon cultured cells secrete an appreciable portion of triacylglycerol (24-38% of total triacylglycerol), composed predominantly of saturated fatty acids. Moreover, in vitro reconstitution assay showed that triacylglycerol encapsulates shikonin derivatives with phospholipids to form lipid droplet-like structures. These findings suggest a novel role for triacylglycerol as a matrix lipid, a molecular component involved in the secretion of specialized lipophilic metabolites.

Overcoming the challenges of preserving lipid-rich Cannabis sativa L. glandular trichomes for transmission electron microscopy

Cannabis glandular trichomes produce and store an abundance of lipidic specialised metabolites (e.g. cannabinoids and terpenes) that are consumed by humans for medicinal and recreational purposes. Due to a lack of genetic resources and inherent autofluorescence of cannabis glandular trichomes, our knowledge of cannabinoid trafficking and secretion is limited to transmission electron microscopy (TEM). Advances in cryofixation methods has resulted in ultrastructural observations closer to the 'natural state' of the living cell, and recent reports of cryofixed cannabis trichome ultrastructure challenge the long-standing model of cannabinoid trafficking proposed by ultrastructural reports using chemically fixed samples. Here, we compare the ultrastructural morphology of cannabis glandular trichomes preserved using conventional chemical fixation and ultrarapid cryofixation. We show that chemical fixation results in amorphous metabolite inclusions surrounding the organelles of glandular trichomes that were not present in cryofixed samples. Vacuolar morphology in cryofixed samples exhibited homogenous electron density, while chemically fixed samples contained a flocculent electron dense periphery and electron lucent lumen. In contrast to the apparent advantages of cryopreservation, fine details of cell wall fibre orientation could be observed in chemically fixed glandular trichomes that were not seen in cryofixed samples. Our data suggest that chemical fixation results in intracellular artefacts that impact the interpretation of lipid production and trafficking, while enabling greater detail of extracellular polysaccharide organisation.

Roles of Calcium Signaling in Gene Expression and Photosynthetic Acclimatization of Solanum lycopersicum Micro-Tom (MT) after Mechanical Damage

A momentary increase in cytoplasmic Ca²⁺ generates an oscillation responsible for the activation of proteins, such as calmodulin and kinases, which interact with reactive oxygen species (ROS) for the transmission of a stress signal. This study investigated the influence of variations in calcium concentrations on plant defense signaling and photosynthetic acclimatization after mechanical damage. Solanum lycopersicum Micro-Tom was grown with 0, 2 and 4 mM Ca²⁺, with and without mechanical damage. The expression of stress genes was evaluated, along with levels of antioxidant enzymes, hydrogen peroxide, lipid peroxidation, histochemistry, photosynthesis and dry mass of organs. The ROS production generated by mechanical damage was further enhanced by calcium-free conditions due to the inactivation of the oxygen evolution complex, contributing to an increase in reactive species. The results indicated that ROS affected mechanical damage signaling because calcium-free plants exhibited high levels of H₂O₂ and enhanced expression of kinase and RBOH1 genes, necessary conditions for an efficient response to stress. We conclude that the plants without calcium supply recognized mechanical damage but did not survive. The highest expression of the RBOH1 gene and the accumulation of H₂O₂ in these plants signaled cell death. Plants grown in the presence of calcium showed higher expression of SlCaM2 and control of H₂O₂ concentration, thus overcoming the stress caused by mechanical damage, with photosynthetic acclimatization and without damage to dry mass production.

Volatile organic compounds as mediators of plant communication and adaptation to climate change

Plant volatile organic compounds are the most abundant and structurally diverse plant secondary metabolites. They play a key role in plant lifespan via direct and indirect plant defenses, attracting pollinators, and mediating various interactions between plants and their environment. The ecological diversity and context-dependence of plant-plant communication driven by volatiles are crucial elements that influence plant performance in different habitats. Plant volatiles are also valued for their multiple applications in food, flavor, pharmaceutical, and cosmetics industries. In the current review, we summarize recent advances that have elucidated the functions of plant volatile organic compounds as mediators of plant interaction at community and individual levels, highlighting the complexities of plant receiver feedback to various signals and cues. This review emphasizes volatile terpenoids, the most abundant class of plant volatile organic compounds, highlighting their role in plant adaptability to global climate change and stress-response pathways that are integral to plant growth and survival. Finally, we identify research gaps and suggest future research directions.

