Archaeal basal transcription factors: DNA and protein interactions

The archaeal basal transcription system is a stripped-down model of the complex eucaryal one, having only one RNA polymerase and two known and characterized basal factors: Transcription Factor B (TFB) and TATA-Binding Protein (TBP). After the first sequence analysis of an archaeal genome (Bult et al., 1996), transcription in Archaea became a more attractive territory to explore since there were no other clear homologs of basal transcription factors in the genome leaving a lot of open questions regarding gene expression. This work utilizes the TFB and TBP proteins from thermophilic and mesophilic archaeal species to determine the affinity of this basal factors towards different promoters in order to gain insights into the mechanism of differential gene expression. These experiments lead to the conclusion that TBP alone does not play a role in favoring transcription from different classes of genes through DNA contacts in the promoter region. Hence, other proteins and/or DNA elements would be required to favor the recruitment of the archaeal RNA polymerase to one gene class promoter over the other. The other part of this work focused in the search of proteins interacting with TFB and TBP using the yeast two-hybrid system. Screening for interactors with TBP and TFB from mesophilic species lead to the identification of proteins interacting with these basal factors. These included previously unreported TFB interactions with RNA polymerase subunits D and A′ (bacterial α and β ′ homologues respectively). These interactions lead to a transcription initiation model in which TFB plays an important role in transcription directionality determination and a possible role on start site selection.