Introduction

With the quote "Natura nonfacit saltum", Darwin's theory states that species do not evolve with leaps, but with small steps by vertical inheritance from parent to offspring with periodic selection. Currently, there is a general agreement that also lateral or horizontal gene transfer (HGT) are important evolutionary mechanisms (Kurland et al. 2003; Lawrence and Hendrickson 2003; Gal-Mor and Finlay 2006). HGT is defined as any process in which an organism transfers genetic material to another cell that is not its offspring, via natural transformation, conjugation, or transduction (Gal-Mor and Fin-lay 2006). HGT can enable rapid acquisition of new traits that improve fitness under specific environmental conditions and even occupation of new ecological niches. Because pathogenicity can be considered as an adaptation to a specific niche, the host, it is not surprising that virulence factors of bacteria that are pathogenic to animals or plants are often encoded on transmissible genetic elements, such as transposons, plasmids, bacteriophages, and pathogenicity islands (Frost et al. 2005).

The term pathogenicity island (PAI), introduced by Hacker et al. (1990), specifies a region in the chromosome that contains one or commonly many virulence genes present in pathogenic bacteria but absent in not or less pathogenic bacteria of the same or related species. Within PAIs the genes have often a G+C content and codon usage that differ from those of the rest of the chromosome. PAIs are usually flanked by specific genetic elements, such as direct repeats, insertion sequence elements, and transfer RNA genes, and frequently possess genes coding for genetic mobility factors, such as integrases, transposases, and origins of replication. These features indicate that these particular genetic elements are or have previously been able to spread among bacterial populations and contribute to microbial evolution (Hacker et al. 1997; Gal-Mor and Finlay 2006). The recent availability of multiple ge-nomic sequences and the use of various comparative genomic approaches have revealed that PAIs are widespread and can be found in Gram-negative and Gram-positive human, mammalian, and plant pathogens (Hacker and

Kaper 2000; Oelschlaeger and Hacker 2004; Gal-Mor and Finlay 2006). PAIs of phytopathogenic bacteria are found in diverse genera, such as Streptomyces (Kers et al. 2005), Pseudomonas (Alfano et al. 2000; Araki et al. 2006), Xan-thomonas (Kim et al. 2003), and Erwinia (Oh and Beer 2005). The generation of new pathogenic species through mobilizable PAIs is illustrated by the recent and independent emergence of two new phytopathogenic Streptomyces species, S. acidiscabies and S. turgidiscabies (Kers et al. 2005; Loria et al. 2006).

Plasmids are stable self-replicating extrachromosomal elements that usually do not contain genes for essential cellular functions. The occurrence of virulence genes on circular plasmids and their role in dissemination of virulence traits has been recognized for decades (Vivian et al. 2001). However, it is becoming increasingly clear that virulence determinants are often clustered on the plasmids in typical PAIs, as in Pantoa agglomerans (Barash and Man-ulis 2005) and Pseudomonas syringae pv. phaseolicola (Oguiza et al. 2004).

Since the discovery by Hayakawa et al. (1979) of the first bacterial linear plasmid in S. rochei, many linear double-stranded DNA plasmids of various sizes have been isolated from Streptomyces species (Netolitzky et al. 1995; Mochizuki et al. 2003; Chater and Kinashi, in this volume; see also Chen, in this volume) and other bacteria, such as Clavibacter michiganensis subspecies sepedonicus (Brown et al. 2002) and the actinomycetes Mycobacterium (Pi-cardeau and Vincent 1997; Le Dantec et al. 2001; Kobryn, in this volume), Rhodococcus (Crespi et al. 1992; Stecker et al. 2003; Sekine et al. 2006), and Planobispora (Polo et al. 1998). Two types of linear plasmids exist: the so-called hairpin plasmids with covalently closed ends, and the invertron-type linear plasmids with terminal inverted repeats (TIRs) and proteins cova-lently linked to the 5' termini. The latter type forms the largest group of extrachromosomal linear replicons and is predominantly found in actino-mycetes (Meinhardt et al. 1997; Chater and Kinashi, in this volume; see also Chen, in this volume). These linear plasmids confer advantageous abilities on their hosts, but until now there is only one example of a plant pathogenic bacterium whose virulence genes are located on a linear plasmid. This phy-topathogen, the subject of this chapter, is Rhodococcus fascians, an actino-mycete that provokes leafy gall formation on host plants.

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