Protein-induced fit: the CRP activator protein changes sequence-specific DNA recognition by the CytR repressor, a highly flexible LacI member

Abstract

The CytR repressor and the cAMP receptor protein (CRP) bind cooperatively to several promoters in Escherichia coli to repress transcription initiation. The synergistic binding is mediated by protein-protein interactions between the two regulators. Here, in vitro selection experiments have been used to examine the DNA-binding characteristics of CytR, by itself and when co-binding with cAMP-CRP. We show that the optimal CytR-binding site consists of two octamer repeats, in direct or inverted orientation, and separated by 2 bp. However, when co-binding with cAMP-CRP, CytR instead recognizes inverted repeats separated by 10-13 bp, or direct repeats separated by 1 bp. The configurations of the latter set of operators correlate well with the configurations of natural CytR targets. Thus, cAMP-CRP induces conformational changes in CytR so that the repressor fits the natural targets. Most strikingly, CytR can adopt widely different conformations that are equally favored energetically for complex formation with cAMP-CRP. We propose that this structural adaptability is essential for CytR repression of promoters with diverse architectures. We discuss these novel concepts in the context of the CRP/CytR regulatory system, as well as the structural and functional implications for multiprotein-DNA complex formation in general.