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

dos Reis, M. and Wernisch, Lorenz and Savva, Renos (2003) Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome. Nucleic Acids Research 31 (23), pp. 6976-6985. ISSN 0305-1048.

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Official URL: http://dx.doi.org/10.1093/nar/gkg897

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.

Item Type: Article
Additional Information: This is a pre-copy-editing, author-produced PDF of an article accepted for publication in Nucleic Acids Research following peer review. The definitive publisher-authenticated version, v.31 (23), Pp. 6976-6985 is available online at http://dx.doi.org/10.1093/nar/gkg897
School or Research Centre: Birkbeck Schools and Research Centres > School of Science > Biological Sciences
Depositing User: Administrator
Date Deposited: 20 Jul 2010 10:46
Last Modified: 17 Apr 2013 12:33
URI: http://eprints.bbk.ac.uk/id/eprint/970

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