Genomic localization of a T serotype locus to a recombinatorial zone encoding extracellular matrix-binding proteins in Streptococcus pyogenes

Abstract

Streptococcus pyogenes is an important bacterial pathogen afflicting humans. A striking feature is its extraordinary biological diversity, evident in the wide range of diseases it can cause and the antigenic heterogeneity present on its surface. The T antigens form the basis of a major serological typing scheme that is often used as an alternative or supplement to M typing. Unlike M typing, the genetic basis for T typing is poorly understood. In this report, the tee6 gene is localized to a position approximately equal to 3.3 kb downstream from prtF1 (or sfbI), which encodes the Fn-binding protein, protein F, a key virulence factor. Comparison of this portion of the genome with those of four additional strains reveals the presence of genes encoding a collagen-binding protein (Cpa) and a second Fn-binding protein (PrtF2 or PfbpI). This chromosomal region--here designated the FCT region--is approximately 11 to 16 kb in length and is flanked at both ends by long stretches of highly conserved sequence. For each of the five strains, the FCT region contains a unique combination of semiconserved loci, indicative of extensive intergenomic recombination. The data provide evidence that the highly recombinatorial FCT region of the S. pyogenes genome is under strong selection for change in response to the host environment.

FIG. 1.

Partial genome maps of strains SF370, Manfredo, and CS101. ORFs are indicated by open boxes placed above the line (transcribed left to right) or below the line (oppositely transcribed). The percent nucleotide identity (nt id) between pairs of sequences was established by pairwise BlastN 2 and is depicted for regions showing ≥70% identity. The percent nucleotide identity is presented for SF370 versus Manfredo and for Manfredo versus CS101. Strain CS101 displays 98% nucleotide identity with SF370 at bp 112089 through 114912 (data not shown). The vertical dotted lines depict the boundaries for high nucleotide sequence identity. The distance scale (in kilobases) is shown for strain SF370; distances for Manfredo and CS101 are presented for easy visual alignment but are not drawn precisely to scale. In SF370, the emm locus lies ≈283 kb from SPy0123 (hsp33).

FIG. 2.

Complete FCT region of strain D471 and comparison to SF370. The percent nucleotide identity (nt id) between D471 and SF370 was established by pairwise BlastN 2 and is depicted for regions having ≥70% identity. The vertical dotted lines mark the FCT region boundaries for high nucleotide sequence identity. The distance scale (in kilobases) is shown for strain SF370; distances for D471 are presented for easy visual alignment but are not drawn precisely to scale. The sources for strain D471 sequences are GenBank (Table 1) and this study. The nomenclature for the protein F gene (prtF1) indicates its source as being an M type 6 strain (prtF1.6).

FIG. 3.

Alignments of the prtF2/pfbpI gene and flanking regions in three strains. The percent nucleotide identity (nt id) between pairs of sequences was established by pairwise BlastN 2 and is depicted for regions having ≥70% identity. The percent nucleotide identity is presented for Manfredo versus A735 and for A735 versus B737. Since A735 and B737 are highly related in sequence, the percent nucleotide identity between Manfredo and B737 closely parallels that between A735 and B737. The prtF2/pfbpI.5 allele of Manfredo is ≈1.4 kb smaller than the prtF2/pfbpI.12 and prtF2/pfbpI.49 alleles.

FIG. 4.

Complete FCT region of strain A735 and a possible hot spot for recombination. The complete FCT region for strain A735 is shown. The categories for each locus, and homology to other FCT region loci, are summarized in Table 3. The vertical lines indicate ≈4-kb intervals. The percent nucleotide sequence identity (nt id) to FCT region genes from other strains is shown for a 1.8-kb region spanning from the 3′-end region of prtF1.12 through the 5′-end region of cpa.12. The relative positions of the aligned regions are shown in Fig. 1 (for strain SF370) and 2 (for strain D471) and indicate genomic rearrangements.