Metabolomics as a Prospective Tool for Soybean (Glycine max) Crop Improvement.

Global demand for soybean and its products has stimulated research into the production of novel genotypes with higher yields, greater drought and disease tolerance, and shorter growth times. Genetic research may be the most effective way to continue developing high-performing cultivars with desirable agronomic features and improved nutritional content and seed performance. Metabolomics, which predicts the metabolic marker for plant performance under stressful conditions, is rapidly gaining interest in plant breeding and has emerged as a powerful tool for driving crop improvement. The development of increasingly sensitive, automated, and high-throughput analytical technologies, paired with improved bioinformatics and other omics techniques, has paved the way for wide characterization of genetic characteristics for crop improvement. The combination of chromatography (liquid and gas-based) with mass spectrometry has also proven to be an indisputable efficient platform for metabolomic studies, notably plant metabolic fingerprinting investigations. Nevertheless, there has been significant progress in the use of nuclear magnetic resonance (NMR), capillary electrophoresis, and Fourier-transform infrared spectroscopy (FTIR), each with its own set of benefits and drawbacks. Furthermore, utilizing multivariate analysis, principal components analysis (PCA), discriminant analysis, and projection to latent structures (PLS), it is possible to identify and differentiate various groups. The researched soybean varieties may be correctly classified by using the PCA and PLS multivariate analyses. As metabolomics is an effective method for evaluating and selecting wild specimens with desirable features for the breeding of improved new cultivars, plant breeders can benefit from the identification of metabolite biomarkers and key metabolic pathways to develop new genotypes with value-added features.

Ambrafuran (AmbroxTM) Synthesis from Natural Plant Product Precursors.

Ambergris, an excretion product of sperm whales, has been a valued agent in the formulation of perfumes. The composition of ambergris consists of two major components: 40-46% cholestanol type steroids and approximately 25-45% of a triterpenoid known as ambrein. Ambergris undergoes oxidative decomposition in the environment to result in odorous compounds, such as ambraoxide, methylambraoxide, and ambracetal. Its oxidized form, ambrafuran (IUPAC name: 3a,6,6,9a-tetramethyl-2,4,5,5a,7,8,9,9b-octahydro-1H-benzo[e][1]benzofuran), is a terpene furan with a pleasant odor and unique olfactive and fixative properties. The current state of the fragrance industry uses ambrafuran materials entirely from synthetic or semisynthetic sources. However, natural compounds with the potential to be converted to ambergris-like odorants have been extracted from several different types of plants. Here we review plant terpenoids suitable as starting materials for the semisyntheses of ambrafuran or intermediates, such as ambradiol, that can be used in biocatalytic transformations to yield ambrafuran.

GC-MS based profiling of alkanes in the filamentous yeast Hyphozyma roseoniger (Moesziomyces antarcticus).

OBJECTIVES: Hyphozyma roseoniger, a filamentous yeast, is used as a biocatalyst in the bio-transformation of terpenoids; however, the microorganism's endogenous ability to synthesise and metabolise hydrophobic terpenes and alkanes has not been characterised. RESULTS: When grown in potato dextrose broth the organism reached the stationary phase at 14 d. The non-polar fraction from cells, harvested every second day, were obtained with ethyl acetate extraction and analysed by gas chromatography with mass-spectrometric detection. Principal component-and hierarchical cluster analysis indicated growth-dependent clustering of the sample groups. A total of 26 alkanes were annotated across the different developmental stages. CONCLUSIONS: The major hydrocarbons comprised linear and branched structures. The dominant alkanes were all odd- or even-carbon numbered long-chain n-alkanes, C15 > C18 > C24.

Similar, but different: structurally related azelaic acid and hexanoic acid trigger differential metabolomic and transcriptomic responses in tobacco cells.

