Membrane recruitment of scaffold proteins drives specific signaling

Exploring the influence of cytosolic and membrane FAK activation on YAP/TAZ nuclear translocation

Membrane binding and unbinding dynamics play a crucial role in the biological activity of several nonintegral membrane proteins, which have to be recruited to the membrane to perform their functions. By localizing to the membrane, these proteins are able to induce downstream signal amplification in their respective signaling pathways. Here, we present a 3D computational approach using reaction-diffusion equations to investigate the relation between membrane localization of focal adhesion kinase (FAK), Ras homolog family member A (RhoA), and signal amplification of the YAP/TAZ signaling pathway. Our results show that the theoretical scenarios in which FAK is membrane bound yield robust and amplified YAP/TAZ nuclear translocation signals. Moreover, we predict that the amount of YAP/TAZ nuclear translocation increases with cell spreading, confirming the experimental findings in the literature. In summary, our in silico predictions show that when the cell membrane interaction area with the underlying substrate increases, for example, through cell spreading, this leads to more encounters between membrane-bound signaling partners and downstream signal amplification. Because membrane activation is a motif common to many signaling pathways, this study has important implications for understanding the design principles of signaling networks.

Simple synthetic protein scaffolds can create adjustable artificial MAPK circuits in yeast and mammalian cells

As hubs for eukaryotic cell signaling, scaffold proteins are attractive targets for engineering and manipulating signaling circuits. We designed synthetic scaffolds with a repeated PDZ domain that interacted with engineered kinases of the mitogen-activated protein kinase (MAPK) cascade involved in yeast mating to investigate how modular interactions mediate kinase cascades. The synthetic scaffolds functioned as logic gates of signaling circuits. We replaced the endogenous yeast scaffold Ste5 with designer scaffolds with a variable numbers of a PDZ domain that bound kinases or phosphatases engineered with a PDZ-binding motif. Although association with the membrane was necessary for pathway activity, surprisingly, mating responses occurred when the circuit contained a scaffold with only two PDZ domains, which could only bind two of the three kinases simultaneously. Additionally, the three tiers of the MAPK pathway exhibited decreasing positional plasticity from the top [MAPK kinase kinase (MAPKKK)] to the bottom (MAPK) tier such that binding of a MAPKKK, but not a MAPK, from the osmoregulatory pathway or protein kinase C pathway to the synthetic scaffold activated a reporter of the mating response. We also showed that the output duration and intensity could be altered by recruiting phosphatases or varying the affinity of the recruited proteins for the scaffold and that a designer MAPK scaffold functioned in mammalian cells. Thus, this synthetic approach with designer scaffolds should enable the rational manipulation or engineering of signaling pathways and provide insight into the functional roles of scaffold proteins.

On the inscrutable role of Inscuteable: structural basis and functional implications for the competitive binding of NuMA and Inscuteable to LGN

Alignment of the mitotic spindle to the cellular polarity axis is a prerequisite for asymmetric cell divisions. The protein network coordinating the spindle position with cortical polarity includes the molecular machinery pulling on astral microtubules, which is assembled on conserved NuMA:LGN:Gαi complexes, the polarity proteins Par3:Par6:aPKC and an adaptor molecule known as Inscuteable (Insc). To date, all these components were assumed to enter a macromolecular complex localized at polarity sites in mitosis. However, recent structural studies revealed the Insc and NuMA are mutually exclusive interactors of LGN, implying that the molecular mechanism of spindle coupling to polarity is more sophisticated than has been believed to date.

Recent insights into the complexity of Tank-binding kinase 1 signaling networks: the emerging role of cellular localization in the activation and substrate specificity of TBK1

Tank-binding kinase 1 (TBK1) serves as an important component of multiple signaling pathways. While the majority of research on TBK1 has focused on its role in innate immunity, critical functions for TBK1 in autophagy and cancer are beginning to emerge. This review highlights recent structural and biochemical studies that provide insights into the molecular mechanism of TBK1 activation and summarizes what is known to date about TBK1 substrate selection. Growing evidence suggests that both processes rely on TBK1 subcellular localization, with a variety of adaptor proteins each directing TBK1 to discrete signaling complexes for different cellular responses. Further study of TBK1-mediated pathways will require careful consideration of TBK1 mechanisms of activation and specificity for proper dissection of these distinct signaling cascades.

