ArticleProceedings of the National Academy of Sciences of the United States of America2010
Promoter melting triggered by bacterial RNA polymerase occurs in three steps.
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 37 papers.
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37 citing papers in PubMed, 72 citations in OpenAlex.
- Recent advances in mycobacterial transcription: insights beyond the general pathway.Journal of bacteriology · 2025Review
- Single-stranded DNA drives σ subunit loading onto mycobacterial RNA polymerase to unlock initiation-competent conformations.Nucleic acids research · 2025Article
- Epigenetic control of tetrapyrrole biosynthesis by m4C DNA methylation in a cyanobacterium.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Resistance mechanism of Escherichia coli strains with different ampicillin resistance levels.Applied microbiology and biotechnology · 2024Article
- Anisotropic scrunching of SMC with a baton-pass mechanism.Communications biology · 2024Review
- Coarse-Grained Models to Study Protein-DNA Interactions and Liquid-Liquid Phase Separation.Journal of chemical theory and computation · 2024Article
- Regulatory fine-tuning of mcr-1 increases bacterial fitness and stabilises antibiotic resistance in agricultural settings.The ISME journal · 2023Article
- Brewing COFFEE: A sequence-specific coarse-grained energy function for simulations of DNA-protein complexes.bioRxiv : the preprint server for biology · 2023Article
- Theory and simulations of condensin mediated loop extrusion in DNA.Nature communications · 2021Article
- Asymmetry in histone rotation in forced unwrapping and force quench rewrapping in a nucleosome.Nucleic acids research · 2021Article
- Modeling DNA Opening in the Eukaryotic Transcription Initiation Complexes via Coarse-Grained Models.Frontiers in molecular biosciences · 2021Article
- Learning the Regulatory Code of Gene Expression.Frontiers in molecular biosciences · 2021Review
- Stepwise Promoter Melting by Bacterial RNA Polymerase.Molecular cell · 2020Article
- Vitamin B and Vitamin C Affect DNA Methylation and Amino Acid Metabolism inFrontiers in microbiology · 2020Article
- Recent Advances in Understanding σ70-Dependent Transcription Initiation Mechanisms.Journal of molecular biology · 2019Review
- Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA.Journal of chemical theory and computation · 2018Article
- Forced-rupture of cell-adhesion complexes reveals abrupt switch between two brittle states.The Journal of chemical physics · 2018Article
- Studying transcription initiation by RNA polymerase with diffusion-based single-molecule fluorescence.Protein science : a publication of the Protein Society · 2017Review
- A model for genesis of transcription systems.Transcription · 2016Article
- Initial events in bacterial transcription initiation.Biomolecules · 2015Review
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3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA synthesis, carried out by DNA-dependent RNA polymerase (RNAP) in a process called transcription, involves several stages. In bacteria, transcription initiation starts with promoter recognition and binding of RNAP holoenzyme, resulting in the formation of the closed (R.P(c)) RNAP-promoter DNA complex. Subsequently, a transition to the open R.P(o) complex occurs, characterized by separation of the promoter DNA strands in an approximately 12 base-pair region to form the transcription bubble. Using coarse-grained self-organized polymer models of Thermus aquatics RNAP holoenzyme and promoter DNA complexes, we performed Brownian dynamics simulations of the R.P(c) --> R.P(o) transition. In the fast trajectories, unwinding of the promoter DNA begins by local melting around the -10 element, which is followed by sequential unzipping of DNA till the +2 site. The R.P(c) --> R.P(o) transition occurs in three steps. In step I, dsDNA melts and the nontemplate strand makes stable interactions with RNAP. In step II, DNA scrunches into RNA polymerase and the downstream base pairs sequentially open to form the transcription bubble, which results in strain build up. Subsequently, downstream dsDNA bending relieves the strain as R.P(o) forms. Entry of the dsDNA into the active-site channel of RNAP requires widening of the channel, which occurs by a swing mechanism involving transient movements of a subdomain of the beta subunit caused by steric repulsion with the DNA template strand. If premature local melting away from the -10 element occurs first then the transcription bubble formation is slow involving reformation of the opened base pairs and subsequent sequential unzipping as in the fast trajectories.
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