Letter

A semi-synthetic organism that stores and retrieves increased genetic information

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Abstract

Since at least the last common ancestor of all life on Earth, genetic information has been stored in a four-letter alphabet that is propagated and retrieved by the formation of two base pairs. The central goal of synthetic biology is to create new life forms and functions1, and the most general route to this goal is the creation of semi-synthetic organisms whose DNA harbours two additional letters that form a third, unnatural base pair. Previous efforts to generate such semi-synthetic organisms2 culminated in the creation of a strain of Escherichia coli that, by virtue of a nucleoside triphosphate transporter from Phaeodactylum tricornutum, imports the requisite unnatural triphosphates from its medium and then uses them to replicate a plasmid containing the unnatural base pair dNaM–dTPT3. Although the semi-synthetic organism stores increased information when compared to natural organisms, retrieval of the information requires in vivo transcription of the unnatural base pair into mRNA and tRNA, aminoacylation of the tRNA with a non-canonical amino acid, and efficient participation of the unnatural base pair in decoding at the ribosome. Here we report the in vivo transcription of DNA containing dNaM and dTPT3 into mRNAs with two different unnatural codons and tRNAs with cognate unnatural anticodons, and their efficient decoding at the ribosome to direct the site-specific incorporation of natural or non-canonical amino acids into superfolder green fluorescent protein. The results demonstrate that interactions other than hydrogen bonding can contribute to every step of information storage and retrieval. The resulting semi-synthetic organism both encodes and retrieves increased information and should serve as a platform for the creation of new life forms and functions.

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Accessions

Primary accessions

NCBI Reference Sequence

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Acknowledgements

We thank P. G. Schultz for the pEVOL-pAzF plasmid. This work was supported by the National Institutes of Health (GM118178 to F.E.R.). A.W.F. was supported by a National Science Foundation Graduate Research Fellowship (NSF/DGE-1346837).

Author information

Affiliations

  1. Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA

    • Yorke Zhang
    • , Emil C. Fischer
    • , Aaron W. Feldman
    •  & Floyd E. Romesberg
  2. Synthorx, Inc., La Jolla, California 92037, USA

    • Jerod L. Ptacin
    • , Hans R. Aerni
    • , Carolina E. Caffaro
    • , Kristine San Jose
    •  & Court R. Turner

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Contributions

Y.Z., J.L.P. and F.E.R. designed experiments. Y.Z. and J.L.P. designed plasmids. Y.Z., E.C.F. and J.L.P. performed and interpreted translation experiments. H.R.A. conducted and interpreted MS experiments. C.E.C. developed methods. A.W.F. and K.S.J. provided technical assistance. C.R.T. and F.E.R. provided project leadership. F.E.R. provided overall project supervision. Y.Z. and F.E.R. wrote the manuscript, with input from the other authors.

Competing interests

A provisional patent application has been filed by Synthorx and The Scripps Research Institute (application no. 62/531,325; inventors J.L.P., C.E.C., H.R.A., Y.Z., E.C.F., A.W.F., V.T. Dien and F.E.R.) covering the use of UBPs in tRNAs and mRNAs to produce proteins containing ncAAs. J.L.P., C.E.C., H.R.A., K.S.J., C.R.T. and F.E.R. have shares in Synthorx, Inc., a company that has commercial interests in the UBP.

Corresponding author

Correspondence to Floyd E. Romesberg.

Reviewer Information Nature thanks A. Chatterjee, A. Deiters and P. Herdewyn for their contribution to the peer review of this work.

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Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains Supplementary Figure 1, the uncropped source images of the blots and Supplementary Tables 1 and 2, a description of the plasmids and primers used in this study.

  2. 2.

    Life Sciences Reporting Summary

Text files

  1. 1.

    Supplementary Notes

    This file contains annotated sequences of plasmids denoted in Supplementary Table 1 suitable for direct import into sequence analysis software.

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