Modularity and functional plasticity of scaffold proteins as p(l)acemakers in cell signaling

Cells coordinate and integrate various functional modules that control their dynamics, intracellular trafficking, metabolism and gene expression. Such capacity is mediated by specific scaffold proteins that tether multiple components of signaling pathways at plasma membrane, Golgi apparatus, mitochondria, endoplasmic reticulum, nucleus and in more specialized subcellular structures such as focal adhesions, cell-cell junctions, endosomes, vesicles and synapses. Scaffold proteins act as "pacemakers" as well as "placemakers" that regulate the temporal, spatial and kinetic aspects of protein complex assembly by modulating the local concentrations, proximity, subcellular dispositions and biochemical properties of the target proteins through the intricate use of their modular protein domains. These regulatory mechanisms allow them to gate the specificity, integration and crosstalk of different signaling modules. In addition to acting as physical platforms for protein assembly, many professional scaffold proteins can also directly modify the properties of their targets while they themselves can be regulated by post-translational modifications and/or mechanical forces. Furthermore, multiple scaffold proteins can form alliances of higher-order regulatory networks. Here, we highlight the emerging themes of scaffold proteins by analyzing their common and distinctive mechanisms of action and regulation, which underlie their functional plasticity in cell signaling. Understanding these mechanisms in the context of space, time and force should have ramifications for human physiology and for developing new therapeutic approaches to control pathological states and diseases.

Protein scaffolds can enhance the bistability of multisite phosphorylation systems

The phosphorylation of a substrate at multiple sites is a common protein modification that can give rise to important structural and electrostatic changes. Scaffold proteins can enhance protein phosphorylation by facilitating an interaction between a protein kinase enzyme and its target substrate. In this work we consider a simple mathematical model of a scaffold protein and show that under specific conditions, the presence of the scaffold can substantially raise the likelihood that the resulting system will exhibit bistable behavior. This phenomenon is especially pronounced when the enzymatic reactions have sufficiently large K(M), compared to the concentration of the target substrate. We also find for a closely related model that bistable systems tend to have a specific kinetic conformation. Using deficiency theory and other methods, we provide a number of necessary conditions for bistability, such as the presence of multiple phosphorylation sites and the dependence of the scaffold binding/unbinding rates on the number of phosphorylated sites.

RssAB signaling coordinates early development of surface multicellularity in Serratia marcescens

Bacteria can coordinate several multicellular behaviors in response to environmental changes. Among these, swarming and biofilm formation have attracted significant attention for their correlation with bacterial pathogenicity. However, little is known about when and where the signaling occurs to trigger either swarming or biofilm formation. We have previously identified an RssAB two-component system involved in the regulation of swarming motility and biofilm formation in Serratia marcescens. Here we monitored the RssAB signaling status within single cells by tracing the location of the translational fusion protein EGFP-RssB following development of swarming or biofilm formation. RssAB signaling is specifically activated before surface migration in swarming development and during the early stage of biofilm formation. The activation results in the release of RssB from its cognate inner membrane sensor kinase, RssA, to the cytoplasm where the downstream gene promoters are located. Such dynamic localization of RssB requires phosphorylation of this regulator. By revealing the temporal activation of RssAB signaling following development of surface multicellular behavior, our findings contribute to an improved understanding of how bacteria coordinate their lifestyle on a surface.

GIV/Girdin is a rheostat that fine-tunes growth factor signals during tumor progression

GIV/Girdin is a multidomain signaling molecule that enhances PI3K-Akt signals downstream of both G protein-coupled and growth factor receptors. We previously reported that GIV triggers cell migration via its C-terminal guanine-nucleotide exchange factor (GEF) motif that activates Gαi. Recently we discovered that GIV's C-terminus directly interacts with the epidermal growth factor receptor (EGFR), and when its GEF function is intact, a Gαi-GIV-EGFR signaling complex assembles. By coupling G proteins to growth factor receptors, GIV is uniquely poised to intercept the incoming receptor-initiated signals and modulate them via G protein intermediates. Subsequent work has revealed that expression of the highly specialized C-terminus of GIV undergoes a bipartite dysregulation during oncogenesis-full length GIV with an intact C-terminus is expressed at levels ~20-50-fold above normal in highly invasive cancer cells and metastatic tumors, but its C-terminus is truncated by alternative splicing in poorly invasive cancer cells and non-invasive tumors. The consequences of such dysregulation on graded signal transduction and cellular phenotypes in the normal epithelium and its implication during tumor progression are discussed herein. Based on the fact that GIV grades incoming signals initiated by ligand-activated receptors by linking them to cyclical activation of G proteins, we propose that GIV is a molecular rheostat for signal transduction.

