ArticleBiochemistry2012
Key roles of the downstream mobile jaw of Escherichia coli RNA polymerase in transcription initiation.
Article in Biochemistry, 2012. 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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Who cites it
19 citing papers in PubMed, 31 citations in OpenAlex.
- Architecture of the spinach plastid-encoded RNA polymerase.Nature communications · 2024Article
- Step-by-Step Regulation of Productive and Abortive Transcription Initiation by Pyrophosphorolysis.Journal of molecular biology · 2022Article
- Structural origins ofProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Temperature effects on RNA polymerase initiation kinetics reveal which open complex initiates and that bubble collapse is stepwise.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation.Journal of bacteriology · 2021Review
- Fluorescence-Detected Conformational Changes in Duplex DNA in Open Complex Formation byBiochemistry · 2020Article
- Recent Advances in Understanding σ70-Dependent Transcription Initiation Mechanisms.Journal of molecular biology · 2019Review
- Conformational heterogeneity and bubble dynamics in single bacterial transcription initiation complexes.Nucleic acids research · 2018Article
- Mechanism of transcription initiation and promoter escape byProceedings of the National Academy of Sciences of the United States of America · 2017Article
- Fluorescence Resonance Energy Transfer Characterization of DNA Wrapping in Closed and Open Escherichia coli RNA Polymerase-λP(R) Promoter Complexes.Biochemistry · 2016Article
- RNA polymerase molecular beacon as tool for studies of RNA polymerase-promoter interactions.Methods (San Diego, Calif.) · 2015Review
- Crosslink Mapping at Amino Acid-Base Resolution Reveals the Path of Scrunched DNA in Initial Transcribing Complexes.Molecular cell · 2015Article
- E. coli RNA Polymerase Determinants of Open Complex Lifetime and Structure.Journal of molecular biology · 2015Article
- Initial events in bacterial transcription initiation.Biomolecules · 2015Review
- Using solutes and kinetics to probe large conformational changes in the steps of transcription initiation.Methods in molecular biology (Clifton, N.J.) · 2015Article
- Coupling of downstream RNA polymerase-promoter interactions with formation of catalytically competent transcription initiation complex.Journal of molecular biology · 2014Article
- Probing the protein-folding mechanism using denaturant and temperature effects on rate constants.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- RNA polymerase: in search of promoters.Annals of the New York Academy of Sciences · 2013Review
- Quantifying functional group interactions that determine urea effects on nucleic acid helix formation.Journal of the American Chemical Society · 2013Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
Abstract
Differences in kinetics of transcription initiation by RNA polymerase (RNAP) at different promoters tailor the pattern of gene expression to cellular needs. After initial binding, large conformational changes occur in promoter DNA and RNAP to form initiation-capable complexes. To understand the mechanism and regulation of transcription initiation, the nature and sequence of these conformational changes must be determined. Escherichia coli RNAP uses binding free energy to unwind and separate 13 base pairs of λP(R) promoter DNA to form the unstable open intermediate I(2), which rapidly converts to much more stable open complexes (I(3), RP(o)). Conversion of I(2) to RP(o) involves folding/assembly of several mobile RNAP domains on downstream duplex DNA. Here, we investigate effects of a 42-residue deletion in the mobile β' jaw (ΔJAW) and truncation of promoter DNA beyond +12 (DT+12) on the steps of initiation. We find that in stable ΔJAW open complexes the downstream boundary of hydroxyl radical protection shortens by 5-10 base pairs, as compared to wild-type (WT) complexes. Dissociation kinetics of open complexes formed with ΔJAW RNAP and/or DT+12 DNA resemble those deduced for the structurally uncharacterized intermediate I(3). Overall rate constants (k(a)) for promoter binding and DNA opening by ΔJAW RNAP are much smaller than for WT RNAP. Values of k(a) for WT RNAP with DT+12 and full-length λP(R) are similar, though contributions of binding and isomerization steps differ. Hence, the jaw plays major roles both early and late in RP(o) formation, while downstream DNA functions primarily as the assembly platform after DNA opening.
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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.