The role of an upstream promoter interaction in initiation of bacterial transcription

Abstract

The bacterial RNA polymerase (RNAP) recognizes promoters through sequence-specific contacts of its promoter-specificity components (σ) with two DNA sequence motifs. Contacts with the upstream ('-35') promoter motif are made by σ domain 4 attached to the flap domain of the RNAP β subunit. Bacteriophage T4 late promoters consist solely of an extended downstream ('-10') motif specifically recognized by the T4 gene 55 protein (gp55). Low level basal transcription is sustained by gp55-RNAP holoenzyme. The late transcription coactivator gp33 binds to the β flap and represses this basal transcription. Gp33 can also repress transcription by Escherichia coli σ70-RNAP holoenzyme mutated to allow gp33 access to the β flap. We propose that repression is due to gp33 blocking an upstream sequence-independent DNA-binding site on RNAP (as σ70 domain 4 does) but, unlike σ70 domain 4, providing no new DNA interaction. We show that this upstream interaction is essential only at an early step of transcription initiation, and discuss the role of this interaction in promoter recognition and transcriptional regulation. © 2006 European Molecular Biology Organization | All Rights Reserved.