Journal article
Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes
Genetics (Austin), Vol.168(4), pp.2245-2260
12/2004
DOI: 10.1534/genetics.104.030866
PMCID: PMC1448744
PMID: 15611189
Abstract
To study the roles of translational accuracy, translational efficiency, and the Hill-Robertson effect in codon usage bias, we studied the intragenic spatial distribution of synonymous codon usage bias in four prokaryotic (Escherichia coli, Bacillus subtilis, Sulfolobus tokodaii, and Thermotoga maritima) and two eukaryotic (Saccharomyces cerevisiae and Drosophila melanogaster) genomes. We generated supersequences at each codon position across genes in a genome and computed the overall bias at each codon position. By quantitatively evaluating the trend of spatial patterns using isotonic regression, we show that in yeast and prokaryotic genomes, codon usage bias increases along translational direction, which is consistent with purifying selection against nonsense errors. Fruit fly genes show a nearly symmetric M-shaped spatial pattern of codon usage bias, with less bias in the middle and both ends. The low codon usage bias in the middle region is best explained by interference (the Hill-Robertson effect) between selections at different codon positions. In both yeast and fruit fly, spatial patterns of codon usage bias are characteristically different from patterns of GC-content variations. Effect of expression level on the strength of codon usage bias is more conspicuous than its effect on the shape of the spatial distribution.
Details
- Title: Subtitle
- Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes
- Creators
- Hong Qin - Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USAWei Biao WuJosep M ComeronMartin KreitmanWen-Hsiung Li
- Resource Type
- Journal article
- Publication Details
- Genetics (Austin), Vol.168(4), pp.2245-2260
- Publisher
- United States
- DOI
- 10.1534/genetics.104.030866
- PMID
- 15611189
- PMCID
- PMC1448744
- ISSN
- 0016-6731
- eISSN
- 1943-2631
- Grant note
- GM30998 / NIGMS NIH HHS R37 GM030998 / NIGMS NIH HHS R01 GM030998 / NIGMS NIH HHS
- Language
- English
- Date published
- 12/2004
- Academic Unit
- Biology
- Record Identifier
- 9983992064302771
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