UPLC-TOF-MS for plant metabolomics: a sequential approach for wound marker analysis in Arabidopsis thaliana

Mass spectrometry-based metabolomics oriented by correlation analysis for wound-induced molecule discovery: identification of a novel jasmonate glucoside

INTRODUCTION

Jasmonates are members of the oxylipin family involved in various plant regulatory processes, particularly in the response to biotic and abiotic stresses. They are present in very low amounts in wounded plants, which complicates their detection within complex plant extracts. Therefore, advanced analytical methods are needed for the profiling and characterisation of novel jasmonate derivatives.

OBJECTIVE

To use metabolomics to search for original wound-induced metabolites belonging to the jasmonate family.

METHODOLOGY

Numerous Arabidopsis specimens harvested at various time points after wounding were analysed by ultra-high pressure liquid chromatography coupled to time-of-flight mass spectrometry (UHPLC/TOFMS). A correlation analysis based on kinetic profile similarities with known jasmonates was applied to find wound-induced molecules having a potential role in defence signalling. Their characterisation was performed by tandem mass spectrometry and capillary nuclear magnetic resonance spectroscopy.

RESULTS

The statistical data treatment highlighted several previously reported jasmonates as well as a new glucoside derivative of the jasmonate 3-oxo-2-(2Z-pentenyl) cyclopentane-1-butyric acid (OPC-4). The monitoring of its kinetics in response to wounding revealed a delayed accumulation compared to the profile of OPC-4. This suggests an inactivation or elimination of OPC-4 through the formation of a polar glucosylated metabolite.

CONCLUSION

The metabolomic approach developed has proved useful in the discovery of original jasmonates synthesised in response to plant wounding.

Metabolic profiling of bioactive Pancratium canariense extracts by GC-MS

INTRODUCTION

Pancratium canariense Ker Gawler is a plant species belonging to family Amaryllidaceae. Plants from this family are known to synthesise a particular type of bioactive compounds, named Amaryllidaceae alkaloids, which have shown AChE inhibitory activity.

OBJECTIVE

To perform the metabolite profiling of methanolic extracts from P. canariense in order to identify bioactive compounds.

METHODOLOGY

Methanolic extracts from bulbs, leaves and fruits were separated into alkaloid-free apolar and polar fractions, as well as alkaloid fractions, and subjected to AChE assay. Metabolite profiling of extracts and fractions of P. canariense was carried out by GC-EI-MS and LC-ESI-TOF-MS.

RESULTS

AChE inhibitory activities of the alkaloid fractions at a concentration of 10 microg/mL were 29.80 +/- 0.91, 40.93 +/- 4.60 and 58.06 +/- 1.18% for the bulbs, leaves and fruits, respectively. Seventy-six metabolites-mono-, di- and trisaccharides, fatty acids, amino acids, sterols as well as several Amaryllidaceae alkaloids-were detected. Further purification of the alkaloids from the methanolic extracts resulted in the detection of 31 compounds including several potent AChE inhibitors such as habranthine and galanthamine, and the structural elucidation of 3-O-acetylhabranthine, a new natural compound with potential AChE inhibitory activity.

CONCLUSION

The described method resulted in effective integration of both GC-EI-MS and LC-ESI-TOF-MS strategies, which permitted the identification of many metabolites, as well as the structural elucidation of new compounds with potential AChE inhibitory activity.

MS-based Plant Metabolomic Approaches for Biomarker Discovery

Metabolomics, which aims at the comprehensive and quantitative analysis of wide arrays of metabolites in biological samples, is playing an increasingly important role in plant science. Various biological issues have been successfully studied by this holistic approach that includes global metabolite composition assessment, mutant characterization, taxonomy, developmental processes, stress response, interaction with environment, quality control assessment and mode of action of herbal medicine. This review summarizes the main mass spectrometry methods used for performing these studies and discusses the potential, but also the current limitations of the various approaches. The intention is not to cover exhaustively the field, which has considerably grown over about one decade, but to give a brief insight into the methods commonly employed and discuss some applications that reveal the potential of metabolomics in phytochemistry and systems biology.

Methods for the analysis of oxylipins in plants

Plant oxylipins comprise a highly diverse and complex class of molecules that are derived from lipid oxidation. The initial oxidation of unsaturated fatty acids may either occur by enzymatic or chemical reactions. A large variety of oxylipin classes are generated by an array of alternative reactions further converting hydroperoxy fatty acids. The structural diversity of oxylipins is further increased by their occurrence either as free fatty acid derivatives or as esters in complex lipids. Lipid peroxidation is common to all biological systems, appearing in developmentally regulated processes and as a response to environmental changes. The oxylipins formed may perform various biological roles; some of them have signaling functions. In order to elucidate the roles of oxylipins in a given biological context, comprehensive analytical assays are available for determining the oxylipin profiles of plant tissues. This review summarizes indirect methods to estimate the general peroxidation state of a sample and more sophisticated techniques for the identification, structure determination and quantification of oxylipins.

