Identification of base pairs important for OmpR-DNA interaction

OmpR, the transcriptional regulator of the ompF and ompC porin genes, is a member of a novel class of DNA-binding proteins. The mechanism(s) by which this class of proteins interacts with target DNA sites is not understood. To address this issue, we investigated the nature of the DNA sequences recognized by OmpR. A 36 bp DNA fragment was identified that is capable of supporting OmpR-DNA interaction in vivo. The base pairs within this region of DNA that are critical to this interaction were identified by isolating mutations within the fragment that hinder normal OmpR-DNA binding. The results obtained provide insights concerning the nature of the sequences recognized by OmpR and also support a model in which co-operative binding is involved in OmpR-DNA interaction.