Cell fate decisions are specified by the dynamic ERK interactome

Abstract

Extracellular signal-regulated kinase (ERK) controls fundamental cellular functions, including cell fate decisions 1,2 . In PC12, cells shifting ERK activation from transient to sustained induces neuronal differentiation 3 . As ERK associates with both regulators and effectors 4 , we hypothesized that the mechanisms underlying the switch could be revealed by assessing the dynamic changes in ERK-interacting proteins that specifically occur under differentiation conditions. Using quantitative proteomics, we identified 284 ERK-interacting proteins. Upon induction of differentiation, 60 proteins changed their binding to ERK, including many proteins that were not known to participate in differentiation. We functionally characterized a subset, showing that they regulate the pathway at several levels and by different mechanisms, including signal duration, ERK localization, feedback, crosstalk with the Akt pathway and differential interaction and phosphorylation of transcription factors. Integrating these data with a mathematical model confirmed that ERK dynamics and differentiation are regulated by distributed control mechanisms rather than by a single master switch.

Complexity of Receptor Tyrosine Kinase Signal Processing

“…For instance, negative feedback loops from ERK to SOS and from ERK to Raf-1 and EGFR degradation are redundant because each of these processes is sufficient for signal termination (Orton et al 2008). In fact, mathematical models show that the system control is always distributed over multiple processes (von Kriegsheim et al 2009). …”

“…ERK, which is the terminal kinase in the threelayered MAPK/ERK cascade, phosphorylates multiple signaling molecules and transcription factors (Yoon and Seger 2006;von Kriegsheim et al 2009;Yang et al 2013). An example of ERKmediated negative feedback is the phosphorylation of the guanine nucleotide exchange factor SOS.…”

“…Although early genetic experiments seem to support a linear pathway view, the current biochemical and imaging data suggest that any given RTK, downstream adaptors, small Gproteins (small GTPases, such as Ras, Rac, Rho, or Cdc42), and activated kinases interact with a large variety of signaling molecules resulting in highly interconnected networks (von Kriegsheim et al 2009). These signaling networks not only transmit but also process and integrate signals.…”

Calpain interacts with class IA phosphoinositide 3-kinases regulating their stability and signaling activity

“…Accordingly, several mechanisms to control PI3K activity have evolved, some of which (highlighted in the introduction) are relatively well characterized (9,10,15,19,21,37). Regulation by protein-protein interactions is a recurrent theme in biochemistry (12,13) and several signaling pathway components are known to be regulated by the formation of protein complexes (14)(15)(16)(17). However, the extent by which protein interactors regulate class IA PI3Ks is not completely understood, perhaps because of the lack of off-the-shelf analytical tools to study transient and low-affinity binding partners.…”

“…Regulation of signaling processes by protein-protein interactions is gradually being elucidated for several signaling nodes including ERK (14), Akt (15), and mTOR (16,17), to cite some examples. However, the extent by which protein-protein interactions may modulate the activity of PI3K enzymes is currently underexplored.…”