In the wild-type phage λ, binding of CI to OR2 helps polymerase bound to PRm transition from a closed to open complex. Activators on other promoters increase the polymerase-DNA binding energy, or affect both the binding energy and the closed- open transition probability. Using a validated mathematical model, we show that these two modes of upregulation have very different effects on the promoter function. We predict that if CI2 bound to OR2 produced equal increase in RNAP-DNA binding constant (compared to wild-type increase in the closed-open transition probability), the lysogen would be significantly less stable.
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