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Resource-aware construct design in mammalian cells

Author

Listed:
  • Roberto Di Blasi

    (Imperial College London, South Kensington Campus
    South Kensington Campus)

  • Mara Pisani

    (Instituto Italiano di Tecnologia-IIT, Largo Barsanti e Matteucci
    Open University affiliated centre)

  • Fabiana Tedeschi

    (Instituto Italiano di Tecnologia-IIT, Largo Barsanti e Matteucci
    University of Naples Federico II)

  • Masue M. Marbiah

    (Imperial College London, South Kensington Campus
    South Kensington Campus)

  • Karen Polizzi

    (Imperial College London, South Kensington Campus
    South Kensington Campus)

  • Simone Furini

    (University of Bologna)

  • Velia Siciliano

    (Instituto Italiano di Tecnologia-IIT, Largo Barsanti e Matteucci)

  • Francesca Ceroni

    (Imperial College London, South Kensington Campus
    South Kensington Campus)

Abstract

Resource competition can be the cause of unintended coupling between co-expressed genetic constructs. Here we report the quantification of the resource load imposed by different mammalian genetic components and identify construct designs with increased performance and reduced resource footprint. We use these to generate improved synthetic circuits and optimise the co-expression of transfected cassettes, shedding light on how this can be useful for bioproduction and biotherapeutic applications. This work provides the scientific community with a framework to consider resource demand when designing mammalian constructs to achieve robust and optimised gene expression.

Suggested Citation

  • Roberto Di Blasi & Mara Pisani & Fabiana Tedeschi & Masue M. Marbiah & Karen Polizzi & Simone Furini & Velia Siciliano & Francesca Ceroni, 2023. "Resource-aware construct design in mammalian cells," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-39252-4
    DOI: 10.1038/s41467-023-39252-4
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    References listed on IDEAS

    as
    1. Timothy Frei & Federica Cella & Fabiana Tedeschi & Joaquín Gutiérrez & Guy-Bart Stan & Mustafa Khammash & Velia Siciliano, 2020. "Characterization and mitigation of gene expression burden in mammalian cells," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    2. Hsin-Ho Huang & Yili Qian & Domitilla Del Vecchio, 2018. "A quasi-integral controller for adaptation of genetic modules to variable ribosome demand," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
    3. 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.
    4. 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.
    5. Chenrui Qin & Yanhui Xiang & Jie Liu & Ruilin Zhang & Ziming Liu & Tingting Li & Zhi Sun & Xiaoyi Ouyang & Yeqing Zong & Haoqian M. Zhang & Qi Ouyang & Long Qian & Chunbo Lou, 2023. "Precise programming of multigene expression stoichiometry in mammalian cells by a modular and programmable transcriptional system," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    6. Roberto Di Blasi & Masue M. Marbiah & Velia Siciliano & Karen Polizzi & Francesca Ceroni, 2021. "A call for caution in analysing mammalian co-transfection experiments and implications of resource competition in data misinterpretation," Nature Communications, Nature, vol. 12(1), pages 1-6, December.
    7. Ross D. Jones & Yili Qian & Velia Siciliano & Breanna DiAndreth & Jin Huh & Ron Weiss & Domitilla Del Vecchio, 2020. "An endoribonuclease-based feedforward controller for decoupling resource-limited genetic modules in mammalian cells," Nature Communications, Nature, vol. 11(1), pages 1-16, December.
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    Cited by:

    1. Andras Gyorgy, 2023. "Competition and evolutionary selection among core regulatory motifs in gene expression control," Nature Communications, Nature, vol. 14(1), pages 1-12, December.

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