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Following translation by single ribosomes one codon at a time

Author

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  • Jin-Der Wen

    (University of California, Berkeley, California 94720, USA)

  • Laura Lancaster

    (Cell, and Developmental Biology, and Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA)

  • Courtney Hodges

    (Biophysics Graduate Group, University of California, Berkeley, California 94720, USA)

  • Ana-Carolina Zeri

    (Brazilian Synchrotron Light Laboratory, Caixa Postal 6192, Campinas SP 13083-970, Brazil)

  • Shige H. Yoshimura

    (Graduate School of Biostudies, Kyoto University, Yoshida-honmachi, Sakyo-ku, Kyoto, 606-8501, Japan)

  • Harry F. Noller

    (Cell, and Developmental Biology, and Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA)

  • Carlos Bustamante

    (University of California, Berkeley, California 94720, USA
    Biophysics Graduate Group, University of California, Berkeley, California 94720, USA
    Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA)

  • Ignacio Tinoco

    (University of California, Berkeley, California 94720, USA)

Abstract

We have followed individual ribosomes as they translate single messenger RNA hairpins tethered by the ends to optical tweezers. Here we reveal that translation occurs through successive translocation-and-pause cycles. The distribution of pause lengths, with a median of 2.8 s, indicates that at least two rate-determining processes control each pause. Each translocation step measures three bases—one codon—and occurs in less than 0.1 s. Analysis of the times required for translocation reveals, surprisingly, that there are three substeps in each step. Pause lengths, and thus the overall rate of translation, depend on the secondary structure of the mRNA; the applied force destabilizes secondary structure and decreases pause durations, but does not affect translocation times. Translocation and RNA unwinding are strictly coupled ribosomal functions.

Suggested Citation

  • Jin-Der Wen & Laura Lancaster & Courtney Hodges & Ana-Carolina Zeri & Shige H. Yoshimura & Harry F. Noller & Carlos Bustamante & Ignacio Tinoco, 2008. "Following translation by single ribosomes one codon at a time," Nature, Nature, vol. 452(7187), pages 598-603, April.
    • Handle: RePEc:nat:nature:v:452:y:2008:i:7187:d:10.1038_nature06716
    DOI: 10.1038/nature06716
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    Cited by:

    1. Yosuke Ito & Yuhei Chadani & Tatsuya Niwa & Ayako Yamakawa & Kodai Machida & Hiroaki Imataka & Hideki Taguchi, 2022. "Nascent peptide-induced translation discontinuation in eukaryotes impacts biased amino acid usage in proteomes," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    2. Chen Bao & Mingyi Zhu & Inna Nykonchuk & Hironao Wakabayashi & David H. Mathews & Dmitri N. Ermolenko, 2022. "Specific length and structure rather than high thermodynamic stability enable regulatory mRNA stem-loops to pause translation," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    3. Chris H. Hill & Lukas Pekarek & Sawsan Napthine & Anuja Kibe & Andrew E. Firth & Stephen C. Graham & Neva Caliskan & Ian Brierley, 2021. "Structural and molecular basis for Cardiovirus 2A protein as a viral gene expression switch," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    4. Shuting Yan & Qiyao Zhu & Swati Jain & Tamar Schlick, 2022. "Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression," Nature Communications, Nature, vol. 13(1), pages 1-13, December.

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