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Abstract

The discovery of the archaeal domain of life is tightly connected to an
in-depth analysis of the prokaryotic RNA world. In addition to Carl
Woese's approach to use the sequence of the 16S rRNA gene as
phylogenetic marker, the finding of Karl Stetter and Wolfram Zillig that
archaeal RNA polymerases (RNAPs) were nothing like the bacterial RNAP
but are more complex enzymes that resemble the eukaryotic RNAPII was one
of the key findings supporting the idea that archaea constitute the
third major branch on the tree of life. This breakthrough in
transcriptional research 40 years ago paved the way for in-depth studies
of the transcription machinery in archaea. However, although the
archaeal RNAP and the basal transcription factors that fine-tune the
activity of the RNAP during the transcription cycle are long known, we
still lack information concerning the architecture and dynamics of
archaeal transcription complexes. In this context, single-molecule
measurements were instrumental as they provided crucial insights into
the process of transcription initiation, the architecture of the
initiation complex and the dynamics of mobile elements of the RNAP. In
this review, we discuss single-molecule approaches suitable to examine
molecular mechanisms of transcription and highlight findings that shaped
our understanding of the archaeal transcription apparatus. We
furthermore explore the possibilities and challenges of next-generation
single-molecule techniques, for example, super-resolution microscopy and
single-molecule tracking, and ask whether these approaches will
ultimately allow us to investigate archaeal transcription in vivo. (C)
2019 Elsevier Ltd. All rights reserved.