Hye Kyong Kim

NMR-based metabolomic analysis of plants

Nuclear magnetic resonance (NMR)-based metabolomics has many applications in plant science. Metabolomics can be used in functional genomics and to differentiate plants from different origin, or after different treatments. In this protocol, the following steps of plant metabolomics using NMR spectroscopy are described: sample preparation (freeze drying followed by extraction by ultrasonication with 1:1 CD3OD:KH2PO4 buffer in D2O), NMR analysis (standard 1H, J-resolved, 1H–1H correlation spectroscopy (COSY) and heteronuclear multiple bond correlation (HMBC)) and chemometric methods. The main advantage of NMR metabolomic analysis is the possibility of identifying metabolites by comparing NMR data with references or by structure elucidation using two-dimensional NMR. This protocol is particularly suited for the analysis of secondary metabolites such as phenolic compounds (usually abundant in plants), and for primary metabolites (e.g., sugars and amino acids). This procedure is rapid; it takes not more than 30 min for sample preparation (multiple parallel) and a further 10 min for NMR spectrum acquisition.

Metabolic discrimination of Catharanthus roseus leaves infected by phytoplasma using 1H-NMR spectroscopy and multivariate data analysis

A comprehensive metabolomic profiling of Catharanthus roseus L. G. Don infected by 10 types of phytoplasmas was carried out using one-dimensional and two-dimensional NMR spectroscopy followed by principal component analysis (PCA), an unsupervised clustering method requiring no knowledge of the data set and used to reduce the dimensionality of multivariate data while preserving most of the variance within it. With a combination of these techniques, we were able to identify those metabolites that were present in different levels in phytoplasma-infected C. roseus leaves than in healthy ones. The infection by phytoplasma in C. roseus leaves causes an increase of metabolites related to the biosynthetic pathways of phenylpropanoids or terpenoid indole alkaloids: chlorogenic acid, loganic acid, secologanin, and vindoline. Furthermore, higher abundance of Glc, Glu, polyphenols, succinic acid, and Suc were detected in the phytoplasma-infected leaves. The PCA of the 1H-NMR signals of healthy and phytoplasma-infected C. roseus leaves shows that these metabolites are major discriminating factors to characterize the phytoplasma-infected C. roseus leaves from healthy ones. Based on the NMR and PCA analysis, it might be suggested that the biosynthetic pathway of terpenoid indole alkaloids, together with that of phenylpropanoids, is stimulated by the infection of phytoplasma.

Sample preparation for plant metabolomics

Sample preparation in plant metabolomics is a fundamental and critical step with important consequences for the accuracy of results. Depending on the analytical tools and the metabolites of interest, sample preparation has to be decided. However, the various methods reported in the literature have many steps in common and consequently the practical considerations concerning the pros and cons are similar. In this review, each step of the sample preparation - harvesting, drying, extraction and purification - will be discussed in detail.

NMR-based metabolomics at work in phytochemistry

Metabolomics is defined as both the qualitative and quantitative analysis of all metabolites in an organism unraveling correlation with other OMICs data. Many of the technologies used in metabolomics have method-specific advantages and drawbacks in terms of diversity of metabolites detected, sensitivity, or resolution. In this paper, the potential of NMR spectrometry applied to metabolomics is reviewed using examples of Nicotiana tabacum and Catharanthus roseus.

An ABC Transporter Mutation Alters Root Exudation of Phytochemicals That Provoke an Overhaul of Natural Soil Microbiota

Root exudates influence the surrounding soil microbial community, and recent evidence demonstrates the involvement of ATP-binding cassette (ABC) transporters in root secretion of phytochemicals. In this study, we examined effects of seven Arabidopsis (Arabidopsis thaliana) ABC transporter mutants on the microbial community in native soils. After two generations, only the Arabidopsis abcg30 (Atpdr2) mutant had significantly altered both the fungal and bacterial communities compared with the wild type using automated ribosomal intergenic spacer analysis. Similarly, root exudate profiles differed between the mutants; however, the largest variance from the wild type (Columbia-0) was observed in abcg30, which showed increased phenolics and decreased sugars. In support of this biochemical observation, whole-genome expression analyses of abcg30 roots revealed that some genes involved in biosynthesis and transport of secondary metabolites were up-regulated, while some sugar transporters were down-regulated compared with genome expression in wild-type roots. Microbial taxa associated with Columbia-0 and abcg30 cultured soils determined by pyrosequencing revealed that exudates from abcg30 cultivated a microbial community with a relatively greater abundance of potentially beneficial bacteria (i.e. plant-growth-promoting rhizobacteria and nitrogen fixers) and were specifically enriched in bacteria involved in heavy metal remediation. In summary, we report how a single gene mutation from a functional plant mutant influences the surrounding community of soil organisms, showing that genes are not only important for intrinsic plant physiology but also for the interactions with the surrounding community of organisms as well.

Quality control of herbal material and phytopharmaceuticals with MS and NMR based metabolic fingerprinting

Metabolic fingerprinting techniques have received a lot of attention in recent years and the annual amount of publications in this field has increased significantly over the past decade. This increase in publications is due to improvements in the analytical performance, most notably in the field of NMR and MS analysis, and the increased awareness of the different applications of this growing field. Metabolomic fingerprinting or profiling is continuously being applied to new areas of research such as drug discovery from natural resources, quality control of herbal material, and discovering lead compounds. In this review the current state of the art of metabolic fingerprinting, focussing on NMR and MS technologies will be discussed. The application of these two analytical tools in the quality control of herbal material and phytopharmaceuticals forms the major part of this review. Finally we will look at the future developments and perspectives of these two technologies in the quality control of herbal material.

