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DNA Research Advance Access published online on January 8, 2009
DNA Research, doi:10.1093/dnares/dsn029
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© The Author 2009. Kazusa DNA Research Institute.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

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

Uttam Roymondal1, Shibsankar Das2 and Satyabrata Sahoo3,*

1 Department of Mathematics, Raidighi College, South 24 Parganas, Raidighi, West Bengal, India
2 Department of Mathematics, Uluberia College, Uluberia, Howrah, West Bengal, India
3 Department of Physics, Raidighi College, South 24 Parganas, Raidighi, West Bengal, India

Received 21 March 2008 ; accepted 16 October 2008.

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.

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

* To whom correspondence should be addressed. Tel. +91 3324-180575. Fax. +91 3174-270761. E-mail: dr_s_sahoo{at}yahoo.com

Edited by Hiroyuki Toh


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