A Nutrient-Driven tRNA Modification Alters Translational Fidelity and Genome-wide Protein Coding across an Animal Genus

Use of the nutrient queuine to modify tRNA anticodons can change the accuracy of certain codons during protein synthesis, resulting in evolutionary recoding of fruit fly genomes.

• Publication year

  2014

• Venue

  PLoS Biology

• Publication date

  2014-12-01

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1371/journal.pbio.1002015PMID 25489848PMCID 4260829
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• Queuine-linked changes in tRNA anticodons can lead to evolutionary recoding of fruit fly genomes.

  Confidence 0.93

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewB (s683577b42) reviewq (76h6bfydm6) review
• Queuine-mediated tRNA anticodon modification can change the decoding accuracy of specific codons during protein synthesis.

  Confidence 0.96

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewB (s683577b42) reviewq (76h6bfydm6) review

• codon decoding accuracy

  property

  The precision with which a codon is matched to the correct tRNA and amino acid during translation.

  Aliases: codon accuracy

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewB (s683577b42) reviewq (76h6bfydm6) review
• evolutionary recoding

  genomic phenomenon

  A genome-level change in how codons are interpreted or used over evolutionary time.

  Aliases: genome recoding

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewB (s683577b42) reviewq (76h6bfydm6) review
• fruit fly genomes

  genome, organism

  The genomes of fruit fly species examined in the genus-level comparison.

  Aliases: Drosophila genomes

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewB (s683577b42) reviewq (76h6bfydm6) review
• protein synthesis

  biological process

  The cellular process of assembling proteins from mRNA templates.

  Aliases: translation

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewB (s683577b42) reviewq (76h6bfydm6) review
• queuine

  molecule, nutrient

  A nutrient-derived base used here to modify tRNA anticodons.

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewB (s683577b42) reviewq (76h6bfydm6) review
• translational fidelity

  biological process

  The overall accuracy of translation in producing the intended protein sequence.

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewB (s683577b42) reviewq (76h6bfydm6) review
• trna anticodon modification

  modification

  A chemical alteration of the tRNA anticodon region that affects how codons are read.

  Aliases: anticodon modification

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewB (s683577b42) reviewq (76h6bfydm6) review

• Correction: A Nutrient-Driven tRNA Modification Alters Translational Fidelity and Genome-wide Protein Coding across an Animal Genus

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• A Nutrient-Driven tRNA Modification Alters Translational Fidelity and Genome-wide Protein Coding across an Animal Genus

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• Nuclear tRNA gene predictions for 12 species in the genus Drosophila

  2014cited by this paper
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  2013cited by this paper
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  2013cited by this paper
• Estimating selection on synonymous codon usage from noisy experimental data.

  2013cited by this paper
• Strong Purifying Selection at Synonymous Sites in D. melanogaster

  2013cited by this paper
• Role of wobble base pair geometry for codon degeneracy: purine-type bases at the anticodon wobble position

  2012cited by this paper
• A role for tRNA modifications in genome structure and codon usage.

  2012cited by this paper
• Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency

  2012cited by this paper
• Good Codons, Bad Transcript: Large Reductions in Gene Expression and Fitness Arising from Synonymous Mutations in a Key Enzyme

  2012cited by this paper
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  2012cited by this paper
• Synonymous but not the same: the causes and consequences of codon bias

  2011cited by this paper
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  2011cited by this paper
• An evolutionarily conserved mechanism for controlling the efficiency of protein translation.

  2010cited by this paper
• Effect of Correlated tRNA Abundances on Translation Errors and Evolution of Codon Usage Bias

  2010cited by this paper
• A Universal Trend of Reduced mRNA Stability near the Translation-Initiation Site in Prokaryotes and Eukaryotes

  2010cited by this paper
• A comprehensive analysis of translational missense errors in the yeast Saccharomyces cerevisiae.

