Identification of type II restriction and modification systems in Helicobacter pylori reveals their substantial diversity among strains

Abstract

A total of 22 type II restriction endonucleases with 18 distinct specificities have been identified in six Helicobacter pylori strains. Among these 18 specificities are three completely new endonucleases, Hpy178III, Hpy99I, and Hpy188I, that specifically cleave DNA at TCNNGA, CGWCG, and TCNGA sites, respectively. The set of endonucleases identified in each strain varies, but all have four- or five-base recognition sequences. Among 16 H. pylori strains, examination of the DNA modification status at the recognition sites of 15 restriction endonucleases reveals that each strain has a substantially different complement of type II modification systems. We conclude that the type II restriction-modification systems in H. pylori are highly diverse between strains, a unique characteristic of H. pylori. The diverse methylation status of H. pylori chromosomal DNA may serve as a new typing system to discriminate H. pylori isolates for epidemiological and clinical purposes. This study also demonstrates that H. pylori is a rich source of type II restriction endonucleases.

Figure 1

Digestion of chromosomal DNA from 16 H. pylori strains by 15 different type II REs. The digests, resolved in a 1% agarose gel, are listed in the right panel. “+” indicates digestible by the RE whereas “−” indicates resistant to digestion. The name, recognition site, and prototype of each RE are listed in the left panel. The sources of the chromosomal DNA are listed at the top of the figure. The iceA genotypes of the DNA are also indicated.