Polymerase arrest at the lambdaP(R) promoter during transcription initiation.
During transcription initiation by Escherichia 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 lambdaP(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 sigma(70) subunit. Exonuclease III footprints of the arrested complexes are backtracked compared with that of the binary complex, and KMnO(4) footprinting reveals a decrease in the melting of DNA in the promoter region. Protein footprints of the retained sigma(70) 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.
Sen
R
R
Structural Biology Center, National Institute of Genetics, Mishima, Shizuoka-ken, Japan 411-8540, USA.
Nagai
H
H
Shimamoto
N
N
D012321:DNA-Directed RNA Polymerases / Q000737:chemistry*; D011401:Promoter Regions, Genetic; D011487:Protein Conformation; D012808:Sigma Factor / Q000737:chemistry; D014158:Transcription, Genetic
D012808:Sigma Factor; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases