COMMON FEATURES OF GENOMIC ISLANDS

The genome of a bacterium consists of a core that is common to all strains of a taxon and an accessory part that varies within and among clones of a taxon. The accessory genome represents the flexible gene pool that frequently undergoes acquisition and loss of genetic information and hence plays an important role for the adaptive evolution of bacteria (Dobrindt et al., 2004). The flexible gene pool is made up of accessory elements such as bacteriophages, plasmids, IS elements, transposons, conjugative transposons, integrons and genomic islands (GEIs).

GEIs are chromosomal regions that are typically flanked by direct repeats and inserted at the 3′ end of a tRNA gene. They contain transposase or integrase genes that are required for chromosomal integration and excision and further mobility-related genes. GEIs are clone- or strain-specific and are never found in all clones of a taxon. Most GEIs are easily differentiated from the core genome by their atypical G+C contents and atypical oligonucleotide composition, with steep gradients thereof at their boundaries (Reva & Tümmler, 2005). First identified in pathogenic bacteria (‘pathogenicity islands’), GEIs have since been detected in numerous non-pathogenic species. GEIs may confer fitness traits, increase metabolic versatility or adaptability or promote bacterium–host interaction in terms of symbiosis, commensalism or virulence (Dobrindt et al., 2004).

GEIs have been found in the majority of all currently completely sequenced bacterial genomes, but there is a bias towards Gram-negative bacteria and life in microbial communities.