Pathogenicity islands in bacterial pathogenesis

Abstract

In this review, we focus on a group of mobile genetic elements designated pathogenicity islands (PAI). These elements play a pivotal role in the virulence of bacterial pathogens of humans and are also essential for virulence in pathogens of animals and plants. Characteristic molecular features of PAI of important human pathogens and their role in pathogenesis are described. The availability of a large number of genome sequences of pathogenic bacteria and their benign relatives currently offers a unique opportunity for the identification of novel pathogen-specific genomic islands. However, this knowledge has to be complemented by improved model systems for the analysis of virulence functions of bacterial pathogens. PAI apparently have been acquired during the speciation of pathogens from their nonpathogenic or environmental ancestors. The acquisition of PAI not only is an ancient evolutionary event that led to the appearance of bacterial pathogens on a timescale of millions of years but also may represent a mechanism that contributes to the appearance of new pathogens within a human life span. The acquisition of knowledge about PAI, their structure, their mobility, and the pathogenicity factors they encode not only is helpful in gaining a better understanding of bacterial evolution and interactions of pathogens with eukaryotic host cells but also may have important practical implications such as providing delivery systems for vaccination, tools for cell biology, and tools for the development of new strategies for therapy of bacterial infections.

FIG. 1.

General structure of PAI. (A) Typical PAI are distinct regions of DNA that are present in the genome of pathogenic bacteria but absent in nonpathogenic strains of the same or related species. PAI are mostly inserted in the backbone genome of the host strain (dark grey bars) in specific sites that are frequently tRNA or tRNA-like genes (hached grey bar). Mobility genes, such as integrases (int), are frequently located at the beginning of the island, close to the tRNA locus or the respective attachment site. PAI harbor one or more genes that are linked to virulence (V1 to V4) and are frequently interspersed with other mobility elements, such as IS elements (Is_c, complete insertion element) or remnants of IS elements (IS_d, defective insertion element). The PAI boundaries are frequently determined by DRs (triangle), which are used for insertion and deletion processes. (B) A characteristic feature of PAI is a G+C content different from that of the core genome. This feature is often used to identify new PAI (see the text for details).

FIG. 2.

Model of the development of PAI of pathogenic E. coli. In this basic model, foreign DNA is acquired by an ancient nonpathogenic E. coli strain, e.g., a normal inhabitant of the gut of vertebrates. In EHEC, a virulence-associated plasmid and at least one Stx-converting phage and several PAI have been acquired and maintained due to the specific adaptation to different environments. Genomic islands, which are present in a specific live environment may specialize and are involved in the development of disease such as (A), diarrhea and hemolytic-uremic syndrome after colonization of the large intestine (A), watery diarrhea after colonization of the small intestine (B), and UTI after survival and colonization of E. coli in the bladder (C). Such events probably have led to the development of specific pathotypes of E. coli, examples of which are EHEC (A), EPEC (B), and UPEC (C). In the model described here, the evolutionary sequence of uptake and incorporation of mobile genetic elements has not been considered. tRNA genes and bacterial phage attachment sites are depicted by grey rectangles with dots and hatched dark grey rectangles, respectively. stx, Shiga toxin gene; OI, O-island; espC, E. coli secreted protease gene.

FIG. 3.

Regulation of S. enterica SPI-1 and LEE of EPEC. (A) SPI-1 of S. enterica encodes a number of transcriptional regulators. Current genetic evidence is most consistent with a cascade of transcriptional activation in which HilD/HilC, HilA, and InvF (dark grey bars) act in sequence to activate SPI-1 genes. First, HilD and HilC bind to several sites within P_hilA and derepress hilA transcription. Then HilA binds to invF and prgH transcription start sites and activates the expression of invD and prgH. This results in expression of the genes encoding the T3SS (white bars). InvF is also required for expression of sptP, so it is possible that sicP sptP may be cotranscribed with the sip genes. Two other SPI-1 effectors, SigD (SopB), SopE, SopE2, and other unidentified factors are also expressed from InvF/SicA-dependent promoters. Whereas the HilD-HilA-InvF cascade is most plausible, deviations may occur. A number of environmental signals such as oxygen, osmolarity, growth phase, bile salts, and short-chain fatty acids have been described to modulate SPI-1 expression, probably dependent on the function of the component regulatory systems EnvZ-OmpR, BarA-SirA, PhoPQ, and PhoRB as well as FliZ, and Hha (for reviews, see references 134 and 214). (B) LEE1, LEE2, and LEE3 (light grey bars) represent three polycistronic operons encoding the T3SS. LEE4 (grey bar) encodes the secreted LEE effectors, and LEE5 (dark grey bar) encodes intimin and Tir. The first gene of LEE1 is ler, encoding a regulatory protein which is part of the regulatory cascade. Ler activates LEE2, LEE3, LEE4, and LEE5 expression. LEE1 is not regulated by Ler. The expression of ler itself is regulated by the plasmid-encoded regulator Per, which is encoded by the perABC operon. Per-mediated regulation of LEE is modulated due to different environmental signals. Expression of LEE genes is also dependent on the histone-like protein, H-NS, that usually down-regulates genes; here it down-regulates the LEE2 and LEE3 operons. LEE is also regulated by IHF, a global regulator which is essential for ler expression. Molecules that are produced by the quorum-sensing machinery activate LEE1 and LEE2 operons. Up-regulation of LEE1, in turn, increases the expression of LEE3 and LEE4.

