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Pseudomonas aeruginosa SutA wedges RNAP lobe domain open to facilitate promoter DNA unwinding

Author

Listed:
  • Dingwei He

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Linlin You

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Xiaoxian Wu

    (Chinese Academy of Sciences)

  • Jing Shi

    (Nanjing University of Chinese Medicine)

  • Aijia Wen

    (Zhejiang University School of Medicine)

  • Zhi Yan

    (Chinese Academy of Sciences)

  • Wenhui Mu

    (Chinese Academy of Sciences
    Henan University)

  • Chengli Fang

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Yu Feng

    (Zhejiang University School of Medicine)

  • Yu Zhang

    (Chinese Academy of Sciences)

Abstract

Pseudomonas aeruginosa (Pae) SutA adapts bacteria to hypoxia and nutrition-limited environment during chronic infection by increasing transcription activity of an RNA polymerase (RNAP) holoenzyme comprising the stress-responsive σ factor σS (RNAP-σS). SutA shows no homology to previously characterized RNAP-binding proteins. The structure and mode of action of SutA remain unclear. Here we determined cryo-EM structures of Pae RNAP-σS holoenzyme, Pae RNAP-σS holoenzyme complexed with SutA, and Pae RNAP-σS transcription initiation complex comprising SutA. The structures show SutA pinches RNAP-β protrusion and facilitates promoter unwinding by wedging RNAP-β lobe open. Our results demonstrate that SutA clears an energetic barrier to facilitate promoter unwinding of RNAP-σS holoenzyme.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31871-7
    DOI: 10.1038/s41467-022-31871-7
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    References listed on IDEAS

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    1. Dmitry G. Vassylyev & Shun-ichi Sekine & Oleg Laptenko & Jookyung Lee & Marina N. Vassylyeva & Sergei Borukhov & Shigeyuki Yokoyama, 2002. "Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution," Nature, Nature, vol. 417(6890), pages 712-719, June.
    2. Hande Boyaci & James Chen & Rolf Jansen & Seth A. Darst & Elizabeth A. Campbell, 2019. "Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding," Nature, Nature, vol. 565(7739), pages 382-385, January.
    3. Dmitry G. Vassylyev & Marina N. Vassylyeva & Anna Perederina & Tahir H. Tahirov & Irina Artsimovitch, 2007. "Structural basis for transcription elongation by bacterial RNA polymerase," Nature, Nature, vol. 448(7150), pages 157-162, July.
    4. 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.
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    Cited by:

    1. 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.
    2. Jie Li & Haonan Zhang & Dongyu Li & Ya-Jun Liu & Edward A. Bayer & Qiu Cui & Yingang Feng & Ping Zhu, 2023. "Structure of the transcription open complex of distinct σI factors," Nature Communications, Nature, vol. 14(1), pages 1-12, December.

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