Year: 1996
Type: article
Abstract: “I am the beneficiary of a lucky break in the genetic sweepstakes” Isaac Asimov For most bacterial pathogens virulence is a multifactorial process requiring two general classes of determinants. The first encompasses genes that participate in physiological processes necessary for survival in host and non-host environments, and these genes are generally found in both pathogenic and non-pathogenic organisms. In Salmonella, this set includes regulatory genes, such as phoP/phoQ, that control expression of more than 20 loci in response to low magnesium environments; biosynthetic genes, such as aroA, that encodes the ability to synthesize aromatic amino acids not found in host tissues; and several additional genes required for cell maintenance and DNA repair (9Groisman E.A Ochman H Trends Microbiol. 1994; 2: 289-294Abstract Full Text PDF PubMed Scopus (46) Google Scholar). The second class of virulence genes specifies traits that are unique to pathogens, and, not surprisingly, these genes are rarely detected in non-pathogenic organisms. Based on the initial characterizations of plasmids from Yersinia and Shigella, such sequences were originally thought to be confined to extrachromosomal elements; but recently, several virulence cassettes have been mapped to the chromosome of pathogenic organisms. These segments of the chromosome, termed pathogenicity islands (11Hacker J Bender L Ott M Wingender J Lund B Marre R Goebel W Microb. Pathogen. 1990; 8: 213-225Crossref PubMed Scopus (209) Google Scholar, 13Lee C.A Infect. Agents Dis. 1996; 5: 1-7PubMed Google Scholar; see Figure 1), can be of any length, but, most often, they accommodate large clusters of genes contributing a particular virulence phenotype. Pathogenicity islands have been recognized by their association with transmissible DNA, their sporadic distribution in a set of related pathogenic and non-pathogenic organisms, or the unusual features of their encoded genes, and their recent characterization has provided clues regarding their origins, distribution, mode of transfer, and genetic stability. Incorporation of a pathogenicity island can, in a single step, transform a normally benign organism into a pathogen. For example, enteropathogenic E. coli contain a chromosomal segment that mediates attaching and effacing lesions on intestinal epithelial cells (14McDaniel T.K Jarvis K.G Donnenberg M.S Kaper J.B Proc. Natl. Acad. Sci. USA. 1995; 92: 1664-1668Crossref PubMed Scopus (996) Google Scholar; Figure 1). This 35 kb region—termed LEE for locus of enterocyte effacement—is absent from laboratory strains and codes for an outer membrane protein that promotes contact with host cells and a type III secretion system that exports proteins known to modify host cell functions. Type III secretion systems are prevalent among animal and plant pathogens—homologous export systems are responsible for the secretion of virulence proteins by Yersinia, Erwinia, Pseudomonas, Xanthomonas, Shigella, and Salmonella (18Van Gijsegem F Genin S Boucher C Trends Microbiol. 1993; 1: 175-180Abstract Full Text PDF PubMed Scopus (171) Google Scholar)—and these systems differ from the sec-dependent pathway in that their effector molecules lack a typical signal sequence. At the same location where LEE has inserted into enteropathogenic strains (14McDaniel T.K Jarvis K.G Donnenberg M.S Kaper J.B Proc. Natl. Acad. Sci. USA. 1995; 92: 1664-1668Crossref PubMed Scopus (996) Google Scholar) a distinct pathogenicity island, PAI-1, has been identified in a uropathogenic strain of E. coli (2Blum G Ott M Lischewski A Ritter A Imrich H Tschäpe H Hacker J Infect. Immun. 1994; 62: 606-614PubMed Google Scholar; Figure 1). Both islands are targeted to the same basepair downstream of the selC gene, which codes for the selenocysteine-specific tRNA. LEE and PAI-1 contain different sets of genes: PAI-1 is 70 kb in length and encodes a hemolysin. Thus, the specific cassette incorporated at the selC locus determines whether strains of E. coli are converted into entero- or uropathogens. Aside from PAI-1 and LEE, three other pathogenicity islands have been identified in E. coli (Figure 1); and, in fact, certain uropathogenic strains contain more than one pathogenicity island. In addition to PAI-1, E. coli strain 536 also harbors a 190-kb pathogenicity island, PAI-2, that has integrated at the tRNAleuX locus and contains genes for an alternate hemolysin and Prf-type fimbriae (2Blum G Ott M Lischewski A Ritter A Imrich H Tschäpe H Hacker J Infect. Immun. 