ArticleProceedings of the National Academy of Sciences of the United States of America2011
Templated nucleoside triphosphate binding to a noncatalytic site on RNA polymerase regulates transcription.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 19 citations in OpenAlex.
- Transcription co-inhibition alters drug resistance evolution and enhances Mycobacterium tuberculosis clearance from granulomas.Nature microbiology · 2026Article
- An NTP-driven mechanism for the nucleotide addition cycle of Escherichia coli RNA polymerase during transcription.PloS one · 2022Article
- Nucleotide Loading Modes of Human RNA Polymerase II as Deciphered by Molecular Simulations.Biomolecules · 2020Article
- Multisubunit RNA Polymerase Cleavage Factors Modulate the Kinetics and Energetics of Nucleotide Incorporation: An RNA Polymerase I Case Study.Biochemistry · 2017Article
- Transient-State Kinetic Analysis of the RNA Polymerase I Nucleotide Incorporation Mechanism.Biophysical journal · 2015Article
- Mutations in the CRE pocket of bacterial RNA polymerase affect multiple steps of transcription.Nucleic acids research · 2015Article
- Structural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry Routes.PLoS computational biology · 2015Article
- Computational simulation strategies for analysis of multisubunit RNA polymerases.Chemical reviews · 2013Review
- The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation.Biochimica et biophysica acta · 2013Article
- Single-molecule studies of RNAPII elongation.Biochimica et biophysica acta · 2013Review
- Basic mechanisms of RNA polymerase II activity and alteration of gene expression in Saccharomyces cerevisiae.Biochimica et biophysica acta · 2013Review
- Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase.BMC biophysics · 2012Article
- Interaction of RNA polymerase II fork loop 2 with downstream non-template DNA regulates transcription elongation.The Journal of biological chemistry · 2011Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The regulation of RNA synthesis by RNA polymerase (RNAP) is essential for proper gene expression. Crystal structures of RNAP reveal two channels: the main channel that contains the downstream DNA and a secondary channel that leads directly to the catalytic site. Although nucleoside triphosphates (NTPs) have been seen only in the catalytic site and the secondary channel in these structures, several models of transcription elongation, based on biochemical studies, propose that template-dependent binding of NTPs in the main channel regulates RNA synthesis. These models, however, remain controversial. We used transient state kinetics and a mutant of RNAP to investigate the role of the main channel in regulating nucleotide incorporation. Our data indicate that a NTP specific for the i + 2 template position can bind to a noncatalytic site and increase the rate of RNA synthesis and that the NTP bound to this site can be shuttled directly into the catalytic site. We also identify fork loop 2, which lies across from the downstream DNA, as a functional component of this site. Taken together, our data support the existence of a noncatalytic template-specific NTP binding site in the main channel that is involved in the regulation of nucleotide incorporation. NTP binding to this site could promote high-fidelity processive synthesis under a variety of environmental conditions and allow DNA sequence-mediated regulatory signals to be communicated to the active site.
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