ArticleProceedings of the National Academy of Sciences of the United States of America2007
Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by Escherichia coli RNA polymerase.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed.
- Recent advances in mycobacterial transcription: insights beyond the general pathway.Journal of bacteriology · 2025Review
- Structurally distinct manganese-sensing riboswitch aptamers regulate different expression platform architectures.Nucleic acids research · 2025Article
- 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
- Automated model-predictive design of synthetic promoters to control transcriptional profiles in bacteria.Nature communications · 2022Article
- Quantitative parameters of bacterial RNA polymerase open-complex formation, stabilization and disruption on a consensus promoter.Nucleic acids research · 2022Article
- Auxotrophic and prototrophic conditional genetic networks reveal the rewiring of transcription factors in Escherichia coli.Nature communications · 2022Article
- Article
- 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
- The Impact of Leadered and Leaderless Gene Structures on Translation Efficiency, Transcript Stability, and Predicted Transcription Rates in Mycobacterium smegmatis.Journal of bacteriology · 2020Article
- Recent Advances in Understanding σ70-Dependent Transcription Initiation Mechanisms.Journal of molecular biology · 2019Review
- Distinct Modes of Promoter Recognition by Two Iron Starvation σ Factors with Overlapping Promoter Specificities.Journal of bacteriology · 2019Article
- Kinetic Basis of the Bifunctionality of SsoII DNA Methyltransferase.Molecules (Basel, Switzerland) · 2018Article
- Conformational heterogeneity and bubble dynamics in single bacterial transcription initiation complexes.Nucleic acids research · 2018Article
- Article
- Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation.Molecular cell · 2017Article
- RNA polymerase motions during promoter melting.Science (New York, N.Y.) · 2017Article
- RNA polymerase gate loop guides the nontemplate DNA strand in transcription complexes.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Local and global regulation of transcription initiation in bacteria.Nature reviews. Microbiology · 2016Review
Corrections and comments
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Authors and funding
5 authors.
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Abstract
The architecture of cellular RNA polymerases (RNAPs) dictates that transcription can begin only after promoter DNA bends into a deep channel and the start site nucleotide (+1) binds in the active site located on the channel floor. Formation of this transcriptionally competent "open" complex (RP(o)) by Escherichia coli RNAP at the lambdaP(R) promoter is greatly accelerated by DNA upstream of base pair -47 (with respect to +1). Here we report real-time hydroxyl radical (*OH) and potassium permanganate (KMnO4) footprints obtained under conditions selected for optimal characterization of the first kinetically significant intermediate (I(1)) in RP(o) formation. .OH footprints reveal that the DNA backbone from -71 to -81 is engulfed by RNAP in I(1) but not in RP(o); downstream protection extends to approximately +20 in both complexes. KMnO4 footprinting detects solvent-accessible thymine bases in RP(o), but not in I(1). We conclude that upstream DNA wraps more extensively on RNAP in I(1) than in RP(o) and that downstream DNA (-11 to +20) occupies the active-site channel in I(1) but is not yet melted. Mapping of the footprinting data onto available x-ray structures provides a detailed model of a kinetic intermediate in bacterial transcription initiation and suggests how transient contacts with upstream DNA in I(1) might rearrange the channel to favor entry of downstream duplex DNA.
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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.