Modular and tunable biological feedback control using a de novo protein switch

Andrew H. Ng, Taylor H. Nguyen, Mariana Gómez-Schiavon, Galen Dods, Robert A. Langan, Scott E. Boyken, Jennifer A. Samson, Lucas M. Waldburger, John E. Dueber, David Baker and Hana El-Samad ()
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Andrew H. Ng: University of California, San Francisco
Taylor H. Nguyen: University of California, San Francisco
Mariana Gómez-Schiavon: University of California, San Francisco
Galen Dods: University of California, San Francisco
Robert A. Langan: University of Washington
Scott E. Boyken: University of Washington
Jennifer A. Samson: University of California, Berkeley
Lucas M. Waldburger: University of California, Berkeley
John E. Dueber: University of California, Berkeley
David Baker: University of Washington
Hana El-Samad: University of California, San Francisco

Nature, 2019, vol. 572, issue 7768, 265-269

Abstract: Abstract De novo-designed proteins1–3 hold great promise as building blocks for synthetic circuits, and can complement the use of engineered variants of natural proteins4–7. One such designer protein—degronLOCKR, which is based on ‘latching orthogonal cage–key proteins’ (LOCKR) technology8—is a switch that degrades a protein of interest in vivo upon induction by a genetically encoded small peptide. Here we leverage the plug-and-play nature of degronLOCKR to implement feedback control of endogenous signalling pathways and synthetic gene circuits. We first generate synthetic negative and positive feedback in the yeast mating pathway by fusing degronLOCKR to endogenous signalling molecules, illustrating the ease with which this strategy can be used to rewire complex endogenous pathways. We next evaluate feedback control mediated by degronLOCKR on a synthetic gene circuit9, to quantify the feedback capabilities and operational range of the feedback control circuit. The designed nature of degronLOCKR proteins enables simple and rational modifications to tune feedback behaviour in both the synthetic circuit and the mating pathway. The ability to engineer feedback control into living cells represents an important milestone in achieving the full potential of synthetic biology10,11,12. More broadly, this work demonstrates the large and untapped potential of de novo design of proteins for generating tools that implement complex synthetic functionalities in cells for biotechnological and therapeutic applications.

Date: 2019
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DOI: 10.1038/s41586-019-1425-7

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