The Metabolome as Phenotype

Source: Fiehn, O., Kopka, J., Dormann, P., Altmann, T., Trethewey, R.N., and Willmitzer, L. Metabolite profiling for plant functional genomics. 2000. Nature Biotechnology, 18: 1157 – 61

The authors grew up three strains of Arabidopsis: one wild-type, one with a DGD mutation, and one with a stomatal density mutation. They used GC/MS to profile the strains with 300+ metabolites in an unbiased approach that picked up a number of unknown molecules. Nearly 60 compounds were found to be significantly different between wt and the DGD mutation. The authors used an unbiased approach and found that a number of unidentified compounds were also noticeably different. Each strain has a unique metabolic profile, as determined through principal component analysis.


Significant ( p < 0.01) metabolite differences, between dgd and wt, sdd1-1 and wt. Known or high-fold different metabolites shown.

Other notes:
-used internal standards for correcting and as normalization
-also normalized to 1 mg plant leaf fresh weight
-testing reproducibility in samples that were measured multiple times found deviations for same day analysis at 8 +/- 6% over 149 polar compounds
-tested biological variability and found it in clear excess of preparation variability, averaging 40%
-single gene change showed 153 of 326 significant differences in metabolites

“This analysis demonstrates the power of the metabolite profiling method to identify and quantify previously overlooked alterations, following a more comprehensive interpretation of the consequences of genetic modifications.”