BACKGROUND: Plants respond to various stress stimuli by activating an enhanced broad-spectrum defensive ability. The development of novel resistance inducers represents an attractive, alternative crop protection strategy. In this regard, hexanoic acid (Hxa, a chemical elicitor) and azelaic acid (Aza, a natural signaling compound) have been proposed as inducers of plant defense, by means of a priming mechanism. Here, we investigated both the mode of action and the complementarity of Aza and Hxa as priming agents in Nicotiana tabacum cells in support of enhanced defense. RESULTS: Metabolomic analyses identified signatory biomarkers involved in the establishment of a pre-conditioned state following Aza and Hxa treatment. Both inducers affected the metabolomes in a similar manner and generated common biomarkers: caffeoylputrescine glycoside, cis-5-caffeoylquinic acid, feruloylglycoside, feruloyl-3-methoxytyramine glycoside and feruloyl-3-methoxytyramine conjugate. Subsequently, quantitative real time-PCR was used to investigate the expression of inducible defense response genes: phenylalanine ammonia lyase, hydroxycinnamoyl CoA quinate transferase and hydroxycinnamoyl transferase to monitor activation of the early phenylpropanoid pathway and chlorogenic acids metabolism, while ethylene response element-binding protein, small sar1 GTPase, heat shock protein 90, RAR1, SGT1, non-expressor of PR genes 1 and thioredoxin were analyzed to report on signal transduction events. Pathogenesis-related protein 1a and defensin were quantified to investigate the activation of defenses regulated by salicylic acid and jasmonic acid respectively. The qPCR results revealed differential expression kinetics and, in general (except for NPR1, Thionin and PR1a), the relative gene expression ratios observed in the Hxa-treated cells were significantly greater than the expression observed in the cells treated with Aza. CONCLUSIONS: The results indicate that Aza and Hxa have a similar priming effect through activation of genes involved in the establishment of systemic acquired resistance, associated with enhanced synthesis of hydroxycinnamic acids and related conjugates.

Insights into the wound-healing properties of medicinally important South African Bulbine species - A comparative study.

ETHNOPHARMACOLOGICAL RELEVANCE: South Africa harbours a large number of Bulbine (Xanthorrhoeaceae) species, which includes ethnobotanically important indigenous species. Traditionally, Bulbine leaves are used by several ethnic groups in South Africa to treat dermatological conditions including wounds, which led to the development of Bulbine-containing cosmetic products. However, scientific evidence is needed to support the claims in treating skin conditions and wound-healing. AIM OF THE STUDY: This comparative study was undertaken to investigate the wound-healing properties of five Bulbine species indigenous to South Africa, using in vitro and in vivo models. MATERIALS AND METHODS: Five Bulbine species, B. abyssinica, B. asphodeloides, B. frutescens, B. latifolia and B. narcissifolia were collected from natural populations in the Eastern Cape Province of South Africa. The chemical profiles of the methanol leaf extracts were acquired using ultra-performance liquid chromatography with photodiode array detection in tandem with quadrupole time-of-flight mass spectrometry. The methyl thiazolyl tetrazolium (MTT) assay and maximum tolerated concentration (MTC) assay were used to assess the in vitro and in vivo toxicity of the extracts, respectively. The in vitro scratch assay was employed to monitor cell migration and wound-closure in a HaCaT cell monolayer, following treatment with the plant extracts for 48 h. In vivo wound-healing potential was determined using the zebrafish larvae caudal fin amputation assay, assessed in three-days post fertilization larvae and various concentrations of the plant extracts were tested in both assays to determine the concentration-response effect. Data were analysed using MS Excel® enhanced with the Real Statistics add-in. RESULTS AND DISCUSSION: Using UPLC-MS, 11 major compounds were tentatively identified in the five Bulbine species. Although the compounds varied between species, all five Bulbine species contained the phenylanthraquinone, knipholone. Kaempferol glucoside was identified in four species, but not in B. abyssinica. The five Bulbine species were non-cytotoxic (cell viability > 80%) towards keratinocytes at all three tested concentrations. However, B. latifolia was toxic towards zebrafish larvae at all the tested concentrations, while the other four species were non-toxic at low concentrations. The results of the scratch assay revealed that B. abyssinica was the most active extract at 100 µg/mL. Compared to the untreated control, wound-closure notably increased by 28% (p < 0.05), 44% (p < 0.01) and 34% (p < 0.05) after 12 h, 24 h and 36 h post-treatment, respectively. Although none of the species achieved 100% caudal fin regeneration by the end of the treatment period, B. frutescens demonstrated the highest regeneration (90%) and most significant difference (p < 0.01) compared to the untreated control. CONCLUSION: The results revealed that the five Bulbine species have complex chemical profiles, however, they share major compound classes (i.e. phenylanthroquinones and flavonoid analogues) across the species. The study highlights the wound-healing properties of the five species, which is consistent with their traditional use.

Defence-related metabolic changes in wheat (Triticum aestivum L.) seedlings in response to infection by Puccinia graminis f. sp. tritici.