  2010cited by this paper
• On the Possible Role of tRNA Base Modifications in the Evolution of Codon Usage: Queuosine and Drosophila

  2010cited by this paper
• Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast

  2010cited by this paper
• The influence of anticodon-codon interactions and modified bases on codon usage bias in bacteria.

  2010influential reference
• The evolutionary consequences of erroneous protein synthesis

  2009cited by this paper
• On the application of statistical physics to evolutionary biology.

  2009cited by this paper
• Coding-Sequence Determinants of Gene Expression in Escherichia coli

  2009cited by this paper
• Translationally optimal codons associate with structurally sensitive sites in proteins.

  2009cited by this paper
• Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution.

  2008cited by this paper
• Developmental stage and level of codon usage bias in Drosophila.

  2008cited by this paper
• Coevolution of codon usage and tRNA genes leads to alternative stable states of biased codon usage.

  2008influential reference
• Selection on codon bias.

  2008cited by this paper
• A "Silent" Polymorphism in the MDR1 Gene Changes Substrate Specificity

  2007cited by this paper
• Evolution of genes and genomes on the Drosophila phylogeny

  2007cited by this paper
• Codon usage in twelve species of Drosophila

  2007influential reference
• Splicing and the Evolution of Proteins in Mammals

  2007cited by this paper
• Variable Strength of Translational Selection Among 12 Drosophila Species

  2007cited by this paper
• High Guanine and Cytosine Content Increases mRNA Levels in Mammalian Cells

  2006cited by this paper
• Synonymous codon usage in Escherichia coli: selection for translational accuracy.

  2006cited by this paper
• Minor shift in background substitutional patterns in the Drosophila saltans and willistoni lineages is insufficient to explain GC content of coding sequences

  2006cited by this paper
• The frequency of translational misreading errors in E. coli is largely determined by tRNA competition.

  2006cited by this paper
• Variation in the strength of selected codon usage bias among bacteria

  2005cited by this paper
• The application of statistical physics to evolutionary biology.

  2005cited by this paper
• Hypomodification of Transfer RNA in Cancer with Respect to Queuosine

  2005cited by this paper
• Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization.

  2004cited by this paper
• Decoding the genome: a modified view.

  2004cited by this paper
• A Gene Expression Map for the Euchromatic Genome of Drosophila melanogaster

  2004cited by this paper
• Analysis of a Shift in Codon Usage in Drosophila

  2003cited by this paper
• Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome.

  2003cited by this paper
• Evolution of synonymous codon usage in metazoans.

  2002cited by this paper
• Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy.

  1994cited by this paper
• Queuine metabolism and cadmium toxicity in Drosophila melanogaster.

  1991influential reference
• The selection-mutation-drift theory of synonymous codon usage.

  1991influential reference
• Estimators of the Mantel-Haenszel variance consistent in both sparse data and large-strata limiting models.

  1986cited by this paper
• The nucleotide sequence of two homogeneic Drosophila melanogaster tRNATyr isoacceptors: application of a rapid tRNA anticodon sequencing method using S-1 nuclease.

  1986cited by this paper
• Affinity electrophoresis for monitoring terminal phosphorylation and the presence of queuosine in RNA. Application of polyacrylamide containing a covalently bound boronic acid.

  1985influential reference
• Queuosine modification of the wobble base in tRNAHis influences ‘in vivo’ decoding properties.

  1985cited by this paper
• Queuine salvage in mammalian cells. Evidence that queuine is generated from queuosine 5'-phosphate.

  1984cited by this paper
• Isolation and characterization of an Escherichia coli mutant lacking tRNA-guanine transglycosylase. Function and biosynthesis of queuosine in tRNA.

  1982cited by this paper
• Presence of queuine in Drosophila melanogaster: correlation of free pool with queuosine content of tRNA and effect of mutations in pteridine metabolism.

  1981cited by this paper
• Three-dimensional structure of hyper-modified nucleoside Q located in the wobbling position of tRNA

  1979cited by this paper
• On the physical basis for ambiguity in genetic coding interactions.

  1978influential reference
• Evidence for a high proportion of inactive ribosomes in slow-growing yeast cells.

