Modelling of gene expression and Regulation Analysis.

Our current gene-expression model (Haanstra et al. 2008 PMID: 19008351) will be parameterized for the different genes of interest. The framework of this gene expression model has been used to include mRNA half life data into the model of glycolysis For the enzymes of redox metabolism we will use newly measured rates of transcription, RNA precursor degradation, mRNA degradation, concentrations of mature mRNAs and proteins, enzyme turnover, Vmax values and metabolic fluxes (WP3&5). Regulation Analysis (Daran-Lapujade 2007 PMID: 17898166; Haanstra et al. 2008 PMID: 19008351) gives a quantitative framework to calculate from the gene-expression and flux data the relative importance of changes in metabolite concentrations (metabolic regulation) and changes in various processes in the gene-expression cascade for flux regulation. We will quantify to which extent changes in the redox fluxes (as a function of differentiation stage, growth rate, oxidative stress, mutations) are caused by various processes in the gene expression cascade (RNA splicing and stability, protein synthesis and degradation and protein modifications) and metabolism. Based on the newly measured metabolite data and kinetic descriptions of each enzyme we will also determine the relative importance of the individual metabolites in regulation of the enzymes. Gaps in total regulation (e.g. enzymes whose rate is heavily regulated by metabolism, while measured metabolite changes cannot account for this) will point to the existence of unknown regulatory interactions.