IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v12y2021i1d10.1038_s41467-020-20776-y.html
   My bibliography  Save this article

Structural basis of ribosomal RNA transcription regulation

Author

Listed:
  • Yeonoh Shin

    (Pennsylvania State University)

  • M. Zuhaib Qayyum

    (Pennsylvania State University)

  • Danil Pupov

    (Russian Academy of Sciences)

  • Daria Esyunina

    (Russian Academy of Sciences)

  • Andrey Kulbachinskiy

    (Russian Academy of Sciences)

  • Katsuhiko S. Murakami

    (Pennsylvania State University)

Abstract

Ribosomal RNA (rRNA) is most highly expressed in rapidly growing bacteria and is drastically downregulated under stress conditions by the global transcriptional regulator DksA and the alarmone ppGpp. Here, we determined cryo-electron microscopy structures of the Escherichia coli RNA polymerase (RNAP) σ70 holoenzyme during rRNA promoter recognition with and without DksA/ppGpp. RNAP contacts the UP element using dimerized α subunit carboxyl-terminal domains and scrunches the template DNA with the σ finger and β’ lid to select the transcription start site favorable for rapid promoter escape. Promoter binding induces conformational change of σ domain 2 that opens a gate for DNA loading and ejects σ1.1 from the RNAP cleft to facilitate open complex formation. DksA/ppGpp binding also opens the DNA loading gate, which is not coupled to σ1.1 ejection and impedes open complex formation. These results provide a molecular basis for the exceptionally active rRNA transcription and its vulnerability to DksA/ppGpp.

Suggested Citation

  • Yeonoh Shin & M. Zuhaib Qayyum & Danil Pupov & Daria Esyunina & Andrey Kulbachinskiy & Katsuhiko S. Murakami, 2021. "Structural basis of ribosomal RNA transcription regulation," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-020-20776-y
    DOI: 10.1038/s41467-020-20776-y
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-020-20776-y
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-020-20776-y?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Jin Qian & Bing Wang & Irina Artsimovitch & David Dunlap & Laura Finzi, 2024. "Force and the α-C-terminal domains bias RNA polymerase recycling," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    2. Tomáš Kovaľ & Nabajyoti Borah & Petra Sudzinová & Barbora Brezovská & Hana Šanderová & Viola Vaňková Hausnerová & Alena Křenková & Martin Hubálek & Mária Trundová & Kristýna Adámková & Jarmila Dušková, 2024. "Mycobacterial HelD connects RNA polymerase recycling with transcription initiation," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    3. Linggang Yuan & Qingyang Liu & Liqiao Xu & Bing Wu & Yu Feng, 2024. "Structural basis of promoter recognition by Staphylococcus aureus RNA polymerase," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    4. Dingwei He & Linlin You & Xiaoxian Wu & Jing Shi & Aijia Wen & Zhi Yan & Wenhui Mu & Chengli Fang & Yu Feng & Yu Zhang, 2022. "Pseudomonas aeruginosa SutA wedges RNAP lobe domain open to facilitate promoter DNA unwinding," Nature Communications, Nature, vol. 13(1), pages 1-10, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-020-20776-y. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.