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Snapshots of the second-step self-splicing of Tetrahymena ribozyme revealed by cryo-EM

Author

Listed:
  • Shanshan Li

    (University of Science and Technology of China)

  • Michael Z. Palo

    (Stanford University)

  • Xiaojing Zhang

    (University of Science and Technology of China)

  • Grigore Pintilie

    (Stanford University)

  • Kaiming Zhang

    (University of Science and Technology of China)

Abstract

Group I introns are catalytic RNAs that coordinate two consecutive transesterification reactions for self-splicing. To understand how the group I intron promotes catalysis and coordinates self-splicing reactions, we determine the structures of L-16 Tetrahymena ribozyme in complex with a 5′-splice site analog product and a 3′-splice site analog substrate using cryo-EM. We solve six conformations from a single specimen, corresponding to different splicing intermediates after the first ester-transfer reaction. The structures reveal dynamics during self-splicing, including large conformational changes of the internal guide sequence and the J5/4 junction as well as subtle rearrangements of active-site metals and the hydrogen bond formed between the 2′-OH group of A261 and the N2 group of guanosine substrate. These results help complete a detailed structural and mechanistic view of this paradigmatic group I intron undergoing the second step of self-splicing.

Suggested Citation

  • Shanshan Li & Michael Z. Palo & Xiaojing Zhang & Grigore Pintilie & Kaiming Zhang, 2023. "Snapshots of the second-step self-splicing of Tetrahymena ribozyme revealed by cryo-EM," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-36724-5
    DOI: 10.1038/s41467-023-36724-5
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    References listed on IDEAS

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    1. Zhaoming Su & Kaiming Zhang & Kalli Kappel & Shanshan Li & Michael Z. Palo & Grigore D. Pintilie & Ramya Rangan & Bingnan Luo & Yuquan Wei & Rhiju Das & Wah Chiu, 2021. "Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 Å resolution," Nature, Nature, vol. 596(7873), pages 603-607, August.
    2. Peter L. Adams & Mary R. Stahley & Anne B. Kosek & Jimin Wang & Scott A. Strobel, 2004. "Crystal structure of a self-splicing group I intron with both exons," Nature, Nature, vol. 430(6995), pages 45-50, July.
    3. Lara B. Weinstein & B. C. N. M. Jones & Richard Cosstick & Thomas R. Cech, 1997. "A second catalytic metal ion in a group I ribozyme," Nature, Nature, vol. 388(6644), pages 805-808, August.
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