Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Designed cell consortia as fragrance-programmable analog-to-digital converters

Nature Chemical Biology volume 13, pages 309–316 (2017)Cite this article

Subjects

Abstract

Synthetic biology advances the rational engineering of mammalian cells to achieve cell-based therapy goals. Synthetic gene networks have nearly reached the complexity of digital electronic circuits and enable single cells to perform programmable arithmetic calculations or to provide dynamic remote control of transgenes through electromagnetic waves. We designed a synthetic multilayered gaseous-fragrance-programmable analog-to-digital converter (ADC) allowing for remote control of digital gene expression with 2-bit AND-, OR- and NOR-gate logic in synchronized cell consortia. The ADC consists of multiple sampling-and-quantization modules sensing analog gaseous fragrance inputs; a gas-to-liquid transducer converting fragrance intensity into diffusible cell-to-cell signaling compounds; a digitization unit with a genetic amplifier circuit to improve the signal-to-noise ratio; and recombinase-based digital expression switches enabling 2-bit processing of logic gates. Synthetic ADCs that can remotely control cellular activities with digital precision may enable the development of novel biosensors and may provide bioelectronic interfaces synchronizing analog metabolic pathways with digital electronics.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Design of the fragrance-programmable ADC with Boolean expression logic.
Figure 2: Characterization of the fragrance-sampling-and-quantization module and the gas-to-liquid transducer.
Figure 3: Characterization of the digitizer with integrated signal amplifier.
Figure 4: Expression logic by receiver-digitizer cells.
Figure 5: Fragrance-programmable analog-to-digital conversion.

Similar content being viewed by others

Accession codes

Primary accessions

NCBI Reference Sequence

References

  1. Brophy, J.A.N. & Voigt, C.A. Principles of genetic circuit design. Nat. Methods 11, 508–520 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Moon, T.S., Lou, C., Tamsir, A., Stanton, B.C. & Voigt, C.A. Genetic programs constructed from layered logic gates in single cells. Nature 491, 249–253 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Gitzinger, M., Kemmer, C., El-Baba, M.D., Weber, W. & Fussenegger, M. Controlling transgene expression in subcutaneous implants using a skin lotion containing the apple metabolite phloretin. Proc. Natl. Acad. Sci. USA 106, 10638–10643 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Gitzinger, M. et al. The food additive vanillic acid controls transgene expression in mammalian cells and mice. Nucleic Acids Res. 40, e37 (2012).

    Article  CAS  PubMed  Google Scholar 

  5. Weber, W., Bacchus, W., Daoud-El Baba, M. & Fussenegger, M. Vitamin H-regulated transgene expression in mammalian cells. Nucleic Acids Res. 35, e116 (2007).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  6. Weber, W. et al. Conditional human VEGF-mediated vascularization in chicken embryos using a novel temperature-inducible gene regulation (TIGR) system. Nucleic Acids Res. 31, e69 (2003).

    Article  PubMed  PubMed Central  Google Scholar 

  7. Boorsma, M. et al. A temperature-regulated replicon-based DNA expression system. Nat. Biotechnol. 18, 429–432 (2000).

    Article  CAS  PubMed  Google Scholar 

  8. Ausländer, D. et al. A synthetic multifunctional mammalian pH sensor and CO2 transgene-control device. Mol. Cell 55, 397–408 (2014).

    Article  PubMed  CAS  Google Scholar 

  9. Stanley, S.A. et al. Radio-wave heating of iron oxide nanoparticles can regulate plasma glucose in mice. Science 336, 604–608 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Folcher, M. et al. Mind-controlled transgene expression by a wireless-powered optogenetic designer cell implant. Nat. Commun. 5, 5392 (2014).

    Article  CAS  PubMed  Google Scholar 

  11. Weber, W. & Fussenegger, M. Inducible product gene expression technology tailored to bioprocess engineering. Curr. Opin. Biotechnol. 18, 399–410 (2007).

    Article  CAS  PubMed  Google Scholar 

  12. Weber, W. & Fussenegger, M. Emerging biomedical applications of synthetic biology. Nat. Rev. Genet. 13, 21–35 (2011).

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  13. Tigges, M., Marquez-Lago, T.T., Stelling, J. & Fussenegger, M. A tunable synthetic mammalian oscillator. Nature 457, 309–312 (2009).

    Article  CAS  PubMed  Google Scholar 

  14. Benenson, Y. Biomolecular computing systems: principles, progress and potential. Nat. Rev. Genet. 13, 455–468 (2012).

    Article  CAS  PubMed  Google Scholar 

  15. Ausländer, S., Ausländer, D., Müller, M., Wieland, M. & Fussenegger, M. Programmable single-cell mammalian biocomputers. Nature 487, 123–127 (2012).

