PROTEIN-INDUCED FIT - THE CRP ACTIVATOR PROTEIN-CHANGES SEQUENCE-SPECIFIC DNA RECOGNITION BY THE CYTR REPRESSOR, A HIGHLY FLEXIBLE LACL MEMBER

The CytR repressor and the cAMP receptor protein (CRP) bind cooperativ ely to several promoters in Escherichia coil to repress transcription initiation, The synergistic binding is mediated by protein-protein int eractions between the two regulators, Here, in vitro selection experim ents have been used to examine the DNA-binding characteristics of CytR , by itself and when co-binding with cAMP-CRP. We show that the optima l CytR-binding site consists of two octamer repeats, in direct or inve rted 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 la tter set of operators correlate well with the configurations of natura l 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 ener getically for complex formation with cAMP-CRP. We propose that this st ructural adaptability is essential for CytR repression of promoters wi th diverse architectures, We discuss these novel concepts in the conte xt of the CRP/CytR regulatory system, as well as the structural and fu nctional implications for multiprotein-DNA complex formation in genera l.