Pathogenicity islands (PAIs) are gene clusters incorporated in the
genome, chromosomally or extrachromosomally, of pathogenic organisms, but are usually absent from those
nonpathogenic organisms of the same or closely related species. They may be located on a bacterial chromosome or may be transferred within a
plasmid or can be found in bacteriophage genomes. Bacteriophage integrases also found on pathogenicity islands (PAIs) are enzymes produced by bacteriophages to enable site-specific recombination between two
recognition sequences, serving as another form of mobility element to enable PAIs insertion into host DNA. PAIs are often associated with
tRNA genes, which target sites for this integration event. Given that integration may result in tRNA truncation, it is probable that only non-essential tRNA loci found in multiple locations, or those possessing wobble capacity (the ability of a 5' base of a tRNA anticodon to mispair with the third base of an mRNA codon) can become common integration sites. They can be transferred as a single unit to new bacterial cells, thus conferring virulence to formerly benign strains. Pathogenicity islands carry genes encoding one or more virulence factors, including, but not limited to,
adhesins,
secretion systems (type III and IV secretion system),
toxins,
invasins,
modulins,
effectors,
superantigens, iron uptake systems, o-antigen synthesis, serum resistance,
immunoglobulin A proteases,
apoptosis,
capsule synthesis, and plant tumorigenesis via
Agrobacterium tumefaciens. Type III and type IV secretion systems, which are both expressed in Gram-negative bacteria, are the secretion systems most frequently linked to PAIs. The bacterial membranes contain the
type III secretion system (T3SS), which functions essentially as a molecular syringe. The needle-like apparatus secretes effectors, which go from the bacterial cell to the host cell via the tip of the apparatus, creating a hole in the membrane of the host cell. There are various combinations of regulation involving pathogenicity islands. The first combination is that the pathogenicity island contains the genes to regulate the virulence genes encoded on the PAI. The second combination is that the pathogenicity island contains the genes to regulate genes located outside of the pathogenicity island. Additionally, regulatory genes outside of the PAI may regulate virulence genes in the pathogenicity island. Regulation genes typically encoded on PAIs include AraC-like proteins and two-component response regulators. PAIs can be considered unstable DNA regions as they are susceptible to deletions or mobilization. This may be due to the structure of PAIs, with direct repeats, insertion sequences and association with tRNA that enables deletion and mobilization at higher frequencies. Additionally, deletions of pathogenicity islands inserted in the genome can result in disrupting tRNA and subsequently affect the metabolism of the cell. ==Examples==