The role of feedback control mechanisms on the establishment of oscillatory regimes in the Ras/cAMP/PKA pathway in S. cerevisiae

Daniela Besozzi,Paolo Cazzaniga,Dario Pescini,Giancarlo Mauri,Enzo Martegani,Sonia Colombo

doi:10.1186/1687-4153-2012-10

Abstract

In the yeast Saccharomyces cerevisiae, the Ras/cAMP/PKA pathway is involved in the regulation of cell growth and proliferation in response to nutritional sensing and stress conditions. The pathway is tightly regulated by multiple feedback loops, exerted by the protein kinase A (PKA) on a few pivotal components of the pathway. In this article, we investigate the dynamics of the second messenger cAMP by performing stochastic simulations and parameter sweep analysis of a mechanistic model of the Ras/cAMP/PKA pathway, to determine the effects that the modulation of these feedback mechanisms has on the establishment of stable oscillatory regimes. In particular, we start by studying the role of phosphodiesterases, the enzymes that catalyze the degradation of cAMP, which represent the major negative feedback in this pathway. Then, we show the results on cAMP oscillations when perturbing the amount of protein Cdc25 coupled with the alteration of the intracellular ratio of the guanine nucleotides (GTP/GDP), which are known to regulate the switch of the GTPase Ras protein. This multi-level regulation of the amplitude and frequency of oscillations in the Ras/cAMP/PKA pathway might act as a fine tuning mechanism for the downstream targets of PKA, as also recently evidenced by some experimental investigations on the nucleocytoplasmic shuttling of the transcription factor Msn2 in yeast cells.

Highlights

In living cells many processes are regulated by negative and positive feedback mechanisms, which are usually interlaced in complex regulatory networks and can function to either attenuate, amplify or even exploit molecular noise and stochasticity
The Ras/cAMP/PKA pathway controls more than 90% of all genes that are regulated by glucose through the activation of the protein kinase A (PKA), that is able to phosphorylate a plethora of downstream proteins [11]
Our previous analysis on the Ras/cAMP/PKA model suggested that stable oscillatory regimes in the amount of cAMP can be regulated by the ratio between Cdc25 and Ira2 proteins, which both control the activation of the adenylate cyclase by means of the active fraction of Ras proteins [17]

Summary

Introduction

In living cells many processes are regulated by negative and positive feedback mechanisms, which are usually interlaced in complex regulatory networks and can function to either attenuate, amplify or even exploit molecular noise and stochasticity (see, e.g., [1,2,3] and references therein). Five interlocked systems are known to participate in glucose signaling, which altogether result in a massive restructuring of the transcriptional state of the genome, as well as in a rapid change in the pattern of protein phosphorylation when glucose is added to cells growing on a non-fermentable carbon source [11]. Among these five pathways, the Ras/cAMP/PKA system plays a central role in responding to changes in glucose concentration and in turning on the processes that lead to cellular growth and division. Experimental evidences suggest that the negative feedback loop exerted by PKA operates at the level of Ras2-GTP [13,14,15]: PKA can phosphorylate Cdc, reducing its exchange activity, as well as Ira proteins, increasing the Ras-GAP activity (in both cases, this regulation results in a decrease of the activity of the adenylate cyclase)

Methods

Results

Conclusion