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Autonomous ribosome biogenesis in vitro

Author

Listed:
  • Yuishin Kosaka

    (Kyoto University
    Japan Society for the Promotion of Science)

  • Yumi Miyawaki

    (Kyoto University)

  • Megumi Mori

    (Kyoto University)

  • Shunsuke Aburaya

    (Kyushu University)

  • Chisato Nishizawa

    (Kyoto University)

  • Takeshi Chujo

    (Kumamoto University
    JST FOREST)

  • Tatsuya Niwa

    (Institute of Science Tokyo)

  • Takumi Miyazaki

    (Kyoto University)

  • Takashi Sugita

    (Company)

  • Mao Fukuyama

    (JST FOREST
    Tohoku University)

  • Hideki Taguchi

    (Institute of Science Tokyo)

  • Kazuhito Tomizawa

    (Kumamoto University)

  • Kenji Sugase

    (Kyoto University)

  • Mitsuyoshi Ueda

    (Kyoto University
    Kyoto Integrated Science & Technology Bio-Analysis Center)

  • Wataru Aoki

    (JST FOREST
    Kyoto Integrated Science & Technology Bio-Analysis Center
    Osaka University)

Abstract

Ribosome biogenesis is pivotal in the self-replication of life. In Escherichia coli, three ribosomal RNAs and 54 ribosomal proteins are synthesized and subjected to cooperative hierarchical assembly facilitated by numerous accessory factors. Realizing ribosome biogenesis in vitro is a critical milestone for understanding the self-replication of life and creating artificial cells. Despite its importance, this goal has not yet been achieved owing to its complexity. In this study, we report the successful realization of ribosome biogenesis in vitro. Specifically, we developed a highly specific and sensitive reporter assay for the detection of nascent ribosomes. The reporter assay allowed for combinatorial and iterative exploration of reaction conditions for ribosome biogenesis, leading to the simultaneous, autonomous synthesis of both small and large subunits of ribosomes in vitro through transcription, translation, processing, and assembly in a single reaction space. Our achievement represents a crucial advancement toward revealing the fundamental principles underlying the self-replication of life and creating artificial cells.

Suggested Citation

  • Yuishin Kosaka & Yumi Miyawaki & Megumi Mori & Shunsuke Aburaya & Chisato Nishizawa & Takeshi Chujo & Tatsuya Niwa & Takumi Miyazaki & Takashi Sugita & Mao Fukuyama & Hideki Taguchi & Kazuhito Tomizaw, 2025. "Autonomous ribosome biogenesis in vitro," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-55853-7
    DOI: 10.1038/s41467-025-55853-7
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    References listed on IDEAS

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    1. Takahiro Tsuji & Hiroaki Ozasa & Wataru Aoki & Shunsuke Aburaya & Tomoko Yamamoto Funazo & Koh Furugaki & Yasushi Yoshimura & Masatoshi Yamazoe & Hitomi Ajimizu & Yuto Yasuda & Takashi Nomizo & Hirono, 2020. "YAP1 mediates survival of ALK-rearranged lung cancer cells treated with alectinib via pro-apoptotic protein regulation," Nature Communications, Nature, vol. 11(1), pages 1-16, December.
    2. Natalie S. Kolber & Ranan Fattal & Sinisa Bratulic & Gavriela D. Carver & Ahmed H. Badran, 2021. "Orthogonal translation enables heterologous ribosome engineering in E. coli," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    3. Cédric Orelle & Erik D. Carlson & Teresa Szal & Tanja Florin & Michael C. Jewett & Alexander S. Mankin, 2015. "Protein synthesis by ribosomes with tethered subunits," Nature, Nature, vol. 524(7563), pages 119-124, August.
    4. Hajin Kim & Sanjaya C. Abeysirigunawarden & Ke Chen & Megan Mayerle & Kaushik Ragunathan & Zaida Luthey-Schulten & Taekjip Ha & Sarah A. Woodson, 2014. "Protein-guided RNA dynamics during early ribosome assembly," Nature, Nature, vol. 506(7488), pages 334-338, February.
    5. Megan W. T. Talkington & Gary Siuzdak & James R. Williamson, 2005. "An assembly landscape for the 30S ribosomal subunit," Nature, Nature, vol. 438(7068), pages 628-632, December.
    6. Shijie Huang & Nikolay A. Aleksashin & Anna B. Loveland & Dorota Klepacki & Kaspar Reier & Amira Kefi & Teresa Szal & Jaanus Remme & Luc Jaeger & Nora Vázquez-Laslop & Andrei A. Korostelev & Alexander, 2020. "Ribosome engineering reveals the importance of 5S rRNA autonomy for ribosome assembly," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
    7. Nikolay A. Aleksashin & Margus Leppik & Adam J. Hockenberry & Dorota Klepacki & Nora Vázquez-Laslop & Michael C. Jewett & Jaanus Remme & Alexander S. Mankin, 2019. "Assembly and functionality of the ribosome with tethered subunits," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
    8. Erik D. Carlson & Anne E. d’Aquino & Do Soon Kim & Emily M. Fulk & Kim Hoang & Teresa Szal & Alexander S. Mankin & Michael C. Jewett, 2019. "Engineered ribosomes with tethered subunits for expanding biological function," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
    9. Michael J. Hammerling & Brian R. Fritz & Danielle J. Yoesep & Do Soon Kim & Erik D. Carlson & Michael C. Jewett, 2020. "In vitro ribosome synthesis and evolution through ribosome display," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    10. Tadepalli Adilakshmi & Deepti L. Bellur & Sarah A. Woodson, 2008. "Concurrent nucleation of 16S folding and induced fit in 30S ribosome assembly," Nature, Nature, vol. 455(7217), pages 1268-1272, October.
    11. Bo Qin & Simon M. Lauer & Annika Balke & Carlos H. Vieira-Vieira & Jörg Bürger & Thorsten Mielke & Matthias Selbach & Patrick Scheerer & Christian M. T. Spahn & Rainer Nikolay, 2023. "Cryo-EM captures early ribosome assembly in action," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
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