Polymerase Arrest at the λP_R Promoter during Transcription Initiation*

Abstract

During transcription initiation byEscherichia coli RNA polymerase, a fraction of the homogeneous enzyme population has been kinetically shown to form two types of nonproductive complexes at some promoters: moribund complexes, which produce only abortive transcripts, and fully inactive ternary complexes (Kubori, T., and Shimamoto, N. (1996) J. Mol. Biol. 256, 449–457). Here we report biochemical isolation of the complexes arrested at the λP _R promoter and an analysis of their structure by DNA and protein footprintings. We found that the isolated promoter-arrested complexes retain a stoichiometric amount of ς⁷⁰ subunit. Exonuclease III footprints of the arrested complexes are backtracked compared with that of the binary complex, and KMnO₄ footprinting reveals a decrease in the melting of DNA in the promoter region. Protein footprints of the retained ς⁷⁰ have shown a more exposed conformation in region 3, compared with binary complexes. This feature is similar to that of the complexes arrested in inactive state during transcription elongation, indicating the existence of a common inactivating mechanism during transcription initiation and elongation. The possible involvement of the promoter arrest in transcriptional regulation is discussed.