Abstract
In the process of transcription initiation, the bacterial RNA polymerase binds double-stranded (ds) promoter DNA and subsequently effects strand separation of 12 to 14 base pairs (bp), including the start site of transcription, to form the so-called “open complex” (also referred to as RPo). This complex is competent to initiate RNA synthesis. Here we will review the role of σ70 and its homologs in the strand separation process, and evidence that strand separation is initiated at the −11A (the A of the non-template strand that is 11 bp upstream from the transcription start site) of the promoter. By using the fluorescent adenine analog, 2-aminopurine, it was demonstrated that the −11A on the non-template strand flips out of the DNA helix and into a hydrophobic pocket where it stacks with tyrosine 430 of σ70. Open complexes are remarkably stable, even though in vivo, and under most experimental conditions in vitro, dsDNA is much more stable than its strand-separated form. Subsequent structural studies of other researchers have confirmed that in the open complex the −11A has flipped into a hydrophobic pocket of σ70. It was also revealed that RPo was stabilized by three additional bases of the non-template strand being flipped out of the helix and into hydrophobic pockets, further preventing re-annealing of the two complementary DNA strands.
Highlights
The bacterial transcription apparatus is simple in comparison to that of eukaryotes or archaea.There is one type of RNA polymerase (RNAP), which is referred to as the “core” RNAP
This review focuses on the mechanism of formation of the open complex, as well as its structure
In 1988, when it was not yet clear which subunits of the bacterial RNAP were involved in the strand separation process, Helmann and Chamberlin postulated in a review article that the sigma factor was the responsible subunit
Summary
The bacterial transcription apparatus is simple in comparison to that of eukaryotes or archaea. The 35 and 10 hexamers (consensus sequences TTGACA and TATAAT, respectively), which are respectively 35 base pairs (bp) and 10 bp upstream from the transcription start site, designated +1 (Figure 1). Another important region of contact is a stretch of Gs immediately downstream of the 10 hexamer. Several additional intermediate complexes form, with conformational changes in both the RNAP and the promoter, resulting in the “open complex” (RPo) In this complex 12–14 base pairs have been disrupted [11,12,13], enabling the template strand to reach the active site of the RNAP [8,14]. 4G7O coordinate set; it is likely base paired in the native promoter
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