Modular, robust, and extendible multicellular circuit design in yeast

Elife. 2022 Mar 21;11:e74540. doi: 10.7554/eLife.74540.


Division of labor between cells is ubiquitous in biology but the use of multicellular consortia for engineering applications is only beginning to be explored. A significant advantage of multicellular circuits is their potential to be modular with respect to composition but this claim has not yet been extensively tested using experiments and quantitative modeling. Here, we construct a library of 24 yeast strains capable of sending, receiving or responding to three molecular signals, characterize them experimentally and build quantitative models of their input-output relationships. We then compose these strains into two- and three-strain cascades as well as a four-strain bistable switch and show that experimentally measured consortia dynamics can be predicted from the models of the constituent parts. To further explore the achievable range of behaviors, we perform a fully automated computational search over all two-, three-, and four-strain consortia to identify combinations that realize target behaviors including logic gates, band-pass filters, and time pulses. Strain combinations that are predicted to map onto a target behavior are further computationally optimized and then experimentally tested. Experiments closely track computational predictions. The high reliability of these model descriptions further strengthens the feasibility and highlights the potential for distributed computing in synthetic biology.

Keywords: S. cerevisiae; automated circuit design; computational biology; parallel computing; synthetic multicellular circuit; systems biology.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Gene Library
  • Logic
  • Reproducibility of Results
  • Saccharomyces cerevisiae* / genetics
  • Synthetic Biology* / methods

Grant support

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.