ReviewJournal of bacteriology2021
The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation.
Review in Journal of bacteriology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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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.
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Who cites it
19 citing papers in PubMed, 32 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
- The divergentMicrobiology (Reading, England) · 2026Article
- Core elements play distinct roles in promoter birth and transcriptional regulation.Nature communications · 2026Article
- A unified computational framework for quantitative design and optimization of transcriptional regulation across bacterial species.Nucleic acids research · 2026Article
- Design of bacterial DNT sensors based on computational models.Nucleic acids research · 2026Article
- Synthetic promoter design in plants: integration of computational and experimental approaches.Frontiers in plant science · 2026Review
- Advanced applications of synthetic biology technology in biosynthesis of bioactive compounds from medicinal plants.Chinese herbal medicines · 2026Review
- Computational Pipeline for Targeted Integration and Variable Payload Expression in Bacteriophage Engineering.ACS synthetic biology · 2025Article
- Generating information-dense promoter sequences with optimal string packing.PLoS computational biology · 2024Article
- Regulatory properties of transcription factors with diverse mechanistic function.PLoS computational biology · 2024Article
- High-throughput, fluorescent-aptamer-based measurements of steady-state transcription rates for the Mycobacterium tuberculosis RNA polymerase.Nucleic acids research · 2023Article
- An Efficient Prephenate Dehydrogenase Gene for the Biosynthesis of L-tyrosine: Gene Mining, Sequence Analysis, and Expression Optimization.Foods (Basel, Switzerland) · 2023Article
- High-throughput, fluorescent-aptamer-based measurements of steady-state transcription rates forbioRxiv : the preprint server for biology · 2023Article
- An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Genetic engineering for enhanced production of a novel alkaline protease BSP-1 inFrontiers in bioengineering and biotechnology · 2022Article
- Quantifying the regulatory role of individual transcription factors in Escherichia coli.Cell reports · 2021Article
- Structural origins ofProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Rhodobacter sphaeroides CarD Negatively Regulates Its Own Promoter.Journal of bacteriology · 2021Article
- RNA Polymerase and Transcription Mechanisms: The Forefront of Physicochemical Studies of Chemical Reactions.Biomolecules · 2020Review
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 1 country.
Funding
Abstract
The fitness of an individual bacterial cell is highly dependent upon the temporal tuning of gene expression levels when subjected to different environmental cues. Kinetic regulation of transcription initiation is a key step in modulating the levels of transcribed genes to promote bacterial survival. The initiation phase encompasses the binding of RNA polymerase (RNAP) to promoter DNA and a series of coupled protein-DNA conformational changes prior to entry into processive elongation. The time required to complete the initiation phase can vary by orders of magnitude and is ultimately dictated by the DNA sequence of the promoter. In this review, we aim to provide the required background to understand how promoter sequence motifs may affect initiation kinetics during promoter recognition and binding, subsequent conformational changes which lead to DNA opening around the transcription start site, and promoter escape. By calculating the steady-state flux of RNA production as a function of these effects, we illustrate that the presence/absence of a consensus promoter motif cannot be used in isolation to make conclusions regarding promoter strength. Instead, the entire series of linked, sequence-dependent structural transitions must be considered holistically. Finally, we describe how individual transcription factors take advantage of the broad distribution of sequence-dependent basal kinetics to either increase or decrease RNA flux.
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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.