ArticleProceedings of the National Academy of Sciences of the United States of America2005
Sequence-independent upstream DNA-alphaCTD interactions strongly stimulate Escherichia coli RNA polymerase-lacUV5 promoter association.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed, 80 citations in OpenAlex.
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- Automated model-predictive design of synthetic promoters to control transcriptional profiles in bacteria.Nature communications · 2022Article
- Some novel features of strong promoters discovered in Cytophaga hutchinsonii.Applied microbiology and biotechnology · 2022Article
- Real-Time Single-Molecule Studies of RNA Polymerase-Promoter Open Complex Formation Reveal Substantial Heterogeneity Along the Promoter-Opening Pathway.Journal of molecular biology · 2022Article
- Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins.Molecular cell · 2021Article
- The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation.Journal of bacteriology · 2021Review
- The RNA Polymerase α Subunit Recognizes the DNA Shape of the Upstream Promoter Element.Biochemistry · 2020Article
- The Phage-EncodedViruses · 2020Article
- Fluorescence-Detected Conformational Changes in Duplex DNA in Open Complex Formation byBiochemistry · 2020Article
- Stepwise Promoter Melting by Bacterial RNA Polymerase.Molecular cell · 2020Article
- Design and synthesis of synthetic UP elements for modulation of gene expression inSynthetic and systems biotechnology · 2019Article
- Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria.Nature communications · 2018Article
- Conformational heterogeneity and bubble dynamics in single bacterial transcription initiation complexes.Nucleic acids research · 2018Article
- Study of in vitro transcriptional binding effects and noise using constitutive promoters combined with UP element sequences inJournal of biological engineering · 2017Article
- Fluorescence Resonance Energy Transfer Characterization of DNA Wrapping in Closed and Open Escherichia coli RNA Polymerase-λP(R) Promoter Complexes.Biochemistry · 2016Article
- Initial events in bacterial transcription initiation.Biomolecules · 2015Review
- Sequence elements upstream of the core promoter are necessary for full transcription of the capsule gene operon in Streptococcus pneumoniae strain D39.Infection and immunity · 2015Article
- Phage-encoded inhibitor of Staphylococcus aureus transcription exerts context-dependent effects on promoter function in a modified Escherichia coli-based transcription system.Journal of bacteriology · 2013Article
- Role of cis-acting sites in stimulation of the phage λ P(RM) promoter by CI-mediated looping.Journal of bacteriology · 2013Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The C-terminal domains of the two alpha-subunits (alphaCTD) in Escherichia coli RNA polymerase (RNAP) recognize specific sequences called UP elements in some promoters. These interactions can increase transcription dramatically. Previously, effects of upstream DNA-alphaCTD interactions on transcription were quantified relative to control promoters with nonspecific DNA sequences substituted for UP elements. However, contributions of nonspecific upstream DNA-alphaCTD interactions to promoter activity have not been evaluated extensively. Here, we examine effects of removal of alphaCTD, upstream promoter DNA, or both on the rate of open-complex formation with promoters that lack UP elements. Deletion of alphaCTD decreased the composite second-order association rate constant, k(a), of RNAP for the lacUV5 promoter by approximately 10-fold. Much of this effect was attributable to a decrease in the isomerization rate constant, k(2). Removal of promoter DNA upstream of the -35 element also decreased both k(a) and k(2) approximately 10-fold. Upstream DNA extending approximately to base pair -100 was sufficient for maximal association rates of wild-type RNAP with lacUV5 promoter fragments. The alphaCTD and upstream DNA did not affect dissociation rates from the open complex. We suggest that sequence-independent upstream DNA interactions with alphaCTD are major contributors to initiation at many (or all) promoters (not merely promoters containing UP elements) and that these interactions facilitate isomerization events occurring well downstream of the alpha-binding sites. In addition to highlighting the functional importance of nonspecific protein-DNA interactions, these results suggest also that UP element-alphaCTD interactions play an even larger role in transcription initiation than appreciated previously.
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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.