Metabolic Profiling Allows Comprehensive Phenotyping of Genetically or Environmentally Modified Plant Systems

Abstract

Metabolic profiling using gas chromatography-mass spectrometry technologies is a technique whose potential in the field of functional genomics is largely untapped. To demonstrate the general usefulness of this technique, we applied to diverse plant genotypes a recently developed profiling protocol that allows detection of a wide range of hydrophilic metabolites within a single chromatographic run. For this purpose, we chose four independent potato genotypes characterized by modifications in sucrose metabolism. Using data-mining tools, including hierarchical cluster analysis and principle component analysis, we were able to assign clusters to the individual plant systems and to determine relative distances between these clusters. Extraction analysis allowed identification of the most important components of these clusters. Furthermore, correlation analysis revealed close linkages between a broad spectrum of metabolites. In a second, complementary approach, we subjected wild-type potato tissue to environmental manipulations. The metabolic profiles from these experiments were compared with the data sets obtained for the transgenic systems, thus illustrating the potential of metabolic profiling in assessing how a genetic modification can be phenocopied by environmental conditions. In summary, these data demonstrate the use of metabolic profiling in conjunction with datamining tools as a technique for the comprehensive characterization of a plant genotype.

Quantitative metabolic profiling by 1-dimensional 1H-NMR analyses: application to plant genetics and functional genomics

“…Metabolic profiling is defined as the identification and quantification of several predefined metabolites in a plant sample. Many chromatographic methods such as gas chromatography-mass spectroscopy (GC-MS), liquid chromatography-ultraviolet light (LC-UV) and liquid chromatography-mass spectroscopy (LC-MS) have been used recently for this purpose (Fraser et al 2000;Roessner et al 2001Roessner et al , 2002Fiehn 2002). Highresolution NMR methods are generally less sensitive than MS-based methods, but have been developed for metabolic fingerprinting (Belton et al 1998;Noteborn et al 2000;Ward et al 2003).…”

Principal component analysis of HPLC–MS/MS patterns of wheat (Triticum aestivum) varieties

“…The most common separation and detection techniques for the profiling of metabolites are liquid chromatography (LC) in its high performance (HPLC) or ultra performance (UPLC) forms, gas chromatography (GC), capillary electrophoresis (CE), as well as the coupling of these instruments with detection techniques such as mass spectrometry (MS) [10][11][12][13][14][15] and nuclear magnetic resonance (NMR) [16,17]. Different techniques used in metabolomic analysis are described in several reviews [8,9,[18][19][20].…”

Metabolic dynamics ofDesulfovibrio vulgarisbiofilm grown on a steel surface

“…The dried residue from the previous step was redissolved in 10 μl of methoxyamine hydrochloride (40 mg ml −1 in pyridine) and derivatized for 90 min under intensive oscillation (450 rpm) at 30°C in 10 μl of 40 mg ml −1 of methoxyamine hydrochloride in pyridine, followed by a 30 min treatment at 37°C with 90 μl of N-methyl-Ntrimethylsilyltrifluoroacetamide (MSTFA) (Roessner et al 2001). The derivate supernatant samples were collected by centrifugation at 10,000 × g for 10 min before GC-MS determination.…”