ReviewBiomolecules2015
Initial events in bacterial transcription initiation.
Review in Biomolecules, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 114 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
114 citing papers in PubMed, 189 citations in OpenAlex.
- An inducer-independent, single-plasmid CRISPR-Cas9 system for genome editing in Bacillus species.Applied microbiology and biotechnology · 2026Article
- Modular synthetic cross-kingdom promoters enable coordinated expression in Escherichia coli and Saccharomyces cerevisiae.Nucleic acids research · 2026Article
- Structural basis of pausing during transcription initiation in mycobacterium tuberculosis.Nature communications · 2026Article
- Article
- Inducible transposon mutagenesis identifies bacterial fitness determinants during infection in mice.Nature microbiology · 2025Article
- A systematic survey of TF function in E. coli suggests RNAP stabilization is a prevalent strategy for both repressors and activators.Nucleic acids research · 2025Article
- KorB switching from DNA-sliding clamp to repressor mediates long-range gene silencing in a multi-drug resistance plasmid.Nature microbiology · 2025Article
- Article
- Promoter recognition specificity of Corynebacterium glutamicum stress response sigma factors σJournal of computer-aided molecular design · 2024Article
- Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy.Nature structural & molecular biology · 2024Article
- House of CarDs: Functional insights into the transcriptional regulator CdnL.Molecular microbiology · 2024Review
- Mycobacterial HelD connects RNA polymerase recycling with transcription initiation.Nature communications · 2024Article
- Evidence for a compact σiScience · 2024Article
- Article
- Design of a tunable bacterial gene expression system using engineered σ factors.Applied and environmental microbiology · 2024Article
- Macromolecular crowding has opposite effects on two critical sub-steps of transcription initiation.FEBS letters · 2024Article
- Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy.bioRxiv : the preprint server for biology · 2024Article
- Towards a rational approach to promoter engineering: understanding the complexity of transcription initiation in prokaryotes.FEMS microbiology reviews · 2024Review
- Single-molecule visualization of twin-supercoiled domains generated during transcription.Nucleic acids research · 2024Article
- Systems-wide analysis of the ROK-family regulatory geneApplied and environmental microbiology · 2023Article
54 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Transcription initiation is a highly regulated step of gene expression. Here, we discuss the series of large conformational changes set in motion by initial specific binding of bacterial RNA polymerase (RNAP) to promoter DNA and their relevance for regulation. Bending and wrapping of the upstream duplex facilitates bending of the downstream duplex into the active site cleft, nucleating opening of 13 bp in the cleft. The rate-determining opening step, driven by binding free energy, forms an unstable open complex, probably with the template strand in the active site. At some promoters, this initial open complex is greatly stabilized by rearrangements of the discriminator region between the -10 element and +1 base of the nontemplate strand and of mobile in-cleft and downstream elements of RNAP. The rate of open complex formation is regulated by effects on the rapidly-reversible steps preceding DNA opening, while open complex lifetime is regulated by effects on the stabilization of the initial open complex. Intrinsic DNA opening-closing appears less regulated. This noncovalent mechanism and its regulation exhibit many analogies to mechanisms of enzyme catalysis.
Indexed as
Identifiers
What OpenQuestion holds
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.