ArticleGenome biology and evolution2018
The Codon Usage of Lowly Expressed Genes Is Subject to Natural Selection.
Article in Genome biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed, 63 citations in OpenAlex.
- The transcriptional and translational outcomes for pseudogenes in bacterial endosymbionts.Molecular biology and evolution · 2026Article
- Uncovering evolutionary and phylogenetic relationships in Glyptothorax species through comparative mitochondrial genomics.Journal, genetic engineering & biotechnology · 2026Article
- Hurdles to horizontal gene transfer: species-specific effects of synonymous variation and plasmid copy number determine antibiotic resistance phenotype.Microbiology (Reading, England) · 2026Article
- Integrative genomic and machine learning approaches reveal evolutionary signatures in the winged bean mitochondrial genome.BMC plant biology · 2025Article
- Identification and Functional Analysis of a Key Gene in the CHH Gene Family for Glucose Metabolism in the Pacific White ShrimpInternational journal of molecular sciences · 2025Article
- Discovery and investigation of the truncation of the (GGGGS)n linker and its effect on the productivity of bispecific antibodies expressed in mammalian cells.Bioprocess and biosystems engineering · 2025Article
- Compositional Features and Codon Usage Pattern of Genes Associated with Parkinson's Disease.Molecular neurobiology · 2024Article
- Comparative Analysis of Codon Usage Bias in SixInternational journal of molecular sciences · 2024Article
- Synonymous Codon Variant Analysis for Autophagic Genes Dysregulated in Neurodegeneration.Molecular neurobiology · 2023Article
- Mitogenomic Codon Usage Patterns of Superfamily Certhioidea (Aves, Passeriformes): Insights into Asymmetrical Bias and Phylogenetic Implications.Animals : an open access journal from MDPI · 2022Article
- Using phenotypic plasticity to understand the structure and evolution of the genotype-phenotype map.Genetica · 2022Review
- Preferred synonymous codons are translated more accurately: Proteomic evidence, among-species variation, and mechanistic basis.Science advances · 2022Article
- Intragenomic variation in non-adaptive nucleotide biases causes underestimation of selection on synonymous codon usage.PLoS genetics · 2022Article
- Kingdom-Wide Analysis of Fungal Protein-Coding and tRNA Genes Reveals Conserved Patterns of Adaptive Evolution.Molecular biology and evolution · 2022Article
- Article
- Elevated expression of the adhesion GPCR ADGRL4/ELTD1 promotes endothelial sprouting angiogenesis without activating canonical GPCR signalling.Scientific reports · 2021Article
- Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Article
- Article
- Hidden patterns of codon usage bias across kingdoms.Journal of the Royal Society, Interface · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Codon usage bias affects the genomes of organisms from all kingdoms of life and results from both background substitution biases and natural selection. Natural selection on codon usage to increase translation accuracy and efficiency has long been known to affect gene sequences. Such selection is stronger on highly, compared with lowly expressed genes, resulting in higher levels of codon bias within genes with higher expression levels. Additionally, selection on translation accuracy affects more strongly codons encoding conserved amino acids, since these will more often affect protein folding and/or function. By applying tests of selection on the gene sequences of the bacterium Escherichia coli, we demonstrate that both highly and lowly expressed genes display signals of selection on codon usage. Such signals are found for both conserved and less conserved amino acid positions, even within the 10% of E. coli genes expressed at the lowest levels. We further demonstrate experimentally that single synonymous codon replacements within a lowly expressed, essential gene can carry substantial effects on bacterial fitness. Combined, our results demonstrate that even within genes expressed at relatively low levels there is substantial selection on codon usage and that single synonymous codon replacements within such genes can have a marked effect on bacterial fitness.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.