Different Mechanisms Confer Gradual Control and Memory at Nutrient- and Stress-Regulated Genes in Yeast

Abstract

c Cells respond to environmental stimuli by fine-tuned regulation of gene expression. Here we investigated the dose-dependent modulation of gene expression at high temporal resolution in response to nutrient and stress signals in yeast. The GAL1 activity in cell populations is modulated in a well-defined range of galactose concentrations, correlating with a dynamic change of histone remodeling and RNA polymerase II (RNAPII) association. This behavior is the result of a heterogeneous induction delay caused by decreasing inducer concentrations across the population. Chromatin remodeling appears to be the basis for the dynamic GAL1 expression, because mutants with impaired histone dynamics show severely truncated dose-response profiles. In contrast, the GRE2 promoter operates like a rapid off/on switch in response to increasing osmotic stress, with almost constant expression rates and exclusively temporal regulation of histone remodeling and RNAPII occupancy. The Gal3 inducer and the Hog1 mitogen-activated protein (MAP) kinase seem to determine the different dose-response strategies at the two promoters. Accordingly, GAL1 becomes highly sensitive and dose independent if previously stimulated because of residual Gal3 levels, whereas GRE2 expression diminishes upon repeated stimulation due to acquired stress resistance. Our analysis reveals important differences in the way dynamic signals create dose-sensitive gene expression outputs.C ells continuously adapt their protein composition to changing environmental conditions. The regulation of gene expression is one of the fundamental mechanisms to adjust the global protein repertoire of the cell in order to maintain cell function and integrity in response to environmental challenges. Budding yeast is a powerful model to unravel the modes of transcriptional adaptation at the levels both of specific genes and of the whole organism (1, 2). Additionally, the basic structure of the signaling cascades responding to environmental perturbations is conserved from yeast to humans. It implies the alteration of core kinase activities, which modulate the expression of defense genes through a range of specific transcription factors. Extensive knowledge which precisely describes the molecular machinery and its global impact on gene expression in response to many types of stress has accumulated (3-7). However, the vast majority of these studies are performed with harsh environmental insults and therefore saturating stimulation. As a consequence, only very limited information or approaches are available to understand how cells adapt their gene expression programs to small or gradual changes in their environment.It is assumed that cells have acquired mechanisms that ensure a transcriptional response which is finely adjusted according to the strength of the stress or stimulation. However, the nature of the signaling molecules which confer gradual transcription outputs remains to be determined in most cases. Fine-tuning of gene expression responses can occur with different purposes, and th...

Indirect monitoring of TORC1 signalling pathway reveals molecular diversity among different yeast strains

“…( Figure 2). This behaviour is commonly observed for yeast promoters, with activity during a transient period at the exponential growth phase (Dolz-Edo, Rienzo, Poveda-Huertes, Pascual-Ahuir, & Proft, 2013; Rienzo et al, 2012;Rienzo et al, 2015). Interestingly, the WA strain showed a slower growth in comparison with the other three strains in this medium, reaching OD 600~0 .8 at later time points ( Figure 2).…”

“…Initially, we evaluated the growth and luciferase expression under the control of P RPL26A in the four strains expressing the reporter gene in YMM + Pro medium, showing a maximum level of luciferase expression at the beginning of the exponential phase and before OD 600 ~ 0.8 (Figure ). This behaviour is commonly observed for yeast promoters, with activity during a transient period at the exponential growth phase (Dolz‐Edo, Rienzo, Poveda‐Huertes, Pascual‐Ahuir, & Proft, ; Rienzo et al, ; Rienzo et al, ). Interestingly, the WA strain showed a slower growth in comparison with the other three strains in this medium, reaching OD 600 ~ 0.8 at later time points (Figure ).…”

“…In general, the destabilized version of the firefly luciferase reporter gene has become an ideal tool to assess gene expression dynamics in living cells, allowing to measure the transcriptional activity of genes regulated by nutrient availability, osmotic stress, and oxidative stress in yeasts (Dolz‐Edo et al, ; Rienzo et al, ). In this sense, we used the luciferase reporter gene to record the transcriptional activity of RPL26A gene—which is a gene known to be expressed upon TORC1 activation—using nitrogen upshift experiments, and the results showed strong activation RPL26A only by a preferred nitrogen source (glutamine).…”

“…In the case of Rps6, phosphorylated (pRps6) and total Rps6 protein levels were evaluated using specific antibodies. In the Sch9 phosphorylation, an antibody that recognizes the 3xHA epitope was used, which gives an upper band and a lower band that are representative of phosphorylated (pSch9) In general, the destabilized version of the firefly luciferase reporter gene has become an ideal tool to assess gene expression dynamics in living cells, allowing to measure the transcriptional activity of genes regulated by nutrient availability, osmotic stress, and oxidative stress in yeasts (Dolz-Edo et al, 2013;Rienzo et al, 2015).…”

The memory of hyperosmotic stress response in yeast is modulated by gene-positioning

“…This process is defined as memory. Biological mechanisms known to underlie cellular memory involve chromatin remodeling (epigenetic memory) or proteins synthesized during the first stress, which might leave a trace of the first event (cytoplasmic memory) [5–7].…”