Emerging trends in genomic and epigenomic regulation of plant specialised metabolism

Regulation of specialised metabolism genes is multilayered and complex, influenced by an array of genomic, epigenetic and epigenomic mechanisms. Here, we review the most recent knowledge in this field, drawing from discoveries in several plant species. Our aim is to improve understanding of how plant genome structure and function influence specialised metabolism. We also highlight key areas for future exploration. Gene regulatory mechanisms influencing specialised metabolism include gene duplication and neo-functionalization, conservation of operon-like clusters of specialised metabolism genes, local chromatin modifications, and the organisation of higher order chromatin structures within the nucleus. Genomic and epigenomic research to-date in the discipline have focused on a relatively small number of plant species, primarily at whole organ or tissue level. This is largely due to the technical demands of the experimental methods needed. However, a high degree of cell-type specificity of function exists in specialised metabolism, driven by similarly specific gene regulation. In this review we focus on the genomic characteristics of genes that are found in different types of clusters within the genome. We propose that acquisition of cell-resolution epigenomic datasets in emerging models, such as the glandular trichomes of Cannabis sativa, will yield important advances. Data such as chromatin accessibility and histone modification profiles can pinpoint which regulatory sequences are active in individual cell types and at specific times in development. These could provide fundamental biological insight as well as novel targets for genetic engineering and crop improvement.

Acoustic radiation force on a long cylinder, and potential sound transduction by tomato trichomes

Acoustic transduction by plants has been proposed as a mechanism to enable just-in-time up-regulation of metabolically expensive defensive compounds. Although the mechanisms by which this "hearing" occurs are unknown, mechanosensation by elongated plant hair cells known as trichomes is suspected. To evaluate this possibility, we developed a theoretical model to evaluate the acoustic radiation force that an elongated cylinder can receive in response to sounds emitted by animals, including insect herbivores, and applied it to the long, cylindrical stem trichomes of the tomato plant Solanum lycopersicum. Based on perturbation theory and validated by finite element simulations, the model quantifies the effects of viscosity and frequency on this acoustic radiation force. Results suggest that acoustic emissions from certain animals, including insect herbivores, may produce acoustic radiation force sufficient to trigger stretch-activated ion channels.

Multi-omics analysis reveals the molecular changes accompanying heavy-grazing-induced dwarfing of Stipa grandis

Heavy grazing significantly reduces Stipa grandis growth. To enhance our understanding of plant responses to heavy grazing, we conducted transcriptomic, proteomic, and metabolic analyses of the leaves of non-grazed plants (NG) and heavy-grazing-induced dwarf plants (HG) of S. grandis. A total of 101 metabolites, 167 proteins, and 1,268 genes differed in abundance between the HG and NG groups. Analysis of Kyoto Encyclopedia of Genes and Genomes pathways among differentially accumulated metabolites (DAMs) revealed that the most enriched pathways were flavone and flavonol biosynthesis, tryptophan metabolism, and phenylpropanoid biosynthesis. An integrative analysis of differentially expressed genes (DEGs) and proteins, and DAMs in these three pathways was performed. Heavy-grazing-induced dwarfism decreased the accumulation of DAMs enriched in phenylpropanoid biosynthesis, among which four DAMs were associated with lignin biosynthesis. In contrast, all DAMs enriched in flavone and flavonol biosynthesis and tryptophan metabolism showed increased accumulation in HG compared with NG plants. Among the DAMs enriched in tryptophan metabolism, three were involved in tryptophan-dependent IAA biosynthesis. Some of the DEGs and proteins enriched in these pathways showed different expression trends. The results indicated that these pathways play important roles in the regulation of growth and grazing-associated stress adaptions of S. grandis. This study enriches the knowledge of the mechanism of heavy-grazing-induced growth inhibition of S. grandis and provides valuable information for restoration of the productivity in degraded grassland.

