Transcript profiling of Saccharomyces cerevisiae cells overexpressing YOX1 before and after 2 and 4 hours of hydroxyurea (HU) treatment (200 mM)

mRNA processing bodies (P-bodies) are cytoplasmic granules that form in eukaryotic cells in response to numerous stresses to serve as sites of degradation and storage of mRNAs. Functional P-bodies are critical for the DNA replication stress response in yeast, yet the repertoire of P-body targets and the mechanisms by which P-bodies promote replication stress resistance are unknown. In this study, we identify the complete complement of mRNA targets of P-bodies during replication stress induced by hydroxyurea treatment. The key P-body protein Lsm1 controls the abundance of HHT1, ACF4, ARL3, TMA16, RRS1 and YOX1 mRNAs to prevent their toxic accumulation during replication stress. Accumulation of YOX1 mRNA causes aberrant down-regulation of a network of genes critical for DNA replication stress resistance. Among these genes we identify ALD6, whose de-repression is critical to prevent accumulation of acetaldehyde, a strongly toxic molecule during DNA replication stress. Overall design: WT containing pBY011 (control) or pBY011-YOX1 vectors were cultured in synthetic medium containing raffinose as unique carbon source. Cultures were then treated with hydroxyurea (HU) at a final concentration of 200 mM and galactose was added at the same time to induce YOX1 overexpression. Samples were collected before and after 2 and 4h of galactose induction and hydroxyurea treatment. Experiment was repeated twice.

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Loll-Krippleber R, Brown GW