The flow of genes among prokaryotes plays a fundamental role in shaping bacterial evolution, and restriction-modification systems can modulate this flow. However, relatively little is known about the distribution and movement of restriction-modification systems themselves. We have isolated and characterized the genes for restriction-modification systems from two species of Salmonella, S. enterica serovar Paratyphi A and S. enterica serovar Bareilly. Both systems are closely related to the PvuII restriction-modification system and share its target specificity. In the case of S. enterica serovar Paratyphi A, the restriction endonuclease is inactive, apparently due to a mutation in the subunit interface region. Unlike the chromosomally located Salmonella systems, the PvuII system is plasmid borne. We have completed the sequence characterization of the PvuII plasmid pPvu1, originally from Proteus vulgaris, making this the first completely sequenced plasmid from the genus Proteus. Despite the pronounced similarity of the three restriction-modification systems, the flanking sequences in Proteus and Salmonella are completely different. The SptAI and SbaI genes lie between an equivalent pair of bacteriophage P4-related open reading frames, one of which is a putative integrase gene, while the PvuII genes are adjacent to a mob operon and a XerCD recombination (cer) site.Restriction-modification (RM) systems are nearly ubiquitous among bacteria (both eubacteria and archaea). To date, the only complete bacterial genome sequences lacking candidate RM systems are from the obligate intracellular parasites Chlamydia and Rickettsia. Chlamydia trachomatis is the only known cellular organism that lacks an S-adenosyl-L-methionine (AdoMet) synthetase (63), and a type II RM system with separately active endonuclease and AdoMet-dependent methyltransferase proteins could be dangerous in this context. The other bacterial genomes have between 1 and 22 predicted RM systems (74,75). Even bacteria with the smallest genomes, Mycoplasma and Ureaplasma, have made room for these systems. RM systems provide a defense against DNA bacteriophages, as revealed both by direct experiment and indirectly by the fact that many bacteriophages take specific countermeasures against RM systems (9). In addition to initiating the destruction of some foreign DNAs, RM systems may also promote recombination (6, 51) and improve the spread of some genes by separating them from linked deleterious alleles (4, 42), thus playing both positive and negative roles in modulating the flow of genes among prokaryotes. In the case of type II RM systems, selfish behavior also contributes to their ubiquity (24,45,46). RM system ubiquity is consistent with the selectable phenotypes just summarized, but these phenotypes only help to explain why the systems are maintained once they have entered a given bacterium. It is less clear how these systems move throughout the microbial biosphere. To this end, it would be useful to track the movement of a given RM system by finding very clos...