ArticleNucleic acids research2015
Mutations in the CRE pocket of bacterial RNA polymerase affect multiple steps of transcription.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 29 citations in OpenAlex.
- Mutations in RNA polymerase that drive the emergence of antibiotic resistance.Current opinion in microbiology · 2026Review
- Advances and Mechanisms of RNA-Ligand Interaction Predictions.Life (Basel, Switzerland) · 2025Review
- DNA synthesis across DNA hairpins by human PrimPol.DNA repair · 2024Article
- Compensatory evolution of chromosomes and plasmids counteracts the plasmid fitness cost.Ecology and evolution · 2024Article
- Deep mutational scanning reveals the molecular determinants of RNA polymerase-mediated adaptation and tradeoffs.Nature communications · 2023Article
- RPflex: A Coarse-Grained Network Model for RNA Pocket Flexibility Study.International journal of molecular sciences · 2023Article
- The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation.Journal of bacteriology · 2021Review
- The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase.Journal of molecular biology · 2019Review
- Source of the Fitness Defect in Rifamycin-Resistant Mycobacterium tuberculosis RNA Polymerase and the Mechanism of Compensation by Mutations in the β' Subunit.Antimicrobial agents and chemotherapy · 2018Article
- DNA template sequence control of bacterial RNA polymerase escape from the promoter.Nucleic acids research · 2018Article
- Article
- Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA.Molecular cell · 2018Article
- Conserved functions of the trigger loop and Gre factors in RNA cleavage by bacterial RNA polymerases.The Journal of biological chemistry · 2017Article
- A link between transcription fidelity and pausing in vivo.Transcription · 2017Article
- RNA polymerase gate loop guides the nontemplate DNA strand in transcription complexes.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Rifampin Resistance rpoB Alleles or Multicopy Thioredoxin/Thioredoxin Reductase Suppresses the Lethality of Disruption of the Global Stress Regulator spx in Staphylococcus aureus.Journal of bacteriology · 2016Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
During transcription, the catalytic core of RNA polymerase (RNAP) must interact with the DNA template with low-sequence specificity to ensure efficient enzyme translocation and RNA extension. Unexpectedly, recent structural studies of bacterial promoter complexes revealed specific interactions between the nontemplate DNA strand at the downstream edge of the transcription bubble (CRE, core recognition element) and a protein pocket formed by core RNAP (CRE pocket). We investigated the roles of these interactions in transcription by analyzing point amino acid substitutions and deletions in Escherichia coli RNAP. The mutations affected multiple steps of transcription, including promoter recognition, RNA elongation and termination. In particular, we showed that interactions of the CRE pocket with a nontemplate guanine immediately downstream of the active center stimulate RNA-hairpin-dependent transcription pausing but not other types of pausing. Thus, conformational changes of the elongation complex induced by nascent RNA can modulate CRE effects on transcription. The results highlight the roles of specific core RNAP-DNA interactions at different steps of RNA synthesis and suggest their importance for transcription regulation in various organisms.
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