Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review
  • Published:

Systems biology analysis of G protein and MAP kinase signaling in yeast

Abstract

Approximately a third of all drugs act by binding directly to cell surface receptors coupled to G proteins. Other drugs act indirectly on these same pathways, for example, by inhibiting neurotransmitter reuptake or by blocking the inactivation of intracellular second messengers. These drugs have revolutionized the treatment of human disease. However, the complexity of G protein signaling mechanisms has significantly hampered our ability to identify additional new drug targets. Moreover, today's molecular pharmacologists are accustomed to working on narrowly focused problems centered on a single protein or enzymatic process. Here we describe emerging efforts in yeast aimed at identifying proteins and processes that modulate the function of receptors, G proteins and MAP kinase effectors. The scope of these efforts is far more systematic, comprehensive and quantitative than anything attempted previously, and includes integrated approaches in genetics, proteomics and computational biology.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6

Similar content being viewed by others

References

  • Alon U, Surette MG, Barkai N, Leibler S . (1999). Robustness in bacterial chemotaxis. Nature 397: 168–171.

    Article  CAS  Google Scholar 

  • Alon U . (2006). An Introduction to Systems Biology. Chapman & Hall: London ISBN 1-58488-642-0.

    Google Scholar 

  • Apanovitch DM, Iiri T, Karasawa T, Bourne HR, Dohlman HG . (1998a). Second site suppressor mutations of a GTPase-deficient G-protein α- subunit. Selective inhibition of βγ-mediated signaling. J Biol Chem 273: 28597–28602.

    Article  CAS  Google Scholar 

  • Apanovitch DM, Slep KC, Sigler PB, Dohlman HG . (1998b). Sst2 is a GTPase-activating protein for Gpa1: purification and characterization of a cognate RGS-Gα protein pair in yeast. Biochemistry 37: 4815–4822.

    Article  CAS  Google Scholar 

  • Barnes DJ, Melo JV . (2003). Management of chronic myeloid leukemia: targets for molecular therapy. Semin Hematol 40: 34–49.

    Article  CAS  Google Scholar 

  • Bhalla US, Ram PT, Iyengar R . (2002). MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network. Science 297: 1018–1023.

    Article  CAS  Google Scholar 

  • Bornheimer SJ, Maurya MR, Farquhar MG, Subramaniam S . (2004). Computational modeling reveals how interplay between components of a GTPase-cycle module regulates signal transduction. Proc Natl Acad Sci USA 101: 15899–15904.

    Article  CAS  Google Scholar 

  • Brewster JL, de Valoir T, Dwyer ND, Winter E, Gustin MC . (1993). An osmosensing signal transduction pathway in yeast. Science 259: 1760–1763.

    Article  CAS  Google Scholar 

  • Chan RK, Otte CA . (1982a). Isolation and genetic analysis of Saccharomyces cerevisiae mutants supersensitive to G1 arrest by a factor and α factor pheromones. Mol Cell Biol 2: 11–20.

    Article  CAS  Google Scholar 

  • Chan RK, Otte CA . (1982b). Physiological characterization of Saccharomyces cerevisiae mutants supersensitive to G1 arrest by a factor and α factor pheromones. Mol Cell Biol 2: 21–29.

    Article  CAS  Google Scholar 

  • Chasse SA, Dohlman HG . (2003). RGS proteins: G protein-coupled receptors meet their match. Assay Drug Dev Technol 1: 357–364.

    Article  CAS  Google Scholar 

  • Chasse SA, Flanary P, Parnell SC, Hao N, Cha JY, Siderovski DP et al. (2006). Genome-scale analysis reveals Sst2 as the principal regulator of mating pheromone signaling in the yeast Saccharomyces cerevisiae. Eukaryot Cell 5: 330–346.

    Article  CAS  Google Scholar 

  • Dohlman HG, Thorner JW . (2001). Regulation of G protein-initiated signal transduction in yeast: Paradigms and principles. Annu Rev Biochem 70: 703–754.