1994; 62: 606-614PubMed Google Scholar). The other pathogenicity islands detected in E. coli also contain hemolysin genes but are associated with different tRNA loci: the island at the pheV locus contains genes for P-fimbriae, which allow the pathogen to adhere to cells lining the urinary tract, whereas the island at the pheR locus codes for Prs fimbriae, which bind Gal Nac-1–3-Gal Nac–containing receptors rather the Gal-β-1–4-Gal residues recognized by the P fimbrial adhesins (1Blum G Falbo V Caprioli A Hacker J FEMS Microbiol. Lett. 1995; 126: 189-196PubMed Google Scholar). In addition, the island at the pheR locus codes for a type 1 cytotoxic necrotizing factor, which causes multinucleation and enlargement of eukaryotic cells and can trigger phagocytosis by epithelial cells (4Falzano L Fiorentini C Donelli G.E.M Kocks C.P.C Cabanie L Oswald E Boquet P Mol. Microbiol. 1993; 9: 1247-1254Crossref PubMed Scopus (156) Google Scholar). Sequences similar to those present in the pathogenicity islands of uropathogenic strains have been detected in plasmids of hemolytic strains of E. coli, highlighting the mobile nature of these sequences. Two pathogenicity islands have been identified in Salmonella, each contributing to a specific step in the course of infection. The island at 63', designated SPI-1 (Figure 1), governs the ability of Salmonella to invade epithelial cells (15Mills D.M Bajaj V Lee C.A Mol. Microbiol. 1995; 15: 749-759Crossref PubMed Scopus (274) Google Scholar, 6Galán J.E Mol. Microbiol. 1996; 20: 263-272Crossref PubMed Scopus (363) Google Scholar), and a second island at 31', designated SPI-2, mediates survival within macrophages (16Ochman H Soncini F.C Solomon F Groisman E.A Proc. Natl. Acad. Sci. USA. 1996; 93: 7800-7804Crossref PubMed Scopus (505) Google Scholar, 17Shea J.E Hensel M Gleeson C Holden D.W Proc. Natl. Acad. Sci. USA. 1996; 93: 2593-2597Crossref PubMed Scopus (619) Google Scholar). Both islands are 40 kb in length and appear to have been acquired by horizontal gene transfer because their G+C contents are lower than those typical of Salmonella (10Groisman E.A Sturmoski M.A Solomon F.R Lin R Ochman H Proc. Natl. Acad. Sci. USA. 1993; 90: 1033-1037Crossref PubMed Scopus (62) Google Scholar). The nucleotide sequence of the SPI-1 island is nearly complete, and this region includes at least 25 genes, the majority of which encode components of a Type III secretion system and its effector proteins (6Galán J.E Mol. Microbiol. 1996; 20: 263-272Crossref PubMed Scopus (363) Google Scholar). The assemblage of genes specifying this export apparatus in Salmonella is similar in size, sequence, and organization to a set of genes in the Shigella virulence plasmid (8Groisman E.A Ochman H EMBO J. 1993; 12: 3779-3787PubMed Google Scholar), and several of the proteins encoded by these gene clusters are capable of cross-species complementation. However, certain genes within the Salmonella invasion island, such as orgA and hil, have no counterparts in the Shigella virulence plasmid and may be responsible for the differential regulation of invasion in Shigella and Salmonella: this property is controlled by temperature in Shigella and by oxygen tension, osmolarity, and pH in Salmonella. The vast differences in G+C contents and the phylogenetic distribution of the invasion gene clusters argue that Salmonella and Shigella gained these sequences independently from an as yet unidentified organism. The SPI-2 island of Salmonella harbors at least 15 genes that code for a distinct Type III secretion system and for a two-component regulatory system (16Ochman H Soncini F.C Solomon F Groisman E.A Proc. Natl. Acad. Sci. USA. 1996; 93: 7800-7804Crossref PubMed Scopus (505) Google Scholar, 17Shea J.E Hensel M Gleeson C Holden D.W Proc. Natl. Acad. Sci. USA. 1996; 93: 2593-2597Crossref PubMed Scopus (619) Google Scholar). Unlike the invasion island, the SPI-2 region is not needed for invasion of epithelial cells but is essential for intramacrophage survival (16Ochman H Soncini F.C Solomon F Groisman E.A Proc. Natl. Acad. Sci. USA. 1996; 93: 7800-7804Crossref PubMed Scopus (505) Google Scholar). Moreover, the SPI-2 island is necessary to cause a lethal infection in mice when inoculated either orally or intraperitoneally (16Ochman H Soncini F.C Solomon F Groisman E.A Proc. Natl. Acad. Sci. USA. 1996; 93: 7800-7804Crossref PubMed Scopus (505) Google Scholar, 17Shea J.E Hensel M Gleeson C Holden D.W Proc. Natl. Acad. Sci. USA. 1996; 93: 2593-2597Crossref PubMed Scopus (619) Google Scholar), whereas mutants defective in SPI-1 are attenuated only when inoculated orally (6Galán J.E Mol. Microbiol. 