Transcriptional activation mechanisms of the PRM promoter of λ phage

We investigate the transcriptional activity associated with the PRM promoter of λ phage. The probability for formation of a transcriptionally active (open) RNA polymerase-DNA complex is calculated by means of an equilibrium statistical-mechanical model. In particular, we study two different models of the transcriptional activation mechanism when the OR2 site is occupied by a CI dimer (typical for a lysogen) compared to the situation when OR2 is vacant: (1) transcription rate increases (wild-type mechanism) or (2) RNA polymerase becomes stronger (or weaker) bound to DNA (mutant mechanism). By applying experimental determined protein-DNA binding energies we show that these two mechanisms exhibit different characteristics when we study the activity versus CI concentration. We also show that our model may be fitted to in vivo activity data satisfactorily despite that the activated transcription rate is significantly reduced compared to the wild-type value. The model is consistent with experimental determined activities based upon mutations of CI and RNA polymerase.