    Article  CAS  Google Scholar 

  • Dohlman HG, Apaniesk D, Chen Y, Song J, Nusskern D . (1995). Inhibition of G-protein signaling by dominant gain-of-function mutations in Sst2p, a pheromone desensitization factor in Saccharomyces cerevisiae. Mol Cell Biol 15: 3635–3643.

    Article  CAS  Google Scholar 

  • Dohlman HG, Song J, Ma D, Courchesne WE, Thorner J . (1996). Sst2, a negative regulator of pheromone signaling in the yeast Saccharomyces cerevisiae: expression, localization, and genetic interaction and physical association with Gpa1 (the G-protein α subunit). Mol Cell Biol 16: 5194–5209.

    Article  CAS  Google Scholar 

  • Dohlman HG . (2002). Diminishing returns. Nature 418: 591.

    Article  CAS  Google Scholar 

  • Farfel Z, Bourne HR, Iiri T . (1999). The expanding spectrum of G protein diseases. N Engl J Med 340: 1012–1020.

    Article  CAS  Google Scholar 

  • Ferrell JE, Xiong W . (2001). Bistability in cell signaling: how to make continuous processes discontinuous, and reversible processes irreversible? Chaos 11: 227–236.

    Article  CAS  Google Scholar 

  • Force T, Kuida K, Namchuk M, Parang K, Kyriakis JM . (2004). Inhibitors of protein kinase signaling pathways: emerging therapies for cardiovascular disease. Circulation 109: 1196–1205.

    Article  CAS  Google Scholar 

  • Garrison TR, Zhang Y, Pausch M, Apanovitch D, Aebersold R, Dohlman HG . (1999). Feedback phosphorylation of an RGS protein by MAP kinase in yeast. J Biol Chem 274: 36387–36391.

    Article  CAS  Google Scholar 

  • Gelperin DM, White MA, Wilkinson ML, Kon Y, Kung LA, Wise KJ et al. (2005). Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev 19: 2816–2826.

    Article  CAS  Google Scholar 

  • Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, Dephoure N et al. (2003). Global analysis of protein expression in yeast. Nature 425: 737–741.

    Article  CAS  Google Scholar 

  • Gibbs JB, Oliff A . (1994). Pharmaceutical research in molecular oncology. Cell 79: 193–198.

    Article  CAS  Google Scholar 

  • Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H et al. (1996). Life with 6000 genes [see comments]. Science 274: 546 563-7.

    Article  CAS  Google Scholar 

  • Gold SJ, Ni YG, Dohlman HG, Nestler EJ . (1997). Regulators of G-protein signaling (RGS) proteins: region-specific expression of nine subtypes in rat brain. J Neurosci 17: 8024–8037.

    Article  CAS  Google Scholar 

  • Goldbeter A, Koshland Jr DE . (1981). An amplified sensitivity arising from covalent modification in biological systems. Proc Natl Acad Sci USA 78: 6840–6844.

    Article  CAS  Google Scholar 

  • Guo M, Aston C, Burchett SA, Dyke C, Fields S, Rajarao SJ et al. (2003). The yeast G protein α subunit Gpa1 transmits a signal through an RNA binding effector protein Scp160. Mol Cell 12: 517–524.

    Article  CAS  Google Scholar 

  • Gutkind JS . (1998). The pathways connecting G protein-coupled receptors to the nucleus through divergent mitogen-activated protein kinase cascades. J Biol Chem 273: 1839–1842.

    Article  CAS  Google Scholar 

  • Hao N, Behar M, Parnell SC, Torres MP, Borchers CH, Elston TC et al. (2007). Experimental and computational analysis of feedback inhibition of the Sho1 osmotic stress-response pathway. Curr Biol (in press).

  • Hao N, Yildirim N, Wang Y, Elston TC, Dohlman HG . (2003). Regulators of G protein signaling and transient activation of signaling: experimental and computational analysis reveals negative and positive feedback controls on G protein activity. J Biol Chem 278: 46506–46515.

