ArticleThe Journal of biological chemistry2011
A critical role of downstream RNA polymerase-promoter interactions in the formation of initiation complex.
Article in The Journal of biological chemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- G-Quadruplex Structures in Bacteria: Biological Relevance and Potential as an Antimicrobial Target.Journal of bacteriology · 2021Review
- The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation.Journal of bacteriology · 2021Review
- Direct binding of TFEα opens DNA binding cleft of RNA polymerase.Nature communications · 2020Article
- Rewiring of growth-dependent transcription regulation by a point mutation in region 1.1 of the housekeeping σ factor.Nucleic acids research · 2020Article
- NovelViruses · 2020Article
- Mix-and-matching as a promoter recognition mechanism by ECF σ factors.BMC evolutionary biology · 2017Article
- Analysis of the leakage of gene repression by an artificial TetR-regulated promoter in cyanobacteria.BMC research notes · 2015Article
- RNA polymerase molecular beacon as tool for studies of RNA polymerase-promoter interactions.Methods (San Diego, Calif.) · 2015Review
- E. coli RNA Polymerase Determinants of Open Complex Lifetime and Structure.Journal of molecular biology · 2015Article
- Initial events in bacterial transcription initiation.Biomolecules · 2015Review
- Coupling of downstream RNA polymerase-promoter interactions with formation of catalytically competent transcription initiation complex.Journal of molecular biology · 2014Article
- Insights into the mechanism of initial transcription in Escherichia coli RNA polymerase.The Journal of biological chemistry · 2013Article
- An aromatic residue switch in enhancer-dependent bacterial RNA polymerase controls transcription intermediate complex activity.Nucleic acids research · 2013Article
- A non-bacterial transcription factor inhibits bacterial transcription by a multipronged mechanism.RNA biology · 2013Article
- RNA polymerase-promoter interactions determining different stability of the Escherichia coli and Thermus aquaticus transcription initiation complexes.Nucleic acids research · 2012Article
- Key roles of the downstream mobile jaw of Escherichia coli RNA polymerase in transcription initiation.Biochemistry · 2012Article
- Structural basis of transcription initiation.Science (New York, N.Y.) · 2012Article
- A dual switch controls bacterial enhancer-dependent transcription.Nucleic acids research · 2012Article
- Structural and mechanistic basis for the inhibition of Escherichia coli RNA polymerase by T7 Gp2.Molecular cell · 2012Article
- Molecular mechanism of transcription inhibition by phage T7 gp2 protein.Journal of molecular biology · 2011Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Nucleation of promoter melting in bacteria is coupled with RNA polymerase (RNAP) binding to a conserved -10 promoter element located at the upstream edge of the transcription bubble. The mechanism of downstream propagation of the transcription bubble to include the transcription start site is unclear. Here we introduce new model downstream fork junction promoter fragments that specifically bind RNAP and mimic the downstream segment of promoter complexes. We demonstrate that RNAP binding to downstream fork junctions is coupled with DNA melting around the transcription start point. Consequently, certain downstream fork junction probes can serve as transcription templates. Using a protein beacon fluorescent method, we identify structural determinants of affinity and transcription activity of RNAP-downstream fork junction complexes. Measurements of RNAP interaction with double-stranded promoter fragments reveal that the strength of RNAP interactions with downstream DNA plays a critical role in promoter opening and that the length of the downstream duplex must exceed a critical length for efficient formation of transcription competent open promoter complex.
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Registered trials
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.