ArticlePloS one2012
Contributions of speed and accuracy to translational selection in bacteria.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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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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Who cites it
28 citing papers in PubMed.
- Hierarchical evolution of the proteobacterial essential chaperone SecB reveals non-neutral synonymous evolution under extreme purifying selection.Molecular genetics and genomics : MGG · 2026Article
- Differential Selection for Translation Efficiency Shapes Translation Machineries in Bacterial Species.Microorganisms · 2024Article
- Growth-dependent Gene Expression Variation Influences the Strength of Codon Usage Biases.Molecular biology and evolution · 2023Article
- Growth-dependent gene expression variation influences the strength of codon usage biases.bioRxiv : the preprint server for biology · 2023Article
- Translation Comes First: Ancient and Convergent Selection of Codon Usage Bias Across Prokaryotic Genomes.Journal of molecular evolution · 2022Article
- Translation stalling proline motifs are enriched in slow-growing, thermophilic, and multicellular bacteria.The ISME journal · 2022Article
- Pathogenicity and virulence ofVirulence · 2021Article
- Codon usage bias and environmental adaptation in microbial organisms.Molecular genetics and genomics : MGG · 2021Article
- The effects of codon bias and optimality on mRNA and protein regulation.Cellular and molecular life sciences : CMLS · 2021Review
- Origin and Evolution of H1N1/pdm2009: A Codon Usage Perspective.Frontiers in microbiology · 2020Article
- Selection-driven cost-efficiency optimization of transcripts modulates gene evolutionary rate in bacteria.Genome biology · 2018Article
- Codon usage bias reveals genomic adaptations to environmental conditions in an acidophilic consortium.PloS one · 2018Article
- Hybrid semiparametric systems for quantitative sequence-activity modeling of synthetic biological parts.Synthetic biology (Oxford, England) · 2018Article
- Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms.Genome biology · 2016Article
- Coevolution between Stop Codon Usage and Release Factors in Bacterial Species.Molecular biology and evolution · 2016Article
- Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon.Scientific reports · 2016Article
- Lack of tRNA-i6A modification causes mitochondrial-like metabolic deficiency in S. pombe by limiting activity of cytosolic tRNATyr, not mito-tRNA.RNA (New York, N.Y.) · 2016Article
- Genome Analysis of the Fruiting Body-Forming Myxobacterium Chondromyces crocatus Reveals High Potential for Natural Product Biosynthesis.Applied and environmental microbiology · 2016Article
- Global translational impacts of the loss of the tRNA modification tMicrobial cell (Graz, Austria) · 2016Article
- Codon Bias as a Means to Fine-Tune Gene Expression.Molecular cell · 2015Review
Corrections and comments
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2 authors.
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Abstract
Among bacteria, we have previously shown that species that are capable of rapid growth have stronger selection on codon usage than slow growing species, and possess higher numbers of rRNA and tRNA genes. This suggests that fast-growers are adapted for fast protein synthesis. There is also considerable evidence that codon usage is influenced by accuracy of translation, and some authors have argued that accuracy is more important than speed. Here we compare the strength of the two effects by studying the codon usages in high and low expression genes and on conserved and variable sites within high expression genes. We introduce a simple statistical method that can be used to assess the significance and the strength of the two types of bias in the same sets of sequences. We compare our statistical measure of codon bias to the common used codon adaptation index, and show that the new measure is preferable for three reasons for the purposes of this analysis. Across a large sample of bacterial genomes, both effects from speed and accuracy are clearly visible, although the speed effect appears to be much stronger than the accuracy effect and is found to be significant in a larger proportion of genomes. It is also difficult to explain the correlation of codon bias in the high expression genes with growth rates and numbers of copies of tRNA and rRNA genes on the basis of selection for accuracy. Hence we conclude that selection for translational speed is a dominant effect in driving codon usage bias in fast-growing bacteria, with selection for accuracy playing a small supplementary role.
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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.