    Article  CAS  Google Scholar 

  • Hardman JG, Limbird LE, Gilman AG . (2001). Goodman & Gilman's The Pharmacological Basis of Therapeutics. McGraw-Hill: New York ISBN 0-07-135469-7.

    Google Scholar 

  • Hartwell LH, Szankasi P, Roberts CJ, Murray AW, Friend SH . (1997). Integrating genetic approaches into the discovery of anticancer drugs. Science 278: 1064–1068.

    Article  CAS  Google Scholar 

  • Heinrich R, Neel BG, Rapoport TA . (2002). Mathematical models of protein kinase signal transduction. Mol Cell 9: 957–970.

    Article  CAS  Google Scholar 

  • Hohmann S . (2002). Osmotic stress signaling and osmoadaptation in yeasts. Microbiol Mol Biol Rev 66: 300–372.

    Article  CAS  Google Scholar 

  • Hornberg JJ, Bruggeman FJ, Binder B, Geest CR, de Vaate AJ, Lankelma J et al. (2005). Principles behind the multifarious control of signal transduction. ERK phosphorylation and kinase/phosphatase control. FEBS J 272: 244–258.

    Article  CAS  Google Scholar 

  • Huang CY, Ferrell Jr JE . (1996). Ultrasensitivity in the mitogen-activated protein kinase cascade. Proc Natl Acad Sci USA 93: 10078–10083.

    Article  CAS  Google Scholar 

  • Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS et al. (2003). Global analysis of protein localization in budding yeast. Nature 425: 686–691.

    Article  CAS  Google Scholar 

  • Jacoby T, Flanagan H, Faykin A, Seto AG, Mattison C, Ota I . (1997). Two protein-tyrosine phosphatases inactivate the osmotic stress response pathway in yeast by targeting the mitogen-activated protein kinase, Hog1. J Biol Chem 272: 17749–17755.

    Article  CAS  Google Scholar 

  • Johnson GL, Dohlman HG, Graves LM . (2005). MAPK kinase kinases (MKKKs) as a target class for small-molecule inhibition to modulate signaling networks and gene expression. Curr Opin Chem Biol 9: 325–331.

    Article  CAS  Google Scholar 

  • Kenakin T . (2004). Principles: receptor theory in pharmacology. Trends Pharmacol Sci 25: 186–192.

    Article  CAS  Google Scholar 

  • Kholodenko BN . (2000). Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades. Eur J Biochem 267: 1583–1588.

    Article  CAS  Google Scholar 

  • Klipp E, Nordlander B, Kruger R, Gennemark P, Hohmann S . (2005). Integrative model of the response of yeast to osmotic shock. Nat Biotechnol 23: 975–982.

    Article  CAS  Google Scholar 

  • Kofahl B, Klipp E . (2004). Modelling the dynamics of the yeast pheromone pathway. Yeast 21: 831–850.

    Article  CAS  Google Scholar 

  • Komarova NL, Zou X, Nie Q, Bardwell L . (2005). A theoretical framework for specificity in cell signaling. Mol Syst Biol 1: 0023.

    Article  Google Scholar 

  • Kumar S, Boehm J, Lee JC . (2003). p38 MAP kinases: key signalling molecules as therapeutic targets for inflammatory diseases. Nat Rev Drug Discov 2: 717–726.

    Article  CAS  Google Scholar 

  • Lin FT, Miller WE, Luttrell LM, Lefkowitz RJ . (1999). Feedback regulation of beta-arrestin1 function by extracellular signal-regulated kinases [in process citation]. J Biol Chem 274: 15971–15974.

    Article  CAS  Google Scholar 

  • Marinissen MJ, Gutkind JS . (2001). G-protein-coupled receptors and signaling networks: emerging paradigms. Trends Pharmacol Sci 22: 368–376.

    Article  CAS  Google Scholar 

  • Markevich NI, Hoek JB, Kholodenko BN . (2004). Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades. J Cell Biol 164: 353–359.

