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Designing customized cell signalling circuits

Nature Reviews Molecular Cell Biology volume 11, pages 393–403 (2010)Cite this article

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Key Points

  • Efforts to engineer cells with customized signalling circuits will teach us about the design principles underlying natural signalling networks and could lead to important applications in medicine and biotechnology, such as specialized anti-cancer cells.

  • There have been exciting recent developments in engineering synthetic or modified sensors and receptors that allow novel inputs to control complex natural responses or allow natural inputs to control novel responses. Engineered sensors have also been developed that allow small molecules or light to precisely control biological responses.

  • Engineering highly diverse sensors remains a big challenge in synthetic biology. However, some examples, such as chimeric T cell receptors that incorporate a single-chain antibody as the extracellular domain, offer a strategy for custom receptor design.

  • The modularity of intracellular signalling proteins can be exploited to generate diverse signal processing circuits. Many protein circuits are dependent on the organization of key proteins into specific complexes and assemblies. Thus, recombination and reorganization of specific catalytic domains with different interaction domains provides a way for both evolution and engineering to generate novel circuit wiring.

  • The modification of spatially controlled signalling circuits can lead to cells with new morphological behaviours.

  • Advances that may facilitate the engineering of customized signalling include improved molecular tool kits that are optimized for predictability, and incorporation of combinatorial library design into the engineering process.

Abstract

Living cells have evolved a broad array of complex signalling responses, which enables them to survive diverse environmental challenges and execute specific physiological functions. Our increasingly sophisticated understanding of the molecular mechanisms of cell signalling networks in eukaryotes has revealed a remarkably modular organization and synthetic biologists are exploring how this can be exploited to engineer cells with novel signalling behaviours. This approach is beginning to reveal the logic of how cells might evolve innovative new functions and moves us towards the exciting possibility of engineering custom cells with precise sensing–response functions that could be useful in medicine and biotechnology.

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Figure 1: The general organization and behaviour of cell signalling circuits.
Figure 2: Applications of rewired cell signalling circuits.
Figure 3: Engineering novel signalling sensors.
Figure 4: The modular logic of intracellular signalling components.
Figure 5: Engineering signal processing circuits.
Figure 6: Engineering spatial regulation.
Figure 7: Improving the tool kit for predictable engineering of cell signalling: orthogonal interaction parts.

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Acknowledgements

I thank the following colleagues for many insightful discussions: C. Bashor, B. Conklin, J. Dueber, M. Dustin, D. Fletcher, C. June, A. Levskaya, M. Milone, R.D. Mullins, J. Onuffer, J. Park, B. Rhau, C. Voigt, O. Weiner, W. Wong and B. Yeh. This work was supported by grants from the National Institutes of Health (the Institute of General Medicine and the Nanomedicine Development Centers), the National Science Foundation Engineering Research Centers, the Packard Foundation and the Howard Hughes Medical Institute.

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  1. Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 94158, California, USA

    Wendell A. Lim

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Bart Vanhaesebroeck is an advisor to Intellikine (San Diego, uSA) and Karus Therapeutics (Southampton, uK).

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Glossary

Adoptive immunotherapy

A therapeutic strategy in which a patient's lymphocytes are removed, modified or manipulated ex vivo and retransfused to the patient. This is often used in the treatment of cancer.

T lymphocyte

A lymphocyte that expresses heterodimeric receptors associated with the CD3 complex. Effector T lymphocytes (or T cells) carry out a variety of functions, acting through interactions with other cells (for example, activating macrophages or helping B cells produce antibodies). Cytotoxic T cells kill cells infected with intracellular pathogens.

Natural killer cell

A class of lymphocytes that is crucial in the innate immune response. Natural killer cells exert a cytotoxic activity on target cells (such as virus-infected cells) that is enhanced by cytokines such as interferons.

SH2 domain

(SRC homology 2 domain). A protein motif that recognizes and binds Tyr-phosphorylated sequences and thereby has a key role in relaying cascades of signal transduction.

Orthogonal signal

A signal that only reacts with its cognate ligand and does not cross react with the host proteome.

Heterotrimeric G protein

A protein complex of three proteins (Gα, Gβ and Gγ). Gβ and Gγ form a tight complex, which Gα is a part of when the complex is in its inactive GDP-bound form, but dissociates from when the complex is in its active GTP-bound form. Both Gα and Gβγ can transmit downstream signals after activation.

PIF domain

(Phytochrome-interacting bHLH factor domain). A plant protein interaction domain that selectively binds to the light-activated state of the phytochrome domain. The phytochrome–PIF interaction is normally involved in transcriptional regulation of plants, but can be introduced into diverse organisms and cell types to control the recruitment and activity of fused protein activities.

Guanine nucleotide exchange factor

(GEF). A protein that activates a specific small GTPase by catalysing the exchange of bound GDP for GTP.

Michaelis constant (Km)

A kinetic parameter for a specific substrate in an enzyme-catalysed reaction. Km equals the concentration of substrate that yields half-maximal velocity of the reaction. Providing certain conditions are met, the Km for a substrate can equate to its binding constant, and the lower the value of Km, the tighter the substrate binds.

PDZ domain

(Postsynaptic density protein of 95 kDa, Discs large and Zona occludens 1 domain). A protein-interaction domain that often occurs in scaffolding proteins and is named after the founding members of the protein family.

AND gate

A Boolean logical operation in an output is produced only if two (or more) specific inputs are present. Many important signalling proteins and networks approximate AND gates, although none show an absolute all or none behaviour of the idealized Boolean operator.

SH3 domain

(SRC homology 3 domain). A protein module of ∼50 amino acids that recognizes and binds to sequences that are typically Pro-rich.

Leu zipper

A Leu-rich domain in a protein that binds to other proteins with a similar domain.

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Lim, W. Designing customized cell signalling circuits. Nat Rev Mol Cell Biol 11, 393–403 (2010). https://doi.org/10.1038/nrm2904

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