Restriction and Modification Systems

Prokaryotic restriction-modification (R-M) systems were first recognized in Escherichia coli nearly 50 years ago and are now known to be ubiquitous among bacterial species. This chapter summarizes the current state of knowledge regarding the structure and function of the large number of putative restriction-modification (R-M) genes and systems that are now recognized to be present in Helicobacter pylori. Restriction enzyme activity is catalyzed by a complex containing both Mod and Res subunits; however, the mod gene product can function independently as a modification methylase. The genetic organization of type I R-M systems is similar to that found in E. coli and other enteric bacteria, in which each subunit is encoded by contiguous hsdR, hsdM, and hsdS genes. The HsdS subunit of type I R-M systems determines the DNA sequence specificity for both restriction and modification reactions. The HsdS proteins (S1, S2, S3) in either strain share no significant amino acid homology to each other. Type II and IIS R-M systems are generally encoded by contiguous genes and, unlike type I and III R-M systems, are composed of independent restriction endonuclease and methyltransferase enzymes. Expression of functional type III R-M systems has not yet been demonstrated in H. pylori. The apparent requirement for slipped-strand repair of frameshift mutations in mod-2 and mod-4 suggests that these two putative type III systems may not be expressed.