Condition-specific genetic interaction maps reveal crosstalk between the cAMP/PKA and the HOG MAPK pathways in the activation of the general stress response

Cells must quickly respond and efficiently adapt to environmental changes. The yeast Saccharomyces cerevisiae has multiple pathways that respond to specific environmental insults, as well as a generic stress response program. The later is regulated by two transcription factors, Msn2 and Msn4, that integrate information from upstream pathways to produce fast, tunable, and robust response to different environmental changes. To understand this integration, we employed a systematic approach to genetically dissect the contribution of various cellular pathways to Msn2/4 regulation under a range of stress and growth conditions. We established a high‐throughput liquid handling and automated flow cytometry system and measured GFP levels in 68 single‐knockout and 1,566 double‐knockout strains that carry an HSP12‐GFP allele as a reporter for Msn2/4 activity. Based on the expression of this Msn2/4 reporter in five different conditions, we identified numerous genetic and epistatic interactions between different components in the network upstream to Msn2/4. Our analysis gains new insights into the functional specialization of the RAS paralogs in the repression of stress response and identifies a three‐way crosstalk between the Mediator complex, the HOG MAPK pathway, and the cAMP/PKA pathway.

[1]  Mehdi M. Kashani,et al.  Large-Scale Genetic Perturbations Reveal Regulatory Networks and an Abundance of Gene-Specific Repressors , 2014, Cell.

[2]  J. Broach,et al.  A dynamic interplay of nucleosome and Msn2 binding regulates kinetics of gene activation and repression following stress , 2014, Nucleic acids research.

[3]  Melissa Gymrek,et al.  LoQAtE—Localization and Quantitation ATlas of the yeast proteomE. A new tool for multiparametric dissection of single-protein behavior in response to biological perturbations in yeast , 2013, Nucleic Acids Res..

[4]  J. Hahn,et al.  Rim15‐dependent activation of Hsf1 and Msn2/4 transcription factors by direct phosphorylation in Saccharomyces cerevisiae , 2013, FEBS letters.

[5]  Michael M. Desai,et al.  Pervasive Genetic Hitchhiking and Clonal Interference in 40 Evolving Yeast Populations , 2013, Nature.

[6]  Alexandre V. Morozov,et al.  Noise and interlocking signaling pathways promote distinct transcription factor dynamics in response to different stresses , 2013, Molecular biology of the cell.

[7]  M. Khammash,et al.  Systematic Identification of Signal-Activated Stochastic Gene Regulation , 2013, Science.

[8]  Jeremy Gunawardena,et al.  Tunable Signal Processing Through Modular Control of Transcription Factor Translocation , 2013, Science.

[9]  A. Gasch,et al.  Cellular Memory of Acquired Stress Resistance in Saccharomyces cerevisiae , 2012, Genetics.

[10]  Anne-Claude Gingras,et al.  Global Gene Deletion Analysis Exploring Yeast Filamentous Growth , 2012, Science.

[11]  E. O’Shea,et al.  Hog1 Controls Global Reallocation of RNA Pol II upon Osmotic Shock in Saccharomyces cerevisiae , 2012, G3: Genes | Genomes | Genetics.

[12]  J. Broach.  Nutritional Control of Growth and Development in Yeast , 2012, Genetics.

[13]  Hana El-Samad,et al.  Cellular noise regulons underlie fluctuations in Saccharomyces cerevisiae. , 2012, Molecular cell.

[14]  Erin K O'Shea,et al.  Signal-dependent dynamics of transcription factor translocation controls gene expression , 2011, Nature Structural &Molecular Biology.

[15]  G. Ammerer,et al.  Controlling gene expression in response to stress , 2011, Nature Reviews Genetics.

[16]  Amir Aharoni,et al.  Fine-tuning of the Msn2/4–mediated yeast stress responses as revealed by systematic deletion of Msn2/4 partners , 2011, Molecular biology of the cell.

[17]  A. Gasch,et al.  Molecular Systems Biology Peer Review Process File a Dynamic Model of Proteome Changes Reveals New Roles for Transcript Alteration in Yeast Transaction Report , 2022 .

[18]  Damian Szklarczyk,et al.  The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored , 2010, Nucleic Acids Res..

[19]  Hana El-Samad,et al.  Coordinate control of gene expression noise and interchromosomal interactions in a MAPK pathway , 2010, Nature Cell Biology.

[20]  Gary D Bader,et al.  The Genetic Landscape of a Cell , 2010, Science.

[21]  Y. Pilpel,et al.  Adaptive prediction of environmental changes by microorganisms , 2009, Nature.

