Comprehensive LC-MS-Based Metabolite Fingerprinting Approach for Plant and Fungal-Derived Samples

Unlocking Potentially Therapeutic Phytochemicals in Capadulla (Doliocarpus dentatus) from Guyana Using Untargeted Mass Spectrometry-Based Metabolomics

Doliocarpus dentatus is thought to have a wide variety of therapeutic phytochemicals that allegedly improve libido and cure impotence. Although a few biomarkers have been identified with potential antinociceptive and cytotoxic properties, an untargeted mass spectrometry-based metabolomics approach has never been undertaken to identify therapeutic biofingerprints for conditions, such as erectile dysfunction, in men. This study executes a preliminary phytochemical screening of the woody vine of two ecotypes of D. dentatus with renowned differences in therapeutic potential for erectile dysfunction. Liquid chromatography-mass spectrometry-based metabolomics was used to screen for flavonoids, terpenoids, and other chemical classes found to contrast between red and white ecotypes. Among the metabolite chemodiversity found in the ecotype screens, using a combination of GNPS, MS-DIAL, and SIRIUS, approximately 847 compounds were annotated at levels 2 to 4, with the majority of compounds falling under lipid and lipid-like molecules, benzenoids and phenylpropanoids, and polyketides, indicative of the contributions of the flavonoid, shikimic acid, and terpenoid biosynthesis pathways. Despite the extensive annotation, we report on 138 tentative compound identifications of potentially therapeutic compounds, with 55 selected compounds at a level-2 annotation, and 22 statistically significant therapeutic biomarkers, the majority of which were polyphenols. Epicatechin methyl gallate, catechin gallate, and proanthocyanidin A2 had the greatest significant differences and were also relatively abundant among the red and white ecotypes. These putatively identified compounds reportedly act as antioxidants, neutralizing damaging free radicals, and lowering cell oxidative stress, thus aiding in potentially preventing cellular damage and promoting overall well-being, especially for treating erectile dysfunction (ED).

Screening out Biomarkers of Tetrastigma hemsleyanum for Anti-Cancer and Anti-Inflammatory Based on Spectrum-Effect Relationship Coupled with UPLC-Q-TOF-MS

Tetrastigma hemsleyanum Diels et Gilg. (T. hemsleyanum) is an economically and medicinally valuable species within the genus Tetrastigma. However, the material basis of its pharmacological action and the biomarkers associated with its anti-cancer and anti-inflammatory effects are still unclear. Additionally, the T. hemsleyanum industry cannot grow because there is a lack of a scientific, universal, and measurable quality control system. This study aimed to explore the chemical basis quality markers related to the anti-cancer and anti-inflammatory effects of T. hemsleyanum to establish an effective quality evaluation method. UPLC-Q-TOF-MSE fingerprint profiles of T. hemsleyanum from different origins were established. Pharmacodynamic studies used HepG2 and HuH-7 cells and LPS-induced RAW264.7 to evaluate the anti-tumor and anti-inflammatory effects of the active ingredients. The spectrum-effect relationships between UPLC fingerprints and anti-cancer and anti-inflammatory activities were evaluated using PCA and PLSR statistical methods. Moreover, docking analysis was performed to identify specific active biomarkers with molecular targets associated with cancer and inflammation. Chlorogenic acid, quinic acid, catechin, kaempferol 3-rutinoside, apigenin-8-C-glucoside, and linolenic acid were associated with anticancer activity, while chlorogenic acid, quercetin, quinic acid, kaempferol 3-rutinoside, rutinum, apigenin-8-C-glucoside, and linolenic acid were associated with anti-inflammatory activity. The spectrum-effect relationship of T. hemsleyanum was successfully established, and the biomarkers for anti-cancer and anti-inflammatory effects were preliminary confirmed. These findings provide a theoretical basis for the elucidation of the substance basis of T. hemsleyanum and lay the foundation for its rapid identification, quality control, industrial research, and utilization.

A non-targeted metabolomics analysis identifies wound-induced oxylipins in Physcomitrium patens

Plant oxylipins are a class of lipid-derived signaling molecules being involved in the regulation of various biotic and abiotic stress responses. A major class of oxylipins are the circular derivatives to which 12-oxo-phytodienoic acid (OPDA) and its metabolite jasmonic acid (JA) belong. While OPDA and its shorter chain homologue dinor-OPDA (dnOPDA) seem to be ubiquitously found in land plants ranging from bryophytes to angiosperms, the occurrence of JA and its derivatives is still under discussion. The bryophyte Physcomitrium patens has received increased scientific interest as a non-vascular plant model organism over the last decade. Therefore, we followed the metabolism upon wounding by metabolite fingerprinting with the aim to identify jasmonates as well as novel oxylipins in P. patens. A non-targeted metabolomics approach was used to reconstruct the metabolic pathways for the synthesis of oxylipins, derived from roughanic, linoleic, α-linolenic, and arachidonic acid in wild type, the oxylipin-deficient mutants of Ppaos1 and Ppaos2, the mutants of Ppdes being deficient in all fatty acids harboring a Δ6-double bond and the C20-fatty acid-deficient mutants of Ppelo. Beside of OPDA, iso-OPDA, dnOPDA, and iso-dnOPDA, three additional C18-compounds and a metabolite being isobaric to JA were identified to accumulate after wounding. These findings can now serve as foundation for future research in determining, which compound(s) will serve as native ligand(s) for the oxylipin-receptor COI1 in P. patens.

