ArticleMolecular cell2013
Cys-pair reporters detect a constrained trigger loop in a paused RNA polymerase.
Article in Molecular cell, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Widespread epistasis shapes RNA polymerase II active site function and evolution.Nature communications · 2025Article
- Article
- Higher-order epistasis within Pol II trigger loop haplotypes.bioRxiv : the preprint server for biology · 2024Article
- Thiolutin has complex effects in vivo but is a direct inhibitor of RNA polymerase II in vitro.Nucleic acids research · 2024Article
- Single-molecule visualization of twin-supercoiled domains generated during transcription.Nucleic acids research · 2024Article
- In Vitro Transcription Assay to Quantify Effects of H-NS Filaments on RNA Chain Elongation by RNA Polymerase.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Bacterial H-NS contacts DNA at the same irregularly spaced sites in both bridged and hemi-sequestered linear filaments.iScience · 2022Article
- Obligate movements of an active site-linked surface domain control RNA polymerase elongation and pausing via a Phe pocket anchor.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Closing and opening of the RNA polymerase trigger loop.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase.Journal of molecular biology · 2019Review
- Mechanisms of Transcriptional Pausing in Bacteria.Journal of molecular biology · 2019Review
- A Novel Assay for RNA Polymerase I Transcription Elongation Sheds Light on the Evolutionary Divergence of Eukaryotic RNA Polymerases.Biochemistry · 2019Article
- Functional assays for transcription mechanisms in high-throughput.Methods (San Diego, Calif.) · 2019Review
- RNA Polymerase Clamp Movement Aids Dissociation from DNA but Is Not Required for RNA Release at Intrinsic Terminators.Journal of molecular biology · 2019Article
- Article
- Transcriptional Responses to ppGpp and DksA.Annual review of microbiology · 2018Review
- Reading of the non-template DNA by transcription elongation factors.Molecular microbiology · 2018Article
- RNA Polymerase Accommodates a Pause RNA Hairpin by Global Conformational Rearrangements that Prolong Pausing.Molecular cell · 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
- Trigger loop of RNA polymerase is a positional, not acid-base, catalyst for both transcription and proofreading.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
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5 authors.
Funding
Abstract
Transcriptional pausing, which regulates transcript elongation in both prokaryotes and eukaryotes, is thought to involve formation of alternative RNA polymerase conformations in which nucleotide addition is inhibited in part by restriction of trigger loop (TL) folding. The polymorphous TL must convert from a random coil to a helical hairpin that contacts the nucleotide triphosphate (NTP) substrate to allow rapid nucleotide addition. Understanding the distribution of TL conformations in different enzyme states is made difficult by the TL's small size and sensitive energetics. Here, we report a Cys-pair reporter strategy to elucidate the relative occupancies of different TL conformations in E. coli RNA polymerase based on the ability of Cys residues engineered into the TL and surrounding regions to form disulfide bonds. Our results indicate that a paused complex stabilized by a nascent RNA hairpin favors nonproductive TL conformations that persist after NTP binding but can be reversed by the elongation factor RfaH.
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