Transcription Regulation in Archaea

Abstract

The known diversity of metabolic strategies and physiological adaptations of archaeal species to extreme environments is extraordinary. Accurate and responsive mechanisms to ensure that gene expression patterns match the needs of the cell necessitate regulatory strategies that control the activities and output of the archaeal transcription apparatus. Archaea are reliant on a single RNA polymerase for all transcription, and many of the known regulatory mechanisms employed for archaeal transcription mimic strategies also employed for eukaryotic and bacterial species. Novel mechanisms of transcription regulation have become apparent by increasingly sophisticated in vivo and in vitro investigations of archaeal species. This review emphasizes recent progress in understanding archaeal transcription regulatory mechanisms and highlights insights gained from studies of the influence of archaeal chromatin on transcription.

FIG 1

The archaeal transcription cycle. (A) The euryarchaeal RNA polymerase crystal structure from Thermococcus kodakarensis (PDB ID no. 4QIW) is shown in a surface representation. The clamp and stalk domains are highlighted. A simplified cartoon structure of RNA polymerase is shown below this in light green; the bipartite active site and RNA exit channel are highlighted in dark green. (B) Steps in the transcription cycle. (i) RNAP is recruited to the promoter by transcription factors TFB, TFE, and TBP during transcription initiation. (ii) RNAP escapes the promoter, and early elongation begins with TFE bound to RNAP. (iii) TFE is replaced by elongation factor Spt5 during elongation. (iv) Factor-dependent termination is predicted to occur in archaea by an unknown factor. (v) Intrinsic termination sequences are characterized by a run of T's on the nontemplate strand. (vi) The transcript is released, and RNAP is recycled for another round of transcription.

FIG 2

Transcription in the context of archaeal chromatin. (A) The structure of histone A from Methothermus fervidus (PDB ID no. 1B67) is overlaid by a cartoon representation of each histone dimer with ∼60 bp of DNA wrapping the complex. (B) The crystal structure of an Alba dimer from Sulfolobus solfataricus (PDB ID no. 1H0X) bound to DNA is overlaid by a cartoon representation. (C) Transcription elongation continues in a chromatin environment. Accessibility of the TATA box and BRE is altered by localized chromatin structure.