D’Auria et al. BMC Genomics 2010, 11:181 http://www.biomedcentral.com/1471-2164/11/181 PR2 is specific to the Philadelphia strain and relies on a probable hot spot region. It contains six residual transposase-related ORFs followed by four hypothetical proteins that correspond to the beginning of the DT1ac islands. PR3, as stated above, has been found only in the Corby and Alcoy strains. It begins with an ankyrin repeat-containing protein (LPC_1606, lpa03089). Ankyrin-domain-containing proteins have a eukaryotic origin and are related to intracellular trafficking. In Legionella ankyrin-containing proteins may be secreted by the Dot/Icm system and could play a role in intracel- lular bacterial replication [14,38]. The island also contains several hypothetical proteins (LPC_1607- LPC_1615, lpa03090-lpa03095) and a transposase (LPC_1616, lpa03096). PR4 is specific to the Lens strain genome and spans around 29 kb. It seems to be a residual plasmid inte- grated into the chromosome, based on the presence of several proteins relating to DNA organization, such as lpl1068 containing SNF2-related protein domains that seem to be similar to helicases, and an Omp/MotB domain-containing protein (lpl1070) that may be related to structural flagella membrane proteins. Several phage- related proteins and transposases were found, together with another predicted inner membrane protein (lpl1073). Moreover, this island contains an ORF similar to DNA damage-inducible protein J (lpl1084), and the last two ORFs (lpl1092 and lpl1093) have high homology to other plasmid maintenance killer/antidote systems. The latter has been identified in several gram-negative- related plasmids and it is known as a regulator of bacter- ial programmed cellular death, although in some cases (e. g. E. coli) it is also integrated into the chromosome [39]. The Alcoy-specific island PR5 is integrated into a [CAT]-tRNAile site. The first three ORFs code for pro- teins related to transposases, whereas the remainder code for hypothetical proteins with no clear function. None of these proteins appear to have any relationship with other Legionella-related ORFs, and seem to be a clear case of acquisition by HGT. Three genes with no clear function, TraK gene (lpa03390), an inner mem- brane protein (lpa03394), and one hypothetical protein (lpa03395), have been found to be syntenic with the Lpg and Lpl genomes (lpg2365, lpg2366, and lpg2367; lpl0071, lpl0070, and lpl006, respectively). lpa03400 is similar to a phage-related integrase. The next ORFs (on the reverse strand) are related to a cluster of genes involved in bacilysin synthesis, known as one of the sim- plest antibiotic peptides active against some bacteria and fungi [40] (see Additional file 5). PR6 in the Philadelphia genome includes homologs of a type IV secretion system, mobile genetic elements, and Page 9 of 13 virulence factors. It has been described in detail by Bras- singa and collaborator (2003) as a 65 kb pathogenicity island [41]. Finally, the island PR7 in the Paris genome codes almost exclusively for hypothetical proteins. Only a putative primase/helicase (lpp2117), and a phage inte- grase (lpp2123) homolog seems to relate this island to phage integration with an unpredicted function. Not defined island (ND) Up to thirteen islands, for which it has not been possi- ble to establish a clear role, have been identified. Interestingly, all but one (ND11 in Lpa and Lpc), are strain-specific islands. ND1, ND2, ND3, ND8, ND9, and ND10 are found in the Paris genome. ND1 hosts a complete cytochrome o cluster (subunits II, I, III, IV on lpp0294, lpp0295, lpp0296, lpp0297, respectively) and a glycine/betaine transporter. ND2 contains hypothetical proteins, a CsrA (Carbon storage regula- tor), and is located close to the chromosomal heavy metals regulatory genes (HelABC). ND3 is formed by two hypothetical proteins followed by the HupE/UreJ membrane protein (lpp12118), homologs of Nickel/ Cobalt type II transport systems [42]. These elements are followed by a thiocyanate hydrolase cluster for subunits gamma, alpha and beta (lpp1219, lpp1220 and lpp122, respectively) that were previously identi- fied as unique to the Paris genome when compared to that from Lens [6]. This enzyme is the first key step in thiocyanate degradation and it is important in the detoxification processes [43]. ND8 is a small island composed mainly of transposases. Finally, for ND9 and ND10, it was not possible to propose a role. ND4 and ND5 are specific to the Philadelphia strains. ND4 is a small island containing hypothetical proteins and transposases, whereas ND5 contains a whole set of transposases and phage integrases as well as hypothe- tical proteins. ND6 and ND13 are specific to the Corby strain. ND6 spans a 7 kb region in the Corby genome with no apparently exogenous genes; it con- tains mainly hypothetical proteins, although some ORFs seem to be related to acetyltransferases. ND13 is syntenic with the terminal part of the Lpp island ND10 and, similarly, consists of hypothetical proteins. ND11 was found to be syntenic in both the Alcoy and Corby genomes and contains transposases and hypothetical proteins. ND7 and ND12 islands were found only in the Lens strains. ND7 is another not well-defined island consisting mostly of hypothetical proteins. It contains an ORF related to filamentation induced by a cAMP protein (lpl2288), an incomplete homolog of a HipA system, as well as the R1p island HipA/HipB system. Finally ND12 is made up exclu- sively of hypothetical proteins.