Robust and tunable signal processing in mammalian cells via engineered covalent modification cycles

Ross D. Jones, Yili Qian, Katherine Ilia, Benjamin Wang, Michael T. Laub, Domitilla Del Vecchio () and Ron Weiss ()
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Ross D. Jones: Massachusetts Institute of Technology
Yili Qian: Massachusetts Institute of Technology
Katherine Ilia: Massachusetts Institute of Technology
Benjamin Wang: Massachusetts Institute of Technology
Michael T. Laub: Massachusetts Institute of Technology
Domitilla Del Vecchio: Massachusetts Institute of Technology
Ron Weiss: Massachusetts Institute of Technology

Nature Communications, 2022, vol. 13, issue 1, 1-17

Abstract: Abstract Engineered signaling networks can impart cells with new functionalities useful for directing differentiation and actuating cellular therapies. For such applications, the engineered networks must be tunable, precisely regulate target gene expression, and be robust to perturbations within the complex context of mammalian cells. Here, we use bacterial two-component signaling proteins to develop synthetic phosphoregulation devices that exhibit these properties in mammalian cells. First, we engineer a synthetic covalent modification cycle based on kinase and phosphatase proteins derived from the bifunctional histidine kinase EnvZ, enabling analog tuning of gene expression via its response regulator OmpR. By regulating phosphatase expression with endogenous miRNAs, we demonstrate cell-type specific signaling responses and a new strategy for accurate cell type classification. Finally, we implement a tunable negative feedback controller via a small molecule-stabilized phosphatase, reducing output expression variance and mitigating the context-dependent effects of off-target regulation and resource competition. Our work lays the foundation for establishing tunable, precise, and robust control over cell behavior with synthetic signaling networks.

Date: 2022
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DOI: 10.1038/s41467-022-29338-w

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