The MAPK pathways are a collection of protein signaling cascades stimulated by a wide variety of extra-cellular signals, including growth factors, cytokines, and environmental stress1, 2
. Upon activation, MAPK pathways regulate a large number of fundamental cellular functions, including differentiation, proliferation, and apoptosis, through the activation of specific transcription factors and other regulatory proteins3
. Because of this central role in signal transduction, MAPK proteins have been repeatedly implicated in the pathogenesis of cancer and autoimmune diseases, leading to their selection as targets for drug development4
. MAPK pathways are also well conserved over the eukaryotic kingdom from yeast to man, enabling study of their structure and kinetics through genetic analysis of model organisms2
The canonical MAPK pathway consists of three sequentially-activated MAPK family members: a MAPK kinase kinase (MAP3K) which activates a MAPK kinase (MAP2K) which, in turn, activates a MAP kinase (MAPK). However, it is clear that this canonical pathway is embedded in a rich network of interactions with a wide variety of other components, including membrane receptors, transcription factors, kinase scaffolds, and extensive cross-talk with other activators and inhibitors of signaling5
. It has been suggested that a systems-level approach will ultimately be necessary to map these additional components and to understand their MAPK-related functions3, 6
Towards this goal, we pursued a combined experimental and computational approach to assemble a large resource of MAPK protein interactions and to illustrate methods to functionally explore this network. This work involved four steps: (1) A screen for physical interactions between MAPK proteins and the rest of the proteome, (2) An assessment of network quality and functional assessment of MAPK interactors through siRNA screening, (3) A specific analysis of the MAPK network to identify kinase scaffolds, illustrating how the network can be used as a resource to guide the discovery of novel protein functions, and (4) Identification of interaction modules and evolutionary conservation to aid in functional interpretation. Based on the MAPK network resource, we find evidence that the Na+/H+ exchanger NHE1 functions as a kinase scaffold, and we identify a conserved signaling cascade mediated by the signaling mucin MUC12.