    Article  PubMed  CAS  Google Scholar 

  16. Ausländer, S., Wieland, M. & Fussenegger, M. Smart medication through combination of synthetic biology and cell microencapsulation. Metab. Eng. 14, 252–260 (2012).

    Article  PubMed  CAS  Google Scholar 

  17. Kemmer, C. et al. Self-sufficient control of urate homeostasis in mice by a synthetic circuit. Nat. Biotechnol. 28, 355–360 (2010).

    Article  CAS  PubMed  Google Scholar 

  18. Rössger, K., Charpin-El-Hamri, G. & Fussenegger, M. Bile acid-controlled transgene expression in mammalian cells and mice. Metab. Eng. 21, 81–90 (2014).

    Article  PubMed  CAS  Google Scholar 

  19. Saxena, P., Charpin-El Hamri, G., Folcher, M., Zulewski, H. & Fussenegger, M. Synthetic gene network restoring endogenous pituitary-thyroid feedback control in experimental Graves' disease. Proc. Natl. Acad. Sci. USA 113, 1244–1249 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Schukur, L., Geering, B., Charpin-El Hamri, G. & Fussenegger, M. Implantable synthetic cytokine converter cells with AND-gate logic treat experimental psoriasis. Sci. Transl. Med. 7, 318ra201 (2015).

    Article  PubMed  CAS  Google Scholar 

  21. Riccione, K.A., Smith, R.P., Lee, A.J. & You, L. A synthetic biology approach to understanding cellular information processing. ACS Synth. Biol. 1, 389–402 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Regot, S. et al. Distributed biological computation with multicellular engineered networks. Nature 469, 207–211 (2011).

    Article  CAS  PubMed  Google Scholar 

  23. Tamsir, A., Tabor, J.J. & Voigt, C.A. Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'. Nature 469, 212–215 (2011).

    Article  CAS  PubMed  Google Scholar 

  24. Tubio, M.R. et al. Expression of a G protein-coupled receptor (GPCR) leads to attenuation of signaling by other GPCRs: experimental evidence for a spontaneous GPCR constitutive inactive form. J. Biol. Chem. 285, 14990–14998 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Bushdid, C., Magnasco, M.O., Vosshall, L.B. & Keller, A. Humans can discriminate more than 1 trillion olfactory stimuli. Science 343, 1370–1372 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Nern, A., Pfeiffer, B.D., Svoboda, K. & Rubin, G.M. Multiple new site-specific recombinases for use in manipulating animal genomes. Proc. Natl. Acad. Sci. USA 108, 14198–14203 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Fenno, L.E. et al. Targeting cells with single vectors using multiple-feature Boolean logic. Nat. Methods 11, 763–772 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Yang, L. et al. Permanent genetic memory with >1-byte capacity. Nat. Methods 11, 1261–1266 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Friedland, A.E. et al. Synthetic gene networks that count. Science 324, 1199–1202 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Lapique, N. & Benenson, Y. Digital switching in a biosensor circuit via programmable timing of gene availability. Nat. Chem. Biol. 10, 1020–1027 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Schönhuber, N. et al. A next-generation dual-recombinase system for time- and host-specific targeting of pancreatic cancer. Nat. Med. 20, 1340–1347 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  32. Xie, Z., Wroblewska, L., Prochazka, L., Weiss, R. & Benenson, Y. Multi-input RNAi-based logic circuit for identification of specific cancer cells. Science 333, 1307–1311 (2011).

    Article  CAS  PubMed  Google Scholar 

  33. Morel, M., Shtrahman, R., Rotter, V., Nissim, L. & Bar-Ziv, R.H. Cellular heterogeneity mediates inherent sensitivity-specificity tradeoff in cancer targeting by synthetic circuits. Proc. Natl. Acad. Sci. USA 113, 8133–8138 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Nissim, L. & Bar-Ziv, R.H. A tunable dual-promoter integrator for targeting of cancer cells. Mol. Syst. Biol. 6, 444 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  35. Toh-e, A. & Utatsu, I. Physical and functional structure of a yeast plasmid, pSB3, isolated from Zygosaccharomyces bisporus. Nucleic Acids Res. 13, 4267–4283 (1985).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Bonnet, J., Yin, P., Ortiz, M.E., Subsoontorn, P. & Endy, D. Amplifying genetic logic gates. Science 340, 599–603 (2013).

    Article  CAS  PubMed  Google Scholar 

  37. Hartwell, L.H., Hopfield, J.J., Leibler, S. & Murray, A.W. From molecular to modular cell biology. Nature 402 Suppl: C47–C52 (1999).

