Σ38-dependent promoter-proximal pausing by bacterial RNA polymerase

Abstract

Transcription initiation by bacterial RNA polymerase (RNAP) requires a variable subunit that directs it to promoters for site-specific priming of RNA synthesis. The principal subunit responsible for expression of house-keeping genes can bind the transcription elongation complex after initiation and induce RNAP pausing through specific interactions with promoterlike motifs in transcribed DNA. We show that the stationary phase and stress response38 subunit can also induce pausing by Escherichia coli RNAP on DNA templates containing promoter-like motifs in the transcribed regions. The pausing depends on38 contacts with the DNA template and RNAP core enzyme and results in formation of backtracked transcription elongation complexes, which can be reactivated by Gre factors that induce RNA cleavage by RNAP. Our data suggest that38 can bind the transcription elongation complex in trans but likely acts in cis during transcription initiation, by staying bound to RNAP and recognizing promoter-proximal pause signals. Analysis of38-dependent promoters reveals that a substantial fraction of them contain potential pause-inducingmotifs, suggesting that38-depended pausing may be a common phenomenon in bacterial transcription.