title: 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 (sigma) with two DNA sequence motifs. Contacts with the upstream ('-35') promoter motif are made by sigma domain 4 attached to the flap domain of the RNAP beta 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 beta flap and represses this basal transcription. Gp33 can also repress transcription by Escherichia coli sigma70-RNAP holoenzyme mutated to allow gp33 access to the beta flap. We propose that repression is due to gp33 blocking an upstream sequence-independent DNA-binding site on RNAP (as sigma70 domain 4 does) but, unlike sigma70 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.
authors.affiliation: Division of Biological Sciences and Center for Molecular Genetics, University of California, San Diego, La Jolla, CA 92093-0634, USA. netchaev@biomail.ucsd.edu
authors.forename: Sergei
authors.initials: S
authors.lastname: Nechaev
authors.forename: E Peter
authors.initials: EP
authors.lastname: Geiduschek
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D017122:Bacteriophage T4 / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics; D020035:Holoenzymes / Q000235:genetics / Q000502:physiology; D009154:Mutation; D011401:Promoter Regions, Genetic; D017434:Protein Structure, Tertiary; D012808:Sigma Factor / Q000235:genetics*; D014158:Transcription, Genetic; D014764:Viral Proteins / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D020035:Holoenzymes; D012808:Sigma Factor; D014764:Viral Proteins; C085859:gene 33 protein, Enterobacteria phage T4; C106892:gene 55 protein, Enterobacteria phage T4; D012321:DNA-Directed RNA Polymerases