Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome.

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 in

SUBMITTER: dos Reis M 

PROVIDER: S-EPMC290265 | biostudies-literature | 2003 Dec

REPOSITORIES: biostudies-literature