5 The role of quorum-sensing in the virulence of Pseudomonas ...

Figure 1-1 shows a schematic of the typical structure of a pathogenicity island
Key: mob (mobility genes), vir (virulence gene); DR (direct DNA sequence repeats)
1.2.2 Genomic islands in Pseudomonas aeruginosa
A number of large genomic islands have been identified within P. aeruginosa and
are shown in Table 1-2. The abbreviation PAGI refers to Pseudomonas aeruginosa
genomic island and PAPI refers to Pseudomonas aeruginosa pathogenicity island.
All the large genomic islands are associated with tRNA sites with the exception of
PAGI-1.
Core genome Core genome
tRNA
At present only PAPI-1 and PAPI-2 are explicitly named pathogenicity islands in
the literature. P. aeruginosa is one of the more recently sequenced genomes, and
there are only 4 complete genome sequences available, PAO1 (2001), PA14 (2005),
PAS7 (2007) and LES (2008). It was reported that PAO1 had 44.2% of predicted
ORFs in class 4 (Lee et al. 2006), which is defined as ORFs with unknown function.
In order for genomic islands to be labelled pathogenicity islands they need to
contain proven virulence genes, but if the functions of the genes present are
unknown this is difficult.
DR
mob
Figure 1-1
The annotation process of P. aeruginosa genomes is still in its infancy, so tRNA
sites are referenced by referring to the gene preceding the tRNA gene in the
reference genome of P. aeruginosa PAO1. PAGI-1 is adjacent to the gene PA2217
and the full length island is found within isolate P. aeruginosa X24509. A number
of analysed P. aeruginosa strains contain a truncated version of PAGI-1 (Salunkhe
et al. 2005, Smart et al. 2006). The large genomic islands identified in the literature
6
vir (1)
vir (2)
DR