ArticleGenome biology2005
Do universal codon-usage patterns minimize the effects of mutation and translation error?
Article in Genome biology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- SWPhylo - A Novel Tool for Phylogenomic Inferences by Comparison of Oligonucleotide Patterns and Integration of Genome-Based and Gene-Based Phylogenetic Trees.Evolutionary bioinformatics online · 2018Article
- Inclusion of the fitness sharing technique in an evolutionary algorithm to analyze the fitness landscape of the genetic code adaptability.BMC bioinformatics · 2017Article
- Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes.Computational and structural biotechnology journal · 2017Article
- Article
- Genetic code evolution reveals the neutral emergence of mutational robustness, and information as an evolutionary constraint.Life (Basel, Switzerland) · 2015Article
- Optimization of Mutation Pressure in Relation to Properties of Protein-Coding Sequences in Bacterial Genomes.PloS one · 2015Article
- Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid.Nucleic acids research · 2014Article
- Simulated evolution applied to study the genetic code optimality using a model of codon reassignments.BMC bioinformatics · 2011Article
- A model-independent approach to infer hierarchical codon substitution dynamics.BMC bioinformatics · 2010Article
- Certain non-standard coding tables appear to be more robust to error than the standard genetic code.Journal of molecular evolution · 2010Article
- Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage.Nucleic acids research · 2009Article
- You're one in a googol: optimizing genes for protein expression.Journal of the Royal Society, Interface · 2009Review
- Evidence of bias towards buffered codons in human transcripts.Proceedings of the ... IEEE International Symposium on Signal Processing and Information Technology. IEEE International Symposium on Signal Processing and Information Technology · 2008Article
- The tri-frame model.Journal of theoretical biology · 2008Article
- Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape.Biology direct · 2007Article
- Identification of conflicting selective effects on highly expressed genes.Evolutionary bioinformatics online · 2007Article
- Using the nucleotide substitution rate matrix to detect horizontal gene transfer.BMC bioinformatics · 2006Article
- Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species.Genome biology · 2006Article
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundDo species use codons that reduce the impact of errors in translation or replication? The genetic code is arranged in a way that minimizes errors, defined as the sum of the differences in amino-acid properties caused by single-base changes from each codon to each other codon. However, the extent to which organisms optimize the genetic messages written in this code has been far less studied. We tested whether codon and amino-acid usages from 457 bacteria, 264 eukaryotes, and 33 archaea minimize errors compared to random usages, and whether changes in genome G+C content influence these error values.
resultsWe tested the hypotheses that organisms choose their codon usage to minimize errors, and that the large observed variation in G+C content in coding sequences, but the low variation in G+U or G+A content, is due to differences in the effects of variation along these axes on the error value. Surprisingly, the biological distribution of error values has far lower variance than randomized error values, but error values of actual codon and amino-acid usages are actually greater than would be expected by chance.
conclusionThese unexpected findings suggest that selection against translation error has not produced codon or amino-acid usages that minimize the effects of errors, and that even messages with very different nucleotide compositions somehow maintain a relatively constant error value. They raise the question: why do all known organisms use highly error-minimizing genetic codes, but fail to minimize the errors in the mRNA messages they encode?
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