Interactions between the Escherichia coli cAMP receptor protein and the C-terminal domain of the alpha subunit of RNA polymerase at Class I promoters

The Escherichia coli cAMP receptor protein (CRP) is a factor that activates transcription at over 100 target promoters. At Class I CRP-dependent promo ters, CRP binds immediately upstream of RNA polymerase and activates transc ription by making direct contacts with the C-terminal domain of the RNA pol ymerase alpha subunit (alpha CTD). Since alpha CTD is also known to interac t with DNA sequence elements (known as UP elements), we have constructed a series of semi-synthetic Class I CRP-dependent promoters, carrying both a c onsensus DNA-binding site for CRP and a UP element at different positions. We previously showed that, at these promoters, the CRP-dCTD interaction and the CRP-UP element interaction contribute independently and additively to transcription initiation. In this study, we show that the two halves of the UP element can function independently, and that, in the presence of the UP element, the best location for the DNA site for CRP is position -69.5. Thi s suggests that, at Class I CRP-dependent promoters where the DNA site for CRP is located at position -61.5, the two alpha CTDs of RNA polymerase are not optimally positioned. Two experiments to test this hypothesis are prese nted.