Repression by Cyclic AMP Receptor Protein at a Distance

ABSTRACT In a previous study of promoters dependent on the Escherichia coli cyclic AMP receptor protein (CRP), carrying tan-demDNA sites for CRP, we found that the upstream-bound CRP could either enhance or repress transcription, depending on its location. Here, we have analyzed the interactions between CRP and the C-terminal domains of the RNA polymerase subunits at some of these promoters. We report that the upstream-bound CRP interacts with these domains irrespective of whether it up-or downregulates promoter activity. Hence, disruption of this interaction can lead to either down- or upregulation, depending on its location. IMPORTANCE Many bacterial promoters carry multiple DNA sites for transcription factors. While most factors that downregulate promoter activity bind to targets that overlap or are downstream of the transcription start and10 element, very few cases of repression from upstream locations have been reported. Since more Escherichia coli promoters are regulated by cyclic AMP re-ceptor protein (CRP) than by any other transcription factor, and since multiple DNA sites for CRP are commonplace at promot-ers, our results suggest that promoter downregulation by transcription factors may be more prevalent than hitherto thought, and this will have implications for the annotation of promoters from new bacterial genome sequences