Plastidic membrane lipids are oxidized by a lipoxygenase in Lobosphaera incisa

Green microalgae can accumulate neutral lipids, as part of a general lipid remodeling mechanism under stress such as nitrogen starvation. Lobosphaera incisa is of special interest because of its unique TAG acyl chain composition, especially 20:4 (n-6) can reach up to 21% of dry weight after nitrogen starvation. In order to identify factors that may influence the accumulation of polyunsaturated fatty acids (PUFAs), we identified recently a linoleate 13-lipoxygenase (LiLOX). It shares highest identity with plastidic enzymes from vascular plants and is induced upon nitrogen starvation. Here, we confirmed the localization of LiLOX in the stroma of plastids via transient expression in epithelial onion cells. In order to further characterize this enzyme, we focused on the identification of the endogenous substrate of LiLOX. In this regard, an ex vivo enzymatic assay, coupled with non-targeted analysis via mass spectrometry allowed the identification of MGDG, DGDG and PC as three substrate candidates, later confirmed via in vitro assays. Further investigation revealed that LiLOX has preferences towards the lipid class MGDG, which seems in agreement with its localization in the galactolipid rich plastid. Altogether, this study shows the first characterization of plastidic LOX from green algae, showing preference for MGDGs. However, lipidomics analysis did neither reveal an endogenous LiLOX product nor the final end product of MGDG oxidation. Nevertheless, the latter is a key to understanding the role of this enzyme and since its expression is highest during the degradation of the plastidic membrane, it is tempting to assume its involvement in this process.

A pilot study for fragment identification using 2D NMR and deep learning

This paper presents a proof of concept of a method to identify substructures in 2D NMR spectra of mixtures using a bespoke image-based convolutional neural network application. This is done using HSQC and HMBC spectra separately and in combination. The application can reliably detect substructures in pure compounds, using a simple network. Results indicate that it can work for mixtures when trained on pure compounds only. HMBC data and the combination of HMBC and HSQC show better results than HSQC alone in this pilot study.

Identification of active compounds in Ophiopogonis Radix from different geographical origins by UPLC-Q/TOF-MS combined with GC-MS approaches

Ophiopogonis Radix, also known as Maidong in Chinese, is largely produced in the Sichuan and Zhejiang provinces: “Chuan-maidong (CMD)” and “Zhe-maidong (ZMD),” respectively. This study aimed to distinguish and evaluate the quality of CMD and ZMD. In this study, the tubers of CMD and ZMD were investigated using UPLC-Q/TOF-MS, GC-MS, and LC-MS methods, respectively. Overall, steroidal saponins, homoisoflavonoids, amino acids, and nucleosides were quickly identified. Furthermore, multivariate statistical analysis revealed that CMD and ZMD could be separated. Moreover, CMD showed higher levels of 4-aminobutanoic acid, glycine, l-proline, monoethanolamine, and serine than ZMD. Besides, the levels of chlorogenic acid, traumatic acid, cytidine, cadaverine, pyridoxine 5-phosphate, glutinone, and pelargonidin 3-O-(6-O-malonyl-β-d-glucoside) were remarkably higher in ZMD than in CMD. Furthermore, these different constituents were mainly associated with galactose metabolism; starch and sucrose metabolism; cysteine and methionine metabolism; valine, leucine, and isoleucine biosynthesis; and glycerophospholipid metabolism. In general, these results showed many differences between the bioactive chemical constituents of Ophiopogon japonicus from different production areas, where ZMD performed better in the quality assessment than CMD, and that UPLC-Q/TOF-MS, GC-MS, and LC-MS are effective methods to discriminate medicinal herbs from different production areas.

