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Coevolution of Codon Usage and tRNA Genes Leads to Alternative Stable States of Biased Codon Usage

https://doi.org/10.1093/molbev/msn173
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Co-variation of tRNA Abundance and Codon Usage inEscherichia coliat Different Growth Rates
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The Evolution of tRNA-Leu Genes in Animal Mitochondrial Genomes
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Coevolution of codon usage and transfer RNA abundance
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Synonymous Codon Usage in Escherichia coli: Selection for Translational Accuracy
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Codon Usage in Mitochondrial Genomes: Distinguishing Context-Dependent Mutation from Translational Selection
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The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications
inferredcites →https://doi.org/10.1093/nar/16.17.8207openalex-snapshot
Codon usage patterns inEscherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogasterandHomo sapiens; a review of the considerable within-species diversity
inferredcites →https://doi.org/10.1093/nar/gkg897openalex-snapshot
Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome
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RPG: the Ribosomal Protein Gene database
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inferredcites →https://doi.org/10.1093/nar/gki242openalex-snapshot
Variation in the strength of selected codon usage bias among bacteria
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040335openalex-snapshot
Codon usage and tRNA content in unicellular and multicellular organisms.
inferredcites →https://doi.org/10.1101/gr.2896904openalex-snapshot
Codon usage bias from tRNA's point of view: Redundancy, specialization, and efficient decoding for translation optimization
inferredcites →https://doi.org/10.1126/science.279.5357.1665openalex-snapshot
Evolution of a Transfer RNA Gene Through a Point Mutation in the Anticodon
inferredcites →https://doi.org/10.1146/annurev.biochem.70.1.415openalex-snapshot
Fidelity of Aminoacyl-tRNA Selection on the Ribosome: Kinetic and Structural Mechanisms
inferredcites →https://doi.org/10.1186/1471-2148-8-211openalex-snapshot
The cost of wobble translation in fungal mitochondrial genomes: integration of two traditional hypotheses
inferredcites →https://doi.org/10.1261/rna.2272306openalex-snapshot
Archaeology and evolution of transfer RNA genes in the Escherichia coli genome
inferredcites →https://doi.org/10.1261/rna.294907openalex-snapshot
The frequency of translational misreading errors in E. coli is largely determined by tRNA competition
inferredcites →https://doi.org/10.1371/journal.pcbi.0010012openalex-snapshot
The Genomic Pattern of tDNA Operon Expression in E. coli

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Contributions of Speed and Accuracy to Translational Selection in Bacteria
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scnRCA: A Novel Method to Detect Consistent Patterns of Translational Selection in Mutationally-Biased Genomes
inferred← citeshttps://doi.org/10.1534/g3.116.033308openalex-snapshot
Genomic, Transcriptomic, and Proteomic Analysis Provide Insights Into the Cold Adaptation Mechanism of the Obligate Psychrophilic Fungus Mrakia psychrophila
inferred← citeshttps://doi.org/10.1534/genetics.114.162842openalex-snapshot
The Effect of Mutation and Selection on Codon Adaptation in Escherichia coli Bacteriophage
inferred← citeshttps://doi.org/10.20381/ruor-3483openalex-snapshot
Differential Selection and Mutation Shape Codon Usage of Escherichia coli ssDNA and dsDNA Bacteriophages
inferred← citeshttps://doi.org/10.20381/ruor-487openalex-snapshot
The Roles of Stop Codons and 3’ Flanking Base in Bacterial Translation Termination Efficiency
inferred← citeshttps://doi.org/10.20381/ruor-4888openalex-snapshot
