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Association of Putative Restriction Modification Geneswith Large Genome Polymorphisms Suggested from Comparison of Pyrococcus horikoshii and Pyrococcus abyssi Genome Sequences

Restriction-modification (RM) gene complexes encode two enzymatic functions, restriction and modification. A restriction enzyme will recognize a specific sequence in DNA and cut the DNA unless it is methylated by a cognate modification enzyme. RM systems will defend bacterial cells by attacking incoming foreign DNA. It is widely held that bacteria have evolved RM systems and maintain them in order to protect their genome from invasion by foreign DNA such as bacteriophages and plasmids. We earlier reported that carrying a type II RM gene complex can increase the stability of a plasmid because cells that have lost the plasmid die [4]. From this and other observations, it was proposed that the relative frequency of RM gene complexes has increased through this post-segregational killing, in competitive exclusion, as well as through direct attack on invading DNA [4]. This selfish-gene concept for the RM gene complexes implies a certain degree of independence from the rest of the genome and would be in accordance with movement of RM gene complexes between genomes. Indeed, there are various lines of evidence for their potential mobility [3]. The complete genome sequences of eubacteria and archaea (archaebacteria), especially those of closely related organisms, have been providing further evidence for their mobility and involvement in genome rearrangements. Comparison of two H. pylori genome sequences revealed that RM gene homologues are present at the end-point of an inversion and/or translocation at three loci [1]. This is consistent with a possible role for RM in generating these differences. Their comparison has suggested the presence of a mechanism for bacterial gene mobility insertion with long target duplications often associated with RMs [5]. Recently the complete genome sequences of two different species in the genus Pyrococcus, hyperthermophilic archaeon (archaebacterium), became available those of Pyrococcus horikoshii [2, 6] and of Pyrococcus abyssi [7]. In this communication, we compared these two genome sequences in a search for large genome polymorphisms linked with RM genes.