Bistability, Stochasticity, and Oscillations in the Mitogen-Activated Protein Kinase Cascade

Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7365, USA.
Biophysical Journal (Impact Factor: 3.97). 04/2006; 90(6):1961-78. DOI: 10.1529/biophysj.105.073874
Source: PubMed


Signaling pathways respond to stimuli in a variety of ways, depending on the magnitude of the input and the physiological status of the cell. For instance, yeast can respond to pheromone stimulation in either a binary or graded fashion. Here we present single cell transcription data indicating that a transient binary response in which all cells eventually become activated is typical. Stochastic modeling of the biochemical steps that regulate activation of the mitogen-activated protein kinase Fus3 reveals that this portion of the pathway can account for the graded-to-binary conversion. To test the validity of the model, genetic approaches are used to alter expression levels of Msg5 and Ste7, two of the proteins that negatively and positively regulate Fus3, respectively. Single cell measurements of the genetically altered cells are shown to be consistent with predictions of the model. Finally, computational modeling is used to investigate the effects of protein turnover on the response of the pathway. We demonstrate that the inclusion of protein turnover can lead to sustained oscillations of protein concentrations in the absence of feedback regulation. Thus, protein turnover can profoundly influence the output of a signaling pathway.

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Available from: Henrik G Dohlman, Oct 08, 2015
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    • "criptional in - duction using Hill kinetics . The Hill coeffi cient was taken to be 2 and the K m and V max values were free parameters determined by fi tting the models to experimental data . We did not include a term for degradation of Fus3 , because its half - life was measured to greater than 2 h and increased upon stimulation with pheromone ( Wang et al . , 2006 ) . The equation for the phosphorylated ( active ) Fus3 concentration , [ p - Fus3 ] , is given by stored at – 80°C . Alternatively , in Figure 5B , cells were collected in prechilled 50 - ml tubes containing trichloroacetic acid ( TCA ; 5% fi nal concentration ) . For preparation of extracts , cell pellets were thawed on ice and resusp"
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    ABSTRACT: Different environmental stimuli often use the same set of signaling proteins to achieve very different physiological outcomes. The mating and invasive growth pathways in yeast each employ a mitogen-activated protein (MAP) kinase cascade that includes Ste20, Ste11, and Ste7. Whereas proper mating requires Ste7 activation of the MAP kinase Fus3, invasive growth requires activation of the alternate MAP kinase Kss1. To determine how MAP kinase specificity is achieved, we used a series of mathematical models to quantitatively characterize pheromone-stimulated kinase activation. In accordance with the computational analysis, MAP kinase feedback phosphorylation of Ste7 results in diminished activation of Kss1, but not Fus3. These findings reveal how feedback phosphorylation of a common pathway component can limit the activity of a competing MAP kinase through feedback phosphorylation of a common activator, and thereby promote signal fidelity.
    Molecular biology of the cell 08/2012; 23(19):3899-910. DOI:10.1091/mbc.E12-04-0333 · 4.47 Impact Factor
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    • "We do not consider the effect of protein degradation either. Our model is however a first theoretical fully stochastic study of the MAPK cascade, modelled earlier, to our knowledge, only via rate equations [9] [16] [18] [23] [24] or stochastic simulations [25] [26]. "
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    ABSTRACT: We study a mechanism for reliable switching in biomolecular signal-transduction cascades. Steady bistable states are created by system-size cooperative effects in populations of proteins, in spite of the fact that the phosphorylation-state transitions of any molecule, by means of which the switch is implemented, are highly stochastic. The emergence of switching is a nonequilibrium phase transition in an energetically driven, dissipative system described by a master equation. We use operator and functional integral methods from reaction-diffusion theory to solve for the phase structure, noise spectrum, and escape trajectories and first-passage times of a class of minimal models of switches, showing how all critical properties for switch behavior can be computed within a unified framework.
    Physical Review E 11/2011; 84(5 Pt 1):051917. DOI:10.1103/PhysRevE.84.051917 · 2.29 Impact Factor
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    • "In particular, the yeast Saccharomyces cerevisiae has served as an important eukaryotic model for cellular functions as fundamental as gene regulation and as complex as cell cycle orchestration (13–16). Models of gene regulation have been developed to elucidate sources of noise in gene expression and the effect of noise on fitness, to study the role of feedback in cellular networks, and have led to discoveries of novel network structure (6,17–29). "
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    ABSTRACT: Computational modeling of biological systems has become an effective tool for analyzing cellular behavior and for elucidating key properties of the intricate networks that underlie experimental observations. While most modeling techniques rely heavily on the concentrations of intracellular molecules, little attention has been paid to tracking and simulating the significant volume fluctuations that occur over each cell division cycle. Here, we use fluorescence microscopy to acquire single cell volume trajectories for a large population of Saccharomyces cerevisiae cells. Using this data, we generate a comprehensive set of statistics that govern the growth and division of these cells over many generations, and we discover several interesting trends in their size, growth and protein production characteristics. We use these statistics to develop an accurate model of cell cycle volume dynamics, starting at cell birth. Finally, we demonstrate the importance of tracking volume fluctuations by combining cell division dynamics with a minimal gene expression model for a constitutively expressed fluorescent protein. The significant oscillations in the cellular concentration of a stable, highly expressed protein mimic the observed experimental trajectories and demonstrate the fundamental impact that the cell cycle has on cellular functions.
    Nucleic Acids Research 12/2009; 38(8):2676-81. DOI:10.1093/nar/gkp1069 · 9.11 Impact Factor
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