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

Abstract

Different strains of Streptococcus suis serotypes 1 and 2 isolated from pigs either contained a restrictionmodification (R-M) system or lacked it. The R-M system was an isoschizomer of Streptococcus pneumoniae DpnII, which recognizes nucleotide sequence 5-GATC-3. The nucleotide sequencing of the genes encoding the R-M system in S. suis DAT1, designated SsuDAT1I, showed that the SsuDAT1I gene region contained two methyltransferase genes, designated ssuMA and ssuMB, as does the DpnII system. The deduced amino acid sequences of M.SsuMA and M.SsuMB showed 70 and 90% identity to M.DpnII and M.DpnA, respectively. However, the SsuDAT1I system contained two isoschizomeric restriction endonuclease genes, designated ssuRA and ssuRB. The deduced amino acid sequence of R.SsuRA was 49% identical to that of R.DpnII, and R.SsuRB was 72% identical to R.LlaDCHI of Lactococcus lactis subsp. cremoris DCH-4. The four SsuDAT1I genes overlapped and were bounded by purine biosynthetic gene clusters in the following gene order: purF-purMpurN-purH-ssuMA-ssuMB-ssuRA-ssuRB-purD-purE. The G؉C content of the SsuDAT1I gene region (34.1%) was lower than that of the pur region (48.9%), suggesting horizontal transfer of the SsuDAT1I system. No transposable element or long-repeat sequence was found in the flanking regions. The SsuDAT1I 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 SsuDAT1I. No notable substitutions or insertions could be found, and the structures were conserved among all the strains. These results suggest that the SsuDAT1I system could have been integrated into the S. suis chromosome by an illegitimate recombination mechanism.More than 3,000 restriction-modification (R-M) systems have been identified in a wide variety of microorganisms, where they are thought to protect the host from invasion by foreign DNA. Only a minority of R-M systems have been sequenced (6,37,56). Among them, some type II R-M systems, which recognize 4-bp palindromic sequence 5Ј-GATC-3Ј, involve a variety of isoschizomers. Three classes can be distinguished by their manners of DNA cleavage and susceptibilities to DNA methylation. The first class of isoschizomers, represented by Sau3AI, which was described for Staphylococcus aureus, is prevented from digesting host DNA by a cognate 5-methylcytosine methyltransferase and is not influenced by the modification of N 6 -methyladenine (48, 56). The second class, represented by DpnI, which was described for Streptococcus pneumoniae, is unique among restriction endonucleases in that it cleaves only at methylated DNA sequence 5Ј-GmeATC-3Ј, and thus the cells producing DpnI do not carry the corresponding methyltransferase gene (22,23). The third class, including MboI, DpnII, and LlaDCHI...

Evidence for Lateral Transfer of the Suilysin Gene Region of Streptococcus suis

“…1). The codon usage patterns for the sly and orf102 genes were not anomalous compared to those previously reported for purine and cysteine biosynthetic genes (26,32). No transposable element or long-repeat sequence was found in the 5,545 or 4,257-bp sequence.…”

“…However, there are several variants of these markers and some S. suis isolates from diseased pigs do not possess one or more of them (1,3,4,13,19,38,41), indicating genetic heterogeneity with respect to these markers. Recently, it was shown that some S. suis strains possess a type II restriction-modification (R-M) system, designated SsuDAT1I, which is an isoschizomer of Moraxella bovis MboI (10), whereas some other strains lack the system (32). Nucleotide sequence comparison between strains having the SsuDAT1I system and those lacking the system revealed that the SsuDAT1I system was originally inserted into the S. suis chromosome from a foreign source by illegitimate recombination and was subsequently transferred among S. suis strains by homologous recombination (31,32).…”

“…Recently, it was shown that some S. suis strains possess a type II restriction-modification (R-M) system, designated SsuDAT1I, which is an isoschizomer of Moraxella bovis MboI (10), whereas some other strains lack the system (32). Nucleotide sequence comparison between strains having the SsuDAT1I system and those lacking the system revealed that the SsuDAT1I system was originally inserted into the S. suis chromosome from a foreign source by illegitimate recombination and was subsequently transferred among S. suis strains by homologous recombination (31,32). These findings raise the question of whether a series of genetic exchanges, exemplified by the SsuDAT1I system, also occurred in other genes and is one of the typical processes involved in the evolution of this bacterium, which constitutes a population containing strains with various combinations of virulence markers.…”

Loss of capsule among Streptococcus suis isolates from porcine endocarditis and its biological significance

“…All isolates were stored in Luria-Bertani (Becton Dickinson) broth containing 30 % glycerol at 280 uC and minimally passaged for the experiments to avoid changing key traits including capsule production. In addition, S. suis strains S735 (NCTC 10234; serotype 2 reference strain) and 204 (serotype 1 field isolate) (Sekizaki et al, 2001) were used for the production of rabbit antiserum, and S. suis strain 89/1591, isolated from a pig with septicaemia (Salasia et al, 1995), and its isogenic unencapsulated mutant (CPS2B) (Okura et al, 2011) were used to compare their phenotypic characteristics with other encapsulated and unencapsulated cps2J-positive isolates. Enterococcus faecalis NCTC 775 was used as a control for PCR scanning analysis.…”

Bacterial Genome Instability

“…An RM system can transpose into a new locus (264). It can simply insert into an operon-like gene cluster (like in the pur operon in Streptococcus suis [265]) or insert with a short or long and variable target duplication (such as an 8-bp sequence when type II RM genes insert into Xanthomonas oryzae pv. oryzae [247] or a 506-bp-long direct duplication after insertion of a type IIS system in Helicobacter pylori [266]).…”