The cAMP-CRP/CytR nucleoprotein complex in Escherichia coli: two pairs of closely linked binding sites for the cAMP-CRP activator complex are involved in combinatorial regulation of the cdd promoter.
Transcription initiation at CytR regulated promoters in Escherichia coli is controlled by a combinatorial regulatory system in which the cAMP receptor protein (CRP) functions as both an activator and a co‐repressor. By combining genetic studies and footprinting analyses, we demonstrate that regulated expression of the CytR controlled cdd promoter requires three CRP‐binding sites: a high affinity site (CRP‐1) and two overlapping low affinity sites (CRP‐2 and CRP‐3) centred at positions −41, −91 and −93, respectively. In the absence of CytR, cAMP‐CRP interacts at one set of sites (CRP‐1 and CRP‐2) and both of these binding sites are required for full promoter activation. In the presence of CytR, however, the two regulators bind cooperatively to cddP forming a nucleoprotein complex in which cAMP‐CRP binds to CRP‐1 and CRP‐3 and CytR occupies the sequence between these sites. Thus, association of the two regulators involves a repositioning of the cAMP‐CRP complex. Moreover, mutant cdd promoters in which CRP‐2 and CRP‐3 have been deleted are partially regulated by CytR, and cAMP‐CRP and CytR still bind cooperatively to these promoters. These findings provide clues to an understanding of how cAMP‐CRP and CytR interact at a structurally diverse set of promoters.