The role of transcription factor B in transcription initiation and promoter clearance in the archaeon Sulfolobus acidocaldarius

Mechanisms of transcription initiation appear to be remarkably conserved between archaea and eucaryotes, For instance, there is homology between archaeal and eucaryotic basal transcription factors. Also, the archaeal RNA polymerase (RNAP) resembles eucaryotic nuclear RNAPs in subunit composition and at the amino acid sequence level. Here, we examine the role of transcription factor B, the archaeal homologue of eucaryotic transcription factor IIB, in transcription initiation. We show that the N-terminal region of transcription factor B is required for RNAP recruitment. Furthermore, we reveal that mutation of a conserved residue immediately C-terminal of the N-terminal zinc ribbon motif abrogates transcription on certain promoters. Finally, we identify the promoter sequences responsive to this mutation and demonstrate that the effect of the mutation is to block a late stage in transcription initiation, following formation of the promoter open complex.