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Controlling orthogonal ribosome subunit interactions enables evolution of new function

Author

Listed:
  • Wolfgang H. Schmied

    (Medical Research Council Laboratory of Molecular Biology)

  • Zakir Tnimov

    (Medical Research Council Laboratory of Molecular Biology)

  • Chayasith Uttamapinant

    (Medical Research Council Laboratory of Molecular Biology
    Vidyasirimedhi Institute of Science and Technology (VISTEC))

  • Christopher D. Rae

    (Medical Research Council Laboratory of Molecular Biology)

  • Stephen D. Fried

    (Medical Research Council Laboratory of Molecular Biology
    Johns Hopkins University)

  • Jason W. Chin

    (Medical Research Council Laboratory of Molecular Biology)

Abstract

Orthogonal ribosomes are unnatural ribosomes that are directed towards orthogonal messenger RNAs in Escherichia coli, through an altered version of the 16S ribosomal RNA of the small subunit1. Directed evolution of orthogonal ribosomes has provided access to new ribosomal function, and the evolved orthogonal ribosomes have enabled the encoding of multiple non-canonical amino acids into proteins2–4. The original orthogonal ribosomes shared the pool of 23S ribosomal RNAs, contained in the large subunit, with endogenous ribosomes. Selectively directing a new 23S rRNA to an orthogonal mRNA, by controlling the association between the orthogonal 16S rRNAs and 23S rRNAs, would enable the evolution of new function in the large subunit. Previous work covalently linked orthogonal 16S rRNA and a circularly permuted 23S rRNA to create orthogonal ribosomes with low activity5,6; however, the linked subunits in these ribosomes do not associate specifically with each other, and mediate translation by associating with endogenous subunits. Here we discover engineered orthogonal ‘stapled’ ribosomes (with subunits linked through an optimized RNA staple) with activities comparable to that of the parent orthogonal ribosome; they minimize association with endogenous subunits and mediate translation of orthogonal mRNAs through the association of stapled subunits. We evolve cells with genomically encoded stapled ribosomes as the sole ribosomes, which support cellular growth at similar rates to natural ribosomes. Moreover, we visualize the engineered stapled ribosome structure by cryo-electron microscopy at 3.0 Å, revealing how the staple links the subunits and controls their association. We demonstrate the utility of controlling subunit association by evolving orthogonal stapled ribosomes which efficiently polymerize a sequence of monomers that the natural ribosome is intrinsically unable to translate. Our work provides a foundation for evolving the rRNA of the entire orthogonal ribosome for the encoded cellular synthesis of non-canonical biological polymers7.

Suggested Citation

  • Wolfgang H. Schmied & Zakir Tnimov & Chayasith Uttamapinant & Christopher D. Rae & Stephen D. Fried & Jason W. Chin, 2018. "Controlling orthogonal ribosome subunit interactions enables evolution of new function," Nature, Nature, vol. 564(7736), pages 444-448, December.
    • Handle: RePEc:nat:nature:v:564:y:2018:i:7736:d:10.1038_s41586-018-0773-z
    DOI: 10.1038/s41586-018-0773-z
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    Citations

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    Cited by:

    1. Wenwen Yu & Ke Jin & Dandan Wang & Nankai Wang & Yangyang Li & Yanfeng Liu & Jianghua Li & Guocheng Du & Xueqin Lv & Jian Chen & Rodrigo Ledesma-Amaro & Long Liu, 2024. "De novo engineering of programmable and multi-functional biomolecular condensates for controlled biosynthesis," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Antje Krüger & Andrew M. Watkins & Roger Wellington-Oguri & Jonathan Romano & Camila Kofman & Alysse DeFoe & Yejun Kim & Jeff Anderson-Lee & Eli Fisker & Jill Townley & Anne E. d’Aquino & Rhiju Das & , 2023. "Community science designed ribosomes with beneficial phenotypes," Nature Communications, Nature, vol. 14(1), pages 1-11, December.

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