ArticleProceedings of the National Academy of Sciences of the United States of America2016
RNA polymerase gate loop guides the nontemplate DNA strand in transcription complexes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Single-stranded DNA drives σ subunit loading onto mycobacterial RNA polymerase to unlock initiation-competent conformations.Nucleic acids research · 2025Article
- Force and the α-C-terminal domains bias RNA polymerase recycling.Nature communications · 2024Article
- Pseudomonas aeruginosa SutA wedges RNAP lobe domain open to facilitate promoter DNA unwinding.Nature communications · 2022Article
- Structural origins ofProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Structural basis of ribosomal RNA transcription regulation.Nature communications · 2021Article
- The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase.Journal of molecular biology · 2019Review
- Ancient Transcription Factors in the News.mBio · 2019Review
- In silico discovery of small molecules that inhibit RfaH recruitment to RNA polymerase.Molecular microbiology · 2018Article
- Locking the nontemplate DNA to control transcription.Molecular microbiology · 2018Article
- Reading of the non-template DNA by transcription elongation factors.Molecular microbiology · 2018Article
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- Article
- Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3).Molecular cell · 2018Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Upon RNA polymerase (RNAP) binding to a promoter, the σ factor initiates DNA strand separation and captures the melted nontemplate DNA, whereas the core enzyme establishes interactions with the duplex DNA in front of the active site that stabilize initiation complexes and persist throughout elongation. Among many core RNAP elements that participate in these interactions, the β' clamp domain plays the most prominent role. In this work, we investigate the role of the β gate loop, a conserved and essential structural element that lies across the DNA channel from the clamp, in transcription regulation. The gate loop was proposed to control DNA loading during initiation and to interact with NusG-like proteins to lock RNAP in a closed, processive state during elongation. We show that the removal of the gate loop has large effects on promoter complexes, trapping an unstable intermediate in which the RNAP contacts with the nontemplate strand discriminator region and the downstream duplex DNA are not yet fully established. We find that although RNAP lacking the gate loop displays moderate defects in pausing, transcript cleavage, and termination, it is fully responsive to the transcription elongation factor NusG. Together with the structural data, our results support a model in which the gate loop, acting in concert with initiation or elongation factors, guides the nontemplate DNA in transcription complexes, thereby modulating their regulatory properties.
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