Using the knowns to discover the unknowns: MS‐based dereplication uncovers structural diversity in 17‐hydroxygeranyllinalool diterpene glycoside production in the Solanaceae

Exploring the diversity of plant secondary metabolism requires efficient methods to obtain sufficient structural insights to discriminate previously known from unknown metabolites. De novo structure elucidation and confirmation of known metabolites (dereplication) remain a major bottleneck for mass spectrometry‐based metabolomic workflows, and few systematic dereplication strategies have been developed for the analysis of entire compound classes across plant families, partly due to the complexity of plant metabolic profiles that complicates cross‐species comparisons. 17‐hydroxygeranyllinalool diterpene glycosides (HGL‐DTGs) are abundant defensive secondary metabolites whose malonyl and glycosyl decorations are induced by jasmonate signaling in the ecological model plant Nicotiana attenuata. The multiple labile glycosidic bonds of HGL‐DTGs result in extensive in‐source fragmentation (IS‐CID) during ionization. To reconstruct these IS‐CID clusters from profiling data and identify precursor ions, we applied a deconvolution algorithm and created an MS/MS library from positive‐ion spectra of purified HGL‐DTGs. From this library, 251 non‐redundant fragments were annotated, and a workflow to characterize leaf, flower and fruit extracts of 35 solanaceous species was established. These analyses predicted 105 novel HGL‐DTGs that were restricted to Nicotiana, Capsicum and Lycium species. Interestingly, malonylation is a highly conserved step in HGL‐DTG metabolism, but is differentially affected by jasmonate signaling among Nicotiana species. This MS‐based workflow is readily applicable for cross‐species re‐identification/annotation of other compound classes with sufficient fragmentation knowledge, and therefore has the potential to support hypotheses regarding secondary metabolism diversification.     

Elemental formula annotation of polar and lipophilic metabolites using (13) C, (15) N and (34) S isotope labelling, in combination with high-resolution mass spectrometry

The unbiased and comprehensive analysis of metabolites in any organism presents a major challenge if proper peak annotation and unambiguous assignment of the biological origin of the peaks are required. Here we provide a comprehensive multi-isotope labelling-based strategy using fully labelled (13) C, (15) N and (34) S plant tissues, in combination with a fractionated metabolite extraction protocol. The extraction procedure allows for the simultaneous extraction of polar, semi-polar and hydrophobic metabolites, as well as for the extraction of proteins and starch. After labelling and extraction, the metabolites and lipids were analysed using a high-resolution mass spectrometer providing accurate MS and all-ion fragmentation data, providing an unambiguous readout for every detectable isotope-labelled peak. The isotope labelling assisted peak annotation process employed can be applied in either an automated database-dependent or a database-independent analysis of the plant polar metabolome and lipidome. As a proof of concept, the developed methods and technologies were applied and validated using Arabidopsis thaliana leaf and root extracts. Along with a large repository of assigned elemental compositions, which is provided, we show, using selected examples, the accuracy and reliability of the developed workflow.     

Metabolomics-assisted refinement of the pathways of steroidal glycoalkaloid biosynthesis in the tomato clade

Steroidal glycoalkaloids (SGAs) are nitrogen-con-taining secondary metabolites of the Solanum species, which are known to have large chemical and bioactive diversity in nature. While recent effort and ...     

Mass spectrometry screening reveals widespread diversity in trichome specialized metabolites of tomato chromosomal substitution lines

Glandular secreting trichomes of cultivated tomato (Solanum lycopersicum) and close relatives produce a variety of structurally diverse volatile and non‐volatile specialized (‘secondary’) metabolites, including terpenes, flavonoids and acyl sugars. A genetic screen is described here to profile leaf trichome and surface metabolite extracts of nearly isogenic chromosomal substitution lines covering the tomato genome. These lines contain specific regions of the Solanum pennellii LA0716 genome in an otherwise ‘wild‐type’ M82 tomato genetic background. Regions that have an impact on the total amount of extractable mono‐ and sesquiterpenes (IL2‐2) or only sesquiterpenes (IL10‐3) or specifically influence accumulation of the monoterpene α‐thujene (IL1‐3 and IL1‐4) were identified using GC‐MS. A rapid LC‐TOF‐MS method was developed and used to identify changes in non‐volatile metabolites through non‐targeted analysis. Metabolite profiles generated using this approach led to the discovery of introgression lines producing different acyl chain substitutions on acyl sugar metabolites (IL1‐3/1‐4 and IL8‐1/8‐1‐1), as well as two regions that influence the quantity of acyl sugars (IL5‐3 and IL11‐3). Chromosomal region 1‐1/1‐1‐3 was found to influence the types of glycoalkaloids that are detected in leaf surface extracts. These results show that direct chemical screening is a powerful way to characterize genetic diversity in trichome specialized metabolism.     

