Signaling in the crowded cell

Abstract

High-resolution technologies have clarified some of the principles underlying cellular actions. However, understanding how cells receive, communicate, and respond to signals is still challenging. Questions include how efficient regulation of assemblies, which execute cell actions at the nanoscales, transmits productively at micrometer scales, especially considering the crowded environment, and how the cell organization makes it happen. Here, we describe how cells can navigate long-range diffusion-controlled signaling via association/dissociation of spatially proximal entities. Dynamic clusters can span the cell, engaging in most signaling steps. Effective local concentration, allostery, scaffolding, affinities, and the chemical and mechanical properties of the macromolecules and the environment play key roles. Signaling strength and duration matter, for example, deciding if a mutation promotes cancer or developmental syndromes.

Fig. 1

A simplified diagram of cell proliferation signaling in the crowded cell. In the presence of the receptor tyrosine kinase (RTK) signal, Ras gets activated (upper left region). Ras activates Raf through the kinase domain dimerization. Active Raf dimer activates MEK, and subsequently activates ERK through cascading phosphorylation, leading to cell proliferation. Oncogenic Ras forms nanoclusters, promoting Raf dimerization (upper right region). In the MAPK pathway, KSR scaffolds MEK and ERK, substituting Raf and forming heterodimer with Raf. In the PI3K/AKT/mTOR pathway, both RTK and Ras recruit PI3K to the plasma membrane and fully activate it (lower right region). PI3K phosphorylates signaling lipid, PIP₂ to PIP₃, leading to cell growth. PTEN dephosphorylates PIP₃ to PIP₂, suppressing the growth signal. In the missing RTK signal, both CaM and KRas4B can fully activate PI3Kα in the KRAS-driven adenocarcinoma (lower left region). PDK1 and mTORC2 phosphorylate and activate AKT, and active AKT phosphorylates multiple sites in TSC (tuberous sclerosis complex) containing TSC1, TSC2, and TBC (Tre2-Bub2-Cdc16). Phosphorylated TSC impairs the GAP activity for RHEB (Ras homolog enriched in brain), increasing the population of active GTP-bound RHEB. At the lysosomal surface in the presence of cytosolic amino acids, RHEB-GTP activates mTORC1 in complex with the LYNUS (lysosome nutrient sensing) machinery. The LYNUS complex involves a heterodimer of Rag isoforms, Ragulator, SLC38A9 (sodium-coupled neutral amino acid transporter 9, an arginine-regulated transporter), and V-ATPase (vacuolar ATPase, a proton pump). IQGAP1 is a scaffolding protein in both MAPK and PI3K/AKT pathways (right region). The multi-domain protein of IQGAP1 is composed of the N-terminal CHD (calponin-homology domain), IQ repeats, WW (polyproline binding region) domain, IQ domain with four IQ motifs, GRD (Ras GTPase activating protein-related domain), and RGCT (RasGAP C-terminus). Here we propose that the entities are not physically separated as shown here, but dynamically physically linked, transiently clustered within phases, in line with high resolution imaging, such as that of the ER and actin [92], and actin, spectrin, and other molecules forming a MPS (membrane-associated periodic skeleton) in neurons to which e.g. GPCRs (G protein-coupled receptors), cell adhesion molecules, RTKs, are recruited to promote ERK signaling [93].

Fig. 2

Ras protein localizations in cell. Ras proteins in cytosol are farnesylated by farnesyltransferase (FTase) and translocated to the endoplasmic reticulum (ER). Ras converting enzyme 1 (RCE1) mediates the cleavage of CAAX motif in the C-terminal end, and isoprenylcysteine carboxylmethyltransferase (ICMT) modifies the carboxymethylation at the farnesylated cysteine. KRas4A in state 1 (only farnesylated) and KRas4B with the farnesyl modification perform a direct traffic to the acidic lipid enriched membrane microdomains of the plasma membrane. In contrast, HRas, NRas, and KRas4A are further palmitoylated by palmitoyl acyltransferase (PAT), such as DHHC9-GCP16 (DHHC domain-containing 9-Golgi complex- associated protein), in the Golgi apparatus. After palmitoylation, HRas, NRas, and KRas4A in state 2 (with both farnesyl and palmitoyl modifications) are translocated to various microdomains including the ordered caveolae and lipid rafts, as well as fluidic disordered (nonraft) regions of the plasma membrane.