Key Concepts and Challenges in Archaeal Transcription

Abstract

Transcription is enabled by RNA polymerase and general factors that allow its progress through the transcription cycle by facilitating initiation, elongation and termination. The transitions between specific stages of the transcription cycle provide opportunities for the global and gene-specific regulation of gene expression. The exact mechanisms and the extent to which the different steps of transcription are exploited for regulation vary between the domains of life, individual species and transcription units. Yet, a surprising degree of conservation is apparent.Similar key steps in the transcription cycle can be targeted by homologous or unrelated factors providing insights into the mechanisms of RNAP and the evolution of the transcription machinery. Archaea are bona fide prokaryotes but employ a eukaryote-like transcription system to express the information of bacteria-like genomes. Thus, archaea not only provide the means to study transcription mechanisms of interesting model systems, but also to test key concepts of regulation in this arena. In this review, we discuss key principles of archaeal transcription, new questions that still await experimental investigation, and how novel integrative approaches hold great promise to fill this gap in our knowledge.

Evolution of Regulated Transcription

“…Bacterial RNAP initiates transcription without the involvement of additional factors with the exception of the σ factor, whereas archaeal RNAP requires a minimal set of GTFs, TBP, and TFB. The archaeal core promoter has minimal structural differences from the eukaryotic core promoter [ 145 ]. The GTFs of archaea and eukaryotes (TFB/TFIIB, TFE/TFIIE, and MBF1) share no similarity between each other and with bacterial σ factors beyond the presence of distinct DNA binding domains (DBDs).…”

Discovery of 20 novel ribosomal leaders in bacteria and archaea

“…The four r-leader motifs in Archaea represent a significant increase in the number of known cisregulatory RNAs in these organisms. Archaea share many characteristics of both eukaryotes and bacteria [47]. The novel r-leaders present rare opportunities to learn about how cis-regulation works at the RNA level in Archaea, and, by extension, how transcription and translation processes may be coopted for use in regulation.…”

“…Three, which are expected to bind the S15 or eL15 proteins, were discussed above. We noticed some poly-U stretches immediately after S15 r-leaders in Methanomicrobia (Additional files 2 and 3) that could correspond to intrinsic termination signals, which are still not well understood in archaea [46,47]. The fourth archaeal rleader appears upstream of operons containing the L4 r-protein (Additional file 1: Figure S2, Additional file 1: Supplementary text), which is the ligand of a previously established r-leader in bacteria [7].…”

aCPSF1 controlled archaeal transcription termination: a prototypical eukaryotic model

“…However, little is known about transcription termination in Archaea 1, 13 , the third domain of life. Archaea are thought to represent ancient earth life and possess eukaryotic-like genetic information processing systems to express bacteria-like genomic information 1, 14 . Particularly, they employ the eukaryotic RNAP II orthologs, archaeal RNAP (aRNAP) 15 , but have compact genomes with short intergenic-regions (IGRs) and polycistronic operons usually co-transcribed.…”

“…However, general transcription termination factors have not been discovered in Archaea thus far 1, 13, 18 . Although Eta was reported to release stalled TECs from damaged DNA sites in Thermococcus kodakarensis 18 , it functions specially in DNA damage response 1, 14, 18 .…”