[22]  Nicholas T. Ingolia,et al.  Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling , 2009, Science.

[23]  Campbell W. Gourlay,et al.  Whi2p links nutritional sensing to actin-dependent Ras-cAMP-PKA regulation and apoptosis in yeast , 2009, Journal of Cell Science.

[24]  James R Broach,et al.  How Saccharomyces responds to nutrients. , 2008, Annual review of genetics.

[25]  Audrey P Gasch,et al.  Stress-activated genomic expression changes serve a preparative role for impending stress in yeast. , 2008, Molecular biology of the cell.

[26]  N. Friedman,et al.  Structure and function of a transcriptional network activated by the MAPK Hog1 , 2008, Nature Genetics.

[27]  J. Hahn,et al.  Yeast Yak1 kinase, a bridge between PKA and stress‐responsive transcription factors, Hsf1 and Msn2/Msn4 , 2008, Molecular microbiology.

[28]  Sean R. Collins,et al.  Conservation and Rewiring of Functional Modules Revealed by an Epistasis Map in Fission Yeast , 2008, Science.

[29]  Albert Goldbeter,et al.  Stochastic modelling of nucleocytoplasmic oscillations of the transcription factor Msn2 in yeast , 2008, Journal of The Royal Society Interface.

[30]  Sean R. Collins,et al.  A comprehensive strategy enabling high-resolution functional analysis of the yeast genome , 2008, Nature Methods.

[31]  G. Giaever,et al.  Yeast Barcoders: a chemogenomic application of a universal donor-strain collection carrying bar-code identifiers , 2008, Nature Methods.

[32]  Robert P. St.Onge,et al.  Defining genetic interaction , 2008, Proceedings of the National Academy of Sciences.

[33]  Jean-Philippe Lambert,et al.  Functional Dissection of the NuA4 Histone Acetyltransferase Reveals Its Role as a Genetic Hub and that Eaf1 Is Essential for Complex Integrity , 2008, Molecular and Cellular Biology.

[34]  A. Erkine,et al.  Different Requirements of the SWI/SNF Complex for Robust Nucleosome Displacement at Promoters of Heat Shock Factor and Msn2- and Msn4-Regulated Heat Shock Genes , 2007, Molecular and Cellular Biology.

[35]  A. Gasch.  Comparative genomics of the environmental stress response in ascomycete fungi , 2007, Yeast.

[36]  Oliver Medvedik,et al.  MSN2 and MSN4 Link Calorie Restriction and TOR to Sirtuin-Mediated Lifespan Extension in Saccharomyces cerevisiae , 2007, PLoS biology.

[37]  N. Friedman,et al.  Natural history and evolutionary principles of gene duplication in fungi , 2007, Nature.

[38]  M. Proft,et al.  The Sch9 kinase is a chromatin‐associated transcriptional activator of osmostress‐responsive genes , 2007, The EMBO journal.

[39]  Albert Goldbeter,et al.  Nucleocytoplasmic Oscillations of the Yeast Transcription Factor Msn2: Evidence for Periodic PKA Activation , 2007, Current Biology.

[40]  Grant W. Brown,et al.  Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map , 2007, Nature.

[41]  Joseph Heitman,et al.  Sensing the environment: lessons from fungi , 2007, Nature Reviews Microbiology.

[42]  M. Jacquet,et al.  Role of Gal11, a component of the RNA polymerase II mediator in stress‐induced hyperphosphorylation of Msn2 in Saccharomyces cerevisiae , 2006, Molecular microbiology.

[43]  K. Struhl,et al.  The stress-activated Hog1 kinase is a selective transcriptional elongation factor for genes responding to osmotic stress. , 2006, Molecular cell.

[44]  Jorge Nocedal,et al.  An interior algorithm for nonlinear optimization that combines line search and trust region steps , 2006, Math. Program..

[45]  J. Derisi,et al.  Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise , 2006, Nature.

[46]  C. Pallotti,et al.  A Downshift in Temperature Activates the High Osmolarity Glycerol (HOG) Pathway, Which Determines Freeze Tolerance in Saccharomyces cerevisiae* , 2006, Journal of Biological Chemistry.

[47]  Mike Tyers,et al.  BioGRID: a general repository for interaction datasets , 2005, Nucleic Acids Res..

[48]  I. Pedruzzi,et al.  Regulation of G0 entry by the Pho80–Pho85 cyclin–CDK complex , 2005, The EMBO journal.

[49]  Gustav Ammerer,et al.  A dual role for PP1 in shaping the Msn2‐dependent transcriptional response to glucose starvation , 2005, The EMBO journal.