Multi-omics analysis of xylem sap uncovers dynamic modulation of poplar defenses by ammonium and nitrate

Xylem sap is the major transport route for nutrients from roots to shoots. In the present study, we investigated how variations in nitrogen (N) nutrition affected the metabolome and proteome of xylem sap and the growth of the xylem endophyte Brennaria salicis, and we also report transcriptional re-wiring of leaf defenses in poplar (Populus × canescens). We supplied poplars with high, intermediate or low concentrations of ammonium or nitrate. We identified 288 unique proteins in xylem sap. Approximately 85% of the xylem sap proteins were shared among ammonium- and nitrate-supplied plants. The number of proteins increased with increasing N supply but the major functional categories (catabolic processes, cell wall-related enzymes, defense) were unaffected. Ammonium nutrition caused higher abundances of amino acids and carbohydrates, whereas nitrate caused higher malate levels in xylem sap. Pipecolic acid and N-hydroxy-pipecolic acid increased, whereas salicylic acid and jasmonoyl-isoleucine decreased, with increasing N nutrition. Untargeted metabolome analyses revealed 2179 features in xylem sap, of which 863 were differentially affected by N treatments. We identified 124 metabolites, mainly from specialized metabolism of the groups of salicinoids, phenylpropanoids, phenolics, flavonoids, and benzoates. Their abundances increased with decreasing N, except coumarins. Brennaria salicis growth was reduced in nutrient-supplemented xylem sap of low- and high- NO₃^- -fed plants compared to that of NH₄⁺ -fed plants. The drastic changes in xylem sap composition caused massive changes in the transcriptional landscape of leaves and recruited defenses related to systemic acquired and induced systemic resistance. Our study uncovers unexpected complexity and variability of xylem composition with consequences for plant defenses.

Metabolome-based profiling of African baobab fruit (Adansonia digitata L.) using a multiplex approach of MS and NMR techniques in relation to its biological activity

Adansonia digitata L. also known as African baobab is one of the most important fruit-producing trees, widely distributed in the African continent. Baobab fruits are known to possess potential health benefits and nutritional value. This study aimed to holistically dissect the metabolome of A. digitata fruits using a novel comparative protocol using three different analytical platforms. Ultra high performance liquid chromatography coupled to high-resolution tandem mass spectrometry (UHPLC-HRMS/MS), and headspace solid-phase microextraction/gas chromatography coupled to mass spectrometry (HS-SPME/GC-MS) were respectively employed for phytonutrients and aroma profiling, whereas GC-MS post silylation provided an overview of nutrients i.e., sugars. UHPLC-HRMS/MS analysis allowed for the assignment of 77 metabolites, among which 50% are reported for the first time in the fruit. While GC-MS of silylated and aroma compounds led to the identification of 74 and 16 compounds, respectively. Finally, NMR-based metabolite fingerprinting permitted the quantification of the major metabolites for future standardization. In parallel, in vivo antidiabetic potential of the baobab fruit using a streptozotocin (STZ) induced diabetic rat model was assessed. Histopathological and immune-histochemical investigations revealed hepatoprotective and renoprotective effects of A. digitata fruit along with mitigation against diabetes complications. Moreover, the administration of A. digitata fruits (150 mg kg-1) twice a week lowered fasting blood glucose levels.

The glycosyltransferase UGT76B1 modulates N-hydroxy-pipecolic acid homeostasis and plant immunity

The tradeoff between growth and defense is a critical aspect of plant immunity. Therefore, the plant immune response needs to be tightly regulated. Salicylic acid (SA) is an important plant hormone regulating defense against biotrophic pathogens. Recently, N-hydroxy-pipecolic acid (NHP) was identified as another regulator for plant innate immunity and systemic acquired resistance (SAR). Although the biosynthetic pathway leading to NHP formation is already been identified, how NHP is further metabolized is unclear. Here, we present UGT76B1 as a uridine diphosphate-dependent glycosyltransferase (UGT) that modifies NHP by catalyzing the formation of 1-O-glucosyl-pipecolic acid in Arabidopsis thaliana. Analysis of T-DNA and clustered regularly interspaced short palindromic repeats (CRISPR) knock-out mutant lines of UGT76B1 by targeted and nontargeted ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS) underlined NHP and SA as endogenous substrates of this enzyme in response to Pseudomonas infection and UV treatment. ugt76b1 mutant plants have a dwarf phenotype and constitutive defense response which can be suppressed by loss of function of the NHP biosynthetic enzyme FLAVIN-DEPENDENT MONOOXYGENASE 1 (FMO1). This suggests that elevated accumulation of NHP contributes to the enhanced disease resistance in ugt76b1. Externally applied NHP can move to distal tissue in ugt76b1 mutant plants. Although glycosylation is not required for the long-distance movement of NHP during SAR, it is crucial to balance growth and defense.

