Evolution of secondary metabolites from an ecological and molecular phylogenetic perspective

Specialised metabolites as chemotaxonomic markers of Coptosapelta diffusa, supporting its delimitation as sisterhood phylogenetic relationships with Rubioideae

From the aerial extracts of Coptosapelta diffusa (Champ. ex Benth.) Steenis, twenty-one compounds were isolated and identified by means of column chromatography and NMR and MS techniques, respectively. Amongst, ten ones were determined to be undescribed compounds including six seco-iridoid glucosides (1-6), 2-(hydroxymethyl)-1,2,3,4-tetrahydroanthracene-9,10-dione (7) and three guaiane-type sesquiterpenes (15-17). Compounds 7, 8 and 9 exhibited inhibitory activities against Staphylococcus aureus ATCC25923 with MIC of 8, 4 and 8 μg/mL. The use of 1-6 (iridoids), 7-14 (anthraquinones) and 15-17 (sesquiterpenes) as chemotaxonomic markers for this species was evidenced. Structurally, 7-14 are similar to those anthraquinones isolated from other species of the family Rubiaceae, confirming their close phylogenetic relationship. Whereas, these iridoids and sesquiterpenes with unique structures provided chemotaxonomic evidence to support the genus Coptosapelta (the tribe Coptosapelteae) as a sister of the subfamily Rubioideae. These results contrast with the general producing tendency of indole alkaloids by the species of the subfamily Cinchonoideae, and merit chemotaxonomic significance for the delimitation of Coptosapelta.

Aquatic occurrence of phytotoxins in small streams triggered by biogeography, vegetation growth stage, and precipitation

Toxic plant secondary metabolites (PSMs), so-called phytotoxins, occur widely in plant species. Many of these phytotoxins have similar mobility, persistence, and toxicity properties in the environment as anthropogenic micropollutants, which increasingly contaminate surface waters. Although recent case studies have shown the aquatic relevance of phytotoxins, the overall exposure remains unknown. Therefore, we performed a detailed occurrence analysis covering 134 phytotoxins from 27 PSM classes. Water samples from seven small Swiss streams with catchment areas from 1.7 to 23 km² and varying land uses were gathered over several months to investigate seasonal impacts. They were complemented with samples from different biogeographical regions to cover variations in vegetation. A broad SPE-LC-HRMS/MS method was applied with limits of detection below 5 ng/L for over 80% of the 134 included phytotoxins. In total, we confirmed 39 phytotoxins belonging to 13 PSM classes, which corresponds to almost 30% of all included phytotoxins. Several alkaloids were regularly detected in the low ng/L-range, with average detection frequencies of 21%. This is consistent with the previously estimated persistence and mobility properties that indicated a high contamination potential. Coumarins were previously predicted to be unstable, however, detection frequencies were around 89%, and maximal concentrations up to 90 ng/L were measured for fraxetin produced by various trees. Overall, rainy weather conditions at full vegetation led to the highest total phytotoxin concentrations, which might potentially be most critical for aquatic organisms.

Structural and histochemical attributes of secretory ducts and cavities in leaves of four species of Calophyllaceae J. Agardh in Amazonian savannas

This study represents an important contribution to the structural, histochemical and biological understanding of ducts and cavities in leaves of four species of Calophyllaceae that occur in Amazonian savannas. Samples of adult leaves were processed using light, scanning and transmission electron microscopy, as per usual methods for plant anatomy. In paradermal sections, the lumina of ducts are elongated while those of cavities are short. Ducts occur exclusively in the central rib and are abundant in Kielmeyera rubriflora Cambess and Kielmeyera coriacea Mart. and Zucc and larger than in Calophyllum brasiliense Cambess and Caraipa densifolia Mart. In mesophyll, the type of secretory structure and distribution pattern of the ducts and cavities are distinct. In most species, the secreted metabolites are similar and consist of phenolic compounds, lipids, essential oils with oleoresins, mucilage, neutral polysaccharides, proteins and alkaloids, except in K. coriacea, which does not contain oleoresin. The secretion is probably synthesized by mitochondria, rough endoplasmic reticulum, ribosomes and dictyosomes and is externalized toward the lumen by granulocrine and eccrine processes. In addition to being of diagnostic value for species identification, the attributes of the lumen shape, type of secretory structure, distribution pattern, identified metabolites and secretion mechanism are important for understanding the biological roles of ducts and cavities. The identified metabolites reveal a capacity for adaptation, resistance and protection from the action of herbivores and pathogens, and in water retention.

A Study of Phytochemistry, Genoprotective Activity, and Antitumor Effects of Extracts of the Selected Lamiaceae Species

This study was designed to evaluate the genoprotective, antigenotoxic, as well as antitumor potential of methanolic, ethanolic, and aqueous extracts of Melissa officinalis, Mentha × piperita, Ocimum basilicum, Rosmarinus officinalis, Salvia officinalis, and Satureja montana (Lamiaceae), in different model systems. The polyphenols in these extracts were quantified both spectrophotometrically and using HPLC-DAD technique, while DPPH assay was used to assess the antioxidant activity. The genoprotective potential was tested on pUC19 Escherichia coli XL1-blue, and the antigenotoxicity on Salmonella typhimurium TA1535/pSK1002 and human lung fibroblasts, while the antitumor activity was assessed on colorectal cancer cells. Rosmarinic acid, quercetin, rutin, and luteolin-7-O-glucoside were among the identified compounds. Methanolic extracts had the best DPPH-scavenging and SOS-inducing activities, while ethanolic extracts exhibited the highest antigenotoxicity. Additionally, all extracts exhibited genoprotective potential on plasmid DNA. The antitumor effect was mediated by modulation of reactive oxygen species (ROS), nitric oxide (NO) production, and exhibition of genotoxic effects on tumor cells, especially with O. basilicum ethanolic extract. Generally, the investigated extracts were able to provide antioxidant protection for the acellular, prokaryotic, and normal human DNA, while also modulating the production of ROS and NO in tumor cells, leading to genotoxicity toward these cells and their decrease in proliferation.

Phytochemical, Pharmacological, and Biotechnological Study of Ageratina pichinchensis: A Native Species of Mexico

Ageratina pichinchensis (Asteraceae) has been used for a long time in traditional Mexican medicine for treating different skin conditions and injuries. This review aimed to provide an up-to-date view regarding the traditional uses, chemical composition, and pharmacological properties (in vitro, in vivo, and clinical trials) that have been achieved using crude extracts, fractions, or pure compounds. Moreover, for a critical evaluation of the published literature, key databases (Pubmed, Science Direct, and SciFinder, among others) were systematically searched using keywords to retrieve relevant publications on this plant. Studies that reported on crude extracts, fractions, or isolated pure compounds of A. pichinchensis have found a varied range of biological effects, including antibacterial, curative, antiulcer, antifungal, and anti-inflammatory activities. Phytochemical analyses of different parts of A. pichinchensis revealed 47 compounds belonging to chromenes, furans, glycosylated flavonoids, terpenoids, and essential oils. Furthermore, biotechnological studies of A. pichinchensis such as callus and cell suspension cultures have provided information for future research perspectives to improve the production of valuable bioactive compounds.

Crop host signatures reflected by co-association patterns of keystone Bacteria in the rhizosphere microbiota

BACKGROUND

The native crop bacterial microbiota of the rhizosphere is envisioned to be engineered for sustainable agriculture. This requires the identification of keystone rhizosphere Bacteria and an understanding on how these govern crop-specific microbiome assembly from soils. We identified the metabolically active bacterial microbiota (SSU RNA) inhabiting two compartments of the rhizosphere of wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), rye (Secale cereale), and oilseed rape (Brassica napus L.) at different growth stages.

RESULTS

Based on metabarcoding analysis the bacterial microbiota was shaped by the two rhizosphere compartments, i.e. close and distant. Thereby implying a different spatial extent of bacterial microbiota acquirement by the cereals species versus oilseed rape. We derived core microbiota of each crop species. Massilia (barley and wheat) and unclassified Chloroflexi of group 'KD4-96' (oilseed rape) were identified as keystone Bacteria by combining LEfSe biomarker and network analyses. Subsequently, differential associations between networks of each crop species' core microbiota revealed host plant-specific interconnections for specific genera, such as the unclassified Tepidisphaeraceae 'WD2101 soil group'.

