Investigations into the allosteric mechanism of a trimeric mutant of Clostridial glutamate dehydrogenase

Abstract

Top-down control analysis was used to quantify how different mRNAs cause physiological changes in response to effectors. We analysed published DNA microarray data (Ideker et al., 2001 Science 292,929-934) that reported growth rates and significant changes in the concentrations of 997 mRNAs in wild type yeast and nine mutants in the presence and absence of galactose. Firstly, mRNAs were clustered into eight modules by similarity of expression profile. Multiplication of integrated response coefficients of mRNA modules to galactose by the elasticities of growth rate to each of these modules showed that more than 95% of the galactoseinduced change in doubling time was transmitted by one block, which contained three mRNAs involved in galactose metabolism. Secondly, the mRNAs were clustered into two blocks and the direct and indirect responses of each block of mRNAs to galactose were calculated. Most of the large change in block 2 was shown to be indirect, i.e. mediated by block 1. Top-down control analysis provides a novel and informative way to analyse and quantify gene expression data. The method is generally applicable to modern DNA microarray expression profiling to discover and quantify the relative importance of different groups of mRNA transcripts in mediating physiological responses.