Analysis of the type 1 pilin gene cluster fim in Salmonella: its distinct evolutionary histories in the 5' and 3' regions

Abstract

The type 1 pilin encoded by fim is present in both Escherichia coli and Salmonella natural isolates, but several lines of evidence indicate that similarities at the fim locus may be an example of independent acquisition rather than common ancestry. For example, the fim gene cluster is found at different chromosomal locations and with distinct gene orders in these closely related species. In this work we examined the fim gene cluster of Salmonella, the genes of which show high nucleotide sequence divergence from their E. coli counterparts, as well as a different G+C content and codon usage. DNA hybridization analysis revealed that, among the salmonellae, the fim gene cluster is present in all isolates of S. enterica but is absent from S. bongori. Molecular phylogenetic analyses of the fimA and fimI genes yield an estimate of phylogeny that is in satisfactory congruence with housekeeping and other virulence genes examined in this species. In contrast, phylogenetic analyses of the fimZ, fimY, and fimW genes indicate that horizontal transfer of this region has occurred more than once. There is also size variation in the fimZ, fimY, and fimW intergenic regions in the 3' region, and these genes are absent in isolate S2983 of subspecies IIIa. Interestingly, the G+C contents of the fimZ, fimY, and fimW genes are less than 46%, which is considerably lower than those of the other six genes of the fim cluster. This study demonstrates that horizontal transmission of all or part of the same gene cluster can occur repeatedly, with the result that different regions of a single gene cluster may have different evolutionary histories.

FIG. 1

Schematic representation of the organization of the fim type 1 pilin gene clusters from E. coli K-12 and S. enterica serovar Typhimurium. Each gene is shown as an open arrow, scaled to size. The black bars indicate the positions of the probes (fim1 to fim6) used in DNA hybridization analysis.

FIG. 2

Distribution of polymorphic nucleotide sites in the fimA-fimI coding region among 14 SARC isolates of S. enterica. Numbers at the left are strain designations; those across the top are nucleotide positions along the gene. Dots indicate nucleotide identity. Only variable positions are shown.

FIG. 3

Distribution of polymorphic nucleotide sites in the fimZ gene among 10 SARC isolates of S. enterica. Numbers at the left are strain designations; those across the top are nucleotide positions along the gene. Dots indicate nucleotide identity. Only variable positions are shown.

FIG. 4

Evolutionary relationships based on synonymous site variation in the fimA, fimI, and fimZ genes. The neighbor-joining method was used to construct the trees (48), using the Jukes-Cantor correction for multiple hits (21). The SARC Salmonella strains are indicated by numbers, and the subspecies are indicated by roman numerals. Bootstrap values based on 1,000 computer-generated trees are indicated at the nodes. The genetic distance is the Jukes-Cantor distance (21).

FIG. 5

Proposed evolutionary history of horizontal transmission of certain pathogenic determinants into Salmonella. Phylogenetic relationships of the Salmonella subspecies are based on nucleotide sequence data from five housekeeping genes (7). The proposed times of horizontal transmission (arrows) are consistent with the presence in all lineages of Salmonella of the pathogenicity islands SPI-1 (8, 31) and SPI-2 (37), as well as of the pilin gene clusters agf, lpf, and fim (reference and this study). The proposed times for SPI-3 (4) and spv (9) are consistent with their presence in all lineages of Salmonella except S. bongori. The proposed times for the pef and sef (1) gene clusters are consistent with their presence only in isolates of S. enterica subspecies I. The pilin gene clusters are indicated by asterisks.