Fig 4.

Polymorphisms associated with the genetic organization of relBE2 and its neighboring genes found in S. pneumoniae clinical isolates (118) and NCBI databases. In general, the relBE2 operon is flanked by vicX (metal-dependent hydrolase) at its upstream region, whereas a RUP (repeat unit of pneumococcus) element, ldh (lactate dehydrogenase), as well as gyrA (the A subunit of DNA gyrase) are located downstream. (A to D) Variations are found, as follows. (A) Genes that encode the putative restriction-modification (RM) methylase and type II restriction endonuclease (RE) are found immediately downstream of relE2; (B) a gene encoding a K⁺/cation channel protein is located immediately downstream of relE2 instead; (C) same as in panel B but with a gene encoding an IS1167 insertion sequence located immediately upstream of relB2 in the opposite orientation; (D) same as panel B but with an IS1380-SpnI element found downstream of the gene encoding the K⁺/cation channel protein and in the opposite orientation while keeping the RUP element. (E and F) On the other hand, we found strains which harbor a second set of relBE2 genes, which seems to be an acquired foreign DNA. They have totally different organization patterns from the types described above. (E) The relBE2 genes are flanked by another putative set of TA genes, xre-COG2856B. Besides, an unknown hypothetical protein (HP) is found further upstream, and a type I restriction endonuclease and an integrase are found downstream of the COG2856B gene; in certain strains, a stop codon was found within COG2856B, which leads to the truncation of the gene. (F) Similar to panel E, but instead of a type I restriction endonuclease, an unknown hypothetical protein is found downstream of the COG2856B gene.