Journal Article

Predicting Gene Expression Level from Relative Codon Usage Bias: An Application to <i>Escherichia coli</i> Genome

Uttam Roymondal, Shibsankar Das and Satyabrata Sahoo

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 16, issue 1, pages 13-30
Published in print February 2009 | ISSN: 1340-2838
Published online January 2009 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/dsn029

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We present an expression measure of a gene, devised to predict the level of gene expression from relative codon bias (RCB). There are a number of measures currently in use that quantify codon usage in genes. Based on the hypothesis that gene expressivity and codon composition is strongly correlated, RCB has been defined to provide an intuitively meaningful measure of an extent of the codon preference in a gene. We outline a simple approach to assess the strength of RCB (RCBS) in genes as a guide to their likely expression levels and illustrate this with an analysis of Escherichia coli (E. coli) genome. Our efforts to quantitatively predict gene expression levels in E. coli met with a high level of success. Surprisingly, we observe a strong correlation between RCBS and protein length indicating natural selection in favour of the shorter genes to be expressed at higher level. The agreement of our result with high protein abundances, microarray data and radioactive data demonstrates that the genomic expression profile available in our method can be applied in a meaningful way to the study of cell physiology and also for more detailed studies of particular genes of interest.

Keywords: codon usage; gene expression; predicted highly expressed genes; Escherichia coli

Journal Article.  11003 words.  Illustrated.

Subjects: Genetics and Genomics

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