A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations

Abstract

A large proportion of the 6,000 genes present in the genome of Saccharomyces cerevisiae, and of those sequenced in other organisms, encode proteins of unknown function. Many of these genes are "silent, " that is, they show no overt phenotype, in terms of growth rate or other fluxes, when they are deleted from the genome. We demonstrate how the intracellular concentrations of metabolites can reveal phenotypes for proteins active in metabolic regulation. Quantification of the change of several metabolite concentrations relative to the concentration change of one selected metabolite can reveal the site of action, in the metabolic network, of a silent gene. In the same way, comprehensive analyses of metabolite concentrations in mutants, providing "metabolic snapshots," can reveal functions when snapshots from strains deleted for unstudied genes are compared to those deleted for known genes. This approach to functional analysis, using comparative metabolomics, we call FANCY-an abbreviation for functional analysis by co-responses in yeast.

Impact of Thermodynamic Principles in Systems Biology

“…An interesting application of a lin-log kinetic model is to identify the function of so-called silent genes [35,36] which shows how lin-log kinetic models could be used to resolve gene-annotation problems.…”

Discrimination of Type 2 diabetic patients from healthy controls by using metabonomics method based on their serum fatty acid profiles

“…This method has recently demonstrated enormous potentials in many fields such as plant genotype discrimination [2][3], toxicological mechanisms, disease processes, and drug discovery [4][5][6][7][8][9][10]. One such recent application of this method included the rapid and noninvasive diagnosis of coronary heart disease [11][12][13][14].…”

Characterisation of the metabolome of ocular tissues and post-mortem changes in the rat retina

“…Metabolite extraction was achieved by adding 800μL of chloroform:methanol (50:50, pre-cooled to -20 o C) followed by 50μL of an internal standard mixture (0.1 mg/ml d 5 Benzoic acid, d 4 Succinic acid and d 5 Glycine dissolved in methanol) to each preweighed sample. Homogenisation/extraction was performed in a TissueLyser (Qiagen; 25Hz, 10 minutes using one 3mm tungsten carbide bead).…”

“…2,3 As metabolites are the end product of biological pathways, the metabolome is a sensitive measure of disease phenotype and a dynamic indicator of genetic, environmental or disease-specific perturbations. 1,4,5 Metabolomics is increasingly being applied as a tool in eye research. It has been used to characterise normal ocular tissues and biofluids including the tear film, lens, vitreous and retina.…”