Common gene expression strategies revealed by genome-wide analysis in yeast

Background: Gene expression is a two-step synthesis process that ends with the necessary amount of each protein required to perform its function. Since the protein is the final product, the main focus of gene regulation should be centered on it. However, because mRNA is an intermediate step and the amounts of both mRNA and protein are controlled by their synthesis and degradation rates, the desired amount of protein can be achieved following different strategies. Results: In this paper we present the first comprehensive analysis of the relationships among the six variables that characterize gene expression in a living organism: transcription and translation rates, mRNA and protein amounts, and mRNA and protein stabilities. We have used previously published data from exponentially growing Saccharomyces cerevisiae cells. We show that there is a general tendency to harmonize the levels of mRNA and protein by coordinating their synthesis rates and that functionally related genes tend to have similar values for the six variables. Conclusion: We propose that yeast cells use common expression strategies for genes acting in the same physiological pathways. This trend is more evident for genes coding for large and stable protein complexes, such as ribosomes or the proteasome. Hence, each functional group can be defined by a 'six variable profile' that illustrates the common strategy followed by the genes included in it. Genes encoding subunits of protein complexes show a tendency to have relatively unstable mRNAs and a less balanced profile for mRNA than for protein, suggesting a stronger regulation at the transcriptional leve