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Background  R.PabI is an exceptional restriction enzyme that functions as a DNA glycosylase. The enzyme excises an unmethylated base from its recognition sequence to generate apurinic/apyrimidinic (AP) sites, and also displays AP lyase activity, cleaving the DNA backbone at the AP site to generate the 3’-phospho alpha, beta-unsaturated aldehyde end in addition to the 5’-phosphate end. The resulting ends are difficult to religate with DNA ligase. The enzyme was originally isolated in  Pyrococcus , a hyperthermophilic archaeon, and additional homologs subsequently identified in the epsilon class of the Gram-negative bacterial phylum Proteobacteria, such as  Helicobacter pylori .    Results  Systematic analysis of R.PabI homologs and their neighboring genes in sequenced genomes revealed co-occurrence of R.PabI with M.PabI homolog methyltransferase genes. R.PabI and M.PabI homolog genes are occasionally found at corresponding (orthologous) loci in different species, such as  Helicobacter pylori ,  Helicobacter acinonychis  and  Helicobacter cetorum , indicating long-term maintenance of the gene pair. One R.PabI and M.PabI homolog gene pair is observed immediately after the GMP synthase gene in both  Campylobacter  and  Helicobacter , representing orthologs beyond genera. The mobility of the PabI family of restriction-modification (RM) system between genomes is evident upon comparison of genomes of sibling strains/species. Analysis of R.PabI and M.PabI homologs in  H. pylori  revealed an insertion of integrative and conjugative elements (ICE), and replacement with a gene of unknown function that may specify a membrane-associated toxin ( hrgC ). In view of the similarity of HrgC with toxins in type I toxin-antitoxin systems, we addressed the biological significance of this substitution. Our data indicate that replacement with  hrgC  occurred in the common ancestor of hspAmerind and hspEAsia. Subsequently,  H. pylori  with and without  hrgC  were intermixed at this locus, leading to complex distribution of  hrgC  in East Asia and the Americas. In Malaysia,  hrgC  was horizontally transferred from hspEAsia to hpAsia2 strains.    Conclusions  The PabI family of RM system behaves as a mobile, selfish genetic element, similar to the other families of Type II RM systems. Our analysis additionally revealed some cases of long-term inheritance. The distribution of the  hrgC  gene replacing the PabI family in the subpopulations of  H. pylori,  hspAmerind, hspEAsia and hpAsia2, corresponds to the two human migration events, one from East Asia to Americas and the other from China to Malaysia.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-2021-3) contains supplementary material, which is available to authorized users.

Transmission of the PabI family of restriction DNA glycosylase genes: mobility and long-term inheritance