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Codon Usage Domains over Bacterial Chromosomes

Bailly-Bechet, Marc, Danchin, Antoine, Iqbal, Musaddar, Marsili, Metteo, Vergassola, Massimo (2006) Codon Usage Domains over Bacterial Chromosomes. PLoS Computational Biology, 2 (4). ISSN 1553-734X. (doi:10.1371/journal.pcbi.0020037) (KAR id:14490)

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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.

Item Type: Article
DOI/Identification number: 10.1371/journal.pcbi.0020037
Uncontrolled keywords: Bioinformatics, Codon Bias, Clustering
Subjects: Q Science > QA Mathematics (inc Computing science) > QA 76 Software, computer programming,
Divisions: Divisions > Division of Computing, Engineering and Mathematical Sciences > School of Computing
Depositing User: Mark Wheadon
Date Deposited: 24 Nov 2008 18:04 UTC
Last Modified: 09 Mar 2023 11:29 UTC
Resource URI: (The current URI for this page, for reference purposes)
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