Transcription: Mechanism and Regulation

The biochemical machinery involved in the processes of DNA replication, transcription, and translation shows a striking similarity and phylogenetic relationship to the equivalent machinery in eucarya. In particular, RNA polymerase (RNAP) and the basal transcriptional machinery of archaea share many properties with the eucaryal RNA polymerase II (RNAP II) transcription apparatus. Regulators of archaeal transcription repress initiation by preventing TFB/TBP access to the TATA-box region or RNAP recruitment to the transcription start site. The DNA-binding site of LrpA overlaps the RNAP-binding site, and DNA-bound LrpA inhibits transcription by blocking RNA polymerase recruitment. NrpR controls the transcription of the nif operon by binding cooperatively to two tandem operator sequences, OR1 and OR2, located downstream of the transcription start site. The stronger and promoter proximal NrpR-binding site (OR1) can mediate repression of nif transcription during growth on ammonia. Heat shock-induced upregulation of some TFB genes from haloarchaea and of TFB2 from Pyrococcus have been reported. In cell-free transcription reactions, the addition of the substrate (maltodextrins) of this transporter system causes TrmB to dissociate from the promoter and relieves inhibition of RNA synthesis. The lack of genetic systems in many archaea hampers analysis of transcriptional regulation in vivo. The striking similarity of the archaeal and eucaryal genetic machinery is described in this chapter.