Polymerase arrest at the lambda P-R promoter during transcription initiation

During transcription initiation by Escherichia coli RNA polymerase, a fract ion 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 compl exes (Kubori, T., and Shimamoto, N, (1996) J, Mol Biol, 256, 449-457), Here we report biochemical isolation of the complexes arrested at the lambda P- R promoter and an analysis of their structure by DNA and protein footprinti ngs, We found that the isolated promoter-arrested complexes retain a stoich iometric amount of sigma(70) subunit, Exonuclease III footprints of the arr ested complexes are backtracked compared with that of the binary complex, a nd KMnO4 footprinting reveals a decrease in the melting of DNA id the promo ter region. Protein footprints of the retained sigma(70) have shown a more exposed conformation in region 3, compared with binary complexes. This feat ure is similar to that of the complexes arrested in inactive state during t ranscription elongation, indicating the existence of a common inactivating mechanism during transcription initiation and elongation. The possible invo lvement of the promoter arrest in transcriptional regulation is discussed.