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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
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    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. Tongtong Wang & Guang-Lei Wang & Ying Fang & Yi Zhang & Wenxin Peng & Yue Zhou & Aihong Zhang & Long-Jiang Yu & Congming Lu, 2024. "Architecture of the spinach plastid-encoded RNA polymerase," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    4. 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.
    5. 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.

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