EXPRESSIVITY OF PROTEIN FAMILIES BY CODON ADAPTATION INDEX ANALYSIS: THE FAMiCOD ANALYSER PROJECT

INTRODUCTION All the organisms that have been studied so far have shown a largely different usage of synonymous codons. These differences seems to be due to the cellular tRNA abundancy and therefore to a different regulation of tRNA and aminoacil tRNA-sintethase transcription and to different aminoacil tRNA-sintethase activity. The codon usage seems not to be an evolutionary constrain since it has been found large differences among strictly related organsims. As a result, highly expressed proteins tends to be coded by species-specific "optimized" coding sequences composed by the most abundant codons. The basic meaning of this behaviour is to minimize the risk of tRNA depletion during intense translation and misincorporation of amino acids from rare codons (1). The analysis of the codons used in the coding sequences of proteins may therefore be an index of protein expression. The codon usage can be measured according to a number of criteria, spanning from raw count of the used codons to complex multivariate analysis. The most simple and sufficiently confident method seems to be the Codon Adaptation Index (CAI), which measures the variability of the codon usage in a gene in respect to the variability of a reference set of genes (2). This reference set must be composed of highly expressed genes in order to give a convenient correlation between CAI and gene expression. It is easy to understand that some protenis are conserved at high level into a cell, such as some ribosome associated protein or some basic transcription factor. It may be an underlaying assumption that all organisms present such proteins at high levels. Many researchers have confirmed through microarray analysis an effective correlation between gene expression and codon usage. Here we present a simple and effective method to predict a set of highly expressed genes to be used in estimatin of protein expression. Thanks to this approach a genome-wide analysis of gene expression may be performed and, thanks to protein classification databases, protein families expression may be estimated. This lead to the evaluatation of the effective role of some interesting pathway in different organisms.