Regulation of the HpyII restriction-modification system of Helicobacter pylori by gene deletion and horizontal reconstitution

Helicobacter pylori, Gram-negative, curved bacteria colonizing the human st omach, possess strain-specific complements of functional restriction-modifi cation (R-M) systems. Restriction-modification systems have been identified in most bacterial species studied and are believed to have evolved to prot ect the host genome from invasion by foreign DNA. The large number of R-Ms homologous to those in other bacterial species and their strain-specificity suggest that H. pylori may have horizontally acquired these genes. A type IIs restriction-modification system, hpyIIRM, was active in two out of the six H. pylori strains studied. We demonstrate now that in most strains lack ing M.HpyII function, there is compete absence of the R-M system. Direct DN A repeat of 80 bp flanking the hpyIIRM system allow its deletion, resulting in an 'empty-site' genotype. We show that strains possessing this empty-si te genotype and strains with a full but inactive hpyIIRM can reacquire the hpyIIRM cassette and functional activity through natural transformation by DNA from the parental R-M+ strain. Identical isolates divergent for the pre sence of an active HpyII R-M pose different restriction barriers to transfo rmation by foreign DNA. That H. pylori can lose HpyII R-M function through deletion or mutation, and can horizontally reacquire the hpyIIRM cassette, is, in composite, a novel mechanism for R-M regulation, supporting the gene ral hypothesis that H. pylori populations use mutation and transformation t o regulate gene function.