Exploring Codon-Anticodon Adaptation in Eukaryotes
inferred← citeshttps://doi.org/10.21203/rs.3.rs-3789171/v1openalex-snapshot
Genetic distribution of bovine viral diarrhea virus in free-living cattle in China
inferred← citeshttps://doi.org/10.2147/rrbc.s83483openalex-snapshot
Synonymous codons influencing gene expression in organisms
inferred← citeshttps://doi.org/10.3389/fcimb.2021.607610openalex-snapshot
Adhesive Functions or Pseudogenization of Type Va Autotransporters in Brucella Species
inferred← citeshttps://doi.org/10.3389/fmicb.2022.828536openalex-snapshot
Response to Cold: A Comparative Transcriptomic Analysis in Eight Cold-Adapted Yeasts
inferred← citeshttps://doi.org/10.3389/fmicb.2024.1412318openalex-snapshot
Impact of the chemical modification of tRNAs anticodon loop on the variability and evolution of codon usage in proteobacteria
inferred← citeshttps://doi.org/10.3389/fmicb.2024.1414422openalex-snapshot
Codon usage bias in yeasts and its correlation with gene expression, growth temperature, and protein structure
inferred← citeshttps://doi.org/10.3390/ani15070901openalex-snapshot
Role Analysis of the scarb1 Gene in the Pigmentation of Neocaridina denticulata sinensis
inferred← citeshttps://doi.org/10.3390/biology12101338openalex-snapshot
Bioinformatic Analysis Reveals the Role of Translation Elongation Efficiency Optimisation in the Evolution of Ralstonia Genus
inferred← citeshttps://doi.org/10.3390/foods9020225openalex-snapshot
Insights into the Identification of the Specific Spoilage Organisms in Chicken Meat
inferred← citeshttps://doi.org/10.3390/ijms231911996openalex-snapshot
Bioinformatic Assessment of Factors Affecting the Correlation between Protein Abundance and Elongation Efficiency in Prokaryotes
inferred← citeshttps://doi.org/10.3390/ijms252111614openalex-snapshot
SARS-CoV-2 Displays a Suboptimal Codon Usage Bias for Efficient Translation in Human Cells Diverted by Hijacking the tRNA Epitranscriptome
inferred← citeshttps://doi.org/10.3897/bdj.11.e99224openalex-snapshot
Diversity of culturable thermophilic bacteria from Tata Pani hotspring of Kotli Azad Jammu and Kashmir
inferred← citeshttps://doi.org/10.4137/ebo.s22911openalex-snapshot
Roles of Solvent Accessibility and Gene Expression in Modeling Protein Sequence Evolution
inferred← citeshttps://doi.org/10.4236/jbise.2013.66078openalex-snapshot
Systematic analysis of diabetes- and glucose metabolism-related proteins and its application to Alzheimer’s disease
inferred← citeshttps://doi.org/10.53846/goediss-6242openalex-snapshot
Ribosome Processivity and Co-translational Protein Folding
inferred← citeshttps://doi.org/10.5772/28719openalex-snapshot
Protein Engineering with Non-Natural Amino Acids
inferred← citeshttps://doi.org/10.5897/ajmr.9000321openalex-snapshot
Factors affecting synonymous codon usage bias in the gC gene of DPV CHv strain
inferred← citeshttps://doi.org/10.70675/8ec8af0cz16e5z475czbbc5z65b57603581copenalex-snapshot
Comparative and functional genome analysis of Acidithiobacillus bacteria
inferred← citeshttps://doi.org/10.70675/ac18005bz20dfz4b21z9e2dz23d9cb9cc451openalex-snapshot
Diversité et évolution des paysages nucléotidiques des plantes
inferred← citeshttps://doi.org/10.71548/9902openalex-snapshot
Factors Involved in the Codon Usage Bias Among Different Genes in a Genome, And Among Different Sites Within a Gene
inferred← citeshttps://doi.org/10.7554/elife.01339openalex-snapshot
tRNA genes rapidly change in evolution to meet novel translational demands
inferred← citeshttps://doi.org/10.7554/elife.49816openalex-snapshot
Genomic adaptations in information processing underpin trophic strategy in a whole-ecosystem nutrient enrichment experiment
inferred← citeshttps://doi.org/10.7554/elife.57947openalex-snapshot
The birth of a bacterial tRNA gene by large-scale, tandem duplication events
inferred← citeshttps://doi.org/10.7554/elife.81005openalex-snapshot
The layered costs and benefits of translational redundancy
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