ArticleNucleic acids research2007
Anatomy of Escherichia coli sigma70 promoters.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 139 papers.
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Who cites it
139 citing papers in PubMed, 206 citations in OpenAlex.
- The Role of torS and torT Transcription in Driving a Bet-Hedging Strategy for Trimethylamine N-Oxide Reductase Expression in Escherichia coli.Molecular microbiology · 2026Article
- A set of constitutive promoters with graded strengths for gene expression in diverse cyanobacterial strains.Applied and environmental microbiology · 2026Article
- Core elements play distinct roles in promoter birth and transcriptional regulation.Nature communications · 2026Article
- Review
- A set of constitutive promoters with graded strengths for gene expression in diverse cyanobacterial strains.bioRxiv : the preprint server for biology · 2026Article
- Cell-free genomics reveals fundamental regulatory principles of the Mycobacterium tuberculosis transcription cycle.Molecular cell · 2026Article
- Supervised clustering of bacterial promoter identifies two groups with different relevant positions at -10.Briefings in functional genomics · 2026Article
- Engineering T7 RNA polymerase-cascaded systems controlled by nisin and theophylline for protein overexpression and targeted gene mutagenesis inSynthetic and systems biotechnology · 2025Article
- Nascent RNA profiling reveals genome-wide productive reiterative initiation regulating gene transcription in bacteria.Nucleic acids research · 2025Article
- Unraveling the start element and regulatory divergence of core promoters across the domain bacteria.Nucleic acids research · 2025Article
- Deep learning guided programmable design of Escherichia coli core promoters from sequence architecture to strength control.Nucleic acids research · 2025Article
- RapA opens the RNA polymerase clamp to disrupt post-termination complexes and prevent cytotoxic R-loop formation.Nature structural & molecular biology · 2025Article
- A transcription factor from the cryptic Escherichia coli Rac prophage controls both phage and host operons.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
- Identification of novel broad host-range promoter sequences functional in diverse Pseudomonadota by a promoter-trap approach.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2024Article
- Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy.Nature structural & molecular biology · 2024Article
- A single rare σ70 variant establishes a unique gene expression pattern in the E. coli pathobiont LF82.Nucleic acids research · 2024Article
- AraC Functional Suppressors of Mutations in the C-Terminal Domain of the RpoA Subunit of theMicroorganisms · 2024Article
- Design of a tunable bacterial gene expression system using engineered σ factors.Applied and environmental microbiology · 2024Article
- Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy.bioRxiv : the preprint server for biology · 2024Article
79 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
4 authors at 2 institutions in 1 country.
Funding
Abstract
Information theory was used to build a promoter model that accounts for the -10, the -35 and the uncertainty of the gap between them on a common scale. Helical face assignment indicated that base -7, rather than -11, of the -10 may be flipping to initiate transcription. We found that the sequence conservation of sigma70 binding sites is 6.5 +/- 0.1 bits. Some promoters lack a -35 region, but have a 6.7 +/- 0.2 bit extended -10, almost the same information as the bipartite promoter. These results and similarities between the contacts in the extended -10 binding and the -35 suggest that the flexible bipartite sigma factor evolved from a simpler polymerase. Binding predicted by the bipartite model is enriched around 35 bases upstream of the translational start. This distance is the smallest 5' mRNA leader necessary for ribosome binding, suggesting that selective pressure minimizes transcript length. The promoter model was combined with models of the transcription factors Fur and Lrp to locate new promoters, to quantify promoter strengths, and to predict activation and repression. Finally, the DNA-bending proteins Fis, H-NS and IHF frequently have sites within one DNA persistence length from the -35, so bending allows distal activators to reach the polymerase.
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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.