  1977cited by this paper
• Letter: The structure of Q* nucleoside isolated from rabbit liver transfer ribonucleic acid.

  1976cited by this paper
• Activity of a transfer RNA modifying enzyme during the development of Drosophila and its relationship to the su(s) locus.

  1973influential reference
• Statistical aspects of the analysis of data from retrospective studies of disease.

  1959cited by this paper
• Competition

  1936cited by this paper
• First published online as a Review in Advance on February 25, 2005 STRUCTURAL INSIGHTS INTO TRANSLATIONAL

  year unknowncited by this paper
• Supporting Online Material Materials and Methods Som Text Figs. S1 to S8 Table S1 Movies S1 to S3 a " Silent " Polymorphism in the Mdr1 Gene Changes Substrate Specificity Corrected 30 November 2007; See Last Page

  year unknowncited by this paper

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  2026cites this paper
• Tissue-specific role of dTrmO in threonine decoding during Drosophila melanogaster development.

  2026cites this paper
• A primer on tRNAs, tRNA-m1A58 modification, and tRNA derivatives in T-cell activation

  2026cites this paper
• Selective profiling of translationally active tRNAs and their dynamics under stress

  2026cites this paper
• Ribosome collisions and ZAKα activation: explores the therapeutic potential of metabolic diseases.

  2025cites this paper
• Exploring metalloproteome remodeling in calprotectin-stressed Acinetobacter baumannii using chemoproteomics

  2025cites this paper
• Two microbiome metabolites compete for tRNA modification to impact mammalian cell proliferation and translation quality control

  2025cites this paper
• Unraveling the microbiome's role in breast cancer progression and treatment response.

  2025cites this paper
• Sex-biased duplicates are rapidly generated during Drosophila tRNA repertoire evolution

  2025cites this paper
• Exploring Metalloproteome Remodeling in Calprotectin-Stressed Acinetobacter baumannii Using Chemoproteomics.

  2025cites this paper
• Queuosine is incorporated into precursor tRNA before splicing

  2025cites this paper
• Key RNA-binding domains in the La protein establish tRNA modification levels in Trypanosoma brucei

  2025cites this paper
• tRNA expression and modifications as critical components in the biology of blood feeding arthropods.

  2025cites this paper
• A survey of dietary effects on tRNA abundance and modifications

  2025cites this paper
• Mammalian queuosine tRNA modification impacts translation to enhance cell proliferation and MHC-II expression.

  2025cites this paper
• A microbiome-derived nutrient underlies tyrosine metabolism and predator avoidance in mosquito larvae

  2025cites this paper
• Dinucleotide preferences underlie apparent codon preference reversals in the Drosophila melanogaster lineage

  2025cites this paper
• Queuine: A Bacterial Nucleobase Shaping Translation in Eukaryotes.

  2025cites this paper
• RNA-modification by Base Exchange: Structure, Function and Application of tRNA-guanine Transglycosylases.

  2025cites this paper
• Genes and Pathways Comprising the Human and Mouse ORFeomes Display Distinct Codon Bias Signatures that Can Regulate Protein Levels

  2025cites this paper
• Quantitative RNA pseudouridine maps reveal multilayered translation control through plant rRNA, tRNA and mRNA pseudouridylation

  2025cites this paper
• Bacterial Metallostasis: Metal Sensing, Metalloproteome Remodeling, and Metal Trafficking

  2024cites this paper
• Queuosine tRNA Modification: Connecting the Microbiome to the Translatome

  2024cites this paper
• Variation in the fitness impact of translationally optimal codons among animals

  2024cites this paper
• Identifying Foods within the UK diet that are rich sources of the micronutrient Queuosine (Q)

  2024cites this paper
• Biosynthesis and function of 7-deazaguanine derivatives in bacteria and phages

  2024cites this paper
• Structural basis of Qng1-mediated salvage of the micronutrient queuine from queuosine-5′-monophosphate as the biological substrate

  2023cites this paper
• Disruption to tRNA Modification by Queuine Contributes to Inflammatory Bowel Disease

  2023cites this paper
• Not Quite Lost in Translation: Mistranslation Alters Adaptive Landscape Topography and the Dynamics of Evolution

  2023cites this paper
• Synthesis and Structure Elucidation of Glutamyl-Queuosine

  2023cites this paper
• Dormant bacterial spores encrypt a long-lasting transcriptional program to be executed during revival.

