Spacing requirements for Class I transcription activation in bacteria are set by promoter elements

Abstract

The Escherichia coli cAMP receptor protein (CRP) activates transcription initiation at many promoters by binding upstream of core promoter elements and interacting with the C-terminal domain of the RNA polymerase α subunit. Previous studies have shown stringent spacing is required for transcription activation by CRP. Here we report that this stringency can be altered by the nature of different promoter elements at target promoters. Several series of CRP-dependent promoters were constructed with CRP moved to different upstream locations, and their activities were measured. The results show that (i) a full UP element, located immediately downstream of the DNA site for CRP, relaxes the spacing requirements for activation and increases the recruitment of RNAP and open complex formation; (ii) the distal UP subsite plays the key role in this relaxation; (iii) modification of the extended -10 element also affects the spacing requirements for CRP-dependent activation. From these results, we conclude that the spacing requirements for CRP-dependent transcription activation vary according to the sequence of different promoter elements, and our results are important for understanding the organization of promoters in many different bacteria which are controlled by transcription factors that use activatory mechanisms similar to CRP. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.