title: Near-cognate suppression of amber, opal and quadruplet codons competes with aminoacyl-tRNAPyl for genetic code expansion.
abstract: Over 300 amino acids are found in proteins in nature, yet typically only 20 are genetically encoded. Reassigning stop codons and use of quadruplet codons emerged as the main avenues for genetically encoding non-canonical amino acids (NCAAs). Canonical aminoacyl-tRNAs with near-cognate anticodons also read these codons to some extent. This background suppression leads to 'statistical protein' that contains some natural amino acid(s) at a site intended for NCAA. We characterize near-cognate suppression of amber, opal and a quadruplet codon in common Escherichia coli laboratory strains and find that the PylRS/tRNA(Pyl) orthogonal pair cannot completely outcompete contamination by natural amino acids.
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, United States.
authors.forename: Patrick
authors.initials: P
authors.lastname: O'Donoghue
authors.forename: Laure
authors.initials: L
authors.lastname: Prat
authors.forename: Ilka U
authors.initials: IU
authors.lastname: Heinemann
authors.forename: Jiqiang
authors.initials: J
authors.lastname: Ling
authors.forename: Keturah
authors.initials: K
authors.lastname: Odoi
authors.forename: Wenshe R
authors.initials: WR
authors.lastname: Liu
authors.forename: Dieter
authors.initials: D
authors.lastname: Söll
mesh_terms: D000926:Anticodon; D003062:Codon; D004926:Escherichia coli / Q000235:genetics*; D005815:Genetic Code; D008239:Lysine / Q000031:analogs & derivatives* / Q000235:genetics; D014176:Protein Biosynthesis; D012346:RNA, Transfer, Amino Acyl / Q000235:genetics*; D021241:Spectrometry, Mass, Electrospray Ionization; D013489:Suppression, Genetic
chemical_list: D000926:Anticodon; D003062:Codon; D012346:RNA, Transfer, Amino Acyl; C456839:pyrrolysine; D008239:Lysine