[50]  Sean R. Collins,et al.  Exploration of the Function and Organization of the Yeast Early Secretory Pathway through an Epistatic Miniarray Profile , 2005, Cell.

[51]  Kevin P. Byrne,et al.  The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. , 2005, Genome research.

[52]  H. Sakurai,et al.  Saccharomyces cerevisiae Heat Shock Transcription Factor Regulates Cell Wall Remodeling in Response to Heat Shock , 2005, Eukaryotic Cell.

[53]  G. Lindsey,et al.  A Rapid Method to Determine the Stress Status of Saccharomyces cerevisiae by Monitoring the Expression of a Hsp12:Green Fluorescent Protein (GFP) Construct under the Control of the Hsp12 Promoter , 2005, Journal of biomolecular screening.

[54]  R. Zitomer,et al.  Genetic Factors That Regulate the Attenuation of the General Stress Response of Yeast , 2005, Genetics.

[55]  L. Altucci,et al.  Tumor-selective action of HDAC inhibitors involves TRAIL induction in acute myeloid leukemia cells , 2005, Nature Medicine.

[56]  G. Church,et al.  Modular epistasis in yeast metabolism , 2005, Nature Genetics.

[57]  G. Ammerer,et al.  Nuclear Localization Destabilizes the Stress-regulated Transcription Factor Msn2*♦ , 2004, Journal of Biological Chemistry.

[58]  J. Broach,et al.  PP2A Phosphatase Activity Is Required for Stress and Tor Kinase Regulation of Yeast Stress Response Factor Msn2p , 2004, Eukaryotic Cell.

[59]  M. Jacquet,et al.  Heat shock-induced degradation of Msn2p, a Saccharomyces cerevisiae transcription factor, occurs in the nucleus , 2004, Molecular Genetics and Genomics.

[60]  A. Ramne,et al.  Rck1 and Rck2 MAPKAP kinases and the HOG pathway are required for oxidative stress resistance , 2004, Molecular microbiology.

[61]  S. R. Green,et al.  Promoter-dependent roles for the Srb10 cyclin-dependent kinase and the Hda1 deacetylase in Tup1-mediated repression in Saccharomyces cerevisiae. , 2004, Molecular biology of the cell.

[62]  Ya-Wen Chang,et al.  The Ras/PKA signaling pathway directly targets the Srb9 protein, a component of the general RNA polymerase II transcription apparatus. , 2004, Molecular cell.

[63]  Gary D Bader,et al.  Global Mapping of the Yeast Genetic Interaction Network , 2004, Science.

[64]  Eulàlia de Nadal,et al.  The MAPK Hog1 recruits Rpd3 histone deacetylase to activate osmoresponsive genes , 2004, Nature.

[65]  Ivo Pedruzzi,et al.  TOR and PKA signaling pathways converge on the protein kinase Rim15 to control entry into G0. , 2003, Molecular cell.

[66]  E. O’Shea,et al.  Global analysis of protein expression in yeast , 2003, Nature.

[67]  E. O’Shea,et al.  Global analysis of protein localization in budding yeast , 2003, Nature.

[68]  Eulàlia de Nadal,et al.  Osmostress‐induced transcription by Hot1 depends on a Hog1‐mediated recruitment of the RNA Pol II , 2003, The EMBO journal.

[69]  Albert Goldbeter,et al.  Oscillatory nucleocytoplasmic shuttling of the general stress response transcriptional activators Msn2 and Msn4 in Saccharomyces cerevisiae , 2003, The Journal of cell biology.

[70]  Akira Kikuchi,et al.  Yeast glycogen synthase kinase-3 activates Msn2p-dependent transcription of stress responsive genes. , 2003, Molecular biology of the cell.

[71]  Paul Tempst,et al.  A Complex of the Srb8, -9, -10, and -11 Transcriptional Regulatory Proteins from Yeast* , 2002, The Journal of Biological Chemistry.

[72]  F. Estruch,et al.  Convergence of the Target of Rapamycin and the Snf1 Protein Kinase Pathways in the Regulation of the Subcellular Localization of Msn2, a Transcriptional Activator of STRE (Stress Response Element)-regulated Genes* , 2002, The Journal of Biological Chemistry.

[73]  Michel B Toledano,et al.  The control of the yeast H2O2 response by the Msn2/4 transcription factors , 2002, Molecular microbiology.

[74]  K. Struhl,et al.  Hog1 kinase converts the Sko1-Cyc8-Tup1 repressor complex into an activator that recruits SAGA and SWI/SNF in response to osmotic stress. , 2002, Molecular cell.

