Codon reassignment in the Escherichia coli genetic code

Most organisms, from Escherichia coli to humans, use the ‘universal’ genetic code, which have been unchanged or ‘frozen’ for billions of years. It has been argued that codon reassignment causes mistranslation of genetic information, and must be lethal. In this study, we successfully reassigned the UAG triplet from a stop to a sense codon in the E. coli genome, by eliminating the UAG-recognizing release factor, an essential cellular component, from the bacterium. Only a few genetic modifications of E. coli were needed to circumvent the lethality of codon reassignment; erasing all UAG triplets from the genome was unnecessary. Thus, UAG was assigned unambiguously to a natural or non-natural amino acid, according to the specificity of the UAG-decoding tRNA. The result reveals the unexpected flexibility of the genetic code.

• Publication year

  2010

• Venue

  Nucleic Acids Research

• Publication date

  2010-08-10

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1093/nar/gkq707PMID 20702426PMCID 3001078
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Functional replacement of the endogenous tyrosyl-tRNA synthetase–tRNATyr pair by the archaeal tyrosine pair in Escherichia coli for genetic code expansion

  2010cited by this paper
• Genetic encoding of non‐natural amino acids in Drosophila melanogaster Schneider 2 cells

  2010cited by this paper
• Translation termination in pyrrolysine‐utilizing archaea

  2009cited by this paper
• Genetic encoding of 3-iodo-L-tyrosine in Escherichia coli for single-wavelength anomalous dispersion phasing in protein crystallography.

  2009cited by this paper
• Tandem Stop Codons in Ciliates That Reassign Stop Codons

  2009cited by this paper
• Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion

  2007cited by this paper
• Reduced action of polypeptide release factors induces mRNA cleavage and tmRNA tagging at stop codons in Escherichia coli

  2007cited by this paper
• Efficient large-scale protein production of larvae and pupae of silkworm by Bombyx mori nuclear polyhedrosis virus bacmid system.

  2005cited by this paper
• Conservation of tandem stop codons in yeasts

  2005cited by this paper
• A temperature-sensitive mutant of Escherichia coli that shows enhanced misreading of UAG/A and increased efficiency for tRNA nonsense suppressors

  2004cited by this paper
• Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome

  2004cited by this paper
• Driving change: the evolution of alternative genetic codes.

  2004cited by this paper
• The Escherichia coli argU10(Ts) Phenotype Is Caused by a Reduction in the Cellular Level of the argU tRNA for the Rare Codons AGA and AGG

  2004cited by this paper
• An Expanded Eukaryotic Genetic Code

  2003cited by this paper
• A New UAG-Encoded Residue in the Structure of a Methanogen Methyltransferase

  2002cited by this paper
• Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells.

  2002cited by this paper
• Expanding the Genetic Code of Escherichia coli

  2001cited by this paper
• Rewiring the keyboard: evolvability of the genetic code

  2001cited by this paper
• Translation termination factor aRF1 from the archaeon Methanococcus jannaschii is active with eukaryotic ribosomes

  2000cited by this paper
• Transfer RNA mutation and the malleability of the genetic code.

  1994cited by this paper
• Recent evidence for evolution of the genetic code

  1992cited by this paper
• Codon reassignment (codon capture) in evolution

  1989cited by this paper
• Characterization of reticulocyte release factor.

  1977cited by this paper
• Release factors differing in specificity for terminator codons.

  1968influential reference
• Origin of the Genetic Code

  1967cited by this paper
• Suppression of mutations in the alkaline phosphatase structural cistron of E. coli.

  1962cited by this paper
• A change from nonsense to sense in the genetic code.