1996; 20: 263-272Crossref PubMed Scopus (363) Google Scholar), indicating that genes within each of the pathogenicity islands direct distinct functions during the progression of disease. The phylogenetic distribution of the SPI-1 and SPI-2 pathogenicity islands reveals that their acquisition was critical in the development of Salmonella as a intracellular pathogen. The SPI-1 invasion island is present in representative strains from all subspecific groups of Salmonella, although sporadic cases of secondary loss have been reported for individual isolates of S. enterica sv. Seftenberg and Litchfield. But, in contrast to SPI-1, SPI-2-hybridizing sequences have not been detected in S. bongori (subspecies V), the most divergent lineage of Salmonella. The incorporation of the SPI-1 and SPI-2 pathogenicity islands enabled Salmonella to invade host cells, evade host defense systems, and cause systemic infections in mammals, while its close relative E. coli evolved as a commensal and opportunistic pathogen. On the other hand, the four nominal species of Shigella, all of which emerged relatively recently from E. coli, gained the ability to enter host cells following the acquisition of the large virulence plasmid, thereby becoming invasive pathogens of primates. The occurrence of pathogenicity islands raises several questions about the evolution of virulence in bacteria. First, what advantage does the incorporation of virulence genes into the chromosome provide over retaining them on episomes? Although many virulence determinants occur on extrachromosomal DNAs, integration into the chromosome circumvents the need for autonomously replicating elements. This also lowers the probability that a given gene will be eliminated because episomes must be under continuous selective pressure to be maintained whereas the spontaneous elimination of chromosomal genes is not as high. However, plasmid integration can result in the inactivation of chromosomal loci or in the alteration of the expression of plasmid-encoded genes: for example, insertion of the Shigella flexneri virulence plasmid into the metB locus leads to methionine auxotrophy and decreased expression of the invasion proteins (20Zagaglia C Casalino M Colonna B Conti C Calconi A Nicoletti M Infect. Immun. 1991; 59: 792-799PubMed Google Scholar). Second, how are pathogenicity islands incorporated into the bacterial chromosome? Analysis of the junctions of pathogenicity islands can reveal the mechanism used to integrate these sequences. As noted above, the genes encoded by PAI-1 and LEE of E. coli are clearly different, but the site of insertion within the selC-tRNA gene is conserved (14McDaniel T.K Jarvis K.G Donnenberg M.S Kaper J.B Proc. Natl. Acad. Sci. USA. 1995; 92: 1664-1668Crossref PubMed Scopus (996) Google Scholar). This suggests that both islands were acquired by a similar mechanism which was likely to be phage-mediated since selC also serves as the site of insertion for the retronphage ΦR73 (12Inouye S Sunshine M.G Six E.W Inouye M Science. 1991; 252: 969-971Crossref PubMed Scopus (68) Google Scholar). Bacteriophages have been implicated in the transfer and acquisition of several other pathogenicity islands. The lysogenic conversion of Corynebacterium diphtheria and E. coli strains to pathogenic variants involves the incorporation of phages harboring toxin genes. Recently, the cholera toxin genes were shown to be encoded by a filamentous bacteriophage that can integrate into the chromosome of Vibrio cholerae or replicate autonomously as a plasmid (19Waldor M.K Mekalanos J.J Science. 1996; 272: 1910-1914Crossref PubMed Scopus (1257) Google Scholar). Furthermore, the virulence-associated region (vap) of Dichelobacter nodosus occurs within a tRNA locus and contains an open reading frame with high levels of sequence similarity to the integrases of E. coli phages (3Cheetham B.F Katz M.E Mol. Microbiol. 1995; 18: 201-208Crossref PubMed Scopus (196) Google Scholar). Features of tRNA genes promote their use as integration sites for phages and other episomes: these sequences are conserved across species and occur in multiple copies within a genome. The PAI-1 and PAI-2 islands of E. coli are flanked by direct repeats of 16 and 18 nucleotides, respectively (2Blum G Ott M Lischewski A Ritter A Imrich H Tschäpe H Hacker J Infect. Immun. 1994; 62: 606-614PubMed Google Scholar), and although these islands integrate at different tRNA genes, the repeats contain a motif, TTCGA, that is within the conserved loop of tRNA genes. PAI-1 and PAI-2 are spontaneously deleted from the E. coli chromosome at frequencies of 10−4 to 10−5, leaving a single copy of the repeat at the excision site and rendering the organism avirulent (2Blum G Ott M Lischewski A Ritter A Imrich H Tschäpe H Hacker J Infect. Immun. 1994; 62: 606-614PubMed Google Scholar). Deletion of these pathogenicity islands can also modify metabolic properties of the cell by disrupting the tRNA gene at the site of insertion; for example, inactivation of selC will impede the synthesis of enzymes containing selenocysteine and prevent growth under anaerobic conditions. Although several islands have resulted from the phage-mediated transfer of virulence loci into tRNA genes (3Cheetham B.F Katz M.E Mol. Microbiol. 