Visualization of two architectures in class-II CAP-dependent transcription activation

Abstract

Transcription activation by cyclic AMP receptor protein (CAP) is the classic paradigm of transcription regulation in bacteria. CAP was suggested to activate transcription on class-II promoters via a recruitment and isomerization mechanism. However, whether and how it modifies RNA polymerase (RNAP) to initiate transcription remains unclear. Here we report cryo-EM structures of an intact E. coli class-II CAP-dependent transcription activation complex (TAC) with and without de novo RNA transcript. The structures reveal two distinct architectures of TAC and show that CAP-binding induces substantial conformational changes in all the subunits of RNAP and consequently widens the main cleft of RNAP considerably to facilitate DNA promoter entering and formation of initiation open complex. These structural changes vanish during further RNA transcript synthesis. The observations in this study suggest a unique activation mechanism on class-II promoters that CAP activates transcription by first remodeling RNAP conformation and then stabilizing initiation complex.