Four-dimensional dynamics of MAPK information processing systems

Mitogen activated protein kinase (MAPK) cascades process a myriad of stimuli received by cell-surface receptors and generate precise spatio-temporal guidance for multiple target proteins, dictating receptor-specific cellular outcomes. Computational modelling reveals that the intrinsic topology of MAPK cascades enables them to amplify signal sensitivity and amplitude, reduce noise and display intricate dynamic properties, which include toggle switches, excitation pulses and oscillations. Specificity of signaling responses can be brought about by signal-induced feedback and feedforward wiring imposed on the MAPK cascade backbone. Intracellular gradients of protein activities arise from the spatial separation of opposing reactions in kinase-phosphatase cycles. The membrane confinement of the initiating kinase in MAPK cascades and cytosolic localization of phosphatases can result in precipitous gradients of phosphorylated signal-transducers if they spread solely by diffusion. Endocytotic trafficking of active kinases driven by molecular motors and traveling waves of protein phosphorylation can propagate phosphorylation signals from the plasma membrane to the nucleus, especially in large cells, such as Xenopus eggs.

Scaffolds are 'active' regulators of signaling modules

Signaling cascades, in addition to proteins with obvious signaling-relevant activities (e.g. protein kinases or receptors), also employ dedicated 'inactive' proteins whose functions appear to be the organization of the former components into higher order complexes through protein-protein interactions. The core function of signaling adaptors, anchors and scaffolds is the recruitment of proteins into one macromolecular complex. Several recent studies have demonstrated that the recruiter and the recruited molecules mutually influence each other in a scaffolded complex. This yields fundamentally novel properties for the signaling complex as a whole. Because these are not merely additive to the properties of the individual components, scaffolded signaling complexes may behave as functionally distinct modules.

Strategies for protein synthetic biology

Proteins are the most versatile among the various biological building blocks and a mature field of protein engineering has lead to many industrial and biomedical applications. But the strength of proteins—their versatility, dynamics and interactions—also complicates and hinders systems engineering. Therefore, the design of more sophisticated, multi-component protein systems appears to lag behind, in particular, when compared to the engineering of gene regulatory networks. Yet, synthetic biologists have started to tinker with the information flow through natural signaling networks or integrated protein switches. A successful strategy common to most of these experiments is their focus on modular interactions between protein domains or domains and peptide motifs. Such modular interaction swapping has rewired signaling in yeast, put mammalian cell morphology under the control of light, or increased the flux through a synthetic metabolic pathway. Based on this experience, we outline an engineering framework for the connection of reusable protein interaction devices into self-sufficient circuits. Such a framework should help to ‘refacture’ protein complexity into well-defined exchangeable devices for predictive engineering. We review the foundations and initial success stories of protein synthetic biology and discuss the challenges and promises on the way from protein- to protein systems design.

Scaffold proteins and immune-cell signalling

Over the past 20 years great progress has been made in defining most of the key signalling pathways that functionally regulate immune cells. Recently, it has become clear that scaffold proteins have a crucial role in regulating many of these signalling cascades. By binding two or more components of a signalling pathway, scaffold proteins can help to localize signalling molecules to a specific part of the cell or to enhance the efficacy of a signalling pathway. Scaffold proteins can also affect the thresholds and the dynamics of signalling reactions by coordinating positive and negative feedback signals. In this Review, we focus on recent progress in the understanding of the function of scaffold proteins in immune cells.

Membrane localization of scaffold proteins promotes graded signaling in the yeast MAP kinase cascade

BACKGROUND

Signaling through mitogen-activated protein kinase (MAPK) cascade pathways can show various input-output behaviors, including either switch-like or graded responses to increasing levels of stimulus. Prior studies suggest that switch-like behavior is promoted by positive feedback loops and nonprocessive phosphorylation reactions, but it is unclear whether graded signaling is a default behavior or whether it must be enforced by separate mechanisms. It has been hypothesized that scaffold proteins promote graded behavior.

RESULTS

Here, we experimentally probe the determinants of graded signaling in the yeast mating MAPK pathway. We find that graded behavior is robust in that it resists perturbation by loss of several negative-feedback regulators. However, the pathway becomes switch-like when activated by a crosstalk stimulus that bypasses multiple upstream components. To dissect the contributing factors, we developed a method for gradually varying the signal input at different pathway steps in vivo. Input at the beginning of the kinase cascade produced a sharp, threshold-like response. Surprisingly, the scaffold protein Ste5 increased this threshold behavior when limited to the cytosol. However, signaling remained graded whenever Ste5 was allowed to function at the plasma membrane.

CONCLUSIONS

The results suggest that the MAPK cascade module is inherently ultrasensitive but is converted to a graded system by the pathway-specific activation mechanism. Scaffold-mediated assembly of signaling complexes at the plasma membrane allows faithful propagation of weak signals, which consequently reduces pathway ultrasensitivity. These properties help shape the input-output properties of the system to fit the physiological context.