Abstract
Genetic interaction screens have been applied with great success in several organisms to study gene function and the genetic architecture of the cell. However, most studies have been performed under optimal growth conditions even though many functional interactions are known to occur under specific cellular conditions. In this study, we have performed a large-scale genetic interaction analysis in Saccharomyces cerevisiae involving approximately 49 × 1,200 double mutants in the presence of five different stress conditions, including osmotic, oxidative and cell wall-altering stresses. This resulted in the generation of a differential E-MAP (or dE-MAP) comprising over 250,000 measurements of conditional interactions. We found an extensive number of conditional genetic interactions that recapitulate known stress-specific functional associations. Furthermore, we have also uncovered previously unrecognized roles involving the phosphatase regulator Bud14, the histone methylation complex COMPASS and membrane trafficking complexes in modulating the cell wall integrity pathway. Finally, the osmotic stress differential genetic interactions showed enrichment for genes coding for proteins with conditional changes in phosphorylation but not for genes with conditional changes in gene expression. This suggests that conditional genetic interactions are a powerful tool to dissect the functional importance of the different response mechanisms of the cell.
Highlights
Genetic interaction screens have been applied with great success in several organisms to study gene function and the genetic architecture of the cell
A quantitative differential genetic map, or dE-MAP, of yeast MAPK stress response pathways was constructed based on two experimental screens (Materials and Methods)
The query genes are comprised of stress-sensing proteins, kinases, phosphatases, transcription factors and a few additional adaptor proteins (Fig 1A)
Summary
Genetic interaction screens have been applied with great success in several organisms to study gene function and the genetic architecture of the cell. We have performed a large-scale genetic interaction analysis in Saccharomyces cerevisiae involving approximately 49 × 1,200 double mutants in the presence of five different stress conditions, including osmotic, oxidative and cell wall-altering stresses. This resulted in the generation of a differential E-MAP (or dE-MAP) comprising over 250,000 measurements of conditional interactions. Large-scale gene expression studies have been used to identify the transcriptional responses to different sets of conditions (Gasch & Werner-Washburne, 2002), and proteomic approaches have contributed to our understanding of MAPK-mediated phosphorylation (Soufi et al, 2009; Mascaraque et al, 2013) These regulatory networks result in functional inter-dependencies that can be studied by large-scale genetic approaches. We have compared osmotic differential genetic interactions with large-scale condition-dependent phosphoproteomics and gene expression information to dissect the contribution of these different types of regulation to the conditional fitness measurements
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