Designing new cellular signaling pathways

Abstract

All cells respond to signals from the environment. Extracellular stimuli activate intracellular signal transduction pathways that make decisions about cell identity, behavior, and survival. A nascent field aims to design and construct new signaling pathways beyond those found in nature. Current strategies exploit the structural modularity of many signaling proteins, which makes them inherently amenable to domain-swapping tactics that exchange their input and output connections. The results reveal a remarkable degree of functional plasticity in signaling proteins and pathways, as well as regulatory logic that can be transported to new proteins. Modified adaptor and scaffold proteins can reroute signal traffic and adjust the response behavior of the pathway circuit. These synthetic biology approaches promise to deepen our understanding of existing signaling pathways and spur the development of new cellular tools for research, industry, and medicine.

Figure 1. Modular architecture of signaling proteins

A. Natural signaling proteins often combine a catalytic (“output”) domain with interaction domains that determine its connections. Exchanging interaction domains can create synthetic chimeras that connect to new stimuli or targets. B. Interaction domains can link output domains to activators (i), substrates (ii), or subcellular locations (iii). They can also regulate protein activity by autoinhibitory binding (iv).

Figure 2. Regulating protein activity with foreign autoinhibitory interactions

A. N-WASP stimulates the actin nucleation complex Arp2/3. The GTPase Cdc42 and the phospholipid PIP₂ activate N-WASP by relief of autoinhibition. B. The normal autoinhibitory interactions in N-WASP can be replaced with foreign sequences such as a PDZ domain and its binding peptide. (It is unclear if the foreign interactions block catalytic activity by a steric or conformational effect.) C. Regulation of Rho GEF activity with foreign autoinhibitory interactions. Phosphorylation of the target peptide by PKA disrupts PDZ binding and hence activates the GEF.

Figure 3. Adaptors, scaffolds, and pathway re-wiring

A. Adaptor proteins are intermediary linkers that allow one protein to indirectly control another protein without their direct contact; this often regulates localization (e.g., to a membrane). Scaffolds serve as signal transfer platforms by binding multiple proteins and promoting their mutual interaction. Synthetic hybrids could create new connections and pathways. B. Phosphotyrosines in the tail of activated EGF receptor bind the SH2 domain of the adaptor protein Grb2, whose linked SH3 domains lead to activation of Ras and proliferative signaling (left). The Fas receptor recruits the DD domain of the adaptor protein Fadd, whose linked DED domain leads to activation of caspases and apoptosis (middle). When a hybrid adaptor protein was constructed in which the SH2 domain from Grb2 was linked to the DED domain from Fadd (right), stimulation with EGF now led to cell death (Howard et al., 2003).

Figure 4. Controlling circuit behavior

A. Creation of an irreversible, self-perpetuating signaling circuit in a MAP kinase cascade by placing a constitutively-active form of one pathway component (KKK*) under transcriptional control of the pathway (Ingolia and Murray, 2007). B. A modified scaffold alters response dynamics in a MAP kinase cascade. Using leucine zippers to recruit new pathway regulators to the scaffold, signaling could be enhanced or dampened. Then, by placing expression of the recruited regulator under transcriptional control of the pathway itself, positive or negative feedback loops were established (Bashor et al., 2008). Several types of feedback circuit were constructed. Here, a pathway-induced positive regulator displaces a pre-existing negative regulator, creating a response that is switch-like rather than graded.