ArticleNucleic acids research2013
Cooperativity and interaction energy threshold effects in recognition of the -10 promoter element by bacterial RNA polymerase.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 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
10 citing papers in PubMed, 13 citations in OpenAlex.
- Development of a bacterial gene transcription activating strategy based on transcriptional activator positive feedback.Journal of advanced research · 2024Article
- The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation.Journal of bacteriology · 2021Review
- Genome-Scale Transcription-Translation Mapping Reveals Features of Zymomonas mobilis Transcription Units and Promoters.mSystems · 2020Article
- 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 molecular beacon as tool for studies of RNA polymerase-promoter interactions.Methods (San Diego, Calif.) · 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
- Coupling of downstream RNA polymerase-promoter interactions with formation of catalytically competent transcription initiation complex.Journal of molecular biology · 2014Article
- Next generation sequencing-based parallel analysis of melting kinetics of 4096 variants of a bacterial promoter.Biochemistry · 2014Article
- The whole set of constitutive promoters recognized by RNA polymerase RpoD holoenzyme of Escherichia coli.PloS one · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 2 countries.
Funding
Abstract
RNA polymerase (RNAP) melts promoter DNA to form transcription-competent open promoter complex (RPo). Interaction of the RNAP σ subunit with non-template strand bases of a conserved -10 element (consensus sequence T-12A-11T-10A-9A-8T-7) is an important source of energy-driving localized promoter melting. Here, we used an RNAP molecular beacon assay to investigate interdependencies of RNAP interactions with -10 element nucleotides. The results reveal a strong cooperation between RNAP interactions with individual -10 element non-template strand nucleotides and indicate that recognition of the -10 element bases occurs only when free energy of the overall RNAP -10 element binding reaches a certain threshold level. The threshold-like mode of the -10 element recognition may be related to the energetic cost of attaining a conformation of the -10 element that is recognizable by RNAP. The RNAP interaction with T/A-12 base pair was found to be strongly stimulated by RNAP interactions with other -10 element bases and with promoter spacer between the -10 and -35 promoter elements. The data also indicate that unmelted -10 promoter element can impair RNAP interactions with promoter DNA upstream of the -11 position. We suggest that cooperativity and threshold effects are important factors guiding the dynamics and selectivity of RPo formation.
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.