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

The type 1 pilin encoded by fim is present in both Escherichia coli and Sal monella natural isolates, but several lines of evidence indicate that simil arities at the fim locus may be an example of independent acquisition rathe r than common ancestry. For example, the fim gene cluster is found at diffe rent chromosomal locations and with distinct gene orders in these closely r elated 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 pm gene c luster is present in all isolates of S. enterica but is absent from S. bong ori. Molecular phylogenetic analyses of the fimA and fimI genes yield an es timate of phylogeny that is in satisfactory congruence with housekeeping an d other virulence genes examined in this species. In contrast, phylogenetic analyses of the fimZ, fimY, and fimW genes indicate that horizontal transf er 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 c onsiderably lower than those of the other six genes of the fim cluster. Thi s study demonstrates that horizontal transmission of all or part of the sam e gene cluster can occur repeatedly, with the result that different regions of a single gene cluster may have different evolutionary histories.