Theoretical analysis of gene expression regulation by sRNAs. (A) Schematic representation of the mathematical model. The target mRNA associates with an sRNA to form a heteroduplex (pair). Molecular species and events relevant for the cyanobacterial stress response (ROSs; iron depletion; isiA and IsrR) and kinetic parameters are indicated in gray. (B) Steady-state (top) and dynamical (bottom) response to varying stimulus strength. The top graph indicates the steady-state levels of (free) sRNA (dashed-dotted line) and target mRNA (solid line), and reveals a mutually exclusive expression pattern characterized by a sharp threshold. For comparison, the gradual target mRNA dose-response curve in the absence of sRNA expression is also shown (dotted line). The bottom graph shows the response time of total target expression (i.e., sum of target and pair) as a function of the stimulus level. The solid line (upregulation) depicts the response time t₅₀ required to reach 50% of the difference between old and new steady state upon a step-like increase in the stimulus level from no stimulation to the level indicated on the x axis. Similarly, t₅₀ was also calculated for a step-like drop in the stimulus level from the value on the x axis to no stimulation (downregulation). The dotted line depicts the response time of a reference system with the same kinetic parameters, but without sRNA and is valid for both up- and downregulation. See Table S1 in Data S1 for kinetic parameters.

Experimental verification of simulated dynamical behavior (A and B) and physiological relevance (C and D). (A) Regulation by sRNAs establishes a delay in target mRNA accumulation. The time course of isiA target mRNA accumulation in response to H₂O₂ treatment was measured in wild-type cells (circles), in cells harboring reduced amounts of IsrR sRNA (squares), and in cells overexpressing IsrR sRNA (crosses). The measurements agree well with the corresponding simulations (lines; see Table 1 for kinetic parameters). (B) The decline in target mRNA (isiA) levels is faster in wild-type cells (circles) when compared to cells depleted of IsrR sRNA (squares), as expected from corresponding simulations (lines; see Table 1 for kinetic parameters). Accumulation of isiA target mRNA was induced by iron starvation (48 h), and then isiA expression was blocked by iron readdition at t = 0 (see text). (C) Regulation by sRNAs gives rise to a sharp, spike-like time course of free target mRNA in response to step-like pulse stimulation (solid line), when compared to a corresponding system without sRNA (dashed line). In particular, target mRNA accumulation is completely suppressed until all sRNA is degraded (indicated by black circle). (D) sRNAs establish pulse filtering in gene expression. Target mRNA accumulation in response to step-like stimuli of different duration (but of constant strength) was simulated, and the time course maximum or the integral similar to the hatched area in C (inset) is plotted as a function of pulse length. Highly ultrasensitive pulse duration decoding (Hill coefficient n_H ≈ 3.5) is seen in the presence (solid line) but not in the absence (dashed line) of sRNA-mediated regulation. See Table S1 in Data S1 for kinetic parameters.