Codon reassignment in the Escherichia coli genetic code.

PubWeight™: 1.68‹?› | Rank: Top 3%

🔗 View Article (PMC 3001078)

Published in Nucleic Acids Res on August 11, 2010

Authors

Takahito Mukai1, Akiko Hayashi, Fumie Iraha, Aya Sato, Kazumasa Ohtake, Shigeyuki Yokoyama, Kensaku Sakamoto

Author Affiliations

1: RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.

Articles citing this

Genomically recoded organisms expand biological functions. Science (2013) 2.73

Biocontainment of genetically modified organisms by synthetic protein design. Nature (2015) 2.06

RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites. Nat Chem Biol (2011) 1.83

Reversion of a fungal genetic code alteration links proteome instability with genomic and phenotypic diversification. Proc Natl Acad Sci U S A (2013) 1.75

Efficient genetic encoding of phosphoserine and its nonhydrolyzable analog. Nat Chem Biol (2015) 1.52

Enhanced phosphoserine insertion during Escherichia coli protein synthesis via partial UAG codon reassignment and release factor 1 deletion. FEBS Lett (2012) 1.46

Upgrading protein synthesis for synthetic biology. Nat Chem Biol (2013) 1.32

Efficient decoding of the UAG triplet as a full-fledged sense codon enhances the growth of a prfA-deficient strain of Escherichia coli. J Bacteriol (2012) 1.12

Near-cognate suppression of amber, opal and quadruplet codons competes with aminoacyl-tRNAPyl for genetic code expansion. FEBS Lett (2012) 1.11

Release factor one is nonessential in Escherichia coli. ACS Chem Biol (2012) 1.05

Efficient multisite unnatural amino acid incorporation in mammalian cells via optimized pyrrolysyl tRNA synthetase/tRNA expression and engineered eRF1. J Am Chem Soc (2014) 1.05

Genetic code flexibility in microorganisms: novel mechanisms and impact on physiology. Nat Rev Microbiol (2015) 0.98

Cell-free protein synthesis from a release factor 1 deficient Escherichia coli activates efficient and multiple site-specific nonstandard amino acid incorporation. ACS Synth Biol (2014) 0.96

Cell-free co-production of an orthogonal transfer RNA activates efficient site-specific non-natural amino acid incorporation. Nucleic Acids Res (2013) 0.95

Revealing the amino acid composition of proteins within an expanded genetic code. Nucleic Acids Res (2014) 0.95

Cell-free biology: exploiting the interface between synthetic biology and synthetic chemistry. Curr Opin Biotechnol (2012) 0.93

Non-standard amino acid incorporation into proteins using Escherichia coli cell-free protein synthesis. Front Chem (2014) 0.92

Reassignment of a rare sense codon to a non-canonical amino acid in Escherichia coli. Nucleic Acids Res (2015) 0.90

Improving cell-free protein synthesis through genome engineering of Escherichia coli lacking release factor 1. Chembiochem (2015) 0.86

Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids. Nat Biotechnol (2015) 0.86

Sense codon emancipation for proteome-wide incorporation of noncanonical amino acids: rare isoleucine codon AUA as a target for genetic code expansion. FEMS Microbiol Lett (2014) 0.85

Non-Standard Genetic Codes Define New Concepts for Protein Engineering. Life (Basel) (2015) 0.84

Expanded cellular amino acid pools containing phosphoserine, phosphothreonine, and phosphotyrosine. ACS Chem Biol (2014) 0.83

Rational design of an evolutionary precursor of glutaminyl-tRNA synthetase. Proc Natl Acad Sci U S A (2011) 0.83

Highly reproductive Escherichia coli cells with no specific assignment to the UAG codon. Sci Rep (2015) 0.83

Response and adaptation of Escherichia coli to suppression of the amber stop codon. Chembiochem (2014) 0.82

Evolving tRNA(Sec) for efficient canonical incorporation of selenocysteine. J Am Chem Soc (2014) 0.81