Metabolite Profile of Xylem Sap in Cotton Seedlings Is Changed by K Deficiency

Xylem sap, belonging to the plant apoplast, not only provides plant tissues with inorganic and organic substances but also facilitates communication between the roots and the leaves and coordinates their development. This study investigated the effects of potassium (K) deficiency on the morphology and the physiology of cotton seedlings as well as pH, mineral nutrient contents, and metabolites of xylem sap. In particular, we compared changes in root-shoot communication under low K (LK) and normal K (NK, control) levels. Compared to control, LK stress significantly decreased seedling biomass (leaf, stem, and root dry weight; stem and root length; root surface area and root volume) and the levels of K, Na (sodium), Mg (magnesium), Fe (iron), and Zn (zinc) in xylem sap. A total of 82 metabolites in sap analyzed by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) showed significant differences between the two conditions; among these, 38 were up-regulated more than 2-fold, while the others were down-regulated less than 0.5-fold. In particular, several metabolites found in the cell membrane including three cholines (glycerophosphatecholine, 2-hexenylcholine, and caproylcholine) and desglucocoroloside and others such as malondialdehyde, α-amino acids and derivatives, sucrose, and sugar alcohol significantly increased under LK stress, indicating that cell membranes were damaged and protein metabolism was abnormal. It is worth noting that glycerophosphocholine was up-regulated 29-fold under LK stress, indicating that it can be used as an important signal of root-shoot communication. Furthermore, in pathway analyses, 26 metabolites were matched to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways; L-aspartic acid, which was associated with 10 KEGG pathways, was the most involved metabolite. Overall, K deficiency reduced the antioxidant capacity of cotton seedlings and led to a metabolic disorder including elevated levels of primary metabolites and inhibited production of secondary metabolites. This eventually resulted in decreased biomass of cotton seedlings under LK stress. This study lays a solid foundation for further research on targeted metabolites and signal substances in the xylem sap of cotton plants exposed to K deficiency.

Lolium perenne apoplast metabolomics for identification of novel metabolites produced by the symbiotic fungus Epichloë festucae

Epichloë festucae is an endophytic fungus that forms a symbiotic association with Lolium perenne. Here we analysed how the metabolome of the ryegrass apoplast changed upon infection of this host with sexual and asexual isolates of E. festucae. A metabolite fingerprinting approach was used to analyse the metabolite composition of apoplastic wash fluid from uninfected and infected L. perenne. Metabolites enriched or depleted in one or both of these treatments were identified using a set of interactive tools. A genetic approach in combination with tandem MS was used to identify a novel product of a secondary metabolite gene cluster. Metabolites likely to be present in the apoplast were identified using MarVis in combination with the BioCyc and KEGG databases, and an in-house Epichloë metabolite database. We were able to identify the known endophyte-specific metabolites, peramine and epichloëcyclins, as well as a large number of unknown markers. To determine whether these methods can be applied to the identification of novel Epichloë-derived metabolites, we deleted a gene encoding a NRPS (lgsA) that is highly expressed in planta. Comparative MS analysis of apoplastic wash fluid from wild-type- vs mutant-infected plants identified a novel Leu/Ile glycoside metabolite present in the former.

Isochorismate-derived biosynthesis of the plant stress hormone salicylic acid

The phytohormone salicylic acid (SA) controls biotic and abiotic plant stress responses. Plastid-produced chorismate is a branch-point metabolite for SA biosynthesis. Most pathogen-induced SA derives from isochorismate, which is generated from chorismate by the catalytic activity of ISOCHORISMATE SYNTHASE1. Here, we ask how and in which cellular compartment isochorismate is converted to SA. We show that in Arabidopsis, the pathway downstream of isochorismate requires only two additional proteins: ENHANCED DISEASE SUSCEPTIBILITY5, which exports isochorismate from the plastid to the cytosol, and the cytosolic amidotransferase avrPphB SUSCEPTIBLE3 (PBS3). PBS3 catalyzes the conjugation of glutamate to isochorismate to produce isochorismate-9-glutamate, which spontaneously decomposes into SA and 2-hydroxy-acryloyl-N-glutamate. The minimal requirement of three compartmentalized proteins controlling unidirectional forward flux may protect the pathway against evolutionary forces and pathogen perturbations.

Quantitative Jasmonate Profiling Using a High-Throughput UPLC-NanoESI-MS/MS Method

Jasmonic acid (JA) and its many derivatives-collectively referred as jasmonates-occur ubiquitously in land plants and regulate a wide range of stress-responses and development. Measuring these signaling compounds is complicated by the large number of jasmonate derivatives and the comparatively low concentration of these metabolites in plant tissues. We, here, present a selective and sensitive method consisting of a two-phase extraction coupled with liquid chromatography, nanoelectrospray ionization, and mass spectrometry to determine jasmonate levels in tissues and fluids of various plant species. The application of stable deuterium-labelled standards in combination with authentic standards allows the absolute quantification of a multitude of jasmonates and, additionally, the semi-quantitative analysis of further metabolites from the jasmonate pathway.