ArticleNucleic acids research2012
Predicting the strength of UP-elements and full-length E. coli σE promoters.
Article in Nucleic acids research, 2012. 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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Who cites it
37 citing papers in PubMed, 78 citations in OpenAlex.
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Unraveling the start element and regulatory divergence of core promoters across the domain bacteria.Nucleic acids research · 2025Article
- Physiological roles of anmBio · 2025Article
- Peering into the Bacterial Cell: From Transcription to Functional Genomics.Journal of molecular biology · 2025Review
- Engineering artificial cross-species promoters with different transcriptional strengths.Synthetic and systems biotechnology · 2025Article
- Physiological Roles of anbioRxiv : the preprint server for biology · 2024Article
- Context-dependent redesign of robust synthetic gene circuits.Trends in biotechnology · 2024Review
- Targeted mutagenesis and high-throughput screening of diversified gene and promoter libraries for isolating gain-of-function mutations.Frontiers in bioengineering and biotechnology · 2023Article
- ProD: A Tool for Predictive Design of Tailored Promoters in Escherichia coli.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems.Nature communications · 2021Article
- Insight to Gene Expression From Promoter Libraries With the Machine Learning Workflow Exp2Ipynb.Frontiers in bioinformatics · 2021Review
- Rewiring the specificity of extracytoplasmic function sigma factors.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Predictive design of sigma factor-specific promoters.Nature communications · 2020Article
- Article
- Dynamic insights on transcription initiation and RNA processing during bacterial adaptation.RNA (New York, N.Y.) · 2020Article
- Realization of Robust and Precise Regulation of Gene Expression by Multiple Sigma Recognizable Artificial Promoters.Frontiers in bioengineering and biotechnology · 2020Article
- Recent advances in genetic engineering tools based on synthetic biology.Journal of microbiology (Seoul, Korea) · 2020Review
- Design and synthesis of synthetic UP elements for modulation of gene expression inSynthetic and systems biotechnology · 2019Article
- Distinct Modes of Promoter Recognition by Two Iron Starvation σ Factors with Overlapping Promoter Specificities.Journal of bacteriology · 2019Article
- Tuning the dynamic range of bacterial promoters regulated by ligand-inducible transcription factors.Nature communications · 2018Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Predicting the location and strength of promoters from genomic sequence requires accurate sequenced-based promoter models. We present the first model of a full-length bacterial promoter, encompassing both upstream sequences (UP-elements) and core promoter modules, based on a set of 60 promoters dependent on σ(E), an alternative ECF-type σ factor. UP-element contribution, best described by the length and frequency of A- and T-tracts, in combination with a PWM-based core promoter model, accurately predicted promoter strength both in vivo and in vitro. This model also distinguished active from weak/inactive promoters. Systematic examination of promoter strength as a function of RNA polymerase (RNAP) concentration revealed that UP-element contribution varied with RNAP availability and that the σ(E) regulon is comprised of two promoter types, one of which is active only at high concentrations of RNAP. Distinct promoter types may be a general mechanism for increasing the regulatory capacity of the ECF group of alternative σ's. Our findings provide important insights into the sequence requirements for the strength and function of full-length promoters and establish guidelines for promoter prediction and for forward engineering promoters of specific strengths.
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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.