Diversity of restriction–modification gene homologues in Helicobacter pylori

The complete genome sequences of two Helicobacter pylori strains have recently become available. We have searched them for homologues of restriction–modification genes. One strain (26695) carried 52 such homologues, and the other (J99) carried 53. Their sequence alignments were arranged in the form of a phylogenetic tree and compared with the tree based on rRNA. The trees showed that the homologues are scattered among diverse groups of bacteria. They also revealed high polymorphism within the species — there are 42 pairs with high homology, 10 specific to 26695, and 11 specific to J99. Many of the restriction–modification homologues were characterized by a GC content lower than that of the average gene in the genome. Some of the restriction–modification homologues showed a different codon use bias from the average genes. These observations are interpreted in terms of horizontal transfer of the restriction–modification genes.