  2023cites this paper
• Queuosine‐tRNA promotes sex‐dependent learning and memory formation by maintaining codon‐biased translation elongation speed

  2023cites this paper
• Analysis of queuosine and 2-thio tRNA modifications by high throughput sequencing

  2022cites this paper
• tRNA modification dynamics from individual organisms to metaepitranscriptomics of microbiomes.

  2022cites this paper
• Functional integration of a semi-synthetic azido-queuosine derivative into translation and a tRNA modification circuit

  2022cites this paper
• tRNA-m1A modification promotes T cell expansion via efficient MYC protein synthesis

  2022cites this paper
• Arsenite toxicity is regulated by queuine availability and oxidation-induced reprogramming of the human tRNA epitranscriptome

  2022cites this paper
• The absence of the queuosine tRNA modification leads to pleiotropic phenotypes revealing perturbations of metal and oxidative stress homeostasis in Escherichia coli K12

  2022cites this paper
• Impact of queuosine modification of endogenous E. coli tRNAs on sense codon reassignment

  2022cites this paper
• Queuosine salvage in fission yeast by Qng1-mediated hydrolysis to queuine.

  2022cites this paper
• Dysfunction of transfer RNA modifications in inflammatory bowel disease

  2022cites this paper
• Dynamic queuosine changes in tRNA couple nutrient levels to codon choice in Trypanosoma brucei

  2021cites this paper
• Synonymous but not Silent: The Codon Usage Code for Gene Expression and Protein Folding.

  2021cites this paper
• Queuine, a bacterial-derived hypermodified nucleobase, shows protection in in vitro models of neurodegeneration

  2021cites this paper
• Tissue-specific reprogramming of host tRNA transcriptome by the microbiome

  2021cites this paper
• Analysis of Queuosine tRNA Modification Using APB Northern Blot Assay.

  2021cites this paper
• Genomic differentiation within East Asian Helicobacter pylori

  2021cites this paper
• Variations in transfer and ribosomal RNA epitranscriptomic status can adapt eukaryote translation to changing physiological and environmental conditions

  2021cites this paper
• Synthesis and structure elucidation of the human tRNA nucleoside mannosyl-queuosine

  2021cites this paper
• Structural and functional insights into human tRNA guanine transglycosylase

  2021cites this paper
• Preferential import of queuosine-modified tRNAs into Trypanosoma brucei mitochondrion is critical for organellar protein synthesis

  2021cites this paper
• Quantitative probing of glycosylated queuosine modifications in tRNA.

  2021cites this paper
• The Importance of the Epi-Transcriptome in Translation Fidelity

  2021cites this paper
• Epoxyqueuosine Reductase QueH in the Biosynthetic Pathway to tRNA Queuosine Is a Unique Metalloenzyme.

  2021cites this paper
• The importance of RNA modifications: From cells to muscle physiology

  2021cites this paper
• A versatile tRNA modification-sensitive northern blot method with enhanced performance

  2021cites this paper
• Cecum methylome response to Salmonella enterica serovar Enteritidis infection in chicken through whole genome bisulfite sequencing

  2020cites this paper
• Breast and gut microbiome in health and cancer

  2020cites this paper
• Detection and quantification of glycosylated queuosine modified tRNAs by acid denaturing and APB gels

  2020cites this paper
• Dynamic changes in tRNA modifications and abundance during T cell activation

  2020cites this paper
• Queuine Micronutrient Deficiency Promotes Warburg Metabolism and Reversal of the Mitochondrial ATP Synthase in Hela Cells

  2020cites this paper
• From canonical to modified nucleotides: balancing translation and metabolism

  2020cites this paper
• Broad-range RNA modification analysis of complex biological samples using rapid C18-UPLC-MS

  2020cites this paper
• tRNA Queuosine Modification Enzyme Modulates the Growth and Microbiome Recruitment to Breast Tumors

  2020cites this paper
• Chicken cecal DNA methylome alteration in the response to Salmonella enterica serovar Enteritidis inoculation

  2020cites this paper
• Probing the diversity and regulation of tRNA modifications.

