ArticleProceedings of the National Academy of Sciences of the United States of America2020
RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 49 citations in OpenAlex.
- The prokaryotic origins of the COMMD protein family involved in eukaryotic membrane trafficking.Nature communications · 2026Article
- Structural basis of pausing during transcription initiation in mycobacterium tuberculosis.Nature communications · 2026Article
- Structural insights into σ28-dependent transcription initiation and its regulation by anti-sigma factor in Pseudomonas aeruginosa.Nucleic acids research · 2026Article
- Nascent RNA profiling reveals genome-wide productive reiterative initiation regulating gene transcription in bacteria.Nucleic acids research · 2025Article
- Structural Insights into De Novo Promoter Escape by Mycobacterium tuberculosis RNA Polymerase.Nature communications · 2025Article
- Pol III escapes the promoter using a "protein spring" mechanism.Science China. Life sciences · 2025Article
- The displacement of the σ70 finger in initial transcription is highly heterogeneous and promoter-dependent.Nucleic acids research · 2025Article
- Article
- Single-stranded DNA drives σ subunit loading onto mycobacterial RNA polymerase to unlock initiation-competent conformations.Nucleic acids research · 2025Article
- RapA opens the RNA polymerase clamp to disrupt post-termination complexes and prevent cytotoxic R-loop formation.Nature structural & molecular biology · 2025Article
- How does the polymerase of non-segmented negative strand RNA viruses commit to transcription or genome replication?Journal of virology · 2024Review
- Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Structural basis of σProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Article
- DomainMapper: Accurate domain structure annotation including those with non-contiguous topologies.Protein science : a publication of the Protein Society · 2022Article
- Step-by-Step Regulation of Productive and Abortive Transcription Initiation by Pyrophosphorolysis.Journal of molecular biology · 2022Article
- Structural and mechanistic basis of σ-dependent transcriptional pausing.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Design, Synthesis, and Characterization of TNP-2198, a Dual-Targeted Rifamycin-Nitroimidazole Conjugate with Potent Activity against Microaerophilic and Anaerobic Bacterial Pathogens.Journal of medicinal chemistry · 2022Article
- Structural and mechanistic basis of reiterative transcription initiation.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Universal functions of the σ finger in alternative σ factors during transcription initiation by bacterial RNA polymerase.RNA biology · 2021Article
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
All organisms-bacteria, archaea, and eukaryotes-have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center. This transcription initiation-factor structural module preorganizes template-strand ssDNA to engage the RNAP active center, thereby facilitating binding of initiating nucleotides and enabling transcription initiation from initiating mononucleotides. However, this transcription initiation-factor structural module occupies the path of nascent RNA and thus presumably must be displaced before or during initial transcription. Here, we report four sets of crystal structures of bacterial initially transcribing complexes that demonstrate and define details of stepwise, RNA-extension-driven displacement of the "σ-finger" of the bacterial transcription initiation factor σ. The structures reveal that-for both the primary σ-factor and extracytoplasmic (ECF) σ-factors, and for both 5'-triphosphate RNA and 5'-hydroxy RNA-the "σ-finger" is displaced in stepwise fashion, progressively folding back upon itself, driven by collision with the RNA 5'-end, upon extension of nascent RNA from ∼5 nt to ∼10 nt.
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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.