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Complete chemical structures of human mitochondrial tRNAs

Author

Listed:
  • Takeo Suzuki

    (University of Tokyo)

  • Yuka Yashiro

    (University of Tokyo)

  • Ittoku Kikuchi

    (University of Tokyo)

  • Yuma Ishigami

    (University of Tokyo)

  • Hironori Saito

    (RIKEN
    University of Tokyo)

  • Ikuya Matsuzawa

    (University of Tokyo)

  • Shunpei Okada

    (University of Tokyo
    Tokyo University of Science)

  • Mari Mito

    (RIKEN)

  • Shintaro Iwasaki

    (RIKEN
    University of Tokyo)

  • Ding Ma

    (University of Tokyo)

  • Xuewei Zhao

    (University of Tokyo)

  • Kana Asano

    (University of Tokyo)

  • Huan Lin

    (University of Tokyo
    Hainan University)

  • Yohei Kirino

    (Thomas Jefferson University)

  • Yuriko Sakaguchi

    (University of Tokyo)

  • Tsutomu Suzuki

    (University of Tokyo)

Abstract

Mitochondria generate most cellular energy via oxidative phosphorylation. Twenty-two species of mitochondrial (mt-)tRNAs encoded in mtDNA translate essential subunits of the respiratory chain complexes. mt-tRNAs contain post-transcriptional modifications introduced by nuclear-encoded tRNA-modifying enzymes. They are required for deciphering genetic code accurately, as well as stabilizing tRNA. Loss of tRNA modifications frequently results in severe pathological consequences. Here, we perform a comprehensive analysis of post-transcriptional modifications of all human mt-tRNAs, including 14 previously-uncharacterized species. In total, we find 18 kinds of RNA modifications at 137 positions (8.7% in 1575 nucleobases) in 22 species of human mt-tRNAs. An up-to-date list of 34 genes responsible for mt-tRNA modifications are provided. We identify two genes required for queuosine (Q) formation in mt-tRNAs. Our results provide insight into the molecular mechanisms underlying the decoding system and could help to elucidate the molecular pathogenesis of human mitochondrial diseases caused by aberrant tRNA modifications.

Suggested Citation

  • Takeo Suzuki & Yuka Yashiro & Ittoku Kikuchi & Yuma Ishigami & Hironori Saito & Ikuya Matsuzawa & Shunpei Okada & Mari Mito & Shintaro Iwasaki & Ding Ma & Xuewei Zhao & Kana Asano & Huan Lin & Yohei K, 2020. "Complete chemical structures of human mitochondrial tRNAs," Nature Communications, Nature, vol. 11(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-18068-6
    DOI: 10.1038/s41467-020-18068-6
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    Citations

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    Cited by:

    1. Yuta Noda & Shunpei Okada & Tsutomu Suzuki, 2022. "Regulation of A-to-I RNA editing and stop codon recoding to control selenoprotein expression during skeletal myogenesis," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    2. Sunita Maharjan & Howard Gamper & Yuka Yamaki & Thomas Christian & Robert Y. Henley & Nan-Sheng Li & Takeo Suzuki & Tsutomu Suzuki & Joseph A. Piccirilli & Meni Wanunu & Erin Seifert & Douglas C. Wall, 2024. "Post-transcriptional methylation of mitochondrial-tRNA differentially contributes to mitochondrial pathology," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    3. Zhangli Su & Ida Monshaugen & Briana Wilson & Fengbin Wang & Arne Klungland & Rune Ougland & Anindya Dutta, 2022. "TRMT6/61A-dependent base methylation of tRNA-derived fragments regulates gene-silencing activity and the unfolded protein response in bladder cancer," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    4. Vincent Meynier & Steven W. Hardwick & Marjorie Catala & Johann J. Roske & Stephanie Oerum & Dimitri Y. Chirgadze & Pierre Barraud & Wyatt W. Yue & Ben F. Luisi & Carine Tisné, 2024. "Structural basis for human mitochondrial tRNA maturation," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    5. Bernhard Kuhle & Marscha Hirschi & Lili K. Doerfel & Gabriel C. Lander & Paul Schimmel, 2022. "Structural basis for shape-selective recognition and aminoacylation of a D-armless human mitochondrial tRNA," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    6. Paula Clemente & Javier Calvo-Garrido & Sarah F. Pearce & Florian A. Schober & Megumi Shigematsu & Stefan J. Siira & Isabelle Laine & Henrik Spåhr & Christian Steinmetzger & Katja Petzold & Yohei Kiri, 2022. "ANGEL2 phosphatase activity is required for non-canonical mitochondrial RNA processing," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    7. Bernhard Kuhle & Marscha Hirschi & Lili K. Doerfel & Gabriel C. Lander & Paul Schimmel, 2023. "Structural basis for a degenerate tRNA identity code and the evolution of bimodal specificity in human mitochondrial tRNA recognition," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    8. Annika Krüger & Cristina Remes & Dmitrii Igorevich Shiriaev & Yong Liu & Henrik Spåhr & Rolf Wibom & Ilian Atanassov & Minh Duc Nguyen & Barry S. Cooperman & Joanna Rorbach, 2023. "Human mitochondria require mtRF1 for translation termination at non-canonical stop codons," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    9. Vivek Singh & Yuzuru Itoh & Samuel Del’Olio & Asem Hassan & Andreas Naschberger & Rasmus Kock Flygaard & Yuko Nobe & Keiichi Izumikawa & Shintaro Aibara & Juni Andréll & Paul C. Whitford & Antoni Barr, 2024. "Mitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk," Nature Communications, Nature, vol. 15(1), pages 1-22, December.

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