  1962cited by this paper

• Essential Logic and Facts Behind the Expansion of the Genetic Code: A Critical Assessment

  2025cites this paper
• Design and evolution of artificial enzyme with in-situ biosynthesized non-canonical amino acid

  2025cites this paper
• Boosting Reversible Photocontrol of a Photoxenase by an Engineered Conformational Shift

  2025cites this paper
• Bacteria employ lysine acetylation of transcriptional regulators to adapt gene expression to cellular metabolism

  2024cites this paper
• Engineering Pyrrolysine Systems for Genetic Code Expansion and Reprogramming

  2024cites this paper
• Cracking the Code: Reprogramming the Genetic Script in Prokaryotes and Eukaryotes to Harness the Power of Noncanonical Amino Acids

  2024cites this paper
• Genetic Code Expansion: Recent Developments and Emerging Applications

  2024cites this paper
• The Great Codon Escape: Vacating Codons for Genetic Code Expansion and Ribosome Stalling

  2024cites this paper
• Genetic Code Expansion History and Modern Innovations.

  2024cites this paper
• Creating a System of Dual Regulation of Translation and Transcription to Enhance the Production of Recombinant Protein

  2024cites this paper
• Genetic Encoding of Phosphorylated Amino Acids into Proteins.

  2024cites this paper
• Simplified Construction of Engineered Bacillus subtilis Host for Improved Expression of Proteins Harboring Noncanonical Amino Acids.

  2023cites this paper
• Potential Impact of Genetic-Code Mutations on Medicine and Health

  2023cites this paper
• Site‐specific photo‐crosslinking/cleavage for protein–protein interface identification reveals oligomeric assembly of lysosomal‐associated membrane protein type 2A in mammalian cells

  2023cites this paper
• Artificial Small Molecules as Cofactors and Biomacromolecular Building Blocks in Synthetic Biology: Design, Synthesis, Applications, and Challenges

  2023cites this paper
• Crystal Structure of Pyrrolysyl-tRNA Synthetase from a Methanogenic Archaeon ISO4-G1 and Its Structure-Based Engineering for Highly-Productive Cell-Free Genetic Code Expansion with Non-Canonical Amino Acids

  2023cites this paper
• A novel vaccine strategy using quick and easy conversion of bacterial pathogens to unnatural amino acid-auxotrophic suicide derivatives

  2023cites this paper
• Rebooting life: engineering non-natural nucleic acids, proteins and metabolites in microorganisms

  2022cites this paper
• Genetic Code Expansion: Another Solution to Codon Assignments

  2022cites this paper
• Building biomaterials through genetic code expansion.

  2022cites this paper
• Improving the Efficiency and Orthogonality of Genetic Code Expansion

  2022cites this paper
• Genetic Code Engineering by Natural and Unnatural Base Pair Systems for the Site-Specific Incorporation of Non-Standard Amino Acids Into Proteins

  2022cites this paper
• Optimizing eRF1 to Enable the Genetic Encoding of Three Distinct Noncanonical Amino Acids in Mammalian Cells

  2022cites this paper
• Directed Evolution Pipeline for the Improvement of Orthogonal Translation Machinery for Genetic Code Expansion at Sense Codons

  2022cites this paper
• Creation, Optimization, and Use of Semi-Synthetic Organisms that Store and Retrieve Increased Genetic Information.

  2021cites this paper
• Directed Evolution of the Methanosarcina barkeri Pyrrolysyl tRNA/aminoacyl tRNA Synthetase Pair for Rapid Evaluation of Sense Codon Reassignment Potential

  2021cites this paper
• Assays to Study Enzymatic and Non‐Enzymatic Protein Lysine Acetylation In Vitro

  2021cites this paper
• Post-translational Lysine Ac(et)ylation in Bacteria: A Biochemical, Structural, and Synthetic Biological Perspective

  2021cites this paper
• Comparative Analyses of the Transcriptome and Proteome of Escherichia coli C321.△A and Further Improving Its Noncanonical Amino Acids Containing Protein Expression Ability by Integration of T7 RNA Polymerase

  2021cites this paper
• Genetic Code Expansion: Inception, Development, Commercialization.

  2021cites this paper
• Engineering translation components for genetic code expansion.

  2021cites this paper
• Recent Technologies for Genetic Code Expansion and their Implications on Synthetic Biology Applications.

