Modeling mutant phenotypes and oscillatory dynamics in the Saccharomyces cerevisiae cAMP-PKA pathway

BackgroundThe cyclic AMP-Protein Kinase A (cAMP-PKA) pathway is an evolutionarily conserved signal transduction mechanism that regulates cellular growth and differentiation in animals and fungi. We present a mathematical model that recapitulates the short-term and long-term dynamics of this pathway in the budding yeast, Saccharomyces cerevisiae. Our model is aimed at recapitulating the dynamics of cAMP signaling for wild-type cells as well as single (pde1Δ and pde2Δ) and double (pde1Δpde2Δ) phosphodiesterase mutants.ResultsOur model focuses on PKA-mediated negative feedback on the activity of phosphodiesterases and the Ras branch of the cAMP-PKA pathway. We show that both of these types of negative feedback are required to reproduce the wild-type signaling behavior that occurs on both short and long time scales, as well as the the observed responses of phosphodiesterase mutants. A novel feature of our model is that, for a wide range of parameters, it predicts that intracellular cAMP concentrations should exhibit decaying oscillatory dynamics in their approach to steady state following glucose stimulation. Experimental measurements of cAMP levels in two genetic backgrounds of S. cerevisiae confirmed the presence of decaying cAMP oscillations as predicted by the model.ConclusionsOur model of the cAMP-PKA pathway provides new insights into how yeast respond to alterations in their nutrient environment. Because the model has both predictive and explanatory power it will serve as a foundation for future mathematical and experimental studies of this important signaling network.

[1]  P. Cohen,et al.  Amino acid sequences at the two sites on glycogen synthetase phosphorylated by cyclic AMP‐dependent protein kinase and their dephosphorylation by protein phosphatase‐III , 1977, FEBS letters.

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

[3]  M. Jacquet,et al.  SDC25, a dispensable Ras guanine nucleotide exchange factor of Saccharomyces cerevisiae differs from CDC25 by its regulation. , 1996, Molecular biology of the cell.

[4]  M. Jacquet,et al.  Membrane‐anchoring domains of Cdc25p, a Saccharomyces cerevisiae ras exchange factor , 1996, Biology of the cell.

[5]  G. Mills,et al.  Phosphorylation and inactivation of glycogen synthase kinase 3 by protein kinase A. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[6]  L. Buck,et al.  Information coding in the vertebrate olfactory system. , 1996, Annual review of neuroscience.

[7]  J. Beavo,et al.  Biochemistry and physiology of cyclic nucleotide phosphodiesterases: essential components in cyclic nucleotide signaling. , 2007, Annual review of biochemistry.

[8]  E. Martegani,et al.  Modeling and stochastic simulation of the Ras/cAMP/PKA pathway in the yeast Saccharomyces cerevisiae evidences a key regulatory function for intracellular guanine nucleotides pools. , 2008, Journal of biotechnology.

[9]  J. Heitman,et al.  Yeast pseudohyphal growth is regulated by GPA2, a G protein α homolog , 1997 .

[10]  E. Sutherland,et al.  The role of cyclic adenylic acid in hormone action. , 1960, Recent progress in hormone research.

[11]  J. D. de Winde,et al.  Glucose‐induced cAMP signalling in yeast requires both a G‐protein coupled receptor system for extracellular glucose detection and a separable hexose kinase‐dependent sensing process , 2000, Molecular microbiology.

[12]  J. Field,et al.  The SH3 domain of the S. cerevisiae Cdc25p binds adenylyl cyclase and facilitates Ras regulation of cAMP signalling. , 1999, Cellular signalling.

[13]  M. Elowitz,et al.  Frequency-modulated nuclear localization bursts coordinate gene regulation , 2008, Nature.

[14]  J. Kehrl,et al.  RGS2: a multifunctional regulator of G-protein signaling. , 2002, The international journal of biochemistry & cell biology.

[15]  E. Sutherland,et al.  Formation of a cyclic adenine ribonucleotide by tissue particles. , 1958, The Journal of biological chemistry.

