Specific Recognition of the -10 Promoter Element by the Free RNA Polymerase σ Subunit

• Published in: The Journal of biological chemistry 2007-07, Vol.282 (30), p.22033
• Main Authors: Anastasiya Sevostyanova, Andrey Feklistov, Nataliya Barinova, Ewa Heyduk, Irina Bass, Saulius Klimasauskas, Tomasz Heyduk, Andrey Kulbachinskiy
• Format: Article
• Language: English
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M702495200

Bacterial RNA polymerase holoenzyme relies on its σ subunit for promoter recognition and opening. In the holoenzyme, regions 2 and 4 of the σ subunit are positioned at an optimal distance to allow specific recognition of the -10 and -35 promoter elements, respectively. In free σ, the promoter binding regions are positioned closer to each other and are masked for interactions with the promoter, with σ region 1 playing a role in the masking. To analyze the DNA-binding properties of the free σ, we selected single-stranded DNA aptamers that are specific to primary σ subunits from several bacterial species, including Escherichia coli and Thermus aquaticus . The aptamers share a consensus motif, TGTAGAAT, that is similar to the extended -10 promoter. We demonstrate that recognition of this motif by σ region 2 occurs without major structural rearrangements of σ observed upon the holoenzyme formation and is not inhibited by σ regions 1 and 4. Thus, the complex process of the -10 element recognition by RNA polymerase holoenzyme can be reduced to a simple system consisting of an isolated σ subunit and a short aptamer oligonucleotide.