TY - JOUR T1 - Codon Usage Domains over Bacterial Chromosomes A1 - Bailly-Bechet, Marc A1 - Danchin, Antoine A1 - Iqbal, Mudassar A1 - Marsili, Matteo A1 - Vergassola, Massimo Y1 - 2006/04/21 N2 - The geography of codon bias distributions over prokaryotic genomes and its impact upon chromosomal organization are analyzed. To this aim, we introduce a clustering method based on information theory, specifically designed to cluster genes according to their codon usage and apply it to the coding sequences of Escherichia coli and Bacillus subtilis. One of the clusters identified in each of the organisms is found to be related to expression levels, as expected, but other groups feature an over-representation of genes belonging to different functional groups, namely horizontally transferred genes, motility, and intermediary metabolism. Furthermore, we show that genes with a similar bias tend to be close to each other on the chromosome and organized in coherent domains, more extended than operons, demonstrating a role of translation in structuring bacterial chromosomes. It is argued that a sizeable contribution to this effect comes from the dynamical compartimentalization induced by the recycling of tRNAs, leading to gene expression rates dependent on their genomic and expression context. JF - PLOS Computational Biology JA - PLOS Computational Biology VL - 2 IS - 4 UR - https://doi.org/10.1371/journal.pcbi.0020037 SP - e37 EP - PB - Public Library of Science M3 - doi:10.1371/journal.pcbi.0020037 ER -