CONCLUSIONS

Our results provide keystone rhizosphere Bacteria derived from for crop hosts and revealed that cohort subnetworks and differential associations elucidated host species effect that was not evident from differential abundance of single bacterial genera enriched or unique to a specific plant host. Thus, we underline the importance of co-occurrence patterns within the rhizosphere microbiota that emerge in crop-specific microbiomes, which will be essential to modify native crop microbiomes for future agriculture and to develop effective bio-fertilizers.

Bioactive properties of Persea lingue Ness (Lauraceae) fruit and leaf extracts

Persea lingue Ness is a tree species that lives mainly in temperate forests of south-central Chile. Its leaves are used in ethnomedicine, the fruit is a drupe similar to that of the avocado and has not been studied. The aim of this study was to determine the cytotoxicity in leukemia cell and antibacterial activity, along with some chemical content characteristics of P. lingue fruit and leaf extracts. The antibacterial activity was determined by the inhibition of bacterial growth in liquid medium assay against Gram-positive and Gram-negative bacteria. The leukemia cell lines Kasumi-1 and Jurkat were used to evaluate the cytotoxic activity by using propidium iodide and AlamarBlue assays. Total phenolic, flavonoid, condensed tannin, alkaloid and lipid contents were evaluated in the fruit and in the leaf extracts. The antioxidant activity of both extracts were also elavaluated. Leaf extract presented the highest content of total phenols, condensed tannins and flavonoids, and also the highest antioxidant activity. While the fruit extract has a higher amount of lipids and alkaloids and the high antibacterial activity against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Bacillus megaterium and Micrococcus luteus. The leaf extract only showed activity against M. luteus. Concerning the cytotoxic activity, only the fruit extract showed cytotoxicity against the cell lines Jurkat and Kasumi-1. P. lingue fruit extract is a potential source of biologically active molecules for the development of new drugs to be used in some types of leukemia, as well as antibacterial agent.

Protective effect of Callistemon citrinus on oxidative stress in rats with 1,2-dimethylhydrazine-induced colon cancer

Callistemon citrinus has terpenes effective in inducing antioxidant enzymes, an important mechanism involved in cancer chemoprevention. This study investigated the chemopreventive efficacy of herbal preparation of C. citrinus leaves against the oxidative stress produced during the colorectal cancer (CRC) in male Wistar rats. The amelioration of toxicity in a model of CRC induced with 1,2-dimethylhydrazine (DMH) was determined by assessing antioxidant enzymes, phase II enzymes activities and lipid peroxidation (LPO) products after 22 weeks of treatment. C. citrinus was administered at a daily oral dose of 250 mg/kg. The activities in proximal, middle and distal colon, liver, kidney and heart were determined. C. citrinus showed a strong antioxidant activity that correlated with the high content of phenolics and terpenoids. DMH treated animals showed a decrease of the enzymes activity in most tissues and the level of reduced glutathione (GSH). Conversely, the levels of lipid peroxidation products were increased. Macroscopic examination revealed the protective effect of C. citrinus in damaged organs caused by DMH. Moreover, histopathological examination of the liver displayed normal structure in the C. citrinus-treated group, unlike the DMH-treated group. C. citrinus supplementation significantly maintained or increased the antioxidant enzyme activities, whereas lipid peroxidation products levels were reduced to values similar to the level of control group. The ability of C. citrinus to induce the antioxidant system reduced the damage of oxidative stress, which makes this plant a good candidate to be used as a prevention agent in treatment of diseases such as colorectal cancer.

Phytochemistry reflects different evolutionary history in traditional classes versus specialized structural motifs

Foundational hypotheses addressing plant-insect codiversification and plant defense theory typically assume a macroevolutionary pattern whereby closely related plants have similar chemical profiles. However, numerous studies have documented variation in the degree of phytochemical trait lability, raising the possibility that phytochemical evolution is more nuanced than initially assumed. We utilize proton nuclear magnetic resonance (1H NMR) data, chemical classification, and double digest restriction-site associated DNA sequencing (ddRADseq) to resolve evolutionary relationships and characterize the evolution of secondary chemistry in the Neotropical plant clade Radula (Piper; Piperaceae). Sequencing data substantially improved phylogenetic resolution relative to past studies, and spectroscopic characterization revealed the presence of 35 metabolite classes. Metabolite classes displayed phylogenetic signal, whereas the crude 1H NMR spectra featured little evidence of phylogenetic signal in multivariate tests of chemical resonances. Evolutionary correlations were detected in two pairs of compound classes (flavonoids with chalcones; p-alkenyl phenols with kavalactones), where the gain or loss of a class was dependent on the other's state. Overall, the evolution of secondary chemistry in Radula is characterized by strong phylogenetic signal of traditional compound classes and weak phylogenetic signal of specialized chemical motifs, consistent with both classic evolutionary hypotheses and recent examinations of phytochemical evolution in young lineages.

Metabolomic analysis reveals reliance on secondary plant metabolites to facilitate carnivory in the Cape sundew, Drosera capensis

BACKGROUND AND AIMS

Secondary metabolites are integral to multiple key plant processes (growth regulation, pollinator attraction and interactions with conspecifics, competitors and symbionts) yet their role in plant adaptation remains an underexplored area of research. Carnivorous plants use secondary metabolites to acquire nutrients from prey, but the extent of the role of secondary metabolites in plant carnivory is not known. We aimed to determine the extent of the role of secondary metabolites in facilitating carnivory of the Cape sundew, Drosera capensis.

METHODS

We conducted metabolomic analysis of 72 plants in a time-series experiment before and after simulated prey capture. We used ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) and the retention time index to identify compounds in the leaf trap tissue that changed up to 72 h following simulated prey capture. We identified associated metabolic pathways, and cross-compared these compounds with metabolites previously known to be involved in carnivorous plants across taxa.

KEY RESULTS

For the first time in a carnivorous plant, we have profiled the whole-leaf metabolome response to prey capture. Reliance on secondary plant metabolites was higher than previously thought - 2383 out of 3257 compounds in fed leaves had statistically significant concentration changes in comparison with unfed controls. Of these, ~34 compounds are also associated with carnivory in other species; 11 are unique to Nepenthales. At least 20 compounds had 10-fold changes in concentration, 12 of which had 30-fold changes and are typically associated with defence or attraction in non-carnivorous plants.

CONCLUSIONS

Secondary plant metabolites are utilized in plant carnivory to an extent greater than previously thought - we found a whole-metabolome response to prey capture. Plant carnivory, at the metabolic level, likely evolved from at least two distinct functions: attraction and defence. Findings of this study support the hypothesis that secondary metabolites play an important role in plant diversification and adaptation to new environments.

Fruit Colour and Novel Mechanisms of Genetic Regulation of Pigment Production in Tomato Fruits

Fruit colour represents a genetic trait with ecological and nutritional value. Plants mainly use colour to attract animals and favour seed dispersion. Thus, in many species, fruit colour coevolved with frugivories and their preferences. Environmental factors, however, represented other adaptive forces and further diversification was driven by domestication. All these factors cooperated in the evolution of tomato fruit, one of the most important in human nutrition. Tomato phylogenetic history showed two main steps in colour evolution: the change from green-chlorophyll to red-carotenoid pericarp, and the loss of the anthocyanic pigmentation. These events likely occurred with the onset of domestication. Then spontaneous mutations repeatedly occurred in carotenoid and phenylpropanoid pathways, leading to colour variants which often were propagated. Introgression breeding further enriched the panel of pigmentation patterns. In recent decades, the genetic determinants underneath tomato colours were identified. Novel evidence indicates that key regulatory and biosynthetic genes undergo mechanisms of gene expression regulation that are much more complex than what was imagined before: post-transcriptional mechanisms, with RNA splicing among the most common, indeed play crucial roles to fine-tune the expression of this trait in fruits and offer new substrate for the rise of genetic variables, thus providing further evolutionary flexibility to the character.

