ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2017
Evidence of translation efficiency adaptation of the coding regions of the bacteriophage lambda.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 20 citations in OpenAlex.
- DNA viruses are constrained to ecological niches and share similar environmental adaptations with hosts.Nature communications · 2026Article
- Bacteriophage Infection of the Marine BacteriumMicroorganisms · 2023Article
- Unique properties of spacer acquisition by the type III-A CRISPR-Cas system.Nucleic acids research · 2022Article
- Translational adaptation of human viruses to the tissues they infect.Cell reports · 2021Article
- Variability in mRNA translation: a random matrix theory approach.Scientific reports · 2021Article
- Phage-specific metabolic reprogramming of virocells.The ISME journal · 2020Article
- Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages.Nature communications · 2020Article
- The Critical Role of Codon Composition on the Translation Efficiency Robustness of the Hepatitis A Virus Capsid.Genome biology and evolution · 2019Article
- Modelling and measuring intracellular competition for finite resources during gene expression.Journal of the Royal Society, Interface · 2019Article
- Generation and comparative genomics of synthetic dengue viruses.BMC bioinformatics · 2018Article
- Significant differences in terms of codon usage bias between bacteriophage early and late genes: a comparative genomics analysis.BMC genomics · 2017Article
- The Landscape of the Emergence of Life.Life (Basel, Switzerland) · 2017Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Deciphering the way gene expression regulatory aspects are encoded in viral genomes is a challenging mission with ramifications related to all biomedical disciplines. Here, we aimed to understand how the evolution shapes the bacteriophage lambda genes by performing a high resolution analysis of ribosomal profiling data and gene expression related synonymous/silent information encoded in bacteriophage coding regions.We demonstrated evidence of selection for distinct compositions of synonymous codons in early and late viral genes related to the adaptation of translation efficiency to different bacteriophage developmental stages. Specifically, we showed that evolution of viral coding regions is driven, among others, by selection for codons with higher decoding rates; during the initial/progressive stages of infection the decoding rates in early/late genes were found to be superior to those in late/early genes, respectively. Moreover, we argued that selection for translation efficiency could be partially explained by adaptation to Escherichia coli tRNA pool and the fact that it can change during the bacteriophage life cycle.An analysis of additional aspects related to the expression of viral genes, such as mRNA folding and more complex/longer regulatory signals in the coding regions, is also reported. The reported conclusions are likely to be relevant also to additional viruses.
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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.