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The mechanism of discriminative aminoacylation by isoleucyl-tRNA synthetase based on wobble nucleotide recognition

Author

Listed:
  • Bingyi Chen

    (Sun Yat-sen University
    Sun Yat-sen University)

  • Fang Yi

    (Sun Yat-sen University
    Sun Yat-sen University)

  • Zhiteng Luo

    (Sun Yat-sen University
    Sun Yat-sen University)

  • Feihu Lu

    (Sun Yat-sen University
    Sun Yat-sen University)

  • Hongwei Liu

    (Guangzhou Medical University)

  • Siting Luo

    (Sun Yat-sen University
    Sun Yat-sen University)

  • Qiong Gu

    (Sun Yat-sen University)

  • Huihao Zhou

    (Sun Yat-sen University
    Sun Yat-sen University)

Abstract

The faithful charging of amino acids to cognate tRNAs by aminoacyl-tRNA synthetases (AARSs) determines the fidelity of protein translation. Isoleucyl-tRNA synthetase (IleRS) distinguishes tRNAIle from tRNAMet solely based on the nucleotide at wobble position (N34), and a single substitution at N34 could exchange the aminoacylation specificity between two tRNAs. Here, we report the structural and biochemical mechanism of N34 recognition-based tRNA discrimination by Saccharomyces cerevisiae IleRS (ScIleRS). ScIleRS utilizes a eukaryotic/archaeal-specific arginine as the H-bond donor to recognize the common carbonyl group (H-bond acceptor) of various N34s of tRNAIle, which induces mutual structural adaptations between ScIleRS and tRNAIle to achieve a preferable editing state. C34 of unmodified tRNAIle(CAU) (behaves like tRNAMet) lacks a relevant H-bond acceptor, which disrupts key H-bonding interactions and structural adaptations and suspends the ScIleRS·tRNAIle(CAU) complex in an initial non-reactive state. This wobble nucleotide recognition-based structural adaptation provides mechanistic insights into selective tRNA aminoacylation by AARSs.

Suggested Citation

  • Bingyi Chen & Fang Yi & Zhiteng Luo & Feihu Lu & Hongwei Liu & Siting Luo & Qiong Gu & Huihao Zhou, 2024. "The mechanism of discriminative aminoacylation by isoleucyl-tRNA synthetase based on wobble nucleotide recognition," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-55183-0
    DOI: 10.1038/s41467-024-55183-0
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    References listed on IDEAS

    as
    1. A. Brkic & M. Leibundgut & J. Jablonska & V. Zanki & Z. Car & V. Petrovic Perokovic & A. Marsavelski & N. Ban & I. Gruic-Sovulj, 2023. "Antibiotic hyper-resistance in a class I aminoacyl-tRNA synthetase with altered active site signature motif," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    2. Masahiro Naganuma & Shun-ichi Sekine & Yeeting Esther Chong & Min Guo & Xiang-Lei Yang & Howard Gamper & Ya-Ming Hou & Paul Schimmel & Shigeyuki Yokoyama, 2014. "The selective tRNA aminoacylation mechanism based on a single G•U pair," Nature, Nature, vol. 510(7506), pages 507-511, June.
    3. Bingyi Chen & Siting Luo & Songxuan Zhang & Yingchen Ju & Qiong Gu & Jun Xu & Xiang-Lei Yang & Huihao Zhou, 2021. "Author Correction: Inhibitory mechanism of reveromycin A at the tRNA binding site of a class I synthetase," Nature Communications, Nature, vol. 12(1), pages 1-1, December.
    4. Bingyi Chen & Siting Luo & Songxuan Zhang & Yingchen Ju & Qiong Gu & Jun Xu & Xiang-Lei Yang & Huihao Zhou, 2021. "Inhibitory mechanism of reveromycin A at the tRNA binding site of a class I synthetase," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    5. Scisung Chung & Mi-Sun Kang & Dauren S. Alimbetov & Gil-Im Mun & Na-Oh Yunn & Yunjin Kim & Byung-Gyu Kim & Minwoo Wie & Eun A. Lee & Jae Sun Ra & Jung-Min Oh & Donghyun Lee & Keondo Lee & Jihan Kim & , 2022. "Regulation of BRCA1 stability through the tandem UBX domains of isoleucyl-tRNA synthetase 1," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    6. Susan M. Rueter & T. Renee Dawson & Ronald B. Emeson, 1999. "Regulation of alternative splicing by RNA editing," Nature, Nature, vol. 399(6731), pages 75-80, May.
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