MAPK-mediated bimodal gene expression and adaptive gradient sensing in yeast

Abstract

The mating pathway in Saccharomyces cerevisiae has been the focus of considerable research effort, yet many quantitative aspects of its regulation still remain unknown. Using an integrated approach involving experiments in microfluidic chips and computational modelling, we studied gene expression and phenotypic changes associated with the mating response under well-defined pheromone gradients. Here we report a combination of switch-like and graded pathway responses leading to stochastic phenotype determination in a specific range of pheromone concentrations. Furthermore, we show that these responses are critically dependent on mitogen-activated protein kinase (MAPK)-mediated regulation of the activity of the pheromone-response-specific transcription factor, Ste12, as well as on the autoregulatory feedback of Ste12. In particular, both the switch-like characteristics and sensitivity of gene expression in shmooing cells to pheromone concentration were significantly diminished in cells lacking Kss1, one of the MAP kinases activated in the mating pathway. In addition, the dynamic range of gradient sensing of Kss1-deficient cells was reduced compared with wild type. We thus provide unsuspected functional significance for this kinase in regulation of the mating response.

Modulating the frequency and bias of stochastic switching to control phenotypic variation

“…Therefore, the expression levels of the states do not affect the frequency and bias of switching. Systems that generate bimodality through feedback can, under the right conditions, produce some behaviours that have been observed, such as a graded unimodal response [41][42][43][44][45][46] . However, the feedback makes it more difficult to tune phenotypic variation and mean expression.…”

Dynamic analysis of MAPK signaling using a high-throughput microfluidic single-cell imaging platform

“…The combination of fluorescent reporters and quantitative microscopy has recently been used to address cell-cell variability in the yeast mating response under constant environmental conditions (2,16). Such techniques are scalable to highthroughput formats in multiwell plates but provide only crude control over the microenvironment and are poorly suited to the study of response dynamics or history effects.…”

“…These networks feature emergent properties, including bistability, adaptation, and memory that make their behavior inherently dependent on previous stimulation and current cell states. As examples, system bistability provides a selective advantage by allowing populations of cells to test the responses of alternative states to a given condition (1,2); network adaptation to a sustained change in stimulant concentration limits the metabolic cost of a sustained response (3,4); and network memory allows more rapid accommodation of recurrent stimulations (5,6). Because of experimental tractability, these emergent properties were first studied in model systems and have recently been uncovered in key mammalian regulatory networks, including those dysregulated in disease (7).…”

“…In yeast, the precise microfluidic control of conditions has been applied to investigations of modest number of genotypes or chemical conditions under both constant (2,18) or changing (19-21) media conditions. More scalable devices have been applied to the culture and analysis of mammalian cells on-chip (22,23) although these have to date be focused primarily on adherent cell types (22,24,25).…”

Fluorescent-Based Quantitative Measurements of Signal Transduction in Single Cells

“…Due to the small volume present in these devices, the media switching times can be in the order of a few seconds. Using diffusion between two different media, it is also possible to generate stable concentration gradients for example to study the establishment of oriented cell polarity 40 . Another benefit of the small dimensions of microfluidic devices is the possibility to keep all cells in the same focal plane for multiple generations by designing chambers with a height of only a few microns 41,42 .…”