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Pseudoknot length modulates the folding, conformational dynamics, and robustness of Xrn1 resistance of flaviviral xrRNAs

Author

Listed:
  • Xiaolin Niu

    (Tsinghua University)

  • Ruirui Sun

    (Tsinghua University
    Tsinghua University)

  • Zhifeng Chen

    (Tsinghua University
    Guangxi Normal University)

  • Yirong Yao

    (Tsinghua University
    Tsinghua University)

  • Xiaobing Zuo

    (X-ray Science Division, Argonne National Laboratory)

  • Chunlai Chen

    (Tsinghua University
    Tsinghua University)

  • Xianyang Fang

    (Tsinghua University)

Abstract

To understand how RNA dynamics is regulated and connected to its function, we investigate the folding, conformational dynamics and robustness of Xrn1 resistance of a set of flaviviral xrRNAs using SAXS, smFRET and in vitro enzymatic assays. Flaviviral xrRNAs form discrete ring-like 3D structures, in which the length of a conserved long-range pseudoknot (PK2) ranges from 2 bp to 7 bp. We find that xrRNAs’ folding, conformational dynamics and Xrn1 resistance are strongly correlated and highly Mg2+-dependent, furthermore, the Mg2+-dependence is modulated by PK2 length variations. xrRNAs with long PK2 require less Mg2+ to stabilize their folding, exhibit reduced conformational dynamics and strong Xrn1 resistance even at low Mg2+, and tolerate mutations at key tertiary motifs at high Mg2+, which generally are destructive to xrRNAs with short PK2. These results demonstrate an unusual regulatory mechanism of RNA dynamics providing insights into the functions and future biomedical applications of xrRNAs.

Suggested Citation

  • Xiaolin Niu & Ruirui Sun & Zhifeng Chen & Yirong Yao & Xiaobing Zuo & Chunlai Chen & Xianyang Fang, 2021. "Pseudoknot length modulates the folding, conformational dynamics, and robustness of Xrn1 resistance of flaviviral xrRNAs," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-26616-x
    DOI: 10.1038/s41467-021-26616-x
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    References listed on IDEAS

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    Cited by:

    1. Yuan Liang & Yunkai Qie & Jing Yang & Ranfeng Wu & Shuang Cui & Yuliang Zhao & Greg J. Anderson & Guangjun Nie & Suping Li & Cheng Zhang, 2023. "Programming conformational cooperativity to regulate allosteric protein-oligonucleotide signal transduction," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    2. Xiang Chen & Yan Wang & Zhonghe Xu & Meng-Li Cheng & Qing-Qing Ma & Rui-Ting Li & Zheng-Jian Wang & Hui Zhao & Xiaobing Zuo & Xiao-Feng Li & Xianyang Fang & Cheng-Feng Qin, 2023. "Zika virus RNA structure controls its unique neurotropism by bipartite binding to Musashi-1," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    3. Xiaolin Niu & Zhonghe Xu & Yufan Zhang & Xiaobing Zuo & Chunlai Chen & Xianyang Fang, 2023. "Structural and dynamic mechanisms for coupled folding and tRNA recognition of a translational T-box riboswitch," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

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