Studies on the binding of the Escherichia coli MelR transcription activator protein to operator sequences at the MelAB promoter

Escherichia coli MelR protein binds to two sites located upstream of the melAB transcription start site. Although both sites are required for optimal melibiose-dependent expression from the melAB promoter, some MelR-dependent expression is found if the upstream site is deleted or if the spacing between the two sites is altered. Gel retardation assays have been exploited to study MelR binding to a DNA fragment carrying just the upstream site. Methylation interference analysis was used to identify one guanine (at -104) which is important for MelR binding. Mutational analysis confirmed the importance of this base and revealed a second position (at -110) where mutations interfere with melAB promoter activity. Experiments using potassium permanganate as a probe suggested that the DNA sequence around -110 adopts a distorted conformation. We propose that the mutation at -104 alters MelR binding by interfering with a direct contact, whereas the mutation at -110 primarily affects DNA conformation. The binding of purified MelR protein to a melAB promoter fragment carrying both binding sites has also been studied: binding results in four retarded bands in gel assays. Methylation interference experiments have been exploited to identify the binding sites occupied in each complex. Although both binding sites share a common 18 bp sequence, MelR binding to the more upstream site is stronger. We could find no evidence for co-operative interactions between MelR and RNA polymerase and no major effects of melibiose. Some evidence for melibiose-dependent distortion in complexes between MelR and the melAB promoter is discussed.