The Escherichia coli RNA polymerase a subunit linker: length requirements for transcription activation at CRP-dependent promoters

The C-terminal domain of the Escherichia coli RNA polymerase alpha subunit (alpha CTD) plays a key role in transcription initiation at many activator- dependent promoters. This domain is connected to the N-terminal domain by a n unstructured linker, which is proposed to confer a high degree of mobilit y on alpha CTD. To investigate the role of this linker in transcription act ivation we tested the effect of altering the linker length on promoters dep endent on the cyclic AMP receptor protein (CRP). Short deletions within the a linker decrease CRP-dependent transcription at a Class I promoter while increasing the activity of a Class II promoter. Linker extension impairs CR P-dependent transcription from both promoters, with short extensions exerti ng a more marked effect on the Class II promoter. Activation at both classe s of promoter was shown to remain dependent upon activating region 1 of CRP . These results show that the response to CRP of RNA polymerase containing linker-modified a subunits is class specific. These observations have impor tant implications for the architecture of transcription initiation complexe s at CRP-dependent promoters.