[16]  L. Stateva,et al.  Candida albicans Pde1p and Gpa2p comprise a regulatory module mediating agonist-induced cAMP signalling and environmental adaptation. , 2010, Fungal genetics and biology : FG & B.

[17]  E. Martegani,et al.  The large N-terminal domain of Cdc25 protein of the yeast Saccharomyces cerevisiae is required for glucose-induced Ras2 activation. , 2007, FEMS yeast research.

[18]  E. Krebs,et al.  An adenosine 3',5'-monophosphate-dependant protein kinase from rabbit skeletal muscle. , 1968, The Journal of biological chemistry.

[19]  C. Arrieumerlou,et al.  Glucose-induced cyclic AMP oscillations regulate pulsatile insulin secretion. , 2008, Cell metabolism.

[20]  Enzo Martegani,et al.  Activation State of the Ras2 Protein and Glucose-induced Signaling in Saccharomyces cerevisiae* , 2004, Journal of Biological Chemistry.

[21]  Gerald R. Fink,et al.  Unipolar cell divisions in the yeast S. cerevisiae lead to filamentous growth: Regulation by starvation and RAS , 1992, Cell.

[22]  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.

[23]  J. Heitman,et al.  Yeast pseudohyphal growth is regulated by GPA2, a G protein alpha homolog. , 1997, The EMBO journal.

[24]  P. Sassone-Corsi,et al.  Cyclic AMP signalling. , 2001, Journal of cell science.

[25]  K. Matsumoto,et al.  IRA1, an inhibitory regulator of the RAS-cyclic AMP pathway in Saccharomyces cerevisiae , 1989, Molecular and cellular biology.

[26]  J. D. de Winde,et al.  Novel sensing mechanisms and targets for the cAMP–protein kinase A pathway in the yeast Saccharomyces cerevisiae , 1999, Molecular microbiology.

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

[28]  Paul Shannon,et al.  Derivation of genetic interaction networks from quantitative phenotype data , 2005, Genome Biology.

[29]  J. Beavo,et al.  Cyclic nucleotide research — still expanding after half a century , 2002, Nature Reviews Molecular Cell Biology.

[30]  P. S. Lazo,et al.  Activation of adenylate cyclase in cdc25 mutants of Saccharomyces cerevisiae , 1993, FEBS letters.

[31]  P. Ma,et al.  The PDE1-encoded low-affinity phosphodiesterase in the yeast Saccharomyces cerevisiae has a specific function in controlling agonist-induced cAMP signaling. , 1999, Molecular biology of the cell.

[32]  Mike Tyers,et al.  Systematic Identification of Pathways That Couple Cell Growth and Division in Yeast , 2002, Science.

[33]  K. Matsumoto,et al.  IRA2, a second gene of Saccharomyces cerevisiae that encodes a protein with a domain homologous to mammalian ras GTPase-activating protein. , 1990, Molecular and cellular biology.

[34]  H. Mitsuzawa.  Responsiveness to exogenous cAMP of a Saccharomyces cerevisiae strain conferred by naturally occurring alleles of PDE1 and PDE2. , 1993, Genetics.

[35]  Michael Wigler,et al.  Three different genes in S. cerevisiae encode the catalytic subunits of the cAMP-dependent protein kinase , 1987, Cell.

[36]  Novel mechanisms in nutrient activation of the yeast protein kinase A pathway. , 2008, Acta microbiologica et immunologica Hungarica.

[37]  Susan S. Taylor,et al.  cAMP-dependent protein kinase: framework for a diverse family of regulatory enzymes. , 1990, Annual review of biochemistry.

[38]  I. H. Segel.  Enzyme Kinetics: Behavior and Analysis of Rapid Equilibrium and Steady-State Enzyme Systems , 1975 .

[39]  A. Levitzki,et al.  Phosphorylation of the S. cerevisiae Cdc25 in response to glucose results in its dissociation from Ras , 1992, Nature.