Metabolomics: back to basics

Metabolomics has developed into a major tool in functional genomics and plant systems biology. The various methods used for metabolomic analysis will be discussed from the analytical methods back to the preanalytical phase and the biological experiment. Particularly aspects of the preanalytical phase of the analysis is dealt with, including the risks of artefact formation with the various commonly used solvents. Metabolomics is like a snap shot, and conclusions from dynamic systems must be drawn with great care as demonstrated with a biosynthetic study of salicylate in Catharanthus roseus cell cultures.

Metabolic classification of South American Ilex species by NMR-based metabolomics.

The genus Ilex to which mate (Ilex paraguariensis) belongs, consists of more than 500 species. A wide range of metabolites including saponins and phenylpropanoids has been reported from Ilex species. However, despite the previous works on the Ilex metabolites, the metabolic similarities between species which can be used for chemotaxonomy of the species are not clear yet. In this study, nuclear magnetic resonance (NMR) spectroscopy-based metabolomics was applied to the classification of 11 South American Ilex species, namely, Ilex argentina, Ilex brasiliensis, Ilex brevicuspis, Ilex dumosa var. dumosa, I. dumosa var. guaranina, Ilex integerrima, Ilex microdonta, I. paraguariensis var. paraguariensis, Ilex pseudobuxus, Ilex taubertiana, and Ilex theezans. (1)H NMR combined with principal component analysis (PCA), partial least square-discriminant analysis (PLS-DA) and hierarchical cluster analysis (HCA) showed a clear separation between species and resulted in four groups based on metabolomic similarities. The signal congestion of (1)H NMR spectra was overcome by the implementation of two-dimensional (2D)-J-resolved and heteronuclear single quantum coherence (HSQC). From the results obtained by 1D- and 2D-NMR-based metabolomics it was concluded that species included in group A (I. paraguariensis) were metabolically characterized by a higher amount of xanthines, and phenolics including phenylpropanoids and flavonoids; group B (I. dumosa var. dumosa and I. dumosa var. guaranina) with oleanane type saponins; group C (I. brasiliensis, I. integerrima, I. pseudobuxus and I. theezans) with arbutin and dicaffeoylquinic acids, and group D (I. argentina, I. brevicuspis, I. microdonta and I. taubertiana) with the highest level of ursane-type saponins. Clear metabolomic discrimination of Ilex species and varieties in this study makes the chemotaxonomic classification of Ilex species possible.

Metabolic response of tomato leaves upon different plant-pathogen interactions.

INTRODUCTION Plants utilise various defence mechanisms against their potential biotic stressing agents such as viroids, viruses, bacteria or fungi and abiotic environmental challenges. Among them metabolic alteration is a common response in both compatible and incompatible plant-pathogen interactions. However, the identification of metabolic changes associated with defence response is not an easy task due to the complexity of the metabolome and the plant response. To address the problem of metabolic complexity, a metabolomics approach was employed in this study. OBJECTIVE To identify a wide range of pathogen (citrus exocortis viroid, CEVd, or Pseudomonas syringae pv. tomato)-induced metabolites of tomato using metabolomics. METHODOLOGY Nuclear magnetic resonance (NMR) spectroscopy in combination with multivariate data analysis were performed to analyse the metabolic changes implicated in plant-pathogen interaction. RESULTS NMR-based metabolomics of crude extracts allowed the identification of different metabolites implicated in the systemic (viroid) and hypersensitive response (bacteria) in plant-pathogen interactions. While glycosylated gentisic acid was the most important induced metabolite in the viroid infection, phenylpropanoids and a flavonoid (rutin) were found to be associated with bacterial infection. CONCLUSIONS NMR metabolomics is a potent platform to analyse the compounds involved in different plant infections. A broad response to different pathogenic infections was revealed at metabolomic levels in the plant. Also, metabolic specificity against each pathogen was observed.

Metabolomic Differentiation of Brassica rapa Following Herbivory by Different Insect Instars using Two-Dimensional Nuclear Magnetic Resonance Spectroscopy

The metabolic alterations of Brassica rapa (L.) leaves attacked by larvae of the specialist Plutella xylostella L. (Lepidoptera: Yponomeutidae) and the generalist Spodoptera exigua Hubner (Lepidoptera: Noctuidae) were investigated with nuclear magnetic resonance (NMR) spectroscopy, followed by a multivariate data analysis. The principal component analysis (PCA) of 1H NMR spectra showed that metabolic changes in B. rapa leaves induced by the 2nd and the 4th instars were different from each other. However, the congestion of the one-dimensional 1H NMR spectrum made it difficult to identify discriminating metabolites. To overcome the spectral complexity, several two-dimensional NMR techniques were applied. Of those evaluated, J-resolved spectroscopy, which affords an additional coupling constant, provided a wide range of structure information on differentiating the metabolites. Based on the J-resolved spectra combined with PCA, the major signals contributing to the discrimination were alanine, threonine, glucose, sucrose, feruloyl malate, sinapoyl malate, and gluconapin.