1995; 18: 201-208Crossref PubMed Scopus (196) Google Scholar), pathogenicity islands can arise by any mechanism that promotes horizontal gene transfer. In Yersinia pestis, incorporation of a 102 kb island encoding determinants required for growth in iron-deprived environments were probably mediated by an insertion sequence (5Fetherston J.D Schuetze P Perry R.D Mol. Microbiol. 1992; 6: 2693-2704Crossref PubMed Scopus (209) Google Scholar). This island is flanked by direct repeats of IS100, an element that is present in some 30 copies per genome and can integrate plasmids into the Y. pestis chromosome. Recombination between the directly-repeated IS100 is apparently responsible for the spontaneous loss of the Yersinia island, which occurs at a frequency of 10−5. Is the acquisition of a pathogenicity island sufficient to transform an organism into a pathogen? Three factors determine the virulence role of pathogenicity islands: the genes within the island, the status of the recipient microorganism, and features of the host that promote the progression of disease. The incorporation of certain genes, such as those encoding cholera toxin, would be sufficient to convert any organism into a pathogen because administration of the toxin itself is sufficient to produce the symptoms of the disease. But for most other cases, the utility of sequences obtained through gene transfer varies with the organism. E. coli is a benign constituent of the mammalian intestinal flora and is apparently predisposed to become a pathogen by the introduction of several types of virulence genes. The LEE island is likely to encode all of the genes necessary to produce attachment and effacement lesions, and the acquisition of this island could probably render any strain of E. coli pathogenic. And, not surprisingly, pathogenicity islands causing these lesions have been detected in genetically diversed strains of E. coli. The acquisition of pathogenicity islands offers a rapid method of evolving novel functions; however, the introgressed sequences, even when they encode their specific regulators as part of complete functional units, must interact with rest of the genome. Expression of six invasion genes within the SPI-1 island of Salmonella is governed by the PhoP/PhoQ regulatory system (6Galán J.E Mol. Microbiol. 1996; 20: 263-272Crossref PubMed Scopus (363) Google Scholar), which is not encoded within the SPI-1 island and is present in both pathogenic and non-pathogenic microorganisms. And even sequences that are maintained on extrachromosomal elements can be regulated by chromosomal loci: the invasion genes on the Shigella virulence plasmid are controlled by the chromosomally-encoded histone-like protein H1. The association of pathogenicity islands with mobile DNA elements suggests that these sequences could be incorporated into a wide variety of bacterial species. However, presence of a pathogenicity island does not assure the transformation of an organism into a pathogen. A 10 kb region that harbors most known virulence genes in the pathogenic species of Listeria (L. monocytogenes and L. ivanovii) is also present in the chromosome of the nonpathogenic L. seeligeri (7Gouin E Mengaud J Cossart P Infect. Immun. 1994; 62: 3550-3553PubMed Google Scholar). While this gene cluster also encodes a pleiotropic activator, the attenuated phenotype of L. seeligeri has been ascribed to down regulation of most virulence genes. Furthermore, due to the coevolution between microbes and their hosts, the virulence potential of pathogenicity islands will only manifest in suitable animals and plants. Finally, it has been suggested that the deletion of pathogenicity islands may represent a regulatory mechanism to control expression of virulence genes (2Blum G Ott M Lischewski A Ritter A Imrich H Tschäpe H Hacker J Infect. Immun. 1994; 62: 606-614PubMed Google Scholar). This presupposes that the elimination of pathogenicity islands will circumvent the immune response to the encoded determinants and allow rapid microbial replication by reducing chromosome size. While this is a plausible scenario, both pathogenic and non-pathogenic strains of E. coli contain surface antigens that can promote an immune response, and the growth rates of natural strains of E. coli under lab conditions are not associated with genome size. Therefore, the deletion of pathogenicity islands is probably not a mechanism employed by bacteria to modulate virulence, but simply reflects the intrinsic genetic instability of these sequences.
Source: Cell
Authors: Eduardo A Groisman, Howard Ochman
Institutions: Washington University in St. Louis, University of Rochester
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $11,400
OpenAlex ID: W2004690000