Metabolomics of Arabidopsis Thaliana

Abstract

Since the publication of the complete genome sequence of the model plant Arabidopsis thaliana, the precision annotation of the exact function of each gene has become a major research activity. Metabolomic analysis has much to offer in this endeavour and the small physical size and generation time of Arabidopsis make it a particularly attractive system for large-scale metabolomic data collection and analysis. In this review, we summarize the known phytochemistry of Arabidopsis, with particular emphasis on recent discoveries that indicate that the complexity of this plant's secondary metabolome is much greater than originally realized. We survey how the different analytical technologies, used in metabolomic analysis, are applied to quantify both primary and secondary metabolites of Arabidopsis. The use of isotope labelling to derive empirical formulae for unknown metabolites is highlighted, as is co-expression analysis of transcriptome and metabolome data, as both of these technologies are well suited to this species. The application of the various techniques to study the molecular plant physiology, genetics and functional genomics of Arabidopsis is reviewed, with particular reference to the use of mutants and other genetic resources, such as recombinant inbred lines.

Plant Metabolomics in a Nutshell: Potential and Future Challenges

“…For more detailed information the reader is referred to seminal volumes such as: Saito et al (2006), Weckwerth (2007) and Hardy and Hall (2011). Compact summaries have also been provided by Browne et al (2011) and Beale and Sussman (2011).…”

“…The significant short life cycle and genetic advantages of this compact species have transformed a common weed into the most studied plant species on the planet. Inevitably, Arabidopsis has also rapidly become a favoured target for metabolomics studies (Beale & Sussman, 2011). Much functional genomics research has also been extended to include metabolic fingerprinting and profiling in the quest to understand better the function and molecular impact of specific gene mutations on the molecular patterning of plants.…”

“…Furthermore, its importance in a crop production context enhances the value of this fundamental research (Browne et al, 2011;Draper et al, 2011). Metabolomics research has shown that changes in plant physiology, be they related to genetic or environmental perturbation, often involve widespread alteration in plant biochemistry not specifically restricted to particular pathways (Beale & Sussman, 2011). Abiotic stress for example, be it induced by temperature, drought or sub-optimal nutrient supply, has been shown to induce extensive reprogramming of the plant metabolome (see review by Browne et al, 2011).…”

Genetics, Genomics and Metabolomics

“…Monitoring such differences can greatly assist in determining the causal factors of natural variation in traits (Keurentjes, 2009). Linking metabolic profiles to phenotypic traits has only been reported by a small number of studies (as discussed by de Vos et al (2011) Beale et al (2011) Stewart et al (2011) and functional or regulatory analyses of metabolites are even rarer. Yet, these pioneering studies have shown that metabolism is strongly interlinked with complex genetic traits and may hold the key for their regulatory dissection.…”

An Efficient High Throughput Metabotyping Platform for Screening of Biomass Willows

“…Hence, the development of robust protocols for sample handling and data collection are essential components of any mQTL screen, where many hundreds of samples are involved. Willow (and other tree species) present a range of problems to large-scale screening and metabolomics data collection, which has been established on more tractable species such as Arabidopsis [ 21 , 22 , 23 ], with other significant studies on Solanaceae [ 24 , 25 ], cereals [ 26 , 27 ] and Medicago [ 28 ]. Metabolite screening of perennial woody plants has been reported for loblolly pine (for milled stem tissue) [ 29 ], but generally the heterogeneity of tissue types and physical/chemical properties requires considerable re-thinking of the protocols developed for annual crops.…”