    Article  CAS  Google Scholar 

  • Marshall CJ . (1995). Specificity of receptor tyrosine kinase signaling: transient versus sustained extracellular signal-regulated kinase activation. Cell 80: 179–185.

    Article  CAS  Google Scholar 

  • Martin H, Flandez M, Nombela C, Molina M . (2005). Protein phosphatases in MAPK signalling: we keep learning from yeast. Mol Microbiol 58: 6–16.

    Article  CAS  Google Scholar 

  • Martzen MR, McCraith SM, Spinelli SL, Torres FM, Fields S, Grayhack EJ et al. (1999). A biochemical genomics approach for identifying genes by the activity of their products. Science 286: 1153–1155.

    Article  CAS  Google Scholar 

  • Morrison DK, Davis RJ . (2003). Regulation of MAP kinase signaling modules by scaffold proteins in mammals. Annu Rev Cell Dev Biol 19: 91–118.

    Article  CAS  Google Scholar 

  • Neubig RR, Siderovski DP . (2002). Regulators of G-protein signalling as new central nervous system drug targets. Nat Rev Drug Discov 1: 187–197.

    Article  CAS  Google Scholar 

  • Neves SR, Ram PT, Iyengar R . (2002). G protein pathways. Science 296: 1636–1639.

    Article  CAS  Google Scholar 

  • Ogier-Denis E, Pattingre S, El Benna J, Codogno P . (2000). Erk1/2-dependent phosphorylation of Galpha-interacting protein stimulates its GTPase accelerating activity and autophagy in human colon cancer cells. J Biol Chem 275: 39090–39095.

    Article  CAS  Google Scholar 

  • Parnell SC, Marotti Jr LA, Kiang L, Torres MP, Borchers CH, Dohlman HG . (2005). Phosphorylation of the RGS protein Sst2 by the MAP kinase Fus3 and use of Sst2 as a model to analyze determinants of substrate sequence specificity. Biochemistry 44: 8159–8166.

    Article  CAS  Google Scholar 

  • Pitcher JA, Tesmer JJ, Freeman JL, Capel WD, Stone WC, Lefkowitz RJ . (1999). Feedback inhibition of G protein-coupled receptor kinase 2 (GRK2) activity by extracellular signal-regulated kinases. J Biol Chem 274: 34531–34534.

    Article  CAS  Google Scholar 

  • Roberts CJ, Nelson B, Marton MJ, Stoughton R, Meyer MR, Bennett HA et al. (2000). Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287: 873–880.

    Article  CAS  Google Scholar 

  • Roman DL, Talbot JN, Roof RA, Sunahara RK, Traynor JR, Neubig RR . (2006). Identification of small molecule inhibitors of Regulator of G-protein Signaling 4 (RGS4) using a high throughput flow cytometry protein interaction assay (FCPIA). Mol Pharmacol 71: 169–175.

    Article  Google Scholar 

  • Sabbagh Jr W, Flatauer LJ, Bardwell AJ, Bardwell L . (2001). Specificity of MAP kinase signaling in yeast differentiation involves transient versus sustained MAPK activation. Mol Cell 8: 683–691.

    Article  CAS  Google Scholar 

  • Sasagawa S, Ozaki Y, Fujita K, Kuroda S . (2005). Prediction and validation of the distinct dynamics of transient and sustained ERK activation. Nat Cell Biol 7: 365–373.

    Article  CAS  Google Scholar 

  • Schaber J, Kofahl B, Kowald A, Klipp E . (2006). A modelling approach to quantify dynamic crosstalk between the pheromone and the starvation pathway in baker's yeast. FEBS J 273: 3520–3533.

    Article  CAS  Google Scholar 

  • Schoeberl B, Eichler-Jonsson C, Gilles ED, Muller G . (2002). Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nat Biotechnol 20: 370–375.

    Article  Google Scholar 

  • Sebolt-Leopold JS, English JM . (2006). Mechanisms of drug inhibition of signalling molecules. Nature 441: 457–462.

