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The δ subunit and NTPase HelD institute a two-pronged mechanism for RNA polymerase recycling

Author

Listed:
  • Hao-Hong Pei

    (Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin)

  • Tarek Hilal

    (Institute of Chemistry and Biochemistry, Research Center of Electron Microscopy and Core Facility BioSupraMol, Freie Universität Berlin)

  • Zhuo A. Chen

    (Bioanalytics, Institute of Biotechnology, Technische Universität Berlin)

  • Yong-Heng Huang

    (Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin)

  • Yuan Gao

    (Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin)

  • Nelly Said

    (Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin)

  • Bernhard Loll

    (Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin)

  • Juri Rappsilber

    (Bioanalytics, Institute of Biotechnology, Technische Universität Berlin
    University of Edinburgh, Wellcome Centre for Cell Biology)

  • Georgiy A. Belogurov

    (Department of Biochemistry, University of Turku)

  • Irina Artsimovitch

    (Department of Microbiology and Center for RNA Biology, The Ohio State University)

  • Markus C. Wahl

    (Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin
    Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography)

Abstract

Cellular RNA polymerases (RNAPs) can become trapped on DNA or RNA, threatening genome stability and limiting free enzyme pools, but how RNAP recycling into active states is achieved remains elusive. In Bacillus subtilis, the RNAP δ subunit and NTPase HelD have been implicated in RNAP recycling. We structurally analyzed Bacillus subtilis RNAP-δ-HelD complexes. HelD has two long arms: a Gre cleavage factor-like coiled-coil inserts deep into the RNAP secondary channel, dismantling the active site and displacing RNA, while a unique helical protrusion inserts into the main channel, prying the β and β′ subunits apart and, aided by δ, dislodging DNA. RNAP is recycled when, after releasing trapped nucleic acids, HelD dissociates from the enzyme in an ATP-dependent manner. HelD abundance during slow growth and a dimeric (RNAP-δ-HelD)2 structure that resembles hibernating eukaryotic RNAP I suggest that HelD might also modulate active enzyme pools in response to cellular cues.

Suggested Citation

  • Hao-Hong Pei & Tarek Hilal & Zhuo A. Chen & Yong-Heng Huang & Yuan Gao & Nelly Said & Bernhard Loll & Juri Rappsilber & Georgiy A. Belogurov & Irina Artsimovitch & Markus C. Wahl, 2020. "The δ subunit and NTPase HelD institute a two-pronged mechanism for RNA polymerase recycling," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-20159-3
    DOI: 10.1038/s41467-020-20159-3
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    Cited by:

    1. Zakia Morichaud & Stefano Trapani & Rishi K. Vishwakarma & Laurent Chaloin & Corinne Lionne & Joséphine Lai-Kee-Him & Patrick Bron & Konstantin Brodolin, 2023. "Structural basis of the mycobacterial stress-response RNA polymerase auto-inhibition via oligomerization," Nature Communications, Nature, vol. 14(1), pages 1-13, December.

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