ArticleProceedings of the National Academy of Sciences of the United States of America2009
Mechanism of sequence-specific pausing of bacterial RNA polymerase.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers.
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81 citing papers in PubMed, 120 citations in OpenAlex.
- Structure-to-function relationships of RNA polymerases: recent advances in bacterial transcription termination.Transcription · 2026Review
- Intergenic accumulation of RNA polymerase II maintains the potential for swift transcriptional restart upon release from quiescence.Genome research · 2025Article
- Kinetic mechanisms for the sequence dependence of transcriptional errors.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The chromatin landscape of the histone-possessingGenome research · 2025Article
- Bacteroides expand the functional versatility of a conserved transcription factor and transcribed DNA to program capsule diversity.Nature communications · 2024Article
- RNA polymerase SI3 domain modulates global transcriptional pausing and pause-site fluctuations.Nucleic acids research · 2024Article
- Distinct negative elongation factor conformations regulate RNA polymerase II promoter-proximal pausing.Molecular cell · 2024Article
- The landscape of the histone-organized chromatin of Bdellovibrionota bacteria.bioRxiv : the preprint server for biology · 2023Article
- Robust regulation of transcription pausing inProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Structural advances in transcription elongation.Current opinion in structural biology · 2022Review
- Inverse folding based pre-training for the reliable identification of intrinsic transcription terminators.PLoS computational biology · 2022Article
- Article
- Basic mechanisms and kinetics of pause-interspersed transcript elongation.Nucleic acids research · 2021Review
- Mfd regulates RNA polymerase association with hard-to-transcribe regions in vivo, especially those with structured RNAs.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- The torpedo effect in Bacillus subtilis: RNase J1 resolves stalled transcription complexes.The EMBO journal · 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
- Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation.Genes & development · 2019Review
- The Role of Pyrophosphorolysis in the Initiation-to-Elongation Transition by E. coli RNA Polymerase.Journal of molecular biology · 2019Article
- Transcription factor regulation of RNA polymerase's torque generation capacity.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
21 more citing papers are in PubMed but not listed here.
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2 authors at 2 institutions in 1 country.
Funding
Abstract
Sequence-specific pausing of multisubunit RNA polymerases (RNAPs) represents a rate-limiting step during transcription elongation. Pausing occurs on average every 100 bases of DNA. Several models have been proposed to explain pausing, including backtracking of the ternary elongation complex, delay of translocation of the enzyme along DNA, or a conformational change in the active site preventing formation of the phosphodiester bond. Here, we performed biochemical characterization of previously-reported pauses of Escherichia coli RNAP and found that they are not associated with backtracking or a translocation delay. Instead, the paused complex contains the 3' end of the transcript in the active center and is capable of binding the next cognate NTP. However, bond formation occurs much slower in the paused complex compared with its fully-active counterpart. The pausing is dramatically decreased by a substitution of the base encoding the next incoming NTP and the base encoding the 3' end of the nascent RNA, suggesting that (mis)-alignment of the 3' end of the RNA and the incoming NTP in the active site is crucial for pausing. These pause sites are conserved between E. coli and Thermus thermophilus RNAPs, but are not recognized by Saccharomyces cerevisiae RNAP II, indicating that prokaryotic RNAPs might be more sensitive to the changes in the alignment of the nascent transcript and the substrate NTP in the active site.
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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.