ArticleProceedings of the National Academy of Sciences of the United States of America2010
One-step DNA melting in the RNA polymerase cleft opens the initiation bubble to form an unstable open complex.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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43 citing papers in PubMed.
- Article
- Targeting Bacterial RNA Polymerase: Harnessing Simulations and Machine Learning to Design Inhibitors for Drug-Resistant Pathogens.Biochemistry · 2025Review
- Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy.Nature structural & molecular biology · 2024Article
- Macromolecular crowding has opposite effects on two critical sub-steps of transcription initiation.FEBS letters · 2024Article
- Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy.bioRxiv : the preprint server for biology · 2024Article
- Review
- Quantitative parameters of bacterial RNA polymerase open-complex formation, stabilization and disruption on a consensus promoter.Nucleic acids research · 2022Article
- Step-by-Step Regulation of Productive and Abortive Transcription Initiation by Pyrophosphorolysis.Journal of molecular biology · 2022Article
- Structural origins ofProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Temperature effects on RNA polymerase initiation kinetics reveal which open complex initiates and that bubble collapse is stepwise.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Role of bacterial RNA polymerase gate opening dynamics in DNA loading and antibiotics inhibition elucidated by quasi-Markov State Model.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Article
- Fluorescence-Detected Conformational Changes in Duplex DNA in Open Complex Formation byBiochemistry · 2020Article
- Stepwise Promoter Melting by Bacterial RNA Polymerase.Molecular cell · 2020Article
- Mechanisms of σJournal of molecular biology · 2019Review
- Structures of Bacterial RNA Polymerase Complexes Reveal the Mechanism of DNA Loading and Transcription Initiation.Molecular cell · 2018Article
- High-throughput detection of RNA processing in bacteria.BMC genomics · 2018Article
- Conformational heterogeneity and bubble dynamics in single bacterial transcription initiation complexes.Nucleic acids research · 2018Article
- Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation.Molecular cell · 2017Article
- Mechanism of transcription initiation and promoter escape byProceedings of the National Academy of Sciences of the United States of America · 2017Article
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5 authors.
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Abstract
Though opening of the start site (+1) region of promoter DNA is required for transcription by RNA polymerase (RNAP), surprisingly little is known about how and when this occurs in the mechanism. Early events at the lambdaP(R) promoter load this region of duplex DNA into the active site cleft of Escherichia coli RNAP, forming the closed, permanganate-unreactive intermediate I(1). Conversion to the subsequent intermediate I(2) overcomes a large enthalpic barrier. Is I(2) open? Here we create a burst of I(2) by rapidly destabilizing open complexes (RP(o)) with 1.1 M NaCl. Fast footprinting reveals that thymines at positions from -11 to +2 in I(2) are permanganate-reactive, demonstrating that RNAP opens the entire initiation bubble in the cleft in a single step. Rates of decay of all observed thymine reactivities are the same as the I(2) to I(1) conversion rate determined by filter binding. In I(2), permanganate reactivity of the +1 thymine on the template (t) strand is the same as the RP(o) control, whereas nontemplate (nt) thymines are significantly less reactive than in RP(o). We propose that: (i) the +1(t) thymine is in the active site in I(2); (ii) conversion of I(2) to RP(o) repositions the nt strand in the cleft; and (iii) movements of the nt strand are coupled to the assembly and DNA binding of the downstream clamp and jaw that occurs after DNA opening and stabilizes RP(o). We hypothesize that unstable open intermediates at the lambdaP(R) promoter resemble the unstable, transcriptionally competent open complexes formed at ribosomal promoters.
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