  2021cites this paper
• An expanded genetic code facilitates antibody chemical conjugation involving the lambda light chain.

  2021cites this paper
• Multi‐Site Incorporation of Nonstandard Amino Acids into Protein‐Based Biomaterials

  2020cites this paper
• Reprogramming the genetic code

  2020cites this paper
• A photo-cross-linking approach to monitor protein dynamics in living cells.

  2020cites this paper
• Genome recoding strategies to improve cellular properties: mechanisms and advances

  2020cites this paper
• Emerging Methods for Efficient and Extensive Incorporation of Non-canonical Amino Acids Using Cell-Free Systems

  2020cites this paper
• Release Factor Inhibiting Antimicrobial Peptides Improve Nonstandard Amino Acid Incorporation in Wild-type Bacterial Cells.

  2020cites this paper
• Expanding the enzyme universe with genetically encoded unnatural amino acids

  2020cites this paper
• Collateral Toxicity Limits the Evolution of Bacterial Release Factor 2 toward Total Omnipotence

  2020cites this paper
• Better together: building protein oligomers naturally and by design

  2019cites this paper
• Engineering the Ribosomal Translation System to Introduce Non-proteinogenic Amino Acids into Peptides

  2019cites this paper
• Contingency’s causality and structural diversity

  2019cites this paper
• Strategies for in vitro engineering of the translation machinery

  2019cites this paper
• Cell-Free Protein Synthesis Using S30 Extracts from Escherichia coli RFzero Strains for Efficient Incorporation of Non-Natural Amino Acids into Proteins

  2019cites this paper
• Translational Control using an Expanded Genetic Code

  2019cites this paper
• Total synthesis of Escherichia coli with a recoded genome

  2019cites this paper
• Site-Specific Incorporation of Unnatural Amino Acids into Escherichia coli Recombinant Protein: Methodology Development and Recent Achievement

  2019cites this paper
• Genetic code expansion in mammalian cells

  2019cites this paper
• Expanding the Genetic Code for Site-Directed Spin-Labeling

  2019cites this paper
• Contingency’s causality and structural diversity

  2019cites this paper
• The Role of Orthogonality in Genetic Code Expansion

  2019cites this paper
• Novel routes to defined post translational modifications using non-canonical amino acids

  2018cites this paper
• Biochemische Charakterisierung des archäellen Argonaute-Proteins aus Methanocaldococcus jannaschii und strukturelle Untersuchungen mit Einzelmolekül-Förster-Resonanz-Energie-Transfer-Studien

  2018cites this paper
• Effects of Heterologous tRNA Modifications on the Production of Proteins Containing Noncanonical Amino Acids

  2018cites this paper
• Expansion of the genetic code via expansion of the genetic alphabet.

  2018cites this paper
• Engineering an Automaturing Transglutaminase with Enhanced Thermostability by Genetic Code Expansion with Two Codon Reassignments.

  2018cites this paper
• Orthogonal Protein Translation Using Pyrrolysyl-tRNA Synthetases for Single- and Multiple-Noncanonical Amino Acid Mutagenesis.

  2018cites this paper
• Context effects of genetic code expansion by stop codon suppression.

  2018cites this paper
• Auxotrophy to Xeno-DNA: an exploration of combinatorial mechanisms for a high-fidelity biosafety system for synthetic biology applications

  2018cites this paper
• Playing with the Molecules of Life.

  2018cites this paper
• Variants of the industrially relevant protease KP-43 with suppressed activity under alkaline conditions developed using expanded genetic codes

  2018cites this paper
• Adaptive evolution of genomically recoded Escherichia coli

  2018cites this paper
• Ribosomal incorporation of unnatural amino acids: lessons and improvements from fast kinetics studies.

  2018cites this paper
• Cell-Free Protein Synthesis for Multiple Site-Specific Incorporation of Noncanonical Amino Acids Using Cell Extracts from RF-1 Deletion E. coli Strains.

