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Structures and mechanisms of tRNA methylation by METTL1–WDR4

Author

Listed:
  • Victor M. Ruiz-Arroyo

    (University of Texas Southwestern Medical Center
    University of Texas Southwestern Medical Center
    University of Texas Southwestern Medical Center)

  • Rishi Raj

    (University of Texas Southwestern Medical Center
    University of Texas Southwestern Medical Center
    University of Texas Southwestern Medical Center)

  • Kesavan Babu

    (University of Texas Southwestern Medical Center
    University of Texas Southwestern Medical Center
    University of Texas Southwestern Medical Center)

  • Otgonbileg Onolbaatar

    (University of Texas Southwestern Medical Center
    University of Texas Southwestern Medical Center
    University of Texas Southwestern Medical Center)

  • Paul H. Roberts

    (University of Texas Southwestern Medical Center
    University of Texas Southwestern Medical Center
    University of Texas Southwestern Medical Center)

  • Yunsun Nam

    (University of Texas Southwestern Medical Center
    University of Texas Southwestern Medical Center
    University of Texas Southwestern Medical Center)

Abstract

Specific, regulated modification of RNAs is important for proper gene expression1,2. tRNAs are rich with various chemical modifications that affect their stability and function3,4. 7-Methylguanosine (m7G) at tRNA position 46 is a conserved modification that modulates steady-state tRNA levels to affect cell growth5,6. The METTL1–WDR4 complex generates m7G46 in humans, and dysregulation of METTL1–WDR4 has been linked to brain malformation and multiple cancers7–22. Here we show how METTL1 and WDR4 cooperate to recognize RNA substrates and catalyse methylation. A crystal structure of METTL1–WDR4 and cryo-electron microscopy structures of METTL1–WDR4–tRNA show that the composite protein surface recognizes the tRNA elbow through shape complementarity. The cryo-electron microscopy structures of METTL1–WDR4–tRNA with S-adenosylmethionine or S-adenosylhomocysteine along with METTL1 crystal structures provide additional insights into the catalytic mechanism by revealing the active site in multiple states. The METTL1 N terminus couples cofactor binding with conformational changes in the tRNA, the catalytic loop and the WDR4 C terminus, acting as the switch to activate m7G methylation. Thus, our structural models explain how post-translational modifications of the METTL1 N terminus can regulate methylation. Together, our work elucidates the core and regulatory mechanisms underlying m7G modification by METTL1, providing the framework to understand its contribution to biology and disease.

Suggested Citation

  • Victor M. Ruiz-Arroyo & Rishi Raj & Kesavan Babu & Otgonbileg Onolbaatar & Paul H. Roberts & Yunsun Nam, 2023. "Structures and mechanisms of tRNA methylation by METTL1–WDR4," Nature, Nature, vol. 613(7943), pages 383-390, January.
  • Handle: RePEc:nat:nature:v:613:y:2023:i:7943:d:10.1038_s41586-022-05565-5
    DOI: 10.1038/s41586-022-05565-5
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    Cited by:

    1. Shunya Kaneko & Keita Miyoshi & Kotaro Tomuro & Makoto Terauchi & Ryoya Tanaka & Shu Kondo & Naoki Tani & Kei-Ichiro Ishiguro & Atsushi Toyoda & Azusa Kamikouchi & Hideki Noguchi & Shintaro Iwasaki & , 2024. "Mettl1-dependent m7G tRNA modification is essential for maintaining spermatogenesis and fertility in Drosophila melanogaster," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    2. Yudong Fu & Fan Jiang & Xiao Zhang & Yingyi Pan & Rui Xu & Xiu Liang & Xiaofen Wu & Xingqiang Li & Kaixuan Lin & Ruona Shi & Xiaofei Zhang & Dominique Ferrandon & Jing Liu & Duanqing Pei & Jie Wang & , 2024. "Perturbation of METTL1-mediated tRNA N7- methylguanosine modification induces senescence and aging," Nature Communications, Nature, vol. 15(1), pages 1-21, December.

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