Figure 9. Surprises in class II regulation by CRP.

(A) Regulation by CRP centered at −41.5 bp was assayed using an allelic series of RNAP binding sites that have variant −10 elements (gradient). (B) The observed allelic manifold plateaus at the value of $t_{\mathrm{sat}}=15.1$ a.u. (dashed lines) determined for Figure 5B, thus indicating no detectable acceleration by CRP. This lack of acceleration is at odds with prior in vitro studies (Niu et al., 1996; Rhodius et al., 1997). (C) Regulation by CRP centered at −40.5 bp was assayed in an analogous manner. (D) Unexpectedly, data from the promoters in panel C do not collapse to a 1D allelic manifold. This finding falsifies the biophysical models in Figures 4A and 7B and indicates that CRP can either activate or repress transcription from this position, depending on as-yet-unidentified features of the RNAP binding site. Error bars in panel D indicate 95% confidence intervals estimated from replicate experiments.