The HMG-box mitochondrial transcription factor xl-mtTFA binds DNA as a tetramer to activate bidirectional transcription

The mitochondrial HMG-box transcription factor xl-mtTFA activates bidirectional transcription by binding to a site separating two core promoters in Xenopus laevis mitochondrial DNA (mtDNA). Three independent approaches were used to study the higher order structure of xl-mtTFA binding to this site. First, coimmunoprecipitation of differentially tagged recombinant mtTFA derivatives established that the protein exists as a multimer. Second, in vitro chemical crosslinking experiments provided evidence of cross-linked dimers, trimers and tetramers of xl-mtTFA. Finally, high resolution scanning transmission electron microscopy (STEM) established that xl-mtTFA binds to the specific promoter-proximal site predominantly as a tetramer. Computer analysis of several previously characterized binding sites for xl-mtTFA revealed a fine structure consisting of two half-sites in a symmetrical orientation. The predominant sequence of this dyad symmetry motif shows homology to binding sites of sequence-specific EMG-box-containing proteins such as Sry and Lef-1. We suggest that bidirectional activation of transcription results from the fact that binding of a tetramer of xl-mtTFA permits symmetrical interactions with other components of the transcription machinery at the adjacent core promoters.