    Article  CAS  Google Scholar 

  • Shao D, Zheng W, Qiu W, Ouyang Q, Tang C . (2006). Dynamic studies of scaffold-dependent mating pathway in yeast. Biophys J 91: 3986–4001.

    Article  CAS  Google Scholar 

  • Shenoy SK, Lefkowitz RJ . (2005). Seven-transmembrane receptor signaling through beta-arrestin. Sci STKE 2005: cm10.

    PubMed  Google Scholar 

  • Slessareva JE, Routt SM, Temple B, Bankaitis VA, Dohlman HG . (2006). Activation of the phosphatidylinositol 3-kinase Vps34 by a G protein alpha subunit at the endosome. Cell 126: 191–203.

    Article  CAS  Google Scholar 

  • Somsen OJ, Siderius M, Bauer FF, Snoep JL, Westerhoff HV . (2002). Selectivity in overlapping MAP kinase cascades. J Theor Biol 218: 343–354.

    Article  CAS  Google Scholar 

  • Spiegel AM . (2000). G protein defects in signal transduction. Horm Res 53: 17–22.

    CAS  PubMed  Google Scholar 

  • Sprang SR . (1997). G protein mechanisms: insights from structural analysis. Annu Rev Biochem 66: 639–678.

    Article  CAS  Google Scholar 

  • Tyson JJ, Chen KC, Novak B . (2003). Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol 15: 221–231.

    Article  CAS  Google Scholar 

  • Wang X, Hao N, Dohlman HG, Elston TC . (2006). Bistability, stochasticity, and oscillations in the mitogen-activated protein kinase cascade. Biophys J 90: 1961–1978.

    Article  CAS  Google Scholar 

  • Wang Y, Dohlman HG . (2002). Pheromone-dependent ubiquitination of the mitogen-activated protein kinase kinase Ste7. J Biol Chem 277: 15766–15772.

    Article  CAS  Google Scholar 

  • Wang Y, Ge Q, Houston D, Thorner J, Errede B, Dohlman HG . (2003). Regulation of Ste7 ubiquitination by Ste11 phosphorylation and the Skp1-Cullin-F-box complex. J Biol Chem 278: 22284–22289.

    Article  CAS  Google Scholar 

  • Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, Andre B et al. (1999). Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285: 901–906.

    Article  CAS  Google Scholar 

  • Wurgler-Murphy SM, Maeda T, Witten EA, Saito H . (1997). Regulation of the Saccharomyces cerevisiae HOG1 mitogen-activated protein kinase by the PTP2 and PTP3 protein tyrosine phosphatases. Mol Cell Biol 17: 1289–1297.

    Article  CAS  Google Scholar 

  • Xiong W, Ferrell Jr JE . (2003). A positive-feedback-based bistable ‘memory module’ that governs a cell fate decision. Nature 426: 460–465.

    Article  CAS  Google Scholar 

  • Yi TM, Huang Y, Simon MI, Doyle J . (2000). Robust perfect adaptation in bacterial chemotaxis through integral feedback control. Proc Natl Acad Sci USA 97: 4649–4653.

    Article  CAS  Google Scholar 

  • Yi TM, Kitano H, Simon MI . (2003). A quantitative characterization of the yeast heterotrimeric G protein cycle. Proc Natl Acad Sci USA 100: 10764–10769.

    Article  CAS  Google Scholar 

  • Zhong H, Wade SM, Woolf PJ, Linderman JJ, Traynor JR, Neubig RR . (2003). A spatial focusing model for G protein signals. Regulator of G protein signaling (RGS) protien-mediated kinetic scaffolding. J Biol Chem 278: 7278–7284.

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to T C Elston or H G Dohlman.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Hao, N., Behar, M., Elston, T. et al. Systems biology analysis of G protein and MAP kinase signaling in yeast. Oncogene 26, 3254–3266 (2007). https://doi.org/10.1038/sj.onc.1210416

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/sj.onc.1210416

Keywords

This article is cited by

Search

Quick links