MarVis: a tool for clustering and visualization of metabolic biomarkers

BACKGROUND

A central goal of experimental studies in systems biology is to identify meaningful markers that are hidden within a diffuse background of data originating from large-scale analytical intensity measurements as obtained from metabolomic experiments. Intensity-based clustering is an unsupervised approach to the identification of metabolic markers based on the grouping of similar intensity profiles. A major problem of this basic approach is that in general there is no prior information about an adequate number of biologically relevant clusters.

RESULTS

We present the tool MarVis (Marker Visualization) for data mining on intensity-based profiles using one-dimensional self-organizing maps (1D-SOMs). MarVis can import and export customizable CSV (Comma Separated Values) files and provides aggregation and normalization routines for preprocessing of intensity profiles that contain repeated measurements for a number of different experimental conditions. Robust clustering is then achieved by training of an 1D-SOM model, which introduces a similarity-based ordering of the intensity profiles. The ordering allows a convenient visualization of the intensity variations within the data and facilitates an interactive aggregation of clusters into larger blocks. The intensity-based visualization is combined with the presentation of additional data attributes, which can further support the analysis of experimental data.

CONCLUSION

MarVis is a user-friendly and interactive tool for exploration of complex pattern variation in a large set of experimental intensity profiles. The application of 1D-SOMs gives a convenient overview on relevant profiles and groups of profiles. The specialized visualization effectively supports researchers in analyzing a large number of putative clusters, even though the true number of biologically meaningful groups is unknown. Although MarVis has been developed for the analysis of metabolomic data, the tool may be applied to gene expression data as well.

MS/MS spectral tag-based annotation of non-targeted profile of plant secondary metabolites

The MS/MS spectral tag (MS2T) library-based peak annotation procedure was developed for informative non-targeted metabolic profiling analysis using LC-MS. An MS2T library of Arabidopsis metabolites was created from a set of MS/MS spectra acquired using the automatic data acquisition function of the mass spectrometer. By using this library, we obtained structural information for the detected peaks in the metabolic profile data without performing additional MS/MS analysis; this was achieved by searching for the corresponding MS2T accession in the library. In the case of metabolic profile data for Arabidopsis tissues containing more than 1000 peaks, approximately 50% of the peaks were tagged by MS2Ts, and 90 peaks were identified or tentatively annotated with metabolite information by searching the metabolite databases and manually interpreting the MS2Ts. A comparison of metabolic profiles among the Arabidopsis tissues revealed that many unknown metabolites accumulated in a tissue-specific manner, some of which were deduced to be unusual Arabidopsis metabolites based on the MS2T data. Candidate genes responsible for these biosyntheses could be predicted by projecting the results to the transcriptome data. The method was also used for metabolic phenotyping of a subset of Ds transposon-inserted lines of Arabidopsis, resulting in clarification of the functions of reported genes involved in glycosylation of flavonoids. Thus, non-targeted metabolic profiling analysis using MS2T annotation methods could prove to be useful for investigating novel functions of secondary metabolites in plants.

High-resolution profiling of oxylipin-containing galactolipids in Arabidopsis extracts by ultra-performance liquid chromatography/time-of-flight mass spectrometry

A high-resolution ultra-performance liquid chromatography/time-of-flight mass spectrometry (UPLC/TOFMS) method using in-source collision-induced dissociation (CID) was developed for globally profiling oxylipin-containing galactolipids in Arabidopsis wounded leaves. MS and pseudo-MS/MS spectra were obtained during a single analytical run by switching a lens of the TOFMS transfer optics from low to high voltage. Numerous known galactolipids were observed, and four novel mono- or di-galactosyl monoacylglycerides (MGMGs or DGMGs) containing oxophytodienoic acid (OPDA) or dinor-oxophytodienoic acid (dn-OPDA), esterified respectively at the sn1 and the sn2 positions, were identified. Rapid microisolation of the galactolipids followed by alkaline and enzymatic hydrolyses enabled the release of the esterified oxylipins, which allowed for the unambiguous characterization of the oxylipin-containing monoacylglycerides. Their strong induction in response to wounding indicates that these compounds are probably lysogalactolipids formed from galactosyldiglycerides in the injured tissues.