Comparative transcriptomics of Pinus massoniana organs provides insights on terpene biosynthesis regulation

Terpenoids are the most important natural products collected from conifer species. However, the molecular mechanisms and core factors underlying terpenoid biosynthesis in Pinus massoniana remain unclear. To clarify these mechanisms, this study aimed to identify potential genes that might participate in the terpenoid biosynthesis of P. massoniana. In this study, single molecule real-time (SMRT) sequencing and expression analysis were used to confirm the expression patterns of genes involved in the cones, immature needles, mature needles, immature branches, and mature branches of P. massoniana. A total of 31,331 lncRNAs and 71,240 mRNAs were identified from these organs, and the greatest number of differentially expressed genes (DEGs) was discovered between needles and branches. Weighted gene coexpression network analysis (WGCNA) classified all expressed genes into nine typical modules with 11 kinds of transcription factors (TFs), namely, AP2-ERF, ARF, AUX-IAA, C2H2, Dof, F-box, SBP, WRKY, bHLH, bZIP, and GRAS, and seven kinds of functional genes, namely, ABC transporter, cellulose synthase (CesA), leucine-rich repeats (LRR), cytochrome P450 (CYT P450), pathogenesis-related protein (PR), terpene synthase (TPS), and chlorophyllase enzyme. A molecular network was constructed for hub genes, TFs, and functional genes in three modules. The potential function of eight candidate genes, including PmbHLH2, PmERF1, PmRGA, PmGAI, PmbZIP1, PmLOB1, PmMADS1, and PmMYB1, was validated through correlation analysis between terpenoid contents and expression levels, subcellular localization, and transcriptional activation activity, which provides us with probable regulators of terpenoid biosynthesis in conifers.

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.

Histochemical Evidence for Nitrogen-Transfer Endosymbiosis in Non-Photosynthetic Cells of Leaves and Inflorescence Bracts of Angiosperms

Simple Summary

We used light and confocal microscopy to visualize bacteria in leaf and bract cells of more than 30 species in 18 families of seed plants. We detected chemical exchanges between intracellular bacteria and plant cells. We found that endophytic bacteria that show evidence of the transfer of nitrogen to plants are present in non-photosynthetic cells of leaves and bracts of diverse plant species. Nitrogen transfer from bacteria was observed in epidermal cells, various filamentous and glandular trichomes, and other non-photosynthetic cells. The most efficient of the nitrogen-transfer endosymbioses were seen to involve glandular trichomes, as seen in hops (Humulus lupulus) and hemp (Cannabis sativa). Trichome chemistry is hypothesized to function to scavenge oxygen around bacteria to facilitate nitrogen fixation.

Abstract

We used light and confocal microscopy to visualize bacteria in leaf and bract cells of more than 30 species in 18 families of seed plants. Through histochemical analysis, we detected hormones (including ethylene and nitric oxide), superoxide, and nitrogenous chemicals (including nitric oxide and nitrate) around bacteria within plant cells. Bacteria were observed in epidermal cells, various filamentous and glandular trichomes, and other non-photosynthetic cells. Most notably, bacteria showing nitrate formation based on histochemical staining were present in glandular trichomes of some dicots (e.g., Humulus lupulus and Cannabis sativa). Glandular trichome chemistry is hypothesized to function to scavenge oxygen around bacteria and reduce oxidative damage to intracellular bacterial cells. Experiments to assess the differential absorption of isotopic nitrogen into plants suggest the assimilation of nitrogen into actively growing tissues of plants, where bacteria are most active and carbohydrates are more available. The leaf and bract cell endosymbiosis types outlined in this paper have not been previously reported and may be important in facilitating plant growth, development, oxidative stress resistance, and nutrient absorption into plants. It is unknown whether leaf and bract cell endosymbioses are significant in increasing the nitrogen content of plants. From the experiments that we conducted, it is impossible to know whether plant trichomes evolved specifically as organs for nitrogen fixation or if, instead, trichomes are structures in which bacteria easily colonize and where some casual nitrogen transfer may occur between bacteria and plant cells. It is likely that the endosymbioses seen in leaves and bracts are less efficient than those of root nodules of legumes in similar plants. However, the presence of endosymbioses that yield nitrate in plants could confer a reduced need for soil nitrogen and constitute increased nitrogen-use efficiency, even if the actual amount of nitrogen transferred to plant cells is small. More research is needed to evaluate the importance of nitrogen transfer within leaf and bract cells of plants.