Stem rust caused by the pathogen Puccinia graminis f. sp. tritici is a destructive fungal disease-causing major grain yield losses in wheat. Therefore, understanding the plant defence regulation and function in response to the pathogen attack is required. As such, an untargeted LC-MS-based metabolomics approach was employed as a tool to dissect and understand the biochemical responses of Koonap (resistant) and Morocco (susceptible) wheat varieties infected with two different races of P. graminis (2SA88 [TTKSF] and 2SA107 [PTKST]). Data was generated from the infected and non-infected control plants harvested at 14- and 21- days post-inoculation (dpi), with 3 biological replicates per sample under a controlled environment. Chemo-metric tools such as principal component analysis (PCA), orthogonal projection to latent structures-discriminant analysis (OPLS-DA) were used to highlight the metabolic changes using LC-MS data of the methanolic extracts generated from the two wheat varieties. Molecular networking in Global Natural Product Social (GNPS) was further used to analyse biological networks between the perturbed metabolites. PCA and OPLS-DA analysis showed cluster separations between the varieties, infection races and the time-points. Distinct biochemical changes were also observed between the races and time-points. Metabolites were identified and classified using base peak intensities (BPI) and single ion extracted chromatograms from samples, and the most affected metabolites included flavonoids, carboxylic acids and alkaloids. Network analysis also showed high expression of metabolites from thiamine and glyoxylate, such as flavonoid glycosides, suggesting multi-faceted defence response strategy by understudied wheat varieties towards P. graminis pathogen infection. Overall, the study provided the insights of the biochemical changes in the expression of wheat metabolites in response to stem rust infection.

Identification of Plant-Derived Bioactive Compounds Using Affinity Mass Spectrometry and Molecular Networking.

Affinity selection-mass spectrometry (AS-MS) is a label-free binding assay system that uses UHPLC-MS size-based separation methods to separate target-compound complexes from unbound compounds, identify bound compounds, classify compound binding sites, quantify the dissociation rate constant of compounds, and characterize affinity-extracted ligands. This label-free binding assay, in contrast to conventional biochemical (i.e., high-throughput screening (HTS)) approaches, is applicable to any drug target, and is also concise, accurate, and adaptable. Although AS-MS is an innovative approach for identifying lead compounds, the possibilities of finding bioactive compounds are limited by competitive binding, which occurs during the equilibration of extracts with the target protein(s). Here, we discuss the potential for metabolite profiling complemented with molecular networking to be used alongside AS-MS to improve the identification of bioactive compounds in plant extracts. AS-MS has gained significant prominence in HTS labs and shows potential to emerge as the driving force behind novel drug development in the future.

Highlighting mass spectrometric fragmentation differences and similarities between hydroxycinnamoyl-quinic acids and hydroxycinnamoyl-isocitric acids.

BACKGROUND: Plants contain a myriad of metabolites which exhibit diverse biological activities. However, in-depth analyses of these natural products with current analytical platforms remains an undisputed challenge due to the multidimensional chemo-diversity of these molecules, amplified by both isomerization and conjugation. In this study, we looked at molecules such as hydroxyl-cinnamic acids (HCAs), which are known to exist as positional and geometrical isomers conjugated to different organic acids namely quinic- and isocitric acid. OBJECTIVE: The study aimed at providing a more defined distinction between HCA conjugates from Amaranthus viridis and Moringa oleifera, using mass spectrometry (MS) approaches. METHODS: Here, we used a UHPLC-MS/MS targeted approach to analyze isobaric HCA conjugates extracted from the aforementioned plants. RESULTS: Mass spectrometry results showed similar precursor ions and fragmentation pattern; however, distinct differences were seen with ions at m/z 155 and m/z 111 which are associated with isocitric acid conjugates. CONCLUSION: Our results highlight subtle differences between these two classes of compounds based on the MS fingerprints, enabling confidence differentiation of the compounds. Thus, these findings provide a template reference for accurate and confident annotation of such compounds in other plants.

Stimulatory Effects of Acibenzolar-S-Methyl on Chlorogenic Acids Biosynthesis in Centella asiatica Cells.

Centella asiatica is a perrenial herb that grows in tropical regions with numerous medicinal properties mostly attributed to the presence of pentacyclic triterpenoids. Interestingly, this plant also possess a significant amount of phenylpropanoid-derived chlorogenic acids (CGAs) that have recently been reported to confer neuroprotective properties. In a biotechnological attempt to increase the biosynthesis of CGA-derivatives in cultured Centella cells, acibenzolar-S-methyl was applied as a xenobiotic inducer in combination with quinic acid and shikimic acid as precursor molecules. Applying a semi-targeted metabolomics-based approach, time and concentration studies were undertaken to evaluate the effect of the manipulation on cellular metabolism leading to CGA production. Phytochemical extracts were prepared using methanol and analyzed using a UHPLC-qTOF-MS platform. Data was processed and analyzed using multivariate data models. A total of four CGA-derivatives, annotated as trans-5-feruloylquinic acid, 3,5 di-caffeoylquinic acid, 3,5-O-dicaffeoyl-4-O-malonylquinic acid (irbic acid) and 3-caffeoyl, 5-feruloylquinic acid, were found to be upregulated by the acibenzolar-S-methyl treatment. To the best of our knowledge, this is the first report on the induction of CGA derivatives in this species. Contrary to expectations, the effects of precursor molecules on the levels of the CGAs were insignificant. However, a total of 16 metabolites, including CGA derivatives, were up-regulated by precursor treatment. Therefore, this study shows potential to biotechnologically manipulate C. asiatica cells to increase the production of these health beneficial CGAs.

