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

We present an expression measure of a gene, devised to predictthe level of gene expression from relative codon bias (RCB).There are a number of measures currently in use that quantifycodon usage in genes. Based on the hypothesis that gene expressivityand codon composition is strongly correlated, RCB has been definedto provide an intuitively meaningful measure of an extent ofthe codon preference in a gene. We outline a simple approachto assess the strength of RCB (RCBS) in genes as a guide totheir likely expression levels and illustrate this with an analysisof Escherichia coli (E. coli) genome. Our efforts to quantitativelypredict gene expression levels in E. coli met with a high levelof success. Surprisingly, we observe a strong correlation betweenRCBS and protein length indicating natural selection in favourof the shorter genes to be expressed at higher level. The agreementof our result with high protein abundances, microarray dataand radioactive data demonstrates that the genomic expressionprofile available in our method can be applied in a meaningfulway to the study of cell physiology and also for more detailedstudies of particular genes of interest.