Delineating genetic regulation of cannabinoid biosynthesis during female flower development in Cannabis sativa

Cannabinoids are predominantly produced in the glandular trichomes on cannabis female flowers. There is little known on how cannabinoid biosynthesis is regulated during female flower development. We aim to understand the rate-limiting step(s) in the cannabinoid biosynthetic pathway. We investigated the transcript levels of cannabinoid biosynthetic genes together with cannabinoid contents during 7 weeks of female flower development. We demonstrated that the enzymatic steps for producing cannabigerol (CBG), which involve genes GPPS, PT, TKS, and OAC, could rate limit cannabinoid biosynthesis. Our findings further suggest that upregulation of cannabinoid synthases, CBDAS and THCAS in a commercial hemp and medical marijuana variety, respectively, is not critical for cannabinoid biosynthesis. The cannabinoid biosynthetic genes are generally upregulated during flower maturation; increased expression occurs coincident with glandular trichome development and cannabinoid production in the maturing flower. The results also suggest that different cannabis varieties may experience discrete transcriptional regulation of cannabinoid biosynthetic genes. In addition, we showed that methyl jasmonate (MeJA) can potentially increase cannabinoid production. We propose that biweekly applications of 100 μM MeJA starting from flower initiation would be efficacious for promoting cannabinoid biosynthesis. Our findings provide important genetic information for cannabis breeding to generate new varieties with favorable traits.

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.

Triiron Tetrairon Phosphate (Fe7(PO4)6) Nanomaterials Enhanced Flavonoid Accumulation in Tomato Fruits

Flavonoids contribute to fruit sensorial and nutritional quality. They are also highly beneficial for human health and can effectively prevent several chronic diseases. There is increasing interest in developing alternative food sources rich in flavonoids, and nano-enabled agriculture provides the prospect for solving this action. In this study, triiron tetrairon phosphate (Fe₇(PO₄)₆) nanomaterials (NMs) were synthesized and amended in soils to enhance flavonoids accumulation in tomato fruits. 50 mg kg⁻¹ of Fe₇(PO₄)₆ NMs was the optimal dose based on its outstanding performance on promoting tomato fruit flavonoids accumulation. After entering tomato roots, Fe₇(PO₄)₆ NMs promoted auxin (IAA) level by 70.75 and 164.21% over Fe-EDTA and control, and then up-regulated the expression of genes related to PM H⁺ ATPase, leading to root proton ef-flux at 5.87 pmol cm⁻² s⁻¹ and rhizosphere acidification. More Mg, Fe, and Mn were thus taken up into plants. Subsequently, photosynthate was synthesized, and transported into fruits more rapidly to increase flavonoid synthesis potential. The metabolomic and transcriptomic profile in fruits further revealed that Fe₇(PO₄)₆ NMs regulated sucrose metabolism, shi-kimic acid pathway, phenylalanine synthesis, and finally enhanced flavonoid biosynthesis. This study implies the potential of NMs to improve fruit quality by enhancing flavonoids synthesis and accumulation.

