Brief Communication

Quantifying cellular capacity identifies gene expression designs with reduced burden

  • Nature Methods volume 12, pages 415418 (2015)
  • doi:10.1038/nmeth.3339
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Abstract

Heterologous gene expression can be a significant burden for cells. Here we describe an in vivo monitor that tracks changes in the capacity of Escherichia coli in real time and can be used to assay the burden imposed by synthetic constructs and their parts. We identify construct designs with reduced burden that predictably outperformed less efficient designs, despite having equivalent output.

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Change history

  • Corrected online 25 June 2015

    In the version of the Supplementary Software originally posted online, some files needed to run the software were missing. These files have been included as of 25 June 2015.

References

  1. 1.

    & Bioinformatics 22, 2790–2799 (2006).

  2. 2.

    et al. Microbiology 159, 1236–1253 (2013).

  3. 3.

    & Nat. Methods 11, 508–520 (2014).

  4. 4.

    & Adv. Biochem. Eng. Biotechnol. 89, 73–92 (2004).

  5. 5.

    , , & Mol. Cell 38, 758–767 (2010).

  6. 6.

    , , , & ACS Synth. Biol. 3, 129–139 (2014).

  7. 7.

    & Biotechnol. J. 7, 856–866 (2012).

  8. 8.

    & ACS Synth. Biol. 2, 519–528 (2013).

  9. 9.

    et al. ACS Synth. Biol. 1, 555–564 (2012).

  10. 10.

    , & Nat. Chem. Biol. 5, 842–848 (2009).

  11. 11.

    , & Cell Rep. 4, 231–237 (2013).

  12. 12.

    , , , & ACS Synth. Biol. 3, 416–425 (2014).

  13. 13.

    , & Cell 139, 1366–1375 (2009).

  14. 14.

    , , , & Science 330, 1099–1102 (2010).

  15. 15.

    , , , & Biotechnol. J. 6, 773–783 (2011).

  16. 16.

    , , & Mol. Syst. Biol. 9, 658 (2013).

  17. 17.

    , , & J. Mol. Biol. 231, 678–688 (1993).

  18. 18.

    , & In Proc. 53rd IEEE Conference on Decision and Control (IEEE, 2014).

  19. 19.

    , , , & J. Biol. Chem. 289, 28160–28171 (2014).

  20. 20.

    et al. Biotechnol. J. 8, 1379–1395 (2013).

  21. 21.

    , , & Nature 497, 619–623 (2013).

  22. 22.

    , , , & Nature 491, 249–253 (2012).

  23. 23.

    & Science 346, 1256272 (2014).

  24. 24.

    , & Nature 403, 339–342 (2000).

  25. 25.

    & J. Bacteriol. 183, 6384–6393 (2001).

  26. 26.

    , , , & Nat. Biotechnol. 24, 79–88 (2006).

  27. 27.

    , & J. Biol. Eng. 2, 5 (2008).

  28. 28.

    , & Nat. Biotechnol. 26, 787–793 (2008).

  29. 29.

    et al. Nat. Methods 6, 343–345 (2009).

  30. 30.

    & Nucleic Acids Res. 37, 184–192 (2009).

  31. 31.

    et al. Nucleic Acids Res. 42, D459–D471 (2014).

  32. 32.

    , , , & Protein Eng. 14, 529–532 (2001).

  33. 33.

    Methods Enzymol. 498, 19–42 (2011).

  34. 34.

    & Nat. Protoc. 6, 242–251 (2011).

  35. 35.

    et al. PLoS ONE 4, e7002 (2009).

  36. 36.

    & Nat. Rev. Genet. 12, 32–42 (2011).

  37. 37.

    , & J. Mol. Biol. 382, 236–245 (2008).

  38. 38.

    & Biotechnol. Bioeng. 90, 116–126 (2005).

  39. 39.

    , & Nature 484, 538–541 (2012).

  40. 40.

    , , & Cell 157, 624–635 (2014).

  41. 41.

    & Genome Biol. 12, R12 (2011).

  42. 42.

    , & Science 342, 475–479 (2013).

  43. 43.

    et al. Nucleic Acids Res. 33, W526–W531 (2005).

  44. 44.

    , , & Nucleic Acids Res. 35, W126–W131 (2007).

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Acknowledgements

The authors thank J.J. Collins, M. Scott, D. Goodman, A. Wipat, D. Siegal-Gaskins, J. Lucks, J. Chappell, C. Hirst, K. Royle and colleagues at the Centre for Synthetic Biology and Innovation for thoughts and advice during this project. This work was supported by grants from the UK Engineering and Physical Research Council (EP/G036004/1, EP/J021849/1 and EP/J02175X/1).

Author information

Affiliations

  1. Centre for Synthetic Biology and Innovation, Imperial College London, London, UK.

    • Francesca Ceroni
    • , Rhys Algar
    • , Guy-Bart Stan
    •  & Tom Ellis
  2. Department of Bioengineering, Imperial College London, London, UK.

    • Francesca Ceroni
    • , Rhys Algar
    • , Guy-Bart Stan
    •  & Tom Ellis

Authors

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Contributions

F.C., R.A., G.-B.S. and T.E. designed the research; F.C. and R.A. performed the experiments; R.A. and G.-B.S. developed and performed model simulations; F.C., G.-B.S. and T.E. analyzed data; F.C., G.-B.S. and T.E. wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Tom Ellis.

Integrated supplementary information

Supplementary information

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    Supplementary Text and Figures

    Supplementary Figures 1–15, Supplementary Tables 1–6 and Supplementary Notes 1–5

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    Supplementary Software

    Supplementary Software