Allosteric Control of RNA Polymerase by a Site That Contacts Nascent RNA Hairpins

@article{Toulokhonov2001AllostericCO,
  title={Allosteric Control of RNA Polymerase by a Site That Contacts Nascent RNA Hairpins},
  author={Innokenti Toulokhonov and Irina Artsimovitch and Robert Landick},
  journal={Science},
  year={2001},
  volume={292},
  pages={730 - 733}
}
DNA, RNA, and regulatory molecules control gene expression through interactions with RNA polymerase (RNAP). We show that a short α helix at the tip of the flaplike domain that covers the RNA exit channel of RNAP contacts a nascent RNA stem-loop structure (hairpin) that inhibits transcription, and that this flap-tip helix is required for activity of the regulatory protein NusA. Protein-RNA cross-linking, molecular modeling, and effects of alterations in RNAP and RNA all suggest that a tripartite… 
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192 Citations
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192 Citations

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RNA Polymerase Accommodates a Pause RNA Hairpin by Global Conformational Rearrangements that Prolong Pausing.
The flap domain is required for pause RNA hairpin inhibition of catalysis by RNA polymerase and can modulate intrinsic termination.
RNA polymerase pausing and nascent RNA structure formation are linked through clamp domain movement
TLDR
It is reported that exit-channel RNA structures slow pause escape by favoring clamp opening through interactions with the flap that slow translocation.
An allosteric path to transcription termination.
A Two-Way Street: Regulatory Interplay between RNA Polymerase and Nascent RNA
TLDR
The evolutionary origin, mechanistic underpinnings, and regulatory consequences of this interplay between RNAP and nascent RNA structure are reviewed, and the extensive linkage between the transcriptional machinery and its product is categorized and rationalized.
A Two-Way Street: Regulatory Interplay between RNA Polymerase and Nascent RNA Structure.
Antisense Oligonucleotide-stimulated Transcriptional Pausing Reveals RNA Exit Channel Specificity of RNA Polymerase and Mechanistic Contributions of NusA and RfaH*
TLDR
The authors' results favor direct NusA stabilization of exit channel duplexes, which consequently affect RNAP clamp conformation, suggesting that RfaH and exit channel Duplexes compete via opposing effects on RNAP clamped conformation.
RNA polymerase mutations that impair conversion to a termination-resistant complex by Q antiterminator proteins.
TLDR
The positions of amino acid substitutions in the modeled RNAP/DNA/RNA ternary elongation complex suggest that they do not define a binding site for Q in RNAP, but instead act by impairing interactions among core RNAP subunits and nucleic acids that are essential for Q modification.
Pulling on the nascent RNA during transcription does not alter kinetics of elongation or ubiquitous pausing.
Shortening of RNA:DNA hybrid in the elongation complex of RNA polymerase is a prerequisite for transcription termination.
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References

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TLDR
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TLDR
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TLDR
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