Control of resource allocation between primary and specialized metabolism in glandular trichomes

Plant specialized metabolites are often synthesized and stored in dedicated morphological structures such as glandular trichomes, resin ducts, or laticifers where they accumulate in large concentrations. How this high productivity is achieved is still elusive, in particular, with respect to the interface between primary and specialized metabolism. Here, we focus on glandular trichomes to survey recent progress in understanding how plant metabolic cell factories manage to balance homeostasis of essential central metabolites while producing large quantities of compounds that constitute a metabolic sink. In particular, we review the role of gene duplications, transcription factors and photosynthesis.

Coenzymes and the primary and specialized metabolism interface

In plants, primary and specialized metabolism have classically been distinguished as either essential for growth or required for survival in a particular environment. Coenzymes (organic cofactors) are essential for growth but their importance to specialized metabolism is often not considered. In line with the recent proposal of viewing primary and specialized metabolism as an integrated whole rather than segregated lots with a defined interface, we highlight here the importance of collating information on the regulation of coenzyme supply with metabolic demands using examples of vitamin B derived coenzymes. We emphasize that coenzymes can have enormous influence on the outcome of metabolic as well as engineered pathways and should be taken into account in the era of synthetic biology.

Engineering of tomato type VI glandular trichomes for trans-chrysanthemic acid biosynthesis, the acid moiety of natural pyrethrin insecticides

Glandular trichomes, known as metabolic cell factories, have been proposed as highly suitable for metabolically engineering the production of plant high-value specialized metabolites. Natural pyrethrins, found only in Dalmatian pyrethrum (Tanacetum cinerariifolium), are insecticides with low mammalian toxicity and short environmental persistence. Type I pyrethrins are esters of the monoterpenoid trans-chrysanthemic acid with one of the three rethrolone-type alcohols. To test if glandular trichomes can be made to synthesize trans-chrysanthemic acid, we reconstructed its biosynthetic pathway in tomato type VI glandular trichomes, which produce large amounts of terpenoids that share the precursor dimethylallyl diphosphate (DMAPP) with this acid. This was achieved by coexpressing the trans-chrysanthemic acid pathway related genes including TcCDS encoding chrysanthemyl diphosphate synthase and the fusion gene of TcADH2 encoding the alcohol dehydrogenase 2 linked with TcALDH1 encoding the aldehyde dehydrogenase 1 under the control of a newly identified type VI glandular trichome-specific metallocarboxypeptidase inhibitor promoter. Whole tomato leaves harboring type VI glandular trichomes expressing all three aformentioned genes had a concentration of total trans-chrysanthemic acid that was about 1.5-fold higher (by mole number) than the levels of β-phellandrene, the dominant monoterpene present in non-transgenic leaves, while the levels of β-phellandrene and the representative sesquiterpene β-caryophyllene in transgenic leaves were reduced by 96% and 81%, respectively. These results suggest that the tomato type VI glandular trichome is an alternative platform for the biosynthesis of trans-chrysanthemic acid by metabolic engineering.

Flavonoid deficiency disrupts redox homeostasis and terpenoid biosynthesis in glandular trichomes of tomato

Glandular trichomes (GTs) are epidermal structures that provide the first line of chemical defense against arthropod herbivores and other biotic threats. The most conspicuous structure on leaves of cultivated tomato (Solanum lycopersicum) is the type-VI GT (tVI-GT), which accumulates both flavonoids and volatile terpenoids. Although these classes of specialized metabolites are derived from distinct metabolic pathways, previous studies with a chalcone isomerase 1 (CHI1)-deficient mutant called anthocyanin free (af) showed that flavonoids are required for terpenoid accumulation in tVI-GTs. Here, we combined global transcriptomic and proteomic analyses of isolated trichomes as a starting point to show that the lack of CHI1 is associated with reduced levels of terpenoid biosynthetic transcripts and enzymes. The flavonoid deficiency in af trichomes also resulted in the upregulation of abiotic stress-responsive genes associated with DNA damage and repair. Several lines of biochemical and genetic evidence indicate that the terpenoid defect in af mutants is specific for the tVI-GT and is associated with the absence of bulk flavonoids rather than loss of CHI1 per se. A newly developed genome-scale model of metabolism in tomato tVI-GTs helped identify metabolic imbalances caused by the loss of flavonoid production. We provide evidence that flavonoid deficiency in this cell type leads to increased production of reactive oxygen species (ROS), which may impair terpenoid biosynthesis. Collectively, our findings support a role for flavonoids as ROS-scavenging antioxidants in GTs.

