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

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Abstract
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.