  2018cites this paper
• Genetically encoded amino acids with tert-butyl and trimethylsilyl groups for site-selective studies of proteins by NMR spectroscopy

  2018cites this paper
• Organisms with alternative genetic codes resolve unassigned codons via mistranslation and ribosomal rescue

  2018cites this paper
• Expanding the Genetic Code to Study Protein-Protein Interactions.

  2018cites this paper
• Dissecting the Contribution of Release Factor Interactions to Amber Stop Codon Reassignment Efficiencies of the Methanocaldococcus jannaschii Orthogonal Pair

  2018cites this paper
• Expanding and reprogramming the genetic code

  2017cites this paper
• A molecular engineering toolbox for the structural biologist

  2017cites this paper
• Genetically encoded amino acids with tert-butyl and trimethylsilyl groups for site-selective studies of proteins by NMR spectroscopy

  2017cites this paper
• Selenocysteine Insertion at a Predefined UAG Codon in a Release Factor 1 (RF1)-depleted Escherichia coli Host Strain Bypasses Species Barriers in Recombinant Selenoprotein Translation*

  2017cites this paper
• Characterization of lysine acetylation of a phosphoenolpyruvate carboxylase involved in glutamate overproduction in Corynebacterium glutamicum

  2017cites this paper
• Rapid and Inexpensive Evaluation of Nonstandard Amino Acid Incorporation in Escherichia coli.

  2017cites this paper
• Protein Engineering: Recent Trends

  2017cites this paper
• Nuclear codon reassignments in the genomics era and mechanisms behind their evolution.

  2017cites this paper
• Long-term adaptive evolution of genomically recoded Escherichia coli

  2017cites this paper
• Two‐Tier Screening Platform for Directed Evolution of Aminoacyl–tRNA Synthetases with Enhanced Stop Codon Suppression Efficiency

  2017cites this paper
• Extensive Survey of Antibody Invariant Positions for Efficient Chemical Conjugation Using Expanded Genetic Codes.

  2017cites this paper
• Increasing the fidelity of noncanonical amino acid incorporation in cell-free protein synthesis.

  2017cites this paper
• The central role of tRNA in genetic code expansion.

  2017cites this paper
• Electron transfer in protein-carbon nanotube hybrid structures

  2017cites this paper
• Rewriting the Genetic Code.

  2017influential citation
• Evolving Bacterial Fitness with an Expanded Genetic Code

  2017cites this paper
• Precise and combinatorial PEGylation generates a low‐immunogenic and stable form of human growth hormone

  2017cites this paper
• Construction of an inducible stable cell line for efficient incorporation of unnatural amino acids in mammalian cells.

  2017cites this paper
• Translation system engineering in Escherichia coli enhances non‐canonical amino acid incorporation into proteins

  2017influential citation
• Generation of phospho‐ubiquitin variants by orthogonal translation reveals codon skipping

  2016cites this paper
• In Vitro Kinetics of Ribosomal Incorporation of Unnatural Amino Acids

  2016cites this paper
• Innovative Technology for Recombinant Protein Production Using Engineered E. coli Genetic Codes

  2016cites this paper
• Protein Building Blocks and the Expansion of the Genetic Code

  2016influential citation
• Expanded Genetic Codes Create New Mutational Routes to Rifampicin Resistance in Escherichia coli.

  2016cites this paper
• Performance of optimized noncanonical amino acid mutagenesis systems in the absence of release factor 1.

  2016cites this paper
• New Genetic Codes

  2016cites this paper
• A Web Interface for Codon Compression.

  2016cites this paper
• Fluorescent Probes to Investigate Homologous Recombination Dynamics

  2016cites this paper
• Engineering the genetic code of Escherichia coli with methionine analogues and bioorthogonal amino acids for protein immobilization

  2016cites this paper
• Modulating Parkin E3 Ubiquitin Ligase Activity Using Phospho-Ubiquitin Variants

  2016cites this paper