ArticleGenetics2014
The effect of mutation and selection on codon adaptation in Escherichia coli bacteriophage.
Article in Genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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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.
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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.
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Who cites it
21 citing papers in PubMed, 40 citations in OpenAlex.
- Evolution of Translational Machinery in Fast- and Slow-Growing Bacteria.Microorganisms · 2026Article
- Comparative analysis of codon usage bias revealed natural selection-driven evolution and host adaptation of infectious haematopoietic necrosis virus.Virus evolution · 2026Article
- The role and application of bioinformatics techniques and tools in drug discovery.Frontiers in pharmacology · 2025Review
- Differential Selection for Translation Efficiency Shapes Translation Machineries in Bacterial Species.Microorganisms · 2024Article
- Specific codons control cellular resources and fitness.Science advances · 2024Article
- Variation in Release Factor Abundance Is Not Needed to Explain Trends in Bacterial Stop Codon Usage.Molecular biology and evolution · 2022Article
- Current Status of Endolysin-Based Treatments against Gram-Negative Bacteria.Antibiotics (Basel, Switzerland) · 2021Review
- Improving Phylogenetic Signals of Mitochondrial Genes Using a New Method of Codon Degeneration.Life (Basel, Switzerland) · 2020Article
- Dissimilation of synonymous codon usage bias in virus-host coevolution due to translational selection.Nature ecology & evolution · 2020Article
- Article
- Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes.Frontiers in microbiology · 2019Article
- The adaptation of codon usage of +ssRNA viruses to their hosts.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2018Article
- The Evolution of Molecular Compatibility between Bacteriophage ΦX174 and its Host.Scientific reports · 2018Article
- How Changes in Anti-SD Sequences Would Affect SD Sequences inG3 (Bethesda, Md.) · 2017Article
- Veterinary pharmaceuticals in aqueous systems and associated effects: an update.Environmental science and pollution research international · 2017Review
- Article
- Bioinformatics and Drug Discovery.Current topics in medicinal chemistry · 2017Review
- Codon usage in Alphabaculovirus and Betabaculovirus hosted by the same insect species is weak, selection dominated and exhibits no more similar patterns than expected.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2016Article
- Coevolution between Stop Codon Usage and Release Factors in Bacterial Species.Molecular biology and evolution · 2016Article
- Escherichia coli and Staphylococcus phages: effect of translation initiation efficiency on differential codon adaptation mediated by virulent and temperate lifestyles.The Journal of general virology · 2015Article
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 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Studying phage codon adaptation is important not only for understanding the process of translation elongation, but also for reengineering phages for medical and industrial purposes. To evaluate the effect of mutation and selection on phage codon usage, we developed an index to measure selection imposed by host translation machinery, based on the difference in codon usage between all host genes and highly expressed host genes. We developed linear and nonlinear models to estimate the C→T mutation bias in different phage lineages and to evaluate the relative effect of mutation and host selection on phage codon usage. C→T-biased mutations occur more frequently in single-stranded DNA (ssDNA) phages than in double-stranded DNA (dsDNA) phages and affect not only synonymous codon usage, but also nonsynonymous substitutions at second codon positions, especially in ssDNA phages. The host translation machinery affects codon adaptation in both dsDNA and ssDNA phages, with a stronger effect on dsDNA phages than on ssDNA phages. Strand asymmetry with the associated local variation in mutation bias can significantly interfere with codon adaptation in both dsDNA and ssDNA phages.
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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.