  2020cites this paper
• Quantification of Queuosine Modification Levels in tRNA from Human Cells Using APB Gel and Northern Blot.

  2019cites this paper
• RNA (C5-cytosine) Methyltransferases

  2019cites this paper
• Queuine links translational control in eukaryotes to a micronutrient from bacteria

  2019influential citation
• Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens

  2019cites this paper
• Nutrigenomics and RNA methylation: role of micronutrients.

  2019cites this paper
• Effects of Arbovirus Multi-Host Life Cycles on Dinucleotide and Codon Usage Patterns

  2019cites this paper
• Repertoires of tRNAs: The Couplers of Genomics and Proteomics.

  2018cites this paper
• A molecular mechanics study on GA codon box translation.

  2018cites this paper
• The role of intracellular compartmentalization on tRNA processing and modification

  2018cites this paper
• The ribosome, (slow) beating heart of cancer (stem) cell

  2018cites this paper
• Visualizing translational errors: one cell at a time

  2018cites this paper
• Queuosine modification protects cognate tRNAs against ribonuclease cleavage

  2018influential citation
• Conservation of location of several specific inhibitory codon pairs in the Saccharomyces sensu stricto yeasts reveals translational selection

  2018cites this paper
• Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses

  2018cites this paper
• Can Protein Expression Be Regulated by Modulation of tRNA Modification Profiles?

  2018cites this paper
• Impact of tRNA Modifications and tRNA-Modifying Enzymes on Proteostasis and Human Disease

  2018cites this paper
• Emerging impacts of biological methylation on genetic information.

  2018cites this paper
• Identification of the minimal bacterial 2′‐deoxy‐7‐amido‐7‐deazaguanine synthesis machinery

  2018cites this paper
• Queuosine‐modified tRNAs confer nutritional control of protein translation

  2018influential citation
• The Epitranscriptome of Noncoding RNAs in Cancer.

  2017cites this paper
• Diverse Mechanisms of Sulfur Decoration in Bacterial tRNA and Their Cellular Functions

  2017cites this paper
• TRMT1-Catalyzed tRNA Modifications Are Required for Redox Homeostasis To Ensure Proper Cellular Proliferation and Oxidative Stress Survival

  2017cites this paper
• Synonymous Codons: Choose Wisely for Expression.

  2017cites this paper
• Metabolic influences on RNA biology and translation

  2017cites this paper
• The Escherichia coli COG1738 Member YhhQ Is Involved in 7-Cyanodeazaguanine (preQ0) Transport

  2017cites this paper
• Insights into soybean transcriptome reconfiguration under hypoxic stress: Functional, regulatory, structural, and compositional characterization

  2017cites this paper
• Cross-Talk between Dnmt2-Dependent tRNA Methylation and Queuosine Modification

  2017influential citation
• Mind over Matter : The Necessity of Metaphysics in a Material World

  2016cites this paper
• Detection of nucleic acid modifications by chemical reagents

  2016cites this paper
• tRNA base methylation identification and quantification via high-throughput sequencing

  2016cites this paper
• Rapid and dynamic transcriptome regulation by RNA editing and RNA modifications

  2016cites this paper
• Dnmt2 in RNA methylation, RNA inheritance, and environmental responses in the mouse

  2016influential citation
• Genome recoding by tRNA modifications

  2016cites this paper
• Recent and Long-Term Selection Across Synonymous Sites in Drosophila ananassae

  2016cites this paper