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. 2012 Aug 21;7(8):e42296. doi: 10.1371/journal.pone.0042296

Figure 3. Regulation by a shared sRNA synchronizes the temporal induction of mRNA expression.

Figure 3

(A) and (B) Dynamics of mRNA accumulation in response to step-like changes in both mRNA synthesis rates (A) or a step-like change in the sRNA synthesis rate (B). Time-dependent changes in the mRNA or sRNA synthesis rates (vsyn) are depicted on the top. The solid lines correspond to the sRNA circuit, while the dashed lines depict the behavior of the corresponding sRNA-less system. See Eq. 15 for model equations and Protocol S3 for kinetic parameters. (C) and (D) Synchronous temporal switching occurs mostly independent of kinetic parameters. Response time alignment in the sRNA circuit was compared to the corresponding sRNA-less system using the synchronization factor (Eq. 16). Synchronization factors smaller than unity indicate that sRNA-mediated regulation enhances synchrony in mRNA expression. Synchronization was analyzed as a function mRNA degradation rates and the relative inhibition strength of mRNAs (α″ = kon,1/kon,2). The heatmaps show simulation results for a regulatory scenario where a coordinate, step-like increase (C) or decrease (panel D) in both mRNA synthesis rates is accompanied by a step-like change in the sRNA synthesis rate in the opposite direction; this counter-regulation assumption was necessary to eliminate delay phases, and to obtain the same steady states in sRNA and sRNA-less systems. Qualitatively similar results are obtained for coordinate regulation of mRNA (but not sRNA) synthesis rates. See Eq. 15 for model equations and Protocol S3 for kinetic parameters. (E) Regulation by a shared sRNAs establishes a delay frame for mRNA induction. Multiple mRNA synthesis rates sequentially increase at different times in a step-like manner (top). Synchronous accumulation of mRNA species occurs upon depletion of the sRNA pool. Late mRNAs whose synthesis starts after the delay period respond immediately due to lack of sRNA buffer (dashed orange line). See Eq. 15 for model equations and Protocol S3 for kinetic parameters.