Functional analysis of putative restriction-modification system genes in the Helicobacter pylori J99 genome

Helicobacter pylori is a gram-negative bacterium, which colonizes the gastr ic mucosa of humans and is implicated in a wide range of gastroduodenal dis eases. The genomic sequences of two H,pylori strains, 26695 and J99, have b een published recently. About two dozen. potential restriction-modification (R-NI) systems have been annotated in both genomes, which is far above the average number of R-M systems in other sequenced genomes. Here we describe a functional analysis of the 16 putative Type II R-WI systems in the H,pyl ori J99 genome. To express potentially toxic endonuclease genes, a unique v ector was constructed, which features repression and antisense transcriptio n as dual control elements. To determine the methylation activities of puta tive DNA methyltransferases, we developed polyclonal antibodies able to det ect DNA containing N6-methyladenine or N4-methylcytosine. We found that <30 % of the potential Type II R-M systems in H. pylori J99 strain were fully f unctional, displaying both endonuclease and methyltransferase activities. H elicobacter pylori may maintain a variety of functional R-M systems, which are believed to be a primitive bacterial 'immune' system, by alternatively turning on/off a subset of numerous R-M systems.