Eukaryotic and archaeal tbp and tfb/tf(ii)b follow different promoter DNA bending pathways. Nucleic Acids Res

During transcription initiation, the promoter DNA is recognized and bent by the basal transcription fac-tor TATA-binding protein (TBP). Subsequent associa-tion of transcription factor B (TFB) with the TBP–DNA complex is followed by the recruitment of the ribonu-cleic acid polymerase resulting in the formation of the pre-initiation complex. TBP and TFB/TF(II)B are highly conserved in structure and function among the eukaryotic-archaeal domain but intriguingly have to operate under vastly different conditions. Employ-ing single-pair fluorescence resonance energy trans-fer, we monitored DNA bending by eukaryotic and ar-chaeal TBPs in the absence and presence of TFB in real-time. We observed that the lifetime of the TBP– DNA interaction differs significantly between the ar-chaeal and eukaryotic system. We show that the eu-karyotic DNA-TBP interaction is characterized by a linear, stepwise bending mechanism with an inter-mediate state distinguished by a distinct bending an-gle. TF(II)B specifically stabilizes the fully bent TBP– promoter DNA complex and we identify this step as a regulatory checkpoint. In contrast, the archaeal TBP–DNA interaction is extremely dynamic and TBP from the archaeal organism Sulfolobus acidocaldar-ius strictly requires TFB for DNA bending. Thus, we demonstrate that transcription initiation follows di-verse pathways on the way to the formation of the pre-initiation complex