[75]  I. Ota,et al.  Heat Stress Activates the Yeast High-Osmolarity Glycerol Mitogen-Activated Protein Kinase Pathway, and Protein Tyrosine Phosphatases Are Essential under Heat Stress , 2002, Eukaryotic Cell.

[76]  Gustav Ammerer,et al.  Acute glucose starvation activates the nuclear localization signal of a stress‐specific yeast transcription factor , 2002, The EMBO journal.

[77]  Gary D Bader,et al.  Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants , 2001, Science.

[78]  E. de Nadal,et al.  Regulation of the Sko1 transcriptional repressor by the Hog1 MAP kinase in response to osmotic stress , 2001, The EMBO journal.

[79]  Galit Shenhar,et al.  A Positive Regulator of Mitosis, Sok2, Functions as a Negative Regulator of Meiosis in Saccharomyces cerevisiae , 2001, Molecular and Cellular Biology.

[80]  E. Lander,et al.  Remodeling of yeast genome expression in response to environmental changes. , 2001, Molecular biology of the cell.

[81]  D. Botstein,et al.  Genomic expression programs in the response of yeast cells to environmental changes. , 2000, Molecular biology of the cell.

[82]  M. Jacquet,et al.  Hyperphosphorylation of Msn2p and Msn4p in response to heat shock and the diauxic shift is inhibited by cAMP in Saccharomyces cerevisiae. , 2000, Microbiology.

[83]  K. Struhl,et al.  Aca1 and Aca2, ATF/CREB Activators in Saccharomyces cerevisiae, Are Important for Carbon Source Utilization but Not the Response to Stress , 2000, Molecular and Cellular Biology.

[84]  I. Pedruzzi,et al.  Saccharomyces cerevisiae Ras/cAMP pathway controls post‐diauxic shift element‐dependent transcription through the zinc finger protein Gis1 , 2000, The EMBO journal.

[85]  J. Thevelein,et al.  The Transcriptional Response of Saccharomyces cerevisiae to Osmotic Shock , 2000, The Journal of Biological Chemistry.

[86]  W. Brandt,et al.  The LEA-like protein HSP 12 in Saccharomyces cerevisiae has a plasma membrane location and protects membranes against desiccation and ethanol-induced stress. , 2000, Biochimica et biophysica acta.

[87]  Michael N. Hall,et al.  The TOR signalling pathway controls nuclear localization of nutrient-regulated transcription factors , 1999, Nature.

[88]  S. Jazwinski,et al.  Role of RAS2 in recovery from chronic stress: effect on yeast life span. , 1998, Experimental cell research.

[89]  M. Ward,et al.  Yeast PKA represses Msn2p/Msn4p‐dependent gene expression to regulate growth, stress response and glycogen accumulation , 1998, The EMBO journal.

[90]  J. D. de Winde,et al.  Involvement of distinct G‐proteins, Gpa2 and Ras, in glucose‐ and intracellular acidification‐induced cAMP signalling in the yeast Saccharomyces cerevisiae , 1998, The EMBO journal.

[91]  M. Jacquet,et al.  Msn2p and Msn4p Control a Large Number of Genes Induced at the Diauxic Transition Which Are Repressed by Cyclic AMP inSaccharomyces cerevisiae , 1998, Journal of bacteriology.

[92]  B Hamilton,et al.  Nuclear localization of the C2H2 zinc finger protein Msn2p is regulated by stress and protein kinase A activity. , 1998, Genes & development.

[93]  R. Lenski,et al.  Test of synergistic interactions among deleterious mutations in bacteria , 1997, Nature.

[94]  A. Marchler-Bauer,et al.  The Saccharomyces cerevisiae zinc finger proteins Msn2p and Msn4p are required for transcriptional induction through the stress response element (STRE). , 1996, The EMBO journal.

[95]  G. Fink,et al.  SOK2 may regulate cyclic AMP-dependent protein kinase-stimulated growth and pseudohyphal development by repressing transcription , 1995, Molecular and cellular biology.

[96]  A. Levitzki,et al.  Differential activation of yeast adenylyl cyclase by Ras1 and Ras2 depends on the conserved N terminus. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[97]  M. Carlson,et al.  Two homologous zinc finger genes identified by multicopy suppression in a SNF1 protein kinase mutant of Saccharomyces cerevisiae , 1993, Molecular and cellular biology.

[98]  M. Wigler,et al.  Differential activation of yeast adenylate cyclase by wild type and mutant RAS proteins , 1985, Cell.

[99]  M. Wigler,et al.  In yeast, RAS proteins are controlling elements of adenylate cyclase , 1985, Cell.

[100]  the original work is properly cited. , 2022 .