Figure 4.

Engineering synthetic circuits for reverse engineering intracellular biochemical systems. (A) Generic pipeline of reverse engineering a protein network, starting from defining its inputs and outputs and ending up with resolving its causal topology, which explains its response properties. Experimentally, reverse engineering requires systematic perturbations of the system components and measuring their effects on each other. (B) Synthetic biology can be applied to construct intracellular circuits enabling generic, acute and flexible perturbations of the system components. (C) Left, an example of a biochemical system in which the states of the acting (i.e., active) components are defined by their conformation, interaction or post-translational modifications (PTM). The causal topology describes how the level of each acting component affects the level of the others acting components. Accordingly, perturbations applied for reverse engineering should alter the levels of the acting components either by converting their states or by depleting them.