ArticleProceedings of the National Academy of Sciences of the United States of America2016
Structures of E. coli σS-transcription initiation complexes provide new insights into polymerase mechanism.
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 47 papers.
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Who cites it
47 citing papers in PubMed, 83 citations in OpenAlex.
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- Widespread epistasis shapes RNA polymerase II active site function and evolution.Nature communications · 2025Article
- Transcription activation inEcoSal Plus · 2024Review
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- Higher-order epistasis within Pol II trigger loop haplotypes.bioRxiv : the preprint server for biology · 2024Article
- RpoS and the bacterial general stress response.Microbiology and molecular biology reviews : MMBR · 2024Review
- Structural basis for transcription activation by the nitrate-responsive regulator NarL.Nucleic acids research · 2024Article
- Structure of the transcription open complex of distinct σNature communications · 2023Article
- Structural Insight into the Mechanism of σ32-Mediated Transcription Initiation of Bacterial RNA Polymerase.Biomolecules · 2023Article
- An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Step-by-Step Regulation of Productive and Abortive Transcription Initiation by Pyrophosphorolysis.Journal of molecular biology · 2022Article
- Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase.Nature communications · 2022Article
- Using cryo-EM to uncover mechanisms of bacterial transcriptional regulation.Biochemical Society transactions · 2021Review
- Conserved Trigger Loop Histidine of RNA Polymerase II Functions as a Positional Catalyst Primarily through Steric Effects.Biochemistry · 2021Article
- Universal functions of the σ finger in alternative σ factors during transcription initiation by bacterial RNA polymerase.RNA biology · 2021Article
- 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
- Mutations Suppressing the Lack of Prepilin Peptidase Provide Insights Into the Maturation of the Major Pilin Protein in Cyanobacteria.Frontiers in microbiology · 2021Article
- Structural basis of bacterial σThe EMBO journal · 2020Article
- Visualization of two architectures in class-II CAP-dependent transcription activation.PLoS biology · 2020Article
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3 authors at 1 institution in 1 country.
Funding
Abstract
In bacteria, multiple σ factors compete to associate with the RNA polymerase (RNAP) core enzyme to form a holoenzyme that is required for promoter recognition. During transcription initiation RNAP remains associated with the upstream promoter DNA via sequence-specific interactions between the σ factor and the promoter DNA while moving downstream for RNA synthesis. As RNA polymerase repetitively adds nucleotides to the 3'-end of the RNA, a pyrophosphate ion is generated after each nucleotide incorporation. It is currently unknown how the release of pyrophosphate affects transcription. Here we report the crystal structures of E coli transcription initiation complexes (TICs) containing the stress-responsive σ(S) factor, a de novo synthesized RNA oligonucleotide, and a complete transcription bubble (σ(S)-TIC) at about 3.9-Å resolution. The structures show the 3D topology of the σ(S) factor and how it recognizes the promoter DNA, including likely specific interactions with the template-strand residues of the -10 element. In addition, σ(S)-TIC structures display a highly stressed pretranslocated initiation complex that traps a pyrophosphate at the active site that remains closed. The position of the pyrophosphate and the unusual phosphodiester linkage between the two terminal RNA residues suggest an unfinished nucleotide-addition reaction that is likely at equilibrium between nucleotide addition and pyrophosphorolysis. Although these σ(S)-TIC crystals are enzymatically active, they are slow in nucleotide addition, as suggested by an NTP soaking experiment. Pyrophosphate release completes the nucleotide addition reaction and is associated with extensive conformational changes around the secondary channel but causes neither active site opening nor transcript translocation.
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