Finishing/ gap closure

19 contigs > 1kbp

Sanger Centre, UK

Acquisition of new traits by HGT (horizontal gene transfer) as well as a complementary loss-of-function mechanism have been proposed [16, 17] to adapt to specialized niches and to increase virulence. Acquisition of the virulence plasmid enabled S.flexneri to enter the intracellular environment in human intestinal epithelial cells. In this new niche, genes required in the intestinal lumen may be deleterious or are no longer beneficial and may accumulate mutations without a selective force to maintain them. Lysine decarboxylase (CadA) produces cadaver-ine, which inhibits the escape of S.flexneri from the vacuole into the cell cytosol [18, 19]. As replication and spread of S.flexneri depends on access to the cytosol, biosynthesis of cadaverine attenuates virulence. The cadA and cadC genes are deleted as well as the surface protease OmpT encoding gene, which determines the intercellular spreading ability of Shigella [9]. Lack of surface structures, e.g., flagella and curli fimbriae, in S.flexneri may provide the advantage of fewer antigens that could be recognized by the host immune system. In strain 2457T, 14 genes of flagellar biosynthesis are nonfunctional due to frameshift and point mutations as well as to IS2-mediated truncation [15]. Pseudogenes result from disruption of coding sequences by point mutations, single nucleotide indels, and insertion of IS elements. IS elements cause disruption and truncation of genes as well as larger deletions and insertions. IS elements are probably the major cause of the S.flexneri genome dynamics. Many other phenotypic characteristics of S.flexneri relative to E. coli (e.g., the loss of utilization of lactose, maltose, and xylose) can be assigned to pseudogenes in Shigella which are still functional in E. coli. With respect to the presence of large numbers of pseudogenes, S.flexneri resembles another enteric pathogen restricted to humans, and that is Salmonella enterica serovar Typhi. The accumulation of pseudogenes is considered to be one of the main reasons why both evolved from the rest of their species to become human restricted pathogens [20].

S.flexneri harbors a large virulence plasmid, pINV, that contains all of the genes (ipa, mxi-spa, virG/lscA, virF) required to express the invasive phenotype. This plasmid is also present in enteroinvasive E. coli strains. Sequence comparison of the four available virulence plasmid sequences of S.flexneri, pINV-2457T, pWR100, pWR501, and pCP301 [14, 15, 21, 22] showed that they are essentially identical. Size differences are mainly due to the presence of IS elements. Interestingly, about 50% of all ORFs located on the invasion plasmid are related to putative IS elements indicative of IS-mediated acquisition of gene blocks of various origins. However, the analysis of non-IS-related coding sequences of different pINV variants also indicated that positive selection is also a major driving force involved in the evolution of pINV variants [23]. In contrast to strain 301, strain 2457Talso contains two small multicopy plasmids as well as another 165-kbp plasmid with high homology to the S. enterica serovar Typhi R27-like plasmid [15]. The latter was considered to be limited to Salmonella implicated in the acquisition and accumulation of antibiotic resistance. However, sequence similarity between pR27 and the large virulence plasmid of Yersinia pestis, pMT1, has been observed, indicative of a common origin.

Comparative genome analysis also provides a powerful means of linking pathogenic processes with specific acquired genes and their encoded products. In addition to the 3.9-Mbp backbone shared with E. coli, several regions unique to Shigella can be found scattered over the chromosome. Sixty-four such Shigella islands (SIs) greater than 1000 base pairs can be detected and many of them exhibit typical features of genomic islands or prophages. Shigella prophages play an important role in serotype conversion, which is an important virulence trait of S. flexneri. Four different temperate bacteriophages involved in O antigen modification have been characterized so far. Compared to E. coli, most prophages found in S. flexneri differ in their DNA sequence, indicating that they were acquired after the separation of the two bacterial lineages [14, 15, 24, 25].

Tab. 5.3 Well-characterized pathogenicity islands of E. coli and Shigella.


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