A basal promoter element recognized by free RNA polymerase sigma subunit determines promoter recognition by RNA polymerase holoenzyme.

Institute of Molecular Genetics, Moscow 123182, Russia.

Molecular cell 2006 Jul 7

filter terms:

During transcription initiation by bacterial RNA polymerase, the sigma subunit recognizes the -35 and -10 promoter elements; free sigma, however, does not bind DNA. We selected ssDNA aptamers that strongly and specifically bound free sigma(A) from Thermus aquaticus. A consensus sequence, GTA(C/T)AATGGGA, was required for aptamer binding to sigma(A), with the TA(C/T)AAT segment making interactions similar to those made by the -10 promoter element (consensus sequence TATAAT) in the context of RNA polymerase holoenzyme. When in dsDNA form, the aptamers function as strong promoters for the T. aquaticus RNA polymerase sigma(A) holoenzyme. Recognition of the aptamer-based promoters depends on the downstream GGGA motif from the aptamers' common sequence, which is contacted by sigma(A) region 1.2 and directs transcription initiation even in the absence of the -35 promoter element. Thus, recognition of bacterial promoters is controlled by independent interactions of sigma with multiple basal promoter elements.

Citation

Andrey Feklistov, Nataliya Barinova, Anastasiya Sevostyanova, Ewa Heyduk, Irina Bass, Irina Vvedenskaya, Konstantin Kuznedelov, Egle Merkiene, Elena Stavrovskaya, Saulius Klimasauskas, Vadim Nikiforov, Tomasz Heyduk, Konstantin Severinov, Andrey Kulbachinskiy. A basal promoter element recognized by free RNA polymerase sigma subunit determines promoter recognition by RNA polymerase holoenzyme. Molecular cell. 2006 Jul 7;23(1):97-107