In the deoP2 promoter of Escherichia coli, a transcription activator, cAMP–CRP, binds at two sites, centered at –41.5 and –93.5 from the start site of transcription, while a repressor, CytR, binds to a space between the two cAMP–CRP complexes. The mechanisms for the cAMP–CRP-mediated transcription activation and CytR-mediated transcription repression were investigated in vitro using purified components. We classified the deoP2 promoter as a class II cAMP–CRP-dependent promoter, primarily by the action of cAMP–CRP at the downstream site. Interestingly, we also found that deoP2 carries an ‘UP-element’ immediately upstream of the downstream cAMP–CRP site. The UP-element overlaps with the DNA site for CytR. However, it was observed that CytR functions with the RNA polymerase devoid of the C-terminal domain of the α-subunit as well as with intact RNA polymerase. The mechanism of repression by CytR proposed in this study is that the cAMP–CRP bound at –41.5 undergoes an allosteric change upon direct interaction with CytR such that it no longer maintains a productive interaction with the N-terminal domain of α, but instead acts as a repressor to interfere with RNA polymerase acting on deoP2
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