[40]  Jong-In Park,et al.  The high-affinity cAMP phosphodiesterase of Saccharomyces cerevisiae is the major determinant of cAMP levels in stationary phase: involvement of different branches of the Ras-cyclic AMP pathway in stress responses. , 2005, Biochemical and biophysical research communications.

[41]  J. D. de Winde,et al.  A novel regulator of G protein signalling in yeast, Rgs2, downregulates glucose‐activation of the cAMP pathway through direct inhibition of Gpa2 , 1999, The EMBO journal.

[42]  A. Levitzki,et al.  The N-terminal half of Cdc25 is essential for processing glucose signaling in Saccharomyces cerevisiae. , 1999, Biochemistry.

[43]  M. Wigler,et al.  Cloning and characterization of BCY1, a locus encoding a regulatory subunit of the cyclic AMP-dependent protein kinase in Saccharomyces cerevisiae , 1987, Molecular and cellular biology.

[44]  F. McCormick,et al.  The ras Superfamily of GTPases , 1993 .

[45]  N. Spitzer,et al.  Dynamic interactions of cyclic AMP transients and spontaneous Ca2+ spikes , 2002, Nature.

[46]  G. Gill,et al.  Role of the receptor in the mechanism of action of adenosine 3':5'-cyclic monophosphate. , 1971, Proceedings of the National Academy of Sciences of the United States of America.

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

[48]  J. Thevelein,et al.  Involvement of the CDC25 gene product in the signal transmission pathway of the glucose-induced RAS-mediated cAMP signal in the yeast Saccharomyces cerevisiae. , 1991, Journal of general microbiology.

[49]  Wayne R. Cowell,et al.  Sources and development of mathematical software , 1984 .

[50]  Jongkyeong Chung,et al.  cAMP signalling in mushroom bodies modulates temperature preference behaviour in Drosophila , 2008, Nature.

[51]  J. Richards,et al.  Functional Interactions, Phosphorylation, and Levels of 3؅,5؅-cyclic Adenosine Monophosphate-regulatory Element Binding Protein and Steroidogenic Factor-1 Mediate Hormone-regulated and Constitutive Expression of Aromatase in Gonadal Cells , 2022 .

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

[53]  J. D. de Winde,et al.  A Saccharomyces cerevisiae G‐protein coupled receptor, Gpr1, is specifically required for glucose activation of the cAMP pathway during the transition to growth on glucose , 1999, Molecular microbiology.

[54]  Xiaojia Bai,et al.  The localization and concentration of the PDE2-encoded high-affinity cAMP phosphodiesterase is regulated by cAMP-dependent protein kinase A in the yeast Saccharomyces cerevisiae. , 2010, FEMS yeast research.

[55]  A. Tengholm,et al.  cAMP oscillations restrict protein kinase A redistribution in insulin-secreting cells. , 2006, Biochemical Society transactions.

[56]  E. Martegani,et al.  Localization of Ras signaling complex in budding yeast. , 2012, Biochimica et biophysica acta.

[57]  Douglas B. Kell,et al.  Deterministic mathematical models of the cAMP pathway in Saccharomyces cerevisiae , 2009, BMC Systems Biology.

[58]  William F. Loomis,et al.  Periodic Signaling Controlled by an Oscillatory Circuit That Includes Protein Kinases ERK2 and PKA , 2004, Science.

[59]  M. Harbeck,et al.  Cell physiology of cAMP sensor Epac , 2006, The Journal of physiology.

[60]  M. Wigler,et al.  The S. cerevisiae CDC25 gene product regulates the RAS/adenylate cyclase pathway , 1987, Cell.

[61]  M. Jacquet,et al.  Enhancement of the GDP-GTP exchange of RAS proteins by the carboxyl-terminal domain of SCD25. , 1990, Science.

[62]  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.

[63]  G. Santangelo,et al.  Glucose Signaling in Saccharomyces cerevisiae , 2006, Microbiology and Molecular Biology Reviews.

[64]  J. Corbin,et al.  Structure and function of cyclic nucleotide-dependent protein kinases. , 1994, Annual review of physiology.