An exploratory method for identifying reactant-product lipid pairs from lipidomic profiles of wild-type and mutant leaves of Arabidopsis thaliana

Abstract

Discerning the metabolic or enzymatic role of a particular gene product, in the absence of information indicating sequence homology to known gene products, is a difficult task. One approach is to compare the levels of metabolites in a wild-type organism to those in an organism with a mutation that causes loss of function of the gene. The goal of this project was to develop an approach to analyze metabolite data on wild-type and mutant organisms for the purpose of identifying the function of a mutated gene. To develop and test statistical approaches to analysis of metabolite data for identification of gene function, levels of 141 lipid metabolites were measured in leaves of wild-type Arabidopsis thaliana plants and in leaves of Arabidopsis thaliana plants with known mutations in genes involved in lipid metabolism. The mutations were primarily in fatty acid desaturases, which are enzymes that catalyze reactions in which double bonds are added to fatty acids. When these enzymes are mutated, leaf lipid composition is altered, and the altered levels of specific lipid metabolites can be detected by a mass spectrometry. A randomization P-Value and other metrics were calculated for all potential reactant product pairs, which included all lipid metabolite pairs. An algorithm was developed to combine these data and rank the results for each pair as to likelihood of being the actual reactant-product pair. This method was designed and tested on data collected on mutants in genes with known functions, fad2 (Okuley et al., 1994), fad3 (Arondel et al., 1992), fad4, fad5 (Mekhedov et al., 2000), fad6 (Falcone et al., 1994), and fad7 (Iba et al., 1993 and Gibson et al., 1994). Application of the method to three additional genes produced by random mutagenesis, sfd1, sfd2, and sfd3, indicated that the significant pairs for fad6 and sfd3 were similar. Consistent with this, genetic evidence has indicated that sfd3 is a mutation in the FAD6 gene. The methods provide a list of putative reactions for an enzyme encoded by an unknown mutant gene. The output lists for unknown genes and known genes can be compared to provide evidence for similar biochemical activities. However, the strength of the current method is that the list of candidate chemical reactions for an enzyme encoded by a mutant gene can be produced without data other than the metabolite profile of the wild-type and mutant organisms, i.e., known gene analysis is not a requirement to obtain the candidate reaction list.