ArticleJournal of molecular biology2009
Evidence for a tyrosine-adenine stacking interaction and for a short-lived open intermediate subsequent to initial binding of Escherichia coli RNA polymerase to promoter DNA.
Article in Journal of molecular biology, 2009. 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.
- Recent advances in mycobacterial transcription: insights beyond the general pathway.Journal of bacteriology · 2025Review
- 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
- Pseudomonas aeruginosa SutA wedges RNAP lobe domain open to facilitate promoter DNA unwinding.Nature communications · 2022Article
- F/YGG-motif is an intrinsically disordered nucleic-acid binding motif.RNA biology · 2022Article
- The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation.Journal of bacteriology · 2021Review
- Recent Advances in Understanding σ70-Dependent Transcription Initiation Mechanisms.Journal of molecular biology · 2019Review
- Structures and mechanism of transcription initiation by bacterial ECF factors.Nucleic acids research · 2019Article
- Conformational heterogeneity and bubble dynamics in single bacterial transcription initiation complexes.Nucleic acids research · 2018Article
- Inter-sigmulon communication through topological promoter coupling.Nucleic acids research · 2016Article
- RNA polymerase molecular beacon as tool for studies of RNA polymerase-promoter interactions.Methods (San Diego, Calif.) · 2015Review
- Article
- Initial events in bacterial transcription initiation.Biomolecules · 2015Review
- Base flipping in open complex formation at bacterial promoters.Biomolecules · 2015Review
- Differential role of base pairs on gal promoters strength.Journal of molecular biology · 2015Article
- Next generation sequencing-based parallel analysis of melting kinetics of 4096 variants of a bacterial promoter.Biochemistry · 2014Article
- Indirect read-out of the promoter DNA by RNA polymerase in the closed complex.Nucleic acids research · 2013Article
- Distinct functions of regions 1.1 and 1.2 of RNA polymerase σ subunits from Escherichia coli and Thermus aquaticus in transcription initiation.The Journal of biological chemistry · 2012Article
- Predicting the strength of UP-elements and full-length E. coli σE promoters.Nucleic acids research · 2012Article
- Structural basis for promoter-10 element recognition by the bacterial RNA polymerase σ subunit.Cell · 2011Article
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Authors and funding
6 authors.
Funding
Abstract
Bacterial RNA polymerase and a "sigma" transcription factor form an initiation-competent "open" complex at a promoter by disruption of about 14 base pairs. Strand separation is likely initiated at the highly conserved -11 A-T base pair. Amino acids in conserved region 2.3 of the main Escherichia coli sigma factor, sigma(70), are involved in this process, but their roles are unclear. To monitor the fates of particular bases upon addition of RNA polymerase, promoters bearing single substitutions of the fluorescent A-analog 2-aminopurine (2-AP) at -11 and two other positions in promoter DNA were examined. Evidence was obtained for an open intermediate on the pathway to open complex formation, in which these 2-APs are no longer stacked onto their neighboring bases. The tyrosine at residue 430 in region 2.3 of sigma(70) was shown to be involved in quenching the fluorescence of a 2-AP substituted at -11, presumably through a stacking interaction. These data refine the structural model for open complex formation and reveal a novel interaction involved in DNA melting by RNA 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.