Comparative genomics of the restriction-modification systems in Helicobacter pylori

Abstract

Helicobacter pylori is a Gram-negative bacterial pathogen with a small genome of 1.64 -1.67 Mb. More than 20 putative DNA restrictionmodification (R-M) systems, comprising more than 4% of the total genome, have been identified in the two completely sequenced H. pylori strains, 26695 and J99, based on sequence similarities. In this study, we have investigated the biochemical activities of 14 Type II R-M systems in H. pylori 26695. Less than 30% of the Type II R-M systems in 26695 are fully functional, similar to the results obtained from strain J99. Although nearly 90% of the R-M genes are shared by the two H. pylori strains, different sets of these R-M genes are functionally active in each strain. Interestingly, all strain-specific R-M genes are active, whereas most shared genes are inactive. This agrees with the notion that strain-specific genes have been acquired more recently through horizontal transfer from other bacteria and selected for function. Thus, they are less likely to be impaired by random mutations. Our results also show that H. pylori has extremely diversified R-M systems in different strains, and that the diversity may be maintained by constantly acquiring new R-M systems and by inactivating and deleting the old ones.H elicobacter pylori is one of the most common bacterial pathogens that colonizes the gastric mucosa of humans. H. pylori is implicated in a wide range of gastroduodenal diseases (1, 2). H. pylori is commonly believed to be a very diverse species. It is believed that, in addition to genetic recombination, de novo mutation could have a role in generating the high level of genetic variation in H. pylori (3). MutH and MutL homologues cannot be found in H. pylori genomes, which suggests H. pylori may not have a functional mismatch repair system (4, 5). Recent analysis of the complete genomic sequences of two unrelated H. pylori isolates reveals that although intraspecies variation does exist, the overall genomic organization, gene order, and predicted proteins of the two strains are quite similar (5, 6). Approximately 6-7% of the genes are specific to each strain (5). The 26695 and J99 strains have a relatively small genome size of 1.67 and 1.64 megabase pairs (4, 5). However, more than twenty DNA restriction-modification (R-M) systems can be identified in each strain based on sequence similarities. The biological significance of this large complement of R-M systems is not clear. The majority of the H. pylori R-M systems are of Type II, which consist of two separate enzymes: the restriction endonucleases, which are responsible for degrading unmodified foreign DNA, and the modification DNA methyltransferases (methylase or M), which protect endogenous DNA from endonucleolytic digestion by methylating them at the endonuclease recognition sites (7).Interesting observations have been reported regarding H. pylori R-M genes. A novel H. pylori gene, iceA (induced when the bacteria contact the host epithelium), was identified recently (8). DNA sequences have revealed two alleles of the iceA locu...

Characterization of the LlaCI methyltransferase from Lactococcus lactis subsp. cremoris W15 provides new insights into the biology of type II restriction–modification systems

“…This indicates that each MTase of a particular R-M system is not a product of gene duplication but was acquired/evolved independently. Recent studies on the diversity of R-M systems in Helicobacter pylori provide facts endorsing such a notion (Nobusato et al, 2000a, b;Lin et al, 2001). In vivo experiments with the BcnI R-M system show that M.BcnIB alone is sufficient to support the growth of E. coli cells carrying the BcnI ENase gene; this could not be demonstrated for M.BcnIA (Vilkaitis et al, 2002).…”

Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense

“…Further analyses revealed that only some of these systems retain enzyme activity (195,198). In some of the inactive systems, REases are truncated while retaining the functional MTase gene.…”

RecBCD Enzyme and the Repair of Double-Stranded DNA Breaks

“…The well-known type II restriction-modification systems constitute the primary defensive mechanism against foreign DNA and can, remarkably, account for greater than 4% of the genome for some bacteria (Helicobacter pylori) (179). The type II restriction enzymes cleave foreign DNA into linear fragments that are substrates for more extensive nucleolytic degradation by the RecBCD enzyme (85,121,171,255).…”