Genome rearrangement by replication-directed translocation

Abstract

Gene order in bacteria is poorly conserved during evolution. For example, although many homologous genes are shared by the proteobacteria Escherichia coli, Haemophilus influenzae and Helicobacter pylori, their relative positions are very different in each genome, except local functional clusters such as operons. The complete sequences of the more closely related bacterial genomes, such as pairs of Chlamydia, H. pylori and Mycobacterium species, now allow identification of the processes and mechanisms involved in genome evolution. Here we provide evidence that a substantial proportion of rearrangements in gene order results from recombination sites that are determined by the positions of the replication forks. Our observations suggest that replication has a major role in directing genome evolution.

Diversity of the genus Lactobacillus revealed by comparative genomics of five species

“…The alignments are made of patched regions following an X-shaped distribution that is symmetric about the origin of replication as previously noted in other bacteria by Eisen et al (2000). This symmetry indicates that matching sequences tend to occur at the same distance from the origin but not necessarily on the same side of the origin, which is explained by the fork replication theory (Tillier & Collins, 2000). These X-shaped regions are not clearly symmetrical with respect to the origin-terminus axis in any of the L. plantarum alignments.…”

Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica

“…The region around the terminus has eight rearranged blocks of DNA. Most chromosomal rearrangements between related bacteria are arranged reciprocally around the origin or terminus of replication, because, it has been suggested, most recombination occurs between, or close to, replication forks 9 or because other rearrangements may occur but are selectively disadvantageous 10 . Most of the rearrangements in B. parapertussis (and B. pertussis) do not follow this pattern, suggesting that any such selection may be overcome by frequent recombination between large perfect repeats.…”

Does Gene Translocation Accelerate the Evolution of Laterally Transferred Genes?

“…translocations play important roles in bacterial genome evolution (Garcia-Vallvé et al 2000;Ochman and Jones 2000;Tillier and Collins 2000a;Fraser-Liggett 2005). Gene insertions and deletions, as the essential driving forces in influencing gene content (Kunin and Ouzounis 2003), have received a great deal of attention.…”