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Genomic Islands and Phages

Microbes often carry a substantial set of genes that are phylogenetically related to genes from distantly related species [40]. It is now widely recognized that many of these genes have been laterally transferred through integration of mobile DNA into a bacterial host chromosome. Clusters of laterally transferred genes were first discovered in pathogenic strains of bacterial species, whilst they were absent from nonpathogens [41, 42], and were therefore termed pathogenicity islands. However, it now seems clear that the concept of islands must be extended to nonpathogens, and could in principle be any distinct and unstable piece of DNA encoding genes used to exploit new environments. One example is the 500-kbp island capable of converting nonsymbiotic strains of the a-proteobacterium Mesorhizobium into legume symbionts [43]. Therefore, "genomic island" is a more appropriate name [44].

In addition to carrying host-adaptive genes and being present in some strains but not in others, genomic islands often have a mosaic structure, carrying cryptic or functional genes encoding integrases or other mobility factors, and have a base composition that differs from the rest of the genome [45]. Genomic islands may

13.5 Genomic Islands and Phages in Bartonella Species | 287

be introduced into the genome via bacteriophages, plasmids, or other accessory DNA [45]. The most commonly observed features associated with genomic islands are phage integrases, tRNAs, and flanking direct repeats [46, 47]. These characteristics suggest a phage origin, since phages are known to integrate site-specifically into tRNAs.

Phages are prevalent in nature and their role in horizontal transfer of genes between bacterial hosts in natural ecosystems is probably very important [48-51]. Phage genomes are mosaic with potential access to a large common gene pool, and recombination between phages appears to be frequent [52-55]. It is therefore likely that they provide a source of innovation, in which new variants and combinations of host-adaptive genes can appear. Several authors have put forward the idea that phages play a role in the evolution of their host [39, 56-58]. The pattern of presence and absence of phages in closely related strains and species suggests that they are generally short-lived in a bacterial genome. This could be the result of a deletion bias in the host, selected as a mechanism for removal of deleterious parasite-encoded DNA [59]. Of course, prophage DNA may be both deleterious and adaptive; the part of the phage that confers no advantage to the host is at most neutral and perhaps a burden. Most of the prophage genes (like the phage structural genes) are expected to be selectively neutral to the bacterium, and once a prophage is immobilized, nonessential parts will be eliminated by purifying selection. This is probably the reason for the observed relationship between geno-mic islands and phages; genomic islands might be remnants of phages that have kept the host-adaptive genes and lost the phage structural proteins.

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