Genomes by design. Nat Rev Genet (2015) 0.81

High-yield, zero-leakage expression system with a translational switch using site-specific unnatural amino Acid incorporation. Appl Environ Microbiol (2013) 0.81

Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation. Sci Rep (2015) 0.81

Orthogonal dual-modification of proteins for the engineering of multivalent protein scaffolds. Beilstein J Org Chem (2015) 0.80

Multiple site-selective insertions of noncanonical amino acids into sequence-repetitive polypeptides. Chembiochem (2013) 0.80

Unnatural amino acid incorporation in E. coli: current and future applications in the design of therapeutic proteins. Front Chem (2014) 0.80

Repurposing the translation apparatus for synthetic biology. Curr Opin Chem Biol (2015) 0.80

Overcoming Challenges in Engineering the Genetic Code. J Mol Biol (2015) 0.80

The genetic code. Rewritten, revised, repurposed. Artif DNA PNA XNA (2014) 0.78

Multiply labeling proteins for studies of folding and stability. Curr Opin Chem Biol (2015) 0.77

Recent developments of engineered translational machineries for the incorporation of non-canonical amino acids into polypeptides. Int J Mol Sci (2015) 0.76

Towards Biocontained Cell Factories: An Evolutionarily Adapted Escherichia coli Strain Produces a New-to-nature Bioactive Lantibiotic Containing Thienopyrrole-Alanine. Sci Rep (2016) 0.76

Genetically encoded libraries of nonstandard peptides. J Nucleic Acids (2012) 0.76

Protein stabilization utilizing a redefined codon. Sci Rep (2015) 0.76

Molecular reconstruction of a fungal genetic code alteration. RNA Biol (2013) 0.75

Genome remodeling. Nat Biotechnol (2011) 0.75

Translation system engineering in Escherichia coli enhances non-canonical amino acid incorporation into proteins. Biotechnol Bioeng (2016) 0.75

Modification of orthogonal tRNAs: unexpected consequences for sense codon reassignment. Nucleic Acids Res (2016) 0.75

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. J Biol Chem (2017) 0.75

Synthetic biology approaches to biological containment: pre-emptively tackling potential risks. Essays Biochem (2016) 0.75

CRISPRi-Manipulation of Genetic Code Expansion via RF1 for Reassignment of Amber Codon in Bacteria. Sci Rep (2016) 0.75

Genetic code expansion as a tool to study regulatory processes of transcription. Front Chem (2014) 0.75

The central role of tRNA in genetic code expansion. Biochim Biophys Acta (2017) 0.75

Articles cited by this

The origin of the genetic code. J Mol Biol (1968) 9.44

Expanding the genetic code of Escherichia coli. Science (2001) 7.25

Suppression of mutations in the alkaline phosphatase structural cistron of E. coli. Proc Natl Acad Sci U S A (1962) 6.33

A change from nonsense to sense in the genetic code. Proc Natl Acad Sci U S A (1962) 5.17

An expanded eukaryotic genetic code. Science (2003) 4.66

Recent evidence for evolution of the genetic code. Microbiol Rev (1992) 4.32

Release factors differing in specificity for terminator codons. Proc Natl Acad Sci U S A (1968) 4.18

A new UAG-encoded residue in the structure of a methanogen methyltransferase. Science (2002) 3.11

Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome. Mol Microbiol (2005) 2.77

Rewiring the keyboard: evolvability of the genetic code. Nat Rev Genet (2001) 2.70

Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion. Nat Biotechnol (2007) 2.51

Codon reassignment (codon capture) in evolution. J Mol Evol (1989) 2.20

A temperature-sensitive mutant of Escherichia coli that shows enhanced misreading of UAG/A and increased efficiency for some tRNA nonsense suppressors. Mol Gen Genet (1984) 2.03

Characterization of reticulocyte release factor. J Biol Chem (1977) 1.76

Transfer RNA mutation and the malleability of the genetic code. J Mol Biol (1994) 1.74

Genetic encoding of 3-iodo-L-tyrosine in Escherichia coli for single-wavelength anomalous dispersion phasing in protein crystallography. Structure (2009) 1.64

Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells. Nucleic Acids Res (2002) 1.64

Driving change: the evolution of alternative genetic codes. Trends Genet (2004) 1.48

Efficient large-scale protein production of larvae and pupae of silkworm by Bombyx mori nuclear polyhedrosis virus bacmid system. Biochem Biophys Res Commun (2005) 1.12

Translation termination factor aRF1 from the archaeon Methanococcus jannaschii is active with eukaryotic ribosomes. FEBS Lett (2000) 1.10

Conservation of tandem stop codons in yeasts. Genome Biol (2005) 0.97

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. J Bacteriol (2004) 0.97

Translation termination in pyrrolysine-utilizing archaea. FEBS Lett (2009) 0.95

Tandem stop codons in ciliates that reassign stop codons. J Mol Evol (2009) 0.94

Reduced action of polypeptide release factors induces mRNA cleavage and tmRNA tagging at stop codons in Escherichia coli. Mol Microbiol (2007) 0.94

Genetic encoding of non-natural amino acids in Drosophila melanogaster Schneider 2 cells. Protein Sci (2010) 0.92

Functional replacement of the endogenous tyrosyl-tRNA synthetase-tRNATyr pair by the archaeal tyrosine pair in Escherichia coli for genetic code expansion. Nucleic Acids Res (2010) 0.92

Articles by these authors

Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution. Nature (2002) 6.74

Structural basis for defects of Keap1 activity provoked by its point mutations in lung cancer. Mol Cell (2006) 6.09

Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa. Cell (2006) 5.70

Crystal structure of the complex of human epidermal growth factor and receptor extracellular domains. Cell (2002) 5.64

An open-and-shut case? Recent insights into the activation of EGF/ErbB receptors. Mol Cell (2003) 5.06

Curved EFC/F-BAR-domain dimers are joined end to end into a filament for membrane invagination in endocytosis. Cell (2007) 4.73

Let-7 microRNA-mediated mRNA deadenylation and translational repression in a mammalian cell-free system. Genes Dev (2007) 4.35

Protein production and purification. Nat Methods (2008) 3.97

Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription. Cell (2004) 3.39

ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding. EMBO J (2003) 3.14

A small-molecule AdipoR agonist for type 2 diabetes and short life in obesity. Nature (2013) 2.74

Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion. Nat Struct Biol (2003) 2.71

Structural basis for substrate selection by t7 RNA polymerase. Cell (2004) 2.62

Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors. Mol Cell (2007) 2.62

Structural basis for transcription regulation by alarmone ppGpp. Cell (2004) 2.60

Structure of a T7 RNA polymerase elongation complex at 2.9 A resolution. Nature (2002) 2.57

An unnatural hydrophobic base pair system: site-specific incorporation of nucleotide analogs into DNA and RNA. Nat Methods (2006) 2.46

Infants show a facilitation effect for native language phonetic perception between 6 and 12 months. Dev Sci (2006) 2.45

Different electrostatic potentials define ETGE and DLG motifs as hinge and latch in oxidative stress response. Mol Cell Biol (2007) 2.38

Adding l-lysine derivatives to the genetic code of mammalian cells with engineered pyrrolysyl-tRNA synthetases. Biochem Biophys Res Commun (2008) 2.29

Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme. Cell (2003) 2.29

Crystal structure of hypothetical protein TTHB192 from Thermus thermophilus HB8 reveals a new protein family with an RNA recognition motif-like domain. Protein Sci (2006) 2.29

Preparation of Escherichia coli cell extract for highly productive cell-free protein expression. J Struct Funct Genomics (2004) 2.14

Multistep engineering of pyrrolysyl-tRNA synthetase to genetically encode N(epsilon)-(o-azidobenzyloxycarbonyl) lysine for site-specific protein modification. Chem Biol (2008) 2.13

Reconstitution reveals the functional core of mammalian eIF3. EMBO J (2007) 2.06

A B-box 2 surface patch important for TRIM5alpha self-association, capsid binding avidity, and retrovirus restriction. J Virol (2009) 2.03

Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein. Nature (2010) 2.01

Parkin binds the Rpn10 subunit of 26S proteasomes through its ubiquitin-like domain. EMBO Rep (2003) 2.01

A computational model on the modulation of mitogen-activated protein kinase (MAPK) and Akt pathways in heregulin-induced ErbB signalling. Biochem J (2003) 2.00

Crystal structure of the homologous-pairing domain from the human Rad52 recombinase in the undecameric form. Mol Cell (2002) 1.98

Structure of the oncoprotein gankyrin in complex with S6 ATPase of the 26S proteasome. Structure (2007) 1.97

Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm. Bioinformatics (2004) 1.96

Interaction of Era with the 30S ribosomal subunit implications for 30S subunit assembly. Mol Cell (2005) 1.93

Structural basis of the substrate-specific two-step catalysis of long chain fatty acyl-CoA synthetase dimer. J Biol Chem (2004) 1.89

The crystal structure of leucyl-tRNA synthetase complexed with tRNALeu in the post-transfer-editing conformation. Nat Struct Mol Biol (2005) 1.87

Aminoacylation complex structures of leucyl-tRNA synthetase and tRNALeu reveal two modes of discriminator-base recognition. Nat Struct Mol Biol (2005) 1.82

Increased Ras expression and caspase-independent neuroblastoma cell death: possible mechanism of spontaneous neuroblastoma regression. J Natl Cancer Inst (2002) 1.78

An enzyme with a deep trefoil knot for the active-site architecture. Acta Crystallogr D Biol Crystallogr (2002) 1.72

Protein photo-cross-linking in mammalian cells by site-specific incorporation of a photoreactive amino acid. Nat Methods (2005) 1.67

UTX and UTY demonstrate histone demethylase-independent function in mouse embryonic development. PLoS Genet (2012) 1.67

Crystal structure of elongation factor P from Thermus thermophilus HB8. Proc Natl Acad Sci U S A (2004) 1.65

Real-time imaging of histone H4K12-specific acetylation determines the modes of action of histone deacetylase and bromodomain inhibitors. Chem Biol (2011) 1.65

Genetic encoding of 3-iodo-L-tyrosine in Escherichia coli for single-wavelength anomalous dispersion phasing in protein crystallography. Structure (2009) 1.64

Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells. Nucleic Acids Res (2002) 1.64

DOCK8 is a Cdc42 activator critical for interstitial dendritic cell migration during immune responses. Blood (2012) 1.63

Structure, interaction and real-time monitoring of the enzymatic reaction of wild-type APOBEC3G. EMBO J (2009) 1.63

Structural evidence for loose linkage between ligand binding and kinase activation in the epidermal growth factor receptor. Mol Cell Biol (2010) 1.63

A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P. Nat Struct Mol Biol (2010) 1.62

Site-specific incorporation of a photo-crosslinking component into RNA by T7 transcription mediated by unnatural base pairs. Chem Biol (2004) 1.59

Structural basis for octameric ring formation and DNA interaction of the human homologous-pairing protein Dmc1. Mol Cell (2004) 1.57

An unnatural base pair system for efficient PCR amplification and functionalization of DNA molecules. Nucleic Acids Res (2008) 1.56

The RAC binding domain/IRSp53-MIM homology domain of IRSp53 induces RAC-dependent membrane deformation. J Biol Chem (2006) 1.56

Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase. Structure (2006) 1.56

Expression and purification of recombinant human histones. Methods (2004) 1.54

Crystal structure of the human BRD2 bromodomain: insights into dimerization and recognition of acetylated histone H4. J Biol Chem (2006) 1.54

Structural basis of replication origin recognition by the DnaA protein. Nucleic Acids Res (2003) 1.54

Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme. Structure (2004) 1.53

Drosophila U6 promoter-driven short hairpin RNAs effectively induce RNA interference in Schneider 2 cells. Biochem Biophys Res Commun (2005) 1.53

Mutation of the plastidial alpha-glucan phosphorylase gene in rice affects the synthesis and structure of starch in the endosperm. Plant Cell (2008) 1.52

Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA. Proc Natl Acad Sci U S A (2007) 1.52

Mammalian GW182 contains multiple Argonaute-binding sites and functions in microRNA-mediated translational repression. RNA (2009) 1.50

The antibiotic kasugamycin mimics mRNA nucleotides to destabilize tRNA binding and inhibit canonical translation initiation. Nat Struct Mol Biol (2006) 1.47

Pin1 and Par14 peptidyl prolyl isomerase inhibitors block cell proliferation. Chem Biol (2003) 1.47

Physical maps and recombination frequency of six rice chromosomes. Plant J (2003) 1.46

A common mechanism for the ATP-DnaA-dependent formation of open complexes at the replication origin. J Biol Chem (2008) 1.46

Solution structure of an Arabidopsis WRKY DNA binding domain. Plant Cell (2005) 1.45

Cytoplasmic destruction of p53 by the endoplasmic reticulum-resident ubiquitin ligase 'Synoviolin'. EMBO J (2006) 1.45

Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation. Nat Struct Mol Biol (2009) 1.45

Psychological factors influencing donors' decision-making pattern in living-donor liver transplantation. Transplantation (2011) 1.45

KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies. J Biomol NMR (2007) 1.44

Functional convergence of two lysyl-tRNA synthetases with unrelated topologies. Nat Struct Biol (2002) 1.43

Mutational separation of two pathways for editing by a class I tRNA synthetase. Mol Cell (2002) 1.42

Highly specific unnatural base pair systems as a third base pair for PCR amplification. Nucleic Acids Res (2011) 1.42

An efficient unnatural base pair for PCR amplification. J Am Chem Soc (2007) 1.41

RAD51 plays a crucial role in halting cell death program induced by ionizing radiation in bovine oocytes. Biol Reprod (2012) 1.40

Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1. Plant Cell (2004) 1.40

Structural basis for histone H3 Lys 27 demethylation by UTX/KDM6A. Genes Dev (2011) 1.40

Structural basis for the exclusive specificity of Slac2-a/melanophilin for the Rab27 GTPases. Structure (2008) 1.38

The interaction of DiaA and DnaA regulates the replication cycle in E. coli by directly promoting ATP DnaA-specific initiation complexes. Genes Dev (2007) 1.37

Structurally designed trans-2-phenylcyclopropylamine derivatives potently inhibit histone demethylase LSD1/KDM1 . Biochemistry (2010) 1.36

Crystal structure of leucyl-tRNA synthetase from the archaeon Pyrococcus horikoshii reveals a novel editing domain orientation. J Mol Biol (2004) 1.35

An engineered Escherichia coli tyrosyl-tRNA synthetase for site-specific incorporation of an unnatural amino acid into proteins in eukaryotic translation and its application in a wheat germ cell-free system. Proc Natl Acad Sci U S A (2002) 1.35

An unnatural base pair for incorporating amino acid analogs into proteins. Nat Biotechnol (2002) 1.35

A two-unnatural-base-pair system toward the expansion of the genetic code. J Am Chem Soc (2004) 1.35

Contribution of E3-ubiquitin ligase activity to HIV-1 restriction by TRIM5alpha(rh): structure of the RING domain of TRIM5alpha. J Virol (2011) 1.34

A short peptide insertion crucial for angiostatic activity of human tryptophanyl-tRNA synthetase. Nat Struct Mol Biol (2004) 1.34

Lessons from structural genomics. Annu Rev Biophys (2009) 1.33

Activation of the pyrrolysine suppressor tRNA requires formation of a ternary complex with class I and class II lysyl-tRNA synthetases. Mol Cell (2003) 1.33

13-Deoxytedanolide, a marine sponge-derived antitumor macrolide, binds to the 60S large ribosomal subunit. Bioorg Med Chem (2005) 1.32

Structural basis for the recognition between the regulatory particles Nas6 and Rpt3 of the yeast 26S proteasome. Biochem Biophys Res Commun (2007) 1.32