Steroidal alkaloids defence metabolism and plant growth are modulated by the joint action of gibberellin and jasmonate signalling

Steroidal glycoalkaloids (SGAs) are protective metabolites constitutively produced by Solanaceae species. Genes and enzymes generating the vast structural diversity of SGAs have been largely identified. Yet, mechanisms of hormone pathways coordinating defence (jasmonate; JA) and growth (gibberellin; GA) controlling SGAs metabolism remain unclear. We used tomato to decipher the hormonal regulation of SGAs metabolism during growth vs defence tradeoff. This was performed by genetic and biochemical characterisation of different JA and GA pathways components, coupled with in vitro experiments to elucidate the crosstalk between these hormone pathways mediating SGAs metabolism. We discovered that reduced active JA results in decreased SGA production, while low levels of GA or its receptor led to elevated SGA accumulation. We showed that MYC1 and MYC2 transcription factors mediate the JA/GA crosstalk by transcriptional activation of SGA biosynthesis and GA catabolism genes. Furthermore, MYC1 and MYC2 transcriptionally regulate the GA signalling suppressor DELLA that by itself interferes in JA-mediated SGA control by modulating MYC activity through protein-protein interaction. Chemical and fungal pathogen treatments reinforced the concept of JA/GA crosstalk during SGA metabolism. These findings revealed the mechanism of JA/GA interplay in SGA biosynthesis to balance the cost of chemical defence with growth.

An advanced method for the release, enrichment and purification of high-quality Arabidopsis thaliana rosette leaf trichomes enables profound insights into the trichome proteome

BACKGROUND

Rosette leaf trichomes of Arabidopsis thaliana have been broadly used to study cell development, cell differentiation and, more recently, cell wall biogenesis. However, trichome-specific biochemical or -omics analyses require a proper separation of trichomes from residual plant tissue. Thus, different strategies were proposed in the past for trichome isolation, which mostly rely on harsh conditions and suffer from low yield, thereby limiting the spectrum of downstream analyses.

RESULTS

To take trichome-leaf separation to the next level, we revised a previously proposed method for isolating A. thaliana trichomes by optimizing the mechanical and biochemical specifications for trichome release. We additionally introduced a density gradient centrifugation step to remove residual plant debris. We found that prolonged, yet mild seedling agitation increases the overall trichome yield by more than 60% compared to the original protocol. We noticed that subsequent density gradient centrifugation further visually enhances trichome purity, which may be advantageous for downstream analyses. Gene expression analysis by quantitative reverse transcriptase-polymerase chain reaction validated a substantial enrichment upon purification of trichomes by density gradient centrifugation. Histochemical and biochemical investigation of trichome cell wall composition indicated that unlike the original protocol gentle agitation during trichome release largely preserves trichome integrity. We used enriched and density gradient-purified trichomes for proteomic analysis in comparison to trichome-depleted leaf samples and present a comprehensive reference data set of trichome-resident and -enriched proteins. Collectively we identified 223 proteins that are highly enriched in trichomes as compared to trichome-depleted leaves. We further demonstrate that the procedure can be applied to retrieve diverse glandular and non-glandular trichome types from other plant species.

CONCLUSIONS

We provide an advanced method for the isolation of A. thaliana leaf trichomes that outcompetes previous procedures regarding yield and purity. Due to the large amount of high-quality trichomes our method enabled profound insights into the so far largely unexplored A. thaliana trichome proteome. We anticipate that our protocol will be of use for a variety of downstream analyses, which are expected to shed further light on the biology of leaf trichomes in A. thaliana and possibly other plant species.

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.