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Codon usage domains over bacterial chromosomes
Marc Bailly-Bechet, Antoine Danchin, Mudassar Iqbal, Matteo Marsili, and Massimo Vergassola
PLoS Computational Biology, 2(4):182-196, April 2006.Abstract
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.
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@article{2600,
author = {Marc Bailly-Bechet and Antoine Danchin and Mudassar Iqbal and Matteo Marsili and Massimo Vergassola},
title = {Codon Usage Domains over Bacterial Chromosomes},
month = {April},
year = {2006},
pages = {182-196},
keywords = {determinacy analysis, Craig interpolants},
note = {},
doi = {},
url = {http://www.cs.kent.ac.uk/pubs/2006/2600},
publication_type = {article},
submission_id = {25754_1187711295},
ISSN = {ISSN 1553-734X},
journal = {PLoS Computational Biology },
volume = {2},
number = {4},
publisher = {Public Library of Science (PLOS)},
}