ArticleProceedings of the National Academy of Sciences of the United States of America2010
Predicting strength and function for promoters of the Escherichia coli alternative sigma factor, sigmaE.
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 61 papers.
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Who cites it
61 citing papers in PubMed, 109 citations in OpenAlex.
- The relationship mammalian p38 with human health and its homolog Hog1 in response to environmental stresses inFrontiers in cell and developmental biology · 2025Review
- The conserved σD envelope stress response monitors multiple aspects of envelope integrity in corynebacteria.PLoS genetics · 2024Article
- Machine Learning and Deep Learning in Synthetic Biology: Key Architectures, Applications, and Challenges.ACS omega · 2024Review
- Decoding a cryptic mechanism of metronidazole resistance among globally disseminated fluoroquinolone-resistant Clostridioides difficile.Nature communications · 2023Article
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- Synthetic Biology Meets Machine Learning.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Alteration of the -35 and -10 sequences and deletion the upstream sequence of the -35 region of the promoter A1 of the phage T7 in dsDNA confirm the contribution of non-specific interactions withFrontiers in molecular biosciences · 2023Article
- Experimental promoter identification of a foodborne pathogenFrontiers in microbiology · 2023Article
- Expanding the genetic toolkit helps dissect a global stress response in the early-branching speciesProceedings of the National Academy of Sciences of the United States of America · 2022Article
- Automated model-predictive design of synthetic promoters to control transcriptional profiles in bacteria.Nature communications · 2022Article
- Promoter Architecture Differences amongmSystems · 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
- The Exploration of Novel Regulatory Relationships Drives Haloarchaeal Operon-Like Structural Dynamics over Short Evolutionary Distances.Microorganisms · 2020Article
- Predictive design of sigma factor-specific promoters.Nature communications · 2020Article
- Dynamic insights on transcription initiation and RNA processing during bacterial adaptation.RNA (New York, N.Y.) · 2020Article
- Context-dependency of synthetic minimal promoters in driving gene expression: a case study.Microbial biotechnology · 2019Article
- Multiplex transcriptional characterizations across diverse bacterial species using cell-free systems.Molecular systems biology · 2019Article
- Structures and mechanism of transcription initiation by bacterial ECF factors.Nucleic acids research · 2019Article
- Alternative Sigma Factor RpoX Is a Part of the RpoE Regulon and Plays Distinct Roles in Stress Responses, Motility, Biofilm Formation, and Hemolytic Activities in the Marine Pathogen Vibrio alginolyticus.Applied and environmental microbiology · 2019Article
1 more citing papers are in PubMed but not listed here.
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2 authors at 1 institution in 1 country.
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Abstract
Sequenced bacterial genomes provide a wealth of information but little understanding of transcriptional regulatory circuits largely because accurate prediction of promoters is difficult. We examined two important issues for accurate promoter prediction: (1) the ability to predict promoter strength and (2) the sequence properties that distinguish between active and weak/inactive promoters. We addressed promoter prediction using natural core promoters recognized by the well-studied alternative sigma factor, Escherichia coli sigma(E), as a representative of group 4 sigmas, the largest sigma group. To evaluate the contribution of sequence to promoter strength and function, we used modular position weight matrix models comprised of each promoter motif and a penalty score for suboptimal motif location. We find that a combination of select modules is moderately predictive of promoter strength and that imposing minimal motif scores distinguished active from weak/inactive promoters. The combined -35/-10 score is the most important predictor of activity. Our models also identified key sequence features associated with active promoters. A conserved "AAC" motif in the -35 region is likely to be a general predictor of function for promoters recognized by group 4 sigmas. These results provide valuable insights into sequences that govern promoter strength, distinguish active and inactive promoters for the first time, and are applicable to both in vivo and in vitro measures of promoter strength.
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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.