Analyses of chlorogenic acids and related cinnamic acid derivatives from Nicotiana tabacum tissues with the aid of UPLC-QTOF-MS/MS based on the in-source collision-induced dissociation method.

BACKGROUND: Chlorogenic acids (CGAs) are a class of phytochemicals that are formed as esters between different derivatives of cinnamic acid and quinic acid molecules. In plants, accumulation of these compounds has been linked to several physiological responses against various stress factors; however, biochemical synthesis differs from one plant to another. Although structurally simple, the analysis of CGA molecules with modern analytical platforms poses an analytical challenge. The objective of the study was to perform a comparison of the CGA profiles and related derivatives from differentiated tobacco leaf tissues and undifferentiated cell suspension cultures. RESULTS: Using an UHPLC-Q-TOF-MS/MS fingerprinting method based on the in-source collision induced dissociation (ISCID) approach, a total of 19 different metabolites with a cinnamic acid core moiety were identified. These metabolites were either present in both leaf tissue and cell suspension samples or in only one of the two plant systems. Profile differences point to underlying biochemical similarities or differences thereof. CONCLUSION: Using this method, the regio- and geometric-isomer profiles of chlorogenic acids of the two tissue types of Nicotiana tabacum were achieved. The method was also shown to be applicable for the detection of other related molecules containing a cinnamic acid core.

Exploring the wound healing potential of Lobostemon fruticosus using in vitro and in vivo bioassays.

ETHNOPHARMACOLOGICAL RELEVANCE: Lobostemon fruticosus (L.) H.Buek is a perennial and woody shrub of the Boraginaceae family, found in the Cape region of South Africa. The leaves and twigs are used to treat dermatological conditions such as wounds, burns, ringworm, erysipelas and eczema. Anti-inflammatory, antibacterial, antiviral and anti-proliferative activities of L. fruticosus have been reported. However, there is a void in research which reports on the wound healing properties of this plant. AIM OF THE STUDY: Aligned with the traditional use of L. fruticosus, our study aimed to use in vitro and in vivo bioassays to confirm the wound healing potential of the plant. MATERIALS AND METHODS: An aqueous methanol extract (80% v/v) of L. fruticosus was prepared using a sample collected from the Western Cape Province of South Africa and chromatographically profiled by ultra-performance liquid chromatography coupled to mass spectrometry (UPLC-MS). The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) cytotoxicity assay was performed to determine the non-toxic concentrations of the extract for subsequent use in the in vitro scratch assay. Both the human keratinocyte (HaCaT) and fibroblast (BJ-5ta) cell lines were employed in the in vitro scratch assay. The in vivo caudal fin amputation assay was used to assess the wound healing potential of L. fruticosus, by monitoring fin regeneration in zebrafish larvae treated with the plant extract at various concentrations. RESULTS: Six major compounds were tentatively identified in the L. fruticosus extract namely; globoidnan A, globoidnan B, rutin, rabdosiin, sagerinic acid and rosmarinic acid. The potentially toxic pyrrolizidine alkaloids were also identified and quantitatively confirmed to be present at a low concentration of 119.58 ppm (m/m). Treatment of HaCaT and BJ-5ta cells with the plant extract in the scratch assay resulted in an increase in cell migration, which translates to accelerated wound closure. After 24 hr treatment with 100 µg/mL of extract, wound closure was recorded to be 91.1 ± 5.7% and 94.1 ± 1.3% for the HaCaT and BJ-5ta cells, respectively, while the untreated (medium) controls showed 72.3 ± 3.3% and 73.0 ± 4.3% for the two cell lines, respectively. Complete wound closure was observed between 24 and 36 hr, while the untreated control group did not achieve 100% wound closure by the end of the observation period (48 hr). In vivo, the crude extract at 100 µg/mL accelerated zebrafish caudal fin regeneration achieving 100.5 ± 3.8% regeneration compared to 68.3 ± 6.6% in the untreated control at two days post amputation. CONCLUSIONS: The study affirms the wound healing properties, as well as low toxicity of L. fruticosus using both in vitro and in vivo assays, which supports the traditional medicinal use. Other in vitro assays that target different mechanisms involved in wound healing should be investigated to support the current findings.