Compartmentalization of specialized metabolites across vegetative and reproductive tissues in two sympatric Psychotria species

Premise

The specialized metabolites of plants are recognized as key chemical traits in mediating the ecology and evolution of sundry plant–biotic interactions, from pollination to seed predation. Intra- and interspecific patterns of specialized metabolite diversity have been studied extensively in leaves, but the diverse biotic interactions that contribute to specialized metabolite diversity encompass all plant organs. Focusing on two species of Psychotria shrubs, we investigated and compared patterns of specialized metabolite diversity in leaves and fruit with respect to each organ's diversity of biotic interactions.

Methods

To evaluate associations between biotic interaction diversity and specialized metabolite diversity, we combined UPLC-MS metabolomic analysis of foliar and fruit specialized metabolites with existing surveys of leaf- and fruit-centered biotic interactions. We compared patterns of specialized metabolite richness and variance among vegetative and reproductive tissues, among plants, and between species.

Results

In our study system, leaves interact with a far larger number of consumer species than do fruit, while fruit-centric interactions are more ecologically diverse in that they involve antagonistic and mutualistic consumers. This aspect of fruit-centric interactions was reflected in specialized metabolite richness—leaves contained more than fruit, while each organ contained over 200 organ-specific specialized metabolites. Within each species, leaf- and fruit-specialized metabolite composition varied independently of one another across individual plants. Contrasts in specialized metabolite composition were stronger between organs than between species.

Conclusions

As ecologically disparate plant organs with organ-specific specialized metabolite traits, leaves and fruit can each contribute to the tremendous overall diversity of plant specialized metabolites.     

Integrated view of plant metabolic defense with particular focus on chewing herbivores

Success of plants largely depends on their ability to defend against herbivores. Since emergence of the first voracious consumers, plants maintained adapting their structures and chemistry to escape from extinction. The constant pressure was further accelerated by adaptation of herbivores to plant defenses, which all together sparked the rise of a chemical empire comprised of thousands of specialized metabolites currently found in plants. Metabolic diversity in the plant kingdom is truly amazing, and although many plant metabolites have already been identified, a large number of potentially useful chemicals remain unexplored in plant bio-resources. Similarly, biosynthetic routes for plant metabolites involve many enzymes, some of which still wait for identification and biochemical characterization. Moreover, regulatory mechanisms that control gene expression and enzyme activities in specialized metabolism of plants are scarcely known. Finally, understanding of how plant defense chemicals exert their toxicity and/or repellency against herbivores remains limited to typical examples, such as proteinase inhibitors, cyanogenic compounds and nicotine. In this review, we attempt summarizing the current status quo in metabolic defense of plants that is predominantly based on the survey of ubiquitous examples of plant interactions with chewing herbivores.     

Plant–plant interactions as a mechanism structuring plant diversity in a Mediterranean semi‐arid ecosystem

Plant–plant interactions are among the fundamental processes that shape structure and functioning of arid and semi‐arid plant communities. Despite the large amount of studies that have assessed the relationship between plant–plant interactions (i.e., facilitation and competition) and diversity, often researchers forget a third kind of interaction, known as allelopathy. We examined the effect of plant–plant interactions of three dominant species: the perennial grass Lygeum spartum, the allelopathic dwarf shrub Artemisia herba‐alba, and the nurse shrub Salsola vermiculata, on plant diversity and species composition in a semi‐arid ecosystem in NE Spain. Specifically, we quantified the interaction outcome (IO) based on species co‐occurrence, we analyzed diversity by calculation of the individual species–area relationship (ISAR), and compositional changes by calculation of the Chao‐Jaccard similarity index. We found that S. vermiculata had more positive IO values than L. spartum, and A. herba‐alba had values between them. Lygeum spartum and A. herba‐alba acted as diversity repellers, whereas S. vermiculata acted as a diversity accumulator. As aridity increased, A. herba‐alba transitioned from diversity repeller to neutral and S. vermiculata transitioned from neutral to diversity accumulator, while L. spartum remained as diversity repeller. Artemisia herba‐alba had more perennial grass species in its local neighborhood than expected by the null model, suggesting some tolerance of this group to its “chemical neighbor”. Consequently, species that coexist with A. herba‐alba were very similar among different A. herba‐alba individuals. Our findings highlight the role of the nurse shrub S. vermiculata as ecosystem engineer, creating and maintaining patches of diversity, as well as the complex mechanism that an allelopathic plant may have on diversity and species assemblage. Further research is needed to determine the relative importance of allelopathy and competition in the overall interference of allelopathic plants.     

