PMID:14627830
| Citation |
dos Reis, M, Wernisch, L and Savva, R (2003) Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome. Nucleic Acids Res. 31:6976-85 |
|---|---|
| Abstract |
Escherichia coli has long been regarded as a model organism in the study of codon usage bias (CUB). However, most studies in this organism regarding this topic have been computational or, when experimental, restricted to small datasets; particularly poor attention has been given to genes with low CUB. In this work, correspondence analysis on codon usage is used to classify E.coli genes into three groups, and the relationship between them and expression levels from microarray experiments is studied. These groups are: group 1, highly biased genes; group 2, moderately biased genes; and group 3, AT-rich genes with low CUB. It is shown that, surprisingly, there is a negative correlation between codon bias and expression levels for group 3 genes, i.e. genes with extremely low codon adaptation index (CAI) values are highly expressed, while group 2 show the lowest average expression levels and group 1 show the usual expected positive correlation between CAI and expression. This trend is maintained over all functional gene groups, seeming to contradict the E.coli-yeast paradigm on CUB. It is argued that these findings are still compatible with the mutation-selection balance hypothesis of codon usage and that E.coli genes form a dynamic system shaped by these factors. |
| Links | |
| Keywords |
Bias (Epidemiology); Codon/genetics; Escherichia coli/genetics; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Genes, Bacterial/genetics; Genome, Bacterial; Molecular Sequence Data; Mutation; Oligonucleotide Array Sequence Analysis; Protein Biosynthesis; RNA, Bacterial/genetics; RNA, Bacterial/metabolism; RNA, Messenger/genetics; RNA, Messenger/metabolism; Regression Analysis; Statistics, Nonparametric |
| edit table |
Significance
You can help EcoliWiki by summarizing why this paper is useful
Useful Materials and Methods
You can help Ecoliwiki by describing the useful materials (strains, plasmids, antibodies, etc) described in this paper.
Annotations
<annotationlinks/>
EcoliWiki Links
Add links to pages that link here (e.g. gene, product, method pages)
References
See Help:References for how to manage references in EcoliWiki.