ArticleBiophysical journal2015
Transient-State Kinetic Analysis of the RNA Polymerase I Nucleotide Incorporation Mechanism.
Article in Biophysical journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 34 citations in OpenAlex.
- TFIIS enhancement of Pol II cleavage is under kinetic control.Nucleic acids research · 2026Article
- Kinetic characterization of RNA synthesis catalyzed by the model hyperthermophilic archaeonmSphere · 2025Article
- NTPs compete in the active site of RNA polymerases I and II.Biophysical chemistry · 2024Article
- Biochemical characterization ofJournal of bacteriology · 2024Article
- Global kinetic mechanism describing single nucleotide incorporation for RNA polymerase I reveals fast UMP incorporation.Biophysical chemistry · 2024Article
- Reversible Kinetics in Multi-nucleotide Addition Catalyzed by S. cerevisiae RNA polymerase II Reveal Slow Pyrophosphate Release.Journal of molecular biology · 2024Article
- Quantifying the impact of initial RNA primer length on nucleotide addition by RNA polymerase I.Biophysical chemistry · 2024Article
- Article
- The A12.2 Subunit Plays an Integral Role in Pyrophosphate Release of RNA Polymerase I.Journal of molecular biology · 2023Article
- Frozen in time: analyzing molecular dynamics with time-resolved cryo-EM.Structure (London, England : 1993) · 2023Review
- Transient-State Kinetic Analysis of the RNA Polymerase II Nucleotide Incorporation Mechanism.Biochemistry · 2023Article
- Uncovering the mechanisms of transcription elongation by eukaryotic RNA polymerases I, II, and III.iScience · 2022Article
- Article
- RNA polymerase I (Pol I) lobe-binding subunit Rpa12.2 promotes RNA cleavage and proofreading.The Journal of biological chemistry · 2022Article
- An NTP-driven mechanism for the nucleotide addition cycle of Escherichia coli RNA polymerase during transcription.PloS one · 2022Article
- Multi-start Evolutionary Nonlinear OpTimizeR (MENOTR): A hybrid parameter optimization toolbox.Biophysical chemistry · 2021Article
- Transient-state kinetic analysis of multi-nucleotide addition catalyzed by RNA polymerase I.Biophysical journal · 2021Article
- The N-terminal domain of the A12.2 subunit stimulates RNA polymerase I transcription elongation.Biophysical journal · 2021Article
- Downstream sequence-dependent RNA cleavage and pausing by RNA polymerase I.The Journal of biological chemistry · 2020Article
- Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Eukaryotes express three or more multisubunit nuclear RNA polymerases (Pols) referred to as Pols I, II, and III, each of which synthesizes a specific subset of RNAs. Consistent with the diversity of their target genes, eukaryotic cells have evolved divergent cohorts of transcription factors and enzymatic properties for each RNA polymerase system. Over the years, many trans-acting factors that orchestrate transcription by the individual Pols have been described; however, little effort has been devoted to characterizing the molecular mechanisms of Pol I activity. To begin to address this gap in our understanding of eukaryotic gene expression, here we establish transient-state kinetic approaches to characterize the nucleotide incorporation mechanism of Pol I. We collected time courses for single turnover nucleotide incorporation reactions over a range of substrate ATP concentrations that provide information on both Pol I's nucleotide addition and nuclease activities. The data were analyzed by model-independent and model-dependent approaches, resulting in, to our knowledge, the first minimal model for the nucleotide addition pathway for Pol I. Using a grid searching approach we provide rigorous bounds on estimated values of the individual elementary rate constants within the proposed model. This work reports the most detailed analysis of Pol I mechanism to date. Furthermore, in addition to their use in transient state kinetic analyses, the computational approaches applied here are broadly applicable to global optimization problems.
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