Towards novel amino acid-base contacts in gene regulatory proteins: AraR--a case study.

AraR is a transcription factor involved in the regulation of carbon catabolism in Bacillus subtilis. This regulator belongs to the vast GntR family of helix-turn-helix (HTH) bacterial metabolite-responsive transcription factors. In this study, AraR-DNA specific interactions were analysed by an in vitro missing-contact probing and validated using an in vivo model. We show that amino acid E30 of AraR, a highly conserved residue in GntR regulators, is indirectly responsible for the specificity of amino acid-base contacts, and that by mutating this residue it will be possible to achieve new specificities towards DNA contacts. The results highlight the importance in DNA recognition and binding of highly conserved residues across certain families of transcription factors that are located in the DNA-binding domain but not predicted to specifically contact bases on the DNA. These new findings not only contribute to a more detailed comprehension of AraR-operator interactions, but may also be useful for the establishment of a framework of rules governing protein-DNA recognition.