ArticleMolecular biology and evolution2012
Gene expression levels are correlated with synonymous codon usage, amino acid composition, and gene architecture in the red flour beetle, Tribolium castaneum.
Article in Molecular biology and evolution, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed, 58 citations in OpenAlex.
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- Comparative Analysis of Codon Usage Bias in SixInternational journal of molecular sciences · 2024Article
- Codon Usage Provide Insights into the Adaptation of Rice Genes under Stress Condition.International journal of molecular sciences · 2023Article
- Co-Expression Network Analysis of Soybean Transcriptome Identify Hub Genes Under Saline-Alkaline and Water Deficit Stress.Iranian journal of biotechnology · 2022Article
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- Comprehensive analysis of coding sequence architecture features and gene expression inPhysiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- Convergent adaptation of the genomes of woody plants at the land-sea interface.National science review · 2020Article
- Absence of a Faster-X Effect in Beetles (G3 (Bethesda, Md.) · 2020Article
- A report on DNA sequence determinants in gene expression.Bioinformation · 2020Article
- Correlation between gene expression levels under drought stress and synonymous codon usage in rice plant by in-silico study.PloS one · 2020Article
- Evidence of multifaceted functions of codon usage in translation within the model beetle Tribolium castaneum.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Comprehensive profiling of codon usage signatures and codon context variations in the genus Ustilago.World journal of microbiology & biotechnology · 2019Article
- Comparative analysis of selection mode reveals different evolutionary rate and expression pattern in Arachis duranensis and Arachis ipaënsis duplicated genes.Plant molecular biology · 2018Article
- Base composition is the primary factor responsible for the variation of amino acid usage in zebra finch (Taeniopygia guttata).PloS one · 2018Article
- Co-adaption of tRNA gene copy number and amino acid usage influences translation rates in three life domains.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- Comprehensive analysis of correlations among codon usage bias, gene expression, and substitution rate in Arachis duranensis and Arachis ipaënsis orthologs.Scientific reports · 2017Article
- Integrated analysis of individual codon contribution to protein biosynthesis reveals a new approach to improving the basis of rational gene design.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
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2 authors at 1 institution in 1 country.
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Abstract
Gene expression levels correlate with multiple aspects of gene sequence and gene structure in phylogenetically diverse taxa, suggesting an important role of gene expression levels in the evolution of protein-coding genes. Here we present results of a genome-wide study of the influence of gene expression on synonymous codon usage, amino acid composition, and gene structure in the red flour beetle, Tribolium castaneum. Consistent with the action of translational selection, we find that synonymous codon usage bias increases with gene expression. However, the correspondence between tRNA gene copy number and optimal codons is weak. At the amino acid level, translational selection is suggested by the positive correlation between tRNA gene numbers and amino acid usage, which is stronger for highly expressed genes. In addition, there is a clear trend for increased use of metabolically cheaper, less complex amino acids as gene expression increases. tRNA gene numbers also correlate negatively with amino acid size/complexity (S/C) score indicating the coupling between translational selection and selection to minimize the use of large/complex amino acids. Interestingly, the analysis of 10 additional genomes suggests that the correlation between tRNA gene numbers and amino acid S/C score is widespread and might be explained by selection against negative consequences of protein misfolding. At the level of gene structure, three major trends are detected: 1) complete coding region length increases across low and intermediate expression levels but decreases in highly expressed genes; 2) the average intron size shows the opposite trend, first decreasing with expression, followed by a slight increase in highly expressed genes; and 3) intron density remains nearly constant across all expression levels. These changes in gene architecture are only in partial agreement with selection favoring reduced cost of biosynthesis.
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