The Mammalian MAPK/ERK Pathway Exhibits Properties of a Negative Feedback Amplifier

Analysis of ERK pathway circuitry suggests appropriate targets for inhibition, providing a guide for drug development. Biological Circuits Inform Drug Development The mitogen-activated protein kinase (MAPK) pathway involves a three-tiered kinase module, which amplifies the signal. Many cells also have negative feedback loops from the last kinase in the module to various points upstream in the pathway. Sturm et al. showed that, with negative feedback loops, the MAPK module results in a system like that of a negative feedback amplifier (NFA), which is an engineering design that smoothens the output to changes in input and makes a system robust to change. These NFA-like properties may explain why some cells are sensitive to inhibition of the second kinase in the cascade (they lack feedback loops), whereas other cells are resistant to inhibition at this point (their feedback loops are intact). These results also have implications for drug development, because inhibitors that target components that are outside the NFA are more effective at inhibiting the pathway. Three-tiered kinase modules, such as the Raf–MEK (mitogen-activated or extracellular signal–regulated protein kinase kinase)–ERK (extracellular signal–regulated kinase) mitogen-activated protein kinase pathway, are widespread in biology, suggesting that this structure conveys evolutionarily advantageous properties. We show that the three-tiered kinase amplifier module combined with negative feedback recapitulates the design principles of a negative feedback amplifier (NFA), which is used in electronic circuits to confer robustness, output stabilization, and linearization of nonlinear signal amplification. We used mathematical modeling and experimental validation to demonstrate that the ERK pathway has properties of an NFA that (i) converts intrinsic switch-like activation kinetics into graded linear responses, (ii) conveys robustness to changes in rates of reactions within the NFA module, and (iii) stabilizes outputs in response to drug-induced perturbations of the amplifier. These properties determine biological behavior, including activation kinetics and the response to drugs.

[1]  W. Kolch,et al.  Activated raf induces the hyperphosphorylation of stathmin and the reorganization of the microtubule network. , 1998, The Journal of biological chemistry.

[2]  Ursula Klingmüller,et al.  Theoretical and experimental analysis links isoform- specific ERK signalling to cell fate decisions , 2009, Molecular systems biology.

[3]  J E Ferrell,et al.  The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. , 1998, Science.

[4]  F. Hobbs,et al.  Identification of a Novel Inhibitor of Mitogen-activated Protein Kinase Kinase* , 1998, The Journal of Biological Chemistry.

[5]  W. Kolch.  Coordinating ERK/MAPK signalling through scaffolds and inhibitors , 2005, Nature Reviews Molecular Cell Biology.

[6]  William Pao,et al.  Genetic predictors of MEK dependence in non-small cell lung cancer. , 2008, Cancer research.

[7]  Todd R. Golub,et al.  BRAF mutation predicts sensitivity to MEK inhibition , 2006, Nature.

[8]  A. Adjei,et al.  Novel Anticancer Agents in Clinical Development , 2003, Cancer biology & therapy.

[9]  C. Springer,et al.  In melanoma, RAS mutations are accompanied by switching signaling from BRAF to CRAF and disrupted cyclic AMP signaling. , 2006, Cancer research.

[10]  Reinhart Heinrich,et al.  Mathematical models of protein kinase signal transduction. , 2002, Molecular cell.

[11]  G. Holdgate,et al.  Enzyme kinetics and binding studies on inhibitors of MEK protein kinase. , 2008, Biochemistry.

[12]  W. Kolch,et al.  Regulation and Role of Raf-1/B-Raf Heterodimerization , 2006, Molecular and Cellular Biology.

[13]  W. Knorre,et al.  M. A. Savageau, Biochemical Systems Analysis. A Study of Function and Design in Molecular Biology. 396 S., 115 Abb., 14 Tab. Reading, Mass. 1976. Addison‐Wesley Pbl. Co./Advanced Book Program. £ 26,50 , 1979 .

[14]  W. R. Burack,et al.  The activating dual phosphorylation of MAPK by MEK is nonprocessive. , 1997, Biochemistry.

[15]  B. Kholodenko,et al.  Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades , 2004, The Journal of cell biology.

[16]  Walter Kolch,et al.  Phosphatase and Feedback Regulation of Raf-1 Signaling , 2007, Cell cycle.

[17]  E. Gilles,et al.  Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors , 2002, Nature Biotechnology.

[18]  Wei Chen,et al.  Differential regulation and properties of MAPKs , 2007, Oncogene.

[19]  M. White,et al.  Stimulus-Coupled Spatial Restriction of Extracellular Signal-Regulated Kinase 1/2 Activity Contributes to the Specificity of Signal-Response Pathways , 2004, Molecular and Cellular Biology.

[20]  P. Cohen,et al.  Specificity and mechanism of action of some commonly used protein kinase inhibitors. , 2000, The Biochemical journal.

[21]  P. Bastiaens,et al.  Growth factor-induced MAPK network topology shapes Erk response determining PC-12 cell fate , 2007, Nature Cell Biology.

[22]  M. Savageau.  Biochemical Systems Analysis: A Study of Function and Design in Molecular Biology , 1976 .

[23]  J. Sebolt-Leopold,et al.  Mechanisms of drug inhibition of signalling molecules , 2006, Nature.

[24]  Richard Marais,et al.  The RAF proteins take centre stage , 2004, Nature Reviews Molecular Cell Biology.

[25]  H. S. Black,et al.  Stabilized feedback amplifiers , 1934 .

[26]  Julian Downward,et al.  EGF induced SOS phosphorylation in PC12 cells involves P90 RSK-2 , 1997, Oncogene.

[27]  H. Sauro,et al.  Quantitative analysis of signaling networks. , 2004, Progress in biophysics and molecular biology.

[28]  Jeffrey P. MacKeigan,et al.  Graded Mitogen-Activated Protein Kinase Activity Precedes Switch-Like c-Fos Induction in Mammalian Cells , 2005, Molecular and Cellular Biology.

[29]  Gaetano Palumbo,et al.  Feedback Amplifiers: Theory and Design , 2002 .

[30]  C. Der,et al.  Targeting the Raf-MEK-ERK mitogen-activated protein kinase cascade for the treatment of cancer , 2007, Oncogene.

[31]  Ming Zhou,et al.  Regulation of Raf-1 by direct feedback phosphorylation. , 2005, Molecular cell.

[32]  J. Ferrell,et al.  Mos Mediates the Mitotic Activation of p42 MAPK in Xenopus Egg Extracts , 2004, Current Biology.

[33]  M. McMahon,et al.  Conditional transformation of cells and rapid activation of the mitogen-activated protein kinase cascade by an estradiol-dependent human raf-1 protein kinase , 1993, Molecular and cellular biology.