ArticleProceedings of the National Academy of Sciences of the United States of America2005
The effects of upstream DNA on open complex formation by Escherichia coli RNA polymerase.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 59 citations in OpenAlex.
- Dynamic landscape of transcription initiation by yeast RNA polymerase I.Nucleic acids research · 2026Article
- Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy.Nature structural & molecular biology · 2024Article
- Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy.bioRxiv : the preprint server for biology · 2024Article
- Determining translocation orientations of nucleic acid helicases.Methods (San Diego, Calif.) · 2022Review
- Quantitative parameters of bacterial RNA polymerase open-complex formation, stabilization and disruption on a consensus promoter.Nucleic acids research · 2022Article
- Real-Time Single-Molecule Studies of RNA Polymerase-Promoter Open Complex Formation Reveal Substantial Heterogeneity Along the Promoter-Opening Pathway.Journal of molecular biology · 2022Article
- The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation.Journal of bacteriology · 2021Review
- Fluorescence-Detected Conformational Changes in Duplex DNA in Open Complex Formation byBiochemistry · 2020Article
- Design and synthesis of synthetic UP elements for modulation of gene expression inSynthetic and systems biotechnology · 2019Article
- Conformational heterogeneity and bubble dynamics in single bacterial transcription initiation complexes.Nucleic acids research · 2018Article
- Study of in vitro transcriptional binding effects and noise using constitutive promoters combined with UP element sequences inJournal of biological engineering · 2017Article
- Fluorescence Resonance Energy Transfer Characterization of DNA Wrapping in Closed and Open Escherichia coli RNA Polymerase-λP(R) Promoter Complexes.Biochemistry · 2016Article
- Initial events in bacterial transcription initiation.Biomolecules · 2015Review
- Phage-encoded inhibitor of Staphylococcus aureus transcription exerts context-dependent effects on promoter function in a modified Escherichia coli-based transcription system.Journal of bacteriology · 2013Article
- Role of cis-acting sites in stimulation of the phage λ P(RM) promoter by CI-mediated looping.Journal of bacteriology · 2013Article
- Key roles of the downstream mobile jaw of Escherichia coli RNA polymerase in transcription initiation.Biochemistry · 2012Article
- Predicting the strength of UP-elements and full-length E. coli σE promoters.Nucleic acids research · 2012Article
- Mechanism of bacterial transcription initiation: RNA polymerase - promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis.Journal of molecular biology · 2011Article
- One-step DNA melting in the RNA polymerase cleft opens the initiation bubble to form an unstable open complex.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
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 lambdaP(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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.