Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids

Amiram, Miriam; Haimovich, Adrian D.; Fan, Chenguang; Wang, Yane-Shih; Aerni, Hans-Rudolf; Ntai, Ioanna; Moonan, Daniel W.; Ma, Natalie J.; Rovner, Alexis J.; Hong, Seok Hoon; Kelleher, Neil L.; Goodman, Andrew L.; Jewett, Michael C.; Söll, Dieter; Rinehart, Jesse; Isaacs, Farren J.

doi:10.1038/nbt.3372

Title: Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids

Journal Article · Mon Nov 16 00:00:00 UTC 2015 · Nature Biotechnology

DOI: https://doi.org/10.1038/nbt.3372 · OSTI ID:1466973

Amiram, Miriam ^[1]; Haimovich, Adrian D. ^[2]; Fan, Chenguang ^[3];

^[3];

^[4]; Ntai, Ioanna ^[5]; Moonan, Daniel W. ^[2]; Ma, Natalie J. ^[2]; Rovner, Alexis J. ^[2];

^[6]; Kelleher, Neil L. ^[5]; Goodman, Andrew L. ^[7]; Jewett, Michael C. ^[6]; Söll, Dieter ^[8];

^[4]; Isaacs, Farren J. ^[2]

Yale Univ., New Haven, CT (United States). Dept.of Molecular, Cellular, and Developmental Biology and Systems Biology Inst.; Yale University
Yale Univ., New Haven, CT (United States). Dept.of Molecular, Cellular, and Developmental Biology and Systems Biology Inst.
Yale Univ., New Haven, CT (United States). Dept. of Molecular Biophysics and Biochemistry
Yale Univ., New Haven, CT (United States). Systems Biology Inst. and Dept. of Cellular and Molecular Physiology
Northwestern Univ., Evanston, IL (United States). Dept. of Chemistry
Northwestern Univ., Evanston, IL (United States). Dept. of Chemical and Biological Engineering
Yale Univ. School of Medicine, New Haven, CT (United States). Dept. of Microbial Pathogenesis and Microbial Sciences Inst.
Yale Univ., New Haven, CT (United States). Dept. of Chemistry and Dept. of Molecular Biophysics and Biochemistry

Expansion of the genetic code with nonstandard amino acids (nsAAs) has enabled biosynthesis of proteins with diverse new chemistries. However, this technology has been largely restricted to proteins containing a single or few nsAA instances. We describe an in vivo evolution approach in a genomically recoded Escherichia coli strain for the selection of orthogonal translation systems capable of multi-site nsAA incorporation. We evolved chromosomal aminoacyl-tRNA synthetases (aaRSs) with up to 25-fold increased protein production for p-acetyl-L-phenylalanine and p-azido-L-phenylalanine (pAzF). We also evolved aaRSs with tunable specificities for 14 nsAAs, including an enzyme that efficiently charges pAzF while excluding 237 other nsAAs. These variants enabled production of elastin-like-polypeptides with 30 nsAA residues at high yields (~50 mg/L) and high accuracy of incorporation (>95%). This approach to aaRS evolution should accelerate and expand our ability to produce functionalized proteins and sequence-defined polymers with diverse chemistries.

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Research Organization:: Harvard Univ., Cambridge, MA (United States)

Sponsoring Organization:: Arnold and Mabel Beckman Foundation; Camille Dreyfus Teacher-Scholar Awards Program; David and Lucile Packard Foundation; Defense Advanced Research Projects Agency (DARPA); National Inst. of Health (NIH); US Army Research Office (ARO); USDOE

Grant/Contract Number:: FG02-02ER63445

OSTI ID:: 1466973

Journal Information:: Nature Biotechnology, Journal Name: Nature Biotechnology Journal Issue: 12 Vol. 33; ISSN 1087-0156

Publisher:: Springer NatureCopyright Statement

Country of Publication:: United States

Language:: English

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Dissecting the Contribution of Release Factor Interactions to Amber Stop Codon Reassignment Efficiencies of the Methanocaldococcus jannaschii Orthogonal Pair Schwark, David; Schmitt, Margaret; Fisk, John Genes, Vol. 9, Issue 11 https://doi.org/10.3390/genes9110546	journal	November 2018
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The Role of Orthogonality in Genetic Code Expansion Arranz-Gibert, Pol; Patel, Jaymin R.; Isaacs, Farren J. Life, Vol. 9, Issue 3 https://doi.org/10.3390/life9030058	journal	July 2019
Organisms with alternative genetic codes resolve unassigned codons via mistranslation and ribosomal rescue Ma, Natalie Jing; Hemez, Colin F.; Barber, Karl W. eLife, Vol. 7 https://doi.org/10.7554/elife.34878	journal	October 2018

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