Abstract
In the wild-type phage λ, binding of CI to O R2 helps polymerase bound to P RM 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 CI 2 bound to O R2 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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