A putative RNA-interference-based immune system in prokaryotes: the epitome of prokaryotic genomic diversity

The extreme diversity and plasticity of prokaryotic genomes, manifest both at the level of gene loss and acquisition via horizontal gene transfer and at the level of gene order rearrangement, are arguably among the major generalizations of comparative genomics (Coenye et al., 2005; Koonin & Galperin, 1997, 2002; Snel et al., 2002). Bacteria and archaea have numerous partially conserved operons, probably thanks, in part, to the ‘selfish’ behaviour of operons, but little conservation of genome organization is seen at large evolutionary distances beyond the operon level (Dandekar et al., 1998; Lawrence, 1999; Mushegian & Koonin, 1996; Watanabe et al., 1997; Wolf et al., 2001). To detect traces of such long-range conservation, specially designed computational methods for detecting ‘überoperons’, or partially conserved gene neighbourhoods, have been developed (Lathe et al., 2000; Rogozin et al., 2002).