A thermostable platform for transcriptional regulation: the DNA-binding properties of two Lrp homologs from the hyperthermophilic archaeon Methanococcus jannaschii

The hyperthermophilic archaeon Methanococcus jannaschii encodes two putativ e transcription regulators, Ptr1 and Ptr2, related to the bacterial Lrp/Asn C family of transcriptional regulators. We show that these two small helix- turn-helix proteins are specific DNA-binding proteins recognizing sites in their respective promoter regions. In vitro selection at high temperature h as been used to isolate sets of high-affinity DNA sites that define a palin dromic consensus binding sequence for each protein. Ptr1 and Ptr2 bind thes e cognate sites from one side of the DNA helix, as dimers, with each protei n monomer making base-specific contacts in the major groove. As the first a rchaeal DNA-binding proteins with clearly defined specificities, Ptr1 and P tr2 provide a thermostable DNA-binding platform for analysis of effector in teractions with the core archaeal transcription apparatus; a platform allow ing manipulation of promoter structure and examination of mechanisms of act ion at heterologous promoters.