Plant metabolomics: analytical platforms and integration with functional genomics

Abstract

As the final downstream product of the genome, the plant metabolome is a highly complex, dynamic assortment of primary and secondary compounds. Although technological platforms to study genomes, transcriptomes and even proteomes are presently available, methods to pursue genuine metabolomics have not yet been developed due to the extensive chemical diversity of plant primary and secondary metabolites. No single analytical method can accurately survey the entire metabolome. However, recent technical, chemometric and bioinformatic advances promise to enhance our global understanding of plant metabolism. Separation-based mass spectrometry (MS) approaches, such as gas (GC) or liquid chromatography (LC)-MS, are relatively inexpensive, highly sensitive and provide excellent identifying capacity. However, Fourier transform-ion cyclotron resonance (FT-ICR)-MS is better suited for rapid, high-throughput applications and is currently the most sensitive method available. Unlike MS-based analyses, nuclear magnetic resonance (NMR) spectroscopy provides a large amount of information regarding molecular structure, and novel software innovations have facilitated the unequivocal identification and absolute quantification of compounds within composite samples. Due to the size and complexity of metabolomics datasets, numerous chemometric methods are used to extract and display systematic variation. Coupled with pattern recognition techniques and plant-specific metabolite databases, broad-scope metabolite analyses have emerged as functional genomics tools for novel gene discovery and functional characterization. In this review, key metabolomics technologies are compared and the applications of FT-ICR-MS and NMR to the study of benzylisoquinoline alkaloid metabolism in opium poppy are discussed. AbbreviationsAPCI Atmospheric pressure chemical ionization BL Batch-learning CE Capillary electrophoresis CAS Chemical Abstract Service CID Collision induced dissociation DIMS Direct injection mass spectrometry ESI Electrospray ionization EST Expressed sequence tag FID Free induction decay J. M. Hagel is the recipient of an Alberta Ingenuity Graduate Student Scholarship. P. J. Facchini holds the Canada Research Chair in Plant Metabolic Processes Biotechnology.

Metabolic movement upon abscisic acid and salicylic acid combined treatments

“…Since plants have complex and highly diverse metabolites, it is difficult to analyze plant metabolites comprehensively by a single analytical method, thus mass spectrometry (MS) and nuclear magnetic resonance (NMR) have mainly been used for metabolite detection (Hagel and Facchini 2008;Hall 2006). NMR provides structural information for metabolites without detailed assignments and is a non-selective and propertyindependent analytical technique, although a drawback is less sensitivity when compared with MS.…”

“…For example, 1 H-NMR metabolic profiling has been shown useful in distinguishing different ecotypes (Ward et al 2003), transgenic plants or their wild types (Choi et al 2004;Manetti et al 2004), and in describing the influence of infection by pathogens on metabolite composition (Abdel-Farid et al 2009;Choi et al 2006). Furthermore, there are some reports on the data process of 1 H-NMR for metabolic analysis (Hagel and Facchini 2008;Krishnan et al 2005). Thus, 1 H-NMR is very useful at the initial stage in metabolite phenotyping.…”

Metabolômica como ferramenta em taxonomia: O modelo em Arnica. Metabolomics in plant taxonomy: The Arnica model

“…The most widely employed methods are mass spectrometry coupled to gas or liquid chromatography (GC-MS and LC-MS) and nuclear magnetic resonance (NMR), but also other methods such as capillary electrophoresis mass spectrometry (CE-MS), high-performance liquid chromatography with photodiode array detection (HPLC-PDA), thin layer chromatography with UV detection (TLC-UV) and Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR-MS) have been described (HAGEL and FACCHINI, 2008;MORITZ and JOHANSSON, 2008). Each method has its own advantages and disadvantages, an appropriate combination of analytical tools with respect to the analysed plant material is therefore essential (MORITZ and JOHANSSON, 2008).…”

“…In these methods, the metabolites are separated via gas chromatography, liquid chromatography, or capillary electrophoresis (CE) prior to mass spectrometric analysis. GC and LC or HPLC (highperformance liquid chromatography) separate compounds due to different interactions of the substances with the stationary phase, while CE separation is based on the size-to-charge ratio of the ionic molecules (HAGEL and FACCHINI, 2008). CE-MS will not be further discussed at this point.…”

“…The separation technique is chosen on the basis of the type of molecules present in the target sample. GC is applicable in the case of hydrophobic, low molecular weight compounds such as essential oils, hydrocarbons, esters, and metabolite derivatives with reduced polarity (HAGEL and FACCHINI, 2008). In order to perform a GC analysis the analytes must be heat-stable and volatile.…”