ArticleJournal of molecular evolution2008
Codon bias is a major factor explaining phage evolution in translationally biased hosts.
Article in Journal of molecular evolution, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers, 1 of them a synthesis that pooled it.
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Who cites it
59 citing papers in PubMed, 1 synthesis or guideline pooled it, 86 citations in OpenAlex.
- Advances in phage-host interaction prediction: in silico method enhances the development of phage therapies.Briefings in bioinformatics · 2024Pooled it
- Phage host range: determinants, dynamics and applications.Nature reviews. Microbiology · 2026Review
- tRNA modifications in viral replication.The Journal of biological chemistry · 2026Review
- Isolation and characterization of a novel lytic phage Artin targeting typhoidal and nontyphoidal Salmonella and evaluation of its antibacterial efficacy in food.Virology journal · 2026Article
- DNA viruses are constrained to ecological niches and share similar environmental adaptations with hosts.Nature communications · 2026Article
- Review
- A comprehensive computational analysis investigating the relationships between phage codon usage, infection style, and number of tRNA genes.bioRxiv : the preprint server for biology · 2026Article
- Contrasting genome composition and codon usage inVirus evolution · 2026Article
- A computational investigation into the role of tRNAs encoded by Shigella phage Sf14.BMC genomics · 2025Article
- Adaptive loss of tRNA gene expression leads to phage resistance in a marine Synechococcus cyanobacterium.Nature microbiology · 2025Article
- Virus-host interactions predictor (VHIP): Machine learning approach to resolve microbial virus-host interaction networks.PLoS computational biology · 2024Article
- Why tRNA acquisition could be relevant to bacteriophages?Microbial biotechnology · 2024Article
- PB-LKS: a python package for predicting phage-bacteria interaction through local K-mer strategy.Briefings in bioinformatics · 2024Article
- Computational host range prediction-The good, the bad, and the ugly.Virus evolution · 2024Article
- Simultaneous entry as an adaptation to virulence in a novel satellite-helper system infecting Streptomyces species.The ISME journal · 2023Article
- Bacteriophage Infection of the Marine BacteriumMicroorganisms · 2023Article
- Article
- Setting Up a Better Infection: Overexpression of the Early Bacteriophage T4 GenePHAGE (New Rochelle, N.Y.) · 2022Article
- CHIKV infection reprograms codon optimality to favor viral RNA translation by altering the tRNA epitranscriptome.Nature communications · 2022Article
- Characterization and Genome Study of Novel Lytic Bacteriophages against Prevailing Saprophytic Bacterial Microflora of Minimally Processed Plant-Based Food Products.International journal of molecular sciences · 2021Article
Corrections and comments
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The size and diversity of bacteriophage populations require methodologies to quantitatively study the landscape of phage differences. Statistical approaches are confronted with small genome sizes forbidding significant single-phage analysis, and comparative methods analyzing full phage genomes represent an alternative but they are of difficult interpretation due to lateral gene transfer, which creates a mosaic spectrum of related phage species. Based on a large-scale codon bias analysis of 116 DNA phages hosted by 11 translationally biased bacteria belonging to different phylogenetic families, we observe that phage genomes are almost always under codon selective pressure imposed by translationally biased hosts, and we propose a classification of phages with translationally biased hosts which is based on adaptation patterns. We introduce a computational method for comparing phages sharing homologous proteins, possibly accepted by different hosts. We observe that throughout phages, independently from the host, capsid genes appear to be the most affected by host translational bias. For coliphages, genes involved in virion morphogenesis, host interaction and ssDNA binding are also affected by adaptive pressure. Adaptation affects long and small phages in a significant way. We analyze in more detail the Microviridae phage space to illustrate the potentiality of the approach. The small number of directions in adaptation observed in phages grouped around phi X174 is discussed in the light of functional bias. The adaptation analysis of the set of Microviridae phages defined around phi MH2K shows that phage classification based on adaptation does not reflect bacterial phylogeny.
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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.