Figure 1. SIM architectures differ in their ability to robustly coordinate gene expression responses.

(A) The single-input module (SIM), where a regulator (R) controls multiple targets (T_i) may establish coordinated expression of all targets (synexpression) or sequential regulation if target affinities differ (prioritization). (B) Threshold of a cooperative repression model is sensitive to changes in regulator affinity. The steady state dose-response of the cooperative repression model (Eq. 1) was calculated while varying the ratio of promoter-regulator affinities α′ = K_D,2/K_D,1 (other parameters: V_max,i = 1; k_deg,i = 1; n = 3). The x-axis is normalized by the regulator concentration where the case α′ = 1 reaches 10% of maximal mRNA expression. (C) An extended cooperative repression model with regulator depletion is less sensitive to parameter alterations. The steady state dose-response of a mass-action model explicitly describing three sequential binding steps of the regulator to the two target promoters was calculated numerically (see Protocol S1 for details). This system is a generalization of the minimal cooperative repression model (Eq. 1). High affinity regulator binding to mRNAs was assumed to ensure that regulator depletion effects are significant. The x-axis is normalized by the regulator concentration where the case α′ = 1 reaches 10% of maximal mRNA expression to allow direct comparison with panel B. (D) Mathematical model for sRNA-mediated co-regulation. The mRNA species (m₁ and m₂) are controlled by reversible binding to the shared sRNA (s), giving rise to inhibitory complexes, c₁ and c₂. The monomeric species m₁, m₂ and s are constantly synthesized, and all molecular species are subject to degradation. Throughout this work we assume that the inhibitory complexes c₁ and c₂ are formed with high affinity.