Molecular Biology and Evolution, Vol 16, 1219-1230, Copyright © 1999 by Society for Molecular Biology and Evolution
EP Rocha, A Danchin and A Viari
Prokaryotic genomes seem to be optimized toward compactness and have
therefore been thought to lack long redundant DNA sequences. However, we
identified a large number of long strict repeats in eight prokaryotic
complete genomes and found that their density is negatively correlated with
genome size. A detailed analysis of the long repeats present in the genome
of Bacillus subtilis revealed a very strict constraint on the spatial
distribution of repeats in this genome. We interpret this as the hallmark
of selection processes leading to the addition of new genetic information.
Such addition is independent of insertion sequences and relies on the
nonspecific DNA uptake by the competent cell and its subsequent integration
in the chromosome in a circular form through a Campbell-like mechanism.
Similar patterns are found in other competent genomes of Gram-negative
bacteria and Archaea, suggesting a similar evolutionary mechanism. The
correlation of the spatial distribution of repeats and the absence of
insertion sequences in a genome may indicate, in the framework of our
model, that mechanisms aiming at their avoidance/elimination have been
developed.
ORIGINAL ARTICLE
Analysis of long repeats in bacterial genomes reveals alternative evolutionary mechanisms in Bacillus subtilis and other competent prokaryotes
Atelier de BioInformatique, Universite Paris VI, France. erocha@abi.snv.jussieu.fr
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