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Martin H, Shales M, Fernandez-Piñar P, Wei P, Molina M, Fiedler D, Shokat KM, Beltrao P, Lim W, Krogan NJ. Differential genetic interactions of yeast stress response MAPK pathways. Mol Syst Biol 2015; 11:800. [PMID: 25888283 PMCID: PMC4422557 DOI: 10.15252/msb.20145606] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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.
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Affiliation(s)
- Humberto Martin
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, Spain
| | - Michael Shales
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA USA
| | - Pablo Fernandez-Piñar
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, Spain
| | - Ping Wei
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Maria Molina
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, Spain
| | - Dorothea Fiedler
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Kevan M Shokat
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, CA, USA
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK iBiMED and Department of Health Sciences, University of Aveiro, Aveiro, Portugal
| | - Wendell Lim
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA USA Howard Hughes Medical Institute, University of California, San Francisco, CA, USA Center for Systems and Synthetic Biology, University of California, San Francisco, CA, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA USA Center for Systems and Synthetic Biology, University of California, San Francisco, CA, USA California Institute for Quantitative Biosciences, QB3, San Francisco, CA, USA J. David Gladstone Institutes, San Francisco, CA, USA
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Fernandez-Piñar P, Alemán A, Sondek J, Dohlman HG, Molina M, Martín H. The Salmonella Typhimurium effector SteC inhibits Cdc42-mediated signaling through binding to the exchange factor Cdc24 in Saccharomyces cerevisiae. Mol Biol Cell 2012; 23:4430-43. [PMID: 23015760 PMCID: PMC3496616 DOI: 10.1091/mbc.e12-03-0243] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Expression of the Salmonella effector SteC in yeast leads to down-regulation of the mating and HOG pathways by Cdc42 inhibition. This is mediated by the SteC N-terminal domain through binding to the GEF Cdc24. SteC alters Cdc24 localization and also interacts with human GEF Vav1, suggesting that SteC could target Cdc42 function in host cells. Intracellular survival of Salmonella relies on the activity of proteins translocated into the host cell by type III secretion systems (T3SS). The protein kinase activity of the T3SS effector SteC is required for F-actin remodeling in host cells, although no SteC target has been identified so far. Here we show that expression of the N-terminal non-kinase domain of SteC down-regulates the mating and HOG pathways in Saccharomyces cerevisiae. Epistasis analyses using constitutively active components of these pathways indicate that SteC inhibits signaling at the level of the GTPase Cdc42. We demonstrate that SteC interacts through its N-terminal domain with the catalytic domain of Cdc24, the sole S. cerevisiae Cdc42 guanine nucleotide exchange factor (GEF). SteC also binds to the human Cdc24-like GEF protein Vav1. Moreover, expression of human Cdc42 suppresses growth inhibition caused by SteC. Of interest, the N-terminal SteC domain alters Cdc24 cellular localization, preventing its nuclear accumulation. These data reveal a novel functional domain within SteC, raising the possibility that this effector could also target GTPase function in mammalian cells. Our results also highlight the key role of the Cdc42 switch in yeast mating and HOG pathways and provide a new tool to study the functional consequences of Cdc24 localization.
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Affiliation(s)
- Pablo Fernandez-Piñar
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, and Instituto Ramón y Cajal de Investigaciones Sanitarias, 28040 Madrid, Spain
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