ArticleProceedings of the National Academy of Sciences of the United States of America2015
Trigger loop folding determines transcription rate of Escherichia coli's RNA polymerase.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- RNA polymerase inhibitors reveal active-site motions essential for the nucleotide addition cycle.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- RNA polymerase inhibitors reveal active-site motions essential for the nucleotide-addition cycle.bioRxiv : the preprint server for biology · 2026Article
- Single-molecule studies reveal the off-pathway early paused state intermediates as a target of streptolydigin inhibition of RNA polymerase and its dramatic enhancement by Gre factors.Nucleic acids research · 2025Article
- Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Article
- Conserved Trigger Loop Histidine of RNA Polymerase II Functions as a Positional Catalyst Primarily through Steric Effects.Biochemistry · 2021Article
- Closing and opening of the RNA polymerase trigger loop.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- High intrinsic hydrolytic activity of cyanobacterial RNA polymerase compensates for the absence of transcription proofreading factors.Nucleic acids research · 2020Article
- Bayesian inference and comparison of stochastic transcription elongation models.PLoS computational biology · 2020Article
- The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase.Journal of molecular biology · 2019Review
- The effect of macromolecular crowding on single-round transcription by Escherichia coli RNA polymerase.Nucleic acids research · 2019Article
- Article
- Active site closure stabilizes the backtracked state of RNA polymerase.Nucleic acids research · 2018Article
- RNA-DNA and DNA-DNA base-pairing at the upstream edge of the transcription bubble regulate translocation of RNA polymerase and transcription rate.Nucleic acids research · 2018Article
- Hinge action versus grip in translocation by RNA polymerase.Transcription · 2018Article
- Trigger loop dynamics can explain stimulation of intrinsic termination by bacterial RNA polymerase without terminator hairpin contact.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- An excited state underlies gene regulation of a transcriptional riboswitch.Nature chemical biology · 2017Article
- Kinetics of nucleotide entry into RNA polymerase active site provides mechanism for efficiency and fidelity.Biochimica et biophysica acta. Gene regulatory mechanisms · 2017Article
- A structure-based kinetic model of transcription.Transcription · 2017Article
- High-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop.PLoS genetics · 2016Article
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3 authors.
Funding
Abstract
Two components of the RNA polymerase (RNAP) catalytic center, the bridge helix and the trigger loop (TL), have been linked with changes in elongation rate and pausing. Here, single molecule experiments with the WT and two TL-tip mutants of the Escherichia coli enzyme reveal that tip mutations modulate RNAP's pause-free velocity, identifying TL conformational changes as one of two rate-determining steps in elongation. Consistent with this observation, we find a direct correlation between helix propensity of the modified amino acid and pause-free velocity. Moreover, nucleotide analogs affect transcription rate, suggesting that their binding energy also influences TL folding. A kinetic model in which elongation occurs in two steps, TL folding on nucleoside triphosphate (NTP) binding followed by NTP incorporation/pyrophosphate release, quantitatively accounts for these results. The TL plays no role in pause recovery remaining unfolded during a pause. This model suggests a finely tuned mechanism that balances transcription speed and fidelity.
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