Selection on codon bias.

@article{Hershberg2008SelectionOC,
  title={Selection on codon bias.},
  author={Ruth Hershberg and Dmitri A. Petrov},
  journal={Annual review of genetics},
  year={2008},
  volume={42},
  pages={
          287-99
        }
}
In a wide variety of organisms, synonymous codons are used with different frequencies, a phenomenon known as codon bias. Population genetic studies have shown that synonymous sites are under weak selection and that codon bias is maintained by a balance between selection, mutation, and genetic drift. It appears that the major cause for selection on codon bias is that certain preferred codons are translated more accurately and/or efficiently. However, additional and sometimes maybe even… 

Figures from this paper

Strong purifying selection on codon usage bias

This work uses site frequency spectrum and polymorphism- level data from deep Drosophila melanogaster population genomic sequencing to measure selection on synonymous sites and suggests a new model where the level of CUB in a gene is determined by distribution of selection coefficients across sites.

Enhanced effective codon numbers to understand codon usage bias

Methods to calculate modified effective codon numbers are presented that allow the investigation of the sources of codon bias and how genes or organisms have their codon biases shaped, and demonstrates that variation in codon usage bias across organisms is likely driven more by likely mutational forces while the variation within genomes is likelydriven by codon selectional forces.

Pervasive Strong Selection at the Level of Codon Usage Bias in Drosophila melanogaster

This is the first study to detect and quantify strong selection specifically at the level of CUB, and finds that CUB-associated polymorphism accounts for the majority of strong selection on synonymous sites, with secondary contributions of splicing and transcription factor binding.

Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift

A nested model of protein translation and population genetics is used to show that observed gene level variation of CUB in Saccharomyces cerevisiae can be explained almost entirely by selection for efficient ribosomal usage, genetic drift, and biased mutation.

Strong selection at the level of codon usage bias: evidence against the Li-Bulmer model

It is suggested that the level of CUB in the genome is determined by the proportion of synonymous sites under no, weak, and strong selection, which challenges the standard Li-Bulmer model and explains some of the longest-standing puzzles in the field.

Estimating Selection Intensity on Synonymous Codon Usage in a Nonequilibrium Population

A matrix model is constructed that includes the effects of a recent change in population size on estimates of selection on preferred vs. unpreferred codons, and analyses of twofold degenerate codons reveal that selection acts in favor of preferred codons.

Analysis of Mutation Bias in Shaping Codon Usage Bias and Its Association with Gene Expression Across Species

The results indicate that prediction of gene expression is significantly improved under the framework, and suggests that quantification of mutation bias is essential for fully understanding synonymous codon usage.

Evidence for Stabilizing Selection on Codon Usage in Chromosomal Rearrangements of Drosophila pseudoobscura

It is found that the interaction between weak stabilizing selection and mutational bias likely plays a role in shaping the composition of synonymous codons across the third chromosome in D. pseudoobscura.

Biased gene conversion affects patterns of codon usage and amino acid usage in the Saccharomyces sensu stricto group of yeasts.

It is shown that an additional neutral process, GC-biased gene conversion (gBGC), plays a part in shaping patterns of both synonymous codon usage and amino acid composition in a manner dependent upon the local recombination rate.

Selection on codon bias in yeast: a transcriptional hypothesis

A computational analysis of codon bias in yeast using experimental and theoretical genome-wide data suggests a role for transcriptional forces in driving codon usage bias via a mechanism that improves gene expression by optimizing mRNA folding structures.
...

References

SHOWING 1-10 OF 57 REFERENCES

The selection-mutation-drift theory of synonymous codon usage.

It is argued that the bias in synonymous codon usage observed in unicellular organisms is due to a balance between the forces of selection and mutation in a finite population, with greater bias in

Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage.

A likelihood ratio test is developed to examine the null hypothesis that codon usage is due to mutation bias alone, not influenced by natural selection, suggesting that natural selection may be a driving force in the evolution of synonymouscodon usage in mammals.

Synonymous codon usage in Escherichia coli: selection for translational accuracy.

It is concluded that selection on synonymous codon use in E. coli is largely due to selection for translational accuracy, to reduce the costs of both missense and nonsense errors.

Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases.

Codon usage data for 56 Bacillus subtilis genes show that synonymous codon usage in B. subtilis is less biased than in Escherichia coli, or in Saccharomyces cerevisiae. Nevertheless, certain genes

"Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons.

The patterns of synonymous codon usage in 91 Drosophila melanogaster genes have been examined, and data discussed are consistent with the effects of translational selection among synonymous codons, as seen in unicellular organisms.

Absence of translationally selected synonymous codon usage bias in Helicobacter pylori.

Despite the lack of selected codon usage, base composition immediately after the translation initiation site is skewed, consistent with selection against secondary structure formation in this region, suggesting that Hel.

Mutation pressure, natural selection, and the evolution of base composition in Drosophila

Patterns of base composition in Drosophila DNA suggest that natural selection may act at ‘silent’ sites, and a relationship between recombination rates and codon usage and comparisons of the evolutionary dynamics of silent mutations support natural selection discriminating among synonymous codons.

Natural selection and the frequency distributions of "silent" DNA polymorphism in Drosophila.

The existence of fitness classes of silent mutations is confirmed and maximum likelihood estimates suggest that selection intensity at silent sites is, on average, very weak in both D. pseudoobscura and D. simulans.

Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy.

Evidence is presented that natural selection biases synonymous codon usage to enhance the accuracy of protein synthesis in Drosophila melanogaster to avoid translational misincorporation and to support functional constraint at the protein level.

Codon catalog usage and the genome hypothesis.

This work indicates that the main factors distinguishing between mRNA sequences relate to choices among degenerate bases, and systematic third base choices can therefore be used to establish a new kind of genetic distance, which reflects differences in coding strategy.
...