Efficient Reassignment of a Frequent Serine Codon in Wild-Type Escherichia coli

Ho, J. M., Reynolds, N. M., Rivera, K., Connolly, M., Guo, L. T., Ling, J. Q., Pappin, D. J., Church, G. M., Soll, D. (February 2016) Efficient Reassignment of a Frequent Serine Codon in Wild-Type Escherichia coli. ACS Synthetic Biology, 5 (2). pp. 163-171. ISSN 2161-5063

URL: http://www.ncbi.nlm.nih.gov/pubmed/26544153
DOI: 10.1021/acssynbio.5b00197

Abstract

Expansion of the genetic code through engineering the translation machinery has greatly increased the chemical repertoire of the proteome. This has been accomplished mainly by read-through of UAG or UGA stop codons by the noncanonical aminoacyl-tRNA of choice. While stop codon read-through involves competition with the translation release factors, sense codon reassignment entails competition with a large pool of endogenous tRNAs. We used an engineered pyrrolysyl-tRNA synthetase to incorporate 3-iodo-L-phenylalanine (3-I-Phe) at a number of different serine and leucine codons in wild-type Escherichia coli. Quantitative LC-MS/MS measurements of amino acid incorporation yields carried out in a selected reaction monitoring experiment revealed that the 3-I-Phe abundance at the Ser(208)AGU codon in superfolder GFP was 65 +/- 17%. This method also allowed quantification of other amino acids (serine, 33 +/- 17%; phenylalanine, 1 +/- 1%; threonine, 1 +/- 1%) that compete with 3-I-Phe at both the aminoacylation and decoding steps of translation for incorporation at the same codon position. Reassignments of different serine (AGU, AGC, UCG) and leucine (CUG) codons with the matching tRNAPYI anticodon variants were met with varying success, and our findings provide a guideline for the choice of sense codons to be reassigned. Our results indicate that the 3-iodo-L-phenylalanyl-tRNA synthetase (IFRS)/tRNA(Pyl) pair can efficiently outcompete the cellular machinery to reassign select sense codons in wild-type E. coli.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics
organism description > bacteria
organism description > bacteria > escherichia coli
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > translation
CSHL Authors:
Communities: CSHL labs > Pappin lab
CSHL Cancer Center Program > Signal Transduction
Depositing User: Matt Covey
Date: February 2016
Date Deposited: 22 Mar 2016 20:48
Last Modified: 05 Mar 2018 15:42
PMCID: PMC4807657
Related URLs:
URI: http://repository.cshl.edu/id/eprint/32445

Actions (login required)

Administrator's edit/view item Administrator's edit/view item
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving