ArticleProceedings of the National Academy of Sciences of the United States of America2009
Allosteric control of catalysis by the F loop of 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 36 papers.
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Who cites it
36 citing papers in PubMed, 47 citations in OpenAlex.
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- Structural basis for multi-subunit DNA-dependent RNA polymerase catalytic activity.Molecular cell · 2026Article
- RNA polymerase inhibitors reveal active-site motions essential for the nucleotide-addition cycle.bioRxiv : the preprint server for biology · 2026Article
- Transcription co-inhibition alters drug resistance evolution and enhances Mycobacterium tuberculosis clearance from granulomas.Nature microbiology · 2026Article
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- Pleomorphic effects of three small-molecule inhibitors on transcription elongation bybioRxiv : the preprint server for biology · 2025Article
- An NTP-driven mechanism for the nucleotide addition cycle of Escherichia coli RNA polymerase during transcription.PloS one · 2022Article
- Nucleotide Loading Modes of Human RNA Polymerase II as Deciphered by Molecular Simulations.Biomolecules · 2020Article
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- Gre-family factors modulate DNA damage sensing byRNA biology · 2019Article
- The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase.Journal of molecular biology · 2019Review
- Structural mechanism of transcription inhibition by lasso peptides microcin J25 and capistruin.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Active site closure stabilizes the backtracked state of RNA polymerase.Nucleic acids research · 2018Article
- Conserved functions of the trigger loop and Gre factors in RNA cleavage by bacterial RNA polymerases.The Journal of biological chemistry · 2017Article
- Regulation of transcriptional pausing through the secondary channel of RNA polymerase.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Bacterial Transcription as a Target for Antibacterial Drug Development.Microbiology and molecular biology reviews : MMBR · 2016Review
- Lineage-specific variations in the trigger loop modulate RNA proofreading by bacterial RNA polymerases.Nucleic acids research · 2016Article
- Allosteric Activation of Bacterial Swi2/Snf2 (Switch/Sucrose Non-fermentable) Protein RapA by RNA Polymerase: BIOCHEMICAL AND STRUCTURAL STUDIES.The Journal of biological chemistry · 2015Article
- CBR antimicrobials inhibit RNA polymerase via at least two bridge-helix cap-mediated effects on nucleotide addition.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Trigger-helix folding pathway and SI3 mediate catalysis and hairpin-stabilized pausing by Escherichia coli RNA polymerase.Nucleic acids research · 2014Article
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
Bacterial RNA polymerases (RNAPs) undergo coordinated conformational changes during catalysis. In particular, concerted folding of the trigger loop and rearrangements of the bridge helix at the RNAP active center have been implicated in nucleotide addition and RNAP translocation. At moderate temperatures, the rate of catalysis by RNAP from thermophilic Thermus aquaticus is dramatically reduced compared with its closest mesophilic relative, Deinococcus radiodurans. Here, we show that a part of this difference is conferred by a third element, the F loop, which is adjacent to the N terminus of the bridge helix and directly contacts the folded trigger loop. Substitutions of amino acid residues in the F loop and in an adjacent segment of the bridge helix in T. aquaticus RNAP for their D. radiodurans counterparts significantly increased the rate of catalysis (up to 40-fold at 20 degrees C). A deletion in the F loop dramatically impaired the rate of nucleotide addition and pyrophosphorolysis, but it had only a moderate effect on intrinsic RNA cleavage. Streptolydigin, an antibiotic that blocks folding of the trigger loop, did not inhibit nucleotide addition by the mutant enzyme. The resistance to streptolydigin likely results from the loss of its functional target, the folding of the trigger loop, which is already impaired by the F-loop deletion. Our results demonstrate that the F loop is essential for proper folding of the trigger loop during nucleotide addition and governs the temperature adaptivity of RNAPs in different bacteria.
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