Robust and tunable signal processing in mammalian cells via engineered covalent modification cycles
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...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2022-03-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-022-29338-w |
| _version_ | 1797743962846396416 |
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| author | Ross D. Jones Yili Qian Katherine Ilia Benjamin Wang Michael T. Laub Domitilla Del Vecchio Ron Weiss |
| author_facet | Ross D. Jones Yili Qian Katherine Ilia Benjamin Wang Michael T. Laub Domitilla Del Vecchio Ron Weiss |
| author_sort | Ross D. Jones |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-12T15:03:03Z |
| format | Article |
| id | doaj.art-07b7c8171973444cb2597e662547c991 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-03-12T15:03:03Z |
| publishDate | 2022-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-07b7c8171973444cb2597e662547c9912023-08-13T11:16:28ZengNature PortfolioNature Communications2041-17232022-03-0113111710.1038/s41467-022-29338-wRobust and tunable signal processing in mammalian cells via engineered covalent modification cyclesRoss D. Jones0Yili Qian1Katherine Ilia2Benjamin Wang3Michael T. Laub4Domitilla Del Vecchio5Ron Weiss6Department of Biological Engineering, Massachusetts Institute of TechnologySynthetic Biology Center, Massachusetts Institute of TechnologyDepartment of Biological Engineering, Massachusetts Institute of TechnologySynthetic Biology Center, Massachusetts Institute of TechnologySynthetic Biology Center, Massachusetts Institute of TechnologySynthetic Biology Center, Massachusetts Institute of TechnologyDepartment of Biological Engineering, Massachusetts Institute of TechnologyAbstract 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.https://doi.org/10.1038/s41467-022-29338-w |
| spellingShingle | Ross D. Jones Yili Qian Katherine Ilia Benjamin Wang Michael T. Laub Domitilla Del Vecchio Ron Weiss Robust and tunable signal processing in mammalian cells via engineered covalent modification cycles Nature Communications |
| title | Robust and tunable signal processing in mammalian cells via engineered covalent modification cycles |
| title_full | Robust and tunable signal processing in mammalian cells via engineered covalent modification cycles |
| title_fullStr | Robust and tunable signal processing in mammalian cells via engineered covalent modification cycles |
| title_full_unstemmed | Robust and tunable signal processing in mammalian cells via engineered covalent modification cycles |
| title_short | Robust and tunable signal processing in mammalian cells via engineered covalent modification cycles |
| title_sort | robust and tunable signal processing in mammalian cells via engineered covalent modification cycles |
| url | https://doi.org/10.1038/s41467-022-29338-w |
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