Dynamic processes at stress promoters regulate the bimodal expression of HOG response genes

Short linear motifs in intrinsically disordered regions modulate HOG signaling capacity

Background

The effort to characterize intrinsically disordered regions of signaling proteins is rapidly expanding. An important class of disordered interaction modules are ubiquitous and functionally diverse elements known as short linear motifs (SLiMs).

Results

To further examine the role of SLiMs in signal transduction, we used a previously devised bioinformatics method to predict evolutionarily conserved SLiMs within a well-characterized pathway in S. cerevisiae. Using a single cell, reporter-based flow cytometry assay in conjunction with a fluorescent reporter driven by a pathway-specific promoter, we quantitatively assessed pathway output via systematic deletions of individual motifs. We found that, when deleted, 34% (10/29) of predicted SLiMs displayed a significant decrease in pathway output, providing evidence that these motifs play a role in signal transduction. Assuming that mutations in SLiMs have quantitative effects on mechanisms of signaling, we show that perturbations of parameters in a previously published stochastic model of HOG signaling could reproduce the quantitative effects of 4 out of 7 mutations in previously unknown SLiMs.

Conclusions

Our study suggests that, even in well-characterized pathways, large numbers of functional elements remain undiscovered, and that challenges remain for application of systems biology models to interpret the effects of mutations in signaling pathways.

Electronic supplementary material

The online version of this article (10.1186/s12918-018-0597-3) contains supplementary material, which is available to authorized users.

A rapid and effective vignetting correction for quantitative microscopy

We describe a novel and versatile algorithm for vignetting correction and demonstrate its usefulness for quantitative microscopy.