Specific and global regulation of mRNA stability during osmotic stress in Saccharomyces cerevisiae

Abstract

Hyperosmotic stress yields reprogramming of gene expression in Saccharomyces cerevisiae cells. Most of this response is orchestrated by Hog1, a stress-activated, mitogen-activated protein kinase (MAPK) homologous to human p38. We investigated, on a genomic scale, the contribution of changes in transcription rates and mRNA stabilities to the modulation of mRNA amounts during the response to osmotic stress in wild-type and hog1 mutant cells. Mild osmotic shock induces a broad mRNA destabilization; however, osmo-mRNAs are up-regulated by increasing both transcription rates and mRNA half-lives. In contrast, mild or severe osmotic stress in hog1 mutants, or severe osmotic stress in wild-type cells, yields global mRNA stabilization and sequestration of mRNAs into P-bodies. After adaptation, the absence of Hog1 affects the kinetics of P-bodies disassembly and the return of mRNAs to translation. Our results indicate that regulation of mRNA turnover contributes to coordinate gene expression upon osmotic stress, and that there are both specific and global controls of mRNA stability depending on the strength of the osmotic stress.

Growth rate controls mRNA turnover in steady and non-steady states

“…7 Now, we have used this algorithm to calculate iGR profiles from the transcriptomes ([mRNAs]) of our previous stress-response GRO studies. [29][30][31][32][33][34] As expected, the common pattern was that iGR lowered immediately after applying stress and later recovered (Fig. S1).…”

“…In most cases the level of each mRNA was determined mainly by its TR, but DR usually plays an important role in fine-tuning the response and could even be a quantitatively important part of the response. 32,34 However, the link between GR and gene expression has never been investigated because calculating GR in such a variable situation is not straightforward. Botstein's group created an algorithm based on a transcriptional signature to calculate an instantaneous growth rate (iGR) from the transcriptome at a particular time point.…”

A genomic view of mRNA turnover in yeast

“…backtracking). Under the assumption that RNA polymerases elongate at a constant rate, the quantification of their density provides a TR measure at the time of RNA labelling [13].This technique has been applied to S. cerevisiae to perform accurate kinetic measures of TR in both standard growing conditions [4,14], and in plenty of different stress responses [3,15,16]. One of the advantages of yeast is that the GRO assay can be performed on whole cells, which allows very rapid and accurate measurements.…”

“…[33] for details). We have used this approach in some experiments in which yeast cells were subjected to osmotic, oxidative or heat stress, and have found that most genes undergo changes in their mRNA stability during the stress response [15,16,34]. This method requires complex calculations, thus the experimental error is more prone to being mathematically amplified.…”

Analysis of osmoadaptation system in budding yeast suggests that regulated degradation of glycerol synthesis enzyme is key to near-perfect adaptation

“…Although in literature there are reports of both transient and persistent regulations of degradation of mRNA (Miller for three conditions of ramp input; Case 1: Stress is increased at 0.0166 M/min NaCl till 45 min and maintained constant then after (solid); Case 2: Stress is increased with a rate of 0.0083 M/min NaCl, which is half that in Case 1, and maintained constant after 90 min (dash-dotted) and; Case 3: Stress is increased at rate 0.00425 M/min NaCl, which is 1/4th that in Case 1, till 180 min (dashed). Note that at the end of the ramp input, the net concentration of NaCl is the same for all the cases Romero-Santacreu et al 2009), the regulated degradation constants of mRNA are still much higher compare to the transcription rate constants. Moreover, from the dynamic data provided by Klipp et al 2005 for both wild type and putative FPS1 mutant, a small value of degradation rate constants for mRNA and Hog1PP is not evident.…”