Exposure and Transport of Alkaloids and Phytoestrogens from Soybeans to Agricultural Soils and Streams in the Midwestern United States

Phytotoxins are naturally produced toxins with potencies similar/higher than many anthropogenic micropollutants. Nevertheless, little is known regarding their environmental fate and off-field transport to streams. To fill this research gap, a network of six basins in the Midwestern United States with substantial soybean production was selected for the study. Stream water (n = 110), soybean plant tissues (n = 8), and soil samples (n = 16) were analyzed for 12 phytotoxins (5 alkaloids and 7 phytoestrogens) and 2 widely used herbicides (atrazine and metolachlor). Overall, at least 1 phytotoxin was detected in 82% of the samples, with as many as 11 phytotoxins detected in a single sample (median = 5), with a concentration range from below detection to 37 and 68 ng/L for alkaloids and phytoestrogens, respectively. In contrast, the herbicides were ubiquitously detected at substantially higher concentrations (atrazine: 99% and metolachlor: 83%; the concentrations range from below detection to 150 and 410 ng/L, respectively). There was an apparent seasonal pattern for phytotoxins, where occurrence prior to and during harvest season (September to November) and during the snow melt season (March) was higher than that in December-January. Runoff events increased phytotoxin and herbicide concentrations compared to those in base-flow conditions. Phytotoxin plant concentrations were orders of magnitude higher compared to those measured in soil and streams. These results demonstrate the potential exposure of aquatic and terrestrial organisms to soybean-derived phytotoxins.

The case of tryptamine and serotonin in plants: a mysterious precursor for an illustrious metabolite

Indolamines are tryptophan-derived specialized metabolites belonging to the huge and ubiquitous indole alkaloids group. Serotonin and melatonin are the best-characterized members of this family, given their many hormonal and physiological roles in animals. Following their discovery in plants, the study of plant indolamines has flourished and their involvement in important processes, including stress responses, growth and development, and reproduction, has been proposed, leading to their classification as a new category of phytohormones. However, the complex indolamine puzzle is far from resolved, particularly the biological roles of tryptamine, the early serotonin precursor representing the central hub of many downstream indole alkaloids. Tryptophan decarboxylase, which catalyzes the synthesis of tryptamine, strictly regulates the flux of carbon and nitrogen from the tryptophan pool into the indolamine pathway. Furthermore, tryptamine accumulates to high levels in the reproductive organs of many plant species and therefore cannot be classed as a mere intermediate but rather as an end product with potentially important functions in fruits and seeds. This review summarizes current knowledge on the role of tryptamine and its close relative serotonin, emphasizing the need for a clear understanding of the functions of, and mutual relations between, these indolamines and their biosynthesis pathways in plants.

Effects of curcumin-loaded poly(lactic-co-glycolic acid) nanoparticles in MDA-MB231 human breast cancer cells

Aim: This study was aimed at evaluating the anticancer potential of curcumin-loaded poly(lactic-co-glycolic acid) (PLGA) based nanoparticles (NPs) in MDA-MB231 human breast cancer cells. Methods: Curcumin-loaded PLGA NPs were developed using a modified solvent evaporation technique. Physical characterization was performed on the formulated NPs. Furthermore, in vitro experiments were conducted to study the biological activity of the curcumin-loaded NPs. Results: Curcumin-loaded PLGA NPs demonstrated high encapsulation efficiency and sustained payload release. Moreover, the NPs exhibited a significant reduction in cell viability, cell migration and cell invasion in the MDA-MB231 cells. Conclusion: The study revealed that the formulated curcumin-loaded PLGA NPs possessed significant anti-metastatic properties. The findings showcased the possible potential of curcumin-loaded NPs in the management of debilitating conditions such as cancer. In addition, this study could form the basis for further research and advancements in this area.

Endophytic Isaria javanica pf185 Persists after Spraying and Controls Myzus persicae (Hemiptera: Aphididae) and Colletotrichum acutatum (Glomerellales: Glomerellaceae) in Pepper

Simple Summary

The green peach aphid (Myzus persicae) and the phytopathogenic fungus Colletotrichum acutatum cause significant losses in a wide variety of crops. To efficiently protect their crops, farmers use chemical pesticides, but this kind of practice is not sustainable because of its negative effects on the environment. This study suggests an environmentally friendly method such as the use of the endophytic Isaria javanica pf185 in pepper plants. Suspension of the endophytic fungus (EF) was sprayed on plants under cage while those same leaves were sampled and assessed under laboratory conditions. The EF can both penetrate inside the leaf tissues and survive on the surface of the leaf after five weeks. The suspension showed an evident insecticidal efficiency against M. persicae and a lower one against C. acutatum. Therefore, its antifungal efficiency against C. acutatum was not correlated with weather patterns. Authors recommend I. javanica pf185 as a potential biocontrol agent against M. persicae and C. acutatum.

Abstract

This study endeavored to sustainably control aphids and anthracnose after spraying endophytic Isaria javanica pf185 under field conditions. Under two different tents; one batch of seedlings was sprayed with a 10⁷ conidia/mL I. javanica pf185 suspension; while another was sprayed with 0.05% Tween 80^® in distilled water. Six leaf discs from the top; middle; and bottom part of the plant canopy were weekly collected and placed on moistened filter paper in a Petri dish for insecticidal and antifungal bioassays against Myzus persicae and Colletotrichum acutatum. Differences were noticed from the 18th day after spraying with mortality (86.67 ± 0.57% versus 36.67 ± 0.64%) and leaf damage (13.45 ± 0.03% versus 41.18 ± 0.06%) on fungus-treated and controlled, respectively. The corrected insecticidal efficacy was 20.43, 39.82, 72.32, 66.43 and 70.04%, while the corrected fungicidal efficacy was 26.07, 38.01, 53.35, 29.08 and 41.81% during five successive weeks. A positive correlation was evident between insecticidal efficacy and relative humidity (r² = 0.620) and temperature (r² = 0.424), respectively. No correlation was found between antifungal activity and relative humidity (r² = 0.061) and temperature (r² = 0), respectively. The entomopathogenic fungus survived on leaf surface area and in tissues after spraying.

The potential of nuclear magnetic resonance (NMR) in metabolomics and lipidomics of microalgae- a review

Microalgae biotechnology has made it possible to derive secondary bioactive metabolites from microalgae strains that have opened up their entire potential to uncover a wide range of novel metabolic capabilities and turn these into bio-products for the development of sustainable bio-refineries. Nuclear Magnetic Resonance Technology (NMR) has been one of the most successful and functional research technology over the past two decades to analyse the composition, structure and functionality of distinct metabolites in the different microalgae strains. This technology offers qualitative as well as quantitative knowledge about the endogenous metabolites and lipids of low molecular mass to offer a good picture of the physiological state of biological samples in metabolomics and lipidomics studies. Henceforth, this review is aimed at introducing the metabolomics and lipidomics studies into the field of NMR technology and also highlights the protocols for the isolation and metabolic measurements of metabolites from microalgae that should be redirected to resource recovery and value-added products with a systematic and holistic approach for scalability or sustainability.

Great chemistry between us: The link between plant chemical defenses and butterfly evolution

Plants constantly cope with insect herbivory, which is thought to be the evolutionary driver for the immense diversity of plant chemical defenses. Herbivorous insects are in turn restricted in host choice by the presence of plant chemical defense barriers. In this study, we analyzed whether butterfly host-plant patterns are determined by the presence of shared plant chemical defenses rather than by shared plant evolutionary history. Using correlation and phylogenetic statistics, we assessed the impact of host-plant chemical defense traits on shaping northwestern European butterfly assemblages at a macroevolutionary scale. Shared chemical defenses between plant families showed stronger correlation with overlap in butterfly assemblages than phylogenetic relatedness, providing evidence that chemical defenses may determine the assemblage of butterflies per plant family rather than shared evolutionary history. Although global congruence between butterflies and host-plant families was detected across the studied herbivory interactions, cophylogenetic statistics showed varying levels of congruence between butterflies and host chemical defense traits. We attribute this to the existence of multiple antiherbivore traits across plant families and the diversity of insect herbivory associations per plant family. Our results highlight the importance of plant chemical defenses in community ecology through their influence on insect assemblages.

Chemical similarity methods for analyzing secondary metabolite structures

The relation that exists between the structure of a compound and its function is an integral part of chemoinformatics. The similarity principle states that “structurally similar molecules tend to have similar properties and similar molecules exert similar biological activities”. The similarity of the molecules can either be studied at the structure level or at the descriptor level (properties level). Generally, the objective of chemical similarity measures is to enhance prediction of the biological activities of molecules. In this article, an overview of various methods used to compare the similarity between metabolite structures has been provided, including two-dimensional (2D) and three-dimensional (3D) approaches. The focus has been on methods description; e.g. fingerprint-based similarity in which the molecules under study are first fragmented and their fingerprints are computed, 2D structural similarity by comparing the Tanimoto coefficients and Euclidean distances, as well as the use of physiochemical properties descriptor-based similarity methods. The similarity between molecules could also be measured by using data mining (clustering) techniques, e.g. by using virtual screening (VS)-based similarity methods. In this approach, the molecules with the desired descriptors or /and structures are screened from large databases. Lastly, SMILES-based chemical similarity search is an important method for studying the exact structure search, substructure search and also descriptor similarity. The use of a particular method depends upon the requirements of the researcher.