Toward better annotation in plant metabolomics: isolation and structure elucidation of 36 specialized metabolites from Oryza sativa (rice) by using MS/MS and NMR analyses

Metabolomics plays an important role in phytochemical genomics and crop breeding; however, metabolite annotation is a significant bottleneck in metabolomic studies. In particular, in liquid chromatography–mass spectrometry (MS)-based metabolomics, which has become a routine technology for the profiling of plant-specialized metabolites, a substantial number of metabolites detected as MS peaks are still not assigned properly to a single metabolite. Oryza sativa (rice) is one of the most important staple crops in the world. In the present study, we isolated and elucidated the structures of specialized metabolites from rice by using MS/MS and NMR. Thirty-six compounds, including five new flavonoids and eight rare flavonolignan isomers, were isolated from the rice leaves. The MS/MS spectral data of the isolated compounds, with a detailed interpretation of MS fragmentation data, will facilitate metabolite annotation of the related phytochemicals by enriching the public mass spectral data depositories, including the plant-specific MS/MS-based database, ReSpect.     

Two birds with one stone: Doing metabolomics with your proteomics kit

Proteomic research facilities and laboratories are facing increasing demands for the integration of biological data from multiple ‘‐OMICS’ approaches. The aim to fully understand biological processes requires the integrated study of genomes, proteomes and metabolomes. While genomic and proteomic workflows are different, the study of the metabolome overlaps significantly with the latter, both in instrumentation and methodology. However, chemical diversity complicates an easy and direct access to the metabolome by mass spectrometry (MS). The present review provides an introduction into metabolomics workflows from the viewpoint of proteomic researchers. We compare the physicochemical properties of proteins and peptides with metabolites/small molecules to establish principle differences between these analyte classes based on human data. We highlight the implications this may have on sample preparation, separation, ionisation, detection and data analysis. We argue that a typical proteomic workflow (nLC‐MS) can be exploited for the detection of a number of aliphatic and aromatic metabolites, including fatty acids, lipids, prostaglandins, di/tripeptides, steroids and vitamins, thereby providing a straightforward entry point for metabolomics‐based studies. Limitations and requirements are discussed as well as extensions to the LC‐MS workflow to expand the range of detectable molecular classes without investing in dedicated instrumentation such as GC‐MS, CE‐MS or NMR.     

In vitro rapid regeneration of plantlets from nodal explants of Mucuna pruriens– a valuable medicinal plant

A rapid and efficient protocol for the large‐scale propagation of a potential medicinal plant, Mucuna pruriens, through in vitro culture of nodal segment explants obtained from 15‐day‐old aseptic seedlings is described. Of the three different cytokinins, 6‐benzyladenine (BA), kinetin (Kin) and 2‐isopentenyl adenine (2‐iP) evaluated as supplements to Murashige and Skoog (MS) medium, BA at an optimal concentration of 5.0 μM was effective in inducing multiple shoots. Strength of the basal media also influenced the efficiency of shoot regeneration. The frequency of shoot regeneration tended to increase when the salt concentration in the basal media was reduced. Highest number of multiple shoots (23.3) and maximum average length (5.6 cm) were standardised on half‐strength MS medium supplemented with 5.0 μM BA along with 0.5 μM α‐naphthalene acetic acid (NAA) at pH 5.8. Rooting was best induced in shoots excised from proliferated shoot cultures on MS medium augmented with an optimal concentration of 1.0 μM indole‐3‐butyric acid (IBA). The in vitro‐raised plantlets with well‐developed shoots and roots were successfully established in earthen pots containing garden soil and were grown in greenhouse with 90% survival rate. The results of this study provide the first report on in vitro plant regeneration of M. pruriens.     

