Codon usage as a tool to predict the cellular location of eukaryotic ribosomal proteins and aminoacyl-tRNA synthetases

In spite of many efforts, the prediction of the location of proteins in euk aryotic cells (cytoplasm, mitochondrion or chloroplast) is still far from s traightforward. In some cases (e,g, ribosomal proteins and aminoacyl-tRNA s ynthetases) both the cytoplasmic proteins and their organellar counterparts are encoded by the nuclear genome. A factorial correspondence analysis of the codon usage in yeast and Caenorhabditis elegans shows that the codon us age of those nuclear genes encoding ribosomal proteins or aminoacyl-tRNA sy nthetases is markedly different, depending on the final location of the pro teins (cytoplasmic or mitochondrial). As a consequence, the location of suc h proteins-whose sequences are now frequently determined by systematic geno mic sequencing-can be easily and quickly predicted. A WWW interface has bee n developed, aimed at providing a user-friendly tool for codon usage patter n analysis. It is available from http://www.genetique.uvsq.f r/afc.html.