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

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

Tropane alkaloids and terpenes synthase genes of Datura stramonium (Solanaceae)

Background

Plants have evolved physical–chemical defense to prevent/diminish damage by their enemies. Chemical defense involves the synthesis’ pathways of specialized toxic, repellent, or anti-nutritive metabolites to herbivores. Molecular evolutionary studies have revealed the origin of new genes, acquisition and functional diversification along time in different plant lineages.

Methods

Using bioinformatic tools we analyze gene divergence of tropane alkaloids (TAs) and terpene synthases (TPSs) in Datura stramonium and other species of Solanaceae; compared gene and amino acids sequence of TAs and TPSs on genomes, cDNA and proteins sequences of Viridiplantae. We analyzed two recently assembled genomes of D. stramonium (Ticumán and Teotihuacán), transcriptomes of Datura metel and genomes of other Solanaceae. Hence, we analyzed variation of TAs and TPSs to infer genes involved in plant defense and plant responses before stress. We analyzed protein modeling and molecular docking to predict interactions between H6H and ligand; we translated the sequences (Teo19488, Tic8550 and Tic8549) obtained from the two genomes of D. stramonium by using Swiss-Model and Ramachandran plot and MolProbity structure validation of Teo19488 protein model.

Results

For TAs, we detected an expansion event in the tropinone reductase II (TRII) and the ratio synonymous/non-synonymous substitutions indicate positive selection. In contrast, a contraction event and negative selection was detected in tropinone reductase I (TRI). In Hy-oscyamine 6 b-hydroxylase (H6H), enzyme involved in the production of tropane alkaloids atropine and scopolamine, the synonymous/non-synonymous substitution ratio in its dominion indicates positive selection. For terpenes (TPS), we found 18 DsTPS in D. stramomiun and seven in D. metel; evolutionary analyses detected positive selection in TPS10.1 and TPS10.2 of D. stramonium and D. metel. Comparison of copies of TPSs in D. stramonium detected variation among them in the binding site. Duplication events and differentiation of TAs and TPSs of D. stramonium, as compared to other Solanaceae, suggest their possible involvement on adaptive evolution of defense to herbivores. Protein modeling and docking show that the three protein structures obtained of DsH6H from Teo19488, Tic-8550 and Tic8549 maintain the same interactions and the union site of 2OG-FeII_Oxy with the Hy-o ligand as in 6TTM of D. metel.

Conclusion

Our results indicate differences in the number of gene copies involved in the synthesis of tropane alkaloids, between the genomes of D. stramonium from two Mexican populations. More copies of genes related to the synthesis of tropane alkaloids (TRI, TRII, H6H, PMT) are found in D. stramonium as compared to Viridiplantae. Likewise, for terpene synthases (TPS), TPS-10 is duplicated in D. stramonium and D. metel. Further studies should be directed to experimentally assess gain (overexpression) or loss (silencing) of function of duplicated genes.

Supercritical Fluid-Based Decellularization Technologies for Regenerative Medicine Applications

Supercritical fluid-based extraction technologies are currently being increasingly utilized in high purity extract products for food industries. In recent years, supercritical fluid-based extraction technology is transformed in biomaterials process fields to be further utilized for tissue engineering and other biomedical applications. In particular, supercritical fluid-based decellularization protocols have great advantage over the conventional decellularization as it may allow preservation of extracellular matrix components and structures. In this review, the latest technological development utilizing the supercritical fluid-based decellularization for regenerative medicine is introduced.

The Influence of Abiotic Stress Factors on the Morphophysiological and Phytochemical Aspects of the Acclimation of the Plant Rhodiola semenowii Boriss

Plants of the Crassulaceae family are natural accumulators of many medicinal secondary metabolites (SM). This article describes the study of morphophysiological, anatomic and phytochemical responses of immature plants of Rhodiolla semenovii under water deficit and (or) cold-stress conditions. Changes in biomass production due to water content in plant tissues such as a decrease in water deficit and an increase in cold stress were revealed. A significant decrease in the efficiency of the photosynthetic apparatus under stress conditions was noted, based on the parameters quantum efficiency of Photosystem II and electron transport rate and energy dissipated in Photosystem II. The greatest decrease in efficiency was pointed out in conditions of water shortage. The anatomical modulations of root and shoot of R. semenovii under stress conditions were found. For the first time, a detailed study of the chemical composition of the ethanol extract of root and shoot of R. semenovii under stress was carried out using gas chromatography-mass spectrometry. The qualitative and quantitative composition of SM associated with acclimation to the effects of abiotic stresses was determined. Both nonspecific and specific phytochemical changes caused by the action of water deficiency and cold treatment were identified. It has been shown that the antioxidant system in plant tissues is complex, multicomponent, depending on a number of natural and climatic factors. Further research should be focused on the use of abiotic stressors for the targeted synthesis of bioactive SMs valuable for pharmaceutical use.

Comparative analysis of antioxidant and antiproliferative activities of crude and purified flavonoid enriched fractions of pods/seeds of two desert legumes Prosopis cineraria and Cyamopsis tetragonoloba

Cyamopsis tetragonoloba and Prosopis cineraria are two legumes of the semi-arid region of Indian subcontinent which are unexplored with respect to their medicinal potential. Moreover, there is considerable lack in the comparative analysis of the biological properties of crude and enriched fractions obtained from the pods and seeds. Therefore, this study aims in investigating the effect of purification on the antioxidant and anticancerous activities of the extracts from the two legumes. This is the first study to purify an enriched methanolic fraction using Amberlite XAD7HP column chromatography followed by analysis using Thin Layer Chromatography. This matrix provided an economic and time efficient isolation of flavonoids and isoflavonoids from the seeds and pods of the above mentioned legumes. In addition, antioxidant activity carried out using DPPH assay showed that purification process did not contributed to enhanced antioxidant potential. However, inverse results were obtained during anticancerous activity assay on Huh-7 cell lines.

Elucidating the Fitness of a Dead-End Trap Crop Strategy against the Tomato Fruitworm, Helicoverpa armigera

Simple Summary

The tomato fruitworm, Helicoverpa armigera Hübner (Lepidoptera: Noctuidae), is a destructive polyphagous insect pest of tomatoes and its control largely depends on chemical pesticides. However, indiscriminate use of chemical pesticides has resulted in the development of resistance and posed serious environmental problems. Alternatively, in search of environmentally friendly pest management techniques, the use of trap crops has recently gained more attention. In this study, we compared different accessions of S. viarum to investigate which of them have the highest potential as a dead-end trap crop for H. armigera. Results from the laboratory experiment showed a significant variation among the S. viarum accessions in terms of H. armigera oviposition, and exhibited a higher level of resistance against H. armigera larvae compared to the tomato plants. Under the semi-field condition, trap cropping of S. viarum significantly reduces the total egg-laying of H. armigera on tomato. This study provides important information about the abilities of S. viarum plants to influence the life parameter of H. armigera and highlighted the possibilities to use S. viarum as a dead-end trap crop for the management of H. armigera. However, the efficacy of S. viarum needs to be tested under large, open-field conditions.

Abstract

Solanum viarum has been proposed as a potential dead-end trap crop for the management of Helicoverpa armigera because of its unsuitability for larval growth and survival despite being overwhelmingly preferred for oviposition. This study delved into the different S. viarum accessions for ovipositional preference and non-suitability for larval growth and survival of H. armigera. Besides, foliage trichomes, acylsugars, and phenolic content of S. viarum plants were assessed and compared with tomato. Since there is no significant variation in the ovipositional preference and larval performance of H. armigera, our result revealed that all those evaluated accessions of S. viarum have the potential to be used as a dead-end trap crop for the management of H. armigera. However, significant variation among the S. viarum accessions in terms of H. armigera oviposition was also evident in a no-choice experiment. Because of high-density glandular trichomes, acylsugars, and phenolic content, S. viarum significantly impaired H. armigera larval growth and survival compared to the tomato. Hence, our study elucidated that the S. viarum plant fits with the criteria for dead-end trap crop, and has the potential as a dead-end trap crop for the H. armigera, which needs to be tested under large, open-field conditions.

