ArticleJournal of molecular biology2015
E. coli RNA Polymerase Determinants of Open Complex Lifetime and Structure.
Article in Journal of molecular biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 52 citations in OpenAlex.
- Gene syntaxes modulate gene expression and circuit behavior on plasmids.Journal of biological engineering · 2025Article
- RNA polymerase SI3 domain modulates global transcriptional pausing and pause-site fluctuations.Nucleic acids research · 2024Article
- Macromolecular crowding has opposite effects on two critical sub-steps of transcription initiation.FEBS letters · 2024Article
- An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Isolation of E. coli RNA polymerase transcription elongation complexes by selective solid-phase photoreversible immobilization.Methods in enzymology · 2023Article
- 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
- The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation.Journal of bacteriology · 2021Review
- Diverse and unified mechanisms of transcription initiation in bacteria.Nature reviews. Microbiology · 2021Review
- Steps toward translocation-independent RNA polymerase inactivation by terminator ATPase ρ.Science (New York, N.Y.) · 2021Article
- Rewiring of growth-dependent transcription regulation by a point mutation in region 1.1 of the housekeeping σ factor.Nucleic acids research · 2020Article
- Fluorescence-Detected Conformational Changes in Duplex DNA in Open Complex Formation byBiochemistry · 2020Article
- Transcription initiation in mycobacteria: a biophysical perspective.Transcription · 2020Review
- Article
- Local DNA Base Conformations and Ligand Intercalation in DNA Constructs Containing Optical Probes.Biophysical journal · 2019Article
- The dormancy-specific regulator, SutA, is intrinsically disordered and modulates transcription initiation in Pseudomonas aeruginosa.Molecular microbiology · 2019Article
- Diversity, versatility and complexity of bacterial gene regulation mechanisms: opportunities and drawbacks for applications in synthetic biology.FEMS microbiology reviews · 2019Review
- The Core and Holoenzyme Forms of RNA Polymerase fromJournal of bacteriology · 2019Article
- Delayed inhibition mechanism for secondary channel factor regulation of ribosomal RNA transcription.eLife · 2019Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
In transcription initiation by Escherichia coli RNA polymerase (RNAP), initial binding to promoter DNA triggers large conformational changes, bending downstream duplex DNA into the RNAP cleft and opening 13bp to form a short-lived open intermediate (I2). Subsequent conformational changes increase lifetimes of λPR and T7A1 open complexes (OCs) by >10(5)-fold and >10(2)-fold, respectively. OC lifetime is a target for regulation. To characterize late conformational changes, we determine effects on OC dissociation kinetics of deletions in RNAP mobile elements σ(70) region 1.1 (σ1.1), β' jaw and β' sequence insertion 3 (SI3). In very stable OC formed by the wild type WT RNAP with λPR (RPO) and by Δσ1.1 RNAP with λPR or T7A1, we conclude that downstream duplex DNA is bound to the jaw in an assembly with SI3, and bases -4 to +2 of the nontemplate strand discriminator region are stably bound in a positively charged track in the cleft. We deduce that polyanionic σ1.1 destabilizes OC by competing for binding sites in the cleft and on the jaw with the polyanionic discriminator strand and downstream duplex, respectively. Examples of σ1.1-destabilized OC are the final T7A1 OC and the λPR I3 intermediate OC. Deleting σ1.1 and either β' jaw or SI3 equalizes OC lifetimes for λPR and T7A1. DNA closing rates are similar for both promoters and all RNAP variants. We conclude that late conformational changes that stabilize OC, like early ones that bend the duplex into the cleft, are primary targets of regulation, while the intrinsic DNA opening/closing step is not.
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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.