Archaeal transcription factors and their role in transcription initiation

Archaeal RNA polymerases show a weak ability in vitro to bind to promoter DNA and/or to initiate transcription with low activity independent of upstream regulatory DNA sequences. Active transcription in vitro and in vivo, however, depends strictly on a TATA box resembling the TATA box of eucaryal polII promoters. This TATA box is recognized by a polypeptide related to eucaryal TATA-binding protein (TBP) that was formerly designated aTFB. Template competition studies showed that this archaeal TATA-binding protein (aTBP) is stably sequestered at the promoter by interaction with the second archaeal transcription factor, aTFA, which is related to eucaryal transcription factor IIB (TFIIB). The association of archaeal TFIIB (aTFIIB) with the aTBP-promoter complex leads to template commitment, indicating that aTFIIB recruits archaeal RNA polymerase to the preinitiation complex. These analyses suggest the following order for assembly of transcription factors on the archaeal promoter: aTBP, aTFIIB, RNA polymerase, and provide evidence for a common molecular mechanism of transcription initiation by eucaryal RNA polymerase II and archaeal RNA polymerases. The sequence of the genes encoding aTBP and aTFIIB (TFB) showed all the characteristics conserved in their eucaryal counterparts. The degree of sequence similarity between archaeal and eucaryal transcription factors is between 27 to 35% for TFIIB and between 36 to 41% for TBP. The findings discussed here indicate that TBP and TFIIB perform analogous functions in Archaea and Eucarya and show that four essential components of archaeal and eucaryal transcriptional machineries. RNA polymerase, TATA box, TBP and TFIIB are homologous.