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The effects of upstream DNA on open complex formation by Escherichia coli RNA polymerase
- Source :
- Proceedings of the National Academy of Sciences. 102:285-290
- Publication Year :
- 2004
- Publisher :
- Proceedings of the National Academy of Sciences, 2004.
-
Abstract
- Binding of activators to upstream DNA sequences regulates transcription initiation by affecting the stability of the initial RNA polymerase (RNAP)–promoter complex and/or the rate of subsequent conformational changes required to form the open complex (RP O ). Here we observe that the presence of nonspecific upstream DNA profoundly affects an early step in formation of the transcription bubble. Kinetic studies with the λP R promoter and Escherichia coli RNAP reveal that the presence of DNA upstream of base pair -47 greatly increases the rate of forming RP O , without significantly affecting its rate of dissociation. We find that this increase is largely due to an acceleration of the rate-limiting step (isomerization) in RP O formation, a step that occurs after polymerase binds. Footprinting experiments reveal striking structural differences downstream of the transcription start site (+1) in the first kinetically significant intermediate when upstream DNA is present. On the template strand, the DNase I downstream boundary of this early intermediate is +20 when upstream DNA is present but is shortened by approximately two helical turns when upstream DNA beyond -47 is removed. KMnO 4 footprinting reveals an identical initiation bubble (-11 to +2), but unusual reactivity of template strand upstream cytosines (-12, -14, and -15) on the truncated promoter. Based on this work, we propose that early wrapping interactions between upstream DNA and the polymerase exterior strongly affect the events that control entry and subsequent unwinding of the DNA start site in the jaws of polymerase.
- Subjects :
- Multidisciplinary
DNA clamp
Transcription, Genetic
biology
Base pair
DNA polymerase
Escherichia coli Proteins
DNA polymerase II
DNA
DNA-Directed RNA Polymerases
Biological Sciences
Molecular biology
Kinetics
Upstream activating sequence
Coding strand
biology.protein
Biophysics
Transcription Initiation Site
Promoter Regions, Genetic
Polymerase
Transcription bubble
Subjects
Details
- ISSN :
- 10916490 and 00278424
- Volume :
- 102
- Database :
- OpenAIRE
- Journal :
- Proceedings of the National Academy of Sciences
- Accession number :
- edsair.doi.dedup.....288dcb6989be298408f34767e0dbc6af