Theobroma cacao L. compounds: Theoretical study and molecular modeling as inhibitors of main SARS-CoV-2 protease

Cocoa beans contain antioxidant molecules with the potential to inhibit type 2 coronavirus (SARS-CoV-2), which causes a severe acute respiratory syndrome (COVID-19). In particular, protease. Therefore, using in silico tests, 30 molecules obtained from cocoa were evaluated. Using molecular docking and quantum mechanics calculations, the chemical properties and binding efficiency of each ligand was evaluated, which allowed the selection of 5 compounds of this series. The ability of amentoflavone, isorhoifolin, nicotiflorin, naringin and rutin to bind to the main viral protease was studied by means of free energy calculations and structural analysis performed from molecular dynamics simulations of the enzyme/inhibitor complex. Isorhoifolin and rutin stand out, presenting a more negative binding ΔG than the reference inhibitor N-[(5-methylisoxazol-3-yl)carbonyl]alanyl-l-valyl-N~1~-((1R,2Z)−4-(benzyloxy)−4-oxo-1-{[(3R)−2-oxopyrrolidin-3-yl]methyl}but-2-enyl)-L-leucinamide (N3). These results are consistent with high affinities of these molecules for the major SARS-CoV-2. The results presented in this paper are a solid starting point for future in vitro and in vivo experiments aiming to validate these molecules and /or test similar substances as inhibitors of SARS-CoV-2 protease.

Chemical Similarity of Co-occurring Trees Decreases With Precipitation and Temperature in North American Forests

Plant diversity varies immensely over large-scale gradients in temperature, precipitation, and seasonality at global and regional scales. This relationship may be driven in part by climatic variation in the relative importance of abiotic and biotic interactions to the diversity and composition of plant communities. In particular, biotic interactions may become stronger and more host specific with increasing precipitation and temperature, resulting in greater plant species richness in wetter and warmer environments. This hypothesis predicts that the many defensive compounds found in plants’ metabolomes should increase in richness and decrease in interspecific similarity with precipitation, temperature, and plant diversity. To test this prediction, we compared patterns of chemical and morphological trait diversity of 140 woody plant species among seven temperate forests in North America representing 16.2°C variation in mean annual temperature (MAT), 2,115 mm variation in mean annual precipitation (MAP), and from 10 to 68 co-occurring species. We used untargeted metabolomics methods based on data generated with liquid chromatography-tandem mass spectrometry to identify, classify, and compare 13,480 unique foliar metabolites and to quantify the metabolomic similarity of species in each community with respect to the whole metabolome and each of five broad classes of metabolites. In addition, we compiled morphological trait data from existing databases and field surveys for three commonly measured traits (specific leaf area [SLA], wood density, and seed mass) for comparison with foliar metabolomes. We found that chemical defense strategies and growth and allocation strategies reflected by these traits largely represented orthogonal axes of variation. In addition, functional dispersion of SLA increased with MAP, whereas functional richness of wood density and seed mass increased with MAT. In contrast, chemical similarity of co-occurring species decreased with both MAT and MAP, and metabolite richness increased with MAT. Variation in metabolite richness among communities was positively correlated with species richness, but variation in mean chemical similarity was not. Our results are consistent with the hypothesis that plant metabolomes play a more important role in community assembly in wetter and warmer climates, even at temperate latitudes, and suggest that metabolomic traits can provide unique insight to studies of trait-based community assembly.

Exploring the phytochemical variation of non-volatile metabolites within three South African Salvia species using UPLC-MS fingerprinting and chemometric analysis

The South African Salvia species, Salvia africana-lutea, S. lanceolata and S. chamelaeagnea, are widely used to treat fever and inflammation associated with skin and lung infections. The aim of this study was to explore the non-volatile secondary metabolites and the phytochemical variation within these lesser known species, to support product development and commercialisation. Chemical profiles of the methanol extracts of 81 wild-harvested samples were obtained using ultra performance-quadrupole-Time-of-Flight-mass spectrometry (UPLC-qToF-MS). Forty-one compounds, including caffeic acid, rosmarinic acid, carnosol, carnosic acid and ursolic acid, were detected and confirmed across the three species. Nineteen compounds were tentatively identified of which 14 have not been reported in these species. Principal component analysis revealed distinct clusters corresponding to the three species, confirming chemical differences. Marker compounds for each species were revealed using orthogonal projection to latent structures-discriminant analysis. Further chemometric analysis reflected a degree of intraspecies variation, although the chemistry within populations was mostly conserved. Potential chemotypes for each species were identified through unique compounds associated with each group. The concentrations of medicinally important metabolites, namely, rosmarinic acid, carnosol, carnosic acid and ursolic acid, were determined, using validated UPLC-PDA methods. Ursolic acid was present at levels up to 38.2 mg/g, confirming that these species are a rich source of this compound. No similar studies combining liquid chromatography with chemometric analysis, and utilising a large sample size from various habitats, have been reported for these three Salvia species. The results will guide selection of cultivars with the best attributes for the intended therapeutic application, thereby protecting wild populations from over-exploitation.

Multiple Molecular Mechanisms to Overcome Multidrug Resistance in Cancer by Natural Secondary Metabolites

Plant secondary metabolites (SMs) common natural occurrences and the significantly lower toxicities of many SM have led to the approaching development and use of these compounds as effective pharmaceutical agents; especially in cancer therapy. A combination of two or three of plant secondary metabolites together or of one SM with specific anticancer drugs, may synergistically decrease the doses needed, widen the chemotherapeutic window, mediate more effective cell growth inhibition, and avoid the side effects of high drug concentrations. In mixtures they can exert additive or even synergistic activities. Many SM can effectively increase the sensitivity of cancer cells to chemotherapy. In phytotherapy, secondary metabolites (SM) of medicinal plants can interact with single or multiple targets. The multi-molecular mechanisms of plant secondary metabolites to overcome multidrug resistance (MDR) are highlighted in this review. These mechanisms include interaction with membrane proteins such as P-glycoprotein (P-gp/MDR1); an ATP-binding cassette (ABC) transporter, nucleic acids (DNA, RNA), and induction of apoptosis. P-gp plays an important role in the development of MDR in cancer cells and is involved in potential chemotherapy failure. Therefore, the ingestion of dietary supplements, food or beverages containing secondary metabolites e.g., polyphenols or terpenoids may alter the bioavailability, therapeutic efficacy and safety of the drugs that are P-gp substrates.

Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook

Manually curated metabolic databases residing at the Sol Genomics Network comprise two taxon-specific databases for the Solanaceae family, i.e. SolanaCyc and the genus Nicotiana, i.e. NicotianaCyc as well as six species-specific databases for Nicotiana tabacum TN90, N. tabacum K326, Nicotiana benthamiana, N. sylvestris, N. tomentosiformis and N. attenuata. New pathways were created through the extraction, examination and verification of related data from the literature and the aid of external database guided by an expert-led curation process. Here we describe the curation progress that has been achieved in these databases since the first release version 1.0 in 2016, the curation flow and the curation process using the example metabolic pathway for cholesterol in plants. The current content of our databases comprises 266 pathways and 36 superpathways in SolanaCyc and 143 pathways plus 21 superpathways in NicotianaCyc, manually curated and validated specifically for the Solanaceae family and Nicotiana genus, respectively. The curated data have been propagated to the respective Nicotiana-specific databases, which resulted in the enrichment and more accurate presentation of their metabolic networks. The quality and coverage in those databases have been compared with related external databases and discussed in terms of literature support and metabolic content.

Influence of Mycosphaerella and Teratosphaeria leaf diseases on chemical composition of essential oils of Eucalyptus globulus and effect of these essential oils on ascospores germination

In a first step, essential oils were extracted from Eucalyptus globulus leaves, healthy and with symptoms and signs of Mycosphaerella leaf disease (MLD) and Teratosphaeria leaf disease (TLD), in two leaf stages. Stage 1: sessile, oval leaves covered by a waxy layer of a bluish colour, with opposite phyllotaxis, inserted along stems of quadrangular section. Stage 2: narrow and sickle leaves with a greyish green surface, mainly on the abaxial surface, inserted in alternating pairs along rounded stems. The essential oils were extracted by hydrodistillation and were analyzed by gas chromatography coupled with mass spectrometry. Chemical composition data and percentages of essential oil constituents were submitted to cluster analysis and principal component analysis. In a second step, under in vitro conditions, was evaluated the germination of Teratosphaeria nubilosa (one of the causal agents of TLD) ascospores in contact with the four types of essential oils extracted. The evaluations were performed at 24, 48 and 72 h after the experiments were assembled. The present study made it possible to distinguish and identify the chemical composition of essential oils from the eucalypt leaves used, and allowed 1,8-cineole to be identified as the major component for the essential oils investigated. The contact between essential oils and T. nubilosa spores allowed to prove the inhibition of the ascospores germination, being more efficient for the essential oils extracted from materials with the disease, which presented high amounts of 1,8-cineole.

Measuring Dietary Botanical Diversity as a Proxy for Phytochemical Exposure

The study of natural plant molecules and their medicinal properties, pharmacognosy, provides a taxonomy for botanical families that represent diverse chemical groupings with potentially distinct functions in relation to human health. Yet, this reservoir of knowledge has not been systematically applied to elucidating the role of patterns of plant food consumption on gut microbial ecology and function. All chemical classes of dietary phytochemicals can affect the composition of the microbes that colonize the gut and their function. In turn, the gut microbiome affects the host via multiple mechanisms including gut barrier function, immune function, satiety and taste regulation and the activity of biological signaling pathways that influence health and disease. Herein, we report the development of a botanical diversity index (BDI) to evaluate plant food consumption as a novel metric for identifying and quantifying phytochemicals to which an individual is exposed. A rationale is advanced for using the BDI to investigate how plant food diversity impacts gut microbial ecology and functionality.

Identification of CYP 2A6 inhibitors in an effort to mitigate the harmful effects of the phytochemical nicotine

AIM

In this study, our goal was to study the inhibition of nicotine metabolism by P450 2A6, as a means for reduction in tobacco use and consequently the prevention of smoking-related cancers. Nicotine, a phytochemical, is an addictive stimulant, responsible for the tobacco-dependence in smokers. Many of the other phytochemicals in tobacco, including polycyclic aromatic hydrocarbons, N-nitrosamines, and aromatic amines, are potent systemic carcinogens. Tobacco smoking causes about one of every five deaths in the United States annually. Nicotine plasma concentration is maintained by the smokers' smoking behavior within a small range. Nicotine is metabolized by cytochrome P450s 2A6 and 2A13 to cotinine. This metabolism causes a decrease in nicotine plasma levels, which in turn leads to increased tobacco smoking, and increased exposure to the tobacco carcinogens.

METHODS

Using the phytochemical nicotine as a lead structure, and taking its interactions with the P450 2A6 binding pocket into consideration, new pyridine derivatives were designed and synthesized as potential selective mechanism-based inhibitors for this enzyme.

RESULTS

The design and synthesis of two series of novel pyridine-based compounds, with varying substituents and substitution locations on the pyridine ring, as well as their inhibitory activities on cytochrome P450 2A6 and their interactions with its active site are discussed here. Substitutions at position 3 of the pyridine ring with an imidazole or propargyl ether containing group showed the most optimal interactions with the P4502A6 active site.

CONCLUSION

The pyridine compounds with an imidazole or propargyl ether containing substituent on position 3 were found to be promising lead compounds for further development. Hydrogen-bonding interactions were determined to be crucial for effective binding of these molecules within the P450 2A6 active site.

An overview of the genus Aloysia Paláu (Verbenaceae): Essential oil composition, ethnobotany and biological activities

Aloysia Paláu is an important herbal genus from the Verbenaceae family and possesses numerous remedial properties in the folk medicine of Asian, European, and, in particular, South American countries. Only a few reports have discussed some phytochemical characteristics associated with Aloysia species. Right the lack of an exhaustive report prompted us to organize this review article. Accordingly, besides the ethnobotanical knowledge of Aloysia species, their essential oil profiles, phytochemistry of the polar isolated fractions, and the relevant biological activities are discussed in detail.

Cluster Analysis of Medicinal Plants and Targets Based on Multipartite Network

Network-based methods for the analysis of drug-target interactions have gained attention and rely on the paradigm that a single drug can act on multiple targets rather than a single target. In this study, we have presented a novel approach to analyze the interactions between the chemicals in the medicinal plants and multiple targets based on the complex multipartite network of the medicinal plants, multi-chemicals, and multiple targets. The multipartite network was constructed via the conjunction of two relationships: chemicals in plants and the biological actions of those chemicals on the targets. In doing so, we introduced an index of the efficacy of chemicals in a plant on a protein target of interest, called target potency score (TPS). We showed that the analysis can identify specific chemical profiles from each group of plants, which can then be employed for discovering new alternative therapeutic agents. Furthermore, specific clusters of plants and chemicals acting on specific targets were retrieved using TPS that suggested potential drug candidates with high probability of clinical success. We expect that this approach may open a way to predict the biological functions of multi-chemicals and multi-plants on the targets of interest and enable repositioning of the plants and chemicals.

Host evolutionary relationships explain tree mortality caused by a generalist pest-pathogen complex

The phylogenetic signal of transmissibility (competence) and attack severity among hosts of generalist pests is poorly understood. In this study, we examined the phylogenetic effects on hosts differentially affected by an emergent generalist beetle-pathogen complex in California and South Africa. Host types (non-competent, competent and killed-competent) are based on nested types of outcomes of interactions between host plants, the beetles and the fungal pathogens. Phylogenetic dispersion analysis of each host type revealed that the phylogenetic preferences of beetle attack and fungal growth were a nonrandom subset of all available tree and shrub species. Competent hosts were phylogenetically narrower by 62 Myr than the set of all potential hosts, and those with devastating impacts were the most constrained by 107 Myr. Our results show a strong phylogenetic signal in the relative effects of a generalist pest-pathogen complex on host species, demonstrating that the strength of multi-host pest impacts in plants can be predicted by host evolutionary relationships. This study presents a unifying theoretical approach to identifying likely disease outcomes across multiple host-pest combinations.

Phytochemical profile and rosmarinic acid purification from two Peruvian Lepechinia Willd. species (Salviinae, Mentheae, Lamiaceae)

The phytochemical profile of Lepechinia meyenii (Walp.) Epling and Lepechina floribunda (Benth.) Epling obtained by liquid chromatography associated with high-resolution mass spectrometry is presented. Forty eight compounds were detected exhibiting a variety of salvianolic acids and abietane phenolic diterpenoids. A simple procedure by cold evaporative crystallization to purify rosmarinic acid from these botanical species was also shown.

Association of Genetic Structure and Diversity in Iranian Wild Germplasms of Mentha longifolia L. Based on Phenotypical, Biochemical, and Molecular Markers

Mentha longifolia L. is well-known to be one of the most pervasive wild-growing species of the Lamiaceae family, which has extensive beneficial properties in the fields of pharmacology and biological products. In the present study, the correlation between Inter-simple sequence repeat (ISSR) markers and morpho-chemical parameters of twenty different M. longifolia accessions (MLACs) were assessed. The geographic information system (GIS) has been employed to interpret the original habitat of the accessions in Iran. ISSR analysis indicated a remarkable difference in the studied accessions, segregated them into three main groups, constructed by an unweighted pair-group method with arithmetic (UPGMA) and principal coordinate analysis (PCoA). A total of 89 bands were generated by 12 ISSR primers, among which 82 (91.97 %) of them were polymorphic. The cluster analysis based on agro-morphological data scattered MLACs into two main groups. The essential oils (EOs) were analyzed through GC/FID/MS, and four chemotypes were characterized according to the major constituents. Pulegone ranged from 0.17 to 69.50 % was the main oil constituent with the highest content. Also, HPLC-PDA was employed to identify and to quantify the phenolic compounds in the MeOH extracts of MLACs. Heatmap cluster based on phenolic compounds produced three main categories of accessions. The components identified in the extracts were rosmarinic acid, rutin, vanillic acid, ferulic acid, chlorogenic acid, caffeic acid, 3,4-dihydroxybenzoic acid, 2,5-dihydroxybenzoic acid, and p-coumaric acid, which among them rosmarinic acid (RA) varied from 39.16 to 261.55 mg/100 g (DW) as a predominant constituent. Subsequently, multiple regression analyses between ISSR fragments and morpho-chemical data illustrated considerable relationships in the plant materials. The high variation and correlation observed in metabolic and phenotypic traits of MLACs establish an adequate source to conduct reserves conservation programs.

