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Regulation of transcription by unnatural amino acids

Nature Biotechnology volume 29, pages 164–168 (2011)Cite this article

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Abstract

Small-molecule regulation of gene expression is intrinsic to cellular function and indispensable to the construction of new biological sensing, control and expression systems1,2. However, there are currently only a handful of strategies for engineering such regulatory components and fewer still that can give rise to an arbitrarily large set of inducible systems whose members respond to different small molecules, display uniformity and modularity in their mechanisms of regulation, and combine to actuate universal logics3,4,5,6,7,8. Here we present an approach for small-molecule regulation of transcription based on the combination of cis-regulatory leader-peptide elements with genetically encoded unnatural amino acids (amino acids that have been artificially added to the genetic code). In our system, any genetically encoded unnatural amino acid (UAA) can be used as a small-molecule attenuator or activator of gene transcription, and the logics intrinsic to the network defined by expanded genetic codes can be actuated.

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Figure 1: A representative molecular recognition network of expanded genetic codes, its integration with cis-regulatory leader-peptide elements and some possible uses of this platform.
Figure 2: Behavior of UAA-controlled transcriptional switches.
Figure 3: Control of transcriptional OFF and transcriptional ON switches with multiple UAAs.

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Acknowledgements

We thank P. Schultz (The Scripps Research Institute) for thoughtful comments and the gift of the pEVOL plasmids. We thank J. Lucks for helpful discussions and advice. This work was funded by the National Science Foundation as part of the Synthetic Biology Engineering Research Center (A.P.A.) and the Miller Institute for Basic Scientific Research (C.C.L.).

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Authors and Affiliations

  1. Department of Bioengineering, University of California at Berkeley, Berkeley, California, USA

    Chang C Liu, Lei Qi & Adam P Arkin

  2. Miller Institute for Basic Research in Science, Berkeley, California, USA

    Chang C Liu

  3. Department of Biological Sciences, Stanford University, Stanford, California, USA

    Charles Yanofsky

  4. Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

    Adam P Arkin

  5. QB3: California Institute for Quantitative Biological Research, University of California at Berkeley, Berkeley, California, USA

    Adam P Arkin

Authors
  1. Chang C Liu
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  2. Lei Qi
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  3. Charles Yanofsky
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Contributions

C.C.L. conceived of the study and C.Y. and A.P.A. advised. All authors were involved in designing the experiments. C.C.L. and L.Q. performed the experiments and interpreted the data. C.C.L. and A.P.A. wrote the manuscript. All authors discussed results and commented on the manuscript.

Corresponding authors

Correspondence to Chang C Liu or Adam P Arkin.

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The authors declare no competing financial interests.

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Supplementary Discussion, Supplementary Sequences, Supplementary List of Plasmids and Supplementary Figs. 1–6 (PDF 4744 kb)

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Liu, C., Qi, L., Yanofsky, C. et al. Regulation of transcription by unnatural amino acids. Nat Biotechnol 29, 164–168 (2011). https://doi.org/10.1038/nbt.1741

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