    Article  CAS  PubMed  Google Scholar 

  38. Sprinzak, D. et al. Cis-interactions between Notch and Delta generate mutually exclusive signalling states. Nature 465, 86–90 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Morsut, L. et al. Engineering customized cell sensing and response behaviors using synthetic Notch receptors. Cell 164, 780–791 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Clark, B. & Häusser, M. Neural coding: hybrid analog and digital signalling in axons. Curr. Biol. 16, R585–R588 (2006).

    Article  CAS  PubMed  Google Scholar 

  41. Dreosti, E., Esposti, F., Baden, T. & Lagnado, L. In vivo evidence that retinal bipolar cells generate spikes modulated by light. Nat. Neurosci. 14, 951–952 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Hahnloser, R.H., Sarpeshkar, R., Mahowald, M.A., Douglas, R.J. & Seung, H.S. Digital selection and analogue amplification coexist in a cortex-inspired silicon circuit. Nature 405, 947–951 (2000).

    Article  CAS  PubMed  Google Scholar 

  43. Firestein, S. How the olfactory system makes sense of scents. Nature 413, 211–218 (2001).

    Article  CAS  PubMed  Google Scholar 

  44. Roybal, K.T. et al. Precision tumor recognition by T cells with combinatorial antigen-sensing circuits. Cell 164, 770–779 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Chen, Y.Y., Jensen, M.C. & Smolke, C.D. Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems. Proc. Natl. Acad. Sci. USA 107, 8531–8536 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Kemmer, C. et al. A designer network coordinating bovine artificial insemination by ovulation-triggered release of implanted sperms. J. Control. Release 150, 23–29 (2011).

    Article  CAS  PubMed  Google Scholar 

  47. Ye, H., Daoud-El Baba, M., Peng, R.W. & Fussenegger, M. A synthetic optogenetic transcription device enhances blood-glucose homeostasis in mice. Science 332, 1565–1568 (2011).

    Article  CAS  PubMed  Google Scholar 

  48. Roquet, N., Soleimany, A.P., Ferris, A.C., Aaronson, S. & Lu, T.K. Synthetic recombinase-based state machines in living cells. Science 353, aad8559 (2016).

    Article  PubMed  CAS  Google Scholar 

  49. Siuti, P., Yazbek, J. & Lu, T.K. Synthetic circuits integrating logic and memory in living cells. Nat. Biotechnol. 31, 448–452 (2013).

    Article  CAS  PubMed  Google Scholar 

  50. Rubens, J.R., Selvaggio, G. & Lu, T.K. Synthetic mixed-signal computation in living cells. Nat. Commun. 7, 11658 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Saito, H., Kubota, M., Roberts, R.W., Chi, Q. & Matsunami, H. RTP family members induce functional expression of mammalian odorant receptors. Cell 119, 679–691 (2004).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank T. Horn, E. Montani, T. Lopes and V. Jaeggin for their support with microscopy and flow cytometry. We thank F. Sedlmayer, V. Viswam, S. Bürgel and P. Buchmann for their generous advice and O. Chepurny and G. Holz (Department of Physiology and Neuroscience, New York University School of Medicine, New York, USA), H. Matsunami (Department of Molecular Genetics and Microbiology, Duke University Medical Center, North Carolina, USA), H. Ye (Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China) and W. Bacchus (Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland) for providing plasmids and genetic components. This work was supported by a European Research Council (ERC) advanced grant (ProNet, no. 321381) and in part by funding from the National Centre of Competence in Research (NCCR) for Molecular Systems Engineering awarded to M.F.

Author information

Authors and Affiliations

  1. Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland

    Marius Müller, Simon Ausländer, Andrea Spinnler, David Ausländer, Julian Sikorski, Marc Folcher & Martin Fussenegger

  2. Faculty of Science, University of Basel, Basel, Switzerland

    Martin Fussenegger

Authors
  1. Marius Müller
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Simon Ausländer
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Andrea Spinnler
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. David Ausländer
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Julian Sikorski
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Marc Folcher
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Martin Fussenegger
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

M.M., S.A., D.A., M. Folcher and M. Fussenegger designed the project and analyzed the results; M.M., J.S. and A.S. performed the experimental work; and M.M. and M. Fussenegger wrote the manuscript.

Corresponding author

Correspondence to Martin Fussenegger.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Results, Supplementary Tables 1–3 and Supplementary Figures 1–13 (PDF 3812 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Müller, M., Ausländer, S., Spinnler, A. et al. Designed cell consortia as fragrance-programmable analog-to-digital converters. Nat Chem Biol 13, 309–316 (2017). https://doi.org/10.1038/nchembio.2281

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nchembio.2281

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing