Kinetic insulation as an effective mechanism for achieving pathway specificity in intracellular signaling networks

Abstract

Intracellular signaling pathways that share common components often elicit distinct physiological responses. In most cases, the biochemical mechanisms responsible for this signal specificity remain poorly understood. Protein scaffolds and cross-inhibition have been proposed as strategies to prevent unwanted cross-talk. Here, we report a mechanism for signal specificity termed "kinetic insulation." In this approach signals are selectively transmitted through the appropriate pathway based on their temporal profile. In particular, we demonstrate how pathway architectures downstream of a common component can be designed to efficiently separate transient signals from signals that increase slowly over time. Furthermore, we demonstrate that upstream signaling proteins can generate the appropriate input to the common pathway component regardless of the temporal profile of the external stimulus. Our results suggest that multilevel signaling cascades may have evolved to modulate the temporal profile of pathway activity so that stimulus information can be efficiently encoded and transmitted while ensuring signal specificity.

Fig. 1.

Kinetic insulation. (A) Pathways A and B share the component C. The terminal kinases, KA and KB, must respond to external cues received by receptors, RA and RB, respectively. (B) Slow kinetics prevents KA from being activated by a short transient signal, whereas the adaptive nature of KB prevents its activation by a slowly varying signal. (C and D) The temporal profiles of KA (black solid lines) and KB (black dashed lines) activity when component C is exposed to a slowly increasing signals (C, gray line) and square pulse lasting 45 min (D, gray line).

Fig. 2.

System response to various input profiles. Species C is exposed to ramped inputs (Left) of various rise times and final amplitudes and square pulses (Right) of various amplitudes and durations. The gray scale indicates maximum activity level of KA (Upper) and KB (Lower) reached during the 8-h period. Black corresponds to activity levels of <10% of the total kinase abundance, and white corresponds to activity levels of >60% of the total kinase abundance.

Fig. 3.

Simple architectures designed to modulate the temporal profile of the input stimulus. (A) Architectures that transform sustained, transient, and slowly increasing inputs into a slowly increasing output signal. (B) Architectures that transform the same set of inputs into a transient signal.

Fig. 4.

A model for kinetic insulation. The upstream components of pathway A transform diverse SA input signals into a slowly varying output signal that activates kinase KA but not KB. The upstream components of pathway B transform diverse SB input signals into a transient output signal, causing the activation of kinase KB but not KA.

Fig. 5.

Response to various stimulus profiles. A–C illustrate the system's response to sustained, transient (45 min), and ramped stimulus profiles, respectively, applied to pathway A. Times series for the stimulus SA (gray lines) and activity levels of C (dashed gray lines), KA (black lines), and KB (dashed black lines) are shown. D–F illustrate the system's response to the same stimulus profiles applied to pathway B. The gray lines are times series for SB. Note that, for this case, both KA and KB reach steady state within 90 min.

Fig. 6.

Simultaneous stimulation of both pathways. (A) Application of a slowly increasing stimulus (Left, gray line) to pathway A and a square pulse lasting 45 min (Left, dashed gray line) to pathway B. Temporal profiles of the shared component C (Left, black line) and the terminal kinases KA (Right, solid line) and KB (Right, dashed line) are shown. (B) The same as in A, except the square pulse is applied to pathway B after a 1-h delay. (C) The same as in A, except the square pulse is applied after a 4-h delay. In this case, saturation of the common component C prevents signaling through pathway B.