Metabolome-Wide, Phylogenetically Controlled Comparison Indicates Higher Phenolic Diversity in Tropical Tree Species

Tropical plants are expected to have a higher variety of defensive traits, such as a more diverse array of secondary metabolic compounds in response to greater pressures of antagonistic interactions, than their temperate counterparts. We test this hypothesis using advanced metabolomics linked to a novel stoichiometric compound classification to analyze the complete foliar metabolomes of four tropical and four temperate tree species, which were selected so that each subset contained the same amount of phylogenetic diversity and evenness. We then built Bayesian phylogenetic multilevel models to test for tropical–temperate differences in metabolite diversity for the entire metabolome and for four major families of secondary compounds. We found strong evidence supporting that the leaves of tropical tree species have a higher phenolic diversity. The functionally closer group of polyphenolics also showed moderate evidence of higher diversity in tropical species, but there were no differences either for the entire metabolome or for the other major families of compounds analyzed. This supports the interpretation that this tropical–temperate contrast must be related to the functional role of phenolics and polyphenolics.

Structural and Chemical Adaptations of Artemisia monosperma Delile and Limbarda crithmoides (L.) Dumort. in Response to Arid Coastal Environments along the Mediterranean Coast of Egypt

Arid coastal habitats are stressful regions subjected to the effects of biotic and abiotic factors. Vascular plants in these habitats display different responses to cope with these environmental fluctuations. This work addressed the morpho-anatomical features and chemical responses of two medicinal vascular plant species Artemisia monosperma Delile and Limbarda crithmoides (L.) Dumort., growing naturally along the Mediterranean coast of Egypt. Soil properties (physical and chemical), morpho-anatomical features and chemical constituents (secondary metabolites, antioxidant activity and essential oils) for the two species were performed. Our results displayed that both species are surviving where soils are alkaline, high saline with low moisture and organic carbon. The morphology of both species appeared woody low shrub with fleshy leaves. The most marked anatomical attributes were the thick cuticle of the epidermal layer in leaves and stems, compact palisade cells and abundant idioblasts (secretory ducts, phenolic compounds and calcium oxalate). Also, sclerenchymatous pericycle fibers in stem and glandular trichomes on the leaf had appeared in A. monosperma. Both plants exhibited a considerable content of phenolics, flavonoids, tannins, alkaloids and antioxidant activity with a higher level in A. monosperma than L. crithmoides. The leaf extracts of both plants showed higher values than the stem extracts. The sesquiterpenes group were the major identified compounds of the essential oils (EOs) in A. monosperma and L. crithmoides, and the majority were oxygenated sesquiterpenes with percentages of 42.63% and 51.49%, respectively. The second major group of EOs was monoterpenes, which were represented in A. monosperma in concentrations (34.04%) much higher than those recorded in L. crithmoides (4.97%). Exploring the local adaptation mechanism used by the target plants helps us to understand how these plants can acclimatize to harsh conditions, and this provides critical insights into the protection and survival strategy of species under extreme conditions.

Chemosystematic and evolutionary trends of the genistoid clade sensu stricto (Papilionoideae, Fabaceae)

The Papilionoideae, which comprises 503 genera and approximately 14,000 species, is the largest and most diverse subfamily of the Fabaceae family. In this subfamily, the Crotalarieae, Genisteae, Podalyrieae, Thermopsideae, Sophoreae and Euchresteae tribes are closely related by micro and macromolecular features, thus forming the genistoid clade. This group combines well-known genera, whereas other genera lack phytochemical and chemotaxonomic studies. Thus, this work aimed to characterize the special metabolites in these genera in order to define the chemical profile, the micromolecular markers and the chemical diversity, as well as to evaluate the group evolutionary trends. Flavonoids and alkaloids were identified as chemosystematic markers for the studied tribes due to high occurrence number and structural diversity. Among flavonoids, the flavones and isoflavones predominated. Low protection indexes of flavonoid hydroxyls by O-glycosylation or O-methylation were observed, whereas C-prenylation and C-glycosylation were frequent, mainly at C-6 and C-8 positions. The flavone/flavonol ratio shows the predominance of the flavones. Quinolizidine and piperidine alkaloids were present in most genera. Pyrrolizidine alkaloids were found in a few genera from Thermopsideae, Genisteae and Crotalarieae, which suggests a mechanism of adaptive convergence. Cluster analysis allowed separation of genera for each tribe by chemical similarities. The micromolecular trends of protection of flavonoid hydroxyls and alkaloid oxidation indicate the genistoid clade is through evolutionary transition, which is consistent with its phylogenetic position in the Papilionoideae subfamily.

PSC-db: A Structured and Searchable 3D-Database for Plant Secondary Compounds

Plants synthesize a large number of natural products, many of which are bioactive and have practical values as well as commercial potential. To explore this vast structural diversity, we present PSC-db, a unique plant metabolite database aimed to categorize the diverse phytochemical space by providing 3D-structural information along with physicochemical and pharmaceutical properties of the most relevant natural products. PSC-db may be utilized, for example, in qualitative estimation of biological activities (Quantitative Structure-Activity Relationship, QSAR) or massive docking campaigns to identify new bioactive compounds, as well as potential binding sites in target proteins. PSC-db has been implemented using the open-source PostgreSQL database platform where all compounds with their complementary and calculated information (classification, redundant names, unique IDs, physicochemical properties, etc.) were hierarchically organized. The source organism for each compound, as well as its biological activities against protein targets, cell lines and different organism were also included. PSC-db is freely available for public use and is hosted at the Universidad de Talca.

Evolutionary history and ecology shape the diversity and abundance of phytochemical arsenals across monkeyflowers

We examine the extent to which phylogenetic effects and ecology are associated with macroevolutionary patterns of phytochemical defence production across the Mimulus phylogeny. We grew plants from 21 species representing the five major sections of the Mimulus phylogeny in a common garden to assess how the arsenals (NMDS groupings) and abundances (concentrations) of a phytochemical defence, phenylpropanoid glycosides (PPGs), vary across the phylogeny. Very few PPGs are widespread across the genus, but many are common to multiple sections of the genus. Phytochemical arsenals cluster among sections in an NMDS and are not associated with total concentration of PPGs. There is a strong phylogenetic signal for phytochemical arsenal composition across the Mimulus genus, whereas ecological variables such as growing season length, latitude, and elevation do not significantly influence arsenal. In contrast, there is little phylogenetic signal for total PPG concentration, and this trait is significantly influenced by several ecological factors. Phytochemical arsenals and abundances are influenced by plant life history form. Both phylogenetic effects and ecology are related to phytochemical patterns across species, albeit in different ways. The independence of phytochemical defence concentrations from arsenal compositions indicates that these aspects of defence may continue to evolve independently of one another.

The Deep Roots of Addiction: A Comparative Perspective

Addiction is a debilitating condition that extracts enormous social and economic tolls. Despite several decades of research, our knowledge of its etiology, preventive measures, and treatments is limited. A relatively recent research field with the potential to provide a more holistic understanding, and subsequently treatments, takes a phylogenetic view of addiction. This perspective is based on deep homologies at the genetic, proteomic, and behavioral levels, which are shared across all metazoan life; particularly those organisms faced with plant secondary metabolites as defensive compounds against insect herbivory. These addictive alkaloids, such as nicotine, cocaine, or cathinone, are commonly referred to as "human drugs of abuse" even though humans had little to no role in the co-evolutionary processes that determined their initial emergence or continued selection. This commentary discusses the overwhelming homologies of addictive alkaloid effects on neural systems across a wide range of taxa, as we aim to develop a broader comparative view of the "addicted brain." Taking nicotine as an example, homologous physiological responses to this compound identify common underlying cellular and molecular mechanisms that advocate for the adoption of a phylogenetic view of addiction.

