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Translational T-box riboswitches bind tRNA by modulating conformational flexibility

Author

Listed:
  • Eduardo Campos-Chavez

    (Northwestern University)

  • Sneha Paul

    (The University of Chicago
    Paris-Saclay University)

  • Zunwu Zhou

    (The University of Chicago)

  • Dulce Alonso

    (Northwestern University)

  • Anjali R. Verma

    (Columbia University
    University of Maryland)

  • Jingyi Fei

    (The University of Chicago)

  • Alfonso Mondragón

    (Northwestern University)

Abstract

T-box riboswitches are noncoding RNA elements involved in genetic regulation of most Gram-positive bacteria. They regulate amino acid metabolism by assessing the aminoacylation status of tRNA, subsequently affecting the transcription or translation of downstream amino acid metabolism-related genes. Here we present single-molecule FRET studies of the Mycobacterium tuberculosis IleS T-box riboswitch, a paradigmatic translational T-box. Results support a two-step binding model, where the tRNA anticodon is recognized first, followed by interactions with the NCCA sequence. Furthermore, after anticodon recognition, tRNA can transiently dock into the discriminator domain even in the absence of the tRNA NCCA-discriminator interactions. Establishment of the NCCA-discriminator interactions significantly stabilizes the fully bound state. Collectively, the data suggest high conformational flexibility in translational T-box riboswitches; and supports a conformational selection model for NCCA recognition. These findings provide a kinetic framework to understand how specific RNA elements underpin the binding affinity and specificity required for gene regulation.

Suggested Citation

  • Eduardo Campos-Chavez & Sneha Paul & Zunwu Zhou & Dulce Alonso & Anjali R. Verma & Jingyi Fei & Alfonso Mondragón, 2024. "Translational T-box riboswitches bind tRNA by modulating conformational flexibility," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-50885-x
    DOI: 10.1038/s41467-024-50885-x
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    References listed on IDEAS

    as
    1. Jinwei Zhang & Adrian R. Ferré-D’Amaré, 2013. "Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA," Nature, Nature, vol. 500(7462), pages 363-366, August.
    2. Krishna C. Suddala & Janghyun Yoo & Lixin Fan & Xiaobing Zuo & Yun-Xing Wang & Hoi Sung Chung & Jinwei Zhang, 2023. "Direct observation of tRNA-chaperoned folding of a dynamic mRNA ensemble," Nature Communications, Nature, vol. 14(1), pages 1-16, 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.
    4. Taekjip Ha & Ivan Rasnik & Wei Cheng & Hazen P. Babcock & George H. Gauss & Timothy M. Lohman & Steven Chu, 2002. "Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase," Nature, Nature, vol. 419(6907), pages 638-641, October.
    5. Krishna C. Suddala & Javier Cabello-Villegas & Malgorzata Michnicka & Collin Marshall & Edward P. Nikonowicz & Nils G. Walter, 2018. "Hierarchical mechanism of amino acid sensing by the T-box riboswitch," Nature Communications, Nature, vol. 9(1), pages 1-14, December.
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