Acute stress puts cells at risk, and rapid adaptation is crucial for maximizing cell survival. Cellular adaptation mechanisms include modification of certain aspects of cell physiology, such as the induction of efficient changes in the gene expression programmes by intracellular signalling networks. Recent studies using genome-wide approaches as well as single-cell transcription measurements, in combination with classical genetics, have shown that rapid and specific activation of gene expression can be accomplished by several different strategies. This article discusses how organisms can achieve generic and specific responses to different stresses by regulating gene expression at multiple stages of mRNA biogenesis from chromatin structure to transcription, mRNA stability and translation.

Adaptation to changes in extracellular salinity is a critical event for cell survival. Genome-wide DNA chip analysis has been used to analyze the transcriptional response of yeast cells to saline stress. About 7% of the genes encoded in the yeast genome are induced more than 5-fold after a mild and brief saline shock (0.4 M NaCl, 10 min). Interestingly, most responsive genes showed a very transient expression pattern, as mRNA levels dramatically declined after 20 min in the presence of stress. A quite similar set of genes increased expression in cells subjected to higher saline concentrations (0.8 M NaCl), although in this case the response was delayed. Therefore, our data show that cells respond to saline stress by inducing the expression of a very large number of genes and suggest that stress adaptation requires regulation of many cellular aspects. The transcriptional induction of most genes that are strongly responsive to salt stress was highly or fully dependent on the presence of the stress-activated mitogen-activated protein kinase Hog1, indicating that the Hog1-mediated signaling pathway plays a key role in global gene regulation under saline stress conditions.

Ongoing efforts within synthetic and systems biology have been directed towards the building of artificial computational devices using engineered biological units as basic building blocks. Such efforts, inspired in the standard design of electronic circuits, are limited by the difficulties arising from wiring the basic computational units (logic gates) through the appropriate connections, each one to be implemented by a different molecule. Here, we show that there is a logically different form of implementing complex Boolean logic computations that reduces wiring constraints thanks to a redundant distribution of the desired output among engineered cells. A practical implementation is presented using a library of engineered yeast cells, which can be combined in multiple ways. Each construct defines a logic function and combining cells and their connections allow building more complex synthetic devices. As a proof of principle, we have implemented many logic functions by using just a few engineered cells. Of note, small modifications and combination of those cells allowed for implementing more complex circuits such as a multiplexer or a 1-bit adder with carry, showing the great potential for re-utilization of small parts of the circuit. Our results support the approach of using cellular consortia as an efficient way of engineering complex tasks not easily solvable using single-cell implementations.

Regulation of gene expression by mitogen-activated protein kinases (MAPKs) is essential for proper cell adaptation to extracellular stimuli. Exposure of yeast cells to high osmolarity results in rapid activation of the MAPK Hog1, which coordinates the transcriptional programme required for cell survival on osmostress. The mechanisms by which Hog1 and MAPKs in general regulate gene expression are not completely understood, although Hog1 can modify some transcription factors. Here we propose that Hog1 induces gene expression by a mechanism that involves recruiting a specific histone deacetylase complex to the promoters of genes regulated by osmostress. Cells lacking the Rpd3-Sin3 histone deacetylase complex are sensitive to high osmolarity and show compromised expression of osmostress genes. Hog1 interacts physically with Rpd3 in vivo and in vitro and, on stress, targets the deacetylase to specific osmostress-responsive genes. Binding of the Rpd3-Sin3 complex to specific promoters leads to histone deacetylation, entry of RNA polymerase II and induction of gene expression. Together, our data indicate that targeting of the Rpd3 histone deacetylase to osmoresponsive promoters by the MAPK Hog1 is required to induce gene expression on stress.

Mitogen-activated protein kinase (MAPK) cascades are conserved signalling modules that control many cellular processes by integrating intra-and extracellular cues. The p38/Hog1 MAPK is transiently activated in response to osmotic stress, leading to rapid translocation into the nucleus and induction of a specific transcriptional program. When investigating the dynamic interplay between Hog1 activation and Hog1-driven gene expression, we found that Hog1 activation increases linearly with stimulus, whereas the transcriptional output is bimodal. Modelling predictions, corroborated by single cell experiments, established that a slow stochastic transition from a repressed to an activated transcriptional state in conjunction with transient Hog1 activation generates this behaviour. Together, these findings provide a molecular mechanism by which a cell can impose a transcriptional threshold in response to a linear signalling behaviour. The authors declare that they have no competing financial interests. Transcriptional activation of mating genes occurs with linear kinetics and high fidelity (5,6), and the observed cell-to-cell variation in protein expression is governed by the ability of cells to express proteins (expression capacity) (5). While the mating pathway can be compared to a cell-fate decision system with sustained MAPK activity, the HOG pathway is an adaptation response, which is only transiently induced like other stress-activated pathways (7). We therefore investigated whether this transient response would trigger different expression behaviour. Mitogen-activated protein kinase (MAPKTo quantitatively measure the transcriptional output induced by osmotic stress, we engineered a reporter system based on a quadruple Venus (qV) fluorescent protein expressed under the control of specific osmo-stress-inducible promoters dependant on the three main transcription factors orchestrating the transcriptional response to osmotic 3 stress (Hot1 and Sko1: pSTL1, Msn2,4: pALD3 or Msn2,4 and Hot1: pHSP12) (8). Flow cytometry revealed a Pbs2-dependent 20-fold increase in pSTL1-qV reporter expression when 0.4M NaCl was added to the growth medium ( Fig. 1 A and B). also generated a bimodal expression output of the Ste12-specific reporter pFIG1-qV.However, signalling in the mating pathway is prevented from "Start" through S phase (9), and expression output became unimodal after relieving this cell-cycle dependent restriction ( Fig. 1B and Fig. S1B).To investigate the source of the HOG pathway bimodal expression behaviour, we integrated two reporters driving the expression of a quadruple cyan fluorescent protein (qCFP) and a qV construct in the same cell. Correlation of the cyan and yellow intensities measures the contribution of cell-to-cell (extrinsic) and intra-cellular (intrinsic) variability to the overall expression noise (5, 10). The two pFIG1-reporters induced by !-factor demonstrated that the mating pathway is governed by extrinsic noise. In contrast,we observed a lack of correlation between the two pSTL1-repor...