FIG. 4.

Comparison of various PAI integrated at the selC locus. This schematic drawing of PAI demonstrates that the selC tRNA locus may have served as an integration site of PAI with different functions in different organisms either by means of a phage integrase or by other unknown events. (A) SHI-1 of S. flexneri; (B) LPA of STEC; (C) LEE of EPEC; (D) SPI-3 of S. enterica; (E) Tia-PAI of ETEC; (F) PAI I₅₃₆ of UPEC. Numbers and gene designations are adapted from the original papers (20, 68, 82, 94, 95, 282, 309). ORF are depicted as rectangles: dotted grey, tRNA selC; white, phage-like integrase gene; dark grey, mobility genes; light grey, all other PAI genes. See the text for details.

FIG. 5.

Examples of PAI of various pathogens. The topology of PAI of various pathogens is depicted to demonstrate different features of PAI. The functional classes of the genes are as indicated in the figure. (A) The cag island of H. pylori harbors genes for a type IV secretion system (T4SS) (grey symbols) that can mediate the translocation of the effector protein CagA (dark grey) into eukaryotic cells modified from reference 92. (B) Salmonella SPI-2 has a mosaic structure. It has been defined as a genetic element of about 40 kb that is absent from the related species E. coli. Only a 25-kb portion is required for systemic infection and encodes a T3SS system (grey), secreted proteins (dark grey), and regulatory proteins (white). Another portion (15 kb) is not required for virulence and harbors genes for metabolic or unknown functions (light grey symbols), such as an enzyme system for alternative electron acceptors during anaerobic growth. Genes associated with mobility are indicated by dark dotted symbols. Modified from reference 134. (C) The HPI of Y. enterocolitica is an example of an unstable PAI. Several is elements are present within this PAI (dotted arrows). Genes in HPI encode an high-affinity iron uptake system (dark grey) that is important for the extracellular proliferation of the pathogen during colonization of the host. Modified from reference 45. (D) The νSal PAI of MRSA is shown. A remarkable feature of PAI in S. aureus is the presence of a large number of genes with related functions, such as genes for enterotoxin (dark grey) or lipoproteins (grey). Modified from reference 9.

FIG. 6.

Relationship of SPI functions of S. enterica. This example shows the complex relationship of the functions of SPI-1, SPI-2, and SPI-5 that play important roles in the virulence of S. enterica. SPI-1 and SPI-2 each encode a secretion apparatus (T3SS) that assembles in the cell envelope (light and dark grey symbols). In addition, substrate proteins that are secreted or translocated by the SPI-1-encoded T3SS (dark grey circles) or the SPI-2-encoded T3SS (light grey circles) are encoded by the respective PAI. Further translocated effector proteins for either system are encoded by various loci outside of SPI-1 or SPI-2. SPI-5 harbors genes encoding effector proteins for the SPI-1 system as well as for the SPI-2 system. There are additional effector loci outside of the PAI that encode substrate proteins that can be secreted by the SPI-1 system as well as by the SPI-2 system (dotted grey symbols). SPI-1 and the cognate substrate proteins have functions in the invasion of eukaryotic host cells and enteropathogenesis. SPI-2 and the substrate proteins of the T3SS are important for the systemic pathogenesis of S. enterica and its intracellular survival and replication.