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E-GEOD-54748 - Characterization of the connection between protein synthesis and amino acid biosynthesis gene expression to growth rate in budding yeast
Released on 7 February 2014, last updated on 15 April 2014
In unicellular organisms, growth rate is the major phenotype that is being selected through evolution. In order to grow efficiently, living cells should synchronize the quantity of their ribosome and RNA polymerase levels according to the respective rates by which amino acids and nucleotides pool are replenished. Gene expression patterns and their relationship with growth rate have been widely investigated in various conditions, and a large set of transcripts which included genes associated with ribosome biogenesis (Ribi) and with the stress response, was shown to be expressed in coordination with cell growth rate. Interestingly, decoupling of this correlation was found for certain mutants and conditions, including in my lab when mutant growth rate was examined and when yeast were grown on xylulose, a carbon source not available in the wild. Under those conditions, amino-acid biosynthesis genes regulated by the GCN4 transcription factor were found to have a strong inverse correlation with growth rate, while Ribi and stress genes showed no such correlation. I hypothesized that this decoupling of the general coupling between growth rate and gene expression is a result of a lack of evolutionary optimization to this carbon source or to genetic mutations. The goal of my study was to examine this hypothesis at a greater depth. To this end, I defined the growth rate and genome-wide expression profile of 328 strains deleted of individual genes that show different levels of growth defect. As predicted, growth rate of those strains was correlated with the expression level of GCN4-dependent genes, but not with the Ribi or stress genes, similar to the correlation observed in our xylulose experiment. 328 S. Cerevisiae deletion strains relatively to the wild type strain
RNA-seq of coding RNA