Adaptive responses of yeast to cell wall stress

To better understand the roles of SR (calculated from the nascent TR by dividing it by cell volume) (Pérez-Ortín, BioEssays 2013), and mRNA stability in stress adaptation, we investigated the yeast cell wall stress response and compared it with other stress responses using the GRO method. In this study, we analyzed genome-wide changes in RNA abundance to determine how synthesis rates and mRNA stabilization influence RA along the treatment with Congo Red. Our findings indicate that alterations in synthesis rates primarily drive changes in RA, whereas mRNA stability remains largely unaffected under our conditions, in contrast to other stress responses. Additionally, the RA of RP, RiBi, and ESRup genes is influenced by both mRNA stability and SR, albeit to a lesser extent than in other stress conditions. Moreover, we identified: a) a small subset of genes whose mRNA levels are co-regulated by both changes in synthesis rates and mRNA stability; b) previously unidentified genes whose mRNA levels increase in the presence of Congo Red; and c) RNA-binding proteins (RBPs) such as Nab2 and Hrp1 as potential regulators of genes induced in response to cell wall stress. We quantified the mRNA abundance (RA) and synthesis rate (SR) for all genes of the yeast over a time course (0, 30, 60, 120, 180, and 240 minutes) of Congo Red treatment (30 µg/ml) using the GRO method (Garcia-Martinez Mol cell 2004; Pérez-Ortín jmb 2013). The SR was derived from the nascent transcription rate (nTR) by normalizing it to the cell volume (no change in samples t0, t30 & t60: 1x factor, and 1.17, 1.44, 1.65x factors for t120, t180 and t240 samples, respectively).