A plant pathogen modulates the effects of secondary metabolites on the performance and immune function of an insect herbivore

Host plant chemical composition critically shapes the performance of insect herbivores feeding on them. Some insects have become specialized on plant secondary metabolites, and even use them to their own advantage such as defense against predators. However, infection by plant pathogens can seriously alter the interaction between herbivores and their host plants. We tested whether the effects of the plant secondary metabolites, iridoid glycosides (IGs), on the performance and immune response of an insect herbivore are modulated by a plant pathogen. We used the IG‐specialized Glanville fritillary butterfly Melitaea cinxia, its host plant Plantago lanceolata, and the naturally occurring plant pathogen, powdery mildew Podosphaera plantaginis, as model system. Pre‐diapause larvae were fed on P. lanceolata host plants selected to contain either high or low IGs, in the presence or absence of powdery mildew. Larval performance was measured by growth rate, survival until diapause, and by investment in immunity. We assessed immunity after a bacterial challenge in terms of phenoloxidase (PO) activity and the expression of seven pre‐selected insect immune genes (qPCR). We found that the beneficial effects of constitutive leaf IGs, that improved larval growth, were significantly reduced by mildew infection. Moreover, mildew presence downregulated one component of larval immune response (PO activity), suggesting a physiological cost of investment in immunity under suboptimal conditions. Yet, feeding on mildew‐infected leaves caused an upregulation of two immune genes, lysozyme and prophenoloxidase. Our findings indicate that a plant pathogen can significantly modulate the effects of secondary metabolites on the growth of an insect herbivore. Furthermore, we show that a plant pathogen can induce contrasting effects on insect immune function. We suspect that the activation of the immune system toward a plant pathogen infection may be maladaptive, but the actual infectivity on the larvae should be tested.     

Relationships among soil fertility,native plant diversity and exotic plant abundance inform restoration of forb‐rich eucalypt woodlands

Aim Water and nutrient availability are major limits to productivity in semi‐arid ecosystems; hence, ecological restoration often focuses on conserving or concentrating soil resources. By contrast, nutrient enrichment can promote invasion by exotic annuals, leading to restoration approaches that target reduction of soil nutrients. We aimed to explore potential biodiversity trade‐offs between these approaches by investigating relationships among soil nutrients, exotic annuals and native plant diversity and composition. In particular, we investigated the hypothesis that native plant diversity in semi‐arid to temperate woodlands reflects the productivity–diversity hypothesis, leading to hump‐backed relationships with soil nutrients such that (1) native plant diversity declines with increasing nutrient enrichment and (2) native diversity is limited at the lowest levels of soil fertility. Location Fragmented, long‐ungrazed Eucalyptus loxophleba subsp. loxophleba (York gum)–Acacia acuminata (jam) woodlands in the wheatbelt of South‐Western Australia. Methods We conducted stratified surveys of floristic composition and topsoil nutrient concentrations in 112 woodland patches. We used generalized linear models, structural equation models and ordinations to characterize relationships among soil nutrients, rainfall, exotic annuals and patch‐scale (100 m²) native plant composition and diversity. Results Patch‐scale native plant diversity declined strongly with increasing exotic abundance. This was partly related to elevated soil nutrient concentrations, particularly total nitrogen and available phosphorus. By contrast, there was little evidence for positive correlations between soil nutrients and native diversity, even at very low soil nutrient concentrations. Main conclusions Minimizing weed invasions is crucial for maximizing native plant diversity in E. loxophleba woodlands and could include nutrient‐depleting treatments without substantially compromising the functional capacity of soils to maintain native plant richness and composition. More broadly we emphasize that understanding relationships among ecosystem productivity, plant diversity and exotic invasions in the context of associated theoretical frameworks is fundamental for informing ecological restoration.     

Biodiesel and poly‐unsaturated fatty acids production from algae and crop plants – a rapid and comprehensive workflow for lipid analysis

Fatty acid methyl ester analysis (FAME) by gas chromatography coupled to mass spectrometry (GC‐MS) is a widely used technique in biodiesel/bioproduct (e.g. poly‐unsaturated fatty acids, PUFA) research but typically does not allow distinguishing between bound and free fatty acids. To understand and optimize biosynthetic pathways, however, the origin of the fatty acid is an important information. Furthermore the annotation of PUFAs is compromised in classical GC‐EI‐MS because the precursor molecular ion is missing. In the present protocol an alkaline methyl esterification step with TMS derivatization enabling the simultaneous analysis of bound and free fatty acids but also further lipids such as sterols in one GC‐MS chromatogram is combined. This protocol is applied to different lipid extracts from single cell algae to higher plants: Chlorella vulgaris, Chlamydomonas reinhardtii, Coffea arabica, Pisum sativum and Cuscuta japonica. Further, field ionization (GC‐FI‐MS) is introduced for a better annotation of fatty acids and exact determination of the number of double bonds in PUFAs. The proposed workflow provides a convenient strategy to analyze algae and other plant crop systems with respect to their capacity for third generation biodiesel and high‐quality bioproducts for nutrition such as PUFAs.     

