Evidence for Horizontal Transfer of Ssu DAT1I Restriction-Modification Genes to the Streptococcus suis Genome

Abstract

ABSTRACT Different strains of Streptococcus suis serotypes 1 and 2 isolated from pigs either contained a restriction-modification (R-M) system or lacked it. The R-M system was an isoschizomer of Streptococcus pneumoniae Dpn II, which recognizes nucleotide sequence 5′-GATC-3′. The nucleotide sequencing of the genes encoding the R-M system in S. suis DAT1, designated Ssu DAT1I, showed that the Ssu DAT1I gene region contained two methyltransferase genes, designated ssuMA and ssuMB , as does the Dpn II system. The deduced amino acid sequences of M. Ssu MA and M. Ssu MB showed 70 and 90% identity to M. Dpn II and M. Dpn A, respectively. However, the Ssu DAT1I system contained two isoschizomeric restriction endonuclease genes, designated ssuRA and ssuRB . The deduced amino acid sequence of R. Ssu RA was 49% identical to that of R. Dpn II, and R. Ssu RB was 72% identical to R. Lla DCHI of Lactococcus lactis subsp. cremoris DCH-4. The four Ssu DAT1I genes overlapped and were bounded by purine biosynthetic gene clusters in the following gene order: purF-purM-purN-purH-ssuMA-ssuMB-ssuRA-ssuRB-purD-purE . The G+C content of the Ssu DAT1I gene region (34.1%) was lower than that of the pur region (48.9%), suggesting horizontal transfer of the Ssu DAT1I system. No transposable element or long-repeat sequence was found in the flanking regions. The Ssu DAT1I genes were functional by themselves, as they were individually expressed in Escherichia coli . Comparison of the sequences between strains with and without the R-M system showed that only the region from 53 bp upstream of ssuMA to 5 bp downstream of ssuRB was inserted in the intergenic sequence between purH and purD and that the insertion target site was not the recognition site of Ssu DAT1I. No notable substitutions or insertions could be found, and the structures were conserved among all the strains. These results suggest that the Ssu DAT1I system could have been integrated into the S. suis chromosome by an illegitimate recombination mechanism.