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 putative transcription regulators, Ptr1 and Ptr2, related to the bacterial Lrp/AsnC 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 has been used to isolate sets of high-affinity DNA sites that define a palindromic consensus binding sequence for each protein. Ptr1 and Ptr2 bind these cognate sites from one side of the DNA helix, as dimers, with each protein monomer making base-specific contacts in the major groove. As the first archaeal DNA-binding proteins with clearly defined specificities, Ptr1 and Ptr2 provide a thermostable DNA-binding platform for analysis of effector interactions with the core archaeal transcription apparatus; a platform allowing manipulation of promoter structure and examination of mechanisms of action at heterologous promoters.