Nucleic Acids Research, 2003, Vol. 31, No. 22 6570-6577
© 2003 Oxford University Press
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Gene essentiality determines chromosome organisation in bacteria
1 Unité Génétique des Génomes Bactériens, Institut Pasteur, 28, rue du Dr Roux, 75724 Paris Cedex 15, France and 2 Atelier de Bioinformatique, Université Pierre et Marie Curie, 12, Rue Cuvier, 75005 Paris, France
*To whom correspondence should be addressed at Atelier de Bioinformatique, Université Pierre et Marie Curie, 12 rue Cuvier, 75005 Paris, France. Tel: +33 1 44 27 65 36; Fax: +33 1 44 27 63 12; Email: erocha{at}abi.snv.jussieu.fr
In Escherichia coli and Bacillus subtilis, essentiality, not expressivity, drives the distribution of genes between the two replicating strands. Although essential genes tend to be coded in the leading replicating strand, the underlying selective constraints and the evolutionary extent of these findings have still not been subject to comparative studies. Here, we extend our previous analysis to the genomes of low G + C firmicutes and 
-proteobacteria, and in a second step to all sequenced bacterial genomes. The inference of essentiality by homology allows us to show that essential genes are much more frequent in the leading strand than other genes, even when compared with non- essential highly expressed genes. Smaller biases were found in the genomes of obligatory intracellular bacteria, for which the assignment of essentiality by homology from fast growing free-living bacteria is most problematic. Cross-comparisons used to assess potential errors in the assignment of essentiality by homology revealed that, in most cases, variations in the assignment criteria have little influence on the overall results. Essential genes tend to be more conserved in the leading strand than average genes, which is consistent with selection for this positioning and may impose a strong constraint on chromosomal rearrangements. These results indicate that essentiality plays a fundamental role in the distribution of genes in most bacterial genomes.
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