Metabolic fingerprinting as an indicator of biodiversity: towards understanding inter-specific relationships among Homoscleromorpha sponges

Sponges are an important source of secondary metabolites showing a great diversity of structures and biological activities. Secondary metabolites can display specificity on different taxonomic levels, from species to phylum, which can make them good taxonomic biomarkers. However, the knowledge available on the metabolome of non-model organisms is often poor. In this study, we demonstrate that sponge chemical diversity may be useful for fundamental issues in systematics or evolutionary biology, by using metabolic fingerprints as indicators of metabolomic diversity in order to assess interspecific relationships. The sponge clade Homoscleromorpha is particularly challenging because its chemistry has been little studied and its phylogeny is still debated. Identification at species level is often troublesome, especially for the highly diversified Oscarella genus which lacks the fundamental characters of sponge taxonomy. An HPLC–DAD–ELSD–MS metabolic fingerprinting approach was developed and applied to 10 Mediterranean Homoscleromorpha species as a rapid assessment of their chemical diversity. A first validation of our approach was to measure intraspecific variability, which was found significantly lower than interspecific variability obtained between two Oscarella sister-species. Interspecific relationships among Homoscleromorpha species were then inferred from the alignment of their metabolic fingerprints. The resulting classification is congruent with phylogenetic trees obtained for a DNA marker (mitochondrial COI) and demonstrates the existence of two distinct groups within Homoscleromorpha. Metabolic fingerprinting proves a useful complementary tool in sponge systematics. Our case study calls for a revision of Homoscleromorpha with further phylogenetic studies and identification of additional chemical synapomorphic characters.     

Fungal volatiles emitted by members of the microbiome of desert plants are diverse and capable of promoting plant growth

Fungi represent a group of eukaryotic microorganisms that are an important part of the plant microbiome. They produce a vast array of metabolites, including fungal volatile organic compounds (fVOCs). However, the diversity and biological activities of fVOCs emitted by the mycobiota of plants native to arid and semi-arid environments remain under-explored. We characterized the chemical diversity of fVOCs produced by 22 representative members of the microbiome of agaves and cacti using SPME-GC–MS. We further tested the effects of pure compounds on the growth and development of Arabidopsis thaliana and host plants. Members of the Sordariomycetes (nine strains), Eurotiomycetes (three), Dothideomycetes (eight), Saccharomycetes (one) and Mucoromycetes (one) were included in our study. We identified 94 fungal organic volatiles classified into nine chemical classes. Terpenes showed the greatest chemical diversity, followed by alcohols and aliphatic compounds. We discovered that camphene and benzyl benzoate, together with the widely distributed and already tested benzyl alcohol, 2-phenylethyl alcohol and 3-methyl-1-butanol, improved plant growth and development of A. thaliana, Agave tequilana and Agave salmiana. Our studies on the fungal VOCs from desert plants underscore an untapped chemical diversity with promising biotechnological applications.     

In Vino Veritas: An Invitation for Ambitious,Collaborative Proteogenomics Campaigns on Plant and Animal Models

Vitis vinifera has been an emblematic plant for humans since the Neolithic period. Human civilization has been shaped by its domestication as both its medicinal and nutritional values were exploited. It is now cultivated on all habitable continents, and more than 5000 varieties have been developed. A global passion for the art of wine fuels innovation and a profound desire for knowledge on this plant. The genome sequence of a homozygotic cultivar and several RNA‐seq datasets on other varieties have been released paving the way to gaining further insight into its biology and tailoring improvements to varieties. However, its genome annotation remains unpolished. In this issue of Proteomics, Chapman and Bellgard (Proteomics 2017, 17, 1700197) discuss how proteogenomics can help improve genome annotation. By mining shotgun proteomics data, they defined new protein‐coding genes, refined gene structures, and corrected numerous mRNA splicing events. This stimulating study shows how large international consortia could work together to improve plant and animal genome annotation on a large scale. To achieve this aim, time should be invested to generate comprehensive, high‐quality experimental datasets for a wide range of well‐defined lineages and exploit them with pipelines capable of handling giant datasets.