Genome-wide identification and analysis of AP2/ERF transcription factors related to camptothecin biosynthesis in Camptotheca acuminata

Camptotheca acuminata produces camptothecin (CPT), a monoterpene indole alkaloid (MIA) that is widely used in the treatment of lung, colorectal, cervical, and ovarian cancers. Its biosynthesis pathway has attracted significant attention, but the regulation of CPT biosynthesis by the APETALA2/ethylene-responsive factor (AP2/ERF) transcription factors (TFs) remains unclear. In this study, a systematic analysis of the AP2/ERF TFs family in C. acuminata was performed, including phylogeny, gene structure, conserved motifs, and gene expression profiles in different tissues and organs (immature bark, cotyledons, young flower, immature fruit, mature fruit, mature leaf, roots, upper stem, and lower stem) of C. acuminata. A total of 198 AP2/ERF genes were identified and divided into five relatively conserved subfamilies, including AP2 (26 genes), DREB (61 genes), ERF (92 genes), RAV (18 genes), and Soloist (one gene). The combination of gene expression patterns in different C. acuminata tissues and organs, the phylogenetic tree, the co-expression analysis with biosynthetic genes, and the analysis of promoter sequences of key enzymes genes involved in CPT biosynthesis pathways revealed that eight AP2/ERF TFs in C. acuminata might be involved in CPT synthesis regulation, which exhibit relatively high expression levels in the upper stem or immature bark. Among these, four genes (CacAP2/ERF123, CacAP2/ERF125, CacAP2/ERF126, and CacAP2/ERF127) belong to the ERF-B2 subgroup; two genes (CacAP2/ERF149 and CacAP2/ERF152) belong to the ERF-B3 subgroup; and two more genes (CacAP2/ERF095 and CacAP2/ERF096) belong to the DREB-A6 subgroup. These results provide a foundation for future functional characterization of the AP2/ERF genes to enhance the biosynthesis of CPT compounds of C. acuminata.

Ecological convergence of secondary phytochemicals along elevational gradients

Biologists still strive to identify the ecological and evolutionary drivers of phytochemical variation that mediate biotic interactions. We hypothesized that plant species growing at sites characterized by high herbivore pressure would converge to produce highly toxic blends of secondary metabolites, independent of phylogenetic constraints. To address the role of shared evolutionary history and ecological niches in driving variation in plant phytochemistry, we combined targeted metabolomics with insect herbivore bioassays and with a set of growth-related traits of several Cardamine species growing along the entire elevational gradient of the Alps. We observed that Cardamine phytochemical profiles grouped according to previously established growth form categorizations within specific abiotic conditions, independently of phylogenetic relationship. We also showed that novel indices summarizing functional phytochemical diversity better explain plant resistance against chewing and sap-feeding herbivores than classic diversity indices. We conclude that multiple functional axes of phytochemical diversity should be integrated with the functional axis of plant growth forms to study phenotypic convergence along large-scale ecological gradients.

Pinpointing secondary metabolites that shape the composition and function of the plant microbiome

One of the major questions in contemporary plant science involves determining the functional mechanisms that plants use to shape their microbiome. Plants produce a plethora of chemically diverse secondary metabolites, many of which exert bioactive effects on microorganisms. Several recent publications have unequivocally shown that plant secondary metabolites affect microbiome composition and function. These studies have pinpointed that the microbiome can be influenced by a diverse set of molecules, including: coumarins, glucosinolates, benzoxazinoids, camalexin, and triterpenes. In this review, we summarize the role of secondary metabolites in shaping the plant microbiome, highlighting recent literature. A body of knowledge is now emerging that links specific plant metabolites with distinct microbial responses, mediated via defined biochemical mechanisms. There is significant potential to boost agricultural sustainability via the targeted enhancement of beneficial microbial traits, and here we argue that the newly discovered links between root chemistry and microbiome composition could provide a new set of tools for rationally manipulating the plant microbiome.

Responses of Lotus corniculatus to environmental change. 4: Root carbohydrate levels at defoliation and regrowth climatic conditions are major drivers of phenolic content and forage quality

Differential accumulation of root carbohydrates at defoliation have a higher impact than regrowth environmental conditions on the phenolic content and feed quality of the perennial forage legume Lotus corniculatus. The unpredictable nature of proanthocyanidin (condensed tannin) accumulation in regrowth vegetation of the perennial forage legume Lotus corniculatus represents a dilemma to the wider use of this species in agriculture, and a potential problem in the nutritional ecology of some terrestrial herbivores, as variable condensed tannin levels can result in either beneficial or detrimental effects on animal nutrition. However, the source of this variation has not been extensively explored. High levels of carbon allocation to roots during low-temperature preconditioning of clonal plants were found to significantly increase condensed tannin and flavonol levels in regrowth foliage, while low levels of carbon allocation to roots during periods of high-temperature preconditioning significantly decreased condensed tannin and flavonol levels. Phenolic accumulation and tissue digestibility were also differentially affected by regrowth of these defoliated plants at high CO₂ concentrations and by drought. Lower rates of digestion generally paralleled increases in tannin levels in regrowth leaves under the different environmental conditions, with rates of digestion falling in high tannin plants, despite correspondingly higher levels of leaf carbohydrates. Differential accumulation of root carbohydrates between seasons and years may therefore explain some of the variability found in the nutritional quality of the forage of this species.

Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis

Plant genomes remain highly fragmented and are often characterized by hundreds to thousands of assembly gaps. Here, we report chromosome-level reference and phased genome assembly of Ophiorrhiza pumila, a camptothecin-producing medicinal plant, through an ordered multi-scaffolding and experimental validation approach. With 21 assembly gaps and a contig N50 of 18.49 Mb, Ophiorrhiza genome is one of the most complete plant genomes assembled to date. We also report 273 nitrogen-containing metabolites, including diverse monoterpene indole alkaloids (MIAs). A comparative genomics approach identifies strictosidine biogenesis as the origin of MIA evolution. The emergence of strictosidine biosynthesis-catalyzing enzymes precede downstream enzymes' evolution post γ whole-genome triplication, which occurred approximately 110 Mya in O. pumila, and before the whole-genome duplication in Camptotheca acuminata identified here. Combining comparative genome analysis, multi-omics analysis, and metabolic gene-cluster analysis, we propose a working model for MIA evolution, and a pangenome for MIA biosynthesis, which will help in establishing a sustainable supply of camptothecin.

Food allergy as a biological food quality control system

Food is simultaneously a source of essential nutrients and a potential source of lethal toxins and pathogens. Consequently, multiple sensory mechanisms evolved to monitor the quality of food based on the presence and relative abundance of beneficial and harmful food substances. These include the olfactory, gustatory, and gut chemosensory systems. Here we argue that, in addition to these systems, allergic immunity plays a role in food quality control by mounting allergic defenses against food antigens associated with noxious substances. Exaggeration of these defenses can result in pathological food allergy.

Analytical Methods for Quantification and Identification of Intact Glucosinolates in Arabidopsis Roots Using LC-QqQ(LIT)-MS/MS

Glucosinolates are biologically active secondary metabolites in Brassicaceae plants that play a critical role in positive and negative interactions between plants and root-associated microbial communities. The aim of this study was to develop a reversed-phase liquid chromatography method to quantify and identify intact glucosinolates in the root of Arabidopsis thaliana (Arabidopsis) grown in non-sterile natural soil by using liquid chromatography-hybrid triple quadruple-linear ion trap (LC-QqQ(LIT)) mass spectrometry. The Synergi Fusion C18-based column was found to be effective for sufficient retention and separation of nine intact glucosinolates without the need for time-consuming desulfation or ion-pairing steps. Method validation results showed satisfactory inter-day and intra-day precision for all glucosinolates except for 4-hydroxyglucobrassicin. Good inter-day and intra-day accuracy and recovery results were observed for glucoiberin, gluconapin, glucobrassicin, 4-methoxyglucobrassicin and neoglucobrassicin. However, for 4-hydroxyglucobrassicin, glucoraphanin and glucoerucin corrections to quantification results might be necessary since the recovery and accuracy results were not optimal. Matrix effects were shown to have a negligible effect on the ionization of all target analytes. The established liquid chromatography–tandem mass spectrometry (LC-MS/MS) method was applied to quantify target intact glucosinolates in Arabidopsis root crude extract of four different wild-type accessions where differences in terms of concentration and composition of intact glucosinolates were observed. Employment of sensitive and selective precursor ion survey scan of m/z 97 in combination with the information-dependent acquisition (IDA) of the enhanced product ion (EPI) dependent scan (Prec97-IDA-EPI) using LC-QqQ(LIT) provided high confidence in structural characterization of diverse intact glucosinolate profiles in complex Arabidopsis root crude extract.