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Understanding resource competition to achieve predictable synthetic gene expression in eukaryotes

Nature Reviews Bioengineering (2024)Cite this article

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Abstract

Synthetic gene expression in engineered cells typically depends on the host cell’s limited pool of intracellular resources, which can lead to resource competition between native and engineered functions and may cause unanticipated effects in the host and synthetic gene circuit. For example, competition for shared resources may lead to cellular overload affecting physiological functions (that is, cellular burden) and negatively affect synthetic construct performance to the point of unreliability. This fundamental problem has implications for the use of synthetic genetic constructs in cell engineering for foundational research, therapy and bioprocessing. Resource competition has mainly been investigated in model bacteria systems, but also considerably affects eukaryotic systems, including mammalian cells. In this Review, we discuss resource competition beyond bacteria, outlining how it can lead to gene expression coupling, gene expression and metabolic burden. We also examine ways to quantify cellular burden in mammalian cells, and investigate circuit-centric and host-centric mitigation strategies, highlighting important implications of resource competition for cell engineering in therapeutic and bioproduction applications as well as in fundamental biology studies.

Key points

  • Synthetic genetic circuits use metabolic, transcriptional, translational and post-translational resources from their engineered host cells, competing with native functions and leading to cellular burden.

  • Resource competition has been well described in prokaryotes, but is often overlooked in eukaryotic organisms, including in mammalian cells.

  • Cellular burden caused by resource competition can be quantified and mitigated in eukaryotic systems to achieve predictability in gene expression.

  • Understanding and mitigating resource competition and cellular burden may improve cell engineering for bioproduction, therapy and fundamental biology.

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Fig. 1: Resource competition between native and engineered cellular functions.
Fig. 2: Tools to quantify cellular burden.
Fig. 3: Mitigation of resource competition by circuit-centric approaches.
Fig. 4: Mitigation of resource competition by host-centric approaches.

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Acknowledgements

The authors acknowledge support from the Engineering and Physical Sciences Research Council (EPSRC) Centre for Doctoral Training in BioDesign Engineering (EP/S022856/1) (to J.G., C.K., T.E., R.L.-A. and F.C.). R.D.B. was supported by the Imperial College Chemical Engineering PhD scholarship. R.L.-A. received funding from the European Research Council (ERC) (DEUSBIO-949080). K.S. acknowledges a postdoctoral fellowship from the European Molecular Biology Organization (EMBO) (ALTF 769-2021) and a UKRI-Marie Skłodowska-Curie Actions (UKRI-MSCA) Postdoctoral Fellowship (UNICOH).

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  1. These authors contributed equally: Roberto Di Blasi, Jacopo Gabrielli, Kiyan Shabestary.

Authors and Affiliations

  1. Department of Chemical Engineering, Imperial College London, London, UK

    Roberto Di Blasi, Jacopo Gabrielli, Ioanna Ziarti, Cleo Kontoravdi & Francesca Ceroni

  2. Imperial College Centre for Synthetic Biology, Imperial College London, London, UK

    Roberto Di Blasi, Jacopo Gabrielli, Kiyan Shabestary, Tom Ellis, Cleo Kontoravdi, Rodrigo Ledesma-Amaro & Francesca Ceroni

  3. Department of Bioengineering, Imperial College London, London, UK

    Kiyan Shabestary, Tom Ellis & Rodrigo Ledesma-Amaro

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R.D.B., T.E. and F.C. conceived the work. I.Z. contributed background literature research. All authors wrote and edited the manuscript.

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Di Blasi, R., Gabrielli, J., Shabestary, K. et al. Understanding resource competition to achieve predictable synthetic gene expression in eukaryotes. Nat Rev Bioeng (2024). https://doi.org/10.1038/s44222-024-00206-0

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