ArticleBMC evolutionary biology2015
The evolutionary dynamics of tRNA-gene copy number and codon-use in E. coli.
Article in BMC evolutionary biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 28 citations in OpenAlex.
- Genome comparison of the bacteria in Mycobacterium avium complex (MAC) reveals the role of translational selection in shaping codon usage patterns.Molecular genetics and genomics : MGG · 2026Article
- Recombinant DNA the Bio-Revolution, Between Promise, Hurdles, and Achievements.International journal of molecular sciences · 2025Article
- Large-scale duplication events underpin population-level flexibility in tRNA gene copy number in Pseudomonas fluorescens SBW25.Nucleic acids research · 2024Article
- MenT nucleotidyltransferase toxins extend tRNA acceptor stems and can be inhibited by asymmetrical antitoxin binding.Nature communications · 2023Article
- On distinguishing between canonical tRNA genes and tRNA gene fragments in prokaryotes.RNA biology · 2023Article
- Distribution, inducibility, and characteristics ofMicrobiome research reports · 2023Article
- Translational demand is not a major source of plasmid-associated fitness costs.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
- Anaerobic Fungal Mevalonate Pathway Genomic Biases Lead to Heterologous Toxicity Underpredicted by Codon Adaptation Indices.Microorganisms · 2021Article
- Evolutionary responses to codon usage of horizontally transferred genes inMicrobial genomics · 2021Article
- Article
- Comparative Genome Analysis ofJournal of microbiology and biotechnology · 2020Article
- Deep sequencing reveals new roles for MuB in transposition immunity and target-capture, and redefines the insular Ter region ofMobile DNA · 2020Article
- Elucidation of Codon Usage Signatures across the Domains of Life.Molecular biology and evolution · 2019Article
- Codon usage revisited: Lack of correlation between codon usage and the number of tRNA genes in enterobacteria.Biochemical and biophysical research communications · 2018Article
- Article
- Transcription by RNA polymerase III: insights into mechanism and regulation.Biochemical Society transactions · 2016Review
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe introduction of foreign DNA by Lateral Gene Transfer (LGT) can quickly and drastically alter genome composition. Problems can arise if the genes introduced by LGT use codons that are not suited to the host's translational machinery. Here we investigate compensatory adaptation of E. coli in response to the introduction of large volumes of codons that are rarely used by the host genome.
resultsWe analyze genome sequences from the E. coli/Shigella complex, and find that certain tRNA genes are present in multiple copies in two pathogenic Shigella and O157:H7 subgroups of E. coli. Furthermore, we show that the codons that correspond to these multi-copy number tRNA genes are enriched in the high copy number Selfish Genetic Elements (SGE's) in Shigella and laterally introduced genes in O157:H7. We analyze the duplicate copies and find evidence for the selective retention of tRNA genes introduced by LGT in response to the changed codon content of the genome.
conclusionThese data support a model where the relatively rapid influx of LGT genes and SGE's introduces a large number of genes maladapted to the host's translational machinery. Under these conditions, it becomes advantageous for the host to retain tRNA genes that are required for the incorporation of amino acids at these codons. Subsequently, the increased number of copies of these specific tRNA genes adjusts the cellular tRNA pool to the demands set by global shifts in codon usage.
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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.