ArticleThe Journal of biological chemistry2011
Interaction of Escherichia coli RNA polymerase σ70 subunit with promoter elements in the context of free σ70, RNA polymerase holoenzyme, and the β'-σ70 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 27 papers.
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Who cites it
27 citing papers in PubMed, 38 citations in OpenAlex.
- Molecular basis of Streptomyces ECF σShbA factors transcribing principal σHrdB genes.Nucleic acids research · 2025Article
- Single-stranded DNA drives σ subunit loading onto mycobacterial RNA polymerase to unlock initiation-competent conformations.Nucleic acids research · 2025Article
- DNA looping mediates cooperative transcription activation.Nature structural & molecular biology · 2024Article
- Construction of Strong Promoters by Assembling Sigma Factor Binding Motifs.Methods in molecular biology (Clifton, N.J.) · 2022Article
- CueR activates transcription through a DNA distortion mechanism.Nature chemical biology · 2021Article
- NovelViruses · 2020Article
- Defining the seed sequence of the Cas12b CRISPR-Cas effector complex.RNA biology · 2019Article
- A Thermus phage protein inhibits host RNA polymerase by preventing template DNA strand loading during open promoter complex formation.Nucleic acids research · 2018Article
- RNA polymerase motions during promoter melting.Science (New York, N.Y.) · 2017Article
- Backtracked and paused transcription initiation intermediate of Escherichia coli RNA polymerase.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- RNA polymerase molecular beacon as tool for studies of RNA polymerase-promoter interactions.Methods (San Diego, Calif.) · 2015Review
- Article
- E. coli RNA Polymerase Determinants of Open Complex Lifetime and Structure.Journal of molecular biology · 2015Article
- Initial events in bacterial transcription initiation.Biomolecules · 2015Review
- Base flipping in open complex formation at bacterial promoters.Biomolecules · 2015Review
- Using solutes and kinetics to probe large conformational changes in the steps of transcription initiation.Methods in molecular biology (Clifton, N.J.) · 2015Article
- Regulatory crosstalk between type I and type II toxin-antitoxin systems in the human pathogen Enterococcus faecalis.RNA biology · 2015Article
- 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
- Cooperativity and interaction energy threshold effects in recognition of the -10 promoter element by bacterial RNA polymerase.Nucleic acids research · 2013Article
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Authors and funding
3 authors at 1 institution in 2 countries.
Funding
Abstract
Promoter recognition by RNA polymerase is a key point in gene expression and a target of regulation. Bacterial RNA polymerase binds promoters in the form of the holoenzyme, with the σ specificity subunit being primarily responsible for promoter recognition. Free σ, however, does not recognize promoter DNA, and it has been proposed that the intrinsic DNA binding ability is masked in free σ but becomes unmasked in the holoenzyme. Here, we use a newly developed fluorescent assay to quantitatively study the interactions of free σ(70) from Escherichia coli, the β'-σ complex, and the σ(70) RNA polymerase (RNAP) holoenzyme with non-template strand of the open promoter complex transcription bubble in the context of model non-template oligonucleotides and fork junction templates. We show that σ(70), free or in the context of the holoenzyme, recognizes the -10 promoter element with the same efficiency and specificity. The result implies that there is no need to invoke a conformational change in σ for recognition of the -10 element in the single-stranded form. In the holoenzyme, weak but specific interactions of σ are increased by contacts with DNA downstream of the -10 element. We further show that region 1 of σ(70) is required for stronger interaction with non-template oligonucleotides in the holoenzyme but not in free σ. Finally, we show that binding of the β' RNAP subunit is sufficient to allow specific recognition of the TG motif of the extended -10 promoter element by σ(70). The new fluorescent assay, which we call a protein beacon assay, will be instrumental in quantitative dissection of fine details of RNAP interactions with promoters.
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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.